BLASTP 2.2.1 [Apr-13-2001]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= gi|15645906|ref|NP_208085.1| DNA-directed RNA
polymerase, alpha subunit (rpoA) [Helicobacter pylori 26695]
(344 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1IW7|A Chain A, Crystal Structure Of The Rna Polymerase... 157 2e-39
pdb|1L9U|A Chain A, Thermus Aquaticus Rna Polymerase Holoen... 150 3e-37
pdb|1I6V|B Chain B, Thermus Aquaticus Core Rna Polymerase-R... 149 3e-37
pdb|1HQM|B Chain B, Crystal Structure Of Thermus Aquaticus ... 145 5e-36
pdb|1BDF|B Chain B, Structure Of Escherichia Coli Rna Polym... 110 3e-25
pdb|1LB2|B Chain B, Structure Of The E. Coli Alpha C-Termin... 47 3e-06
pdb|1COO| The Cooh-Terminal Domain Of Rna Polymerase Alph... 47 3e-06
pdb|1DOQ|A Chain A, The C-Terminal Domain Of The Rna Polyme... 40 3e-04
pdb|1I60|A Chain A, Structural Genomics, Ioli Protein >gi|2... 32 0.14
pdb|1AV1|A Chain A, Crystal Structure Of Human Apolipoprote... 30 0.31
pdb|1DII|A Chain A, Crystal Structure Of P-Cresol Methylhyd... 29 0.68
pdb|1H6E|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adapt... 28 1.5
pdb|1D06|A Chain A, Structural Basis Of Dimerization And Se... 28 2.0
pdb|1K83|J Chain J, Crystal Structure Of Yeast Rna Polymera... 28 2.0
pdb|1DD3|A Chain A, Crystal Structure Of Ribosomal Protein ... 27 3.4
pdb|1JNB|A Chain A, Connector Protein From Bacteriophage Ph... 27 4.4
pdb|1BJQ|B Chain B, The Dolichos Biflorus Seed Lectin In Co... 27 4.4
pdb|1JAD|A Chain A, C-Terminal Domain Of Turkey Plc-Beta >g... 26 5.8
pdb|1HZJ|A Chain A, Human Udp-Galactose 4-Epimerase: Accomm... 26 7.6
pdb|1FOU|A Chain A, Connector Protein From Bacteriophage Ph... 26 7.6
pdb|1LN4|A Chain A, Crystal Structure Of E. Coli Yhby 26 7.6
pdb|1I3K|A Chain A, Molecular Basis For Severe Epimerase-De... 26 7.6
pdb|1LL1| Hydroxo Bridge Met Form Hemocyanin From Limulus 26 7.6
pdb|1HYG|A Chain A, Crystal Structure Of Mj0490 Gene Produc... 26 7.6
pdb|1DGT|B Chain B, Crystal Structure Of Nad+-Dependent Dna... 26 7.6
pdb|1EK6|A Chain A, Structure Of Human Udp-Galactose 4-Epim... 26 7.6
pdb|1IHO|A Chain A, Crystal Apo-Structure Of Pantothenate S... 26 7.6
>pdb|1IW7|A Chain A, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|B Chain B, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|K Chain K, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|L Chain L, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
Length = 315
Score = 157 bits (396), Expect = 2e-39
Identities = 96/296 (32%), Positives = 163/296 (54%), Gaps = 16/296 (5%)
Query: 28 LAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTEDVSLFIMNLKN 87
L P E G+ VTL +P+RR+LL S G A + IE V HEF ++ GV EDV I+NLK
Sbjct: 25 LEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKE 84
Query: 88 --IRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARD-LNSEQIEIVNPEMPLATINED 144
+RF+ +L Q+V + +GP E++ARD L +EI+NP++ +AT+ E
Sbjct: 85 LVVRFLNPSL---------QTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEG 135
Query: 145 AQLNFSLIIYKGMGYVPSENTRELMPEGYMPLDGSFTPIKKVVYEIENVLVEGDPNYEKI 204
+LN + + +G+GYVP+E +P+D F+P+++V +++E+ + + +K+
Sbjct: 136 GRLNMEVRVDRGVGYVPAEKHGIKDRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKL 195
Query: 205 IFDIETDGQIDPYKAFLSAVKVMSKQLGVFGERPIANT----EYSGDYAQRDDAKDLSAK 260
I TDG + P +A AV+++ + L F A E A + ++L
Sbjct: 196 TLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEELDLP 255
Query: 261 IESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGY 316
+E + LS R + L + GI+ V L+ ++ ++LK + +G++S +EI E L G+
