RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1246
(161 letters)
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 42.5 bits (99), Expect = 2e-05
Identities = 18/116 (15%), Positives = 30/116 (25%), Gaps = 3/116 (2%)
Query: 37 KRPPYGQPENTPPYAPAENRPSYGQSENSPSYGQPENKPSYGQPENRPSYGQPGNGASYG 96
K+ Y Q + P ++ P SYGQ P P G
Sbjct: 5 KKRVYPQAQLQYGQNAT---PLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61
Query: 97 QPENKPSYGQPENKPSYGQPENRPSYGQPENRPSYGQPGNGASYGQPENKPSYGQP 152
+ Q ++ + + + +Y QP G P +
Sbjct: 62 LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMA 117
Score = 41.3 bits (96), Expect = 6e-05
Identities = 23/139 (16%), Positives = 36/139 (25%), Gaps = 4/139 (2%)
Query: 19 PANSGLYGNGPSGYTPTEKRPPYGQPENTPPYAPAENRPSYGQSENSPSYGQPENKPSYG 78
P YG + + P P P G +
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69
Query: 79 QPENRPSYGQPGNGASYGQPENKP-SYGQPENKPSYGQPENRPSYGQPENRPSYGQPGNG 137
+ + + + P P +Y QP+ G P + QP P+YGQP
Sbjct: 70 HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQ--QPMAAPAYGQPSAA 127
Query: 138 ASYG-QPENKPSYGQPENG 155
+P N+
Sbjct: 128 MGQNMRPMNQLYPIDLLTE 146
Score = 41.3 bits (96), Expect = 6e-05
Identities = 28/129 (21%), Positives = 37/129 (28%), Gaps = 5/129 (3%)
Query: 25 YGNGPSGYTPTEKRPPYGQPENT-PPYAPAENRPSYGQSENSPSYGQPENKPSYGQPENR 83
Y Y P QP PP PA SYGQ P P +
Sbjct: 9 YPQAQLQYGQN--ATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQ 66
Query: 84 PSYGQPGNGASYGQPENKPSYGQPENKPSYGQPENRPSYGQPENRPSYGQPGNGASYGQP 143
Q + A+ + + +Y QP+ G P + QP +YGQP
Sbjct: 67 EQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQ--QPMAAPAYGQP 124
Query: 144 ENKPSYGQP 152
Sbjct: 125 SAAMGQNMR 133
Score = 40.6 bits (94), Expect = 1e-04
Identities = 14/122 (11%), Positives = 28/122 (22%)
Query: 13 SGPSPTPANSGLYGNGPSGYTPTEKRPPYGQPENTPPYAPAENRPSYGQSENSPSYGQPE 72
P + G G P P GQ + P ++ + +
Sbjct: 28 QFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHN 87
Query: 73 NKPSYGQPENRPSYGQPGNGASYGQPENKPSYGQPENKPSYGQPENRPSYGQPENRPSYG 132
+P Q + + + + GQ + P + +
Sbjct: 88 VPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTEL 147
Query: 133 QP 134
P
Sbjct: 148 PP 149
Score = 38.7 bits (89), Expect = 5e-04
Identities = 21/129 (16%), Positives = 37/129 (28%), Gaps = 4/129 (3%)
Query: 13 SGPSPTPANSGLYGNGPSGYTPTEKRPPYGQPENTPPYAPAENRPSYGQSENSPSYGQPE 72
P+ + G G P G P+ + + P + + + + + +
Sbjct: 33 QDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVD 92
Query: 73 NKPSYGQPENRPSYGQPGNGASYGQPENKPSYGQPENKPSYG-QPENRPSYGQPENRPSY 131
+Y QP+ G P QP P+YGQP +P N+
Sbjct: 93 P-NAYMQPQVPVQMGTPLQQQQ--QPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPP 149
Query: 132 GQPGNGASY 140
Sbjct: 150 PITDLTLPP 158
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 34.7 bits (79), Expect = 0.010
Identities = 30/149 (20%), Positives = 40/149 (26%), Gaps = 8/149 (5%)
Query: 1 MSACPSSFAEACSGPSPTPANSGLYGNGPSGYTPTEKRPPYGQPENTPPYAPAENRPSYG 60
+ F + G SPT S Y Y+PT P P +P Y+P S
Sbjct: 1528 EAPTSPGFGVSSPGFSPT---SPTYSPTSPAYSPT---SPSYSP-TSPSYSPTSPSYSPT 1580
Query: 61 QSENSPSYGQPENKPSYGQPENRPSYGQPGNGASYGQPENKPSYGQPENKPSYGQPENRP 120
SP+ P PSY S P P+ P +
