RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780332|ref|YP_003064745.1| replicative DNA helicase
[Candidatus Liberibacter asiaticus str. psy62]
(504 letters)
>gnl|CDD|30653 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 458 bits (1180), Expect = e-129
Identities = 190/472 (40%), Positives = 281/472 (59%), Gaps = 37/472 (7%)
Query: 21 RESPNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTANP 80
R P +IEAEQA+LG IL++ +A RVS+ L+P F+ H+ I++ + L G+ +
Sbjct: 1 RLPPQDIEAEQAVLGGILLDPDAIERVSERLRPEDFYRPAHRLIYQAILDLYGQGEPIDL 60
Query: 81 VTVKTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEMVN 140
VTV LSD+ +L + YLA L S N + Y +I+ AL R LI G E+VN
Sbjct: 61 VTVSEELSDRGLLTRIGGANYLATLIDRTPSAANIDYYAKIVKEKALLRELIEAGNEIVN 120
Query: 141 AAYEASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVAIDMAGQAFNRDGRLA 200
YE+ D + ++ AE+K+F +AE + F D + +D F G L
Sbjct: 121 LGYESEKDLDEEV-LDAAEKKIFDVAER-KNSEDFVHIGDLLKETMDEIEARFENGG-LI 177
Query: 201 GVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI 260
GV TG LD+ G + DLII+A RPGMGKT+LA NIA N A +
Sbjct: 178 GVPTGFTDLDEITSGFRPGDLIIVAARPGMGKTALALNIALNAAADGRKP---------- 227
Query: 261 NGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYI 320
V +SLEMS EQL R++S ++ + SSK+R G L+ ++E+++ + + + P++I
Sbjct: 228 ----VAIFSLEMSEEQLVMRLLSSESGIESSKLRTGRLSDDEWERLIKAASELSEAPIFI 283
Query: 321 DQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKALA 380
D T G++++++ ++ARRLK + L L+++DY+QLMT KK ENR E++ I+ +LK LA
Sbjct: 284 DDTPGLTITEIRSKARRLKLKHNLGLIVIDYLQLMTGGKK-SENRKQEVSEISRSLKGLA 342
Query: 381 KELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKEPTN 440
KEL +P+IALSQL+R VE R +KRP LSDLRESG++EQDAD+V+F+ RDE Y+++
Sbjct: 343 KELGVPVIALSQLNRSVEQRTDKRPMLSDLRESGALEQDADIVIFLHRDEAYLKDTPD-- 400
Query: 441 KDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRFSALSD 492
+G A++I+AK R+GPTGTV LAF +FT+F L+
Sbjct: 401 -----------------RGEAEVIVAKNRNGPTGTVKLAFDPQFTKFKNLAR 435
>gnl|CDD|29985 cd00984, DnaB_C, DnaB helicase C terminal domain. The hexameric
helicase DnaB unwinds the DNA duplex at the chromosome
replication fork. Although the mechanism by which DnaB
both couples ATP hydrolysis to translocation along DNA
and denatures the duplex is unknown, a change in the
quaternary structure of the protein involving
dimerization of the N-terminal domain has been observed
and may occur during the enzymatic cycle. This
C-terminal domain contains an ATP-binding site and is
therefore probably the site of ATP hydrolysis..
Length = 242
Score = 302 bits (774), Expect = 2e-82
Identities = 134/274 (48%), Positives = 179/274 (65%), Gaps = 34/274 (12%)
Query: 209 LDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFY 268
LD GGLQ DLIIIA RP MGKT+ A NIA N+A G V F+
Sbjct: 3 LDNLTGGLQPGDLIIIAARPSMGKTAFALNIAENIAKKQ--------------GKPVLFF 48
Query: 269 SLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQTGGISM 328
SLEMS EQL R+++ ++ + SK+R G L+ D+E++ +++LP+YID + +++
Sbjct: 49 SLEMSKEQLLQRLLASESGISLSKLRTGSLSDEDWERLAEAIGELKELPIYIDDSSSLTV 108
Query: 329 SQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKALAKELNIPII 388
S + +RARRLK++ GL L+++DY+QLM+ SKK + NR E+ I+ +LK LAKELN+P+I
Sbjct: 109 SDIRSRARRLKKEHGLGLIVIDYLQLMSGSKK-KGNRQQEVAEISRSLKLLAKELNVPVI 167
Query: 389 ALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKEPTNKDDILAYT 448
ALSQLSR VE+R +KRP LSDLRESGSIEQDADVV+F+ RDEYY + E
Sbjct: 168 ALSQLSRGVESRADKRPMLSDLRESGSIEQDADVVMFLYRDEYYNKESE----------- 216
Query: 449 KWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQA 482
KGIA+II+AK R+GPTGTV L F
Sbjct: 217 --------SKGIAEIIVAKNRNGPTGTVELRFDG 242
>gnl|CDD|146436 pfam03796, DnaB_C, DnaB-like helicase C terminal domain. The
hexameric helicase DnaB unwinds the DNA duplex at the
Escherichia coli chromosome replication fork. Although
the mechanism by which DnaB both couples ATP hydrolysis
to translocation along DNA and denatures the duplex is
unknown, a change in the quaternary structure of the
protein involving dimerization of the N-terminal domain
has been observed and may occur during the enzymatic
cycle. This C-terminal domain contains an ATP-binding
site and is therefore probably the site of ATP
hydrolysis.
