RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781149|ref|YP_003065562.1| replicative DNA helicase
[Candidatus Liberibacter asiaticus str. psy62]
(266 letters)
>gnl|CDD|161985 TIGR00665, DnaB, replicative DNA helicase. This model describes
the helicase DnaB, a homohexameric protein required for
DNA replication. The homohexamer can form a ring around
a single strand of DNA near a replication fork. An
intein of > 400 residues is found at a conserved
location in DnaB of Synechocystis PCC6803, Rhodothermus
marinus (both experimentally confirmed), and
Mycobacterium tuberculosis. The intein removes itself by
a self-splicing reaction. The seed alignment contains
inteins so that the model built from the seed alignment
will model a low cost at common intein insertion sites.
Length = 434
Score = 119 bits (300), Expect = 9e-28
Identities = 71/253 (28%), Positives = 108/253 (42%), Gaps = 36/253 (14%)
Query: 5 IISHFESQTKISFSTYLNNLLTLASSISSEVINA---ARRVVQQWAR---ITISQEAKAL 58
+ E K+ L L LA ++ S N A V ++ I E L
Sbjct: 62 VKEELEKDGKLEEVGGLAYLAELADNVPS-AANIEYYAEIVKEKAILRRLIEAGTEIVEL 120
Query: 59 ALHTSDPTCNTATLIRKSMQSFEDIISEVH-----LTKNQCTGSSCISIANAATTAMKSA 113
A E+++ E + +++ T SI ++
Sbjct: 121 AYDPEG--------------DVEELLDEAEQKIFEIAESR-TSGGFKSIKEILKDTVEEI 165
Query: 114 EQ-QKKEGENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGH 171
E+ ++ G + G +D L G+Q +LI++ ARPSMGKT FAL+ A + A+ G
Sbjct: 166 EELYERGGGITGVPTGFTDLDKLTSGLQPSDLIILAARPSMGKTAFALNIAENAAIKEGK 225
Query: 172 GVAFFSLEMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFP 230
VAFFSLEM E+L R LS S SR+ L G+++ E + +++ KL + P
Sbjct: 226 PVAFFSLEMSAEQLAMRMLS-----SESRVDSQKLRTGKLSDEDWEKLTSAA-GKLSEAP 279
Query: 231 LIIDDRPSPGIME 243
L IDD P I E
Sbjct: 280 LYIDDTPGLTITE 292
>gnl|CDD|132639 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family,
HK022 subfamily. Members of this family are phage (or
prophage-region) homologs of the bacterial homohexameric
replicative helicase DnaB. Some phage may rely on host
DnaB, while others encode their own verions. This model
describes the largest phage-specific clade among the
close homologs of DnaB, but there are, or course, other
DnaB homologs from phage that fall outside the scope of
this model.
Length = 421
Score = 95.5 bits (238), Expect = 1e-20
Identities = 54/178 (30%), Positives = 80/178 (44%), Gaps = 13/178 (7%)
Query: 69 TATLIRKSMQSFEDIISEVHLTKNQCTGSS------CISIANAATTAMKSAEQQ-KKEGE 121
Q+ E + E TG S ++ ++ +++ +GE
Sbjct: 114 IDLACSDGGQTAEQKVEEAQAALLALTGMSDGQERGFVTFGEVLEDVVRDLDKRFNPKGE 173
Query: 122 NPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMS-GHGVAFFSLEM 180
+ GL +D L G+ +LI+IGARPSMGKTT AL+ A ++A+ G V FFSLEM
Sbjct: 174 LTGLSTGLPKLDRLTNGLVKGDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLEM 233
Query: 181 DREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDDRPS 238
E+LG R L+ S S I N+ G N + ++L + L IDD
Sbjct: 234 SAEQLGERLLA-----SKSGINTGNIRTGRFNDSDFNRLLNAVDRLSEKDLYIDDTGG 286
>gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional.
