RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780957|ref|YP_003065370.1| dihydrofolate reductase
protein [Candidatus Liberibacter asiaticus str. psy62]
(176 letters)
>gnl|CDD|182714 PRK10769, folA, dihydrofolate reductase; Provisional.
Length = 159
Score = 126 bits (317), Expect = 4e-30
Identities = 55/138 (39%), Positives = 78/138 (56%), Gaps = 6/138 (4%)
Query: 6 IILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIGRLLPGRTNII 65
I LIAA+ + VIG MPW + +DL FK T PV+MG T++SIGR LPGR NI+
Sbjct: 2 ISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIV 61
Query: 66 ITRDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTISLAHTLYITHI 125
I + + + S+ ++L A +I +IGGG +Y Q + A LY+THI
Sbjct: 62 I----SSQPGTDDRVTWVKSVDEALAAAGD--VPEIMVIGGGRVYEQFLPKAQRLYLTHI 115
Query: 126 EKEIEGDVFFPSIDSNIW 143
+ E+EGD FP + + W
Sbjct: 116 DAEVEGDTHFPDYEPDEW 133
>gnl|CDD|185491 PTZ00164, PTZ00164, bifunctional dihydrofolate
reductase-thymidylate synthase; Provisional.
Length = 514
Score = 109 bits (275), Expect = 3e-25
Identities = 57/191 (29%), Positives = 91/191 (47%), Gaps = 29/191 (15%)
Query: 1 MTRPEIILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTT-------------GNPVVMG 47
+ + ++ A+T IG +PW I D+K F +TT N V+MG
Sbjct: 5 SSLKDFSIVVAVTLKRGIGIGNSLPWHIPEDMKFFSKITTYVREEKYEKSPKKQNAVIMG 64
Query: 48 YRTFQSIG---RLLPGRTNIIITRDNTRRASVNPEAVLASSILDSL-DLASKTGSKKIFI 103
+T++SI R L R N++++R +P ++ S+ D+L LA +KIFI
Sbjct: 65 RKTWESIPKKFRPLKNRINVVLSR-TLTEEEADPGVLVFGSLEDALRLLAEDLSIEKIFI 123
Query: 104 IGGGEIYAQTIS--LAHTLYITHIEKEIEGDVFFPSIDSN---IWKKQEKEIITSAGEGD 158
IGG +Y + +S L +Y+T + E E DVFFP I + + + T + G
Sbjct: 124 IGGASVYREALSANLLDKIYLTRVNSEYECDVFFPKIPESFFIVAIVSQ----TFSTNGT 179
Query: 159 DYPTRFVIYDR 169
Y FVIY++
Sbjct: 180 SY--DFVIYEK 188
>gnl|CDD|100572 PRK00478, scpA, segregation and condensation protein A/unknown
domain fusion protein; Provisional.
Length = 505
Score = 63.4 bits (154), Expect = 3e-11
Identities = 41/130 (31%), Positives = 65/130 (50%), Gaps = 3/130 (2%)
Query: 6 IILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIGRLLPGRTNII 65
I LI N I +PWKI +L F TT + +VMGY TFQ++ ++L + NI+
Sbjct: 2 IKLIWCEDLNFGIAKNNQIPWKIDEELNHFHQTTTNHTIVMGYNTFQAMNKILANQANIV 61
Query: 66 ITRDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTISLAHTLYITHI 125
I++ + R N E + + + L S + +FIIGG + Q I A L I+ +
Sbjct: 62 ISKKHQRELKNNNELFVFNDLKKLLIDFS---NVDLFIIGGKKTIEQFIKYADQLIISKL 118
Query: 126 EKEIEGDVFF 135
+ + D+F
Sbjct: 119 NADYKCDLFV 128
>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 = 29.7 bits (67), Expect = 0.38
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 38 LTTGNPVVMGYRTFQSIGRLLPGRTNIIITRDNTRRASVNPEAVLASSILDSLDLASKT 96
LT G+P+V+ R I L ++ I R +TR +P V +++ +L + KT
Sbjct: 142 LTGGDPLVLSPRRLGDIMARLAAIDHVKIVRFHTRVPVADPARVTP-ALIAALKTSGKT 199
>gnl|CDD|179700 PRK03995, PRK03995, hypothetical protein; Provisional.