Length = 186
Score = 256 bits (656), Expect = 1e-68
Identities = 101/200 (50%), Positives = 134/200 (67%), Gaps = 15/200 (7%)
Query: 201 GVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI 260
G+ TG LD+ GGLQ+ DLIIIA RP MGKT+ A NIA N A
Sbjct: 1 GLPTGFTDLDQLTGGLQKGDLIIIAARPSMGKTAFALNIARNAALKQDKP---------- 50
Query: 261 NGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYI 320
V F+SLEMS+EQLA R++S ++ + SSK+R G+L+ D+E++ + + + PLYI
Sbjct: 51 ----VLFFSLEMSAEQLAERLLSSESRISSSKLRSGQLSDEDWERLAEAAGELSEAPLYI 106
Query: 321 DQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSK-KIEENRVLEITGITMALKAL 379
D T G+S+S+L +ARRLKR+ GL L+++DY+QLM SK ENR EI+ I+ +LKAL
Sbjct: 107 DDTPGLSLSELRAQARRLKREHGLGLIVIDYLQLMQGSKASKSENRQQEISEISRSLKAL 166
Query: 380 AKELNIPIIALSQLSRQVEN 399
AKELNIP+IALSQLSR VE
Sbjct: 167 AKELNIPVIALSQLSRAVEQ 186
>gnl|CDD|144390 pfam00772, DnaB, DnaB-like helicase N terminal domain. The
hexameric helicase DnaB unwinds the DNA duplex at the
Escherichia coli chromosome replication fork. Although
the mechanism by which DnaB both couples ATP hydrolysis
to translocation along DNA and denatures the duplex is
unknown, a change in the quaternary structure of the
protein involving dimerization of the N-terminal domain
has been observed and may occur during the enzymatic
cycle. This N-terminal domain is required both for
interaction with other proteins in the primosome and for
DnaB helicase activity.
Length = 103
Score = 115 bits (291), Expect = 2e-26
Identities = 44/100 (44%), Positives = 60/100 (60%)
Query: 24 PNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTANPVTV 83
P++IEAEQA+LGA+L++ EA V+D LKP F++ H+ IFE + +L GK +PVTV
Sbjct: 3 PHSIEAEQAVLGALLLDPEAIDEVADILKPEDFYDPAHRLIFEAILELYDKGKPIDPVTV 62
Query: 84 KTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIY 123
L + L E+ YLA LA S N E Y RI+
Sbjct: 63 AEELERKGKLEEVGGIAYLAELADNVPSAANIEYYARIVK 102
>gnl|CDD|29988 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3'
helicases. Helicases couple NTP hydrolysis to the
unwinding of nucleic acid duplexes into their component
strands..
Length = 271
Score = 76.5 bits (188), Expect = 1e-14
Identities = 52/227 (22%), Positives = 92/227 (40%), Gaps = 23/227 (10%)
Query: 209 LDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFY 268
L+K GL++ +LII+ G+GKT+ A ++ T +G VG
Sbjct: 20 LNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLI--------------TQHGVRVGTI 65
Query: 269 SLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDY-EKIVACSQVMQKLPLYI--DQTGG 325
SLE + A R++ + + + E+ A + D G
Sbjct: 66 SLEEPVVRTARRLLGQYAGKR---LHLPDTVFIYTLEEFDAAFDEFEGTGRLFMYDSFGE 122
Query: 326 ISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKALAKELNI 385
SM + + R + G+ +I+D + +M + ++ + + I L+ A E I
Sbjct: 123 YSMDSVLEKVRYMAVSHGIQHIIIDNLSIMVSDERASGDERKALDEIMTKLRGFATEHGI 182
Query: 386 PIIALSQLSRQVENR---DNKRPQLSDLRESGSIEQDADVVLFVIRD 429
I +S L R ++ + LSD R S +I Q AD V+ + R+
Sbjct: 183 HITLVSHLRRPDGDKTHEEGGEVSLSDFRGSAAIGQLADNVIALERN 229
>gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion..
Length = 165
Score = 55.5 bits (133), Expect = 3e-08
Identities = 43/209 (20%), Positives = 80/209 (38%), Gaps = 45/209 (21%)
Query: 221 LIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMSSEQLATR 280
LI++ G G GKT+LA +A N+A GG V + +E E+L R
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATK---------------GGKVVYVDIEEEIEELTER 45
Query: 281 IISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQTGGISMSQLATRARRLKR 340
+I E + + + + ++L ++A RL+
Sbjct: 46 LIGESLKGALDNLI-----------------------IVFATADDPAAARLLSKAERLRE 82
Query: 341 QRGLDLLIVDYIQLM-TTSKKIEENRVLEITGITMALKALAKELNIPIIALSQLSRQVEN 399
+ G DL+I+D + + ++I E E+ L A++ + +I Q+ +
Sbjct: 83 RGGDDLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSGDKG 142
Query: 400 RDNKRPQLSDLRESGSIEQDADVVLFVIR 428
R + ++E AD V+ + R
Sbjct: 143 DPR------LTRGAQNLEDIADTVIVLSR 165
>gnl|CDD|31265 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 46.0 bits (109), Expect = 3e-05
Identities = 56/288 (19%), Positives = 109/288 (37%), Gaps = 72/288 (25%)
Query: 202 VSTGIQTLDKQMGG-LQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI 260
+STGI+ LD+ +GG L +I+I G PG+GK++L +A +A K
Sbjct: 75 ISTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGKV----------- 123
Query: 261 NGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYI 320
L +S E+ +I K+R L P + ++ + +
Sbjct: 124 ---------LYVSGEESLQQI----------KLRADRLGLPTNNLYLLAETNLEDIIAEL 164
Query: 321 DQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSK-KIEENRVLEITGITMALKAL 379
+ Q DL+++D IQ + + + V ++ + L L
Sbjct: 165 E-------------------QEKPDLVVIDSIQTLYSEEITSAPGSVSQVREVAAELMRL 205
Query: 380 AKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYY------- 432
AK NI I + ++ K ++ R +E D VL+ D +
Sbjct: 206 AKTKNIAIFIVGHVT--------KEGAIAGPR---VLEHMVDTVLYFEGDRHSRYRILRS 254
Query: 433 IRNKE-PTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLA 479
++N+ TN+ + T + L+ V + + ++++ G+ +
Sbjct: 255 VKNRFGATNELGVFEMT--ENGLREVSNPSALFLSERGEQTPGSAVVV 300
>gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 42.4 bits (99), Expect = 3e-04
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 198 RLAGVSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYNVADA 246
+ + TGI LD+ + GGL R +++I G PG GKT A Y A
Sbjct: 1 MMERIPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGARE 50
>gnl|CDD|30003 cd01393, recA_like, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange. While prokaryotes have a single RecA
protein, eukaryotes have multiple RecA homologs such as
Rad51, DMC1 and Rad55/57. Archaea have the RecA-like
homologs radA and radB..