Length = 497
Score = 94.2 bits (235), Expect = 3e-20
Identities = 68/247 (27%), Positives = 97/247 (39%), Gaps = 42/247 (17%)
Query: 18 STYLNNLLTLASSISSEVINA---ARRVVQQWAR---ITISQEAKALALHTSDPTCNTAT 71
YL L T A +I INA R + R I I ++ A
Sbjct: 97 VQYLAKLATEAVTI----INARDYGRIIYDLALRRELINIGEDVVNNAYDAPVD--VAPQ 150
Query: 72 -LIRKSMQSFEDIISEVHLTKNQCTGSSCISIANAATTAMKSAEQQKKEGEN-PDIKWGL 129
I + Q + L + S A T A+ A K + I GL
Sbjct: 151 EQIEDAEQKLYE------LAETGRYEGGFQSFGTAITEAVDMANAAFKRDGHLSGISTGL 204
Query: 130 QSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMS---------------GHGVA 174
+ +D +GG+ +LI++ RPSMGKT A + A + A + G V
Sbjct: 205 RDLDSKLGGLHPSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVG 264
Query: 175 FFSLEMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIID 234
FFSLEM E+L R LS S I + RG+I++E + ++LQ PL ID
Sbjct: 265 FFSLEMSAEQLATRILS-----EQSEISSSKIRRGKISEEDFEKLVDASQELQKLPLYID 319
Query: 235 DRPSPGI 241
D +P +
Sbjct: 320 D--TPAL 324
>gnl|CDD|181451 PRK08506, PRK08506, replicative DNA helicase; Provisional.
Length = 472
Score = 88.9 bits (221), Expect = 1e-18
Identities = 57/177 (32%), Positives = 85/177 (48%), Gaps = 17/177 (9%)
Query: 70 ATLIRK----SMQSFEDIISEVHLTKNQCT-GSSCISIANA---ATTAMKSAEQQKKEGE 121
A I + Q DI+ EV T GS+ ++ + M+ ++QK+ G
Sbjct: 110 ANTIPEQAVEEDQKSSDILDEVERELYSITNGSNSEDFKDSKEVIESTMEHIKKQKRLG- 168
Query: 122 NPDI---KWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSL 178
N DI G ++ + G +LI+I ARPSMGKTT L+ AL GVAFFSL
Sbjct: 169 NKDIIGLDTGFVELNKMTKGFNKGDLIIIAARPSMGKTTLCLNMALKALNQDKGVAFFSL 228
Query: 179 EMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDD 235
EM E+L R LS + + IP NL G+++ +++ C++L L + D
Sbjct: 229 EMPAEQLMLRMLS-----AKTSIPLQNLRTGDLDDDEWERLSDACDELSKKKLFVYD 280
>gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated.
Length = 886
Score = 87.9 bits (218), Expect = 3e-18
Identities = 45/138 (32%), Positives = 75/138 (54%), Gaps = 8/138 (5%)
Query: 120 GENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGH-GVAFFSL 178
G + G +D + G+ +LI++ ARPSMGKTTF L A + A+ VA FSL
Sbjct: 195 GLARGVPTGFTELDAMTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRHRLAVAIFSL 254
Query: 179 EMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDDRP 237
EM +E+L R LS + ++I ++ G ++ + + R+++ + E + + P+ IDD P
Sbjct: 255 EMSKEQLVMRLLS-----AEAKIKLSDMRSGRMSDDDWTRLARAMGE-ISEAPIFIDDTP 308
Query: 238 SPGIMEFVHVANGLRNKH 255
+ +ME A LR +
Sbjct: 309 NLTVMEIRAKARRLRQEA 326
>gnl|CDD|168658 PRK06749, PRK06749, replicative DNA helicase; Provisional.
Length = 428
Score = 76.9 bits (189), Expect = 5e-15
Identities = 46/143 (32%), Positives = 70/143 (48%), Gaps = 5/143 (3%)
Query: 114 EQQKKEGENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGV 173
E + E I+ G S++ + G+Q + +++GARPSMGKT FAL+ LH A SG V
Sbjct: 158 ELHQDAKEITGIETGYTSLNKMTCGLQEGDFVVLGARPSMGKTAFALNVGLHAAKSGAAV 217
Query: 174 AFFSLEMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLI 232
FSLEM ++L R S + S R L + E + ++S+ E + + PL
Sbjct: 218 GLFSLEMSSKQLLKRMASCVGEVSGGR---LKNPKHRFAMEDWEKVSKAFAE-IGELPLE 273
Query: 233 IDDRPSPGIMEFVHVANGLRNKH 255
I D + + L+ KH
Sbjct: 274 IYDNAGVTVQDIWMQTRKLKRKH 296
>gnl|CDD|181547 PRK08760, PRK08760, replicative DNA helicase; Provisional.
