RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780297|ref|YP_003064710.1| peptide deformylase
[Candidatus Liberibacter asiaticus str. psy62]
(170 letters)
>gnl|CDD|178903 PRK00150, def, peptide deformylase; Reviewed.
Length = 165
Score = 225 bits (577), Expect = 3e-60
Identities = 77/166 (46%), Positives = 118/166 (71%), Gaps = 3/166 (1%)
Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60
M P++ + DP+LR+V++P+E+++ ++ LID+M E MY+ G+GLAA Q+GV R++V
Sbjct: 1 MAILPILRYGDPVLRKVAKPVEEVDDELRKLIDDMFETMYAAPGVGLAAPQVGVSKRIIV 60
Query: 61 IDLQDHAHRKNPMVFINPKIITFS-DDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNA 119
ID++D P+V INP+II+ S +++ Y+EGCLS+P +V R +TV+ +D +
Sbjct: 61 IDVEDKE--GEPLVLINPEIISESSEEYLTYEEGCLSVPGVYGEVPRPERVTVKALDRDG 118
Query: 120 QHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKL 165
+ + ADGLLA C+QHE+DHLNG+LFID LS LKR I KK+ K+
Sbjct: 119 KPFELEADGLLARCIQHEIDHLNGVLFIDRLSPLKRFRIKKKLKKI 164
>gnl|CDD|183788 PRK12846, PRK12846, peptide deformylase; Reviewed.
Length = 165
Score = 197 bits (504), Expect = 1e-51
Identities = 78/166 (46%), Positives = 105/166 (63%), Gaps = 3/166 (1%)
Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSD-IMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLV 59
M +P++ PDP LRR + P+ +++ + LID+M E M + DG+GLAA QIGV R+V
Sbjct: 1 MAVRPILKMPDPRLRRPAEPVTAFDTEELQALIDDMFETMRAADGVGLAAPQIGVSLRVV 60
Query: 60 VIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNA 119
VIDL D P V INP+I S + V EGCLS+P R +V+R A + VR D +
Sbjct: 61 VIDLGDDRV--PPTVLINPEITELSPEEEVGWEGCLSVPGLRGEVERPARVRVRAQDRDG 118
Query: 120 QHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKL 165
+ I A+G LA LQHE+DHL+GIL+ D LSRLKR+ KK+ K
Sbjct: 119 KPIEIEAEGFLARVLQHEIDHLDGILYTDRLSRLKRERALKKVEKY 164
>gnl|CDD|161696 TIGR00079, pept_deformyl, peptide deformylase. Peptide deformylase
(EC 3.5.1.88), also called polypeptide deformylase, is a
metalloenzyme that uses water to release formate from
the N-terminal formyl-L-methionine of bacterial and
chloroplast peptides. This enzyme should not be confused
with formylmethionine deformylase (EC 3.5.1.31) which is
active on free N-formyl methionine and has been reported
from rat intestine.
Length = 161
Score = 175 bits (446), Expect = 4e-45
Identities = 69/159 (43%), Positives = 105/159 (66%), Gaps = 1/159 (0%)
Query: 6 LVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQD 65
+V +PD +LR +++P+EK++ I +D+M+E MY+ +GIGLAA Q+G+ R+ VI L+D
Sbjct: 4 VVHYPDDVLRTIAKPVEKVDDKIRQQLDDMIETMYAEEGIGLAAPQVGIWKRMFVIHLED 63
Query: 66 HAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIY 125
+++P+V INPKII S + S +EGCLS+P V R + +R D + I
Sbjct: 64 -DDKEDPLVLINPKIIETSGEKSGLEEGCLSVPGVYGYVPRPEKVKIRGFDRFGKPFTIE 122
Query: 126 ADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSK 164
A GLLA C+QHE+DHLNG+LF+D +S LK + K++
Sbjct: 123 ASGLLARCIQHEMDHLNGVLFVDRISPLKPEKEKKELKV 161
>gnl|CDD|173061 PRK14597, PRK14597, peptide deformylase; Provisional.
Length = 166
Score = 151 bits (384), Expect = 7e-38
Identities = 64/164 (39%), Positives = 98/164 (59%), Gaps = 5/164 (3%)
Query: 6 LVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQD 65
+ +F DP+LR+ ++P+ K + ++ I+ M+E MY DG+GLAA Q+G+ R V+D
Sbjct: 3 IRLFGDPVLRKKAKPVTKFDDNLKKTIEEMIETMYHYDGVGLAAPQVGISLRFFVMDDG- 61
Query: 66 HAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIY 125
P V INP+II S++ + +EGCLS P+ DV+RS ++ VRY D +
Sbjct: 62 ----SGPKVVINPEIIEKSEEKEIAEEGCLSFPEIFEDVERSKWVKVRYQDERGEVVEEL 117
Query: 126 ADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLR 169
+G A QHE DHLNG+LFID L KR ++ KK+ +++
Sbjct: 118 LEGYAARIFQHEYDHLNGVLFIDRLPPAKRLLLRKKLMDIMRTV 161
>gnl|CDD|173062 PRK14598, PRK14598, peptide deformylase; Provisional.
Length = 187
Score = 148 bits (375), Expect = 8e-37
Identities = 61/164 (37%), Positives = 104/164 (63%), Gaps = 5/164 (3%)
Query: 5 PLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDL- 63
P+ + D +LR+ ++P++ ++++I LI +M E MY+ GIGLAA Q+G RL+V+D+
Sbjct: 4 PINTYSDEVLRQKAKPLKGVDAEIEELIASMFESMYNASGIGLAAPQVGRSLRLLVVDVS 63
Query: 64 --QDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQH 121
+++ K PMV INP I+ ++ +EGCLS+P + DV R + IT++Y D + +
Sbjct: 64 CMKEYEDEK-PMVVINPHILAVKG-YNAMEEGCLSVPGVQGDVVRPSSITLKYRDEHFEE 121
Query: 122 QIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKL 165
+ G++A LQHE+DHL+G LF+D + + R I K++ +
Sbjct: 122 RTEEFSGMMARVLQHEIDHLDGTLFVDRMQKRDRRKIQKELDAI 165
>gnl|CDD|184758 PRK14596, PRK14596, peptide deformylase; Provisional.
