RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780129|ref|YP_003064542.1| hypothetical protein
CLIBASIA_00040 [Candidatus Liberibacter asiaticus str. psy62]
(220 letters)
>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 76.4 bits (188), Expect = 6e-15
Identities = 42/177 (23%), Positives = 70/177 (39%), Gaps = 14/177 (7%)
Query: 5 LKPHQIVMVNWLLSHDR-CALWASMGSGKT-VSVLFALSTIKILDPRPVLIIAPLRVAQY 62
L+P+Q + LLS R L A GSGKT ++L AL +K + VL++ P R
Sbjct: 9 LRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAE 68
Query: 63 VWKDEVERWSAFSDMTVSSLIGS---ERQRIKALNTPAHLYIINFENIP-WLVKMKLDHW 118
W +E+++ + V L G Q K + + + + L L+
Sbjct: 69 QWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELS 128
Query: 119 DFATIVVDES--TKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDLW 173
+ +++DE+ F Q L K+ V+ + L+ TP L
Sbjct: 129 NVDLVILDEAHRLLDGGFG-----DQLEKLLKLLPKNVQLLL-LSATPPEEIENLLE 179
>gnl|CDD|162193 TIGR01078, arcA, arginine deiminase. Arginine deiminase is the
first enzyme of the arginine deiminase pathway of
arginine degradation.
Length = 405
Score = 31.6 bits (72), Expect = 0.16
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 84 GSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWDFATIVVDES 128
G E + + TP++L + F++IPW+ + +H FA + D
Sbjct: 17 GRELENL----TPSNLDELLFDDIPWVEDAQKEHDQFANTLRDNG 57
>gnl|CDD|178452 PLN02861, PLN02861, long-chain-fatty-acid-CoA ligase.
Length = 660
Score = 31.0 bits (70), Expect = 0.23
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 166 PNGLIDLWGQIWFLDKGKRLGLSFKSFVERWFHTQQVG 203
P G I L G F KR L+ + ++ WFHT +G
Sbjct: 464 PRGEICLRGNTLFSGYHKRQDLTEEVLIDGWFHTGDIG 501
>gnl|CDD|178687 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 29.0 bits (65), Expect = 0.86
Identities = 47/195 (24%), Positives = 84/195 (43%), Gaps = 40/195 (20%)
Query: 5 LKPHQIVMVNWLL---SHDRCALWA-SMGSGKTVSVLFALSTIKIL----DPR----PVL 52
++ +Q+ +NWL+ + + A MG GKT L TI +L + R P +
Sbjct: 170 MRDYQLAGLNWLIRLYENGINGILADEMGLGKT------LQTISLLGYLHEYRGITGPHM 223
Query: 53 IIAPLRVAQYVWKDEVERWSAFSDMTVSSLIGS--ERQRIKALNTPAHLYIINFENIPWL 110
++AP + W +E+ R+ + G+ ER + A + + +
Sbjct: 224 VVAP-KSTLGNWMNEIRRFCPV--LRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMA 280
Query: 111 VK----MKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVA--FSKVKRFIELTGTP 164
+K +K W + I++DE+ ++K+ + L K FS R + +TGTP
Sbjct: 281 IKEKTALKRFSWRY--IIIDEAHRIKN--------ENSLLSKTMRLFSTNYRLL-ITGTP 329
Query: 165 SPNGLIDLWGQIWFL 179
N L +LW + FL
Sbjct: 330 LQNNLHELWALLNFL 344
>gnl|CDD|179290 PRK01388, PRK01388, arginine deiminase; Provisional.
Length = 406
Score = 28.6 bits (65), Expect = 1.2
Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 84 GSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWDFATI 123
G E +R+ TP++ + F+++PW+ + + +H FA
Sbjct: 24 GLELERL----TPSNCDELLFDDVPWVERAQKEHDAFAQT 59
>gnl|CDD|184388 PRK13909, PRK13909, putative recombination protein RecB;
Provisional.
Length = 910
Score = 28.4 bits (64), Expect = 1.3
Identities = 13/19 (68%), Positives = 13/19 (68%), Gaps = 4/19 (21%)
Query: 23 ALWASMGSGKTVSVLFALS 41
AL AS GSGKT FALS
Sbjct: 2 ALKASAGSGKT----FALS 16
>gnl|CDD|169949 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed.
Length = 402
Score = 28.7 bits (64), Expect = 1.4
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 72 SAFSDMTVSSLIGSERQRI 90
+ F+D V+SL G ERQR+
Sbjct: 130 AQFADRPVTSLSGGERQRV 148
>gnl|CDD|140243 PTZ00216, PTZ00216, acyl-CoA synthetase; Provisional.