Length = 476
Score = 74.2 bits (182), Expect = 3e-14
Identities = 51/146 (34%), Positives = 76/146 (52%), Gaps = 13/146 (8%)
Query: 105 AATTAMKSA-EQQKKEGENPD----IKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFA 159
A A+K A E+ + EN + G D + G+Q +LI++ ARP+MGKTTFA
Sbjct: 187 AMPGALKDAFEELRNRFENGGNITGLPTGYNDFDAMTAGLQPTDLIILAARPAMGKTTFA 246
Query: 160 LSTALHMAM-SGHGVAFFSLEMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRI 218
L+ A + A+ S GVA FS+EM +L R +S S+ RI L G + E +
Sbjct: 247 LNIAEYAAIKSKKGVAVFSMEMSASQLAMRLIS-----SNGRINAQRLRTGALEDEDWAR 301
Query: 219 SQGICEKLQDFPLIIDDRP--SPGIM 242
G + L++ + IDD P SP ++
Sbjct: 302 VTGAIKMLKETKIFIDDTPGVSPEVL 327
>gnl|CDD|180157 PRK05595, PRK05595, replicative DNA helicase; Provisional.
Length = 444
Score = 71.0 bits (174), Expect = 3e-13
Identities = 44/128 (34%), Positives = 63/128 (49%), Gaps = 6/128 (4%)
Query: 117 KKEGENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHGVAF 175
+GE + G + +D G Q ++ILI ARPSMGKTTFAL+ A + A+ G VA
Sbjct: 176 NNKGETTGVASGFRELDAKTSGFQKGDMILIAARPSMGKTTFALNIAEYAALREGKSVAI 235
Query: 176 FSLEMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDD 235
FSLEM +E+L + L S + + L L G + + + L + IDD
Sbjct: 236 FSLEMSKEQLAYKLLC-----SEANVDMLRLRTGNLEDKDWENIARASGPLAAAKIFIDD 290
Query: 236 RPSPGIME 243
+ME
Sbjct: 291 TAGVSVME 298
>gnl|CDD|180232 PRK05748, PRK05748, replicative DNA helicase; Provisional.
Length = 448
Score = 67.7 bits (166), Expect = 3e-12
Identities = 43/118 (36%), Positives = 61/118 (51%), Gaps = 14/118 (11%)
Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGH-GVAFFSLEMDREKLG 186
G +D + G+Q +LI++ ARPS+GKT FAL+ A ++A VA FSLEM E L
Sbjct: 189 GFTDLDKMTSGLQPNDLIIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSLEMGAESLV 248
Query: 187 ARALSNLLYPSSSRIPYLNLIRGEINQE---QYRISQGICEKLQDFPLIIDDRPSPGI 241
R L + I L G++ + + I+ G L D P+ IDD +PGI
Sbjct: 249 MRMLC-----AEGNIDAQRLRTGQLTDDDWPKLTIAMG---SLSDAPIYIDD--TPGI 296
>gnl|CDD|180791 PRK07004, PRK07004, replicative DNA helicase; Provisional.
Length = 460
Score = 61.9 bits (150), Expect = 2e-10
Identities = 35/118 (29%), Positives = 60/118 (50%), Gaps = 8/118 (6%)
Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHGVAFFSLEMDREKLG 186
G +D + G+ ELI++ RPSMGKT F+++ ++A+ G VA FS+EM +L
Sbjct: 199 GFVDLDRMTSGMHGGELIIVAGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSMEMPGTQLA 258
Query: 187 ARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDDRPSPGIME 243
R L S R+ + G + E + +++ + +K+ + L ID+ ME
Sbjct: 259 MRMLG-----SVGRLDQHRMRTGRLTDEDWPKLTHAV-QKMSEAQLFIDETGGLNPME 310
>gnl|CDD|181193 PRK08006, PRK08006, replicative DNA helicase; Provisional.
