RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14660
(375 letters)
>gnl|CDD|238729 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 = 310 bits (795), Expect = e-106
Identities = 127/189 (67%), Positives = 154/189 (81%), Gaps = 4/189 (2%)
Query: 1 MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMA-DSVE 59
MVLE+TMIC+DNS++MRNGD+ PTR QAQ DAVNL+C +KTRSNPENNVGL+ MA +S E
Sbjct: 1 MVLEATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNSPE 60
Query: 60 VLATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDL 119
VL TLT+D G+ILSKLH VQP G NF+TGI+IA LALKHRQ KN K RI+AFVGSP++
Sbjct: 61 VLVTLTNDQGKILSKLHDVQPKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEE 120
Query: 120 EERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHL 179
+E++L KLAKRLKK V+VDI++FGE NTE L FI +NGKD GSH+V+V G +L
Sbjct: 121 DEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDAVNGKD--GSHLVSVPPGENL 178
Query: 180 -SDALISSP 187
SDAL+SSP
Sbjct: 179 LSDALLSSP 187
>gnl|CDD|227477 COG5148, RPN10, 26S proteasome regulatory complex, subunit
RPN10/PSMD4 [Posttranslational modification, protein
turnover, chaperones].
Length = 243
Score = 208 bits (531), Expect = 8e-66
Identities = 109/241 (45%), Positives = 149/241 (61%), Gaps = 9/241 (3%)
Query: 1 MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMAD-SVE 59
MVLE+T++ +DNS+ +NGD+LPTR +AQ+DAV + K NPEN +GL+ +
Sbjct: 1 MVLEATVVLIDNSEASQNGDYLPTRFEAQKDAVESIFSKKFNDNPENTIGLIPLVQAQPN 60
Query: 60 VLATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDL 119
VL+T T G+IL+ LH ++ +G + M ++IA L LKHR K + RI+AFVGSP+
Sbjct: 61 VLSTPTKQRGKILTFLHDIRLHGGADIMRCLQIAQLILKHRDNKGQRQRIVAFVGSPIQE 120
Query: 120 EERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHL 179
E EL +LAK+LKK V +DI+ FG E N L FI N D SH+ P L
Sbjct: 121 SEDELIRLAKQLKKNNVAIDIIFFG-EAANMAGLFEFIDATNFSD--SSHLEVKPPNPEL 177
Query: 180 SDALI-SSPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRVSMEEQRARQESEARRAA 238
D ++ SPI QG G E+GVDPN DPELA ALR+SMEE++ RQE A++++
Sbjct: 178 LDRVLPFSPIGQGVVGDDL----QLEYGVDPNLDPELAEALRLSMEEEKKRQEVAAQKSS 233
Query: 239 E 239
E
Sbjct: 234 E 234
>gnl|CDD|214621 smart00327, VWA, von Willebrand factor (vWF) type A domain. VWA
domains in extracellular eukaryotic proteins mediate
adhesion via metal ion-dependent adhesion sites (MIDAS).
Intracellular VWA domains and homologues in prokaryotes
have recently been identified. The proposed VWA domains
in integrin beta subunits have recently been
substantiated using sequence-based methods.
Length = 175
Score = 65.9 bits (161), Expect = 7e-13
Identities = 31/153 (20%), Positives = 55/153 (35%), Gaps = 12/153 (7%)
Query: 7 MICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATL-- 64
+ +D S M R + ++ V + + VGL+ +D VL L
Sbjct: 3 VFLLDGSGSMG-----GNRFELAKEFVLKLVEQLDIGPDGDRVGLVTFSDDARVLFPLND 57
Query: 65 TSDVGRILSKLHQVQPNGNINFMTG--IRIAHLALKHRQGKNHKMR---IIAFVGSPVDL 119
+ +L L + G ++ A L + + + +I +
Sbjct: 58 SRSKDALLEALASLSYKLGGGTNLGAALQYALENLFSKSAGSRRGAPKVVILITDGESND 117
Query: 120 EERELTKLAKRLKKEKVNVDIVSFGEEVVNTEL 152
++L K AK LK+ V V +V G +V EL
Sbjct: 118 GPKDLLKAAKELKRSGVKVFVVGVGNDVDEEEL 150
>gnl|CDD|222192 pfam13519, VWA_2, von Willebrand factor type A domain.
Length = 172
Score = 61.2 bits (149), Expect = 3e-11
Identities = 37/163 (22%), Positives = 61/163 (37%), Gaps = 13/163 (7%)
Query: 5 STMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATL 64
+I +D S M D P+RL + A+ + P + VGL+A A S ++ L
Sbjct: 1 DLVIVLDVSGSMNATDLKPSRLTRAKAAIADL----LARLPGDRVGLIAFAGSAYLVLPL 56
Query: 65 TSDVGRILSKLHQVQ----PNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLE 120
T D + + L + P G N + LAL+ G I + +
Sbjct: 57 TDDRAALAAALPALSPRIMPGGGTNLAAALA---LALRLLAGAGGGSGAIVLITD--GED 111
Query: 121 ERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGK 163
L + A LK+ V V ++ G + + L G+
Sbjct: 112 TPSLLEAASALKQAGVRVYVLGVGTDEGAEDALQRLAKATGGR 154
>gnl|CDD|238119 cd00198, vWFA, Von Willebrand factor type A (vWA) domain was
originally found in the blood coagulation protein von
Willebrand factor (vWF). Typically, the vWA domain is
made up of approximately 200 amino acid residues folded
into a classic a/b para-rossmann type of fold. The vWA
domain, since its discovery, has drawn great interest
because of its widespread occurrence and its involvement
in a wide variety of important cellular functions. These
include basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains.
Length = 161
Score = 58.0 bits (140), Expect = 3e-10
Identities = 33/151 (21%), Positives = 61/151 (40%), Gaps = 11/151 (7%)
Query: 7 MICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLT- 65
+ +D S M +L ++A+ + S + S P + VGL+ + V+ LT
Sbjct: 4 VFLLDVSGSMG-----GEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARVVLPLTT 58
Query: 66 ----SDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEE 121
+D+ + L + G N +R+A LK + N + II +
Sbjct: 59 DTDKADLLEAIDALKK-GLGGGTNIGAALRLALELLKSAKRPNARRVIILLTDGEPNDGP 117
Query: 122 RELTKLAKRLKKEKVNVDIVSFGEEVVNTEL 152
L + A+ L+K + V + G++ EL
Sbjct: 118 ELLAEAARELRKLGITVYTIGIGDDANEDEL 148
>gnl|CDD|238730 cd01453, vWA_transcription_factor_IIH_type, Transcription factors
IIH type: TFIIH is a multiprotein complex that is one of
the five general transcription factors that binds RNA
polymerase II holoenzyme. Orthologues of these genes are
found in all completed eukaryotic genomes and all these
proteins contain a VWA domain. The p44 subunit of TFIIH
functions as a DNA helicase in RNA polymerase II
transcription initiation and DNA repair, and its
transcriptional activity is dependent on its C-terminal
Zn-binding domains. The function of the vWA domain is
unclear, but may be involved in complex assembly. The
MIDAS motif is not conserved in this sub-group.