Sbjct: 256 LEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGF 311
>pdb|1L9U|A Chain A, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|B Chain B, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|J Chain J, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|K Chain K, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|A Chain A, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1L9Z|B Chain B, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 314
Score = 150 bits (378), Expect = 3e-37
Identities = 93/295 (31%), Positives = 164/295 (55%), Gaps = 15/295 (5%)
Query: 28 LAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTEDVSLFIMNLKN 87
L P E G+ VTL +P+RR+LL S G A + IE V HEF ++ GV EDV I+NLK
Sbjct: 25 LEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKE 84
Query: 88 --IRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLN-SEQIEIVNPEMPLATINED 144
+RF+ D + + ++++ +GP E+RA D S +EI+NP++ +AT+ E
Sbjct: 85 LVVRFL-------DPKMASTTLIL--RAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEG 135
Query: 145 AQLNFSLIIYKGMGYVPSENTRELMPEGYMPLDGSFTPIKKVVYEIENVLVEGDPNYEKI 204
+L + + +G+GYVP+E +P+D F+P+++V +++E+ + + +K+
Sbjct: 136 GKLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKL 195
Query: 205 IFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYAQRDDA-KDLSAKI 261
I TDG + P +A AV ++ + L F E + T +R+ A +DL +
Sbjct: 196 TLRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDLPL 255
Query: 262 ESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGY 316
E + LS R + L + GI+ V L+ ++ ++L+ + +G++S +EI + L G+
Sbjct: 256 EELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGF 310
>pdb|1I6V|B Chain B, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
pdb|1I6V|A Chain A, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 314
Score = 149 bits (377), Expect = 3e-37
Identities = 91/295 (30%), Positives = 161/295 (53%), Gaps = 15/295 (5%)
Query: 28 LAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTEDVSLFIMNLKN 87
L P E G+ VTL +P+RR+LL S G A + IE V HEF ++ GV EDV I+NLK
Sbjct: 25 LEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKE 84
Query: 88 --IRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLN-SEQIEIVNPEMPLATINED 144
+RF+ D + + ++++ +GP E+RA D S +EI+NP++ +AT+ E
Sbjct: 85 LVVRFL-------DPKMASTTLIL--RAEGPKEVRAVDFTPSADVEIMNPDLHIATLEEG 135
Query: 145 AQLNFSLIIYKGMGYVPSENTRELMPEGYMPLDGSFTPIKKVVYEIENVLVEGDPNYEKI 204
+L + + +G+GYVP+E +P+D F+P+++V +++E+ + + +K+
Sbjct: 136 GKLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKL 195
Query: 205 IFDIETDGQIDPYKAFLSAVKVMSKQLGVFGE---RPIANTEYSGDYAQRDDAKDLSAKI 261
I TDG + P +A AV ++ + L F + E S + +DL +
Sbjct: 196 TLRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASSLPTPEVSKGEKRESAEEDLDLPL 255
Query: 262 ESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGY 316
E + LS R + L + GI+ V L+ ++ ++L+ + +G++S +EI + L G+
Sbjct: 256 EELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGF 310
>pdb|1HQM|B Chain B, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
pdb|1HQM|A Chain A, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 313
Score = 145 bits (367), Expect = 5e-36
Identities = 93/295 (31%), Positives = 160/295 (53%), Gaps = 16/295 (5%)
Query: 28 LAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTEDVSLFIMNLKN 87
L P E G+ VTL +P+RR+LL S G A + IE V HEF ++ GV EDV I+NLK
Sbjct: 25 LEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKE 84
Query: 88 --IRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLN-SEQIEIVNPEMPLATINED 144