Length = 226
Score = 42.1 bits (99), Expect = 3e-04
Identities = 43/207 (20%), Positives = 76/207 (36%), Gaps = 44/207 (21%)
Query: 202 VSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI 260
+STG + LD+ + GG+ + I G G GKT L +A E Q G +
Sbjct: 1 ISTGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLA--------VEAQLPGELGGL 52
Query: 261 NGGIVGFYSLEMSS-----EQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQK 315
G +V + E + QLA R + EV + + RP
Sbjct: 53 EGKVV-YIDTEGAFRPERLVQLAVRFGLDPEEVLDNIY----VARPYN------------ 95
Query: 316 LPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEEN----RVLEITG 371
G ++ R+ +DL++VD + + + I R ++
Sbjct: 96 ---------GEQQLEIVEELERIMSSGRVDLVVVDSVAALFRKEFIGRGMLAERARLLSQ 146
Query: 372 ITMALKALAKELNIPIIALSQLSRQVE 398
L LA + N+ ++ +Q+ +V+
Sbjct: 147 ALRKLLRLADKFNVAVVFTNQVRAKVD 173
>gnl|CDD|29987 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules..
Length = 372
Score = 41.8 bits (98), Expect = 5e-04
Identities = 58/288 (20%), Positives = 109/288 (37%), Gaps = 71/288 (24%)
Query: 202 VSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI 260
+ TGI+ LD+ + GGL +I+I G PG+GK++L +A +A L G
Sbjct: 64 IPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSG----- 118
Query: 261 NGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYI 320
E S EQ+ R R ++ + LY+
Sbjct: 119 ----------EESPEQIKLR------------ADRLGISTEN---------------LYL 141
Query: 321 DQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSK-KIEENRVLEITGITMALKAL 379
++ + LK DL+I+D IQ + +S+ V ++ T L
Sbjct: 142 --LAETNLEDILASIEELK----PDLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMRF 195
Query: 380 AKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYY------- 432
AKE NIPI + ++++ + +E D VL+ D +
Sbjct: 196 AKERNIPIFIVGHVTKE-----------GSIAGPKVLEHMVDTVLYFEGDRHSEYRILRS 244
Query: 433 IRNK-EPTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLA 479
++N+ TN ++ + + L+ V +++ ++++ G+
Sbjct: 245 VKNRFGSTN--ELGVFEMRENGLREVSNPSELFLSEREEDVPGSAVTV 290
>gnl|CDD|29989 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 ..
Length = 235
Score = 38.2 bits (89), Expect = 0.006
Identities = 41/208 (19%), Positives = 75/208 (36%), Gaps = 45/208 (21%)
Query: 202 VSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI 260
++TG + LD+ + GG++ + I G G GKT L +A V Q +
Sbjct: 1 LTTGSKALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTV--------QLPIELGGL 52
Query: 261 NGGIVGFYSLEMS-----SEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQK 315
G V + E + Q+A R + EV I + +Q
Sbjct: 53 EGKAV-YIDTEGTFRPERLVQIAERFGLDPEEV-LDNIY--------VARAYNSDHQLQ- 101
Query: 316 LPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYI-----QLMTTSKKIEENRVLEIT 370
+++ I L + L+IVD + ++ E R +
Sbjct: 102 ---LLEELEAI-----------LIESSRIKLVIVDSVTALFRAEFDGRGELAE-RQQHLA 146
Query: 371 GITMALKALAKELNIPIIALSQLSRQVE 398
+ LK LA E N+ ++ +Q++ + +
Sbjct: 147 KLLRTLKRLADEFNVAVVITNQVTARPD 174
>gnl|CDD|37891 KOG2680, KOG2680, KOG2680, DNA helicase TIP49, TBP-interacting
protein [Transcription].
Length = 454
Score = 34.5 bits (79), Expect = 0.069
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 18/88 (20%)
Query: 222 IIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMSSEQLATRI 281
I+IAG+PG GKT++A ++ L D + +I+G + YSLEMS + T+
Sbjct: 69 ILIAGQPGTGKTAIAMGMS--------KSLGDDTPFTSISGSEI--YSLEMSKTEALTQA 118
Query: 282 --------ISEQTEVPSSKIRRGELTRP 301
I E+TEV ++ ++ RP
Sbjct: 119 FRKSIGVRIKEETEVIEGEVVEIQIDRP 146
>gnl|CDD|30816 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 33.7 bits (77), Expect = 0.13
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 188 MAGQAFNRDGRLAGVSTGIQTLDKQMG-GLQRSDLIIIAGRPGMGKTSLATNIAYNV 243
MA R + +STG LD+ +G GL R + I G GKT+LA + N
Sbjct: 28 MALGGDERREDIEAISTGSLALDEALGGGLPRGRITEIYGPESSGKTTLALQLVANA 84
>gnl|CDD|31417 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 33.7 bits (77), Expect = 0.14
Identities = 32/107 (29%), Positives = 45/107 (42%), Gaps = 23/107 (21%)
Query: 222 IIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMSSEQLATRI 281
I+I G PG GKT+LA IA EL D + I+G + YSLE+ + T+
Sbjct: 68 ILIVGPPGTGKTALAMGIA--------RELGEDVPFVAISGSEI--YSLEVKKTEALTQA 117
Query: 282 --------ISEQT-----EVPSSKIRRGELTRPDYEKIVACSQVMQK 315
I E EV +IRR Y K+ + + + K
Sbjct: 118 LRRAIGVRIKETREVYEGEVVELEIRRARNPLNPYGKVPSGAIITLK 164
>gnl|CDD|37999 KOG2788, KOG2788, KOG2788, Glycosyltransferase [Carbohydrate
transport and metabolism].
