RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780546|ref|YP_003064959.1| hypothetical protein
CLIBASIA_02165 [Candidatus Liberibacter asiaticus str. psy62]
(423 letters)
>gnl|CDD|162854 TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase,
N-terminal domain. The only examples in which the
wobble position of a tRNA must discriminate between G
and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop)
vs. UGG (Trp). In all bacteria, the wobble position of
the tRNA(Ile) recognizing AUA is lysidine, a lysine
derivative of cytidine. This family describes a protein
domain found, apparently, in all bacteria in a single
copy. Eukaryotic sequences appear to be organellar. The
domain archictecture of this protein family is variable;
some, including characterized proteins of E. coli and B.
subtilis known to be tRNA(Ile)-lysidine synthetase,
include a conserved 50-residue domain that many other
members lack. This protein belongs to the ATP-binding
PP-loop family ( pfam01171). It appears in the
literature and protein databases as TilS, YacA, and
putative cell cycle protein MesJ (a misnomer).
Length = 189
Score = 175 bits (446), Expect = 2e-44
Identities = 71/192 (36%), Positives = 94/192 (48%), Gaps = 9/192 (4%)
Query: 21 HILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYVSDVCSRL 80
ILVAVSGG DSM LL H +L + KI+ A VDH LR + +E +V C +L
Sbjct: 1 RILVAVSGGVDSMALL---HLLLKLQPKLKIRLIAAHVDHGLRPESDEEAEFVQQFCKKL 57
Query: 81 RIAHSVVSWKNSKPQ----TGLMAAAREARYALISEHAKTINATLIMTAHTFDDQLETVY 136
I + L AAREARY E AK A I+TAH DDQ ET+
Sbjct: 58 NIPLEIKKVDVKALAKGKKKNLEEAAREARYDFFEEIAKKHGADYILTAHHADDQAETIL 117
Query: 137 MRSQRDYAEKGMGLSGMCDTILYDLNLWISRPFLRCRREDIRSFLLQRNISWCEDPSNTD 196
+R R +G LSGM + I RP L + +I +L + + W ED +N D
Sbjct: 118 LRLLRGSGLRG--LSGMKPIRILGNGGQIIRPLLGISKSEIEEYLKENGLPWFEDETNQD 175
Query: 197 DRFERVRVRRFV 208
D++ R R+R +
Sbjct: 176 DKYLRNRIRHEL 187
>gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional.
Length = 436
Score = 83.1 bits (206), Expect = 1e-16
Identities = 60/189 (31%), Positives = 85/189 (44%), Gaps = 9/189 (4%)
Query: 21 HILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYVSDVCSRL 80
ILVA SGG DS LL L ++ + AI V H L A V++ VC +
Sbjct: 17 QILVAFSGGLDSTVLLHLLVQWRTENP--GVTLRAIHVHHGLSPNADSWVKHCEQVCQQW 74
Query: 81 RIAHSVVSWKNSKPQTGLMAAAREARYALISEHAKTINATLIMTAHTFDDQLETVYMRSQ 140
++ V + + G+ AAAR+ARY + L+ TA DDQ ET + +
Sbjct: 75 QVPLVVERVQLDQRGLGIEAAARQARYQAFARTLLP-GEVLV-TAQHLDDQCETFLLALK 132
Query: 141 RDYAEKGMGLSGMCD-TILYDLNLWISRPFLRCRREDIRSFLLQRNISWCEDPSNTDDRF 199
R GLS M + + L RP L RE++ + + W ED SN DDR+
Sbjct: 133 R--GSGPAGLSAMAEVSPFAGTRLI--RPLLARSREELEQYAQAHGLRWIEDDSNQDDRY 188
Query: 200 ERVRVRRFV 208
+R +R V
Sbjct: 189 DRNFLRLRV 197
>gnl|CDD|162088 TIGR00884, guaA_Cterm, GMP synthase (glutamine-hydrolyzing),
C-terminal domain or B subunit. This protein of purine
de novo biosynthesis is well-conserved. However, it
appears to split into two separate polypeptide chains
in most of the Archaea. This C-terminal region would be
the larger subunit.
