RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780939|ref|YP_003065352.1| type I signal peptidase
[Candidatus Liberibacter asiaticus str. psy62]
(248 letters)
>1b12_A Signal peptidase I; serine proteinase, serine-dependant hydrolase,
signal peptide processing, protein translocation,
membrane bound proteinase; HET: 1PN; 1.95A {Escherichia
coli} SCOP: b.87.1.2 PDB: 1t7d_A* 1kn9_A
Length = 248
Score = 149 bits (377), Expect = 5e-37
Identities = 84/260 (32%), Positives = 127/260 (48%), Gaps = 55/260 (21%)
Query: 30 IRTFLFQPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGD 89
+R+F+++P IPSGSM+PTLL+GD+I+V KF+YG + + I P+RGD
Sbjct: 1 VRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKT------LIETGHPKRGD 54
Query: 90 VVVFRYPKDPSIDYVKRVIGLPGDRISLEKGIIYINGAPVVRH----------------- 132
+VVF+YP+DP +DY+KR +GLPGD+++ + + P
Sbjct: 55 IVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEP 114
Query: 133 ---------------MEGYFSYHYKEDWSSNVPIFQEKLSNG-----VLYNVLSQDFLA- 171
G+F E + + + + K + G +L ++QD +
Sbjct: 115 SDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGM 174
Query: 172 ----PSSNISEFLVPKGHYFMMGDNRDKSKDSRWVEVGFVPEENLVGRASFVLFSIGGDT 227
P ++ ++VP G YFMMGDNRD S DSR+ GFVPE NLVGRA+ + S
Sbjct: 175 YYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRY--WGFVPEANLVGRATAIWMSFDKQE 232
Query: 228 PFSKVWLWIPNMRWDRLFKI 247
W +R R+ I
Sbjct: 233 -----GEWPTGLRLSRIGGI 247
>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 = 36.8 bits (85), Expect = 0.005
Identities = 43/252 (17%), Positives = 71/252 (28%), Gaps = 135/252 (53%)
Query: 11 IFGSDTLKS-------ILQALFFAILI---------RTFLFQPSVI----------PSGS 44
I +D+ +S + LFF I T L PS++ PS
Sbjct: 283 IAETDSWESFFVSVRKAITVLFF---IGVRCYEAYPNTSL-PPSILEDSLENNEGVPS-- 336
Query: 45 MIPTLLVGD--------YI-IVNKFSYGYSKYSFP----FSYNLFNGRIFNNQPRRGDVV 91
P L + + Y+ N P +L NG + ++V
Sbjct: 337 --PMLSISNLTQEQVQDYVNKTNS--------HLPAGKQVEISLVNG------AK--NLV 378
Query: 92 V-------------FRYPKDPS------IDYVKR--VIG---LPGDRISLEKGIIYINGA 127
V R K PS I + +R LP ++ +
Sbjct: 379 VSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLP---VA----------S 425
Query: 128 PVVRHMEGYFSYHY--------KED-------WSSN---VPIFQEKLSNGVLYNVLSQDF 169
P F H +D +++ +P++ +G D
Sbjct: 426 P--------FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTF--DG-------SDL 468
Query: 170 LAPSSNISEFLV 181
S +ISE +V
Sbjct: 469 RVLSGSISERIV 480
>3pfd_A Acyl-COA dehydrogenase; structural genomics, seattle structural
genomics center for infectious disease, ssgcid; HET:
FDA; 2.10A {Mycobacterium thermoresistibile}
Length = 393
Score = 28.6 bits (64), Expect = 1.2
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 171 APSSNISEFLVPKGHY-FMMGDNRDKS--KDSRWVEVGF----VPEENLVGR 215
++ IS F+V K F +G K K S E+ F +P + ++G
Sbjct: 189 KGANGISAFMVHKDDEGFTVGPKERKLGIKGSPTTELYFENCRIPGDRIIGE 240
>1fmj_A Retinol dehydratase; sulfotransferase, adenosine 3',5'-
diphosphate; HET: A3P RTL; 2.00A {Spodoptera frugiperda}
SCOP: c.37.1.5 PDB: 1fml_A* 1x8l_A* 1x8k_A* 1x8j_A*
Length = 351
Score = 28.3 bits (62), Expect = 1.6
Identities = 15/91 (16%), Positives = 33/91 (36%), Gaps = 1/91 (1%)
Query: 60 FSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRISLEK 119
G Y Y I+N R DV V Y + + + ++ L + ++ E
Sbjct: 36 VKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTT-MTQELVWLIENDLNFEA 94
Query: 120 GIIYINGAPVVRHMEGYFSYHYKEDWSSNVP 150
Y++ + + +E+++ +P
Sbjct: 95 AKTYMSLRYIYLDGFMIYDPEKQEEYNDILP 125
>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity,
transcription regulator; 1.95A {Enterobacteria phage
186} PDB: 2fkd_A
Length = 189
Score = 27.8 bits (61), Expect = 2.6
Identities = 8/74 (10%), Positives = 17/74 (22%), Gaps = 26/74 (35%)
Query: 44 SMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDY 103
+ G V+K + + SI
Sbjct: 114 DGMAIRSEGKIYFVDK-----------------------QASLSDGLWLVDIKGAISI-- 148
