RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3251
(959 letters)
>gnl|CDD|224037 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase
subunits [DNA replication, recombination, and repair].
Length = 767
Score = 330 bits (848), Expect = e-100
Identities = 206/826 (24%), Positives = 314/826 (38%), Gaps = 71/826 (8%)
Query: 124 CNGRGHTSGSHIINHLVRAKHKEVTLHKDGPLGETVLECYTCGVRNIFVLGFIPAKADSV 183
N + I + + + + E++L C RN F+L K V
Sbjct: 1 ENLKFELLIKKKIENEELSSNLNELTLLIV-IKESLLGCVNNLKRNTFLLEITDLKKKWV 59
Query: 184 VVLLCRTPCAAQNSLKDMNWDQEQWKPLIADRSFLSWLVKVPTEQEQQRGRQVTSAQIAK 243
L+ + D + L LS + E EQ+ + +I K
Sbjct: 60 EALVRLDKLIKSLPSLLLVRDGTLNRELKELIDSLSKKLGKLVEIEQEAEIKTKELEIKK 119
Query: 244 LEEVWKDNAEATFQDLEKPGVDED-PHQVLLRYE-DGYQYQNIFGPLVKLEADYDKRLKE 301
L + L + E+ + L++Y V K K
Sbjct: 120 LRLAKRSFKGRAILGLLAKVLGENLGSEALVKYGRLESYIN--LEEFVGELVLVSKLNKI 177
Query: 302 SQTQENVTVRWDVGLNKKSIAYFSLAKTDGDGYQYQNIFGPLVKLEADYDKRLKESQTQE 361
+ + + L K I P + + E
Sbjct: 178 KSELAGLLIEYLKRLRKVLDK----------------IIPPPLFEK-------------E 208
Query: 362 NVTVRWDVGLNKKSIAYFSLAKTDGDMRLMQGDELKLRYSYDASKTWSGLGHVIKIPDNF 421
V V L + + L++ + L K + F
Sbjct: 209 EVRVDIVENLLEL-----------SESILLRRELELLSKFALILK--------RLLESLF 249
Query: 422 GDEVGLELKSSAGAPTEATTGFSVDFI-WKSTSFDRMQLALRKFAVDDQSVSA-YIYHRL 479
G +L + + + + R+ F +
Sbjct: 250 EILRGKDLPIKLLDVELELVEINKELDNEQKLAVKRLLSLNDLFLIHQGPFGTGKTRSVT 309
Query: 480 LGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATI 539
+ + E+L L +A + ++ + I+ L I P K + T+
Sbjct: 310 ILELIIELLENNKLKILPTAESNAAVDNLLRRLKRTVIKVELLRIGHPSRVLKKLKLDTL 369
Query: 540 VYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVCAKSREAIDSPVSFLALHNQI 599
L K + A +D++ ++ G +++R AK RE ++ H +
Sbjct: 370 EELLEKHEIPGNKIAA-----LDKVIRELREEGERIIREIAKLRERLERKRLDKISHLNV 424
Query: 600 RNMEMNSELKKLLQLKEETGELSSADEKRYRMLKKNAEKSLLDNADVICCTCVGAGDPRL 659
+ L K L E K R LKK A +L+ ADV+ T AG L
Sbjct: 425 ALRGILPALNKSEALWISLEEKQKKILKELRRLKKKAVTKILEAADVVLSTLSIAGFSIL 484
Query: 660 LKIKFHSILIDESMQATEPECMVPVILGAKQLILVGDHCQLGPVVMCKKAARAGLSQSLF 719
K +F ++IDE+ QATEP ++ + AK++ILVGDH QL P V K+++ GLS SLF
Sbjct: 485 KKYEFDYVIIDEASQATEPSALIALSR-AKKVILVGDHKQLPPTVFFKESSPEGLSASLF 543
Query: 720 ERLVVLGIRPFR-LEVQYRMHPELSKFPSNFFYEGSLQNGVCADERKLSKIDFPWPVPDK 778
ERL+ G L VQYRMHP++ F S FY G L+ L + P V
Sbjct: 544 ERLIDNGPEVVYLLRVQYRMHPDIIAFSSKVFYNGRLEVHTSFLAFTLLDGEIPEVVISN 603
Query: 779 PMLFYVTQGQEEIAGSGTSYVNRTEASNVEKITTRFIRCGMKPEQIGVITPYEGQRAFLV 838
P+ FY T G EE S S +N EA V+ I ++ G++ IGVI+PY Q
Sbjct: 604 PLEFYDTLGAEEFFES-KSKLNELEAEIVKVIVDELLKDGLEENDIGVISPYRAQ----- 657
Query: 839 QHMQYQGSLPAKIYQEIEVASVDAFQGREKDLIIMSCVRSN-DHQGIGFLNDPRRLNVAL 897
+ L + + +EV +VD FQGREKD+II+S VRSN D IGFL DPRRLNVAL
Sbjct: 658 --VSLIRRLLNEAGKGVEVGTVDGFQGREKDVIILSLVRSNDDKGEIGFLGDPRRLNVAL 715
Query: 898 TRAKYGIIVIGNPKVLSKQPLWNNLLNFYKEQKVLVEGPLNNLKES 943
TRAK +IV+G+ L PL+ L+N K + +L E L +L+ +
Sbjct: 716 TRAKRKLIVVGSSSTLESDPLYKRLINDLKRKGLLAELNLLDLRLT 761
>gnl|CDD|192286 pfam09416, UPF1_Zn_bind, RNA helicase (UPF2 interacting domain).