Length = 183
Score = 48.1 bits (115), Expect = 1e-06
Identities = 32/143 (22%), Positives = 62/143 (43%), Gaps = 3/143 (2%)
Query: 7 MICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADS-VEVLATLT 65
+I +D S M D P+RL + L NP + +G++++ + E L LT
Sbjct: 7 IIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLT 66
Query: 66 SDVGRILSKLHQVQ-PNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEEREL 124
+ + + L + +G + G+ +A +LKH + +I F S + +
Sbjct: 67 GNPRKHIQALKTARECSGEPSLQNGLEMALESLKHMPSHGSREVLIIF-SSLSTCDPGNI 125
Query: 125 TKLAKRLKKEKVNVDIVSFGEEV 147
+ +LKKE + V ++ E+
Sbjct: 126 YETIDKLKKENIRVSVIGLSAEM 148
>gnl|CDD|190848 pfam04056, Ssl1, Ssl1-like. Ssl1-like proteins are 40kDa subunits
of the Transcription factor II H complex.
Length = 193
Score = 42.8 bits (101), Expect = 8e-05
Identities = 31/142 (21%), Positives = 54/142 (38%), Gaps = 5/142 (3%)
Query: 10 VDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDVG 69
+D S M D P+R + NP + +GL+ D T +
Sbjct: 2 LDCSRSMEEKDLRPSRFACTIKYLETFVEEFFDQNPISQIGLITCKDGRAHRLTDLTGNP 61
Query: 70 RI----LSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELT 125
R+ L L + + G+ + + +A +LKH + +I F GS + ++
Sbjct: 62 RVHIKALKSLREAECGGDPSLQNALELARASLKHVPSHGSREVLIIF-GSLSTCDPGDIY 120
Query: 126 KLAKRLKKEKVNVDIVSFGEEV 147
LKKEK+ ++ EV
Sbjct: 121 STIDTLKKEKIRCSVIGLSAEV 142
>gnl|CDD|227480 COG5151, SSL1, RNA polymerase II transcription
initiation/nucleotide excision repair factor TFIIH,
subunit SSL1 [Transcription / DNA replication,
recombination, and repair].
Length = 421
Score = 41.5 bits (97), Expect = 6e-04
Identities = 29/152 (19%), Positives = 58/152 (38%), Gaps = 11/152 (7%)
Query: 2 VLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVL 61
++ + +D S+ M DFLPTR NP + + ++++ D
Sbjct: 86 IIRHLHLILDVSEAMDESDFLPTRRANVIKYAEGFVPEFFSQNPISQLSIISIRD---GC 142
Query: 62 ATLTSDV-GRILSKLHQV----QPNGNINFMTGIRIAHLALKHRQGKNHKMR-IIAFVGS 115
A TS + G + + Q+ +GN + + +A + L H R ++ GS
Sbjct: 143 AKYTSSMDGNPQAHIGQLKSKRDCSGNFSLQNALEMARIELMKN--TMHGTREVLIIFGS 200
Query: 116 PVDLEERELTKLAKRLKKEKVNVDIVSFGEEV 147
+ ++ + +L + V + EV
Sbjct: 201 TSTRDPGDIAETIDKLVAYNIRVHFIGLCAEV 232
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 39.5 bits (93), Expect = 0.002
Identities = 38/149 (25%), Positives = 60/149 (40%), Gaps = 12/149 (8%)
Query: 223 MEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPD-FAT 281
+E ++A +E+ ++AAE + D A +A K A G +PD A
Sbjct: 462 LEREKAAREARHKKAAEARAAKDKDAVAAALARVKAKKAAATQPIVIKA--GARPDNSAV 519
Query: 282 MTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVLE 341
+ E + + Q AA+ K A AAA AKA+ AA + E
Sbjct: 520 IAAREARKAQARARQAEKQAAAAADPKKAAVAAAIARAKAK---------KAAQQAANAE 570
Query: 342 NLPGVDPQSAEVRHALSSSAEKPAKKKDE 370
VDP+ A V A++ + K A ++
Sbjct: 571 AEEEVDPKKAAVAAAIARAKAKKAAQQAA 599
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 37.2 bits (86), Expect = 0.014
Identities = 48/204 (23%), Positives = 62/204 (30%), Gaps = 23/204 (11%)
Query: 162 GKDGSGSHMVTVAVGPHLSDALISSPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRV 221
G+ G G+ T A P A P A AP + P P A A R
Sbjct: 366 GQSGGGAGPATAAAAPVAQPA----PAAAAPAAAAPAPAAP---PAAPAAAPAAAAAARA 418
Query: 222 SMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFAT 281
R + AA + A + P P A A AA P
Sbjct: 419 VAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRP------- 471
Query: 282 MTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVLE 341
A + PAA+ + A EE E DAA V E
Sbjct: 472 -------VAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAE 524
Query: 342 NLPGVDPQSAEVRHALSSSAEKPA 365
++P DP +A+ A + A PA
Sbjct: 525 SIP--DPATADPDDAFETLAPAPA 546
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 36.9 bits (86), Expect = 0.016
Identities = 31/149 (20%), Positives = 42/149 (28%), Gaps = 9/149 (6%)
Query: 191 GEDGAGGAPGSSYEFGVDPNEDPELALALRVSMEEQRARQESEARRAAEGASGADTSASS 250
G P D A A + A A GA+ A + +
Sbjct: 646 GVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAP 705
Query: 251 AVPKPTAEAKDAPGDMATAAHPVGGQPDFATM-----TEEEQIAFAMQMSMQDTQEPAAS 305
A P +A D AA A E + Q PA
Sbjct: 706 AATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAP- 764
Query: 306 SSKAPASAAASEEAKAEPMDTDEMVNDAA 334
APA+A A+ + P + +EM D A
Sbjct: 765 ---APAAAPAAAPPPSPPSEEEEMAEDDA 790
Score = 32.7 bits (75), Expect = 0.41
Identities = 19/109 (17%), Positives = 31/109 (28%), Gaps = 4/109 (3%)
Query: 227 RARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEE 286
+ A AA + A + P P G+ P +
Sbjct: 409 APAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAP 468
Query: 287 QIAFAMQMSMQDTQEPAASSSKAP--ASAAASEEAKAEPMDTDEMVNDA 333
A A + + PA ++ AP A AA + A D + +
Sbjct: 469 APAAAPEPTAA--PAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRER 515
Score = 31.5 bits (72), Expect = 0.92
Identities = 31/126 (24%), Positives = 39/126 (30%), Gaps = 13/126 (10%)
Query: 211 EDPELALALRVSMEEQR-------------ARQESEARRAAEGASGADTSASSAVPKPTA 257
D E L R+ E+R A + A AA A A A++A P P A
Sbjct: 368 SDDERGLLARLERLERRLGVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAA 427
Query: 258 EAKDAPGDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASE 317
+ AP A P A A A A + APA A +
Sbjct: 428 APQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAA 487
Query: 318 EAKAEP 323
A A
Sbjct: 488 PAPAAA 493
>gnl|CDD|145783 pfam02809, UIM, Ubiquitin interaction motif. This motif is called
the ubiquitin interaction motif. One of the proteins
containing this motif is a receptor for
poly-ubiquitination chains for the proteasome. This
motif has a pattern of conservation characteristic of an
alpha helix.
Length = 18
Score = 31.6 bits (74), Expect = 0.026
Identities = 6/17 (35%), Positives = 13/17 (76%)
Query: 282 MTEEEQIAFAMQMSMQD 298
M+EEE + A+ +S+++
Sbjct: 1 MSEEEDLQLALALSLEE 17
Score = 30.9 bits (72), Expect = 0.047
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 209 PNEDPELALALRVSMEEQ 226
+E+ +L LAL +S+EE
Sbjct: 1 MSEEEDLQLALALSLEEA 18
>gnl|CDD|181613 PRK09019, PRK09019, translation initiation factor Sui1; Validated.
