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|15645936|ref|NP_208115.1| ribonuclease HII (rnhB)
[Helicobacter pylori 26695]
(209 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|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus >... 67 2e-12
pdb|1EKE|B Chain B, Crystal Structure Of Class Ii Ribonucle... 49 3e-07
pdb|1IO2|A Chain A, Crystal Structure Of Type 2 Ribonucleas... 47 1e-06
pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dn... 27 2.3
pdb|1GPU|A Chain A, Transketolase Complex With Reaction Int... 25 5.0
pdb|1TKB|A Chain A, Transketolase (E.C.2.2.1.1) Complexed W... 25 5.0
pdb|1AY0|A Chain A, Identification Of Catalytically Importa... 25 5.0
pdb|1F66|G Chain G, 2.6 A Crystal Structure Of A Nucleosome... 25 5.0
pdb|1PLU|A Chain A, Pectate Lyase C From Erwinia Chrysanthe... 25 8.6
>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus
pdb|1I3A|A Chain A, Rnase Hii From Archaeoglobus Fulgidus With Cobalt
Hexammine Chloride
Length = 225
Score = 66.6 bits (161), Expect = 2e-12
Identities = 57/183 (31%), Positives = 89/183 (48%), Gaps = 17/183 (9%)
Query: 6 MTLGIDEAGRGCLAGSLFVAGVACNEKTALEFLKMGLKDSKKLSLKKRFFLEYKIKTHGE 65
M GIDEAG+GC+ G L VAGVAC+++ L K+G+KDSKKLS +R L +I+
Sbjct: 21 MKAGIDEAGKGCVIGPLVVAGVACSDEDRLR--KLGVKDSKKLSQGRREELAEEIRKICR 78
Query: 66 VGFFVVKKSANEID----SLGLGACLKLAVQEI---LENGCSLVDEIKIDGNTAFGLNKR 118
V+K S +D + + LK EI L+ + VD + +
Sbjct: 79 TE--VLKVSPENLDERMAAKTINEILKECYAEIILRLKPEIAYVDSPDVIPERLSRELEE 136
Query: 119 YPHIQTII--KGDETIAQIAMASVLAKAFKDREMLELHALFKEYGWDKNCGYGTKQHIEA 176
++ + K DE +A AS++AK ++RE+ L F ++G GY +
Sbjct: 137 ITGLRVVAEHKADEKYPLVAAASIIAKVEREREIERLKEKFGDFG----SGYASDPRTRE 192
Query: 177 IIK 179
++K
Sbjct: 193 VLK 195
>pdb|1EKE|B Chain B, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii)
With Mes Ligand
pdb|1EKE|A Chain A, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii)
With Mes Ligand
Length = 230
Score = 49.3 bits (116), Expect = 3e-07
Identities = 53/188 (28%), Positives = 87/188 (46%), Gaps = 34/188 (18%)
Query: 8 LGIDEAGRGCLAGSLFVAGVACNEKTALEFLKMGLKDSKKLSLKKRFFLEYKIKTHGEVG 67
+GIDEAGRG + G V A ++ E K+G+KDSK+L+ KR +L+ ++ G V
Sbjct: 4 IGIDEAGRGPVLGPXVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENLGYVE 63
Query: 68 FFVVKKSANEIDSLG---------LGACLKLAVQEILENGCSLVDEIKIDGNTAFGLNKR 118
+++ A EI+ L + A K+A + ++E DEI+I + K+
Sbjct: 64 KRILE--AEEINQLXNSINLNDIEINAFSKVA-KNLIEKLNIRDDEIEIYIDACSTNTKK 120
Query: 119 Y-----PHIQTII-------------KGDETIAQIAMASVLAKAFKDREMLELHALFKEY 160
+ I+ II K D ++ AS++AKA +D E+ +K+
Sbjct: 121 FEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERD----EIIDYYKKI 176
Query: 161 GWDKNCGY 168
D GY
Sbjct: 177 YGDIGSGY 184