Length = 267
Score = 28.8 bits (65), Expect = 0.77
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 76 VNPEAV--LASSILDSLDLASKTGSKKIFIIGGGEIYA--QT-ISLAHTLYITHI 125
N A LA ++++ LD K IGGG YA T ++L HI
Sbjct: 157 KNERAGEILAEAVIEVLDSIEYEKFKPAIGIGGGH-YAPKFTKLALESEYCFGHI 210
>gnl|CDD|132448 TIGR03407, urea_ABC_UrtA, urea ABC transporter, urea binding
protein. Members of this protein family are ABC
transporter substrate-binding proteins associated with
urea transport and metabolism. This protein is found in
a conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity. Members of this protein family tend
to have the twin-arginine signal for Sec-independent
transport across the plasma membrane.
Length = 359
Score = 27.7 bits (62), Expect = 1.7
Identities = 18/81 (22%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 86 ILDSLD-LASKTGSKKIFIIGGGEIYAQTISLAHTLYITHIEKEIEGDVFFP-------S 137
I+ ++D L SK G+K+ F++G ++ +T + Y+ + + G+ + P +
Sbjct: 121 IIPAVDYLLSKKGAKRFFLLGSDYVFPRTANKIIKAYLKSLGGTVVGEDYTPLGHTDFQT 180
Query: 138 IDSNIWKKQEKEIITSAGEGD 158
I + I K + +++ + GD
Sbjct: 181 IINKI-KAFKPDVVFNTLNGD 200
>gnl|CDD|178012 PLN02387, PLN02387, long-chain-fatty-acid-CoA ligase family
protein.
Length = 696
Score = 27.4 bits (61), Expect = 1.8
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 21 CGGMPWKISSDLKRFKSLTTGNPVVMGY 48
GG P +S D +RF ++ G P+ GY
Sbjct: 427 SGGAP--LSGDTQRFINICLGAPIGQGY 452
>gnl|CDD|179315 PRK01642, cls, cardiolipin synthetase; Reviewed.
Length = 483
Score = 27.4 bits (62), Expect = 2.1
Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 1/45 (2%)
Query: 52 QSIGRLLPGRTNIIITRDNTRRASVNPEAVLASSILDSLDLASKT 96
+ RL I + N R N + +I+ ++LA
Sbjct: 98 APLFRLCERLQGIPGLKGNQLRLLTNGDETFQ-AIIRDIELARHY 141
>gnl|CDD|131341 TIGR02288, PaaN_2, phenylacetic acid degradation protein paaN.
This family includes sequences from Burkholderia,
Bordetella, Streptomyces. Other PaaN enzymes are
represented by a separate model, TIGR02278.
Length = 551
Score = 27.2 bits (60), Expect = 2.4
Identities = 22/67 (32%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 17 VIGSCGGMP-WKISSDLKRFKSLTTGNPVVMGYRTFQSIGRLLPGRTNIIITRDNTRRAS 75
VIG C P W L F SL TGNPV++ G +LP + + R+ A
Sbjct: 199 VIG-CSTFPTWNTYPGL--FASLATGNPVLVKPHP----GAILPLALTVQVAREVLGEAG 251
Query: 76 VNPEAVL 82
+P V
Sbjct: 252 FDPNLVT 258
>gnl|CDD|180667 PRK06718, PRK06718, precorrin-2 dehydrogenase; Reviewed.
Length = 202
Score = 26.9 bits (60), Expect = 3.1
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 12/56 (21%)
Query: 99 KKIFIIGGGEIYAQTISLAHTL--YITHIEKEIEGDVFFPSIDSNIWKK-QEKEII 151
K++ I+GGG++ + TL Y HI V P + N+ K +E +I
Sbjct: 11 KRVVIVGGGKVAGRRAI---TLLKYGAHIV------VISPELTENLVKLVEEGKIR 57
>gnl|CDD|178003 PLN02375, PLN02375, molybderin biosynthesis protein CNX3.
Length = 270
Score = 26.6 bits (58), Expect = 3.6
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 65 IITRDNTRRASVNPEAVLASSILDSLDLASKTGS------KKIFIIGGGEIYAQTISLAH 118
+ ++DN++R ++ V+ + L LA++ G KI I G + + I L H
Sbjct: 130 VSSKDNSKRTALACCKVILGKRVFDLVLANQMGKGDVLGVAKIAGINGAKQTSSLIPLCH 189
Query: 119 TLYITHIEKEI 129
+ +TH+ ++
Sbjct: 190 NIALTHVRVDL 200
>gnl|CDD|161881 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff.