Length = 108
Score = 33.8 bits (78), Expect = 0.026
Identities = 29/82 (35%), Positives = 39/82 (47%), Gaps = 15/82 (18%)
Query: 54 MADSVEVLATLTSDVGRILS-KLHQVQPNGNINFMTGI-RIAHLALKHRQGKNHKMRIIA 111
M+DS L T D GRI K +P G+ GI RI RQ K + +
Sbjct: 1 MSDSNSRLVYST-DTGRIDEEKAKPERPKGD-----GIVRI------QRQTSGRKGKGVC 48
Query: 112 FVGSPVDLEERELTKLAKRLKK 133
+ + +DL++ EL KLA LKK
Sbjct: 49 LI-TGLDLDDAELKKLAAELKK 69
>gnl|CDD|184242 PRK13685, PRK13685, hypothetical protein; Provisional.
Length = 326
Score = 35.1 bits (81), Expect = 0.053
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 7 MICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTS 66
M+ +D S MR D P RL A Q+A T P N+GL+A A + VL + T+
Sbjct: 92 MLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELT---PGINLGLIAFAGTATVLVSPTT 148
Query: 67 D 67
+
Sbjct: 149 N 149
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 35.2 bits (81), Expect = 0.064
Identities = 17/101 (16%), Positives = 30/101 (29%)
Query: 228 ARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQ 287
R E+ A A+ ++ P +A + QP + +
Sbjct: 421 TRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAP 480
Query: 288 IAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDE 328
+ A + + AA+ S A +A A A D
Sbjct: 481 ASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDA 521
Score = 32.9 bits (75), Expect = 0.35
Identities = 26/130 (20%), Positives = 44/130 (33%), Gaps = 14/130 (10%)
Query: 195 AGGAPGSSYEFGVDPNEDP---ELALALRVSMEEQRARQESEARRAAEGASGADTSASSA 251
A AP ++ + G D + R S + + ++++ + AS + A
Sbjct: 428 AAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPD 487
Query: 252 VPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPA 311
A AP AA P P A+ + P A ++ P
Sbjct: 488 AAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPA-----------AAAPPAPEARPPT 536
Query: 312 SAAASEEAKA 321
AAA+ A+A
Sbjct: 537 PAAAAPAARA 546
Score = 32.5 bits (74), Expect = 0.45
Identities = 23/97 (23%), Positives = 34/97 (35%), Gaps = 3/97 (3%)
Query: 228 ARQESEARRAAEGASGADTSASSAVPKPTAE-AKDAPGDMATAAHPVGGQPDFATMTEEE 286
++ AR +A+ + A + A DAP D A P P AT
Sbjct: 449 VPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVP 508
Query: 287 QIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEP 323
S +D PAA++ AP + + A A
Sbjct: 509 DARAPAAASRED--APAAAAPPAPEARPPTPAAAAPA 543
Score = 31.4 bits (71), Expect = 0.89
Identities = 37/180 (20%), Positives = 50/180 (27%), Gaps = 12/180 (6%)
Query: 194 GAGGAPGSSYEFGVD---PNEDPELALALRVSMEEQRARQESEARRAAEGASGADTSASS 250
GGAPG V P A A+ S A A + A +A+
Sbjct: 363 TGGGAPGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATR 422
Query: 251 AVPKPTAEAKDAPGDMATAAHPV-----GGQPDFATMTEEEQIAFAMQMSMQDTQEPAAS 305
A P A A A D A A+ A + + AS
Sbjct: 423 AEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPAS 482
Query: 306 SSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVLENLPGVDPQSAEVRHALSSSAEKPA 365
+ A+ + A A T V DA + D +A A + PA
Sbjct: 483 DAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASRE----DAPAAAAPPAPEARPPTPA 538
>gnl|CDD|238742 cd01465, vWA_subgroup, VWA subgroup: Von Willebrand factor type A
(vWA) domain was originally found in the blood
coagulation protein von Willebrand factor (vWF).
Typically, the vWA domain is made up of approximately
200 amino acid residues folded into a classic a/b
para-rossmann type of fold. The vWA domain, since its
discovery, has drawn great interest because of its
widespread occurrence and its involvement in a wide
variety of important cellular functions. These include
basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains. Not much is known about the function of the VWA
domain in these proteins. The members do have a
conserved MIDAS motif. The biochemical function however
is not known.
Length = 170
Score = 33.8 bits (78), Expect = 0.071
Identities = 27/145 (18%), Positives = 57/145 (39%), Gaps = 19/145 (13%)
Query: 10 VDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVL--ATLTSD 67
+D S M G LP A + V+ + P++ + ++ + E + AT D
Sbjct: 7 IDRSGSMD-GPKLPLVKSALKLLVD-------QLRPDDRLAIVTYDGAAETVLPATPVRD 58
Query: 68 VGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRII------AFVGSPVDLEE 121
IL+ + ++ G+ GI++ + + RI+ VG +
Sbjct: 59 KAAILAAIDRLTAGGSTAGGAGIQLGYQEAQKHFVPGGVNRILLATDGDFNVGET---DP 115
Query: 122 RELTKLAKRLKKEKVNVDIVSFGEE 146
EL +L + ++ + + + FG+
Sbjct: 116 DELARLVAQKRESGITLSTLGFGDN 140
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 34.6 bits (80), Expect = 0.098
Identities = 28/164 (17%), Positives = 44/164 (26%), Gaps = 8/164 (4%)
Query: 207 VDPNEDPELALALRVSMEEQRARQESEARRAAEGASGADTSASSAV---PKPTAEAKDAP 263
V+ + E V E A A + A+ V P+P
Sbjct: 855 VEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVET 914
Query: 264 GDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEP 323
A PV QP + E +A A +++ EP A + E
Sbjct: 915 THPEVIAAPVTEQPQ---VITESDVAVAQEVAEHA--EPVVEPQDETADIEEAAETAEVV 969
Query: 324 MDTDEMVNDAAFLQSVLENLPGVDPQSAEVRHALSSSAEKPAKK 367
+ E+V A + E A + E +
Sbjct: 970 VAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEATVEH 1013
Score = 30.0 bits (68), Expect = 2.3
Identities = 21/153 (13%), Positives = 40/153 (26%), Gaps = 7/153 (4%)
Query: 221 VSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFA 280
V +EEQR +E + + A + + A P +
Sbjct: 853 VQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVV 912
Query: 281 TMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVL 340
T E IA E +++ + A AEP+ + +
Sbjct: 913 ETTHPEVIA-------APVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAET 965
Query: 341 ENLPGVDPQSAEVRHALSSSAEKPAKKKDEKKE 373
+ +P+ A + + E
Sbjct: 966 AEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVE 998
>gnl|CDD|220840 pfam10667, DUF2486, Protein of unknown function (DUF2486). This
family is made up of members from various Burkholderia
spp. The function is unknown.
Length = 245
Score = 33.7 bits (77), Expect = 0.100
Identities = 37/170 (21%), Positives = 53/170 (31%), Gaps = 26/170 (15%)
Query: 177 PHLSDALISSPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRVSMEEQRARQESEARR 236
P L+D L+ + + A G ++ E L ++ ++A +
Sbjct: 10 PTLTDVLVPGHPVPARSSSADAAGP-------HDDAAEPVLTDQIVPGAEQAASAAPVHA 62
Query: 237 AAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQ----PDFATMTEEEQIAFAM 292
A E + + A VP P A PGD A P A M A A
Sbjct: 63 AREATADPEFVAVEPVPTPHVPAVALPGDTDAPAEPGAAPHVVAERAAAMQAPLPSALAA 122
Query: 293 QMS---------------MQDTQEPAASSSKAPASAAASEEAKAEPMDTD 327
D PAA + PA+A A+ A A D D
Sbjct: 123 DDPQAPPAGATAADAGDAAPDATPPAAGDASPPAAAQAAASAAAALTDLD 172
>gnl|CDD|165527 PHA03269, PHA03269, envelope glycoprotein C; Provisional.
