RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780483|ref|YP_003064896.1| putative inner membrane
protein translocase component YidC [Candidatus Liberibacter asiaticus
str. psy62]
(581 letters)
>3blc_A Inner membrane protein OXAA; YIDC, membrane assembly facilitator,
chaperone, periplasmic domain, transmembrane, chaperone;
2.50A {Escherichia coli K12}
Length = 330
Score = 160 bits (405), Expect = 8e-40
Identities = 49/321 (15%), Positives = 112/321 (34%), Gaps = 22/321 (6%)
Query: 41 QTVKQPNQVDNSYAAVLIDDRAQALSMSPRVELKNPSLIGSINLKGAQFDDLNLRGYHLD 100
+Q Q + A D A + +K L +IN +G + L Y +
Sbjct: 7 PQAQQTTQTTTTAAGSAADQGVPASGQGKLISVKTDVLDLTINTRGGDVEQALLPAYPKE 66
Query: 101 VSSNSPIVTLLSPSNTKNAYFAELDYVSTAN-NIELPNSNTVWNLISGKILT----PTTP 155
++S P L ++ + Y A+ + ++N+ +
Sbjct: 67 LNSTQPFQLL--ETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQ 124
Query: 156 IKLVFKNANNILFERTISL-DEHYLFKIVDTVTNNSIDQIRFSPRGRIMRH-------KP 207
+ + + +A F +T L Y + V N + S G++ +
Sbjct: 125 VPMTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHLDT 184
Query: 208 QTATNTFGVQEGFIAVLGDKSLVEQKYSDIEKSSISNFHESNSWLGISDKYWASVFIPSK 267
++ G D + + I + N W+ + +Y+A+ +IP
Sbjct: 185 GSSNFALHTFRGAAYSTPDAAYAAYAFDTIADNENLNISSKGGWVAMLQQYFATAWIPHN 244
Query: 268 ETSFHSQFKYLSDGHARYQAKFSANEITILPGKSITTTNFLFAGAKEFPTIHHYEKDLAI 327
+ + + L +G + + + + PG++ + L+ G + +
Sbjct: 245 DGTNNFYTANLGNG--IAAIGYKSQPVLVQPGQTGAMNSTLWVGPEIQDKMAAVA----- 297
Query: 328 PRFEMLIDWGWFYFIAKPMFM 348
P ++ +D+GW +FI++P+ +
Sbjct: 298 PHLDLTVDYGWLWFISQPLLV 318
>3bs6_A Inner membrane protein OXAA; YIDC/OXA1/ALB3 family, membrane
insertion, chaperone, SEC translocon, periplasmic
domain, beta supersandwich fold; HET: PG4 PGE 2PE; 1.80A
{Escherichia coli}
Length = 280
Score = 131 bits (331), Expect = 3e-31
Identities = 42/278 (15%), Positives = 94/278 (33%), Gaps = 20/278 (7%)
Query: 70 RVELKNPSLIGSINLKGAQFDDLNLRGYHLDVSSNSPIVTLLSPSNTKNAYFAELDYVST 129
+ +K L +IN +G + L Y +++S P LL S
Sbjct: 5 LISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQ-LLETSPQFIYQAQSGLTGRD 63
Query: 130 ANNIELPNSNTVWNLISG----KILTPTTPIKLVFKNANNILFERTISL-DEHYLFKIVD 184
+ ++N+ + + + +A F +T L Y +
Sbjct: 64 GPDNPANGPRPLYNVEKDAYVLAEGQNELQVPMTYTDAAGNTFTKTFVLKRGDYAVNVNY 123
Query: 185 TVTNNSIDQIRFSPRGRIMRH-----KPQTATNTFGVQEGFIAVLG--DKSLVEQKYSDI 237
V N + S G++ + T ++ F + A D+ + K+ I
Sbjct: 124 NVQNAGEKPLEISSFGQLKQSITLPPHLDTGSSNFALHTFRGAAYSTPDEKYEKYKFDTI 183
Query: 238 EKSSISNFHESNSWLGISDKYWASVFIPSKETSFHSQFKYLSDGHARYQAKFSANEITIL 297
+ N W+ + +Y+A+ +IP + + + L +G + + + +
Sbjct: 184 ADNENLNISSKGGWVAMLQQYFATAWIPHNDGTNNFYTANLGNG--IAAIGYKSQPVLVQ 241
Query: 298 PGKSITTTNFLFAGAKEFPTIHHYEKDLAIPRFEMLID 335
PG++ + L+ G + + L ++ +D
Sbjct: 242 PGQTGAMNSTLWVGPEIQDKMAAVAPHL-----DLTVD 274
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 46.5 bits (110), Expect = 2e-05
Identities = 34/228 (14%), Positives = 59/228 (25%), Gaps = 76/228 (33%)
