RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781047|ref|YP_003065460.1| AFG1-family ATPase [Candidatus
Liberibacter asiaticus str. psy62]
(404 letters)
>gnl|CDD|31674 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 333 bits (856), Expect = 4e-92
Identities = 138/371 (37%), Positives = 215/371 (57%), Gaps = 17/371 (4%)
Query: 6 VSSRLISLIQDKKLKYNPAQESVVKSFDRLLVDLYKQQKQEQGIFSWLWNLRGIKRKYCS 65
R L+ + +PAQ + + DRL D + + WL+ R +
Sbjct: 11 PVERYAQLVPAGTFQPDPAQPAAAAALDRLY-DELVAPRSARKALGWLF-----GRDHGP 64
Query: 66 MQGIYLHGDVGQGKSMLMNLFFALVPIEKKCRLHFYEFMKDVHSRIIMYRKKIEFGEILE 125
++G+YL G VG+GK+MLM+LF+ +P E+K RLHF+ FM VH R+ + +
Sbjct: 65 VRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFHRFMARVHQRLHTLQG--------Q 116
Query: 126 SDPIPLVASSIALESRVLCFDEFMITNIADAIILSRLFAALFSHGCIIVMTSNFIPENLY 185
+DP+P +A +A E+RVLCFDEF +T+IADA+IL RL ALF+ G ++V TSN P+NLY
Sbjct: 117 TDPLPPIADELAAETRVLCFDEFEVTDIADAMILGRLLEALFARGVVLVATSNTAPDNLY 176
Query: 186 KDEINRNVLVSFIELLEKKLEIISLDSGQDYRRKEQSILPIYMTPLNSYNRVLMDKLWAH 245
KD + R + I+L++ E++++D DYR ++ P+Y+TPL++ +DKLWA
Sbjct: 177 KDGLQRERFLPAIDLIKSHFEVVNVDGPVDYRLRKLEQAPVYLTPLDAEAEAALDKLWAA 236
Query: 246 ITKGKKSLSLNISTEGGYEIHVPFFCSRVSRFSFFDLCDRPLSANDFVEIANRFDVVIIN 305
++ G + N+ G EI VP + F F LC+ P SA+D++ +A RF V +
Sbjct: 237 LSDGAPEAAANL-EIKGREIRVPAVAGGLLWFDFAQLCEAPRSASDYLALAERFHTVFLT 295
Query: 306 DIPLLKEDRKDWIKRFIMLIDVFYEHKIGLIISSEENIEDLFPYKLRKGAFEIQRTVSRL 365
D+P + +D +RFI L+D Y+ + L+ S+E + +L+ + AFE QRT+SRL
Sbjct: 296 DVPQMDPLDRDEARRFIALVDELYDRGVKLVASAEVPLNELYQGG--RLAFEFQRTLSRL 353
Query: 366 YEMFSAQYIGK 376
EM S +Y+G
Sbjct: 354 QEMQSEEYLGI 364
>gnl|CDD|112768 pfam03969, AFG1_ATPase, AFG1-like ATPase. This family of proteins
contains a P-loop motif and are predicted to be ATPases.
Length = 361
Score = 287 bits (735), Expect = 5e-78
Identities = 131/372 (35%), Positives = 197/372 (52%), Gaps = 19/372 (5%)
Query: 8 SRLISLIQDKKLKYNPAQESVVKSFDRLLVDLYKQQKQEQ-GIFSWLWNLRGIKRKYCSM 66
R + +Q + + AQ + V + DRL L Q G LW G KR + +
Sbjct: 5 QRYTAQLQRGAIFPDVAQANAVPALDRLYQRLQAADFVRQSGAGGKLW---GRKRSHQPV 61
Query: 67 QGIYLHGDVGQGKSMLMNLFFALVPIEKKCRLHFYEFMKDVHSRIIMYRKKIEFGEILES 126
+G+YL G VG+GK+ LM+ FF +P E+K R HF+ FM VH + +
Sbjct: 62 RGLYLWGGVGRGKTHLMDSFFESLPGERKRRTHFHRFMFRVHDEL-TTLQG-------GD 113
Query: 127 DPIPLVASSIALESRVLCFDEFMITNIADAIILSRLFAALFSHGCIIVMTSNFIPENLYK 186
DP+P+ A A E+R+LCFDEF + +I DA+IL RLF ALF+ G +V TSN PE LY+
Sbjct: 114 DPLPIAADRFANEARLLCFDEFEVDDIGDAMILGRLFEALFARGVSLVATSNTAPEQLYR 173
Query: 187 DEINRNVLVSFIELLEKKLEIISLDSGQDYRRKEQSILPIYMTPLNSYNRVLMDKLWAHI 246
+ +NR + I+LLE E++ +D DYR + P+++ PL+ +D+LW +
Sbjct: 174 NGLNRQRFLPAIDLLESHFEVVRVDGPVDYRLRTLEQAPLWLYPLDGAAWAALDRLWDAL 233
Query: 247 TKGKKSLSLNISTE--GGYEIHVPFFCSRVSRFSFFDLCDRPLSANDFVEIANRFDVVII 304
T G+ +ST + FSF DLC P +D++ +A RF V +
Sbjct: 234 TLGEPQ---PLSTLEVAARLARARAAGGDLVWFSFADLCLAPRHPSDYLALAERFSTVFL 290
Query: 305 NDIPLLKEDRKDWIKRFIMLIDVFYEHKIGLIISSEENIEDLFPYKLRKGAFEIQRTVSR 364
D+P + +D +RFI L+D Y+ + L+ S+E ++DL+ AFE QRT+SR
Sbjct: 291 TDVPPMTRCSQDEARRFIALVDELYDRHVKLVASAEAALDDLYRGGR--LAFEFQRTLSR 348
Query: 365 LYEMFSAQYIGK 376
L EM S Y+ +
Sbjct: 349 LLEMQSEDYLAR 360
>gnl|CDD|37594 KOG2383, KOG2383, KOG2383, Predicted ATPase [General function
prediction only].