>pdb|1IO2|A Chain A, Crystal Structure Of Type 2 Ribonuclease H From
Hyperthermophilic Archaeon, Thermococcus Kodakaraensis
Kod1
Length = 213
Score = 47.4 bits (111), Expect = 1e-06
Identities = 44/171 (25%), Positives = 76/171 (43%), Gaps = 26/171 (15%)
Query: 9 GIDEAGRGCLAGSLFVAGVACNEKTALEFLKMGLKDSKKLSLKKRFFLEYKI-------- 60
GIDEAGRG + G + +A V +E + + ++ ++DSKKL+ K+R L +I
Sbjct: 5 GIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEILGVLDDYV 64
Query: 61 ----------KTHGEVGFFVVKKSANEIDSLGLGACLKLAVQEILENGCSLVDEIKIDGN 110
G + F V+ A ++SL + +++ + VDE +
Sbjct: 65 ILELPPDVIGSREGTLNEFEVENFAKALNSLKV-------KPDVIYADAADVDEERFARE 117
Query: 111 TAFGLNKRYPHIQTIIKGDETIAQIAMASVLAKAFKDREMLELHALFKEYG 161
LN + K D+ ++ AS+LAK +DR + +L + E G
Sbjct: 118 LGERLNFE-AEVVAKHKADDIFPVVSAASILAKVTRDRAVEKLKEEYGEIG 167
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 26.6 bits (57), Expect = 2.3
Identities = 22/58 (37%), Positives = 27/58 (45%), Gaps = 7/58 (12%)
Query: 57 EYKIKTHGEVGFFVVK-------KSANEIDSLGLGACLKLAVQEILENGCSLVDEIKI 107
EY +KT G FF VK K A+ L L + VQEI G L +EIK+
Sbjct: 719 EYDLKTRGPGEFFGVKQHGLSGFKVADLYRDLKLLEWAREDVQEIDVEGIELPEEIKL 776
>pdb|1GPU|A Chain A, Transketolase Complex With Reaction Intermediate
pdb|1GPU|B Chain B, Transketolase Complex With Reaction Intermediate
pdb|1TRK|A Chain A, Transketolase (E.C.2.2.1.1)
pdb|1TRK|B Chain B, Transketolase (E.C.2.2.1.1)
pdb|1NGS|A Chain A, Complex Of Transketolase With Thiamin Diphosphate, Ca2+
And Acceptor Substrate Erythrose-4-Phosphate
pdb|1NGS|B Chain B, Complex Of Transketolase With Thiamin Diphosphate, Ca2+
And Acceptor Substrate Erythrose-4-Phosphate
Length = 680
Score = 25.4 bits (54), Expect = 5.0
Identities = 19/57 (33%), Positives = 28/57 (48%), Gaps = 8/57 (14%)
Query: 103 DEIKIDGNTAFGLN----KRYP----HIQTIIKGDETIAQIAMASVLAKAFKDREML 151
++I IDG T+ + KRY + + G+E +A IA A AK KD+ L
Sbjct: 187 NKITIDGATSISFDEDVAKRYEAYGWEVLYVENGNEDLAGIAKAIAQAKLSKDKPTL 243
>pdb|1TKB|A Chain A, Transketolase (E.C.2.2.1.1) Complexed With
1'-Deazo-Thiamin Diphosphate And Calcium
pdb|1TKB|B Chain B, Transketolase (E.C.2.2.1.1) Complexed With
1'-Deazo-Thiamin Diphosphate And Calcium
pdb|1TKA|A Chain A, Transketolase (E.C.2.2.1.1) Complexed With
3'-Deazo-Thiamin Diphosphate And Calcium
pdb|1TKA|B Chain B, Transketolase (E.C.2.2.1.1) Complexed With
3'-Deazo-Thiamin Diphosphate And Calcium
pdb|1TKC|A Chain A, Transketolase (E.C.2.2.1.1) Complexed With
6'-Methyl-Thiamin Diphosphate And Calcium
pdb|1TKC|B Chain B, Transketolase (E.C.2.2.1.1) Complexed With
6'-Methyl-Thiamin Diphosphate And Calcium
Length = 678
Score = 25.4 bits (54), Expect = 5.0
Identities = 19/57 (33%), Positives = 28/57 (48%), Gaps = 8/57 (14%)