Length = 311
Score = 36.2 bits (84), Expect = 0.018
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 7/60 (11%)
Query: 13 VRSLVYPAHILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDH-CLRETAKDEVR 71
+R V A +++A+SGG DS ++ +VL+ R+ G + + + VDH LR+ ++V
Sbjct: 10 IREQVGDAKVIIALSGGVDS-----SVAAVLAHRAIGD-RLTCVFVDHGLLRKGEAEQVV 63
>gnl|CDD|182655 PRK10696, PRK10696, tRNA 2-thiocytidine biosynthesis protein TtcA;
Provisional.
Length = 258
Score = 35.2 bits (82), Expect = 0.028
Identities = 34/148 (22%), Positives = 52/148 (35%), Gaps = 61/148 (41%)
Query: 22 ILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISV----------DHCLRE------- 64
++V +SGG DS LL L ++ + I F ++V +H L E
Sbjct: 32 VMVCLSGGKDSYTLLDILLNL---QKRAPINFELVAVNLDQKQPGFPEHVLPEYLESLGV 88
Query: 65 -----------TAKDEVR----YVSDVCSRLRIAHSVVSWKNSKPQTGLMAAAREARYAL 109
K+++ S +CSRLR R Y
Sbjct: 89 PYHIEEQDTYSIVKEKIPEGKTTCS-LCSRLR---------------------RGILYRT 126
Query: 110 ISEHAKTINATLIMTAHTFDDQLETVYM 137
A+ + AT I H DD LET+++
Sbjct: 127 ----ARELGATKIALGHHRDDILETLFL 150
>gnl|CDD|177981 PLN02347, PLN02347, GMP synthetase.
Length = 536
Score = 30.8 bits (70), Expect = 0.61
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 13 VRSLVYP-AHILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDH-CLR 63
+++ V P H++ A+SGG DS +H + DR + VD+ LR
Sbjct: 222 IKATVGPDEHVICALSGGVDSTVAATLVHKAIGDR------LHCVFVDNGLLR 268
>gnl|CDD|184485 PRK14068, PRK14068, exodeoxyribonuclease VII small subunit;
Provisional.
Length = 76
Score = 29.1 bits (65), Expect = 2.2
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 133 ETVYMRSQRDYAEKGMGLSGMCDTILYD 160
ETV + D ++GM LS CDT L +
Sbjct: 25 ETVSLEESLDLYQRGMKLSAACDTTLKN 52
>gnl|CDD|168382 PRK06077, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 252
Score = 28.5 bits (64), Expect = 3.5
Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 24/93 (25%)
Query: 220 MKKFQDLRVKVNNA---VAM--------LIPKYLTVHMRSIIAISQD----------ILN 258
+ ++ + VNNA + LI K+++ +S+I SQ+ I+N
Sbjct: 79 IDRYGVADILVNNAGLGLFSPFLNVDDKLIDKHISTDFKSVIYCSQELAKEMREGGAIVN 138
Query: 259 IDST---LLFYLLRVSAAICGGQISLPGYRSME 288
I S Y L + A+ I+L Y ++E
Sbjct: 139 IASVAGIRPAYGLSIYGAMKAAVINLTKYLALE 171
>gnl|CDD|162310 TIGR01348, PDHac_trf_long, pyruvate dehydrogenase complex
dihydrolipoamide acetyltransferase, long form. This
model describes a subset of pyruvate dehydrogenase
complex dihydrolipoamide acetyltransferase specifically
close by both phylogenetic and per cent identity (UPGMA)
trees. Members of this set include two or three copies
of the lipoyl-binding domain. E. coli AceF is a member
of this model, while mitochondrial and some other
bacterial forms belong to a separate model.
Length = 546
Score = 27.9 bits (62), Expect = 5.1
Identities = 12/54 (22%), Positives = 28/54 (51%)
Query: 206 RFVRDIDLHALYLKMKKFQDLRVKVNNAVAMLIPKYLTVHMRSIIAISQDILNI 259
+F +DL L +KK+ ++ V V+ +L+P V + I ++ ++ ++
Sbjct: 392 KFNASLDLGGEQLILKKYVNIGVAVDTPNGLLVPVIKDVDRKGITELALELSDL 445
>gnl|CDD|177387 PHA02553, 6, baseplate wedge subunit; Provisional.