Length = 471
Score = 60.8 bits (147), Expect = 4e-10
Identities = 39/110 (35%), Positives = 61/110 (55%), Gaps = 7/110 (6%)
Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHGVAFFSLEMDREKLG 186
G ++ G+Q +LI++ ARPSMGKTTFA++ + AM V FSLEM E++
Sbjct: 210 GYDDLNKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMLQDKPVLIFSLEMPGEQIM 269
Query: 187 ARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDD 235
R L++L SR+ + G+++ E + RIS + L+ + IDD
Sbjct: 270 MRMLASL-----SRVDQTRIRTGQLDDEDWARISGTMGILLEKRNMYIDD 314
>gnl|CDD|181562 PRK08840, PRK08840, replicative DNA helicase; Provisional.
Length = 464
Score = 57.7 bits (139), Expect = 3e-09
Identities = 39/110 (35%), Positives = 61/110 (55%), Gaps = 7/110 (6%)
Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHG-VAFFSLEMDREKLG 186
G ++ G+Q +LI++ ARPSMGKTTFA++ + AM V FSLEM E+L
Sbjct: 203 GFTDLNKKTAGLQGSDLIIVAARPSMGKTTFAMNLCENAAMDQDKPVLIFSLEMPAEQLM 262
Query: 187 ARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDD 235
R L++L SR+ + G+++ E + RIS + ++ + IDD
Sbjct: 263 MRMLASL-----SRVDQTKIRTGQLDDEDWARISSTMGILMEKKNMYIDD 307
>gnl|CDD|136106 PRK06904, PRK06904, replicative DNA helicase; Validated.
Length = 472
Score = 56.2 bits (135), Expect = 8e-09
Identities = 41/111 (36%), Positives = 59/111 (53%), Gaps = 8/111 (7%)
Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHGVAFFSLEMDREKLG 186
G +D G+Q +LI++ ARPSMGKTTFA++ + AM S V FSLEM E++
Sbjct: 207 GFTDLDKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMASEKPVLVFSLEMPAEQIM 266
Query: 187 ARALSNLLYPSSSRIPYLNLIRGEI--NQEQYRISQGICEKLQDFPLIIDD 235
R L++L SR+ + G+ Q+ +IS + Q L IDD
Sbjct: 267 MRMLASL-----SRVDQTKIRTGQNLDQQDWAKISSTVGMFKQKPNLYIDD 312
>gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional.
Length = 505
Score = 54.8 bits (132), Expect = 2e-08
Identities = 35/133 (26%), Positives = 70/133 (52%), Gaps = 14/133 (10%)
Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFAL----STALHMAMSGHGVAFFSLEMDRE 183
G + +D L G++ ++I++ ARP +GK+T AL S ++ + FSLEM +
Sbjct: 251 GFKDLDDLTNGLRGGQMIIVAARPGVGKSTLALDFMRSASIKHNKAS---VIFSLEMSKS 307
Query: 184 KLGARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDDRPSPGIM 242
++ R LS + + + ++ G+++++ + ++ Q + K+ P+ IDD + +M
Sbjct: 308 EIVMRLLS-----AEAEVRLSDMRGGKMDEDAWEKLVQRL-GKIAQAPIFIDDSANLTMM 361
Query: 243 EFVHVANGLRNKH 255
E A L+ KH
Sbjct: 362 EIRSKARRLKQKH 374
>gnl|CDD|180528 PRK06321, PRK06321, replicative DNA helicase; Provisional.
Length = 472
Score = 50.6 bits (121), Expect = 4e-07
Identities = 35/132 (26%), Positives = 63/132 (47%), Gaps = 13/132 (9%)
Query: 132 VDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGH-GVAFFSLEMDREKLGARAL 190
+D ++ G L+++ ARP+MGKT AL+ A + V FSLEM ++L R +
Sbjct: 216 LDKMINGFSPSNLMILAARPAMGKTALALNIAENFCFQNRLPVGIFSLEMTVDQLIHRII 275
Query: 191 SNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDDRPSPGIMEFVHVANG 250
S S + + G+++ ++ + ++Q+ L+IDD+P I
Sbjct: 276 C-----SRSEVESKKISVGDLSGRDFQRIVSVVNEMQEHTLLIDDQPGLKI-------TD 323
Query: 251 LRNKHTKMVQLY 262
LR + +M + Y
Sbjct: 324 LRARARRMKESY 335
>gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional.