Length = 566
Score = 33.5 bits (76), Expect = 0.16
Identities = 30/124 (24%), Positives = 45/124 (36%), Gaps = 10/124 (8%)
Query: 185 SSPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRVSMEEQ--RARQESEARRAAEGAS 242
P A AP + + P+LA A + E+ A +A A +
Sbjct: 40 PDPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPA 99
Query: 243 GADTSASSAVPKP------TAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAFAMQMSM 296
A A++ P A+A +AP D T+A +PD A T+ FA SM
Sbjct: 100 VAPQLAAAPKPDAAEAFTSAAQAHEAPADAGTSA--ASKKPDPAAHTQHSPPPFAYTRSM 157
Query: 297 QDTQ 300
+
Sbjct: 158 EHIA 161
Score = 28.2 bits (62), Expect = 8.0
Identities = 37/156 (23%), Positives = 50/156 (32%), Gaps = 29/156 (18%)
Query: 150 TELLNTFISTLNGKDGSGSHMVTVAVGPHLSDALISSPIIQGEDGAGG------APGSSY 203
LNT I + + A PH + + P + A AP +
Sbjct: 19 IANLNTNIPIPELHTSAATQKPDPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAA 78
Query: 204 EFGVDP----------NEDPELALALRVSMEEQRARQESEARRAAEGASGADTSASSAVP 253
DP DP +A L + + A + A +A E + A TSA+S P
Sbjct: 79 SEKFDPAPAPHQAASRAPDPAVAPQLAAAPKPDAAEAFTSAAQAHEAPADAGTSAASKKP 138
Query: 254 KPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIA 289
P AAH P FA E IA
Sbjct: 139 DP-------------AAHTQHSPPPFAYTRSMEHIA 161
>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase;
Reviewed.
Length = 460
Score = 33.8 bits (77), Expect = 0.16
Identities = 33/165 (20%), Positives = 51/165 (30%), Gaps = 18/165 (10%)
Query: 211 EDPELALALRVSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAA 270
E P ALR S + E+ R AE A+ A SA+SAV P + D A
Sbjct: 280 EAPG---ALRGS---EYVVDEALEREPAELAAAAVASAASAVG-PVGPGEPNQPDDVAEA 332
Query: 271 HPVGGQPDFATMTEEEQIAFAMQM-----SMQDTQEPAASSSKAPASAAASEEAKAEPMD 325
+ E + A + ++++T E + + +A A
Sbjct: 333 VKAEVAEVTDEVAAESVVQVADRDGESTPAVEETSEADI---EREQPGDLAGQAPAAHQV 389
Query: 326 TDEMVNDAAFLQSVLENLPGVDPQSAEVRHALSSSAEKPAKKKDE 370
E A+ L E ++ K DE
Sbjct: 390 DAE---AASAAPEEPAALASEAHDETEPEVPEKAAPIPDPAKPDE 431
Score = 30.3 bits (68), Expect = 1.9
Identities = 25/169 (14%), Positives = 41/169 (24%), Gaps = 17/169 (10%)
Query: 172 TVAVGPHLSDALISSPIIQGEDG---AGGAPGSSYEFGVDPNEDPELALALRVSMEEQRA 228
+A S A P+ GE + V E + + E
Sbjct: 302 ELAAAAVASAASAVGPVGPGEPNQPDDVAEAVKAEVAEVTDEVAAESVVQVADRDGESTP 361
Query: 229 RQESEARRAAEGASGADTSA-SSAVPKPTAE-AKDAPGDMAT--AAHPVGGQPDFATMTE 284
E + E D + + A + AE A AP + A + +P+
Sbjct: 362 AVEETSEADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEKAA 421
Query: 285 EEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDA 333
D +P + P A + D
Sbjct: 422 PI----------PDPAKPDELAVAGPGDDPAEPDGIRRQDDFSSRRRRW 460
>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed.
Length = 1228
Score = 33.7 bits (78), Expect = 0.20
Identities = 19/83 (22%), Positives = 25/83 (30%), Gaps = 14/83 (16%)
Query: 241 ASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQ 300
S A +A++A A A A A P P
Sbjct: 39 GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPA----AAAPAAPPK--------- 85
Query: 301 EPAASSSKAPASAAASEEAKAEP 323
PAA+++ A A AA A A
Sbjct: 86 -PAAAAAAAAAPAAPPAAAAAAA 107
>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated.
Length = 430
Score = 33.0 bits (75), Expect = 0.24
Identities = 27/121 (22%), Positives = 45/121 (37%), Gaps = 9/121 (7%)
Query: 214 ELALALRVSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPV 273
E A A + +A+ + A++ EG +A A A A A A
Sbjct: 89 EKAKAKAKAAAAAKAKAAALAKQKREGTEEVTEEEKAAAKAKAAAAAKAKA-AALAKQKR 147
Query: 274 GGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDA 333
G + EE A + AA+++KA A+A A ++A T+E+ +
Sbjct: 148 EGTEEVTEEEEETDKEKA--------KAKAAAAAKAKAAALAKQKAAEAGEGTEEVTEEE 199
Query: 334 A 334
Sbjct: 200 K 200
Score = 30.3 bits (68), Expect = 1.6
Identities = 30/130 (23%), Positives = 50/130 (38%), Gaps = 5/130 (3%)
Query: 204 EFGVDPNEDPELALALRVSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAP 263
G + + E A A + +A+ + A++ EG T K A+AK A
Sbjct: 113 REGTEEVTEEEKAAAKAKAAAAAKAKAAALAKQKREGTEEV-TEEEEETDKEKAKAKAAA 171
Query: 264 GDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEP 323
A AA + A EE + + AA+++KA A+A A ++A
Sbjct: 172 AAKAKAAALAKQKAAEAGEGTEE----VTEEEKAKAKAKAAAAAKAKAAALAKQKASQGN 227
Query: 324 MDTDEMVNDA 333
D+ + A
Sbjct: 228 GDSGDEDAKA 237
Score = 28.4 bits (63), Expect = 6.5
Identities = 35/165 (21%), Positives = 60/165 (36%), Gaps = 27/165 (16%)
Query: 209 PNEDPELALALRVSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMAT 268
N+D + A R + +A+ + A++ EG + K A+AK A A
Sbjct: 50 KNDDMTIEEAKRRAAAAAKAKAAALAKQKREGTEEV-----TEEEKAKAKAKAAAAAKAK 104
Query: 269 AAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDE 328
AA A+ ++ E KA A A A+ AKA+ +
Sbjct: 105 AA--------------------ALAKQKREGTEEVTEEEKAAAKAKAAAAAKAKAAALAK 144
Query: 329 MVNDAAFLQSVLENLPGVDPQSAEVRHALSSSAEKPAKKKDEKKE 373
+ + V E D + A+ + A ++ A+ A K + E
Sbjct: 145 QKREGT--EEVTEEEEETDKEKAKAKAAAAAKAKAAALAKQKAAE 187
>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 33.0 bits (76), Expect = 0.24
Identities = 21/129 (16%), Positives = 35/129 (27%), Gaps = 12/129 (9%)
Query: 213 PELALALRVSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHP 272
P A A E E A V + A A A A
Sbjct: 64 PPPAAAPAAVSRPAAPAAEPAPWLV-EHAKRLTAQREQLVARAAAPAAPEAQAPAAPAER 122
Query: 273 VGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVND 332
+ + A + A A+ A + +A+ E + D ++ +
Sbjct: 123 AAAENAARRLARAAAAA-----------PRPRVPADAAAAVADAVKARIERIVNDTVMQE 171
Query: 333 AAFLQSVLE 341
L+ +LE
Sbjct: 172 LRSLRGMLE 180
>gnl|CDD|238744 cd01467, vWA_BatA_type, VWA BatA type: Von Willebrand factor type
A (vWA) domain was originally found in the blood
coagulation protein von Willebrand factor (vWF).