Length = 467
Score = 273 bits (700), Expect = 5e-74
Identities = 141/419 (33%), Positives = 215/419 (51%), Gaps = 56/419 (13%)
Query: 12 SLIQDKKLKYNPAQESVVKSFDRL---LVDLY----KQQKQEQGIFSWLWNLR------- 57
L+ LK +P Q V +F+RL L++ Y KQ ++ W++ L+
Sbjct: 42 KLVNTGTLKSDPYQRKTVSAFERLYHELIEYYDPRLKQWSAKREEGRWIFELKKSFDDGK 101
Query: 58 ----GIKRKYCSMQGIYLHGDVGQGKSMLMNLFF-ALVPIEKKCRLHFYEFMKDVHSRII 112
+ +G+YL+G VG GK+MLM+LF+ AL PI +K R+HF+ FM VH R+
Sbjct: 102 LDTPNASGQPGPPKGLYLYGSVGCGKTMLMDLFYDALPPIWRKQRVHFHGFMLSVHKRMH 161
Query: 113 MYRK-----KIEFGEILESDPIPLVASSIALESRVLCFDEFMITNIADAIILSRLFAALF 167
++ K + + E DP+P+VA IA E+ +LCFDEF +T++ADA+IL RLF LF
Sbjct: 162 ELKQEQGAEKPGYAKSWEIDPLPVVADEIAEEAILLCFDEFQVTDVADAMILKRLFEHLF 221
Query: 168 SHGCIIVMTSNFIPENLYKDEINRNVLVSFIELLEKKLEIISLDSGQDYRRKEQSILPIY 227
+G ++V TSN PE+LYK+ + R + FI LLE++ ++I LDSG DYRRK +S Y
Sbjct: 222 KNGVVLVATSNRAPEDLYKNGLQRENFIPFIALLEERCKVIQLDSGVDYRRKAKSAGENY 281
Query: 228 MTPLNSYNRVLMDKLW-AHITKGKKSLSLNISTEGGYEIHVPFFCSRVSRFSFFDLCDRP 286
+ ++ + + G ++ VP C V+ F+F +LC RP
Sbjct: 282 YFISETDVETVLKEWFKLLAADQNDGTRQRTLVVFGRKLIVPKACGGVADFTFEELCGRP 341
Query: 287 LSANDFVEIANRFDVVIINDIPLLKEDRKDWIKRFIMLIDVFYEHKIGLIISSEENIEDL 346
L A D++ +A F +I+ DIP L + +D +RFI LID Y++ + L+ S+ +E+L
Sbjct: 342 LGAADYLGLAKNFHTIIVRDIPQLSLENRDQARRFITLIDALYDNHVRLVCSAATPLEEL 401
Query: 347 FPYK------------LRKG-------------------AFEIQRTVSRLYEMFSAQYI 374
F + L F RT+SRLYEM + Y
Sbjct: 402 FQFTGHSEALSDSPRTLMDDLGIKSDSAGGSPMFSGEEEGFAFDRTLSRLYEMQTELYW 460
>gnl|CDD|37256 KOG2045, KOG2045, KOG2045, 5'-3' exonuclease XRN1/KEM1/SEP1
involved in DNA strand exchange and mRNA turnover
[Replication, recombination and repair, Cell cycle
control, cell division, chromosome partitioning].
Length = 1493
Score = 29.3 bits (65), Expect = 1.7
Identities = 14/83 (16%), Positives = 25/83 (30%), Gaps = 5/83 (6%)
Query: 269 FFCSRVSRFSFFDLCDRPLSANDFVEIANRFDVVIINDIPLLKEDRKDWIK-----RFIM 323
S D D ++F + +ND ++ W K F
Sbjct: 424 LEPGSGSDELLLDNLDADELEDEFAVELATLALSGMNDADFANDEEACWEKTILNKEFQR 483
Query: 324 LIDVFYEHKIGLIISSEENIEDL 346
+Y K+ + EE + +L
Sbjct: 484 WKRNYYRDKLKFDPNDEELLREL 506
>gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter
nucleotide-binding domain; ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins..