+RF+ D ++ +GP E+RA D S +EI+NP++ +AT+ E
Sbjct: 85 LVVRFL-------DPRWRTTLIL---RAEGPKEVRAVDFTPSADVEIMNPDLHIATLEEG 134
Query: 145 AQLNFSLIIYKGMGYVPSENTRELMPEGYMPLDGSFTPIKKVVYEIENVLVEGDPNYEKI 204
+L + + +G+GYVP+E +P+D F+P+++V +++E+ + + +K+
Sbjct: 135 GKLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKL 194
Query: 205 IFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYAQRDDA-KDLSAKI 261
I TDG + P +A AV ++ + L F E + T +R+ A +DL +
Sbjct: 195 TLRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDLPL 254
Query: 262 ESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGY 316
E + LS R + L + GI+ V L+ ++ ++L+ + +G++S +EI + L G+
Sbjct: 255 EELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGF 309
>pdb|1BDF|B Chain B, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
N-Terminal Domain
pdb|1BDF|D Chain D, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
N-Terminal Domain
pdb|1BDF|C Chain C, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
N-Terminal Domain
pdb|1BDF|A Chain A, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
N-Terminal Domain
Length = 235
Score = 110 bits (274), Expect = 3e-25
Identities = 65/232 (28%), Positives = 126/232 (54%), Gaps = 15/232 (6%)
Query: 9 LIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEF 68
L P + + + K++L P E G+ TL + +R +LL S G A ++I+GV HE+
Sbjct: 9 LKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEIDGVLHEY 68
Query: 69 DSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE- 127
+ GV ED+ ++NLK +A + G+D V++ + G + A D+ +
Sbjct: 69 STKEGVQEDILEILLNLKG---LAVRVQGKD------EVILTLNKSGIGPVTAADITHDG 119
Query: 128 QIEIVNPEMPLATI-NEDAQLNFSLIIYKGMGYVPS----ENTRELMPEGYMPLDGSFTP 182
+EIV P+ + + +E+A ++ + + +G GYVP+ + + P G + +D ++P
Sbjct: 120 DVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSP 179
Query: 183 IKKVVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF 234
++++ Y +E VE + +K++ ++ET+G IDP +A A ++++QL F
Sbjct: 180 VERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAF 231
>pdb|1LB2|B Chain B, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna
Polymerase In Complex With Cap And Dna
pdb|1LB2|E Chain E, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna
Polymerase In Complex With Cap And Dna
Length = 84
Score = 47.0 bits (110), Expect = 3e-06
Identities = 24/62 (38%), Positives = 34/62 (54%)
Query: 261 IESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGYPVGT 320
++ + L+ R NCL I Y+G+LV +E EL N+GKKS EI + L G +G
Sbjct: 12 VDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGM 71
Query: 321 EL 322
L
Sbjct: 72 RL 73
>pdb|1COO| The Cooh-Terminal Domain Of Rna Polymerase Alpha Subunit
Length = 98
Score = 47.0 bits (110), Expect = 3e-06
Identities = 24/62 (38%), Positives = 34/62 (54%)
Query: 261 IESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGYPVGT 320
++ + L+ R NCL I Y+G+LV +E EL N+GKKS EI + L G +G
Sbjct: 26 VDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGM 85
Query: 321 EL 322
L
Sbjct: 86 RL 87
>pdb|1DOQ|A Chain A, The C-Terminal Domain Of The Rna Polymerase Alpha Subunit
From Thermus Thermophilus
Length = 69
Score = 40.4 bits (93), Expect = 3e-04
Identities = 19/65 (29%), Positives = 38/65 (58%)
Query: 252 DDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKL 311
+ ++L +E + LS R + L + GI+ V L+ ++ ++LK + +G++S +EI E L
Sbjct: 1 EQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEAL 60
Query: 312 NDLGY 316
G+
Sbjct: 61 EKKGF 65
>pdb|1I60|A Chain A, Structural Genomics, Ioli Protein
