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|15644748|ref|NP_206918.1| hypothetical protein
[Helicobacter pylori 26695]
(395 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|1I84|S Chain S, Cryo-Em Structure Of The Heavy Meromyos... 38 0.002
pdb|1F5N|A Chain A, Human Guanylate Binding Protein-1 In Co... 30 0.36
pdb|1FBN|A Chain A, Crystal Structure Of A Fibrillarin Homo... 29 0.81
pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dn... 27 4.0
pdb|1LPQ|A Chain A, Human Dna Topoisomerase I (70 Kda) In N... 27 5.3
pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomeras... 27 5.3
pdb|1JKW| Structure Of Cyclin Mcs2 27 5.3
pdb|1K83|C Chain C, Crystal Structure Of Yeast Rna Polymera... 27 5.3
pdb|1A36|A Chain A, Human Dna Topoisomerase I (70 Kda) In N... 27 5.3
pdb|1A31|A Chain A, Human Reconstituted Dna Topoisomerase I... 27 5.3
pdb|1A35|A Chain A, Human Reconstituted Dna Topoisomerase I... 27 5.3
pdb|1KXU| Cyclin H, A Positive Regulatory Subunit Of Cdk ... 27 5.3
>pdb|1I84|S Chain S, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
Chicken Gizzard Smooth Muscle Myosin With Regulatory
Light Chain In The Dephosphorylated State. Only C Alphas
Provided For Regulatory Light Chain. Only Backbone Atoms
Provided For S2 Fragment.
pdb|1I84|V Chain V, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
Chicken Gizzard Smooth Muscle Myosin With Regulatory
Light Chain In The Dephosphorylated State. Only C Alphas
Provided For Regulatory Light Chain. Only Backbone Atoms
Provided For S2 Fragment
Length = 1184
Score = 37.7 bits (86), Expect = 0.002
Identities = 59/315 (18%), Positives = 146/315 (45%), Gaps = 38/315 (12%)
Query: 78 KAKELDDKVQDKSKQAEKENQINWWKYSGLTIATSLLLAACSTGDVSEQIELEQEKQKTS 137
K +EL + +++ ++AE E + K++ L +LL Q +L+ E + +
Sbjct: 862 KDEELQ-RTKERQQKAEAELKELEQKHTQLCEEKNLL-----------QEKLQAETELYA 909
Query: 138 NIETNNQIKVEQEKQKTSNIETNNQIKVEQEQQKTSNTQKDLVKEQKDLVKEQKDLVKEQ 197
E ++++ +KQ+ I + ++E+E++++ Q + K Q+ ++ ++ L +E+
Sbjct: 910 EAE-EMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEE 968
Query: 198 KDLVKEQKDLVKTQKDFIKYVEQN---CQENHNQFFIEKGGIKAGIGIEVEAECKTPKPA 254
K Q + V T IK +E + ++ +N+ E+ ++ + + + A
Sbjct: 969 AARQKLQLEKV-TADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKA 1027
Query: 255 KTNQTPIQPKH--LPNSKQPRSQRGSKAQELIAYLQKELEFLPYSQKAIAKQVDFYRPSS 312
K N T ++ KH + + + R ++ K+++ + ++++LE + D +
Sbjct: 1028 K-NLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLE---------GESSDLH--EQ 1075
Query: 313 IAYLELDPRDFKVTEEWQKENLKIRSKAQAKMLEMRNPQAHLSNS-QSLLFVQKIFADVN 371
IA L+ + K ++E L QA + + + + +N+ + + ++ +D+
Sbjct: 1076 IAELQAQIAELKAQLAKKEEEL------QAALARLEDETSQKNNALKKIRELESHISDLQ 1129
Query: 372 KEIEAVANTEKKAEK 386
+++E+ KAEK
Sbjct: 1130 EDLESEKAARNKAEK 1144
>pdb|1F5N|A Chain A, Human Guanylate Binding Protein-1 In Complex With The Gtp
Analogue, Gmppnp.
