RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9417
(161 letters)
>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting
domain, arm repeats phospho-CTD, phosphoprotein,
transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A*
3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A
Length = 145
Score = 97.5 bits (242), Expect = 9e-27
Identities = 61/107 (57%), Positives = 82/107 (76%), Gaps = 1/107 (0%)
Query: 56 VIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPG 115
+ +N EL S+N KPPISKAK+T I K A+KA +YK+VVQSVEKFI KCK +YK+PG
Sbjct: 3 AVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPG 62
Query: 116 LYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
LYVID+I+ Q+R QF + KDV+APRF+ N+ TF +++CP +D+ K
Sbjct: 63 LYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109
Score = 62.1 bits (150), Expect = 4e-13
Identities = 44/128 (34%), Positives = 67/128 (52%), Gaps = 7/128 (5%)
Query: 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEW 60
EL S+N KPPISKAK+T I K A+KA +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct: 10 ELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSI 69
Query: 61 NQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKF-----IWKCKSQYKLPG 115
++ + + + + + + Y+ K +W+ + +K
Sbjct: 70 VRQSRHQFGQEKDVFAPRFSNNIISTF--QNLYRCPGDDKSKIVRVLNLWQKNNVFKSEI 127
Query: 116 LYVIDAII 123
+ + +
Sbjct: 128 IQPLLDMA 135
>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA
polymer binding protein, RNA binding protein; 2.10A
{Saccharomyces cerevisiae}
Length = 157
Score = 82.5 bits (203), Expect = 7e-21
Identities = 17/115 (14%), Positives = 34/115 (29%), Gaps = 12/115 (10%)
Query: 59 EWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYV 118
+ L S K IS ++I + AL ++ + + C +KL LY+
Sbjct: 5 NFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYI 64
Query: 119 IDAIIHQARLQFKYKDV-----------YAPRFARNLYRTFGYVFQC-PDEDRKK 161
ID+I + + + + ++K
Sbjct: 65 IDSIGRAYLDETRSNSNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEK 119
Score = 61.7 bits (149), Expect = 6e-13
Identities = 14/57 (24%), Positives = 23/57 (40%)
Query: 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
L S K IS ++I + AL ++ + + C +KL LY+I
Sbjct: 9 TLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYII 65
>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm
repeats, transcription; 2.10A {Saccharomyces cerevisiae}
SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X
Length = 144
Score = 70.5 bits (172), Expect = 2e-16
Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 10/106 (9%)
Query: 56 VIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPG 115
++ ++N L + PI IT + KLA + +Y V ++E I KC + KL
Sbjct: 8 IVKDFNSILEELTFNSRPI----ITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYA 63
Query: 116 LYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
Y +D+I Y F+RNL+ + + D +
Sbjct: 64 FYALDSICKNV------GSPYTIYFSRNLFNLYKRTYLLVDNTTRT 103
Score = 41.6 bits (97), Expect = 1e-05
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 4/57 (7%)
Query: 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
L + PI IT + KLA + +Y V ++E I KC + KL Y +
Sbjct: 15 ILEELTFNSRPI----ITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYAL 67
>4fld_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural
genomics consortium, SGC, protein binding; 2.00A {Homo
sapiens}
Length = 135
Score = 60.8 bits (147), Expect = 1e-12
Identities = 18/101 (17%), Positives = 40/101 (39%), Gaps = 8/101 (7%)
Query: 61 NQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVID 120
++L +++++ + + + +V + + K KS KL LY+ +
Sbjct: 10 EKKLSELSNSQQSVQTLS-----LWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLAN 64
Query: 121 AIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
+I ++ + + F L F +V + DE KK