Query: 103 DEIKIDGNTAFGLN----KRYP----HIQTIIKGDETIAQIAMASVLAKAFKDREML 151
++I IDG T+ + KRY + + G+E +A IA A AK KD+ L
Sbjct: 185 NKITIDGATSISFDEDVAKRYEAYGWEVLYVENGNEDLAGIAKAIAQAKLSKDKPTL 241
>pdb|1AY0|A Chain A, Identification Of Catalytically Important Residues In
Yeast Transketolase
pdb|1AY0|B Chain B, Identification Of Catalytically Important Residues In
Yeast Transketolase
Length = 680
Score = 25.4 bits (54), Expect = 5.0
Identities = 19/57 (33%), Positives = 28/57 (48%), Gaps = 8/57 (14%)
Query: 103 DEIKIDGNTAFGLN----KRYP----HIQTIIKGDETIAQIAMASVLAKAFKDREML 151
++I IDG T+ + KRY + + G+E +A IA A AK KD+ L
Sbjct: 187 NKITIDGATSISFDEDVAKRYEAYGWEVLYVENGNEDLAGIAKAIAQAKLSKDKPTL 243
>pdb|1F66|G Chain G, 2.6 A Crystal Structure Of A Nucleosome Core Particle
Containing The Variant Histone H2a.Z
pdb|1F66|C Chain C, 2.6 A Crystal Structure Of A Nucleosome Core Particle
Containing The Variant Histone H2a.Z
Length = 128
Score = 25.4 bits (54), Expect = 5.0
Identities = 21/85 (24%), Positives = 36/85 (41%), Gaps = 16/85 (18%)
Query: 56 LEYKIKTHGEVGFFVVKKSANEIDSLGLGACLKLAVQEILENGCSLVDEIKIDGNTAFGL 115
L+ + +HG VG SA A L+ E+LE + ++K+ T
Sbjct: 37 LKSRTTSHGRVGATAAVYSA---------AILEYLTAEVLELAGNASKDLKVKRITP--- 84
Query: 116 NKRYPHIQTIIKGDETIAQIAMASV 140
H+Q I+GDE + + A++
Sbjct: 85 ----RHLQLAIRGDEELDSLIKATI 105
>pdb|1PLU|A Chain A, Pectate Lyase C From Erwinia Chrysanthemi With 1 Lu+3 Ion
In The Putative Calcium Binding Site
pdb|1AIR| Pectate Lyase C From Erwinia Chrysanthemi (Ec16) To A Resolution
Of 2.2 Angstroms With 128 Waters
pdb|2PEC| The Refined Three-Dimensional Structure Of Pectate Lyase C From
Erwinia Chrysanthemi At 2.2 Angstroms Resolution:
Length = 353
Score = 24.6 bits (52), Expect = 8.6
Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 84 GACLKLAVQEILENGCSLVDEIKIDGNTAFGLNKRYPHIQTIIKGDETIAQIAMASVLAK 143
GA K A +++ +++D ++D N YP + T ++++ A A++ +
Sbjct: 17 GAVSKTATS--MQDIVNIIDAARLDANGKKVKGGAYPLVITYTGNEDSLINAAAANICGQ 74
Query: 144 AFKDREMLELHALFK 158
KD +E+ K
Sbjct: 75 WSKDPRGVEIKEFTK 89
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
0.322 0.140 0.405
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,138,302
Number of Sequences: 13198
Number of extensions: 42296
Number of successful extensions: 79
Number of sequences better than 10.0: 9
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 73
Number of HSP's gapped (non-prelim): 10
length of query: 209
length of database: 2,899,336
effective HSP length: 84
effective length of query: 125
effective length of database: 1,790,704
effective search space: 223838000
effective search space used: 223838000
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)