RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5829
(147 letters)
>1rh5_A Preprotein translocase SECY subunit; protein translocation, SECY,
membrane protein, protein channels, protein transport;
3.20A {Methanocaldococcus jannaschii} SCOP: f.41.1.1
PDB: 1rhz_A 2yxq_A 3dkn_A 2yxr_A 3bo0_A 3bo1_A 3kcr_A
Length = 436
Score = 116 bits (292), Expect = 9e-32
Identities = 35/128 (27%), Positives = 62/128 (48%), Gaps = 13/128 (10%)
Query: 11 FLSSLQNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPI 70
+ + N + ++ T++VF +V+Y + RV++P+ R +G YPIK Y SNIP+
Sbjct: 200 LIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPV 259
Query: 71 ILQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENL 130
IL +AL +N+ + L + + +LG + + G+ YYLS P L
Sbjct: 260 ILAAALFANIQLWGLAL-----YRMGIPILGHYEG--------GRAVDGIAYYLSTPYGL 306
Query: 131 GHFLLLLL 138
+ +
Sbjct: 307 SSVISDPI 314
>2wwb_A Protein transport protein SEC61 subunit alpha ISO; ribosome,
protein EXIT tunnel, cotranslational protein
translocation, protein conducting channel; 6.48A {Canis
lupus familiaris}
Length = 476
Score = 110 bits (277), Expect = 1e-29
Identities = 87/121 (71%), Positives = 103/121 (85%)
Query: 22 VMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLY 81
+ ++AT+ VFA+VIYFQGFRVDLPIKSARYRGQY++YPIKLFYTSNIPIILQSALVSNLY
Sbjct: 243 MNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSNLY 302
Query: 82 VISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENLGHFLLLLLLRF 141
VISQML+ +F GN+ V+LLG W+D GGPARAYP+GGLC+YLSPPE+ G L +
Sbjct: 303 VISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFGSVLEDPVHAV 362
Query: 142 V 142
V
Sbjct: 363 V 363
>3mp7_A Preprotein translocase subunit SECY; protein transport, membrane
protein complex, preprotein TRAN membrane insertion,;
2.90A {Pyrococcus furiosus}
Length = 482
Score = 104 bits (262), Expect = 2e-27
Identities = 37/114 (32%), Positives = 59/114 (51%), Gaps = 12/114 (10%)
Query: 22 VMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLY 81
+ ++AT++VF IV+YF+ RV++P+ SYPI+ Y SNIPIIL AL +N+
Sbjct: 242 LSVVATIVVFFIVVYFESMRVEIPLGYRG-VTVRGSYPIRFLYVSNIPIILTFALYANIQ 300
Query: 82 VISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENLGHFLL 135
+ +++L + LG + P PI G Y+ PP N+ +
Sbjct: 301 LWARVL-----DRLGHPWLGRF------DPTTGSPISGFVLYVIPPRNIFSVID 343
>2ww9_A SEC sixty-one protein homolog; ribonucleoprotein, transmembrane,
phospho signal sequence, membrane, ribosome, transport;
8.60A {Saccharomyces cerevisiae} PDB: 2wwa_A
Length = 490
Score = 85.9 bits (212), Expect = 1e-20
Identities = 28/125 (22%), Positives = 48/125 (38%), Gaps = 7/125 (5%)
Query: 22 VMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLY 81
+ + + IV Y Q RV+LPI+S R RG + YPIKL YT + ++ ++ ++
Sbjct: 248 TTTIIVLAIAIIVCYLQSVRVELPIRSTRARGTNNVYPIKLLYTGCLSVLFSYTILFYIH 307
Query: 82 VISQMLAVKFHG----NIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENLGHFLLLL 137
+ + +L +I ++G + A P L P
Sbjct: 308 IFAFVLIQLVAKNEPTHIICKIMGHYE---NANNLLAVPTFPLSLLAPPTSFFKGVTQQP 364
Query: 138 LLRFV 142
L
Sbjct: 365 LTFIT 369
>1kvk_A MK, mevalonate kinase; RMK, ATP, GHMP, transferase; HET: ATP; 2.40A
{Rattus norvegicus} SCOP: d.14.1.5 d.58.26.3 PDB:
2r42_A* 2r3v_A
Length = 395
Score = 31.8 bits (71), Expect = 0.075
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 83 ISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENLGHFLL 135
+S++L V G V L GE A V G A A + + + P++ G L
Sbjct: 2 LSEVLLVSAPGK--VILHGEHAVV-HGKVALAVALNLRTFLVLRPQSNGKVSL 51
>3k17_A LIN0012 protein; protein structure initiative II(PSI II), NYSGXRC,
structural genomics, NEW YORK SGX research center for
structural genomics; HET: PGE; 2.10A {Listeria innocua}
Length = 365
Score = 30.0 bits (67), Expect = 0.25
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 83 ISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPI 117
+ L VK G ++ + GE+A V G A +
Sbjct: 3 LKNKLQVKIPGKLY--VAGEYAVVESGHTAILTAV 35
>3din_C Preprotein translocase subunit SECY; protein translocation,
membrane protein, ATPase, ATP-binding membrane,
nucleotide-binding, protein transport; HET: ADP; 4.50A