Length = 237
Score = 48.5 bits (116), Expect = 2e-06
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 135 LMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGAR 188
L ++ +L+L+GARP GKT L A+ SG FF+LE + + R
Sbjct: 57 LFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLEYTEQDVRDR 110
>gnl|CDD|177377 PHA02542, 41, 41 helicase; Provisional.
Length = 473
Score = 37.4 bits (87), Expect = 0.004
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 137 GGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARALSNLL 194
GG + + L ++ A ++GK+ S A G+ V + S+EM E + R +NLL
Sbjct: 185 GGAERKTLNVLLAGVNVGKSLGLCSLAADYLQQGYNVLYISMEMAEEVIAKRIDANLL 242
>gnl|CDD|161868 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)).
Length = 454
Score = 36.3 bits (84), Expect = 0.007
Identities = 37/115 (32%), Positives = 51/115 (44%), Gaps = 10/115 (8%)
Query: 121 ENPDIKWGLQSVDH-LMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLE 179
E P G +D L GG+ LILIG P +GK+T L A +A + V + S E
Sbjct: 72 EVPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGE 131
Query: 180 MDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIID 234
+++ RA L P P L ++ E N EQ I I E+ +ID
Sbjct: 132 ESLQQIKMRA-IRLGLPE----PNLYVL-SETNWEQ--ICANI-EEENPQACVID 177
>gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 35.5 bits (83), Expect = 0.017
Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 23/105 (21%)
Query: 137 GGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLE-------MDREKLGARA 189
GG+ ++LIG P +GK+T L A +A +G V + S E + E+LG +
Sbjct: 75 GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEESASQIKLRAERLGLPS 134
Query: 190 LSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIID 234
+ L ++ L I I +E+ + ++ID
Sbjct: 135 DNLYLLAETN----LEAILATIEEEKPDL------------VVID 163
>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 32.0 bits (72), Expect = 0.19
Identities = 23/97 (23%), Positives = 36/97 (37%), Gaps = 15/97 (15%)
Query: 142 RELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARA---LSNLLYPSS 198
E+ILI P GKTT A + A + G GV + E E++ + + S
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 199 SRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDD 235
S L L + + + LI+D+
Sbjct: 62 SGELRLRLALALARKLKPDV------------LILDE 86
>gnl|CDD|162777 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 31.6 bits (72), Expect = 0.22
Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 8/67 (11%)
Query: 135 LMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAF-----FSLEMDREKLGA-- 187
L GGV+ + I P GKT + A++ A G V + S E ++
Sbjct: 5 LGGGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEGLSPERFKQIAEDRP 64
Query: 188 -RALSNL 193
RALSN
Sbjct: 65 ERALSNF 71
>gnl|CDD|129627 TIGR00536, hemK_fam, HemK family putative methylases. The gene
hemK from E. coli was found to contribute to heme
biosynthesis and originally suggested to be
protoporphyrinogen oxidase (Medline 95189105).
Functional analysis of the nearest homolog in
Saccharomyces cerevisiae, YNL063w, finds it is not
protoporphyrinogen oxidase and sequence analysis
suggests that HemK homologs have
S-adenosyl-methionine-dependent methyltransferase
activity (Medline 99237242). Homologs are found, usually
in a single copy, in nearly all completed genomes, but
varying somewhat in apparent domain architecture. Both
E. coli and H. influenzae have two members rather than
one. The members from the Mycoplasmas have an additional
C-terminal domain.
Length = 284
Score = 30.4 bits (69), Expect = 0.51
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 67 CNTATLIRKS------MQSFEDIISEVHLTK--NQCTGSSCISIANAATTAMKS 112
N LI + ++ +IS+ + + TGS CI++A A
Sbjct: 87 VNEHVLIPRPETEELVEKALASLISQNPILHILDLGTGSGCIALALAYEFPNAE 140
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 29.8 bits (68), Expect = 0.83
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 145 ILIGARPSMGKTTFA 159
ILI P GK+TFA
Sbjct: 260 ILIAGAPGAGKSTFA 274
>gnl|CDD|183735 PRK12771, PRK12771, putative glutamate synthase (NADPH) small
subunit; Provisional.