Length = 418
Score = 32.6 bits (74), Expect = 0.27
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 301 PDYEKIVACSQVMQKLPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKK 360
P +V C + +LP Y +TG +SMS + LKR L + + + L+ +
Sbjct: 300 PQLFHLVPCPR--HRLPKYDPKTGLLSMSYAEFKLTDLKRPGALFITVCKSLGLIHVKEV 357
Query: 361 IEENRVLEITGITM 374
++ L+I +T+
Sbjct: 358 EKDGIYLQINNLTL 371
>gnl|CDD|37584 KOG2373, KOG2373, KOG2373, Predicted mitochondrial DNA helicase
twinkle [Replication, recombination and repair].
Length = 514
Score = 31.2 bits (70), Expect = 0.67
Identities = 44/225 (19%), Positives = 83/225 (36%), Gaps = 36/225 (16%)
Query: 209 LDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFY 268
L+K + G + +L ++ G G GKT+ + Y +L T G T+ +
Sbjct: 263 LNKYLKGHRPGELTVLTGPTGSGKTTFLSE--------YSLDLFTQG-VNTL------WG 307
Query: 269 SLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYI-----DQT 323
S E+ +++LA ++ + L R + K A ++LPLY Q
Sbjct: 308 SFEIPNKRLAHWMLVQYAGYRL-------LDRLNSYKHWADR--FERLPLYFMTFHGQQF 358
Query: 324 GGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKALAKEL 383
++++A Q +I+D +Q M + +R I + A +
Sbjct: 359 MEKVINEIAHAIYVEDIQH----VIIDNLQFMMGQGMMALDRFHLQDRIIGYFRQFATQN 414
Query: 384 NIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIR 428
NI + + ++ + S Q+AD VL +
Sbjct: 415 NIHVTLVVHPRKE---DGDTELDTQSFFGSAKATQEADNVLIIQD 456
>gnl|CDD|143495 cd06821, PLPDE_III_D-TA, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme D-Threonine Aldolase.
D-threonine aldolase (D-TA, EC 4.3.1.18) reversibly
catalyzes the aldol cleavage of D-threonine into glycine
and acetaldehyde, and the synthesis of D-threonine from
glycine and acetaldehyde. Its activity is present in
several genera of bacteria but not in fungi. It requires
PLP and a divalent cation such as Co2+, Ni2+, Mn2+, or
Mg2+ as cofactors for catalytic activity and thermal
stability. Members of this subfamily show similarity to
bacterial alanine racemase (AR), a fold type III
PLP-dependent enzyme which contains an N-terminal
PLP-binding TIM-barrel domain and a C-terminal
beta-sandwich domain. AR exists as homodimers with
active sites that lie at the interface between the TIM
barrel domain of one subunit and the beta-sandwich
domain of the other subunit. Based on its similarity to
AR, it is possible that low specificity D-TAs also form
dimers in solution. Experimental data show that the
monomeric form of low specificity D-TAs exhibit full
catalytic activity.
Length = 361
Score = 31.1 bits (71), Expect = 0.75
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 459 GIADIIIAKQRHGPTGTVTLAFQAEF--TRFSALSDS 493
G D+++A GP L ++ TRFSAL D
Sbjct: 75 GAPDVLLAYPLVGPNIERFLELAKKYPGTRFSALVDD 111
>gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing
factor (pNORF1) [RNA processing and modification].
Length = 935
Score = 30.7 bits (69), Expect = 0.95
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 216 LQRSDLIIIAGRPGMGKTSLATNIAYNVADAYK 248
LQR L +I G PG GKT + I Y++A +
Sbjct: 423 LQRP-LSLIQGPPGTGKTVTSATIVYHLARQHA 454
>gnl|CDD|31343 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 30.3 bits (68), Expect = 1.2
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 223 IIAGRPGMGKTSLATNIAYNVADAYKAEL 251
+ +G+ G GKT++A N+A + D YK L
Sbjct: 6 VASGKGGTGKTTVAANLAVLLGDKYKLVL 34
>gnl|CDD|36271 KOG1053, KOG1053, KOG1053, Glutamate-gated NMDA-type ion channel
receptor subunit GRIN2A and related subunits [Inorganic
ion transport and metabolism, Amino acid transport and
metabolism, Signal transduction mechanisms].
Length = 1258
Score = 30.0 bits (67), Expect = 1.4
Identities = 18/86 (20%), Positives = 39/86 (45%), Gaps = 7/86 (8%)
Query: 368 EITGITMALKALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVI 427
+ + L ++ + +IPII++ + V K + L+ SIEQ A V+L ++
Sbjct: 111 DTEAVAQILDFISSQTHIPIISIHGGAAMVLT--PKDLGSTFLQLGPSIEQQAQVMLKIL 168
Query: 428 RD-EYY----IRNKEPTNKDDILAYT 448
+ ++Y + + P N+ +
Sbjct: 169 EEYDWYNFSLVTTQFPGNRTFVSLIR 194
>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 = 29.9 bits (68), Expect = 1.6
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 222 IIIAGRPGMGKTSLATNIAYNVADAYK 248
I + G PG GK++LA +A + D
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLDHLG 27
>gnl|CDD|107328 cd06333, PBP1_ABC-type_HAAT_like, Type I periplasmic binding
component of ABC (ATPase Binding Cassette)-type
transport systems that are predicted to be involved in
uptake of amino acids. This subgroup includes the type
I periplasmic binding component of ABC (ATPase Binding
Cassette)-type transport systems that are predicted to
be involved in uptake of amino acids. Members of this
subgroup are sequence-similar to members of the family
of ABC-type hydrophobic amino acid transporters (HAAT),
such as leucine-isoleucine-valine-binding protein
(LIVBP); their ligand specificity has not been
determined experimentally, however.