UPF1 is an essential RNA helicase that detects mRNAs
containing premature stop codons and triggers their
degradation. This domain contains 3 zinc binding motifs
and forms interactions with another protein (UPF2) that
is also involved nonsense-mediated mRNA decay (NMD).
Length = 152
Score = 288 bits (740), Expect = 2e-92
Identities = 101/152 (66%), Positives = 127/152 (83%)
Query: 100 HACKYCGIHDPAYVIMCNICKKWFCNGRGHTSGSHIINHLVRAKHKEVTLHKDGPLGETV 159
HAC YCGIH+PA V+ CN C KWFCNG+G TSGSHI+NHLV++KHKEV+LH + PLG+TV
Sbjct: 1 HACAYCGIHNPACVVKCNSCNKWFCNGKGGTSGSHIVNHLVKSKHKEVSLHPESPLGDTV 60
Query: 160 LECYTCGVRNIFVLGFIPAKADSVVVLLCRTPCAAQNSLKDMNWDQEQWKPLIADRSFLS 219
LECY CG +N+F+LGF+PAK+++VVVLLCR PCA + KDMNWD QW+PLI +R FLS
Sbjct: 61 LECYNCGSKNVFLLGFVPAKSEAVVVLLCRQPCANCKASKDMNWDTSQWQPLIEERQFLS 120
Query: 220 WLVKVPTEQEQQRGRQVTSAQIAKLEEVWKDN 251
WLV VP+E+EQ + R++T QI+KLEE+WK N
Sbjct: 121 WLVPVPSEEEQLKARKITLQQISKLEELWKSN 152
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 291 bits (747), Expect = 6e-87
Identities = 183/552 (33%), Positives = 252/552 (45%), Gaps = 94/552 (17%)
Query: 453 SFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYA 512
+F RM+ ALR ++ S + +LG H + F P+LN SQ A
Sbjct: 114 TFKRMKEALRALT---ENHSRLLE-FILGREAPSKASEIHDFQFFD----PNLNESQKEA 165
Query: 513 VKHAI-QRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRT 571
V A+ + L LI GPPGTGKT T ++ QLVK+ G VLV APSNIAVD L E++
Sbjct: 166 VLFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKR-GLRVLVTAPSNIAVDNLLERLALC 224
Query: 572 GLKVVRVCAKSR--------------EAIDSPVSFLALHNQIRNM--EMNSELKKLLQLK 615
K+VR+ +R E + +I + E N +LK Q +
Sbjct: 225 DQKIVRLGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIDELIEERNKKLKPSPQKR 284
Query: 616 E---ETGELSSADEKR-YRMLKKNAEKS----------------LLDNADVIC------- 648
+ L A +KR R ++ S LL +
Sbjct: 285 RGLSDIKILRKALKKREARGIESLKIASMAEWIETNKSIDRLLKLLPEIEERIENEILAE 344
Query: 649 --CTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVILGAKQLILVGDHCQLGPVVMC 706
L +F +IDE+ QA EP C++P +L A++LIL GDH QL P ++
Sbjct: 345 SDVVQSTNSSAGLKGWEFDVAVIDEASQAMEPSCLIP-LLKARKLILAGDHKQLPPTILS 403
Query: 707 KKAARAGLSQSLFERLVVL-GIRPFRLEVQYRMHPELSKFPSNFFYEGSLQNGVCADE-- 763
A L +LFERL+ R L VQYRM+ ++ +FPS FY G L A E
Sbjct: 404 HDAE--ELELTLFERLIKEYPERSRTLNVQYRMNQKIMEFPSREFYNGKLT----AHESV 457
Query: 764 RKLSKIDFPWPVPDK---------PMLFYVTQGQE----EIAGSGTSYVNRTEASNVEKI 810
+ D P + P+LF T G E + A S TS N EA V +I
Sbjct: 458 ANILLRDLPKVEATESEDDLETGIPLLFIDTSGCELFELKEADS-TSKYNPGEAELVSEI 516
Query: 811 TTRFIRCGMKPEQIGVITPYEGQ----RAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGR 866
++ G+ IGVITPY+ Q R L +IEV+SVD FQGR
Sbjct: 517 IQALVKMGVPANDIGVITPYDAQVDLLRQLLEHRHI-----------DIEVSSVDGFQGR 565