Typically, the vWA domain is made up of approximately
200 amino acid residues folded into a classic a/b
para-rossmann type of fold. The vWA domain, since its
discovery, has drawn great interest because of its
widespread occurrence and its involvement in a wide
variety of important cellular functions. These include
basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses. In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen
by the various molecules it complexes with. Ligand
binding in most cases is mediated by the presence of a
metal ion dependent adhesion site termed as the MIDAS
motif that is a characteristic feature of most, if not
all A domains. Members of this subgroup are bacterial
in origin. They are typified by the presence of a MIDAS
motif.
Length = 180
Score = 32.3 bits (74), Expect = 0.25
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 7 MICVDNSDFMRNGDF-LPTRLQAQQDAV-NLVCHSKTRSNPENNVGLLAMADSVEVLATL 64
MI +D S M DF P+RL+A ++ + + + R N + +GL+ A + A L
Sbjct: 6 MIALDVSGSMLAQDFVKPSRLEAAKEVLSDFI---DRREN--DRIGLVVFAGAAFTQAPL 60
Query: 65 TSDVGRILSKLHQVQP 80
T D + L ++
Sbjct: 61 TLDRESLKELLEDIKI 76
>gnl|CDD|222790 PHA00430, PHA00430, tail fiber protein.
Length = 568
Score = 32.9 bits (75), Expect = 0.28
Identities = 25/105 (23%), Positives = 42/105 (40%), Gaps = 6/105 (5%)
Query: 218 ALRVSMEEQRARQESE-ARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQ 276
A E R+R E++ AR AE + S A T + + + A+ G
Sbjct: 161 AWNARNEANRSRNEADRARNQAERF----NNESGASATNTKQWRSEADGSNSEANRFKGY 216
Query: 277 PDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKA 321
D T + E A S ++ ++KA ASA+A+ ++
Sbjct: 217 ADSMTSSVEAAKGQAES-SSKEANTAGDYATKAAASASAAHASEV 260
Score = 30.6 bits (69), Expect = 1.4
Identities = 25/101 (24%), Positives = 36/101 (35%), Gaps = 6/101 (5%)
Query: 218 ALRVSMEEQRARQESEARRAAEGASGADTSAS-SAVPKPTAEAKDAPGDMATAAHPVGGQ 276
A R E RAR ++E GAS +T S +EA G + V
Sbjct: 168 ANRSRNEADRARNQAERFNNESGASATNTKQWRSEADGSNSEANRFKGYADSMTSSVE-- 225
Query: 277 PDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASE 317
A + E + + + AAS+S A AS +
Sbjct: 226 ---AAKGQAESSSKEANTAGDYATKAAASASAAHASEVNAA 263
>gnl|CDD|197845 smart00726, UIM, Ubiquitin-interacting motif. Present in
proteasome subunit S5a and other ubiquitin-associated
proteins.
Length = 20
Score = 28.6 bits (66), Expect = 0.35
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 210 NEDPELALALRVSMEEQRAR 229
+ED +L AL +S++E
Sbjct: 1 DEDEDLQRALELSLQEAEES 20
Score = 26.3 bits (60), Expect = 1.8
Identities = 6/19 (31%), Positives = 14/19 (73%)
Query: 284 EEEQIAFAMQMSMQDTQEP 302
E+E + A+++S+Q+ +E
Sbjct: 2 EDEDLQRALELSLQEAEES 20
>gnl|CDD|114299 pfam05568, ASFV_J13L, African swine fever virus J13L protein. This
family consists of several African swine fever virus
J13L proteins.
Length = 189
Score = 31.8 bits (71), Expect = 0.36
Identities = 33/102 (32%), Positives = 43/102 (42%), Gaps = 6/102 (5%)
Query: 245 DTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAF--AMQMSMQDTQEP 302
D + P+P AK A A+A PV +P + ++ M P
Sbjct: 76 DQQWAEVTPQP-GIAKPAGASTASAGKPVMDRPATNRLVADKPATNKPVMDNLGMAAGGP 134
Query: 303 AASSSKAPASAAASEEA-KAEPMDTDEMVNDAAFLQSVLENL 343
AA+S APASAAAS+ A AE T N A+ ENL
Sbjct: 135 AAAS--APASAAASDPAHPAELYTTATTQNTASQTMPADENL 174
>gnl|CDD|240337 PTZ00261, PTZ00261, acyltransferase; Provisional.
Length = 355
Score = 32.2 bits (73), Expect = 0.48
Identities = 20/86 (23%), Positives = 33/86 (38%), Gaps = 12/86 (13%)
Query: 196 GGAPGSSY----EFGVDPNEDPELALALRVSMEEQRARQE--------SEARRAAEGASG 243
GG P + + +D + D +A+ + Q+ R E EARR G
Sbjct: 270 GGLPADMHIRIGAYPIDYDRDSSKDVAVGLQQRMQKVRDEIAAEVAAAEEARRRRRGIVA 329
Query: 244 ADTSASSAVPKPTAEAKDAPGDMATA 269
++ + P A++A ATA
Sbjct: 330 EAKASKTLDIAPPHAAREAHATRATA 355
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 32.1 bits (73), Expect = 0.64
Identities = 34/200 (17%), Positives = 58/200 (29%), Gaps = 17/200 (8%)
Query: 186 SPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRVSMEEQRARQESEA---RRAAEGAS 242
SP G P + P+ P+L+ LR S A AS
Sbjct: 105 SPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVAS 164
Query: 243 GADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEP 302
A +S +A+P + E A P P A+ + + + P
Sbjct: 165 DAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAP 224
Query: 303 AASSSKAPASAAASEEAKAEPMDTDEMVNDAAFL-------------QSVLENLPGVDPQ 349
S+ A A++S+ + +E + L ++ N P P
Sbjct: 225 GR-SAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPG 283
Query: 350 SAEVRHALSSSAEKPAKKKD 369
A + + P+
Sbjct: 284 PASSSSSPRERSPSPSPSSP 303
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 31.1 bits (70), Expect = 0.97
Identities = 37/152 (24%), Positives = 55/152 (36%), Gaps = 14/152 (9%)
Query: 218 ALRVSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQP 277
A + + EQ+ ++E + AAE A +A K AEA AA +
Sbjct: 123 AEKQAQLEQKQQEEQARKAAAE----QKKKAEAAKAKAAAEAAKL-----KAAAEAKKKA 173
Query: 278 DFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQ 337
+ A EE A A + + E A ++ A A A +AKAE AA
Sbjct: 174 EEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEKAA--- 230
Query: 338 SVLENLPGVDPQSAEVRHALSSSAEKPAKKKD 369
E A+ A + +AE+ A
Sbjct: 231 --AEKKKAAAKAKADKAAAAAKAAERKAAAAA 260
>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 31.1 bits (70), Expect = 0.98
Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 2/93 (2%)
Query: 231 ESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAF 290
E +RA E + +DT A++A P P +A P A + + + A
Sbjct: 48 EELVQRALE-TARSDTPATAAAPAPAPQAPTKPAAPVHAPLKLSANANMSQRQRVASAAE 106
Query: 291 AMQMSMQDTQEPAASSSKAPASAAASEEAKAEP 323
M +M Q P + +APA+A + P
Sbjct: 107 DMIAAMALRQ-PVSVPRQAPAAAPVRAASIPSP 138
>gnl|CDD|237081 PRK12372, PRK12372, ribonuclease III; Reviewed.