Sbjct: 1581 SPSYSPTSPSYSPTSPSYSP-TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1639
Query: 121 SYGQPENRPSYGQPGNGASYGQPENKPSY 149
+ + S PSY
Sbjct: 1640 YSPTSPSYSPTSPSYSPTSPAYSPTSPSY 1668
Score = 32.8 bits (74), Expect = 0.040
Identities = 32/143 (22%), Positives = 38/143 (26%), Gaps = 6/143 (4%)
Query: 13 SGPSPTPANSGLYGNGPSGYTPTEKRPPYGQPENTPPYAPAENRPS---YGQSENSPSYG 69
G A S G + +P G +P Y+P S S SPSY
Sbjct: 1512 GGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYS 1571
Query: 70 QPENKPSYGQPENRPSYGQP-GNGASYGQPENKPSYGQPENKP-SYGQPENRPSYGQPEN 127
S P P+ SY S P P S PSY
Sbjct: 1572 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1631
Query: 128 RPS-YGQPGNGASYGQPENKPSY 149
S + S PSY
Sbjct: 1632 SYSPTSPSYSPTSPSYSPTSPSY 1654
Score = 32.4 bits (73), Expect = 0.066
Identities = 29/149 (19%), Positives = 40/149 (26%), Gaps = 12/149 (8%)
Query: 1 MSACPSSFAEACSGPSPTPANSGLYGNGPSGYTP-TEKRPPYGQPENTPPYAPAENRPSY 59
F+ S G G + Y T YG+ +P + + S
Sbjct: 1485 DVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVS----SP 1540
Query: 60 GQSENSPSYGQPENKPSYGQPENRPSYGQPGNGASYGQPENKPSYGQPENKPSYGQPENR 119
G S SP+Y P+Y S P + S P P+
Sbjct: 1541 GFSPTSPTYSPTS--PAYSPTSPSYSPTSPSYSPTSPS----YSPTSPSYSPTSPSYSPT 1594
Query: 120 PSYGQPENRPSYGQPGNGASYGQPENKPS 148
P PSY S P P+
Sbjct: 1595 SPSYSP-TSPSYSPTSPSYSPTSPSYSPT 1622
Score = 30.8 bits (69), Expect = 0.17
Identities = 35/153 (22%), Positives = 44/153 (28%), Gaps = 10/153 (6%)
Query: 1 MSACPSSFAEACSGPSP-TPANSGLYGNGPSGYTPTEKRPPYGQPE---NTPPYAPAENR 56
S S + + S SP S Y Y+PT P +P Y+P
Sbjct: 1552 TSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1611
Query: 57 PSYGQSENSPSYGQPENKPSYGQPENRPSYGQPGNGASYGQPENKP-SYGQPENKPSYGQ 115
S SP+ P + PSY S P P S PSY
Sbjct: 1612 YSPTSPSYSPTSPSYSPTSPSYSPTS-PSYSPTSPSYSPTSPSYSPTSPAYSPTSPSY-- 1668
Query: 116 PENRPSYGQPENRPSYGQPGNGASYGQPENKPS 148
+ S PSY S P P+
Sbjct: 1669 --SPTSPSYSPTSPSYSPTSPSYSPTSPNYSPT 1699
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 33.5 bits (76), Expect = 0.022
Identities = 32/136 (23%), Positives = 40/136 (29%), Gaps = 9/136 (6%)
Query: 16 SPTPANSGLYGNGPSGYTPTEKRPPYGQPENTPPYAPAENRPSYGQSENSPSYG--QPEN 73
SP G Y PY ++ +P + S G SPSY P
Sbjct: 1506 SPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGY 1565
Query: 74 KPSYGQPENRPSYGQPGNGASYGQPENKPSYGQPENKPSYGQPENRPSYGQPENRPSYGQ 133
S + PSY + S PSY PSY S P P+
Sbjct: 1566 STSPAYMPSSPSY----SPTSPSYSPTSPSYS--PTSPSYSPTSPSYSATSPSYSPTSPS 1619
Query: 134 PGNGASYGQPENKPSY 149
+ P PSY
Sbjct: 1620 YSPTSPSYSP-TSPSY 1634
Score = 32.4 bits (73), Expect = 0.059
Identities = 33/121 (27%), Positives = 41/121 (33%), Gaps = 12/121 (9%)
Query: 1 MSACPSSFAEACSGPSPTPANSGLYGNGPSGYTPTEKRPPYGQPENTPPYAPAENRPSYG 60
S S++ SPT S Y Y+PT P P +P Y+P PSY
Sbjct: 1585 YSPTSPSYSPTSPSYSPT---SPSYSATSPSYSPT---SPSYSP-TSPSYSPTS--PSY- 1634
Query: 61 QSENSPSYGQPENKPSYGQPENRPSYGQPGNGASYGQPENKPSYGQPENKPSYGQPENRP 120
S SPSY S P P+ + P PSY S P P
Sbjct: 1635 -SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP-TSPSYSPTSPSYSPTSPSYSP 1692
Query: 121 S 121
+
Sbjct: 1693 T 1693
Score = 27.0 bits (59), Expect = 4.2
Identities = 20/107 (18%), Positives = 25/107 (23%), Gaps = 12/107 (11%)
Query: 44 PENTPPYAPAENRPSYGQSENSPSYGQPENKPSYGQPENRPSYGQPGNGASYGQPENKPS 103