Query: 867 EKDLIIMSCVRSNDHQGIGFLNDPRRLNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFY 926
EK++II+S VRSN +GFL D RRLNVALTRA+ +IVIG+ + LS + L+ +
Sbjct: 566 EKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWC 625
Query: 927 KEQKVLVEGPLN 938
K+ + E +
Sbjct: 626 KQHGEVREAFKD 637
>gnl|CDD|221913 pfam13087, AAA_12, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 195
Score = 258 bits (662), Expect = 2e-80
Identities = 93/200 (46%), Positives = 122/200 (61%), Gaps = 7/200 (3%)
Query: 714 LSQSLFERLVVLG-IRPFRLEVQYRMHPELSKFPSNFFYEGSLQNGVCADERKLSKIDFP 772
L +SLFERL G L+ QYRMHP++S+FPS FY G L++G ER L F
Sbjct: 1 LDRSLFERLQEAGPEAVVMLDTQYRMHPDISEFPSELFYGGKLKDGESVAERPLPWD-FH 59
Query: 773 WPVPDKPMLFYVTQGQEEIAGSGTSYVNRTEASNVEKITTRFIRCGM-KPEQIGVITPYE 831
P P P++F G EE TSY N EA V ++ + ++ G K + IG+ITPY
Sbjct: 60 LPDPLGPLVFIDVDGSEEEEEKSTSYSNEAEAELVVQLVEKLLKSGPEKNKDIGIITPYR 119
Query: 832 GQRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGREKDLIIMSCVRSNDHQGIGFLNDPR 891
Q + + ++ + +IEV +VD FQGREKD+II S VRSN+ GIGFL+DPR
Sbjct: 120 AQVRLIKKLLKRKFGGE----PDIEVNTVDGFQGREKDVIIFSTVRSNEKGGIGFLSDPR 175
Query: 892 RLNVALTRAKYGIIVIGNPK 911
RLNVALTRAK G+I++GN K
Sbjct: 176 RLNVALTRAKRGLIIVGNAK 195
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 211 bits (538), Expect = 1e-62
Identities = 87/221 (39%), Positives = 125/221 (56%), Gaps = 18/221 (8%)
Query: 504 DLNRSQVYAVKHAIQRP-LSLIQGPPGTGKTVTSATIVYQLVKQT-GSPVLVCAPSNIAV 561
+LN SQ A+K A+ ++LIQGPPGTGKT T I+ QL+ G VLVCAPSN AV
Sbjct: 1 ELNDSQREAIKKALSSSDITLIQGPPGTGKTTTIVEIIKQLLSNAPGKKVLVCAPSNSAV 60
Query: 562 DQLTEKI--HRTGLKVVRVCAKSREAIDSPVSFLALHNQIRN------------MEMNSE 607
D + E++ + GLK+VR+ + +RE I V +L + + E
Sbjct: 61 DNILERLLEQKFGLKIVRIGSPARE-IHEDVLQYSLEYLLEAKFEQLLKRIRKLKSLLEE 119
Query: 608 LKKLLQLKEETGELSSADEKRYRMLKKNAEKSLLDNADVICCTCVGAGDPRLLKIK-FHS 666
KL + + + +K L+K+ K +LD ADV+C T GAG L +K F
Sbjct: 120 KSKLKRERRKLRSEIKKLKKELERLRKSIRKEILDEADVVCTTLSGAGSSLLEGLKKFDV 179
Query: 667 ILIDESMQATEPECMVPVILGAKQLILVGDHCQLGPVVMCK 707
++IDE+ QATEPE ++P++LG K+++LVGDH QL P V+
Sbjct: 180 VIIDEAAQATEPETLIPLLLGCKKVVLVGDHKQLPPTVLSP 220
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 60.8 bits (148), Expect = 1e-11
Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 2/64 (3%)
Query: 511 YAVKHAI-QRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIH 569
AV+ A R L ++ G PGTGKT T+A I+ +L+ G VLV AP+ A +L E++
Sbjct: 1 EAVEAAASGRSLFVVDGGPGTGKTATAAAIIARLLAA-GRSVLVVAPTGRAARRLRERLA 59
Query: 570 RTGL 573
L
Sbjct: 60 ALDL 63
>gnl|CDD|233417 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model [DNA metabolism, DNA replication, recombination,
and repair].
