RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12912
(185 letters)
>2caz_B Vacuolar protein sorting-associated protein VPS28; protein
transport, ESCRT, MVB, multivesicular bodies, endosome,
lysosome, PH domain, protein sorting; 3.6A
{Saccharomyces cerevisiae} SCOP: a.2.17.2
Length = 155
Score = 144 bits (363), Expect = 1e-44
Identities = 33/117 (28%), Positives = 61/117 (52%), Gaps = 7/117 (5%)
Query: 5 EEVKLFTNT---KEREKFDNQADLYAVINTLQNLEKAYIRDCVTPKEYTAACSKLLVQYK 61
+EV LF N+ K++E + +++Y+++ TL ++EKAY++D + +YT KLL Q+K
Sbjct: 28 DEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFK 87
Query: 62 AAFKQVQGEE----YPTVEHFVKKYRLDCPSALERIREDRPITIKDDKGNTSKCIAD 114
EE + ++E F Y + +A+ R+ PIT + T+ +
Sbjct: 88 VYLNSQNKEEINKHFQSIEAFCDTYNITASNAITRLERGIPITAEHAISTTTSAPSG 144
>2f6m_B Vacuolar protein sorting-associated protein VPS28; endosomes,
trafficking complex, vacuole protei sorting, ESCRT
protein complexes; HET: DDQ; 2.10A {Saccharomyces
cerevisiae} SCOP: a.2.17.2 PDB: 2f66_B
Length = 109
Score = 121 bits (305), Expect = 2e-36
Identities = 28/98 (28%), Positives = 53/98 (54%), Gaps = 7/98 (7%)
Query: 5 EEVKLFTNT---KEREKFDNQADLYAVINTLQNLEKAYIRDCVTPKEYTAACSKLLVQYK 61
+EV LF N+ K++E + +++Y+++ TL ++EKAY++D + +YT KLL Q+K
Sbjct: 11 DEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFK 70
Query: 62 AAFKQVQGE----EYPTVEHFVKKYRLDCPSALERIRE 95
E + ++E F Y + +A+ R+
Sbjct: 71 VYLNSQNKEEINKHFQSIEAFADTYNITASNAITRLER 108
>2p22_B Vacuolar protein sorting-associated protein 28; endosome,
trafficking complex, VPS23, VPS28, VPS37, MVB12; 2.70A
{Saccharomyces cerevisiae}
Length = 118
Score = 120 bits (303), Expect = 6e-36
Identities = 28/98 (28%), Positives = 53/98 (54%), Gaps = 7/98 (7%)
Query: 5 EEVKLFTNT---KEREKFDNQADLYAVINTLQNLEKAYIRDCVTPKEYTAACSKLLVQYK 61
+EV LF N+ K++E + +++Y+++ TL ++EKAY++D + +YT KLL Q+K
Sbjct: 20 DEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFK 79
Query: 62 AAFKQVQGE----EYPTVEHFVKKYRLDCPSALERIRE 95
E + ++E F Y + +A+ R+
Sbjct: 80 VYLNSQNKEEINKHFQSIEAFADTYNITASNAITRLER 117
>2j9w_A VPS28, VPS28-PROV protein; NZF finger, HIV budding, protein
transport; 1.30A {Xenopus laevis}
Length = 102
Score = 111 bits (280), Expect = 1e-32
Identities = 57/80 (71%), Positives = 69/80 (86%)
Query: 104 DKGNTSKCIADIVSLFITTMDKLRLDIKAMDELQPDLRDLMDTMNRLSILPSGFEGKEKV 163
GN ++CIADIVSLFIT MDKLRL+I+AMDE+QPDLR+LM+TMNR+S LP FEG+EKV
Sbjct: 2 HMGNLNRCIADIVSLFITVMDKLRLEIRAMDEIQPDLRELMETMNRMSHLPPDFEGREKV 61
Query: 164 SGWLTTLESMSASDELNETQ 183
S WL L SMSASDEL+++Q
Sbjct: 62 SQWLQKLSSMSASDELDDSQ 81
>2j9u_A VPS28, vacuolar protein sorting-associated protein 28; zinc-finger,
metal-binding, protein transport; 2.00A {Saccharomyces
cerevisiae} SCOP: a.24.28.1 PDB: 2j9v_A 2g3k_A
Length = 96
Score = 91.6 bits (227), Expect = 1e-24
Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 2/76 (2%)
Query: 108 TSKCIADIVSLFITTMDKLRLDIKAMDELQPDLRDLMDTMNRLSILPSGFEGKEKVSGWL 167
+K +A+ FIT MD L+L+ A D+L P L +L+ ++NR++ FE + K+ W+
Sbjct: 3 NAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVT--RDDFENRSKLIDWI 60
Query: 168 TTLESMSASDELNETQ 183
+ +S D L ETQ
Sbjct: 61 VRINKLSIGDTLTETQ 76
>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 = 40.8 bits (95), Expect = 1e-04
Identities = 25/137 (18%), Positives = 37/137 (27%), Gaps = 50/137 (36%)
Query: 66 QVQG---EEY---PTV--------EHFVKKYRLDCPSALERIREDRP--ITIKDDKGNTS 109
Q QG + Y HF Y S L+ + + P +TI G
Sbjct: 1627 QEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGF---SILDIVINN-PVNLTIHFG-GEKG 1681
Query: 110 KCIAD--IVSLFITTMDKLRLDIKAMDELQPDLRDLMDTMNRLSILPSGFEGKEKVSGWL 167
K I + +F T +D K E+ F ++
Sbjct: 1682 KRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYT------------FRSEK------ 1723