Length = 700
Score = 28.4 bits (64), Expect = 1.5
Identities = 27/65 (41%), Positives = 31/65 (47%), Gaps = 13/65 (20%)
Query: 161 TGTPSPNGLIDLWGQIWFLDKG--KRLGLSFKSFVER-WFHTQQVGSS--------IGAV 209
T TP P G I L G FL KG K+ L+ + E WFHT VGS IG V
Sbjct: 501 TDTPEPRGEILLRGP--FLFKGYYKQEELTREVLDEDGWFHTGDVGSIAANGTLRIIGRV 558
Query: 210 KHIPK 214
K + K
Sbjct: 559 KALAK 563
>gnl|CDD|181290 PRK08206, PRK08206, diaminopropionate ammonia-lyase; Provisional.
Length = 399
Score = 27.5 bits (62), Expect = 3.1
Identities = 14/65 (21%), Positives = 21/65 (32%), Gaps = 9/65 (13%)
Query: 135 RTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDL--------WGQIWFLDKGKRLG 186
L + K + F + +P L+ L G I D+ R G
Sbjct: 13 NKPYDGADLPLLSQEEAKKARAFHQSFPGYAPTPLVALPDLAAELGVGSILVKDESYRFG 72
Query: 187 L-SFK 190
L +FK
Sbjct: 73 LNAFK 77
>gnl|CDD|161871 TIGR00420, trmU, tRNA
(5-methylaminomethyl-2-thiouridylate)-methyltransferase.
tRNA
(5-methylaminomethyl-2-thiouridylate)-methyltransferase
(trmU, asuE, or mnmA) is involved in the biosynthesis of
the modified nucleoside
5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in
the wobble position of some tRNAs. This enzyme appears
not to occur in the Archaea.
Length = 352
Score = 27.4 bits (61), Expect = 3.3
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 8/54 (14%)
Query: 152 SKVKRFIELTGTPSPNGLIDLWGQ--------IWFLDKGKRLGLSFKSFVERWF 197
K + F++ P +I + GQ +WF G+R GL E WF
Sbjct: 201 RKFRDFLKKYLPVKPGVIITVDGQSVIGEHDGLWFYTIGQRKGLGIGGAAEPWF 254
>gnl|CDD|132298 TIGR03254, oxalate_oxc, oxalyl-CoA decarboxylase. In a number of
bacteria, including Oxalobacter formigenes from the
human gut, a two-gene operon of oxc (oxalyl-CoA
decarboxylase) and frc (formyl-CoA transferase) encodes
a system for degrading and therefore detoxifying
oxalate. Members of this family are the thiamine
pyrophosphate (TPP)-containing enzyme oxalyl-CoA
decarboxylase.
Length = 554
Score = 27.1 bits (60), Expect = 3.9
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 5/29 (17%)
Query: 3 LVLKPHQIVMV-----NWLLSHDRCALWA 26
L +VM+ NWLLSH + LW
Sbjct: 261 FALAEADVVMLVGARLNWLLSHGKGKLWG 289
>gnl|CDD|166255 PLN02614, PLN02614, long-chain acyl-CoA synthetase.
Length = 666
Score = 26.9 bits (59), Expect = 4.3
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 165 SPNGLIDLWGQIWFLDKGKRLGLSFKSFVERWFHTQQVG 203
+P G I + G+ F KR L+ + ++ W HT VG
Sbjct: 466 TPRGEICIRGKTLFSGYYKREDLTKEVLIDGWLHTGDVG 504
>gnl|CDD|163585 TIGR03873, F420-0_ABC_ATP, proposed F420-0 ABC transporter,
ATP-binding protein. This small clade of ABC-type
transporter ATP-binding protein components is found as a
three gene cassette along with a periplasmic
substrate-binding protein (TIGR03868) and a permease
(TIGR03869). The organisms containing this cassette are
all Actinobacteria and all contain numerous genes
requiring the coenzyme F420. This model was defined
based on five such organisms, four of which are lacking
all F420 biosynthetic capability save the final
side-chain polyglutamate attachment step (via the gene
cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and
marine actinobacterium PHSC20C1 this cassette is in an
apparent operon with the cofE gene and, in PHSC20C1,
also with a F420-dependent glucose-6-phosphate
dehydrogenase (TIGR03554). Based on these observations
we propose that this ATP-binding protein is a component
of an F420-0 (that is, F420 lacking only the
polyglutamate tail) transporter.
