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|15645314|ref|NP_207485.1| 3-oxoadipate
coA-transferase subunit A (yxjD) [Helicobacter pylori 26695]
(232 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|1K6D|A Chain A, Crystal Structure Of Acetate Coa-Transf... 192 4e-50
pdb|1POI|A Chain A, Crystal Structure Of Glutaconate Coenzy... 33 0.022
pdb|3GPD|G Chain G, Twinning In Crystals Of Human Skeletal ... 27 2.0
pdb|1D6T|A Chain A, Rnase P Protein From Staphylococcus Aureus 27 2.6
pdb|1MKX|K Chain K, The Co-Crystal Structure Of Unliganded ... 26 4.5
pdb|1E25|A Chain A, The High Resolution Structure Of Per-1 ... 25 5.9
pdb|1GPD|G Chain G, D-Glyceraldehyde-3-Phosphate Dehydrogen... 25 5.9
pdb|4GPD|1 Chain 1, Apo-D-Gyceraldehyde-3-Phosphate Dehydro... 25 5.9
pdb|1JYL|A Chain A, Catalytic Mechanism Of Ctp:phosphocholi... 25 5.9
pdb|1JYK|A Chain A, Catalytic Mechanism Of Ctp:phosphocholi... 25 5.9
pdb|1QS1|A Chain A, Crystal Structure Of Vegetative Insecti... 25 7.7
pdb|1KEO|A Chain A, Twists And Turns Of The Cd-Mpr: Ligand-... 25 7.7
pdb|1C39|A Chain A, Structure Of Cation-Dependent Mannose 6... 25 7.7
pdb|3PVA|A Chain A, Penicillin V Acylase From B. Sphaericus... 25 7.7
pdb|2PVA|A Chain A, Oxidized Penicillin V Acylase From B. S... 25 7.7
pdb|1QS2|A Chain A, Crystal Structure Of Vip2 With Nad 25 7.7
>pdb|1K6D|A Chain A, Crystal Structure Of Acetate Coa-Transferase Alpha Subunit
pdb|1K6D|B Chain B, Crystal Structure Of Acetate Coa-Transferase Alpha Subunit
Length = 220
Score = 192 bits (487), Expect = 4e-50
Identities = 91/213 (42%), Positives = 140/213 (65%)
Query: 1 MNKVITDLDKALSALKDGDTILVGGFGLCGIPEYAIDYIYKKGIKDLIVVSNNCGVDDFG 60
M + L A +DG TI+VGGF G P ++ + + G++DL +++N+ D G
Sbjct: 1 MKTKLMTLQDATGFFRDGMTIMVGGFMGIGTPSRLVEALLESGVRDLTLIANDTAFVDTG 60
Query: 61 LGILLEKKQIKKIIASYVGENKIFESQMLNGEIEVVLTPQGTLAENLHAGGAGIPAYYTP 120
+G L+ +++K+IAS++G N +M++GE++VVL PQGTL E + GGAG+ + TP
Sbjct: 61 IGPLIVNGRVRKVIASHIGTNPETGRRMISGEMDVVLVPQGTLIEQIRCGGAGLGGFLTP 120
Query: 121 TGVGTLIAQGKESREFNGKEYILERAITGDYGLIKAYKSDTLGNLVFRKTARNFNPLCAM 180
TGVGT++ +GK++ +GK ++LER + D LI+A++ DTLGNL ++ +ARNFNPL A+
Sbjct: 121 TGVGTVVEEGKQTLTLDGKTWLLERPLRADLALIRAHRCDTLGNLTYQLSARNFNPLIAL 180
Query: 181 AAKICVAEVEEIVPAGELDPDEIHLPGIYVQHI 213
AA I + E +E+V GEL PD I PG + HI
Sbjct: 181 AADITLVEPDELVETGELQPDHIVTPGAVIDHI 213
>pdb|1POI|A Chain A, Crystal Structure Of Glutaconate Coenzyme A-Transferase
From Acidaminococcus Fermentans To 2.55 Angstoms
Resolution
pdb|1POI|C Chain C, Crystal Structure Of Glutaconate Coenzyme A-Transferase
From Acidaminococcus Fermentans To 2.55 Angstoms
Resolution
Length = 317
Score = 33.5 bits (75), Expect = 0.022
Identities = 30/120 (25%), Positives = 49/120 (40%), Gaps = 9/120 (7%)
Query: 2 NKVITDLDKALSALKDGDTILVGGFGLCGIPEYAIDYIYKKGIKDLIVVSNNCGVDDFGL 61
+KV+T D + GD I +GGF P A+ I ++GI DL + G D
Sbjct: 1 SKVMTLKDAIAKYVHSGDHIALGGFTTDRKPYAAVFEILRQGITDLTGLGGAAGGD---W 57
Query: 62 GILLEKKQIKKIIASYVGENKI------FESQMLNGEIEVVLTPQGTLAENLHAGGAGIP 115