P P + S + SP + AS + P
Sbjct: 1485 PYERSPMVDSGFVGSPDAAAFSPLVQ------GGSEGREGFGDYGLLGAASPYKGVQSPG 1538
Query: 104 YGQPENKPSYGQPENRPSYGQPENRPSYGQPGNGASYGQPENKPSYG 150
Y P P YG S PG S + PSY
Sbjct: 1539 YTSP------FSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYS 1579
>1n4c_A Auxilin; four helix bundle, protein binding; NMR {Bos taurus}
SCOP: a.2.3.1 PDB: 1xi5_J
Length = 182
Score = 27.5 bits (60), Expect = 1.8
Identities = 15/46 (32%), Positives = 23/46 (50%)
Query: 40 PYGQPENTPPYAPAENRPSYGQSENSPSYGQPENKPSYGQPENRPS 85
P G PE + P++ +NRP+Y S +S GQ E + E +
Sbjct: 2 PLGSPEFSMPHSSPQNRPNYNVSFSSMPGGQNERGKAAANLEGKQK 47
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A*
Length = 448
Score = 27.2 bits (60), Expect = 2.8
Identities = 15/86 (17%), Positives = 22/86 (25%), Gaps = 3/86 (3%)
Query: 5 PSSFAEACSGPSPTPANSGLYGNGPSGYTPTEKRPPYGQPENTPPYAPAENRPSYGQSEN 64
P+ + + + + PP G Y P P +
Sbjct: 355 PAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQG 414
Query: 65 SPSYGQ---PENKPSYGQPENRPSYG 87
P G P+ P G P P G
Sbjct: 415 YPPQGYPPPPQGAPPQGAPPAAPPQG 440
>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus} PDB: 3lvh_A
Length = 624
Score = 26.9 bits (59), Expect = 3.6
Identities = 9/48 (18%), Positives = 14/48 (29%), Gaps = 4/48 (8%)
Query: 13 SGPSPTPANSGLYGNGPSGYTPTEKRPPYGQPENTPPYAPAENRPSYG 60
+ P + GPS P P A + +P +G
Sbjct: 578 TQPIVYGQPQLMLTAGPSVAVP----PQAPFGYGYTAPAYGQPQPGFG 621
>3gdb_A Endo-D, putative uncharacterized protein SPR0440;
alpha-beta-barrels, cell WALL, peptidoglycan-anchor,
secreted, hydrolase; HET: PGE; 1.87A {Streptococcus
pneumoniae} PDB: 2xqx_A
Length = 937
Score = 26.5 bits (57), Expect = 5.5
Identities = 23/144 (15%), Positives = 42/144 (29%), Gaps = 3/144 (2%)
Query: 5 PSSFAEACSGPSPTPANSGLYGNGPSGYTPTEKRPPYGQPENTPPYAPAENRPSYGQSEN 64
+ E SG S N N + G + +PA N + ++
Sbjct: 30 SGANTELVSGESEHSTNEADKQNEGEHARENKLEKAEGVATASETASPASNEAATTETAE 89
Query: 65 SPSYGQPENKPSYGQPENRPSYGQPGNGASYGQPENKPSYGQPENKPSYGQPENRPSYGQ 124
+ S +PE K S E + +P S + E KP ++ N+
Sbjct: 90 AASAAKPEEKASEVVAETPSAEAKP---KSDKETEAKPEATNQGDESKPAAEANKTEKEV 146
Query: 125 PENRPSYGQPGNGASYGQPENKPS 148
+ P + + +
Sbjct: 147 QPDVPKNTEKTLKPKEIKFNSWEE 170
>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring
E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A
{Saccharomyces cerevisiae}
Length = 371
Score = 26.0 bits (56), Expect = 6.8
Identities = 10/71 (14%), Positives = 17/71 (23%)
Query: 33 TPTEKRPPYGQPENTPPYAPAENRPSYGQSENSPSYGQPENKPSYGQPENRPSYGQPGNG 92
+ T + PP ++ QS + S P P +
Sbjct: 1 SLTPLSAITVRSMEGPPTVQQQSPSVIRQSPTQRRKTSTTSSTSRAPPPTNPDASSSSSS 60
Query: 93 ASYGQPENKPS 103
+ K S
Sbjct: 61 FAVPTIHFKES 71
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
0.301 0.128 0.395
Gapped
Lambda K H
0.267 0.0437 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,496,617
Number of extensions: 142565
Number of successful extensions: 508
Number of sequences better than 10.0: 1
Number of HSP's gapped: 353
Number of HSP's successfully gapped: 94
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: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.6 bits)
S2: 53 (24.9 bits)