RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780202|ref|YP_003064615.1| hypothetical protein
CLIBASIA_00435 [Candidatus Liberibacter asiaticus str. psy62]
(211 letters)
>gnl|CDD|132408 TIGR03365, Bsubt_queE, 7-cyano-7-deazaguanosine (preQ0)
biosynthesis protein QueE. This uncharacterized enzyme,
designated QueE, participates in the biosynthesis, from
GTP, of 7-cyano-7-deazaguanosine, also called preQ0
because in many species it is a precursor of queuosine.
In most Archaea, it is instead the precursor of a
different tRNA modified base, archaeosine.
Length = 238
Score = 55.0 bits (133), Expect = 1e-08
Identities = 41/142 (28%), Positives = 61/142 (42%), Gaps = 30/142 (21%)
Query: 6 IKEIF-LTLQGEGGHAGRVAVFCRFSGCNLWSGREQDRLSAQCRFCDTDFVGIQGTKGGR 64
+ EIF T+QGEG G+ +F R GC+ +C +CD+ F T G
Sbjct: 5 VLEIFGPTIQGEGMVIGQKTMFVRTGGCDY-----------RCSWCDSLF-----TWDGS 48
Query: 65 YNVDQLADLIEEQW-----ITGEKEGRYCVLTGGEPLLQVDV-PLIQALNKRGFEIAVET 118
EE W + G + L+GG P LQ + LI +G+ A+ET
Sbjct: 49 AKDTWRPMTAEEVWQELKALGGG-TPLHVSLSGGNPALQKPLGELIDLGKAKGYRFALET 107
Query: 119 NGTIEPPQG----IDWICVSPK 136
G++ Q +D + +SPK
Sbjct: 108 QGSV--WQDWFRDLDDLTLSPK 127
>gnl|CDD|162888 TIGR02495, NrdG2, anaerobic ribonucleoside-triphosphate reductase
activating protein. This enzyme is a member of the
radical-SAM family (pfam04055). It is often gene
clustered with the class III (anaerobic) ribonucleotide
triphosphate reductase (NrdD, TIGR02487) and presumably
fulfills the identical function as NrdG which utilizes
S-adenosyl methionine, an iron-sulfur cluster and a
reductant (dihydroflavodoxin) to produce a
glycine-centered radical in NrdD.
Length = 191
Score = 43.5 bits (103), Expect = 4e-05
Identities = 32/126 (25%), Positives = 61/126 (48%), Gaps = 26/126 (20%)
Query: 21 GRVAVFCRFSGCNLWSGREQDRLSAQCRFC-DTDFVGIQGTKGGRYNVDQLADLIEEQWI 79
G++A F GCNL +C +C + + + +G+ G V+ L + + +
Sbjct: 15 GKLAFTIFFQGCNL-----------KCPYCHNPELIDREGS--GEIEVEFLLEFLRSR-- 59
Query: 80 TGEKEGRYCVLTGGEPLLQVDVP-LIQALNKRGFEIAVETNGTIEPP------QG-IDWI 131
+ V+TGGEP LQ +P ++ + + GFE+ ++TNG+ +G +D++
Sbjct: 60 --QGLIDGVVITGGEPTLQAGLPDFLRKVRELGFEVKLDTNGSNPRVLEELLEEGLVDYV 117
Query: 132 CVSPKA 137
+ KA
Sbjct: 118 AMDVKA 123
>gnl|CDD|131546 TIGR02493, PFLA, pyruvate formate-lyase 1-activating enzyme. An
iron-sulfur protein with a radical-SAM domain
(pfam04055). A single glycine residue in EC 2.3.1.54,
formate C-acetyltransferase (formate-pyruvate lyase), is
oxidized to the corresponding radical by transfer of H
from its CH2 to AdoMet with concomitant cleavage of the
latter. The reaction requires Fe2+. The first stage is
reduction of the AdoMet to give methionine and the
5'-deoxyadenosin-5-yl radical, which then abstracts a
hydrogen radical from the glycine residue.