Query: 396 IDELREKFKQSPPQVLQKAMIQLYKTH-----NINPLAGCWPILLQIPVFFAIYKVISIS 450
+ QVL + ++ +I+ LA + ++I
Sbjct: 69 SSLVEPSKVGQFDQVL-NLCLTEFENCYLEGNDIHALAAKLLQENDTTLV-KTKELIKNY 126
Query: 451 LEMRHA---PFWGWIK----DLAAADPTNIFTLFG--------------ILPFYLPGFMH 489
+ R PF + +FG + Y
Sbjct: 127 ITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHV---L 183
Query: 490 VGIWPIIMSLS-MFIQMKMSPPPADK--GQAM-ILNWM---------------PVVFVFA 530
VG +I + ++ + A+K Q + IL W+ P+
Sbjct: 184 VG--DLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPI----- 236
Query: 531 LSSFPAGLIIYWSWSNVISIVQQAV---IMKMHGAEIGLIDRLRSTFS 575
S P LI VI + V ++ E LRS
Sbjct: 237 --SCP--LI------GVIQLAHYVVTAKLLGFTPGE------LRSYLK 268
Score = 44.9 bits (106), Expect = 4e-05
Identities = 55/343 (16%), Positives = 85/343 (24%), Gaps = 182/343 (53%)
Query: 9 VAIALSVIIVYAWQNFYVYPRIEEMNNERKNIQTVKQPNQVDNSYAAV--L--IDDRAQ- 63
A+A++ +W++F+ + A+ L I R
Sbjct: 279 TAVAIAE--TDSWESFF------------------------VSVRKAITVLFFIGVRCYE 312
Query: 64 ---ALSMSPRV---ELKN----PSLIGSI-NLKGAQFDDLNLRGYHLDVSSNSPIVTLLS 112
S+ P + L+N PS + SI NL Q D +++ +
Sbjct: 313 AYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQD------YVNKT---------- 356
Query: 113 PSNTKNAYFAELDYVSTANNIELPNS--NTVWNLISGKILTPTTPIKLVFKNANNILFER 170
N++ V I L N N V +SG P P L
Sbjct: 357 -----NSHLPAGKQVE----ISLVNGAKNLV---VSG----P--PQSLY----------- 387
Query: 171 TISLDEHYLFKI-VDTVTNNSIDQIR--FSPRGRIMRHKPQTATNTFGVQEGFIAVLGDK 227
L+ L K + +DQ R FS R K
Sbjct: 388 --GLN-LTLRKAKAPS----GLDQSRIPFSER------KL-------------------- 414
Query: 228 SLVEQKYSDIEKSSISNFHESNSWLGISDKYWASVFIPSKETSFHSQFKYLSDGHARYQA 287
F N +L ++ P FHS L
Sbjct: 415 ----------------KFS--NRFLPVA--------SP-----FHSH--LLVPASDLINK 441
Query: 288 KFSANEITILPGKSITTTNFLFAGAKEFPTIHHYEKDLAIPRF 330
N ++ KD+ IP +
Sbjct: 442 DLVKNNVSFNA------------------------KDIQIPVY 460
Score = 40.3 bits (94), Expect = 0.001
Identities = 39/243 (16%), Positives = 68/243 (27%), Gaps = 97/243 (39%)
Query: 219 GFIAVLGDKSLVEQK----YSDIEKSSISNFHESN-----------SWLGISDK------ 257
G+++ SLVE + + ++ F L +D
Sbjct: 66 GYVS-----SLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTK 120
Query: 258 -----YWASVFIPSKETSFHSQ---FKYLSDGHAR-YQAKFSANEITILPGKSITTTNFL 308
Y + + + S F+ + +G+A+ I G+ T F
Sbjct: 121 ELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV---------AIFGGQGNTDDYF- 170
Query: 309 FAGAKEFPTIHH-YEKDLAIPRFEMLIDWGWFYFIAKPMFML------MSYFYNLVGNFG 361
+E ++ Y LI F A+ + L + G
Sbjct: 171 ----EELRDLYQTYH-----VLVGDLIK-----FSAETLSELIRTTLDAEKVFTQ----G 212
Query: 362 IAIM--------------LTTVFVKLLFFP------LAKKQYVSTANMKNIQPKIDELRE 401
+ I+ L ++ + P LA YV TA + P ELR
Sbjct: 213 LNILEWLENPSNTPDKDYLLSIPIS---CPLIGVIQLA--HYVVTAKLLGFTPG--ELRS 265
Query: 402 KFK 404
K
Sbjct: 266 YLK 268
Score = 37.2 bits (86), Expect = 0.011
Identities = 62/281 (22%), Positives = 115/281 (40%), Gaps = 63/281 (22%)