Length = 312
Score = 29.8 bits (68), Expect = 1.9
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 5/38 (13%)
Query: 359 KKIEENRVLEI-----TGITMALKALAKELNIPIIALS 391
K IEE++V I T TMA+ +A+E P+I+L+
Sbjct: 60 KLIEEDKVDAIIGPSTTPATMAVAPVAEEAKTPMISLA 97
>gnl|CDD|31805 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide transport
and metabolism].
Length = 179
Score = 29.4 bits (66), Expect = 2.2
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 222 IIIAGRPGMGKTSLATNIA-------YNVADAYKAELQTDGS 256
I I GRPG+GKT+L IA Y V E++ G
Sbjct: 8 IFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVREGGK 49
>gnl|CDD|36647 KOG1434, KOG1434, KOG1434, Meiotic recombination protein Dmc1
[Energy production and conversion, Replication,
recombination and repair].
Length = 335
Score = 29.6 bits (66), Expect = 2.3
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 198 RLAGVSTGIQTLDKQMGG-LQRSDLIIIAGRPGMGKTSLATNIAYNV 243
+ ++TG LD +GG + + I G GKT L+ + V
Sbjct: 93 TVGSITTGSSALDDILGGGIPSMSITEIFGEFRCGKTQLSHTLCVTV 139
>gnl|CDD|32257 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 29.1 bits (65), Expect = 2.8
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 215 GLQRSDLIIIAGRPGMGKTSLATNIAYN 242
++R +I+I G G+GK+++A +A
Sbjct: 85 KMKRPLIILIGGASGVGKSTIAGELARR 112
>gnl|CDD|33644 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 29.2 bits (65), Expect = 3.1
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 222 IIIAGRPGMGKTSLATNIAYNVADAYKAEL 251
+I G P +GKT+L +IA ++D L
Sbjct: 140 TLIIGPPQVGKTTLLRDIARLLSDGINQFL 169
>gnl|CDD|147593 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus.
The RuvB protein makes up part of the RuvABC revolvasome
which catalyses the resolution of Holliday junctions
that arise during genetic recombination and DNA repair.
Branch migration is catalysed by the RuvB protein that
is targeted to the Holliday junction by the structure
specific RuvA protein. This family contains the
N-terminal region of the protein.
Length = 234
Score = 29.0 bits (66), Expect = 3.2
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 220 DLIIIAGRPGMGKTSLATNIA 240
D +++ G PG+GKT+LA IA
Sbjct: 51 DHVLLYGPPGLGKTTLANIIA 71
>gnl|CDD|144508 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 28.8 bits (65), Expect = 3.5
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 209 LDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYN 242
++K + + ++ I G G+GKT+LA I YN
Sbjct: 9 IEKLLEMSENLGVVGIVGMGGVGKTTLAKQI-YN 41
>gnl|CDD|32040 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 28.7 bits (64), Expect = 3.5
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 216 LQRSDLIIIAGRPGMGKTSLATNIA 240
+R++ I+IAG PG GK++ A +A
Sbjct: 260 EERAEGILIAGAPGAGKSTFAQALA 284
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases..
Length = 151
Score = 28.7 bits (64), Expect = 3.6
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 222 IIIAGRPGMGKTSLATNIAYNVADA 246
+++ G PG GKT+LA IA +
Sbjct: 22 LLLYGPPGTGKTTLARAIANELFRP 46
>gnl|CDD|30004 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear..
Length = 218
Score = 28.8 bits (64), Expect = 3.6
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 202 VSTGIQTLDKQMGG-LQRSDLIIIAGRPGMGKTSLATNIAYNVADAYK 248
+ TG + LD+ +GG ++R + + G PG GKT++A +A A K
Sbjct: 1 LPTGCKGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGK 48
>gnl|CDD|30917 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism].
Length = 218
Score = 28.7 bits (64), Expect = 4.0
Identities = 13/49 (26%), Positives = 23/49 (46%)
Query: 213 MGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTIN 261
M ++ +I IAG G GKT++A ++ + + D YK +
Sbjct: 2 MKKPEKVIIIGIAGGSGSGKTTVAKELSEQLGVEKVVVISLDDYYKDQS 50
>gnl|CDD|147726 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely related
to pfam00931.
Length = 165
Score = 28.8 bits (65), Expect = 4.0
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 220 DLIIIAGRPGMGKTSLATNIAY 241
+I+ G G GKT+L +A
Sbjct: 1 RTVILQGEAGSGKTTLLQKLAL 22
>gnl|CDD|38557 KOG3347, KOG3347, KOG3347, Predicted nucleotide kinase/nuclear
protein involved oxidative stress response [Nucleotide
transport and metabolism].
Length = 176
Score = 28.7 bits (64), Expect = 4.0
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 222 IIIAGRPGMGKTSLATNIA 240
I++ G PG GK++LA +A
Sbjct: 10 ILVTGTPGTGKSTLAERLA 28
>gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 28.6 bits (65), Expect = 4.2
Identities = 18/47 (38%), Positives = 20/47 (42%), Gaps = 13/47 (27%)
Query: 204 TGIQTLDKQMGGL------QRSDLIIIAGRPGMGKTSLATNIAYNVA 244
TGI+ +D L QR I I G G GKT L IA N
Sbjct: 1 TGIRAID----LLLPIGKGQR---IGIFGGSGTGKTVLLGMIARNAK 40
>gnl|CDD|132995 cd00218, GlcAT-I, Beta1,3-glucuronyltransferase I (GlcAT-I) is
involved in the initial steps of proteoglycan synthesis.
Beta1,3-glucuronyltransferase I (GlcAT-I) domain;
GlcAT-I is a Key enzyme involved in the initial steps of
proteoglycan synthesis. GlcAT-I catalyzes the transfer
of a glucuronic acid moiety from the uridine
diphosphate-glucuronic acid (UDP-GlcUA) to the common
linkage region of trisaccharide
Gal-beta-(1-3)-Gal-beta-(1-4)-Xyl of proteoglycans. The
enzyme has two subdomains that bind the donor and
acceptor substrate separately. The active site is
located at the cleft between both subdomains in which
the trisaccharide molecule is oriented perpendicular to
the UDP. This family has been classified as
Glycosyltransferase family 43 (GT-43).