Length = 235
Score = 38.1 bits (89), Expect = 0.002
Identities = 29/120 (24%), Positives = 45/120 (37%), Gaps = 25/120 (20%)
Query: 8 EIFLTLQGEGGHAGRVAVFCRFSGCNLWSGREQDRLSAQCRFC---DTDFVGIQGTKGGR 64
E T+ G G R VF GC L +C++C DT G
Sbjct: 6 ESMGTVDGPGI---RFVVF--MQGCPL-----------RCQYCHNPDT----WDLKGGTE 45
Query: 65 YNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVD--VPLIQALNKRGFEIAVETNGTI 122
++L + + G +GGEPLLQ + L +A + G ++T+G +
Sbjct: 46 VTPEELIKEVGSYKDFFKASGGGVTFSGGEPLLQPEFLSELFKACKELGIHTCLDTSGFL 105
>gnl|CDD|162887 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein
family. This subset of the radical-SAM family
(pfam04055) includes a number of probable activating
proteins acting on different enzymes all requiring an
amino-acid-centered radical. The closest relatives to
this family are the pyruvate-formate lyase activating
enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic
ribonucleotide reductase activating enzyme (TIGR02491).
Included within this subfamily are activators of
hydroxyphenyl acetate decarboxylase (HdpA, ),
benzylsuccinate synthase (BssD, ), gycerol dehydratase
(DhaB2, ) as well as enzymes annotated in E. coli as
activators of different isozymes of pyruvate-formate
lyase (PFLC and PFLE) however, these appear to lack
characterization and may activate enzymes with
distinctive functions. Most of the sequence-level
variability between these forms is concentrated within
an N-terminal domain which follows a conserved group of
three cysteines and contains a variable pattern of 0 to
8 additional cysteines.
Length = 295
Score = 37.7 bits (88), Expect = 0.002
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 59 GTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVD--VPLIQALNKRGFEIAV 116
G V+++ ++ I G L+GGEPLLQ + + L+QA ++RG AV
Sbjct: 100 SIVGEEMTVEEVMRVVLRDSIFYRNSGGGVTLSGGEPLLQPEFALALLQACHERGIHTAV 159
Query: 117 ETNGT 121
ET+G
Sbjct: 160 ETSGF 164
>gnl|CDD|162966 TIGR02666, moaA, molybdenum cofactor biosynthesis protein A,
bacterial. The model for this family describes
molybdenum cofactor biosynthesis protein A, or MoaA, as
found in bacteria. It does not include the family of
probable functional equivalent proteins from the
archaea. MoaA works together with MoaC to synthesize
precursor Z from guanine.
Length = 334
Score = 35.3 bits (82), Expect = 0.012
Identities = 18/35 (51%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 90 LTGGEPLLQVDVP-LIQALNK-RGFE-IAVETNGT 121
LTGGEPLL+ D+ L+ L G E IA+ TNG
Sbjct: 65 LTGGEPLLRKDLVELVARLAALPGIEDIALTTNGL 99
>gnl|CDD|162967 TIGR02668, moaA_archaeal, probable molybdenum cofactor biosynthesis
protein A, archaeal. This model describes an archaeal
family related, and predicted to be functionally
equivalent, to molybdenum cofactor biosynthesis protein
A (MoaA) of bacteria (see TIGR02666).
Length = 302
Score = 35.0 bits (81), Expect = 0.016
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 90 LTGGEPLLQVDVPLIQA-LNKRGF-EIAVETNGT 121
+TGGEPLL+ D+ I + G ++++ TNG
Sbjct: 62 ITGGEPLLRKDLIEIIRRIKDYGIKDVSMTTNGI 95
>gnl|CDD|178909 PRK00164, moaA, molybdenum cofactor biosynthesis protein A;
Reviewed.
Length = 331
Score = 34.7 bits (81), Expect = 0.017
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 90 LTGGEPLLQVDVP-LIQAL--NKRGFEIAVETNGT 121
LTGGEPLL+ D+ +I AL ++A+ TNG
Sbjct: 71 LTGGEPLLRKDLEDIIAALAALPGIRDLALTTNGY 105
>gnl|CDD|184000 PRK13361, PRK13361, molybdenum cofactor biosynthesis protein A;
Provisional.