Length = 256
Score = 26.7 bits (59), Expect = 4.5
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 72 SAFSDMTVSSLIGSERQRI---KALNTPAHLYIIN 103
S +D +S+L G ERQR+ +AL L +++
Sbjct: 128 SHLADRDMSTLSGGERQRVHVARALAQEPKLLLLD 162
>gnl|CDD|129256 TIGR00152, TIGR00152, dephospho-CoA kinase. This model produces
scores in the range of 0-25 bits against adenylate,
guanylate, uridine, and thymidylate kinases.
Length = 188
Score = 26.6 bits (59), Expect = 5.6
Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 4/86 (4%)
Query: 60 AQYVWKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWD 119
+ V+ D E +++ LI +++ A Y++ ++P L + KL
Sbjct: 69 GERVFNDPEEL-KWLNNLL-HPLIREWMKKLLAQFQSKLAYVL--LDVPLLFENKLRSLC 124
Query: 120 FATIVVDESTKLKSFRTHQGTKQTRA 145
IVVD S +L+ R Q T
Sbjct: 125 DRVIVVDVSPQLQLERLMQRDNLTEE 150
>gnl|CDD|150299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is
a conserved membrane protein. The yfhO gene is
transcribed in Difco sporulation medium and the
transcription is affected by the YvrGHb two-component
system. Some members of this family have been annotated
as glycosyl transferases of the PMT family.
Length = 835
Score = 26.4 bits (59), Expect = 6.4
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 59 VAQYVWKDEVERWSAFSDMTVSSLIG 84
+ + ++KD RW F +SSL+
Sbjct: 198 LYRLIFKDIKSRWKQFLRFIISSLLS 223
>gnl|CDD|161832 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
family. Members of this family are assumed to differ
from each other in DNA site specificity.
Length = 667
Score = 26.2 bits (58), Expect = 6.8
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 14/66 (21%)
Query: 3 LVLKPHQIVMVNWLL--------------SHDRCALWASMGSGKTVSVLFALSTIKILDP 48
LV KP+Q M + +W + GSGKT+++LFA L
Sbjct: 233 LVTKPYQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELLK 292
Query: 49 RPVLII 54
P +
Sbjct: 293 NPKVFF 298
>gnl|CDD|183924 PRK13258, PRK13258, 7-cyano-7-deazaguanine reductase; Provisional.
Length = 115
Score = 26.3 bits (59), Expect = 7.2
Identities = 14/32 (43%), Positives = 15/32 (46%), Gaps = 12/32 (37%)
Query: 119 DFATIVVD--------ESTKLK----SFRTHQ 138
DFATIV+D E LK SFR H
Sbjct: 36 DFATIVIDYIPDKKCVELKSLKLYLFSFRNHG 67
>gnl|CDD|149650 pfam08664, YcbB, YcbB domain. YcbB is a DNA-binding domain.
Length = 133
Score = 26.1 bits (58), Expect = 7.4
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 5/24 (20%)
Query: 88 QRI-----KALNTPAHLYIINFEN 106
QRI KALN A L + ++ N
Sbjct: 68 QRIRRAIKKALNNLASLGLEDYSN 91
>gnl|CDD|163398 TIGR03686, pupylate_PafA, proteasome accessory factor PafA.
Members of this family are PafA (proteasome accessory
factor A), a protein shown to regulate steady-state
levels of certain proteasome targets in Mycobacterium
tuberculosis. Iyer, et al (2008) suggest that PafA is
the ligase for Pup, a ubiquitin analog attached to an
epsilon-amino group of a Lys side-chain to direct the
target to the proteasome.
Length = 453
Score = 25.9 bits (57), Expect = 7.7
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 6/40 (15%)
Query: 141 KQTRALG--KVAFSKVKRFIELTGTPSPNGLI----DLWG 174
+ AL + + KVK F+E G +PN I DLWG
Sbjct: 269 RSASALEIQREYYEKVKAFLETRGDGTPNAEIPRVVDLWG 308
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
0.323 0.136 0.426
Gapped
Lambda K H
0.267 0.0636 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,612,891
Number of extensions: 220968
Number of successful extensions: 355
Number of sequences better than 10.0: 1
Number of HSP's gapped: 353
Number of HSP's successfully gapped: 23
Length of query: 220
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 130
Effective length of database: 4,049,753
Effective search space: 526467890
Effective search space used: 526467890
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: 55 (25.2 bits)