Length = 223
Score = 28.4 bits (64), Expect = 4.3
Identities = 16/54 (29%), Positives = 19/54 (35%), Gaps = 11/54 (20%)
Query: 174 GFHTF-SDAMTVAIDMAGQAFN----RDGRLAGVSTGIQTLDKQMGGLQRSDLI 222
G+HT IDMAG AFN D A + G Q S +
Sbjct: 147 GWHTAWKPERPFPIDMAGFAFNSKLLWDPPRAVFPYSAKR------GYQESSFL 194
>gnl|CDD|32436 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 28.6 bits (64), Expect = 4.4
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 220 DLIIIAGRPGMGKTSLATNIAY 241
D +++ G PG+GKT+LA IA
Sbjct: 53 DHVLLFGPPGLGKTTLAHIIAN 74
>gnl|CDD|30814 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 28.2 bits (63), Expect = 5.0
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 4/35 (11%)
Query: 206 IQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIA 240
+Q L K++ G ++ + G PG+GKTSL +IA
Sbjct: 341 VQKLTKKLKG----PILCLVGPPGVGKTSLGKSIA 371
>gnl|CDD|31438 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 28.2 bits (63), Expect = 5.7
Identities = 14/51 (27%), Positives = 24/51 (47%)
Query: 208 TLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYK 258
L+ + G + ++I I G G+GKT+ +A + +E SYK
Sbjct: 356 KLEVEEGEIYDGEVIGILGPNGIGKTTFVKLLAGVIKPDEGSEEDLKVSYK 406
>gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of
proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion..
Length = 99
Score = 28.2 bits (62), Expect = 5.7
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 221 LIIIAGRPGMGKTSLATNIAYNVADA 246
+I++ G+ G+GKT+LA N+A +A
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKR 26
>gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265.
Length = 168
Score = 27.9 bits (63), Expect = 5.9
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 222 IIIAGRPGMGKTSLATNIA 240
I I G PG+GKT+L +
Sbjct: 2 IFITGPPGVGKTTLVKKVI 20
>gnl|CDD|30812 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 28.2 bits (62), Expect = 5.9
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 206 IQTLDKQMGGLQRSDL-----IIIAGRPGMGKTSLATNIA 240
I+T K+ ++ L +++ G PG GKT LA +A
Sbjct: 258 IETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVA 297
>gnl|CDD|144230 pfam00563, EAL, EAL domain. This domain is found in diverse
bacterial signaling proteins. It is called EAL after its
conserved residues. The EAL domain is a good candidate
for a diguanylate phosphodiesterase function. The domain
contains many conserved acidic residues that could
participate in metal binding and might form the
phosphodiesterase active site.
Length = 233
Score = 28.1 bits (63), Expect = 6.0
Identities = 32/155 (20%), Positives = 58/155 (37%), Gaps = 41/155 (26%)
Query: 272 MSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKL-----PLYIDQ--TG 324
+ +++ + E+T ++ + + + +L L +D TG
Sbjct: 96 LLDPSFLEALLALKQGGLPPSRLVLEITESALDEDLRLLEALARLRSLGFRLALDDFGTG 155
Query: 325 GISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITM-----ALKAL 379
S+S L+ L DYI KI+ + + +++ AL AL
Sbjct: 156 YSSLSYLSR-------------LPPDYI-------KIDRSFIKDLSDPESRALLRALIAL 195
Query: 380 AKELNIPIIALSQLSRQVENRDNKRPQLSDLRESG 414
A+EL I ++A VE + QL L+E G
Sbjct: 196 ARELGIKVVA-----EGVETEE----QLELLKELG 221
>gnl|CDD|73339 cd03110, Fer4_NifH_child, This protein family's function is unkown.
It contains nucleotide binding site. It uses NTP as
energy source to transfer electron or ion..
Length = 179
Score = 27.9 bits (62), Expect = 6.1
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 221 LIIIAGRPGMGKTSLATNIAY 241
+ +I+G+ G GKT++ +A
Sbjct: 2 IAVISGKGGTGKTTVTAALAA 22
>gnl|CDD|29984 cd00983, recA, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange..
Length = 325
Score = 27.8 bits (62), Expect = 6.3
Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 17/80 (21%)
Query: 194 NRDGRLAGVSTGIQTLDKQMG--GLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAEL 251
+ + + TG +LD +G G + +I I G GKT+LA + +A+A K
Sbjct: 28 DAVQDVEVIPTGSLSLDIALGIGGYPKGRIIEIYGPESSGKTTLALHA---IAEAQK--- 81
Query: 252 QTDGSYKTINGGIVGFYSLE 271
GG V F E
Sbjct: 82 ---------LGGTVAFIDAE 92
>gnl|CDD|39970 KOG4773, KOG4773, KOG4773, NADPH oxidase [Energy production and
conversion].
Length = 386
Score = 28.1 bits (62), Expect = 6.5
Identities = 18/101 (17%), Positives = 31/101 (30%), Gaps = 13/101 (12%)
Query: 335 ARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKALAKELNIPIIALSQLS 394
+ + R G L ++ + E R L ++K NI + +Q +
Sbjct: 119 SLPIGRLGGPGLRPFFFVSPYDSEDVPEAIRRLRPRTRKWKSDGVSKASNIVLGMAAQRA 178
Query: 395 RQVENRDNKRPQLSDLRESGSIE---QDADVVLFVIRDEYY 432
D + +E DV + RDE Y
Sbjct: 179 E----------ASFDFPGNSKLELNLVAGDVEFLLSRDEKY 209
>gnl|CDD|36498 KOG1284, KOG1284, KOG1284, Bifunctional GTP cyclohydrolase
II/3,4-dihydroxy-2butanone-4-phosphate synthase
[Coenzyme transport and metabolism].