Length = 329
Score = 31.1 bits (71), Expect = 0.19
Identities = 31/113 (27%), Positives = 46/113 (40%), Gaps = 33/113 (29%)
Query: 21 GRVAVFCRFSGCNLWSGREQDRLSAQCRFC---DTDFVGIQGTKGGRYNVDQLADLIEEQ 77
GR + R S DR +C +C D F+ DQ+ L E
Sbjct: 10 GRTVTYLRLS--------VTDRCDFRCVYCMSEDPCFL----------PRDQVLSLEELA 51
Query: 78 WIT------GEKEGRYCVLTGGEPLLQVD-VPLIQALNKRG--FEIAVETNGT 121
W+ G ++ R LTGGEPL++ L+ L K E+++ TNG+
Sbjct: 52 WLAQAFTELGVRKIR---LTGGEPLVRRGCDQLVARLGKLPGLEELSLTTNGS 101
>gnl|CDD|178737 PLN03195, PLN03195, fatty acid omega-hydroxylase; Provisional.
Length = 516
Score = 30.9 bits (70), Expect = 0.22
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 164 IGFDFERFSLQPM--DGPFLE--ENTNLAISYCFQNPKWRL 200
+GF E +L P + PF + + N+ ++ F +P W+L
Sbjct: 185 VGFGVEIGTLSPSLPENPFAQAFDTANIIVTLRFIDPLWKL 225
>gnl|CDD|184309 PRK13762, PRK13762, tRNA-modifying enzyme; Provisional.
Length = 322
Score = 30.2 bits (69), Expect = 0.35
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 93 GEPLLQVDVP-LIQALNKRGFEIAVETNGT 121
GEP L +P LI+ +KRGF + TNGT
Sbjct: 139 GEPTLYPYLPELIEEFHKRGFTTFLVTNGT 168
>gnl|CDD|183551 PRK12484, PRK12484, nicotinate phosphoribosyltransferase;
Provisional.
Length = 443
Score = 29.7 bits (67), Expect = 0.63
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 9/42 (21%)
Query: 84 EGRYCVLTGGEPLLQVDVPLIQA-------LNKRGFEIAVET 118
EG V+ EPLL+V PLI+A LN+ + + +
Sbjct: 97 EGT--VVFPNEPLLEVTAPLIEAQLVETFLLNQINHQSLIAS 136
>gnl|CDD|163534 TIGR03822, AblA_like_2, lysine-2,3-aminomutase-related protein.
Members of this protein form a distinctive clade,
homologous to lysine-2,3-aminomutase (of Bacillus,
Clostridium, and methanogenic archaea) and likely
similar in function. Members of this family are found in
Rhodopseudomonas, Caulobacter crescentus,
Bradyrhizobium, etc.
Length = 321
Score = 29.3 bits (66), Expect = 0.70
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 47 CRFC-DTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLL 97
CRFC + VG +G G + +L +I E +LTGG+PL+
Sbjct: 102 CRFCFRREMVGPEG--LGVLSPAELD--AAFAYIADHPEIWEVILTGGDPLV 149
>gnl|CDD|181722 PRK09243, PRK09243, nicotinate phosphoribosyltransferase;
Validated.
Length = 464
Score = 29.0 bits (66), Expect = 0.91
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 79 ITGEKEGRYCVLTGGEPLLQVDVPLIQA 106
+ EG ++ EPLL+V+ PL +A
Sbjct: 98 VRAVPEGE--LVFPNEPLLRVEGPLAEA 123
>gnl|CDD|163535 TIGR03823, FliZ, flagellar regulatory protein FliZ. FliZ is
involved in the regulation of flagellar assembly and
possibly also the down-regulation of the motile
phenotype. FliZ interacts with the flagellar
translational activator FlhCD complex.
Length = 168
Score = 27.9 bits (62), Expect = 2.0
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 8/36 (22%)
Query: 33 NLWSGREQDRLSAQCRFC-------DTDFVGIQGTK 61
N WS Q L+A CRFC +D+ I K
Sbjct: 59 NGWSV-LQQELAALCRFCSEIYCNTTSDYFDIMAFK 93
>gnl|CDD|162339 TIGR01399, hrcV, type III secretion protein, HrcV family. Members
of this family are closely homologous to the flagellar
biosynthesis protein FlhA (TIGR01398) and should all
participate in type III secretion systems. Examples
include InvA (Salmonella enterica), LcrD (Yersinia
enterocolitica), HrcV (Xanthomonas), etc. Type III
secretion systems resemble flagellar biogenesis systems,
and may share the property of translocating special
classes of peptides through the membrane.