Length = 413
Score = 31.0 bits (70), Expect = 1.2
Identities = 26/104 (25%), Positives = 39/104 (37%), Gaps = 1/104 (0%)
Query: 236 RAAEGASGADTSASSAVPKPTAEAKDAPGDMATAA-HPVGGQPDFATMTEEEQIAFAMQM 294
RAA + AD +A P +A D P D AA + A ++ A
Sbjct: 303 RAAHVETAADKGERAAKPAAADKAADKPADRPDAAEKAAEKPAEAAPRAADKPAGQAADP 362
Query: 295 SMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQS 338
+ +P AS+ A + A + +A A DT A Q+
Sbjct: 363 ASSSADKPGASADAAARTPARARDAAAPDADTPPGGASLAAAQA 406
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 30.6 bits (70), Expect = 1.5
Identities = 25/96 (26%), Positives = 33/96 (34%), Gaps = 1/96 (1%)
Query: 228 ARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQ 287
A A AA G + A ASSA A A G +A V A + +
Sbjct: 300 AAAAGGAAAAARGGAAAAGGASSAYSAGAAGGSGAAG-VAAGLGGVARAGASAAASPLRR 358
Query: 288 IAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEP 323
A SM+ + A S+ A AA+ A
Sbjct: 359 AASRAAESMKSSFRAGARSTGGGAGGAAAAAAAGAA 394
>gnl|CDD|99814 cd06218, DHOD_e_trans, FAD/NAD binding domain in the electron
transfer subunit of dihydroorotate dehydrogenase.
Dihydroorotate dehydrogenases (DHODs) catalyze the only
redox reaction in pyrimidine de novo biosynthesis. They
catalyze the oxidation of (S)-dihydroorotate to orotate
coupled with the reduction of NAD+. In L. lactis, DHOD B
(encoded by pyrDa) is co-expressed with pyrK and both
gene products are required for full activity, as well as
3 cofactors: FMN, FAD, and an [2Fe-2S] cluster.
Length = 246
Score = 30.2 bits (69), Expect = 1.6
Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 13/66 (19%)
Query: 127 LAKRLKKEKVNVDIV--------SFGEEVVNTELLNTFISTLNGKDGSGSH--MVTVAVG 176
LAK+L + + V ++ F E +++T DGS VT +
Sbjct: 116 LAKQLAERGIKVTVLLGFRSADDLFLVEEFEALGAEVYVATD---DGSAGTKGFVTDLLK 172
Query: 177 PHLSDA 182
L++A
Sbjct: 173 ELLAEA 178
>gnl|CDD|236335 PRK08724, fliD, flagellar capping protein; Validated.
Length = 673
Score = 30.6 bits (69), Expect = 1.6
Identities = 31/151 (20%), Positives = 50/151 (33%), Gaps = 18/151 (11%)
Query: 225 EQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTE 284
E R R +AR AA+ T V + D G+ A +
Sbjct: 207 EDRVRALEKARAAAQQVIAPLTPEEQKVAPELS---DEEGNAIPPADQEVAEEIQD---- 259
Query: 285 EEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVLENLP 344
A Q++ Q A ++ + P SA + A A + DAA ++ L
Sbjct: 260 ------AAQIAQQQEATAALAALEEPISAGGATAAAA-----GQAAIDAAEAKAYLRPED 308
Query: 345 GVDPQSAEVRHALSSSAEKPAKKKDEKKEKK 375
+ + L S +P ++ DE K
Sbjct: 309 RIPGWTETASGTLLDSYPEPEEELDEAAIAK 339
>gnl|CDD|237320 PRK13258, PRK13258, 7-cyano-7-deazaguanine reductase; Provisional.
Length = 114
Score = 28.9 bits (66), Expect = 1.7
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 272 PVGGQPDFATMT 283
P GQPDFAT+
Sbjct: 30 PKTGQPDFATIV 41
>gnl|CDD|218615 pfam05504, Spore_GerAC, Spore germination B3/ GerAC like,
C-terminal. The GerAC protein of the Bacillus subtilis
spore is required for the germination response to
L-alanine. Members of this family are thought to be
located in the inner spore membrane. Although the
function of this family is unclear, they are likely to
encode the components of the germination apparatus that
respond directly to this germinant, mediating the
spore's response.
Length = 171
Score = 29.1 bits (66), Expect = 2.6
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 121 ERELTKLAKRLKKEKVNVDIVSFGEEV 147
++E+ KL K+L+KE VDI FGE +
Sbjct: 107 KKEIEKLIKKLQKEY-KVDIFGFGEYL 132
>gnl|CDD|237082 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional.
Length = 400
Score = 29.8 bits (67), Expect = 2.6
Identities = 28/152 (18%), Positives = 44/152 (28%), Gaps = 27/152 (17%)
Query: 224 EEQRARQESEARRAAEGASG---ADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFA 280
E +AR + A + D + + +A P A + + A
Sbjct: 200 EAGKARYNASKALAEDIGDTVKRIDGTEVPLLAPWQGDAAPVPPSEAARPKSADAETNAA 259
Query: 281 TMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVL 340
T + AA ++KAP + S A AEP + AA + L
Sbjct: 260 LKTPA------------TAPKAAAKNAKAPEAQPVSGTAAAEPAPKEAAKAAAAAAKPAL 307
Query: 341 ENLPGVDPQSAEVRHALSSSAEKPAKKKDEKK 372
E+ P +P D K
Sbjct: 308 EDKP------------RPLGIARPGGADDLKL 327
>gnl|CDD|187769 cd09638, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas2 is present in majority of CRISPR/Cas systems along
with Cas1; RNAse specific to U-rich regions; Possesses
an RRM/ferredoxin fold.
Length = 90
Score = 27.7 bits (62), Expect = 2.7
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 107 MRIIAFVGSPVDLEERELTKLAKRLKKE 134
M ++ P D E + KL K L+K
Sbjct: 1 MLVLVVYDIPEDTERKRRRKLRKLLEKY 28
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 29.8 bits (67), Expect = 2.8
Identities = 24/145 (16%), Positives = 44/145 (30%), Gaps = 19/145 (13%)
Query: 224 EEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMT 283
EE R + + A R GA+ K + +A P T + T
Sbjct: 1176 EEAREKLQRAAARGESGAA----------KKVSRQAPKKPAPKKTTKKASESETTEETYG 1225
Query: 284 EEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVLENL 343
+ M ++ E +A A A AK + + + + L++
Sbjct: 1226 -------SSAMETENVAEVVKPKGRAGAKKKAPAAAKEKEEEDEILDLKDRLAAYNLDSA 1278
Query: 344 PGVDPQSAEVRHALSSSAEKPAKKK 368
P + + A + A +K
Sbjct: 1279 P--AQSAKMEETVKAVPARRAAARK 1301
>gnl|CDD|178165 PLN02550, PLN02550, threonine dehydratase.