Query: 168 TTLESMSASDELNETQF 184
L+ TQF
Sbjct: 1724 ---------GLLSATQF 1731
>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 = 0.055
Identities = 24/103 (23%), Positives = 35/103 (33%), Gaps = 37/103 (35%)
Query: 3 NLEEVKLFTN---------TKEREKFDNQADLYAVINTLQNLE--KAYIRD-CVTPKEYT 50
+ E + LF K R +++NTLQ L+ K YI D +
Sbjct: 486 HPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLV 545
Query: 51 AA-------------CSKL--LVQ----------YKAAFKQVQ 68
A CSK L++ ++ A KQVQ
Sbjct: 546 NAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQ 588
Score = 30.6 bits (68), Expect = 0.34
Identities = 34/171 (19%), Positives = 58/171 (33%), Gaps = 30/171 (17%)
Query: 18 KFDNQADLYAVINTLQNLEKAYIRDCVTPKEYTAACSKLLVQYKAAFKQVQGEEYPTVEH 77
+ +++D + I + +A +R + K Y LLV VQ +
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC---LLV-----LLNVQNAK--AWNA 261
Query: 78 FVKKYRLDCPSALERI----REDRPITIKDDKGNTSKCIADIVSLFITTMDKLRLDIKAM 133
F L C +I R + +T T+ D S+ +T + L +K +
Sbjct: 262 F----NLSC-----KILLTTR-FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL 311
Query: 134 DELQPDLRDLMDTMNRLSILPSGFEGKEKVSGWLTTLE--SMSASDELNET 182
D DL + T N + S E + L T + D+L
Sbjct: 312 DCRPQDLPREVLTTNPRRL--SII--AESIRDGLATWDNWKHVNCDKLTTI 358
>2b3w_A Hypothetical protein YBIA; structure, NESG, structural genomics,
COG 3236, PSI, protein structure initiative; NMR
{Escherichia coli} SCOP: d.336.1.1
Length = 168
Score = 30.0 bits (67), Expect = 0.31
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 60 YKAAFKQVQGEEYPTVEHFVKKYRLDCPSALERIRE 95
+V G+ +PT EH+ + + E IR
Sbjct: 33 AAWPI-KVDGKTWPTSEHYFQAQKFLDEKYREEIRR 67
>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 = 26.8 bits (58), Expect = 3.2
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 8/30 (26%)
Query: 61 KAAFKQVQGEEYPTVEHFVKKYRLDCPSAL 90
K A K++Q +K Y D AL
Sbjct: 19 KQALKKLQAS--------LKLYADDSAPAL 40
>3v83_A Serotransferrin; iron binding domain, iron carrier/transporter,
transferrin R serum, metal transport; HET: P6G; 2.10A
{Homo sapiens} PDB: 3v8x_B* 3qyt_A* 3ve1_B 2hav_A*
3s9l_C* 3s9m_C* 3s9n_C* 2hau_A* 1jnf_A 1h76_A*
Length = 698
Score = 26.8 bits (58), Expect = 4.5
Identities = 14/73 (19%), Positives = 24/73 (32%), Gaps = 7/73 (9%)
Query: 25 LYAVINTLQNLEKAYIRDCVTPKEYTAACSKLLVQYKAAFKQVQGEEYPTVEHFVKKYRL 84
+ AV+ + +R C + C + K V + P+V K L
Sbjct: 10 VCAVLGLCLAVPDKTVRWCAVSEHEATKCQSF----RDHMKSVIPSDGPSVACVKKASYL 65
Query: 85 DCPSALERIREDR 97
DC + I +
Sbjct: 66 DC---IRAIAANE 75
>3cmm_A Ubiquitin-activating enzyme E1 1; UBA1, protein turnover, ligase,
conformationa thioester, adenylation,
transthioesterification, ATP-bindin nucleotide-binding;
2.70A {Saccharomyces cerevisiae}
Length = 1015
Score = 26.7 bits (58), Expect = 6.6
Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 7/88 (7%)
Query: 1 MANLEEVKLFTNTKEREKFDNQADLYAVINTLQNLEKAYIRDCVTPKEYTAACSKLLVQY 60
+ NLE KL N + E++ N A+ + A + K+Y + ++
Sbjct: 867 LVNLELYKLIDNKTDIEQYKNGFVNLALPFFGFSEPIASPKGEYNNKKYDKIWDRFDIKG 926
Query: 61 KAAFKQVQGEEYPTVEHFVKKYRLDCPS 88
+ +EHF K L+
Sbjct: 927 DIKLSDL-------IEHFEKDEGLEITM 947
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
0.316 0.132 0.370
Gapped
Lambda K H
0.267 0.0445 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,725,988
Number of extensions: 155533
Number of successful extensions: 403
Number of sequences better than 10.0: 1
Number of HSP's gapped: 398
Number of HSP's successfully gapped: 19
Length of query: 185
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 97
Effective length of database: 4,244,745
Effective search space: 411740265
Effective search space used: 411740265
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: 54 (25.3 bits)