Length = 564
Score = 29.1 bits (66), Expect = 1.4
Identities = 15/40 (37%), Positives = 17/40 (42%), Gaps = 9/40 (22%)
Query: 147 IGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLG 186
IG P+ LS A H+ GH V F E KLG
Sbjct: 143 IGGGPA------GLSAAYHLRRMGHAVTIF--EA-GPKLG 173
>gnl|CDD|181799 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 28.3 bits (64), Expect = 2.2
Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 128 GLQSVDHLMGGVQLRELIL-IGARPSMGKTTFALSTALHMAMSGHGVAF-----FSLE 179
G + +D L+GG R I I P GKT L A+ A +G V + S E
Sbjct: 8 GCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTEGLSPE 65
>gnl|CDD|181823 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 28.0 bits (63), Expect = 2.6
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 149 ARPSMGKTTFALSTALHMAMSG 170
A +GKTTF L +L++A G
Sbjct: 102 APTGVGKTTFGLVMSLYLAKKG 123
>gnl|CDD|162097 TIGR00898, 2A0119, cation transport protein.
Length = 505
Score = 28.1 bits (63), Expect = 2.6
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 4/52 (7%)
Query: 151 PSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARALSNLLYPSSSRIP 202
P++ KTT L M +++ L +D LG +L +P
Sbjct: 323 PNLRKTTLCLM----MLWFTTAFSYYGLVLDLGNLGGNIYLDLFISGLVELP 370
>gnl|CDD|148381 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is one
of the Kai proteins among which direct protein-protein
association may be a critical process in the generation
of circadian rhythms in cyanobacteria.
Length = 231
Score = 28.0 bits (63), Expect = 3.0
Identities = 22/86 (25%), Positives = 33/86 (38%), Gaps = 15/86 (17%)
Query: 133 DHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMS-GHGVAFFSLE------------ 179
+ L GG+ ++LI P GKT F L + A+ G + +LE
Sbjct: 10 EILKGGIPEGRVVLITGGPGTGKTIFGLQFLYNGALEYGEPGVYVTLEEPPEDLRENAKS 69
Query: 180 --MDREKLGARALSNLLYPSSSRIPY 203
D EKL ++ S+S I
Sbjct: 70 FGWDLEKLEEEGKLAIIDASTSGIGI 95
>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family. This
model represents a rather narrowly distributed archaeal
protein family in which members have a single copy of
the KaiC domain. This stands in contrast to the
circadian clock protein KaiC itself, with two copies of
the domain. Members are expected to have weak ATPase
activity, by homology to the
autokinase/autophosphorylase KaiC itself.
Length = 224
Score = 27.7 bits (62), Expect = 3.1
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 128 GLQSVDHLM-GGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLG 186
G+ +D ++ GG +I++ GKTTF+L +G + SLE E++
Sbjct: 1 GIPGLDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLEEREERIL 60
Query: 187 ARALS 191
A S
Sbjct: 61 GYAKS 65
>gnl|CDD|163310 TIGR03533, L3_gln_methyl, protein-(glutamine-N5) methyltransferase,
ribosomal protein L3-specific. Members of this protein
family methylate ribosomal protein L3 on a glutamine
side chain. This family is related to HemK, a
protein-glutamine methyltranferase for peptide chain
release factors.
Length = 284
Score = 27.5 bits (62), Expect = 3.4
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 94 CTGSSCISIANA 105
CTGS CI+IA A
Sbjct: 129 CTGSGCIAIACA 140
>gnl|CDD|181312 PRK08236, PRK08236, hypothetical protein; Provisional.
Length = 212
Score = 27.7 bits (62), Expect = 3.5
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 163 ALHMAMSGHGVAFFSLEMDREKLGARALSNLLYP 196
A+ AM G GVA + L RA+SN + P
Sbjct: 156 AVAEAMEGFGVAEAAAAAGLPVLELRAISNPVGP 189
>gnl|CDD|183320 PRK11805, PRK11805, N5-glutamine S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 307
Score = 27.1 bits (61), Expect = 4.6
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 94 CTGSSCISIANA 105
CTGS CI+IA A
Sbjct: 141 CTGSGCIAIACA 152
>gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein.