Sbjct: 65 DVIQNSK---RKGPEFTREFESVLVDAFSHVAREADEGCKK 102
Score = 38.4 bits (89), Expect = 2e-04
Identities = 10/63 (15%), Positives = 24/63 (38%), Gaps = 5/63 (7%)
Query: 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEW 60
+L +++++ + + + +V + + K KS KL LY+ +
Sbjct: 12 KLSELSNSQQSVQTLS-----LWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDV 66
Query: 61 NQE 63
Q
Sbjct: 67 IQN 69
>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural
genomics consortium, SGC, protein binding; 1.80A {Homo
sapiens}
Length = 132
Score = 56.5 bits (136), Expect = 4e-11
Identities = 14/101 (13%), Positives = 35/101 (34%), Gaps = 9/101 (8%)
Query: 61 NQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVID 120
+++ S+ +T I ++ ++ +V K++ + ++L Y+ +
Sbjct: 11 DRKFQSVTNTMESIQGLS-----SWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLAN 65
Query: 121 AIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
+I + K ++ FA L V K
Sbjct: 66 DVIQNCK--RKNAIIFRESFADVLPEAAALV--KDPSVSKS 102
Score = 38.4 bits (89), Expect = 2e-04
Identities = 8/62 (12%), Positives = 23/62 (37%), Gaps = 5/62 (8%)
Query: 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEW 60
+ S+ +T I ++ ++ +V K++ + ++L Y+ +
Sbjct: 13 KFQSVTNTMESIQGLS-----SWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDV 67
Query: 61 NQ 62
Q
Sbjct: 68 IQ 69
>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain,
RNA polymerase II binding protein, phosphoprotein; NMR
{Saccharomyces cerevisiae} PDB: 2l0i_A*
Length = 142
Score = 49.6 bits (118), Expect = 2e-08
Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 9/103 (8%)
Query: 61 NQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIW--KCKSQYKLPGLYV 118
+L ++ ++ IS A K L V + ++++ ++ KL GLY+
Sbjct: 9 TTKLNTLEDSQESISSAS-----KWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYL 63
Query: 119 IDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
++ ++ QA+ + + F + G + Q D KK
Sbjct: 64 MNHVVQQAK--GQKIIQFQDSFGKVAAEVLGRINQEFPRDLKK 104
>3lod_A Putative acyl-COA N-acyltransferase; structural genomics, PSI2,
MCSG, structure initiative; 2.50A {Klebsiella pneumoniae
subsp}
Length = 162
Score = 30.4 bits (69), Expect = 0.17
Identities = 10/46 (21%), Positives = 15/46 (32%), Gaps = 7/46 (15%)
Query: 115 GLYVIDAIIHQARLQFKYKDVY-----APRFARNLYRTFGYVFQCP 155
G ++ A+ +AR Q + A LY GY
Sbjct: 92 GEKLLAALEAKAR-QRDCHTLRLETGIHQHAAIALYTRNGYQ-TRC 135
>3u1w_A Hypothetical periplasmic protein; BLIP-like, structural genomics,
joint center for structural JCSG, protein structure
initiative; 2.00A {Parabacteroides distasonis}
Length = 253
Score = 28.0 bits (62), Expect = 1.1
Identities = 10/44 (22%), Positives = 20/44 (45%)
Query: 7 STKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYK 50
ST +S+ ++ IV +++ Y VQS+ + + Y
Sbjct: 189 STTWAMSEQEVPQIVMQGFESSAYASDKVQSIYTLLNANGTFYL 232
Score = 28.0 bits (62), Expect = 1.1
Identities = 10/44 (22%), Positives = 20/44 (45%)
Query: 69 STKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYK 112
ST +S+ ++ IV +++ Y VQS+ + + Y
Sbjct: 189 STTWAMSEQEVPQIVMQGFESSAYASDKVQSIYTLLNANGTFYL 232
>3rva_A Organophosphorus acid anhydrolase; PITA-bread fold, binuclea
center, BI-functional, prolidase, nerve agents, XAA-Pro
DIP hydrolase; 1.80A {Alteromonas macleodii}
Length = 451
Score = 27.7 bits (62), Expect = 1.8
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 114 PGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFG 149
PGLY ID+++ + K + Y+ FG
Sbjct: 385 PGLYFIDSLLRDLKATPASKYINWDTIDA--YKPFG 418
>1m4i_A Aminoglycoside 2'-N-acetyltransferase; COA binding motif; HET: COA
KAN PAP; 1.50A {Mycobacterium tuberculosis} SCOP:
d.108.1.1 PDB: 1m4d_A* 1m4g_A* 1m44_A*
Length = 181
Score = 27.3 bits (60), Expect = 2.0
Identities = 8/37 (21%), Positives = 18/37 (48%)
Query: 115 GLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYV 151