+L+ ++K I Y + + F G++ + Q + HA G+P
Sbjct: 58 DMLIGNGRVKAYINCYTANSGVTNVSRRFRKWFEAGKLTMEDYSQDVIYMMWHAAALGLP 117
>pdb|3GPD|G Chain G, Twinning In Crystals Of Human Skeletal Muscle D-
Glyceraldehyde-3-Phosphate Dehydrogenase
pdb|3GPD|R Chain R, Twinning In Crystals Of Human Skeletal Muscle D-
Glyceraldehyde-3-Phosphate Dehydrogenase
Length = 334
Score = 26.9 bits (58), Expect = 2.0
Identities = 33/139 (23%), Positives = 52/139 (36%), Gaps = 15/139 (10%)
Query: 4 VITDLDKALSALKDGDTILVGGFGLCGIPEYAIDYIYKKGIKDLIVVSN-NCGVDDFGLG 62
V T ++KA + LK G +V P + + + K L ++SN +C +
Sbjct: 100 VFTTMEKAGAHLKGGAKRIVISAPSADAPMFVMGVNHFKYANSLKIISNASCTTNCLA-- 157
Query: 63 ILLEKKQIKKIIASYVG--ENKIFESQMLNGEIEVVLTPQGTLAENLHAGGAGIPAYYTP 120
+ K+I + G E + + + V +P G L GG G P
Sbjct: 158 ------PLAKVIHDHFGIVEGLMTTVHAITATQKTVDSPSG----KLWRGGRGAAQNLIP 207
Query: 121 TGVGTLIAQGKESREFNGK 139
G A GK E +GK
Sbjct: 208 ASTGAAKAVGKVIPELDGK 226
>pdb|1D6T|A Chain A, Rnase P Protein From Staphylococcus Aureus
Length = 117
Score = 26.6 bits (57), Expect = 2.6
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 39 IYKKGI-----KDLIVVSNNCGVDDFGLGILLEKK----QIKKIIASYVGEN-KIFESQM 88
IYKKG + ++ NN +D F LGI + KK ++ I + EN K+ +S +
Sbjct: 18 IYKKGHSVANRQFVVYTCNNKEIDHFRLGISVSKKLGNAVLRNKIKRAIRENFKVHKSHI 77
Query: 89 LNGEIEVV 96
L +I V+
Sbjct: 78 LAKDIIVI 85
>pdb|1MKX|K Chain K, The Co-Crystal Structure Of Unliganded Bovine
Alpha-Thrombin And Prethrombin-2: Movement Of The Yppw
Segment And Active Site Residues Upon Ligand Binding
pdb|1MKW|K Chain K, The Co-Crystal Structure Of Unliganded Bovine
Alpha-Thrombin And Prethrombin-2: Movement Of The Yppw
Segment And Active Site Residues Upon Ligand Binding
Length = 308
Score = 25.8 bits (55), Expect = 4.5
Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 10/50 (20%)
Query: 55 GVDDFGLGILLEKKQI-----KKIIASYVGENKIFESQMLNGEIEVVLTP 99
G D GL L EKKQ+ K++ SY+ E +I E Q + EV L+P
Sbjct: 18 GEADCGLRPLFEKKQVQDQTEKELFESYI-EGRIVEGQ----DAEVGLSP 62
>pdb|1E25|A Chain A, The High Resolution Structure Of Per-1 Class A
Beta-Lactamase
Length = 282
Score = 25.4 bits (54), Expect = 5.9
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 26 FGLCGIPEYAIDYIYKKGIKDLIVVSN 52
F L G P DYI GIK+ VV+N
Sbjct: 118 FELVGGPAALHDYIQSMGIKETAVVAN 144
>pdb|1GPD|G Chain G, D-Glyceraldehyde-3-Phosphate Dehydrogenase (E.C.1.2.1.12)
pdb|1GPD|R Chain R, D-Glyceraldehyde-3-Phosphate Dehydrogenase (E.C.1.2.1.12)
Length = 334
Score = 25.4 bits (54), Expect = 5.9
Identities = 36/141 (25%), Positives = 53/141 (37%), Gaps = 19/141 (13%)
Query: 4 VITDLDKALSALKDGDTILVGGFGLCGIPEYAIDYIYKKGIKDLIVVSN-NCGVDDFGLG 62
V T ++KA + K G +V P + +K KD+ VVSN +C +
Sbjct: 98 VFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLA-- 155
Query: 63 ILLEKKQIKKIIASYVGEN-KIFESQMLNGEIEVVLTPQGTL---AENLHAGGAGIPAYY 118
+A + EN +I E M + V Q T+ + GG G
Sbjct: 156 ----------PVAKVLHENFEIVEGLMTT--VHAVTATQKTVDGPSAKDWRGGRGAAQNI 203
Query: 119 TPTGVGTLIAQGKESREFNGK 139
P+ G A GK E +GK
Sbjct: 204 IPSSTGAAKAVGKVIPELDGK 224