Length = 677
Score = 27.7 bits (62), Expect = 2.5
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 7/39 (17%)
Query: 42 RLSAQCRFCDTDFVGIQGTKGGRYNVDQL----ADLIEE 76
RL A +F+GIQ T RY +DQ+ +L++E
Sbjct: 475 RLKATLLRNAQEFIGIQET---RYLLDQMEREYPELVKE 510
>gnl|CDD|152611 pfam12176, MtaB, Methanol-cobalamin methyltransferase B subunit.
This family of proteins is found in bacteria and
archaea. Proteins in this family are approximately 460
amino acids in length. MtaB folds as a TIM barrel and
contains a novel zinc-binding motif. Zinc(II) lies at
the bottom of a funnel formed at the C-terminal
beta-barrel end and ligates to two cysteinyl sulfurs
(Cys-220 and Cys-269) and one carboxylate oxygen
(Glu-164). The function of this protein is to catalyse
the cleavage of the C O bond in methanol by an SN2
mechanism. It complexes with MtaA and MtaC to perform
this function.
Length = 460
Score = 27.4 bits (61), Expect = 2.8
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 131 ICVSP-KAGCDLKIKGGQELKLVFPQVNVSPEN 162
P KAG L+I G V P++N +P
Sbjct: 20 KAKHPVKAGLGLEIGAGY----VIPEINYAPRP 48
>gnl|CDD|185626 PTZ00447, PTZ00447, apical membrane antigen 1-like protein;
Provisional.
Length = 508
Score = 27.3 bits (60), Expect = 2.9
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 184 NTNLAISYCFQNPKWRLSVQTHK 206
NTN I Y +QN K++LS+ + K
Sbjct: 318 NTNANIIYTYQNEKYQLSIHSEK 340
>gnl|CDD|162398 TIGR01513, NAPRTase_put, putative nicotinate
phosphoribosyltransferase. Most members of this family
are Gram-positive bacteria. An additional set of
mutually closely related archaeal sequences score
between the trusted and noise cutoffs.
Length = 443
Score = 26.9 bits (60), Expect = 3.8
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 9/48 (18%)
Query: 79 ITGEKEGRYCVLTGGEPLLQVDVPLIQA-------LNKRGFEIAVETN 119
+ EG ++ EPLLQV+ PLI+A LN F+ + T
Sbjct: 89 VRALPEGS--LVFPNEPLLQVEGPLIEAQLLETLVLNIINFQTLIATK 134
>gnl|CDD|161784 TIGR00238, TIGR00238, KamA family protein. Note that the E. coli
homolog was expressed in E. coli and purified and found
not to display display lysine 2,3-aminomutase activity.
Active site residues are found in 100 residue extension
in B. subtilis. Name changed to KamA family protein.
Length = 331
Score = 26.7 bits (59), Expect = 4.0
Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 5/63 (7%)
Query: 47 CRFCDTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDVPLIQA 106
CR+C + G + + D +I E +++GG+PL+ D L
Sbjct: 127 CRYCFRRHFPYKENPGNKKKWQKALD-----YIAEHPEIIEILISGGDPLMAKDHELEWL 181
Query: 107 LNK 109
L +
Sbjct: 182 LKR 184
>gnl|CDD|179152 PRK00881, purH, bifunctional
phosphoribosylaminoimidazolecarboxamide
formyltransferase/IMP cyclohydrolase; Provisional.
Length = 513
Score = 26.6 bits (60), Expect = 4.4
Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 101 VPLIQALNKRGFEIAVETNGT 121
V +AL + G EI + T GT
Sbjct: 18 VEFAKALVELGVEI-LSTGGT 37
>gnl|CDD|116601 pfam07991, IlvN, Acetohydroxy acid isomeroreductase, catalytic
domain. Acetohydroxy acid isomeroreductase catalyses
the conversion of acetohydroxy acids into dihydroxy
valerates. This reaction is the second in the synthetic
pathway of the essential branched side chain amino acids
valine and isoleucine.