Length = 397
Score = 26.3 bits (59), Expect = 4.3
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 3/49 (6%)
Query: 68 RDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTISL 116
R R V+ + L A K G++ I+G E+ T++L
Sbjct: 346 RKAGIRVEVDLGG---RKLKKQLKYADKLGARFAVILGEDELANGTVTL 391
>gnl|CDD|184767 PRK14611, PRK14611, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 275
Score = 25.9 bits (57), Expect = 5.4
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 91 DLASKTGSKKIFIIGGGEIYAQTISLAHTLYITHIEKEIEGDVFFPSIDSN---IWKKQE 147
+LAS + F + GG + I I +EI + +P+I S+ ++ K
Sbjct: 124 ELASSISADAPFFLKGGFALGRGIGDKLEFLEKPISREIT--LVYPNIKSSTGRVYSKVT 181
Query: 148 KEIITSAGE 156
K+I+T+ +
Sbjct: 182 KQILTNKED 190
>gnl|CDD|153005 pfam12571, DUF3751, Tail fiber protein. This domain family is
found in bacteria and viruses, and is approximately 160
amino acids in length. There are two completely
conserved residues (K and W) that may be functionally
important.
Length = 159
Score = 25.8 bits (57), Expect = 5.8
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 58 LPGRTNIIITRDNTRRASVNPEAVLASSILDS 89
LP I+ + T+ VN AV+ S +LD+
Sbjct: 10 LPAEAQIVHRQAVTQYGYVNENAVVYSVVLDT 41
>gnl|CDD|149852 pfam08915, tRNA-Thr_ED, Archaea-specific editing domain of
threonyl-tRNA synthetase. Archaea-specific editing
domain of threonyl-tRNA synthetase, with marked
structural similarity to D-amino acids deacylases found
in eubacteria and eukaryotes. This domain can bind
D-amino acids, and ensures high fidelity during
translation. It is especially responsible for removing
incorrectly attached serine from tRNA-Thr. The domain
forms a fold that can be be defined as two layers of
beta-sheets (a three-stranded sheet and a five-stranded
sheet), with two alpha-helices located adjacent to the
five-stranded sheet.
Length = 137
Score = 25.6 bits (57), Expect = 6.6
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 77 NPEAVLASSILDSLDLASKTGSKKIFI 103
NPE V+ + + L +ASK + ++ +
Sbjct: 50 NPEEVIEKAAEEILKVASKVKATRVVL 76
>gnl|CDD|161756 TIGR00194, uvrC, excinuclease ABC, C subunit. This family consists
of the DNA repair enzyme UvrC, an ABC excinuclease
subunit which interacts with the UvrA/UvrB complex to
excise UV-damaged nucleotide segments.
Length = 574
Score = 25.4 bits (56), Expect = 7.2
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 11/74 (14%)
Query: 1 MTRPEIILIAAITRNNVIGSC----GGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIGR 56
+ R EI I+ I + +GS G P K S S+T G+ + ++
Sbjct: 381 IKRIEIFDISHIDGSQTVGSMVVFEDGKPLKASYRRYNINSITGGD-------DYAAMRE 433
Query: 57 LLPGRTNIIITRDN 70
+L R + I ++N
Sbjct: 434 VLRRRYSSIQKKNN 447
>gnl|CDD|181618 PRK09038, PRK09038, flagellar motor protein MotD; Reviewed.
Length = 281
Score = 25.4 bits (56), Expect = 8.1
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 7/44 (15%)
Query: 44 VVMGYRTFQSI-------GRLLPGRTNIIITRDNTRRASVNPEA 80
+GY FQ + GR R ++I R+ R S+ P
Sbjct: 211 AAVGYGEFQPVADNDTAEGRARNRRVVLVILRNLDVRRSLTPVG 254
>gnl|CDD|178418 PLN02823, PLN02823, spermine synthase.
Length = 336
Score = 25.0 bits (55), Expect = 9.8
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 92 LASKTGSKKIFIIGGGE 108
L K +FI+GGGE
Sbjct: 98 LLHHPNPKTVFIMGGGE 114
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
0.319 0.137 0.396
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: 2,904,236
Number of extensions: 175726
Number of successful extensions: 335
Number of sequences better than 10.0: 1
Number of HSP's gapped: 330
Number of HSP's successfully gapped: 25
Length of query: 176
Length of database: 5,994,473
Length adjustment: 87
Effective length of query: 89
Effective length of database: 4,114,577
Effective search space: 366197353
Effective search space used: 366197353
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 (21.7 bits)
S2: 54 (24.7 bits)