Length = 157
Score = 29.1 bits (65), Expect = 2.4
Identities = 23/115 (20%), Positives = 41/115 (35%), Gaps = 9/115 (7%)
Query: 73 GDVGQGKSMLMNLFFALV-PIEKKCRLHFYEFMKDVHS---RIIMYRKKIEFGEILESDP 128
G G GKS L+ L+ P + + + K R I Y ++ G+
Sbjct: 32 GPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRV-- 89
Query: 129 IPLVASSIALESRVLCFDEFMI-TNIADAIILSRLFAALFSHGCIIVMTSNFIPE 182
+A ++ L +L DE + A L L L G +++ ++
Sbjct: 90 --ALARALLLNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPEL 142
>gnl|CDD|30938 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 28.7 bits (64), Expect = 3.1
Identities = 27/122 (22%), Positives = 45/122 (36%), Gaps = 21/122 (17%)
Query: 69 IYLHGDVGQGKSMLM----NLFFALVPIEKKCRLHFYEFMKDVHSRIIMYRKKIEFGEIL 124
++++G VG GK+ L+ N A P + L +F D + + +F E
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVK-ALRDNEMEKFKEKY 174
Query: 125 ESDPIPLVASSIALESRVLCFDEFMITNIADAI--ILSRLFAALFSHGCIIVMTSNFIPE 182
D +L D+ + F AL +G IV+TS+ P+
Sbjct: 175 SLD--------------LLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPK 220
Query: 183 NL 184
L
Sbjct: 221 EL 222
>gnl|CDD|144489 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 28.0 bits (63), Expect = 4.5
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 69 IYLHGDVGQGKSMLMNLF 86
I+L+G G GKS L
Sbjct: 1 IWLYGPPGCGKSTLAKYL 18
>gnl|CDD|132906 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polymerase. The
eukaryotic RPB3 subunit of RNA polymerase (RNAP), as
well as its archaeal (D subunit) and bacterial (alpha
subunit) counterparts, is involved in the assembly of
RNAP subunits. RNAP is a large multi-subunit complex
responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III, for the synthesis of
ribosomal RNA precursor, mRNA precursor, and 5S and
tRNA, respectively. A single distinct RNAP complex is
found in prokaryotes and archaea, which may be
responsible for the synthesis of all RNAs. The RPB3
subunit is similar to the bacterial RNAP alpha subunit
in that it contains two subdomains: one subdomain is
similar to the eukaryotic Rpb11/AC19/archaeal L subunit
which is involved in dimerization; and the other is an
inserted beta sheet subdomain. The assembly of the two
largest eukaryotic RNAP subunits that provide most of
the enzyme's catalytic functions depends on the presence
of RPB3/RPB11 heterodimer subunits. This is also true
for the archaeal (D/L subunits) and bacterial (alpha
subunit) counterparts.
Length = 212
Score = 27.9 bits (62), Expect = 4.8
Identities = 14/54 (25%), Positives = 25/54 (46%)
Query: 294 EIANRFDVVIINDIPLLKEDRKDWIKRFIMLIDVFYEHKIGLIISSEENIEDLF 347
+AN V+I ++P + D + +L D H++GLI +I L+
Sbjct: 23 AMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAHRLGLIPLQSMDILQLY 76
>gnl|CDD|144176 pfam00483, NTP_transferase, Nucleotidyl transferase. This family
includes a wide range of enzymes which transfer
nucleotides onto phosphosugars.
Length = 247
Score = 27.6 bits (62), Expect = 7.5
Identities = 8/53 (15%), Positives = 19/53 (35%), Gaps = 6/53 (11%)
Query: 152 NIADAIILSRLFAALFSHGCIIVMTSNFIPENLYKD------EINRNVLVSFI 198
A A+ L+ F ++V+ + I +++ + V+F
Sbjct: 85 GTAPAVALAADFLGDDDPELVLVLGGDHIYRMDFEEAVQKARAKAADGTVTFG 137
>gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 27.4 bits (61), Expect = 7.8
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 282 LCDRPLSANDFVEIANRFDVVIIND 306
+ R +A + A+ FD VI+ND
Sbjct: 143 IARRLENAKKEISHADEFDYVIVND 167
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.326 0.142 0.414
Gapped
Lambda K H
0.267 0.0579 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,999,221
Number of extensions: 279595
Number of successful extensions: 978
Number of sequences better than 10.0: 1
Number of HSP's gapped: 968
Number of HSP's successfully gapped: 20
Length of query: 404
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 308
Effective length of database: 4,189,273
Effective search space: 1290296084
Effective search space used: 1290296084
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 (21.6 bits)
S2: 58 (26.5 bits)