pdb|1DG3|A Chain A, Structure Of Human Guanylate Binding Protein-1 In
Nucleotide Free Form
Length = 592
Score = 30.4 bits (67), Expect = 0.36
Identities = 25/127 (19%), Positives = 57/127 (44%), Gaps = 1/127 (0%)
Query: 77 KKAKELDDKVQDKSKQAEKENQINWWKYSGLTIATSLLLAACSTGDVSEQIELEQEKQKT 136
+K ++L K ++ ++ + +I T +L T E+ E+E E+ K
Sbjct: 438 QKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEK-EIEVERVKA 496
Query: 137 SNIETNNQIKVEQEKQKTSNIETNNQIKVEQEQQKTSNTQKDLVKEQKDLVKEQKDLVKE 196
+ + + ++ E +++ +E + E +Q T + D V+ K+ + ++E
Sbjct: 497 ESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQE 556
Query: 197 QKDLVKE 203
Q+ L+KE
Sbjct: 557 QEQLLKE 563
>pdb|1FBN|A Chain A, Crystal Structure Of A Fibrillarin Homologue From
Methanococcus Jannaschii, A Hyperthermophile, At 1.6 A
Length = 230
Score = 29.3 bits (64), Expect = 0.81
Identities = 11/41 (26%), Positives = 26/41 (62%)
Query: 178 DLVKEQKDLVKEQKDLVKEQKDLVKEQKDLVKTQKDFIKYV 218
D+ K+ K++ KEQK++++ + ++ D+ +KD + +V
Sbjct: 184 DVTKDPKEIFKEQKEILEAGGFKIVDEVDIEPFEKDHVXFV 224
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 26.9 bits (58), Expect = 4.0
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 8/65 (12%)
Query: 177 KDLVKEQKDLVKEQKD------LVKEQKDLVKEQKDLVKTQKDFIKYVEQ--NCQENHNQ 228
++ + E + ++K Q + L+KE D + E KDL + + F+ YV++ N E +
Sbjct: 23 EEFLNEVEKMLKNQVNTRRIHQLLKELDDPLLENKDLEEKLQAFLDYVKEIPNLPEARKR 82
Query: 229 FFIEK 233
+ I+K
Sbjct: 83 YRIQK 87
>pdb|1LPQ|A Chain A, Human Dna Topoisomerase I (70 Kda) In Non-Covalent Complex
With A 22 Base Pair Dna Duplex Containing An 8-Oxog
Lesion
Length = 564
Score = 26.6 bits (57), Expect = 5.3
Identities = 39/218 (17%), Positives = 84/218 (37%), Gaps = 52/218 (23%)
Query: 149 QEKQKTSNIETNNQIKVEQEQQKTSNTQKDLVKEQKDLVKEQKDLVKEQKDLVKEQKDLV 208
+EK +N+ + ++ Q + + +K + KE+K +KE+ +
Sbjct: 88 EEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENE---------------- 131
Query: 209 KTQKDFIKYVEQNCQENHNQFFIEKGGIKAGIG------------------IEVEAECKT 250
K K++ + N +E F IE G+ G G I + K
Sbjct: 132 KLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKV 191
Query: 251 PKPAKTNQTPIQPKHLPNSKQPRSQRGSKAQELIAY---LQKELEFLPYSQKA-IAKQVD 306
P P P K + +K L+++ +Q ++++ + + I + D
Sbjct: 192 PSPP------------PGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKD 239
Query: 307 FYRPSSIAYLE--LDPRDFKVTEEWQKENLKIRSKAQA 342
+ + + L+ +D + E+W+ + +K+R +A A
Sbjct: 240 WQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVA 277
>pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomerase I Dna Complex
Length = 563
Score = 26.6 bits (57), Expect = 5.3
Identities = 39/218 (17%), Positives = 84/218 (37%), Gaps = 52/218 (23%)
Query: 149 QEKQKTSNIETNNQIKVEQEQQKTSNTQKDLVKEQKDLVKEQKDLVKEQKDLVKEQKDLV 208
+EK +N+ + ++ Q + + +K + KE+K +KE+ +
Sbjct: 87 EEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENE---------------- 130
Query: 209 KTQKDFIKYVEQNCQENHNQFFIEKGGIKAGIG------------------IEVEAECKT 250
K K++ + N +E F IE G+ G G I + K
Sbjct: 131 KLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKV 190
Query: 251 PKPAKTNQTPIQPKHLPNSKQPRSQRGSKAQELIAY---LQKELEFLPYSQKA-IAKQVD 306
P P P K + +K L+++ +Q ++++ + + I + D
Sbjct: 191 PSPP------------PGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKD 238
Query: 307 FYRPSSIAYLE--LDPRDFKVTEEWQKENLKIRSKAQA 342
+ + + L+ +D + E+W+ + +K+R +A A
Sbjct: 239 WQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVA 276
>pdb|1JKW| Structure Of Cyclin Mcs2
Length = 323
Score = 26.6 bits (57), Expect = 5.3
Identities = 22/63 (34%), Positives = 28/63 (43%), Gaps = 15/63 (23%)
Query: 49 IAKKVRGLVKKHPKKSSAALVVLT-------------HIACKKAK--ELDDKVQDKSKQA 93
I K +R LVKK+ S + VL ++ KK K E DD V KSK
Sbjct: 251 IMKSMRNLVKKYEPPRSEEVAVLKQKLDRCHSAELALNVITKKRKGYEDDDYVSKKSKHE 310
Query: 94 EKE 96
E+E
Sbjct: 311 EEE 313
>pdb|1K83|C Chain C, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1I50|C Chain C, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I3Q|C Chain C, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I6H|C Chain C, Rna Polymerase Ii Elongation Complex
Length = 318
Score = 26.6 bits (57), Expect = 5.3
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 283 LIAYLQK--ELEFLPYSQKAIAKQVDFYRPSSIAYLELDP-RDFKVTEEWQKENLKIRSK 339