{Thermotoga maritima MSB8}
Length = 431
Score = 29.8 bits (68), Expect = 0.25
Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 9/94 (9%)
Query: 11 FLSSLQNSKMAVMMLATVLVFAIVIYF-QGFRVDLPIKSAR-------YRGQYSSYPIKL 62
+L L + ++ ++ +I Q R + I+ AR Y G + PIK+
Sbjct: 207 YLGGLNLLEWIFLIAVALITIFGIILVQQAER-RITIQYARRVTGRRVYGGASTYLPIKV 265
Query: 63 FYTSNIPIILQSALVSNLYVISQMLAVKFHGNIF 96
IPII SA+VS I+ + + N+F
Sbjct: 266 NQGGVIPIIFASAIVSIPSAIASITNNETLKNLF 299
>2pg9_A Phosphomevalonate kinase; GHMP kinase superfamily, transferase;
HET: PMV ANP; 1.90A {Streptococcus pneumoniae} PDB:
1k47_A* 3gon_A*
Length = 337
Score = 29.6 bits (66), Expect = 0.36
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 86 MLAVKFHGNIFVNLLGEWADVGGGGPARAYPI 117
M+AVK G ++ GE+A + G A I
Sbjct: 3 MIAVKTCGKLY--WAGEYAILEPGQLALIKDI 32
>3dl8_G Preprotein translocase subunit SECY; RECA-type ATPase membrane
protein translocation protein- protein complex,
ATP-binding, cell membrane; 7.50A {Aquifex aeolicus}
Length = 429
Score = 29.4 bits (67), Expect = 0.41
Identities = 17/89 (19%), Positives = 34/89 (38%), Gaps = 9/89 (10%)
Query: 19 KMAVMMLATVLVFAIVIYF-QGFRVDLPIKSAR-------YRGQYSSYPIKLFYTSNIPI 70
+ +++ + + ++Y + R +PI+ Y G+ + PIK+ IPI
Sbjct: 217 TLLLIIALIIAIIVGIVYVQEAER-RIPIQYPGRQVGRQLYAGRKTYLPIKINPAGVIPI 275
Query: 71 ILQSALVSNLYVISQMLAVKFHGNIFVNL 99
I AL+ + + F I
Sbjct: 276 IFAQALLLIPSTLLNFVQNPFIKVIADMF 304
>2zjs_Y Preprotein translocase SECY subunit; translocon, SEC,
protein-conducting-channel, membrane, prote transport,
translocation, transmembrane, transport; 3.20A {Thermus
thermophilus} PDB: 2zqp_Y
Length = 434
Score = 27.9 bits (63), Expect = 1.1
Identities = 26/98 (26%), Positives = 39/98 (39%), Gaps = 13/98 (13%)
Query: 19 KMAVMMLATVLVFAIVIYF-QGFRVDLPIKSAR-------YRGQYSSYPIKLFYTSNIPI 70
+ VL FA + Q R +P++ AR Y GQ + PIKL IPI
Sbjct: 216 AFLFFLAFIVLAFAGMAAVQQAER-RIPVQYARKVVGGRVYGGQATYIPIKLNAAGVIPI 274
Query: 71 ILQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGG 108
I +A++ I LA F N + + + +
Sbjct: 275 IFAAAILQ----IPIFLAAPFQDNPVLQGIANFFNPTR 308
>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 = 28.1 bits (62), Expect = 1.3
Identities = 29/142 (20%), Positives = 46/142 (32%), Gaps = 60/142 (42%)
Query: 15 LQNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQS 74
+ + A+ +L F I G R +YP TS P IL+
Sbjct: 293 FVSVRKAITVL-----FFI-----G-----------VRCY-EAYPN----TSLPPSILED 326
Query: 75 ALVSNLYVISQMLAVK-------------------FHGNIFVNLLGEWADVGGGGPARAY 115
+L +N V S ML++ + ++L V G A+
Sbjct: 327 SLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISL------VNG---AKNL 377
Query: 116 PIGGLCYYLSPPENLGHFLLLL 137
+ G PP++L L L
Sbjct: 378 VVSG------PPQSLYGLNLTL 393
>2hfs_A Mevalonate kinase, putative; GHMP kinase, trypanosomatid parasite,
transferase; 1.75A {Leishmania major} PDB: 2hfu_A*
Length = 332
Score = 26.6 bits (59), Expect = 3.2
Identities = 8/26 (30%), Positives = 8/26 (30%), Gaps = 1/26 (3%)
Query: 97 VNLLGEWADVGGGGPARAYPIGGLCY 122
V L GE V G A I
Sbjct: 22 VILFGEHFVV-HGAEAIVAGISEYTE 46
>3sql_A Glycosyl hydrolase family 3; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG, TIM-barrel,
alpha-beta-alpha sandwich; HET: MSE; 2.25A
{Synechococcus SP} PDB: 3sqm_A*
Length = 535
Score = 25.6 bits (56), Expect = 8.5
Identities = 9/51 (17%), Positives = 16/51 (31%), Gaps = 3/51 (5%)
Query: 83 ISQMLAVKFHGNIFVNLLGEWADVGGGGPARA---YPIGGLCYYLSPPENL 130
I+QM+ V+ G +F + IGG+ +
Sbjct: 21 IAQMIVVRGAGYLFDYERPYPQWEADQTTLQRWIEAGIGGVILLGGSAAEV 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
0.329 0.144 0.444
Gapped
Lambda K H
0.267 0.0525 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,174,851
Number of extensions: 116596
Number of successful extensions: 253
Number of sequences better than 10.0: 1
Number of HSP's gapped: 249
Number of HSP's successfully gapped: 23
Length of query: 147
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 62
Effective length of database: 4,328,508
Effective search space: 268367496
Effective search space used: 268367496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.7 bits)