>pdb|4GPD|1 Chain 1, Apo-D-Gyceraldehyde-3-Phosphate Dehydrogenase
(E.C.1.2.1.12)
pdb|4GPD|2 Chain 2, Apo-D-Gyceraldehyde-3-Phosphate Dehydrogenase
(E.C.1.2.1.12)
pdb|4GPD|3 Chain 3, Apo-D-Gyceraldehyde-3-Phosphate Dehydrogenase
(E.C.1.2.1.12)
pdb|4GPD|4 Chain 4, Apo-D-Gyceraldehyde-3-Phosphate Dehydrogenase
(E.C.1.2.1.12)
Length = 333
Score = 25.4 bits (54), Expect = 5.9
Identities = 36/141 (25%), Positives = 53/141 (37%), Gaps = 19/141 (13%)
Query: 4 VITDLDKALSALKDGDTILVGGFGLCGIPEYAIDYIYKKGIKDLIVVSN-NCGVDDFGLG 62
V T ++KA + K G +V P + +K KD+ VVSN +C +
Sbjct: 97 VFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLA-- 154
Query: 63 ILLEKKQIKKIIASYVGEN-KIFESQMLNGEIEVVLTPQGTL---AENLHAGGAGIPAYY 118
+A + EN +I E M + V Q T+ + GG G
Sbjct: 155 ----------PVAKVLHENFEIVEGLMTT--VHAVTATQKTVDGPSAKDWRGGRGAAQNI 202
Query: 119 TPTGVGTLIAQGKESREFNGK 139
P+ G A GK E +GK
Sbjct: 203 IPSSTGAAKAVGKVIPELDGK 223
>pdb|1JYL|A Chain A, Catalytic Mechanism Of Ctp:phosphocholine
Cytidylytransferase From Streptococcus Pneumoniae
(Licc)
pdb|1JYL|B Chain B, Catalytic Mechanism Of Ctp:phosphocholine
Cytidylytransferase From Streptococcus Pneumoniae
(Licc)
pdb|1JYL|C Chain C, Catalytic Mechanism Of Ctp:phosphocholine
Cytidylytransferase From Streptococcus Pneumoniae
(Licc)
pdb|1JYL|D Chain D, Catalytic Mechanism Of Ctp:phosphocholine
Cytidylytransferase From Streptococcus Pneumoniae
(Licc)
Length = 254
Score = 25.4 bits (54), Expect = 5.9
Identities = 8/18 (44%), Positives = 15/18 (82%)
Query: 33 EYAIDYIYKKGIKDLIVV 50
EY I+++ +KGI D+I++
Sbjct: 60 EYQIEFLKEKGINDIIII 77
>pdb|1JYK|A Chain A, Catalytic Mechanism Of Ctp:phosphocholine
Cytidylytransferase From Streptococcus Pneumoniae
(Licc)
Length = 254
Score = 25.4 bits (54), Expect = 5.9
Identities = 8/18 (44%), Positives = 15/18 (82%)
Query: 33 EYAIDYIYKKGIKDLIVV 50
EY I+++ +KGI D+I++
Sbjct: 60 EYQIEFLKEKGINDIIII 77
>pdb|1QS1|A Chain A, Crystal Structure Of Vegetative Insecticidal Protein2
(Vip2)
pdb|1QS1|B Chain B, Crystal Structure Of Vegetative Insecticidal Protein2
(Vip2)
pdb|1QS1|C Chain C, Crystal Structure Of Vegetative Insecticidal Protein2
(Vip2)
pdb|1QS1|D Chain D, Crystal Structure Of Vegetative Insecticidal Protein2
(Vip2)
Length = 462
Score = 25.0 bits (53), Expect = 7.7
Identities = 18/59 (30%), Positives = 29/59 (48%), Gaps = 3/59 (5%)
Query: 37 DYIYKKGIKDLIVVSNNCGVDDFGLGI---LLEKKQIKKIIASYVGENKIFESQMLNGE 92
D + KK I + I V CG+ +FG I L K ++ + + E+K + S L+ E
Sbjct: 334 DALGKKPIPENITVYRWCGMPEFGYQISDPLPSLKDFEEQFLNTIKEDKGYMSTSLSSE 392
>pdb|1KEO|A Chain A, Twists And Turns Of The Cd-Mpr: Ligand-Bound Versus
Ligand- Free Receptor
pdb|1KEO|B Chain B, Twists And Turns Of The Cd-Mpr: Ligand-Bound Versus
Ligand- Free Receptor
Length = 154
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 108 HAGGAGIPAYYTPTGVGTLIAQGKESREFNGKEYIL 143
H+ GAG+ G T++ + E++ F G +I+
Sbjct: 58 HSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIM 93
>pdb|1C39|A Chain A, Structure Of Cation-Dependent Mannose 6-Phosphate Receptor
Bound To Pentamannosyl Phosphate
