RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15249
(235 letters)
>1f3u_A Transcription initiation factor IIF, beta subunit; general
transcription initiation and elongation factor, RNA
polymerase II; 1.70A {Homo sapiens} SCOP: b.65.1.1
Length = 118
Score = 120 bits (303), Expect = 3e-35
Identities = 46/124 (37%), Positives = 66/124 (53%), Gaps = 17/124 (13%)
Query: 26 VNLDLTQASRGVWLVKVPKYVANKWEKVPGNIEAGKLKIVRNPGQKPVVSLSLSEATMCV 85
++L + + GVWLVKVPKY++ +W K G E GKL+I + G + VS +L+E +
Sbjct: 6 LDLTGAKQNTGVWLVKVPKYLSQQWAKASGRGEVGKLRIAKTQG-RTEVSFTLNEDLANI 64
Query: 86 D-----PNEEKIPKDHRLDVQIVNRQTLGVFSHYIPPVNPDAIVPESEKLMLEGKIVQKL 140
P P++H +Q V QTL VF+ S+KL LEG +VQ+
Sbjct: 65 HDIGGKPASVSAPREHPFVLQSVGGQTLTVFTES-----------SSDKLSLEGIVVQRA 113
Query: 141 ECRP 144
ECRP
Sbjct: 114 ECRP 117
>1bby_A RAP30; average structure transcription regulation, DNA- binding
domain, transcription; NMR {Homo sapiens} SCOP: a.4.5.15
PDB: 2bby_A
Length = 69
Score = 58.6 bits (142), Expect = 6e-12
Identities = 22/33 (66%), Positives = 25/33 (75%)
Query: 188 TYLKEILKEVCNYNLKNPHKNMWELKPEYRCYK 220
YLKEILKE+ N+K HKN WELKPEYR Y+
Sbjct: 37 VYLKEILKEIGVQNVKGIHKNTWELKPEYRHYQ 69
Score = 42.8 bits (101), Expect = 3e-06
Identities = 23/28 (82%), Positives = 26/28 (92%)
Query: 1 MLFAAFEKHQYYNIKDLVKITKQPIVNL 28
MLF+AFEKHQYYN+KDLV ITKQP+V L
Sbjct: 12 MLFSAFEKHQYYNLKDLVDITKQPVVYL 39
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 51.6 bits (123), Expect = 7e-08
Identities = 41/218 (18%), Positives = 78/218 (35%), Gaps = 58/218 (26%)
Query: 30 LTQASRGVWLVKVPKYVANKWEKVPGNIEAGKLKI-----VRNPGQK--PVVSLSLSEAT 82
T S+G+ + V + WE ++ + + VR + P SL S
Sbjct: 270 ATGHSQGL-VTAVAIAETDSWESFFVSVRKA-ITVLFFIGVR--CYEAYPNTSLPPSILE 325
Query: 83 MCVDPNEEKIPKDHRLDVQIVNRQTL----GVFSHYIPP--------VN-PDAIV----P 125
++ N E +P L + + ++ + + ++P VN +V P
Sbjct: 326 DSLE-NNEGVP-SPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPP 383
Query: 126 ESEKLMLEG--KIVQKLECRPYADSCYMKLKLDSIIKASQPLRQVKHLDKIVQNYKPVSN 183
+S L G ++K + D S I S+ R++ K + PV++
Sbjct: 384 QS----LYGLNLTLRKAKAPSGLDQ--------SRIPFSE--RKL----KFSNRFLPVAS 425
Query: 184 HKHLTYLKE----ILKEVCNYNLKNPHKNMWELK-PEY 216
H L I K++ N+ K +++ P Y
Sbjct: 426 PFHSHLLVPASDLINKDLVKNNVSFNAK---DIQIPVY 460
Score = 30.0 bits (67), Expect = 0.90
Identities = 38/248 (15%), Positives = 67/248 (27%), Gaps = 101/248 (40%)
Query: 28 LDLTQAS---RGVWLVKVPKYVANKWEKVPG-NIEAGKLKIVR-NPGQKPVV-----SLS 77
+DL + S + VW N ++ G +I L IV NP +
Sbjct: 1633 MDLYKTSKAAQDVW-----NRADNHFKDTYGFSI----LDIVINNPVNLTIHFGGEKGKR 1683
Query: 78 LSE--ATMCVDPNEEKIPKDHRLDVQIVNRQTLGVFSHYIPPVNPD-----------AIV 124
+ E + M + + K ++ +I T F A+
Sbjct: 1684 IRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRS------EKGLLSATQFTQPALT 1737
Query: 125 PES----EKLMLEGKIVQK-------------LECRPYADSCYMKLKLDSIIK------- 160
E L +G I L AD + ++S+++
Sbjct: 1738 LMEKAAFEDLKSKGLIPADATFAGHSLGEYAALAS--LADV----MSIESLVEVVFYRGM 1791
Query: 161 -------------------ASQPLRQVKHLD-----KIVQNYKPVSNHKHLTYLKEILKE 196
A P R +V+ V ++ E
Sbjct: 1792 TMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVER---VGKRT-----GWLV-E 1842
Query: 197 VCNYNLKN 204
+ NYN++N
Sbjct: 1843 IVNYNVEN 1850
>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 = 32.9 bits (74), Expect = 0.082
Identities = 36/270 (13%), Positives = 81/270 (30%), Gaps = 60/270 (22%)
Query: 2 LFAAFEKH--------QYYNIKDLVKITKQPIVNLDLTQASRGVWL-------VKVPKYV 46