Query: 175 DEH----YLFKIVDTVTNNSID-QIRF-SPRGRIMRHKPQTATNTFGVQEGFIAVLGDKS 228
D H Y F I+D V NN ++ I F +G+ +R F ++ K
Sbjct: 1650 DNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMI--------FETIVDGKL 1701
Query: 229 LVEQKYSDIEKSSISNFHESNSWLGISDKYWASVFIPSKETSFHS-QFKYL--SD----G 281
E+ + +I + S S S L + ++ ++ +F + K L +D G
Sbjct: 1702 KTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAG 1761
Query: 282 HA--RYQAKFS-ANEITILPGKSITTTNFLFAGAKEFPTIHHYEKDLAIPRFEM-LIDWG 337
H+ Y A S A+ ++I +S+ F + G T+ +A+PR E+ ++G
Sbjct: 1762 HSLGEYAALASLADVMSI---ESLVEVVF-YRGM----TMQ-----VAVPRDELGRSNYG 1808
Query: 338 WFYFIA-KPMFMLMS-------YFYNLVGNFGIAIMLTTVFVKLLFFPLAKKQYVSTANM 389
IA P + S Y VG T V+++ + + +QYV+ ++
Sbjct: 1809 ---MIAINPGRVAASFSQEALQYVVERVGK------RTGWLVEIVNYNVENQQYVAAGDL 1859
Query: 390 KNIQPKIDELREKFKQSPPQVLQKA-MIQLYKTHNINPLAG 429
+ + + L F + LQK +I+L K+ ++ + G
Sbjct: 1860 RALDTVTNVL--NFIK-----LQKIDIIELQKSLSLEEVEG 1893
>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 = 36.5 bits (83), Expect = 0.017
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 15/41 (36%)
Query: 36 ER---KNIQ-TVKQPNQVDNSYAAVLIDDRAQALSMSPRVE 72
E+ K +Q ++K YA DD A AL++ +E
Sbjct: 18 EKQALKKLQASLKL-------YA----DDSAPALAIKATME 47
Score = 30.4 bits (67), Expect = 1.1
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 10/31 (32%)
Query: 401 EKFKQSPPQVLQK--AMIQLYKTHNINP-LA 428
EK Q L+K A ++LY + P LA
Sbjct: 18 EK------QALKKLQASLKLYADDSA-PALA 41
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.0 bits (64), Expect = 2.9
Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 18/78 (23%)
Query: 22 QNFYVYPRIEEMNNERKN-IQTVKQPNQVDNSYAAVLIDDRAQALSMSPRVELKNPSLIG 80
QN ++ R E++NE ++ ++ +Q Q N + PR+ P L G
Sbjct: 1283 QNEFLLERTREIHNEAESQLRAAQQ--QWGNDF-----------YKRDPRIA---P-LRG 1325
Query: 81 SINLKGAQFDDLNLRGYH 98
++ G DDL + +H
Sbjct: 1326 ALATYGLTIDDLGVASFH 1343
>2htq_A Neuraminidase; zanamivir, hydrolase; HET: ZMR; 2.20A {Influenza a
virus} PDB: 2ht7_A* 2ht8_A* 2ht5_A* 2htr_A* 2htu_A*
Length = 390
Score = 28.3 bits (63), Expect = 5.0
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 160 FKNANNILFERTISLDEHY---LFKIVDTVTNNSIDQIRFS 197
F+ ++ RTIS + +I + T S +QIR
Sbjct: 271 FRQGTDVWMGRTISRTSRSGFEILRIKNGWTQTSKEQIRKQ 311
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.323 0.137 0.417
Gapped
Lambda K H
0.267 0.0455 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 5,070,268
Number of extensions: 235466
Number of successful extensions: 633
Number of sequences better than 10.0: 1
Number of HSP's gapped: 624
Number of HSP's successfully gapped: 30
Length of query: 581
Length of database: 5,693,230
Length adjustment: 98
Effective length of query: 483
Effective length of database: 3,317,318
Effective search space: 1602264594
Effective search space used: 1602264594
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (27.2 bits)