Length = 357
Score = 28.0 bits (62), Expect = 6.8
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 376 LKALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRES 413
++ A E IP+I++ L R + R K +SD +
Sbjct: 243 CRSFAAEHAIPLISIEDLIRYLTKRPEKVENISDAPQP 280
>gnl|CDD|32701 COG2874, FlaH, Predicted ATPases involved in biogenesis of archaeal
flagella [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 235
Score = 27.9 bits (62), Expect = 6.9
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 196 DGRLAGVSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAY 241
+ + +G LDK++ GG+ LI+I G G GK+ L+ AY
Sbjct: 4 EELKKIIKSGNDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAY 50
>gnl|CDD|31413 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 27.9 bits (62), Expect = 7.0
Identities = 27/101 (26%), Positives = 43/101 (42%), Gaps = 19/101 (18%)
Query: 87 LSDQDMLGELTVP------QYLARLASEAVSIINTEDYGRIIYGLALR----------RT 130
L+ +D LT P QY A L +E V + T+D + I +A + R
Sbjct: 336 LTKEDFERILTEPKASLIKQYKALLKTEGVELEFTDDAIKRIAEIAYQVNEKTENIGARR 395
Query: 131 LITIGEEMV-NAAYEASLDKSPSIQIEEA--ERKLFHLAEN 168
L T+ E ++ + ++EA + I+ E KL L N
Sbjct: 396 LHTVLERLLEDISFEAPDMSGQKVTIDAEYVEEKLGDLVAN 436
>gnl|CDD|143797 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 28.0 bits (63), Expect = 7.2
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 222 IIIAGRPGMGKTSLATNIA 240
+++ G PG GKT+LA +A
Sbjct: 1 LLLYGPPGTGKTTLAKAVA 19
Score = 27.6 bits (62), Expect = 7.9
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 370 TGITMALKALAKELNIPIIALS 391
TG T KA+AKEL P I +S
Sbjct: 9 TGKTTLAKAVAKELGAPFIEIS 30
>gnl|CDD|177080 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 27.7 bits (62), Expect = 7.4
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 222 IIIAGRPGMGKTSLATNIAY 241
+++ G PG GKT LA IA
Sbjct: 219 VLLVGPPGTGKTLLAKAIAG 238
>gnl|CDD|29548 cd00431, cysteine_hydrolases, Cysteine hydrolases; This family
contains amidohydrolases, like CSHase
(N-carbamoylsarcosine amidohydrolase), involved in
creatine metabolism and nicotinamidase, converting
nicotinamide to nicotinic acid and ammonia in the
pyridine nucleotide cycle. It also contains
isochorismatase, an enzyme that catalyzes the conversion
of isochorismate to 2,3-dihydroxybenzoate and pyruvate,
via the hydrolysis of the vinyl ether bond, and other
related enzymes with unknown function..
Length = 161
Score = 27.6 bits (61), Expect = 7.6
Identities = 22/128 (17%), Positives = 42/128 (32%), Gaps = 20/128 (15%)
Query: 346 LLIVDYIQLMTTSKKIEENRVLEITGITMALKALAKELNIPIIALSQLSRQVENRDNKRP 405
LL+VD + E+ L A A+ IP+I + +
Sbjct: 2 LLVVDMQNDFVPGGGLLLPGADELVPNINRLLAAARAAGIPVIFTRDWHPPDDPEFAELL 61
Query: 406 QLSDLRESGSIEQDADVV--LFVIRDEYYIRNK-----EPTNKDDILAYTKWQEDLKRVK 458
+ + A++V L + D+ I T+ D++L R +
Sbjct: 62 WPPHCVKGT---EGAELVPELAPLPDDLVIEKTRYSAFYGTDLDELL----------RER 108
Query: 459 GIADIIIA 466
GI +++
Sbjct: 109 GIDTLVVC 116
>gnl|CDD|29225 cd01452, VWA_26S_proteasome_subunit, 26S proteasome plays a major
role in eukaryotic protein breakdown, especially for
ubiquitin-tagged proteins. It is an ATP-dependent
protease responsible for the bulk of non-lysosomal
proteolysis in eukaryotes, often using covalent
modification of proteins by ubiquitylation. It consists
of a 20S proteolytic core particle (CP) and a 19S
regulatory particle (RP). The CP is an ATP independent
peptidase consisting of hydrolyzing activities. One or
both ends of CP carry the RP that confers both ubiquitin
and ATP dependence to the 26S proteosome. The RP's
proposed functions include recognition of substrates and
translocation of these to CP for proteolysis. The RP can
dissociate into a stable lid and base subcomplexes. The
base is composed of three non-ATPase subunits (Rpn 1, 2
and 10). A single residue in the vWA domain of Rpn10 has
been implicated to be responsible for stabilizing the
lid-base association..
Length = 187
Score = 27.5 bits (61), Expect = 7.6
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 11/74 (14%)
Query: 301 PDYEKIVACSQVMQKLPLY--IDQTGGISMSQLATRARRLKRQRGLDLLIV------DYI 352
D KI++ + + + GI ++QLA + R+ K Q+ + V D
Sbjct: 67 NDQGKILSK---LHDVQPKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEEDEK 123
Query: 353 QLMTTSKKIEENRV 366
L+ +K++++N V
Sbjct: 124 DLVKLAKRLKKNNV 137
>gnl|CDD|30784 COG0435, ECM4, Predicted glutathione S-transferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 324
Score = 27.5 bits (61), Expect = 7.7
Identities = 26/123 (21%), Positives = 48/123 (39%), Gaps = 26/123 (21%)
Query: 86 FLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEMVNAAYEA 145
+D D G +TVP + +I+N E II M N+A++
Sbjct: 118 TRADPDYSGRVTVP---VLWDKKTQTIVNNE-SAEII--------------RMFNSAFDE 159
Query: 146 SLDKSPSI-------QIEEAERKLFHLAENGRYDGGFHTFSDAMTVAIDMAGQAFNR-DG 197
+ + +I+E + ++ NG Y GF T +A A+ +A ++ +
Sbjct: 160 FGASAVDLYPEALRTEIDELNKWIYDTVNNGVYKAGFATTQEAYEEAVKKLFEALDKLEQ 219
Query: 198 RLA 200
L+
Sbjct: 220 ILS 222
>gnl|CDD|35615 KOG0394, KOG0394, KOG0394, Ras-related GTPase [General function
prediction only].