Length = 165
Score = 26.7 bits (60), Expect = 5.1
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 111 GFEIAVETNGTIEPPQGIDWICVSPKA 137
GF I G I+PP+ +D I V+PK
Sbjct: 96 GFNIHF---GQIKPPKDVDVIMVAPKG 119
>gnl|CDD|183213 PRK11582, PRK11582, flagella biosynthesis protein FliZ;
Provisional.
Length = 169
Score = 26.5 bits (59), Expect = 5.7
Identities = 8/18 (44%), Positives = 9/18 (50%), Gaps = 1/18 (5%)
Query: 33 NLWSGREQDRLSAQCRFC 50
N W + Q A CRFC
Sbjct: 59 NGWQ-KLQQEWVALCRFC 75
>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated.
Length = 740
Score = 26.3 bits (58), Expect = 5.8
Identities = 8/32 (25%), Positives = 17/32 (53%)
Query: 34 LWSGREQDRLSAQCRFCDTDFVGIQGTKGGRY 65
L G +D++ +C C +D + + +G R+
Sbjct: 579 LREGLREDKIIGKCPLCGSDLMVRRSKRGSRF 610
>gnl|CDD|180113 PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional.
Length = 330
Score = 26.2 bits (59), Expect = 5.9
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 120 GTIEPPQGIDWICVSPKA 137
G I PP +D I V+PK
Sbjct: 115 GQIVPPADVDVIMVAPKG 132
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 26.2 bits (57), Expect = 6.1
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 44 SAQCRFCDTDFV 55
S QC FCDTDF+
Sbjct: 731 SVQCVFCDTDFL 742
>gnl|CDD|129783 TIGR00700, GABAtrnsam, 4-aminobutyrate aminotransferase,
prokaryotic type. Alternate names include GABA
transaminase, gamma-amino-N-butyrate transaminase, and
beta-alanine--oxoglutarate aminotransferase.
Length = 420
Score = 25.6 bits (56), Expect = 8.8
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 97 LQVDVPLIQALNKRGFEIAVETN--GTIEPPQGI 128
L+ P I + G IAVE GT EP G+
Sbjct: 336 LKAVDPRIGDVRGLGAMIAVELVDPGTTEPDAGL 369
>gnl|CDD|184040 PRK13412, fkp, bifunctional
fucokinase/L-fucose-1-P-guanylyltransferase;
Provisional.
Length = 974
Score = 25.6 bits (56), Expect = 9.0
Identities = 7/27 (25%), Positives = 11/27 (40%)
Query: 178 GPFLEENTNLAISYCFQNPKWRLSVQT 204
G EN L I W+L+ ++
Sbjct: 341 GKLTAENATLWIENSHVGEGWKLASRS 367
>gnl|CDD|180002 PRK05301, PRK05301, pyrroloquinoline quinone biosynthesis protein
PqqE; Provisional.
Length = 378
Score = 25.6 bits (57), Expect = 9.1
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 90 LTGGEPLLQVDVP-LIQALNKRGF 112
+GGEPLL+ D+ L+ + G
Sbjct: 68 FSGGEPLLRKDLEELVAHARELGL 91
>gnl|CDD|172997 PRK14531, PRK14531, adenylate kinase; Provisional.
Length = 183
Score = 25.5 bits (56), Expect = 9.2
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 102 PLIQALNKRGFEIAVETNGTIE 123
PLI +RG +VE G+IE
Sbjct: 151 PLIDHYRQRGLLQSVEAQGSIE 172
>gnl|CDD|184709 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide
biosynthesis protein MobB/FeS domain-containing protein
protein; Provisional.
Length = 229
Score = 25.7 bits (57), Expect = 9.9
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 55 VGIQGTKGGRYNVDQLADLIEE 76
+ I K G +D+LADL+ E
Sbjct: 121 LAIDDFKYGTEEIDELADLVLE 142
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
0.322 0.142 0.450
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,540,607
Number of extensions: 220474
Number of successful extensions: 434
Number of sequences better than 10.0: 1
Number of HSP's gapped: 431
Number of HSP's successfully gapped: 37
Length of query: 211
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 122
Effective length of database: 4,071,361
Effective search space: 496706042
Effective search space used: 496706042
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.2 bits)