Length = 611
Score = 27.7 bits (62), Expect = 5.7
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 118 NATLIMTAHTFDD--QLETVYMRSQ---RDYAEKGMGLSGMCDTILYD 160
I T+ FD+ Y+R+Q +DY +G L+ + D + Y+
Sbjct: 2 MIPDIFTSLDFDEIKSSLIEYLRTQDEFKDYDFEGSRLNVLIDLLAYN 49
>gnl|CDD|181212 PRK08056, PRK08056, threonine-phosphate decarboxylase; Provisional.
Length = 356
Score = 27.7 bits (62), Expect = 6.1
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 169 FLRCRREDI--RSFLLQRN--ISWCEDPSNTDDRFERVRVR 205
FLRC R DI + LL + I C + D R+ RV +R
Sbjct: 297 FLRCERPDIDLQRALLTQRILIRSCANYPGLDSRYYRVAIR 337
>gnl|CDD|132327 TIGR03284, thym_sym, thymidylate synthase. Members of this protein
family are thymidylate synthase, an enzyme that produces
dTMP from dUMP. In prokaryotes, its gene usually is
found close to that for dihydrofolate reductase, and in
some systems the two enzymes are found as a fusion
protein. This model excludes a set of related proteins
(TIGR03283) that appears to replace this family in
archaeal methanogens, where tetrahydrofolate is replaced
by tetrahydromethanopterin.
Length = 296
Score = 27.4 bits (61), Expect = 6.3
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 318 ITRAVRNLPTLILYPEETTVWDGRYQ 343
+TR R LP L L PE+ ++D Y+
Sbjct: 252 LTREPRPLPKLKLNPEKKDIFDFEYE 277
>gnl|CDD|179167 PRK00919, PRK00919, GMP synthase subunit B; Validated.
Length = 307
Score = 27.6 bits (62), Expect = 7.0
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 6 IESVRFFVRSLVYPAHILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCL-RE 64
IE +R + ++A+SGG DS ++ +VL+ R+ G + + + VD L R+
Sbjct: 8 IEEAIEEIREEIGDGKAIIALSGGVDS-----SVAAVLAHRAIGD-RLTPVFVDTGLMRK 61
Query: 65 TAKDEVRYVSDVCSRLRI 82
+ ++ LRI
Sbjct: 62 GETERIKETFSDMLNLRI 79
>gnl|CDD|181483 PRK08576, PRK08576, hypothetical protein; Provisional.
Length = 438
Score = 27.4 bits (61), Expect = 7.6
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 22 ILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYVSDVCSRLR 81
++V SGG DS L+ L+ ++FG + A+ VD DE YV V +L
Sbjct: 237 VIVPWSGGKDSTAALL-----LAKKAFGDVT--AVYVDTGYEMPLTDE--YVEKVAEKLG 287
Query: 82 I 82
+
Sbjct: 288 V 288
>gnl|CDD|162115 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 27.3 bits (61), Expect = 7.6
Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 3/63 (4%)
Query: 321 AVRNLPTLILYPEETTVWDGRYQFQNLSDSLIQI---GPQSYRKADVPSGIPPIIAQRAL 377
+ T I P + + L++ ++ P+ RK + G ++A+ L
Sbjct: 684 ILEQCATKIFLPNPEADREDYAEGFKLTEREFELLKSTPEESRKFLIKQGQSSVVAELNL 743
Query: 378 SSM 380
M
Sbjct: 744 GGM 746
>gnl|CDD|184331 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 27.3 bits (61), Expect = 8.6
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 13/61 (21%)
Query: 24 VAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCL--RETAKDEVRYVSDVCSRLR 81
V+ SGG DS L+ L L+ + F A + L ET V V +V
Sbjct: 248 VSFSGGKDS---LVVLD--LAREALK--DFKAFFNNTGLEFPET----VENVKEVAEEYG 296
Query: 82 I 82
I
Sbjct: 297 I 297
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
0.326 0.139 0.415
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,029,102
Number of extensions: 460238
Number of successful extensions: 1054
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1047
Number of HSP's successfully gapped: 18
Length of query: 423
Length of database: 5,994,473
Length adjustment: 96
Effective length of query: 327
Effective length of database: 3,920,105
Effective search space: 1281874335
Effective search space used: 1281874335
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: 58 (26.3 bits)