Length = 210
Score = 27.6 bits (61), Expect = 7.8
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 213 MGGLQRSDL--IIIAGRPGMGKTSLATNIAYN 242
M L++ L +II G G+GKTSL
Sbjct: 1 MSSLRKRTLLKVIILGDSGVGKTSLMNQYVNK 32
>gnl|CDD|73396 cd04734, OYE_like_3_FMN, Old yellow enzyme (OYE)-related FMN
binding domain, group 3. Each monomer of OYE contains
FMN as a non-covalently bound cofactor, uses NADPH as a
reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Other members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase. One
member of this subgroup, the Sinorhizobium meliloti
stachydrine utilization protein stcD, has been idenified
as a putative N-methylproline demethylase..
Length = 343
Score = 27.5 bits (61), Expect = 8.7
Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 16/77 (20%)
Query: 58 EAIHQKIFEIMGKLVHMGKTANPVTVKTFLSDQDMLGEL---TVPQYLARLASEAVSIIN 114
EA+H IM +L H+G+ + D L L VP+ R +A+
Sbjct: 84 EAVHAHGAVIMIQLTHLGRRGD--------GDGSWLPPLAPSAVPEPRHRAVPKAME--- 132
Query: 115 TEDYGRII--YGLALRR 129
ED II + A RR
Sbjct: 133 EEDIEEIIAAFADAARR 149
>gnl|CDD|39755 KOG4555, KOG4555, KOG4555, TPR repeat-containing protein [Function
unknown].
Length = 175
Score = 27.4 bits (60), Expect = 9.1
Identities = 20/60 (33%), Positives = 24/60 (40%), Gaps = 9/60 (15%)
Query: 136 EEMVNAAYEASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVAIDMAGQAFNR 195
EE A +AS E E K LAE G DG F A+ +A + A NR
Sbjct: 33 EEPDTQAIKASR---------ELELKAIALAEAGDLDGALELFGQALCLAPERASAYNNR 83
>gnl|CDD|37215 KOG2004, KOG2004, KOG2004, Mitochondrial ATP-dependent protease
PIM1/LON [Posttranslational modification, protein
turnover, chaperones].
Length = 906
Score = 27.2 bits (60), Expect = 9.9
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 212 QMGGLQRSDLIIIAGRPGMGKTSLATNIA 240
++ G + ++ G PG+GKTS+A +IA
Sbjct: 431 KLRGSVQGKILCFVGPPGVGKTSIAKSIA 459
>gnl|CDD|107381 cd06386, PBP1_NPR_C_like, Ligand-binding domain of type C
natriuretic peptide receptor. Ligand-binding domain of
type C natriuretic peptide receptor (NPR-C). NPR-C is
found in atrial, mesentery, placenta, lung, kidney,
venous tissue, aortic smooth muscle, and aortic
endothelial cells. The affinity of NPR-C for natriuretic
peptides is ANP>CNP>BNP. The extracellular domain of
NPR-C is about 30% identical to NPR-A and NPR-B.
However, unlike the cyclase-linked receptors, it
contains only 37 intracellular amino acids and no
guanylyl cyclase activity. Major function of NPR-C is to
clear natriuretic peptides from the circulation or
extracellular surroundings through constitutive
receptor-mediated internalization and degradation.
Length = 387
Score = 27.5 bits (61), Expect = 9.9
Identities = 13/44 (29%), Positives = 20/44 (45%)
Query: 460 IADIIIAKQRHGPTGTVTLAFQAEFTRFSALSDSSYQTGEHFDS 503
I I++A R G T + F E S+ D S++ G+ D
Sbjct: 207 IRSIMLAAHRRGLTSGDYIFFNIELFNSSSYGDGSWKRGDKHDF 250
>gnl|CDD|29812 cd00733, GlyRS_alpha_core, Class II Glycyl-tRNA synthetase (GlyRS)
alpha subunit core catalytic domain. GlyRS functions as
a homodimer in eukaryotes, archaea and some bacteria and
as a heterotetramer in the remainder of prokaryotes and
in arabidopsis. It is responsible for the attachment of
glycine to the 3' OH group of ribose of the appropriate
tRNA. This domain is primarily responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. This alignment contains only
sequences from the GlyRS form which heterotetramerizes.
The homodimer form of GlyRS is in a different family of
class II aaRS. Class II assignment is based upon
structure and the presence of three characteristic
sequence motifs..
Length = 279
Score = 27.5 bits (61), Expect = 10.0
Identities = 30/137 (21%), Positives = 55/137 (40%), Gaps = 15/137 (10%)
Query: 211 KQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI---NGGIVGF 267
+Q+GG+ I+ G +A + V + Y E +Y + N
Sbjct: 142 QQVGGI---PCKPISVEITYGLERIAMYLQ-GVDNVYDIEWNKKITYGDVFLQNEIEQSV 197
Query: 268 YSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQTGGIS 327
Y+ E ++ + ++ E E + ++ L P Y+ ++ CS L D G IS
Sbjct: 198 YNFEYANVDMLFQLF-EDYEKEAKRLLELGLPLPAYDYVLKCSHTFNLL----DARGAIS 252
Query: 328 MSQLATRARRLKRQRGL 344
+++ R R + R R L
Sbjct: 253 VTE---RQRYILRIRNL 266
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
0.317 0.133 0.364
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,694,221
Number of extensions: 304382
Number of successful extensions: 1279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1260
Number of HSP's successfully gapped: 103
Length of query: 504
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 406
Effective length of database: 4,146,055
Effective search space: 1683298330
Effective search space used: 1683298330
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: 59 (26.5 bits)