++DA+ R ++ + + AR LY + G++
Sbjct: 96 VSALLDAVEQVMRGAYQLGALSSSARARRLYASRGWL 132
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 26.5 bits (57), Expect = 3.8
Identities = 9/46 (19%), Positives = 15/46 (32%), Gaps = 22/46 (47%)
Query: 98 QSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYKDVYAPRFARN 143
Q+++K ++ KL Y D+ AP A
Sbjct: 20 QALKKL----QASLKL---YADDS---------------APALAIK 43
Score = 26.1 bits (56), Expect = 4.2
Identities = 11/55 (20%), Positives = 18/55 (32%), Gaps = 29/55 (52%)
Query: 36 QSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKITGIVKLALKAT 90
Q+++K ++ KL Y + A LA+KAT
Sbjct: 20 QALKKL----QASLKL---YA---------------DDSAPA-------LAIKAT 45
>3d2y_A N-acetylmuramoyl-L-alanine amidase AMID; zinc amidase, PGRP,
peptidoglycan recognizing protein, AMPD,
acetylmuramyl-L-alanine amidase; HET: AH0; 1.75A
{Escherichia coli} PDB: 2bh7_A 2wkx_A 2bgx_A* 3d2z_A
Length = 261
Score = 26.3 bits (58), Expect = 5.0
Identities = 16/105 (15%), Positives = 31/105 (29%), Gaps = 16/105 (15%)
Query: 72 PPISKAKITGIVKLALKATHYYKYVVQSV---------------EKFIWKCKSQYKLPGL 116
P A+I ++ LA Y ++V F W+ +Q +
Sbjct: 120 APFEPAQIQALIPLAKDIIARYHIKPENVVAHADIAPQRKDDPGPLFPWQQLAQQGIGAW 179
Query: 117 YVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
+ + + V L R +GY + R++
Sbjct: 180 PDAQRVNFYLAGRAPHTPVDTASLLELLAR-YGYDVKPDMTPREQ 223
>2pfm_A Adenylosuccinate lyase; PURB, purine biosynthesis, B anthracis;
2.00A {Bacillus anthracis} PDB: 1f1o_A 2x75_A*
Length = 444
Score = 26.5 bits (59), Expect = 5.1
Identities = 8/35 (22%), Positives = 18/35 (51%)
Query: 118 VIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVF 152
++ ++++ K VY RN+ RT+G ++
Sbjct: 330 ALNYMLNRFGNIVKNLTVYPENMKRNMTRTYGLIY 364
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 26.4 bits (57), Expect = 5.4
Identities = 8/62 (12%), Positives = 20/62 (32%), Gaps = 11/62 (17%)
Query: 100 VEKFIWKCKSQYKLPGLYV-------IDAIIHQARL-QFKYKDVYAPRFARNLYRTFGYV 151
VEK +S +P +Y+ + +H++ + + + Y
Sbjct: 417 VEK--QPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTF-DSDDLIPPYLDQYF 473
Query: 152 FQ 153
+
Sbjct: 474 YS 475
>1c3c_A Protein (adenylosuccinate lyase); purine biosynthesis; 1.80A
{Thermotoga maritima} SCOP: a.127.1.1 PDB: 1c3u_A
Length = 429
Score = 26.1 bits (58), Expect = 7.1
Identities = 9/35 (25%), Positives = 14/35 (40%)
Query: 118 VIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVF 152
+ +I A + V R +N+ T G VF
Sbjct: 318 TLYYMIVTATNVVRNMKVNEERMKKNIDLTKGLVF 352
>1dof_A Adenylosuccinate lyase; purine biosynthesis; 2.10A {Pyrobaculum
aerophilum} SCOP: a.127.1.1
Length = 403
Score = 25.7 bits (57), Expect = 8.1
Identities = 8/34 (23%), Positives = 13/34 (38%)
Query: 119 IDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVF 152
+D I+ A K + R NL + Y+
Sbjct: 320 LDEILTSALRVLKNVYIDEERITENLQKALPYIL 353
>3l24_A XAA-Pro dipeptidase; PITA-bread, detoxification, hydrolase,
manganese, metal-binding, metalloprotease, protease;
2.30A {Alteromonas SP} PDB: 3l7g_A*
Length = 517
Score = 25.5 bits (56), Expect = 9.1
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 114 PGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFG 149
PGLY ID+++ + + + A + FG
Sbjct: 382 PGLYFIDSLLGDLAATDNNQHINWDKVAE--LKPFG 415
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.322 0.137 0.416
Gapped
Lambda K H
0.267 0.0570 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,436,846
Number of extensions: 129830
Number of successful extensions: 287
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 30
Length of query: 161
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 75
Effective length of database: 4,300,587
Effective search space: 322544025
Effective search space used: 322544025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.5 bits)