pdb|1I6N|A Chain A, 1.8 A Crystal Structure Of Ioli Protein With A Binding
Zinc Atom
Length = 278
Score = 31.6 bits (70), Expect = 0.14
Identities = 16/49 (32%), Positives = 32/49 (64%), Gaps = 2/49 (4%)
Query: 277 IGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGYPVGTELSPE 325
+G+KYV + L++E+++ VK KKS ++ +L+D+ P G +++ E
Sbjct: 96 LGVKYVVAVPLVTEQKI--VKEEIKKSSVDVLTELSDIAEPYGVKIALE 142
>pdb|1AV1|A Chain A, Crystal Structure Of Human Apolipoprotein A-I
pdb|1AV1|B Chain B, Crystal Structure Of Human Apolipoprotein A-I
pdb|1AV1|C Chain C, Crystal Structure Of Human Apolipoprotein A-I
pdb|1AV1|D Chain D, Crystal Structure Of Human Apolipoprotein A-I
Length = 201
Score = 30.4 bits (67), Expect = 0.31
Identities = 37/146 (25%), Positives = 63/146 (42%), Gaps = 23/146 (15%)
Query: 214 IDPYKAFLSAVKVMSKQLGVFGERPIANTEYSGDYAQRDDAKDLSAKIESMNLSARCFNC 273
+D + + S + +QLG + N E + +++ +KDL + A+
Sbjct: 5 LDNWDSVTSTFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLE------EVKAKVQPY 58
Query: 274 LDKIGIKYVGELVLMSE--EELKGVKNMG-KKSYDEIAEKLNDLGYPVG----------- 319
LD K+ E+ L + E L+ G ++ E+ EKL+ LG +
Sbjct: 59 LDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEEMRDRARAHVDALR 118
Query: 320 TELSP---EQRESLKKRLEKLEDKGG 342
T L+P E R+ L RLE L++ GG
Sbjct: 119 THLAPYSDELRQRLAARLEALKENGG 144
>pdb|1DII|A Chain A, Crystal Structure Of P-Cresol Methylhydroxylase At 2.5 A
Resolution
pdb|1DII|B Chain B, Crystal Structure Of P-Cresol Methylhydroxylase At 2.5 A
Resolution
pdb|1DIQ|A Chain A, Crystal Structure Of P-Cresol Methylhydroxylase With
Substrate Bound
pdb|1DIQ|B Chain B, Crystal Structure Of P-Cresol Methylhydroxylase With
Substrate Bound
Length = 521
Score = 29.3 bits (64), Expect = 0.68
Identities = 15/27 (55%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 156 GMGYVPSENTRELMPEGYMP-LDGSFT 181
GMG VP NT ++ GY P LDG FT
Sbjct: 198 GMGGVPGSNTWQIFKWGYGPTLDGMFT 224
>pdb|1H6E|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Ctla-4 Internalization Peptide
Ttgvyvkmppt
Length = 288
Score = 28.1 bits (61), Expect = 1.5
Identities = 15/40 (37%), Positives = 24/40 (59%)
Query: 284 ELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGYPVGTELS 323
E L+SEE+L+G+K + + ++ E +N L P G LS
Sbjct: 7 EQKLISEEDLEGIKYRRNELFLDVLESVNLLMSPQGQVLS 46
>pdb|1D06|A Chain A, Structural Basis Of Dimerization And Sensory Mechanisms Of
Oxygen-Sensing Domain Of Rhizobium Meliloti Fixl
Determined At 1.4a Resolution
pdb|1EW0|A Chain A, Crystal Structure Analysis Of The Sensor Domain Of
Rmfixl(Ferrous Form)
Length = 130
Score = 27.7 bits (60), Expect = 2.0
Identities = 17/59 (28%), Positives = 27/59 (44%), Gaps = 4/59 (6%)
Query: 119 LRARDLNSEQIEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSE----NTRELMPEGY 173
+RARD + I P+ + + + ++F+ + GY E N R LMPE Y
Sbjct: 11 VRARDAHLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPY 69
>pdb|1K83|J Chain J, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1I50|J Chain J, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I3Q|J Chain J, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I6H|J Chain J, Rna Polymerase Ii Elongation Complex
Length = 70
Score = 27.7 bits (60), Expect = 2.0
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 264 MNLSARCFNCLDKIGIKYVGELVLMSEEEL---KGVKNMGKKSY 304
M + RCF+C +G K+ L L+ E+EL + +G K Y
Sbjct: 1 MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRY 44
>pdb|1DD3|A Chain A, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritima
pdb|1DD3|B Chain B, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritima
pdb|1DD4|A Chain A, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritima
pdb|1DD4|B Chain B, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritima
pdb|1GIY|I Chain I, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules Are
In The File 1gix
pdb|1GIY|J Chain J, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules Are
In The File 1gix
Length = 128
Score = 26.9 bits (58), Expect = 3.4
Identities = 13/58 (22%), Positives = 30/58 (51%)
Query: 279 IKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGYPVGTELSPEQRESLKKRLEK 336
+K G+ + + ++ + +G K ++ EK + + +S E+ E +KK+LE+
Sbjct: 63 LKSFGQNKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLEE 120
>pdb|1JNB|A Chain A, Connector Protein From Bacteriophage Phi29
pdb|1JNB|B Chain B, Connector Protein From Bacteriophage Phi29
pdb|1JNB|C Chain C, Connector Protein From Bacteriophage Phi29
pdb|1JNB|D Chain D, Connector Protein From Bacteriophage Phi29
pdb|1JNB|E Chain E, Connector Protein From Bacteriophage Phi29
pdb|1JNB|F Chain F, Connector Protein From Bacteriophage Phi29
pdb|1JNB|G Chain G, Connector Protein From Bacteriophage Phi29
pdb|1JNB|H Chain H, Connector Protein From Bacteriophage Phi29
pdb|1JNB|I Chain I, Connector Protein From Bacteriophage Phi29
pdb|1JNB|J Chain J, Connector Protein From Bacteriophage Phi29
pdb|1JNB|K Chain K, Connector Protein From Bacteriophage Phi29
pdb|1JNB|L Chain L, Connector Protein From Bacteriophage Phi29
pdb|1IJG|A Chain A, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|B Chain B, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|C Chain C, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|D Chain D, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|E Chain E, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|F Chain F, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|G Chain G, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|H Chain H, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|I Chain I, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|J Chain J, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|K Chain K, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1IJG|L Chain L, Structure Of The Bacteriophage Phi29 Head-Tail Connector
Protein
pdb|1H5W|B Chain B, 2.1a Bacteriophage Phi-29 Connector
pdb|1H5W|C Chain C, 2.1a Bacteriophage Phi-29 Connector
pdb|1H5W|A Chain A, 2.1a Bacteriophage Phi-29 Connector
Length = 309
Score = 26.6 bits (57), Expect = 4.4
Identities = 15/61 (24%), Positives = 35/61 (56%), Gaps = 1/61 (1%)
Query: 280 KYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDL-GYPVGTELSPEQRESLKKRLEKLE 338
+ V + V ++E+++ + KS +E EK+N+L G V + + E +++ L+++E
Sbjct: 237 RMVTDEVSSNDEQIESSGTVFLKSREEACEKINELYGLNVKVKFRYDIVEQMRRELQQIE 296
Query: 339 D 339
+
Sbjct: 297 N 297
>pdb|1BJQ|B Chain B, The Dolichos Biflorus Seed Lectin In Complex With Adenine
pdb|1BJQ|H Chain H, The Dolichos Biflorus Seed Lectin In Complex With Adenine
pdb|1BJQ|A Chain A, The Dolichos Biflorus Seed Lectin In Complex With Adenine
pdb|1BJQ|G Chain G, The Dolichos Biflorus Seed Lectin In Complex With Adenine
pdb|1LU1| The Structure Of The Dolichos Biflorus Seed Lectin In Complex With
The Forssman Disaccharide
pdb|1LU2|A Chain A, Dolichos Biflorus Seed Lectin In Complex With The Blood
Group A Trisaccharide
pdb|1LU2|B Chain B, Dolichos Biflorus Seed Lectin In Complex With The Blood
Group A Trisaccharide
pdb|1BJQ|C Chain C, The Dolichos Biflorus Seed Lectin In Complex With Adenine