Length = 1394
Score = 26.6 bits (59), Expect = 6.6
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 143 ELILIGARPSMGKTTFALSTA 163
EL ++ RP G +T + A
Sbjct: 88 ELTVVLGRPGSGCSTLLKTIA 108
>gnl|CDD|184171 PRK13598, hisB, imidazoleglycerol-phosphate dehydratase;
Provisional.
Length = 193
Score = 26.3 bits (58), Expect = 7.7
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 168 MSGHGVAFFSLEMDREKLGARALSNL 193
+SG G+AF +L + R ++G A N+
Sbjct: 110 ISGRGMAFVNLNLKRSEIGGLATENI 135
>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
Members of this family contain a single copy of the KaiC
domain (pfam06745) that occurs in two copies of the
circadian clock protein kinase KaiC itself. Members
occur primarily in thermophilic archaea and in
Thermotoga.
Length = 237
Score = 26.3 bits (58), Expect = 8.4
Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 125 IKWGLQSVDHLM-GGVQLRELILIGARPSMGKTTFA 159
+K G+ +D ++ GG+ R ++L+ P GK+ F+
Sbjct: 3 VKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFS 38
>gnl|CDD|163142 TIGR03117, cas_csf4, CRISPR-associated DEAD/DEAH-box helicase Csf4.
Members of this family show up near CRISPR repeats in
Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp.
EbN1, and Rhodoferax ferrireducens DSM 15236. In the
latter two species, the CRISPR/cas locus is found on a
plasmid. This family is one of several characteristic of
a type of CRISPR-associated (cas) gene cluster we
designate Aferr after A. ferrooxidans, where it is both
chromosomal and the only type of cas gene cluster found.
The gene is designated csf4 (CRISPR/cas Subtype as in A.
ferrooxidans protein 1), as it lies farthest (fourth
closest) from the repeats in the A. ferrooxidans genome.
Length = 636
Score = 26.5 bits (58), Expect = 8.7
Identities = 18/123 (14%), Positives = 43/123 (34%), Gaps = 20/123 (16%)
Query: 31 ISSEVINAARRVVQQWARITISQEAKALALHTSDPTCNTATLIRKSMQSFEDIISEVHLT 90
I S + A +Q+ + + + + L L D + + + D S +
Sbjct: 250 IVSAAVAAVSHCIQRLRALDVFGDGQTLCL---DAGNKELETLFADLDAALDACS---VG 303
Query: 91 KNQCTGSSCIS----IANAATTAMKSAEQQKKEGE-----NPDIKW-----GLQSVDHLM 136
+N+ +S + A + + + +PD ++ G + + +M
Sbjct: 304 RNRDENKKALSVVKDVKKARFILDNAITAIQGKASAVLQFSPDRRFPSLIVGREDLGKVM 363
Query: 137 GGV 139
GG+
Sbjct: 364 GGL 366
>gnl|CDD|151380 pfam10933, DUF2827, Protein of unknown function (DUF2827). This is
a family of uncharacterized proteins found in
Burkholderia.
Length = 364
Score = 26.2 bits (58), Expect = 9.6
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 230 PLIIDD---RPSPGIMEFVHVANGLRNK-HTKMVQLYRLL 265
P+++ D R P +EFVHV N L K H + V L
Sbjct: 208 PMLVADEAYRAQPDAVEFVHVTNTLHLKEHPEFVHFANSL 247
>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
Length = 230
Score = 26.2 bits (58), Expect = 9.8
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 135 LMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEM 180
L GG+ LILI S GK+ + A +G+ V++ S ++
Sbjct: 17 LGGGIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQL 62
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
0.318 0.130 0.364
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,064,687
Number of extensions: 243435
Number of successful extensions: 522
Number of sequences better than 10.0: 1
Number of HSP's gapped: 501
Number of HSP's successfully gapped: 49
Length of query: 266
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 174
Effective length of database: 4,006,537
Effective search space: 697137438
Effective search space used: 697137438
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.4 bits)