Length = 591
Score = 29.9 bits (67), Expect = 2.9
Identities = 18/82 (21%), Positives = 28/82 (34%), Gaps = 1/82 (1%)
Query: 213 PELALALRVSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEA-KDAPGDMATAAH 271
P + S + S +R A S +TS + P K +P + A
Sbjct: 12 PLRSHIGSPSKPVVGSTPFSRSRIPAAVDSADETSMAPPPPPSPLPLLKVSPNSLQYPAG 71
Query: 272 PVGGQPDFATMTEEEQIAFAMQ 293
+G P+ E I AM+
Sbjct: 72 YLGAVPERTNEAENGSIPEAME 93
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 29.7 bits (67), Expect = 3.1
Identities = 35/162 (21%), Positives = 55/162 (33%), Gaps = 24/162 (14%)
Query: 204 EFGVDPNEDPELALALRVSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAP 263
E G+ P+E L + L + + + +EA AE + A A++ P A+A AP
Sbjct: 343 ELGLAPDEYAALTMVL-LRLLAFKPAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAP 401
Query: 264 GDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEP 323
A A + P A++ AP +A A+ A P
Sbjct: 402 APAAAPA-----------------------AAASAPAAPPAAAPPAPVAAPAAAAPAAAP 438
Query: 324 MDTDEMVNDAAFLQSVLENLPGVDPQSAEVRHALSSSAEKPA 365
V A + P A++S+A PA
Sbjct: 439 AAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPA 480
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.7 bits (66), Expect = 3.3
Identities = 37/155 (23%), Positives = 56/155 (36%), Gaps = 11/155 (7%)
Query: 226 QRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEE 285
+ AR+ E R+A E D + AV K KDA + A A + E
Sbjct: 1203 EAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDA--EEAKKAEEERNNEEIRKFEEA 1260
Query: 286 EQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVLENLPG 345
FA + + +E + KA A E+ KA+ E A + E
Sbjct: 1261 RMAHFARRQAAIKAEE----ARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKK 1316
Query: 346 VD--PQSAEVRHALSSSAEKPA---KKKDEKKEKK 375
D + AE + +A+K A KK E + +
Sbjct: 1317 ADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAE 1351
Score = 29.3 bits (65), Expect = 4.3
Identities = 35/167 (20%), Positives = 63/167 (37%), Gaps = 6/167 (3%)
Query: 211 EDPELALALRVSMEEQRARQES-----EARRAAEGASGADTSASSAVPKPTAEAKDAPGD 265
E+ + A + EE + E+ EA++A E A+ + + K AE +
Sbjct: 1428 EEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADE 1487
Query: 266 MATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMD 325
A + D A E + A + + + A + KA + A E KAE
Sbjct: 1488 AKKKAEEAKKKADEAKKAAEAKKK-ADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKK 1546
Query: 326 TDEMVNDAAFLQSVLENLPGVDPQSAEVRHALSSSAEKPAKKKDEKK 372
+ + A L+ E + + AE ++ + AKK +E +
Sbjct: 1547 KADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEAR 1593
>gnl|CDD|220678 pfam10293, DUF2405, Domain of unknown function (DUF2405). This is
a conserved region of a family of proteins conserved in
fungi. The function is unknown.
Length = 158
Score = 28.7 bits (65), Expect = 3.4
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 205 FGVDPNEDP---ELALALRVSMEEQRARQESE 233
+ +DP EL L R+ + EQR R E E
Sbjct: 109 LLFELEDDPFEWELGLIYRLGLLEQRERLEKE 140
>gnl|CDD|143398 cd07079, ALDH_F18-19_ProA-GPR, Gamma-glutamyl phosphate reductase
(GPR), aldehyde dehydrogenase families 18 and 19.
Gamma-glutamyl phosphate reductase (GPR), a L-proline
biosynthetic pathway (PBP) enzyme that catalyzes the
NADPH dependent reduction of L-gamma-glutamyl
5-phosphate into L-glutamate 5-semialdehyde and
phosphate. The glutamate route of the PBP involves two
enzymatic steps catalyzed by gamma-glutamyl kinase (GK,
EC 2.7.2.11) and GPR (EC 1.2.1.41). These enzymes are
fused into the bifunctional enzyme, ProA or
delta(1)-pyrroline-5-carboxylate synthetase (P5CS) in
plants and animals, whereas they are separate enzymes in
bacteria and yeast. In humans, the P5CS (ALDH18A1), an
inner mitochondrial membrane enzyme, is essential to the
de novo synthesis of the amino acids proline and
arginine. Tomato (Lycopersicon esculentum) has both the
prokaryotic-like polycistronic operons encoding GK and
GPR (PRO1, ALDH19) and the full-length, bifunctional
P5CS (PRO2, ALDH18B1).
Length = 406
Score = 28.9 bits (66), Expect = 4.0
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 51 LLAMADSVEVLATLTSDVGRILSKLHQVQPNG 82
+ AMA+ + +A L VG +L PNG
Sbjct: 71 IEAMAEGLRQVAALPDPVGEVLRG--WTLPNG 100
>gnl|CDD|235665 PRK05996, motB, flagellar motor protein MotB; Validated.
Length = 423
Score = 28.9 bits (65), Expect = 4.8
Identities = 20/107 (18%), Positives = 27/107 (25%), Gaps = 10/107 (9%)
Query: 238 AEGASGADT--------SASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIA 289
A GA G + S V TA PG A +
Sbjct: 168 ATGADGGEAYRDPFDPDFWSKQVEVTTAGDLLPPGQAREQAQGAKSATAAPATVPQAAPL 227
Query: 290 FAMQMSMQDTQEPAA--SSSKAPASAAASEEAKAEPMDTDEMVNDAA 334
Q T+E + A AA+ A+P + A
Sbjct: 228 PQAQPKKAATEEELIADAKKAATGEPAANAAKAAKPEPMPDDQQKEA 274
>gnl|CDD|182325 PRK10239, PRK10239,
2-amino-4-hydroxy-6-hydroxymethyldihyropteridine
pyrophosphokinase; Provisional.
Length = 159
Score = 28.2 bits (63), Expect = 5.0
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 9/50 (18%)
Query: 104 NHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTELL 153
NH RI +L++ + K A+R +++DI+ FG EV+NTE L
Sbjct: 72 NHTQRI--------ELQQGRVRK-AERWGPRTLDLDIMLFGNEVINTERL 112
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 28.4 bits (64), Expect = 5.4
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 83 NINFMTGIRIAHLALKHRQGKNHKMRIIAFVGS 115
++N+ + +AH L K + I FV S
Sbjct: 111 DVNYFGSLNVAHAVLPL--MKEQRPGHIVFVSS 141
>gnl|CDD|215793 pfam00213, OSCP, ATP synthase delta (OSCP) subunit. The ATP D
subunit from E. coli is the same as the OSCP subunit
which is this family. The ATP D subunit from metazoa are
found in family pfam00401.
Length = 171
Score = 27.9 bits (63), Expect = 5.5
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 11/67 (16%)
Query: 105 HKMRIIAFVGSPVDLEERELTKLAKRLKKE---KVNVDIVSFGEEVVNTELLNTFISTLN 161
H+ + A V S V L E +L L L+K+ KV + E V+ L+ + +
Sbjct: 99 HRGIVEATVTSAVPLSEEQLKALKAALEKKTGKKVKL------ETKVDPSLIGGVVVRVG 152
Query: 162 GK--DGS 166
K DGS
Sbjct: 153 DKVIDGS 159
>gnl|CDD|217511 pfam03358, FMN_red, NADPH-dependent FMN reductase.
Length = 151
Score = 27.9 bits (63), Expect = 5.9
Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 12/46 (26%)
Query: 107 MRIIAFVGSPVDLEERE-------LTKLAKRLKKEKVNVDIVSFGE 145
M+I+ GSP R+ A+ L++ V+++ +
Sbjct: 1 MKILVISGSP-----RKGSNTRKLAEWAAELLEEAGAEVELIDLAD 41
>gnl|CDD|241245 cd01209, PTB_Shc, Shc-like phosphotyrosine-binding (PTB) domain.