pdb|1BJQ|D Chain D, The Dolichos Biflorus Seed Lectin In Complex With Adenine
pdb|1BJQ|E Chain E, The Dolichos Biflorus Seed Lectin In Complex With Adenine
pdb|1BJQ|F Chain F, The Dolichos Biflorus Seed Lectin In Complex With Adenine
Length = 253
Score = 26.6 bits (57), Expect = 4.4
Identities = 31/137 (22%), Positives = 57/137 (40%), Gaps = 15/137 (10%)
Query: 67 EFDSLRGVTEDVSLFIMNLKNIRFIAKALVGQD-SSLENQSVVVDYSFKGPMEL------ 119
EFD+L D S+ + + + A V D ++ EN +++ Y+ + +
Sbjct: 123 EFDTLSNSGWDPSMKHIGIDVNSIKSIATVSWDLANGENAEILITYNAATSLLVASLVHP 182
Query: 120 --RARDLNSEQIEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTRELMPEGYMPLD 177
R + SE+++I N E+P E + FS GY+ + + +P D
Sbjct: 183 SRRTSYILSERVDITN-ELP-----EYVSVGFSATTGLSEGYIETHDVLSWSFASKLPDD 236
Query: 178 GSFTPIKKVVYEIENVL 194
+ P+ Y + NVL
Sbjct: 237 STAEPLDLASYLVRNVL 253
>pdb|1JAD|A Chain A, C-Terminal Domain Of Turkey Plc-Beta
pdb|1JAD|B Chain B, C-Terminal Domain Of Turkey Plc-Beta
Length = 251
Score = 26.2 bits (56), Expect = 5.8
Identities = 19/56 (33%), Positives = 30/56 (52%), Gaps = 7/56 (12%)
Query: 284 ELVLMSEEELKGVKNMGKKSYDEIAEKLNDL----GYPVGTELSPEQRESLKKRLE 335
+L+ E+ELK ++ G K +E+ +K + L YP G + Q LK+RLE
Sbjct: 32 KLLKKQEKELKELERKGSKRREELLQKYSVLFLEPVYPRGLD---SQVVELKERLE 84
>pdb|1HZJ|A Chain A, Human Udp-Galactose 4-Epimerase: Accommodation Of Udp-N-
Acetylglucosamine Within The Active Site
pdb|1HZJ|B Chain B, Human Udp-Galactose 4-Epimerase: Accommodation Of Udp-N-
Acetylglucosamine Within The Active Site
Length = 348
Score = 25.8 bits (55), Expect = 7.6
Identities = 9/26 (34%), Positives = 16/26 (60%)
Query: 151 LIIYKGMGYVPSENTRELMPEGYMPL 176
+++ G GY+ S EL+ GY+P+
Sbjct: 5 VLVTGGAGYIGSHTVLELLEAGYLPV 30
>pdb|1FOU|A Chain A, Connector Protein From Bacteriophage Phi29
pdb|1FOU|B Chain B, Connector Protein From Bacteriophage Phi29
pdb|1FOU|C Chain C, Connector Protein From Bacteriophage Phi29
pdb|1FOU|D Chain D, Connector Protein From Bacteriophage Phi29
pdb|1FOU|E Chain E, Connector Protein From Bacteriophage Phi29
pdb|1FOU|F Chain F, Connector Protein From Bacteriophage Phi29
pdb|1FOU|G Chain G, Connector Protein From Bacteriophage Phi29
pdb|1FOU|H Chain H, Connector Protein From Bacteriophage Phi29
pdb|1FOU|I Chain I, Connector Protein From Bacteriophage Phi29
pdb|1FOU|J Chain J, Connector Protein From Bacteriophage Phi29
pdb|1FOU|K Chain K, Connector Protein From Bacteriophage Phi29
pdb|1FOU|L Chain L, Connector Protein From Bacteriophage Phi29
Length = 309
Score = 25.8 bits (55), Expect = 7.6
Identities = 15/61 (24%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 280 KYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDL-GYPVGTELSPEQRESLKKRLEKLE 338
+ V + V ++E++ + KS +E EK+N+L G V + + E +++ L+++E
Sbjct: 237 RMVTDEVSSNDEQIDSSGTVFLKSREEACEKINELYGLNVKVKFRYDIVEQMRRELQQIE 296
Query: 339 D 339
+
Sbjct: 297 N 297
>pdb|1LN4|A Chain A, Crystal Structure Of E. Coli Yhby
Length = 104
Score = 25.8 bits (55), Expect = 7.6
Identities = 17/42 (40%), Positives = 24/42 (56%), Gaps = 3/42 (7%)
Query: 39 LAHPIRRLLLLSSVGYAP-VGLKIEGV--HHEFDSLRGVTED 77
LAHP++ ++LL S G V +IE HHE ++ TED
Sbjct: 14 LAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATED 55
>pdb|1I3K|A Chain A, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3L|A Chain A, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3N|A Chain A, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3M|A Chain A, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3K|B Chain B, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3L|B Chain B, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3N|B Chain B, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