Length = 199
Score = 129 bits (325), Expect = 4e-31
Identities = 65/170 (38%), Positives = 92/170 (54%), Gaps = 15/170 (8%)
Query: 5 PLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRL-VVIDL 63
P+ ++ DP+LRR +RP++ + I L ++MLE M+ G+GLAA QIG+ RL V ++
Sbjct: 4 PIRLYGDPVLRRKARPVQDFDQGIRRLAEDMLETMFEARGVGLAAPQIGLSVRLFVAVEY 63
Query: 64 QDHAHR------------KNPMVFINPKIITFSDDFSVYQEGCLSIPD-YRADVKRSAFI 110
D V +NP I D S QEGCLSIP Y V R+ +
Sbjct: 64 ADDEEEEEGEEAPLRSRVLREYVMVNPVITYRKGDQS-GQEGCLSIPGLYEEGVPRARQV 122
Query: 111 TVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITK 160
V Y D + Q + + A+G LA QHE+DHL+GILF D L + KR+ +
Sbjct: 123 RVEYQDLDGQKRTLEAEGYLARVFQHEIDHLDGILFFDRLPKAKREAFLE 172
>gnl|CDD|184757 PRK14595, PRK14595, peptide deformylase; Provisional.
Length = 162
Score = 79.5 bits (196), Expect = 4e-16
Identities = 44/156 (28%), Positives = 79/156 (50%), Gaps = 4/156 (2%)
Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60
M K LV PIL + ++ ++ + + L+ ++ + MY+ + L A QIG ++ +
Sbjct: 1 MAIKKLVPASHPILTKKAQAVKTFDDSLKRLLQDLEDTMYAQEAAALCAPQIGQSLQVAI 60
Query: 61 IDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQ 120
ID++ + + +NPKII+ S++ EG +++PD +V RS I V D N
Sbjct: 61 IDME----MEGLLQLVNPKIISQSNETITDLEGSITLPDVYGEVTRSKMIVVESYDVNGN 116
Query: 121 HQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRD 156
+ A +A + H +D +NGI F + R+ D
Sbjct: 117 KVELTAYDDVARMILHIIDQMNGIPFTERADRILTD 152
>gnl|CDD|181704 PRK09218, PRK09218, peptide deformylase; Validated.
Length = 136
Score = 71.9 bits (177), Expect = 7e-14
Identities = 40/101 (39%), Positives = 55/101 (54%), Gaps = 7/101 (6%)
Query: 45 IGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADV 104
+G+AA IGV R+++ L P+V NP I++ S + +EGCLS+ R
Sbjct: 42 VGMAANMIGVQKRIIIFSLGFV-----PVVMFNPVIVSKSGPYET-EEGCLSLTGERP-T 94
Query: 105 KRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGIL 145
KR ITV+Y+D N + Q G A +QHELDH GIL
Sbjct: 95 KRYEEITVKYLDRNWREQTQTFTGFTAQIIQHELDHCEGIL 135
>gnl|CDD|180657 PRK06687, PRK06687, chlorohydrolase; Validated.
Length = 419
Score = 26.5 bits (58), Expect = 3.6
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 74 VFINPKIITFSDDFSVYQEGCLSIPDYR 101
VF + I+T DF VY +G L++ D +
Sbjct: 3 VFQHVNIVTCDQDFHVYLDGILAVKDSQ 30
>gnl|CDD|162900 TIGR02517, type_II_gspD, general secretion pathway protein D. In
Gram-negative bacteria, proteins that have first crossed
the inner member by Sec-dependent protein transport can
be exported across the outer membrane by type II
secretion, also called the main terminal branch of the
general secretion pathway. Members of this family are
general secretion pathway protein D. In Yersinia
enterocolitica, a second member of this family is part
of a novel second type II secretion system specifically
associated with virulence (See PubMed:12654803). This
family is closely homologous to the type IV pilus outer
membrane secretin PilQ (TIGR02515) and to the type III
secretion system pore YscC/HrcC (TIGR02516).
Length = 594
Score = 25.8 bits (57), Expect = 5.3
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 69 RKNPMVFINPKIITFSDDF 87
+ N MVFI P+II +D
Sbjct: 572 KTNLMVFITPRIIRDPEDA 590
>gnl|CDD|180393 PRK06087, PRK06087, short chain acyl-CoA synthetase; Reviewed.
Length = 547
Score = 25.5 bits (56), Expect = 7.0
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 121 HQIIYADGLLATCLQHELDHLNGILFIDHL 150
Q D L LQ++L L I+ +D L
Sbjct: 132 KQTRPVD--LILPLQNQLPQLQQIVGVDKL 159
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.327 0.143 0.418
Gapped
Lambda K H
0.267 0.0801 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,848,883
Number of extensions: 175982
Number of successful extensions: 443
Number of sequences better than 10.0: 1
Number of HSP's gapped: 427
Number of HSP's successfully gapped: 21
Length of query: 170
Length of database: 5,994,473
Length adjustment: 87
Effective length of query: 83
Effective length of database: 4,114,577
Effective search space: 341509891
Effective search space used: 341509891
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 (21.7 bits)
S2: 54 (24.4 bits)