Shc is a substrate for receptor tyrosine kinases, which
can interact with phosphoproteins at NPXY motifs. Shc
contains an PTB domain followed by an SH2 domain. PTB
domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif
with differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Shc-like subgroup.
Length = 170
Score = 27.9 bits (63), Expect = 6.0
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 8 ICVDNSDFMRNGDFLPTRLQAQQDAVNLVC 37
I V S MR+ DF TR Q ++A+N VC
Sbjct: 25 IEVLQS--MRSLDF-NTRTQVTREAINRVC 51
>gnl|CDD|234685 PRK00197, proA, gamma-glutamyl phosphate reductase; Provisional.
Length = 417
Score = 28.5 bits (65), Expect = 6.0
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 51 LLAMADSVEVLATLTSDVGRILSKLHQVQPNG 82
+ +A+ + +A L VG +L PNG
Sbjct: 77 IEGIAEGLRQVAALPDPVGEVLD--GWTLPNG 106
>gnl|CDD|239643 cd03671, Ap4A_hydrolase_plant_like, Diadenosine tetraphosphate
(Ap4A) hydrolase is a member of the Nudix hydrolase
superfamily. Members of this family are well represented
in a variety of prokaryotic and eukaryotic organisms.
Phylogenetic analysis reveals two distinct subgroups
where plant enzymes fall into one group (represented by
this subfamily) and fungi/animals/archaea enzymes fall
into another. Bacterial enzymes are found in both
subfamilies. Ap4A is a potential by-product of aminoacyl
tRNA synthesis, and accumulation of Ap4A has been
implicated in a range of biological events, such as DNA
replication, cellular differentiation, heat shock,
metabolic stress, and apoptosis. Ap4A hydrolase cleaves
Ap4A asymmetrically into ATP and AMP. It is important in
the invasive properties of bacteria and thus presents a
potential target for the inhibition of such invasive
bacteria. Besides the signature nudix motif
(G[X5]E[X7]REUXEEXGU where U is Ile, Leu, or Val), Ap4A
hydrolase is structurally similar to the other members
of the nudix superfamily with some degree of variations.
Several regions in the sequences are poorly defined and
substrate and metal binding sites are only predicted
based on kinetic studies.
Length = 147
Score = 27.6 bits (62), Expect = 6.1
Identities = 12/20 (60%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 206 GVDPNEDPELALALRVSMEE 225
G+D EDPE A ALR EE
Sbjct: 35 GIDEGEDPEQA-ALRELEEE 53
>gnl|CDD|227665 COG5373, COG5373, Predicted membrane protein [Function unknown].
Length = 931
Score = 28.6 bits (64), Expect = 6.2
Identities = 28/95 (29%), Positives = 35/95 (36%), Gaps = 18/95 (18%)
Query: 226 QRARQESEARRAAEGA---SGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATM 282
+A ++ A AAE A + A++ AS VP P A G+ A AA P
Sbjct: 48 AKAAEQMAAPEAAEAAPLPAAAESIASPEVPPPVPPAPAQEGE-APAAEQPSAVP----- 101
Query: 283 TEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASE 317
A A EP S A AAA E
Sbjct: 102 APSAAPAPA---------EPVEPSLAANPFAAAIE 127
>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional.
Length = 209
Score = 27.9 bits (62), Expect = 6.8
Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 1/92 (1%)
Query: 232 SEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAFA 291
S+ ++A + A + + V P E P P A + A
Sbjct: 94 SDLQKATSMSEPATENKPAEVTTPV-EPMGLPETPPAVPVPAPAPAVAAAAAQAAAAPKA 152
Query: 292 MQMSMQDTQEPAASSSKAPASAAASEEAKAEP 323
+ PAA ++ P +++AK
Sbjct: 153 PAKPRAKSPRPAAKAAPKPTETITAKKAKKTA 184
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 28.5 bits (63), Expect = 7.5
Identities = 14/41 (34%), Positives = 16/41 (39%)
Query: 224 EEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPG 264
E +R RQ ARR A + G S V A A G
Sbjct: 94 ERERLRQAYAARRGANTSGGTVGSGRCGVHGDPAAAAATAG 134
>gnl|CDD|223784 COG0712, AtpH, F0F1-type ATP synthase, delta subunit (mitochondrial
oligomycin sensitivity protein) [Energy production and
conversion].
Length = 178
Score = 27.6 bits (62), Expect = 8.1
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 105 HKMRIIAFVGSPVDLEERELTKLAKRLKKE-----KVNVDI 140
+ + A V S +L + +LTKL +L+K+ K+N I
Sbjct: 105 SRGIVEAEVTSAFELSDEQLTKLEAKLEKKFGKKVKLNNKI 145
>gnl|CDD|238446 cd00874, RNA_Cyclase_Class_II, RNA 3' phosphate cyclase domain
(class II). These proteins function as RNA cyclase to
catalyze the ATP-dependent conversion of 3'-phosphate to
a 2'.3'-cyclic phosphodiester at the end of RNA
molecule. A conserved catalytic histidine residue is
found in all members of this subfamily.
Length = 326
Score = 28.0 bits (63), Expect = 8.2
Identities = 24/123 (19%), Positives = 40/123 (32%), Gaps = 43/123 (34%)
Query: 96 ALKHRQGKNHKMRIIAFV-GSPVDLEERELTKLAKRLKKE-KVNVDIV------------ 141
L +G+ K+R I+ P + ER+ A L+K + ++I
Sbjct: 174 LLLEERGEIEKIRGISHAANLPPHVAERQAEAAAALLRKALGLQIEIEPEDQSALGPGSG 233
Query: 142 ---------------SFGE-----EVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHLSD 181
+ G+ E V E ++ L+ AV HL+D
Sbjct: 234 IVLWAEYEHSRLGFSALGKKGVPAEKVGEEAAEELLAYLSSG---------AAVDEHLAD 284
Query: 182 ALI 184
LI
Sbjct: 285 QLI 287
>gnl|CDD|226170 COG3644, COG3644, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 194
Score = 27.6 bits (61), Expect = 8.7
Identities = 22/53 (41%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 233 EARRAAEGASGADTSASSAVPKPTAEAKDAPG-DMATAAHPVGGQPDFATMTE 284
EARRAAEG A + +A +A A D PG + AT A G + FA + E
Sbjct: 113 EARRAAEGPDRARQAQEAAYRFMSAMAGDLPGFEEATRALYAGDEARFAALIE 165
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 27.8 bits (62), Expect = 9.1
Identities = 29/113 (25%), Positives = 51/113 (45%), Gaps = 10/113 (8%)
Query: 220 RVSMEEQRARQESEARRAAE----GASGADTSASSAVPKPTAEAKDAPGDMATAA----- 270
R++ +EQ+ + E A++AA A +A++A K AEAK A AA
Sbjct: 110 RLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKK 169
Query: 271 -HPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAE 322
A +++ A A + + ++ A + +K A+A A ++A AE
Sbjct: 170 KAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAE 222
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.309 0.125 0.337
Gapped
Lambda K H
0.267 0.107 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,505,609
Number of extensions: 1789552
Number of successful extensions: 2491
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2343
Number of HSP's successfully gapped: 161
Length of query: 375
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 277
Effective length of database: 6,590,910
Effective search space: 1825682070
Effective search space used: 1825682070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 60 (26.3 bits)