pdb|1I3M|B Chain B, Molecular Basis For Severe Epimerase-Deficiency
Galactosemia: X-Ray Structure Of The Human V94m-
Substituted Udp-Galactose 4-Epimerase
Length = 348
Score = 25.8 bits (55), Expect = 7.6
Identities = 9/26 (34%), Positives = 16/26 (60%)
Query: 151 LIIYKGMGYVPSENTRELMPEGYMPL 176
+++ G GY+ S EL+ GY+P+
Sbjct: 5 VLVTGGAGYIGSHTVLELLEAGYLPV 30
>pdb|1LL1| Hydroxo Bridge Met Form Hemocyanin From Limulus
Length = 590
Score = 25.8 bits (55), Expect = 7.6
Identities = 15/47 (31%), Positives = 26/47 (54%), Gaps = 6/47 (12%)
Query: 155 KGMGYVPSENTRELMPEGYMPLDGSFTPIKKVVYEIENVLVEGDPNY 201
KG+ YVP +E+ P+ ++P KK++ ++ N+L DP Y
Sbjct: 94 KGL-YVPP--VQEIFPDKFIPSAAINEAFKKILVDVGNIL---DPEY 134
>pdb|1HYG|A Chain A, Crystal Structure Of Mj0490 Gene Product, The Family Of
LactateMALATE DEHYDROGENASE
pdb|1HYG|B Chain B, Crystal Structure Of Mj0490 Gene Product, The Family Of
LactateMALATE DEHYDROGENASE
pdb|1HYE|A Chain A, Crystal Structure Of The Mj0490 Gene Product, The Family
Of LactateMALATE DEHYDROGENASE, DIMERIC STRUCTURE
Length = 313
Score = 25.8 bits (55), Expect = 7.6
Identities = 10/33 (30%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 60 KIEGVHHE-FDSLRGVTEDVSLFIMNLKNIRFI 91
K+EG+ + +D+L G D ++++ + +N+R I
Sbjct: 40 KLEGLREDIYDALAGTRSDANIYVESDENLRII 72
>pdb|1DGT|B Chain B, Crystal Structure Of Nad+-Dependent Dna Ligase
pdb|1DGS|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase From T.
Filiformis
pdb|1DGS|B Chain B, Crystal Structure Of Nad+-Dependent Dna Ligase From T.
Filiformis
pdb|1DGT|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase
Length = 667
Score = 25.8 bits (55), Expect = 7.6
Identities = 11/40 (27%), Positives = 25/40 (62%)
Query: 274 LDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLND 313
L+K ++ V +L + +E+L G++ MG+KS + ++ +
Sbjct: 458 LEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEE 497
>pdb|1EK6|A Chain A, Structure Of Human Udp-Galactose 4-Epimerase Complexed
With Nadh And Udp-Glucose
pdb|1EK5|A Chain A, Structure Of Human Udp-Galactose 4-Epimerase In Complex
With Nad+
pdb|1EK6|B Chain B, Structure Of Human Udp-Galactose 4-Epimerase Complexed
With Nadh And Udp-Glucose
Length = 348
Score = 25.8 bits (55), Expect = 7.6
Identities = 9/26 (34%), Positives = 16/26 (60%)
Query: 151 LIIYKGMGYVPSENTRELMPEGYMPL 176
+++ G GY+ S EL+ GY+P+
Sbjct: 5 VLVTGGAGYIGSHTVLELLEAGYLPV 30
>pdb|1IHO|A Chain A, Crystal Apo-Structure Of Pantothenate Synthetase From E.
Coli
pdb|1IHO|B Chain B, Crystal Apo-Structure Of Pantothenate Synthetase From E.
Coli
Length = 283
Score = 25.8 bits (55), Expect = 7.6
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 1 MKVIKTAPLIPSEIKVLEKEGNRVKI 26
M +I+T PL+ +I+ L EG RV +
Sbjct: 1 MLIIETLPLLRQQIRRLRMEGKRVAL 26
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.315 0.137 0.377
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,991,167
Number of Sequences: 13198
Number of extensions: 84959
Number of successful extensions: 121
Number of sequences better than 10.0: 27
Number of HSP's better than 10.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 91
Number of HSP's gapped (non-prelim): 27
length of query: 344
length of database: 2,899,336
effective HSP length: 89
effective length of query: 255
effective length of database: 1,724,714
effective search space: 439802070
effective search space used: 439802070
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)