+ A + ++ N L I + + L+ + + +P +
Sbjct: 332 IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL 391
Query: 47 ANK-WEKVPGNIE-------AGKLKIVRNPGQKPVVSL-SLSEATMCVDPNEEKIPKDHR 97
+ W V + + + P ++ +S+ S+ NE + HR
Sbjct: 392 LSLIWFDVIKSDVMVVVNKLHKYSLVEKQP-KESTISIPSIYLELKVKLENEYAL---HR 447
Query: 98 LDVQIVNR--QTLGVFSHYIPPVNPD-----------AIVPESEKLMLEGKIVQKLECRP 144
IV+ S + P D + E++ L +
Sbjct: 448 ---SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMV-------- 496
Query: 145 YADSCYMKLKLDSIIKASQPLRQVKHLDKIVQNYKP--VSNHKHLT-YLKEILKEVCNYN 201
+ D +++ K+ A + + + ++ YKP N + IL +
Sbjct: 497 FLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIE 556
Query: 202 ---LKNPHKNMWE--LKPEYRCYKEEEKKE 226
+ + + ++ L E EE K+
Sbjct: 557 ENLICSKYTDLLRIALMAEDEAIFEEAHKQ 586
Score = 27.9 bits (61), Expect = 3.2
Identities = 23/140 (16%), Positives = 43/140 (30%), Gaps = 31/140 (22%)
Query: 88 NEEKIPKDHRLDVQIVNRQTLGVFSHYIPPVNPDAIVPESEKL--------MLEGK---I 136
E+ + D + V + S D I+ + + L K +
Sbjct: 25 FEDAFVDN--FDCKDVQDMPKSILSK----EEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78
Query: 137 VQKL---ECRPYADSCYMKLKLDSIIKASQPLRQVKHLDKI---VQNYKP--VSNHKHLT 188
VQK R +K + + ++ D++ Q + VS +
Sbjct: 79 VQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYL 138
Query: 189 YLKEILKEVCNYNLKNPHKN 208
L++ L E+ P KN
Sbjct: 139 KLRQALLEL------RPAKN 152
>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 = 31.5 bits (70), Expect = 0.14
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 14/36 (38%)
Query: 133 EGKIVQKLEC--RPYADSCYMKLKLDS----IIKAS 162
E + ++KL+ + YAD DS IKA+
Sbjct: 18 EKQALKKLQASLKLYAD--------DSAPALAIKAT 45
>3cue_A Transport protein particle 23 kDa subunit; membrane traffic, GEF,
tethering complex, RAB activation, GU nucleotide
exchange factor; HET: PLM; 3.70A {Saccharomyces
cerevisiae}
Length = 219
Score = 28.9 bits (63), Expect = 1.1
Identities = 22/176 (12%), Positives = 48/176 (27%), Gaps = 10/176 (5%)
Query: 38 WLVKVPKYVANKWEKVPGNIEAG-KLKIVRNPGQKPVVSLSLSEATMCVDPNEEKIPKDH 96
+ K +N++ + + + P + + E T+ P
Sbjct: 21 FTNDEQKLNSNEYLILASTLHGVFAIASQLTPKALQLTQQTNIENTIPYIPYVGMSSNRS 80
Query: 97 RLDVQIVNRQTLGVFSHYIPPVNPDAIVPESEKLMLEGKIVQKLECRPYADSCYM---KL 153
N D G +++L + Y L
Sbjct: 81 DTRNGGGNNNKHTNNEKLGSFKGDDFFKEPFTNWNKSG--LRQLCTDQFTMFIYQTLTGL 138
Query: 154 KLDSIIKASQPLRQVKHLDKIVQNYKPVSNHKHLTYLKEILKEV----CNYNLKNP 205
K +I + P RQ + +++ + L++V +Y +K+P
Sbjct: 139 KFVAISSSVMPQRQPTIATTDKPDRPKSTSNLAIQIADNFLRKVYCLYSDYVMKDP 194
>2xgu_A Relik capsid N-terminal domain; viral protein, retroviral capsid;
1.50A {Oryctolagus cuniculus} PDB: 2xgy_A
Length = 149
Score = 26.5 bits (58), Expect = 6.1
Identities = 4/16 (25%), Positives = 8/16 (50%)
Query: 171 LDKIVQNYKPVSNHKH 186
L + + P+ +H H
Sbjct: 132 LQECQRTISPLEHHHH 147
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
0.315 0.134 0.398
Gapped
Lambda K H
0.267 0.0460 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,608,948
Number of extensions: 206249
Number of successful extensions: 440
Number of sequences better than 10.0: 1
Number of HSP's gapped: 436
Number of HSP's successfully gapped: 19
Length of query: 235
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 144
Effective length of database: 4,160,982
Effective search space: 599181408
Effective search space used: 599181408
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.0 bits)