LI L+K EL+ ++K IAK+ + P++ E DP K T+ W +++ +
Sbjct: 143 LICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQD-SAKEW 201
Query: 340 AQAKMLEMRNP 350
Q+K E +P
Sbjct: 202 PQSKNCEYEDP 212
>pdb|1A36|A Chain A, Human Dna Topoisomerase I (70 Kda) In Non-Covalent Complex
With A 22 Base Pair Dna Duplex
Length = 592
Score = 26.6 bits (57), Expect = 5.3
Identities = 39/218 (17%), Positives = 84/218 (37%), Gaps = 52/218 (23%)
Query: 149 QEKQKTSNIETNNQIKVEQEQQKTSNTQKDLVKEQKDLVKEQKDLVKEQKDLVKEQKDLV 208
+EK +N+ + ++ Q + + +K + KE+K +KE+ +
Sbjct: 116 EEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENE---------------- 159
Query: 209 KTQKDFIKYVEQNCQENHNQFFIEKGGIKAGIG------------------IEVEAECKT 250
K K++ + N +E F IE G+ G G I + K
Sbjct: 160 KLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKV 219
Query: 251 PKPAKTNQTPIQPKHLPNSKQPRSQRGSKAQELIAY---LQKELEFLPYSQKA-IAKQVD 306
P P P K + +K L+++ +Q ++++ + + I + D
Sbjct: 220 PSPP------------PGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKD 267
Query: 307 FYRPSSIAYLE--LDPRDFKVTEEWQKENLKIRSKAQA 342
+ + + L+ +D + E+W+ + +K+R +A A
Sbjct: 268 WQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVA 305
>pdb|1A31|A Chain A, Human Reconstituted Dna Topoisomerase I In Covalent
Complex With A 22 Base Pair Dna Duplex
Length = 538
Score = 26.6 bits (57), Expect = 5.3
Identities = 39/218 (17%), Positives = 84/218 (37%), Gaps = 52/218 (23%)
Query: 149 QEKQKTSNIETNNQIKVEQEQQKTSNTQKDLVKEQKDLVKEQKDLVKEQKDLVKEQKDLV 208
+EK +N+ + ++ Q + + +K + KE+K +KE+ +
Sbjct: 115 EEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENE---------------- 158
Query: 209 KTQKDFIKYVEQNCQENHNQFFIEKGGIKAGIG------------------IEVEAECKT 250
K K++ + N +E F IE G+ G G I + K
Sbjct: 159 KLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKV 218
Query: 251 PKPAKTNQTPIQPKHLPNSKQPRSQRGSKAQELIAY---LQKELEFLPYSQKA-IAKQVD 306
P P P K + +K L+++ +Q ++++ + + I + D
Sbjct: 219 PSPP------------PGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKD 266
Query: 307 FYRPSSIAYLE--LDPRDFKVTEEWQKENLKIRSKAQA 342
+ + + L+ +D + E+W+ + +K+R +A A
Sbjct: 267 WQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVA 304
>pdb|1A35|A Chain A, Human Reconstituted Dna Topoisomerase I In Non-Covalent
Complex With A 22 Base Pair Dna Duplex
Length = 538
Score = 26.6 bits (57), Expect = 5.3
Identities = 39/218 (17%), Positives = 84/218 (37%), Gaps = 52/218 (23%)
Query: 149 QEKQKTSNIETNNQIKVEQEQQKTSNTQKDLVKEQKDLVKEQKDLVKEQKDLVKEQKDLV 208
+EK +N+ + ++ Q + + +K + KE+K +KE+ +
Sbjct: 115 EEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENE---------------- 158
Query: 209 KTQKDFIKYVEQNCQENHNQFFIEKGGIKAGIG------------------IEVEAECKT 250
K K++ + N +E F IE G+ G G I + K
Sbjct: 159 KLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKV 218
Query: 251 PKPAKTNQTPIQPKHLPNSKQPRSQRGSKAQELIAY---LQKELEFLPYSQKA-IAKQVD 306
P P P K + +K L+++ +Q ++++ + + I + D
Sbjct: 219 PSPP------------PGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKD 266
Query: 307 FYRPSSIAYLE--LDPRDFKVTEEWQKENLKIRSKAQA 342
+ + + L+ +D + E+W+ + +K+R +A A
Sbjct: 267 WQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVA 304
>pdb|1KXU| Cyclin H, A Positive Regulatory Subunit Of Cdk Activating Kinase
Length = 333
Score = 26.6 bits (57), Expect = 5.3
Identities = 22/63 (34%), Positives = 28/63 (43%), Gaps = 15/63 (23%)
Query: 49 IAKKVRGLVKKHPKKSSAALVVLT-------------HIACKKAK--ELDDKVQDKSKQA 93
I K +R LVKK+ S + VL ++ KK K E DD V KSK
Sbjct: 261 IMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYVSKKSKHE 320
Query: 94 EKE 96
E+E
Sbjct: 321 EEE 323
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
0.308 0.124 0.330
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,015,121
Number of Sequences: 13198
Number of extensions: 76852
Number of successful extensions: 154
Number of sequences better than 10.0: 12
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 138
Number of HSP's gapped (non-prelim): 17
length of query: 395
length of database: 2,899,336
effective HSP length: 90
effective length of query: 305
effective length of database: 1,711,516
effective search space: 522012380
effective search space used: 522012380
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 55 (25.8 bits)