pdb|1C39|B Chain B, Structure Of Cation-Dependent Mannose 6-Phosphate Receptor
Bound To Pentamannosyl Phosphate
pdb|1M6P|A Chain A, Extracytoplasmic Domain Of Bovine Cation-Dependent Mannose
6-Phosphate Receptor
pdb|1M6P|B Chain B, Extracytoplasmic Domain Of Bovine Cation-Dependent Mannose
6-Phosphate Receptor
Length = 152
Score = 25.0 bits (53), Expect = 7.7
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 108 HAGGAGIPAYYTPTGVGTLIAQGKESREFNGKEYIL 143
H+ GAG+ G T++ + E++ F G +I+
Sbjct: 56 HSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIM 91
>pdb|3PVA|A Chain A, Penicillin V Acylase From B. Sphaericus
pdb|3PVA|B Chain B, Penicillin V Acylase From B. Sphaericus
pdb|3PVA|C Chain C, Penicillin V Acylase From B. Sphaericus
pdb|3PVA|D Chain D, Penicillin V Acylase From B. Sphaericus
pdb|3PVA|E Chain E, Penicillin V Acylase From B. Sphaericus
pdb|3PVA|F Chain F, Penicillin V Acylase From B. Sphaericus
pdb|3PVA|G Chain G, Penicillin V Acylase From B. Sphaericus
pdb|3PVA|H Chain H, Penicillin V Acylase From B. Sphaericus
Length = 335
Score = 25.0 bits (53), Expect = 7.7
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 74 IASYVGENKIFESQMLNGEIEVVLTPQGTLAENLHAGGAGIPAYYTPTGVGTLIAQGKES 133
+ +Y+G ++ G++++ QG AGG G+P +TP+ +A K+
Sbjct: 186 LRAYIGVTPNPPQDIMMGDLDLTPFGQG-------AGGLGLPGDFTPSARFLRVAYWKKY 238
Query: 134 RE 135
E
Sbjct: 239 TE 240
>pdb|2PVA|A Chain A, Oxidized Penicillin V Acylase From B. Sphaericus
pdb|2PVA|B Chain B, Oxidized Penicillin V Acylase From B. Sphaericus
pdb|2PVA|C Chain C, Oxidized Penicillin V Acylase From B. Sphaericus
pdb|2PVA|D Chain D, Oxidized Penicillin V Acylase From B. Sphaericus
Length = 345
Score = 25.0 bits (53), Expect = 7.7
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 74 IASYVGENKIFESQMLNGEIEVVLTPQGTLAENLHAGGAGIPAYYTPTGVGTLIAQGKES 133
+ +Y+G ++ G++++ QG AGG G+P +TP+ +A K+
Sbjct: 196 LRAYIGVTPNPPQDIMMGDLDLTPFGQG-------AGGLGLPGDFTPSARFLRVAYWKKY 248
Query: 134 RE 135
E
Sbjct: 249 TE 250
>pdb|1QS2|A Chain A, Crystal Structure Of Vip2 With Nad
Length = 401
Score = 25.0 bits (53), Expect = 7.7
Identities = 18/59 (30%), Positives = 29/59 (48%), Gaps = 3/59 (5%)
Query: 37 DYIYKKGIKDLIVVSNNCGVDDFGLGI---LLEKKQIKKIIASYVGENKIFESQMLNGE 92
D + KK I + I V CG+ +FG I L K ++ + + E+K + S L+ E
Sbjct: 273 DALGKKPIPENITVYRWCGMPEFGYQISDPLPSLKDFEEQFLNTIKEDKGYMSTSLSSE 331
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
0.317 0.141 0.400
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,444,422
Number of Sequences: 13198
Number of extensions: 65140
Number of successful extensions: 167
Number of sequences better than 10.0: 16
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 155
Number of HSP's gapped (non-prelim): 19
length of query: 232
length of database: 2,899,336
effective HSP length: 85
effective length of query: 147
effective length of database: 1,777,506
effective search space: 261293382
effective search space used: 261293382
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)