Query: 104 VKRVIGLPGDRISL 117
+ + LPG ++ +
Sbjct: 149 -RELTKLPGRKLHV 161
>2vig_A Short-chain specific acyl-COA dehydrogenase,; fatty acid
metabolism, FAD, polymorphism, flavoprotein,
mitochondrion, disease mutation; HET: FAD COS; 1.9A
{Homo sapiens} PDB: 1jqi_A*
Length = 391
Score = 27.5 bits (60), Expect = 2.9
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 168 DFLAPSSNISEFLVPKGHY-FMMGDNRDKS--KDSRWVEVGF----VPEENLVGR 215
D + +IS FLVP +G DK + S + F +P+++++G
Sbjct: 174 DRALQNKSISAFLVPMPTPGLTLGKKEDKLGIRGSSTANLIFEDCRIPKDSILGE 228
>2wnv_A C1Q chain A, complement C1Q subcomponent subunit A; immune system,
secreted, collagen, recognition, disulfide bond, innate
immunity; HET: NAG; 1.25A {Homo sapiens} PDB: 2jg8_A
2wnu_A* 2jg9_A* 1pk6_A
Length = 134
Score = 26.6 bits (58), Expect = 5.1
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 42 SGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNG 78
SG M+ L GD + V K Y + ++F+G
Sbjct: 91 SGGMVLQLQQGDQVWVEKDPKKGHIYQGSEADSVFSG 127
>2uxw_A VERY-long-chain specific acyl-COA dehydrogenase; alternative
splicing, fatty acid metabolism, transit peptide,
disease mutation, lipid metabolism; HET: FAD TH3; 1.45A
{Homo sapiens} PDB: 3b96_A*
Length = 607
Score = 26.8 bits (58), Expect = 5.3
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 176 ISEFLVPKGHY-FMMGDNRDKS--KDSRWVEVGF----VPEENLVGRA 216
I+ F+V +G G K K S EV F VP EN++G
Sbjct: 231 ITAFVVERGFGGITHGPPEKKMGIKASNTAEVFFDGVRVPSENVLGEV 278
>1ges_A Glutathione reductase; oxidoreductase(flavoenzyme); HET: FAD; 1.74A
{Escherichia coli} SCOP: c.3.1.5 c.3.1.5 d.87.1.1 PDB:
1geu_A* 1ger_A* 1get_A*
Length = 450
Score = 26.4 bits (57), Expect = 6.3
Identities = 15/114 (13%), Positives = 35/114 (30%), Gaps = 9/114 (7%)
Query: 40 IPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDP 99
+P M + + I + YG+ F++ R
Sbjct: 48 VPKKVMWHAAQIREAIHMYGPDYGFDTTINKFNWETLIASRTAYIDRIHTSYENVL-GKN 106
Query: 100 SIDYVK--------RVIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHYKEDW 145
++D +K + + + G+ I+ + +I G P + G + +
Sbjct: 107 NVDVIKGFARFVDAKTLEVNGETITADHILIATGGRPSHPDIPGVEYGIDSDGF 160
>3muj_A Transcription factor COE3; immunoglobulin like fold,
helix-loop-helix, structural genom consortium, SGC, DNA
binding protein; 1.92A {Homo sapiens} PDB: 3mqi_A
Length = 138
Score = 26.2 bits (57), Expect = 7.1
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 76 FNGRIFNNQPRRGDVVVFRY--PKDPSIDYV-----KRVIGLPGDRISLEKGIIYINGAP 128
+ + F +G F Y +P+IDY K + PGD L K ++ A
Sbjct: 73 YKSKQFC----KGAPGRFVYTALNEPTIDYGFQRLQKVIPRHPGDPERLPKEVLLKRAAD 128
Query: 129 VVRHM 133
+V +
Sbjct: 129 LVEAL 133
>1q6z_A BFD, BFDC, benzoylformate decarboxylase; lyase, carbon-carbon,
mandelate catabolism, thiamin thiazolone diphosphate,
inhibitor; HET: TZD; 1.00A {Pseudomonas putida} SCOP:
c.31.1.3 c.36.1.5 c.36.1.9 PDB: 1po7_A* 1pi3_A* 3fsj_X*
1mcz_A* 1bfd_A* 2fwn_A* 3fzn_A* 2fn3_A* 2v3w_A* 1yno_A*
3f6b_X* 3f6e_X*
Length = 528
Score = 26.0 bits (56), Expect = 7.5
Identities = 6/34 (17%), Positives = 9/34 (26%), Gaps = 9/34 (26%)
Query: 104 VKRVIGLPGDRI-----SLEKGIIYINGAPVVRH 132
+ V G PG + YI +
Sbjct: 17 IDTVFGNPGSNALPFLKDFPEDFRYI----LALQ 46
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
0.325 0.143 0.454
Gapped
Lambda K H
0.267 0.0642 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,367,958
Number of extensions: 112273
Number of successful extensions: 375
Number of sequences better than 10.0: 1
Number of HSP's gapped: 371
Number of HSP's successfully gapped: 24
Length of query: 248
Length of database: 5,693,230
Length adjustment: 90
Effective length of query: 158
Effective length of database: 3,511,270
Effective search space: 554780660
Effective search space used: 554780660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.1 bits)