Length = 586
Score = 60.9 bits (148), Expect = 2e-09
Identities = 56/210 (26%), Positives = 83/210 (39%), Gaps = 56/210 (26%)
Query: 500 PNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQ---TGSP-VLVCA 555
P L + N Q AV A++ SLI G PGTGKT T A ++ LVKQ G + + A
Sbjct: 142 PLLNEQNW-QKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAA 200
Query: 556 PSNIAVDQLTEKIHRTGLKVVRVCAKSREAIDSPVSFLALHNQIRNMEMNSELKKLLQLK 615
P+ A +L E + + V + A P + +H +LL +K
Sbjct: 201 PTGKAAARLAESLRK---AVKNLAAAEALIAALPSEAVTIH-------------RLLGIK 244
Query: 616 EETGELSSADEKRYRMLKKNAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDE-SM- 673
D KR+R ++N L DV +++DE SM
Sbjct: 245 --------PDTKRFRHHERN---PL--PLDV--------------------LVVDEASMV 271
Query: 674 QATEPECMVPVILGAKQLILVGDHCQLGPV 703
++ + +LIL+GD QL V
Sbjct: 272 DLPLMAKLLKALPPNTKLILLGDKNQLPSV 301
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 55.3 bits (134), Expect = 1e-08
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 505 LNRSQVYAVKHAI--QRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVD 562
L+ Q AV+H + ++++QGP GTGKT TS + + G V+ AP+ A
Sbjct: 2 LSAEQREAVRHVLTSGDRVAVVQGPAGTGKT-TSLKAAREAWEAAGYRVIGLAPTGKAAK 60
Query: 563 QLTEKI 568
L E++
Sbjct: 61 VLGEEL 66
Score = 29.5 bits (67), Expect = 7.3
Identities = 17/53 (32%), Positives = 19/53 (35%), Gaps = 11/53 (20%)
Query: 687 GAKQLILVGDHCQLGPVVMCKKAARAGLSQSLFERLVVLGIRPFRLEVQYRMH 739
GAK ++LVGD QL V AG F L G L R
Sbjct: 120 GAK-VVLVGDPAQLQAVG-------AG---GPFRLLAERGGITAELTEIRRQK 161
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 44.1 bits (105), Expect = 2e-05
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 505 LNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQL 564
L Q A++ +++ LI G+GKT+T+A ++ +L K VL P ++Q
Sbjct: 4 LRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAKG-KKKVLFVVPRKDLLEQA 62
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 44.0 bits (104), Expect = 9e-05
Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 509 QVYAVKHAIQRPLS-LIQGPPGTGKTVTSAT-IVYQLVKQTGSPVLVCAPSNIAVDQLTE 566
Q A++ + ++ P G+GKT+ + + L + G VLV P+ +Q E
Sbjct: 13 QKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAE 72
Query: 567 KIHR 570
++ +
Sbjct: 73 ELKK 76
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 43.1 bits (102), Expect = 1e-04
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 523 LIQGPPGTGKTVTSAT-IVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVC 579
L+ P G+GKT+ + I+ L G VLV AP+ +Q+ E++ + ++V
Sbjct: 4 LLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVG 61
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 44.0 bits (104), Expect = 4e-04
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 505 LNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGS-PVLVCAPSNIAVDQ 563
L+ Q A+ AIQ + ++ G PGTGKT + I+ + G PV + AP+ A +
Sbjct: 324 LSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKR 383
Query: 564 LTE-------KIHR 570
L E IHR
Sbjct: 384 LGEVTGLTASTIHR 397
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 42.0 bits (99), Expect = 0.001
Identities = 17/77 (22%), Positives = 27/77 (35%), Gaps = 5/77 (6%)
Query: 493 LPKHFSAPNLPDLNRSQVYAVKHAIQRPLS-LIQGPPGTGKTVTSATIVYQLVKQTGSPV 551
L + A+ + +I P G GKTV +A + +L
Sbjct: 28 KLIVAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL----KRST 83
Query: 552 LVCAPSNIAVDQLTEKI 568
LV P+ +DQ E +
Sbjct: 84 LVLVPTKELLDQWAEAL 100
>gnl|CDD|236783 PRK10875, recD, exonuclease V subunit alpha; Provisional.
Length = 615
Score = 41.5 bits (98), Expect = 0.002
Identities = 30/89 (33%), Positives = 40/89 (44%), Gaps = 7/89 (7%)
Query: 482 HNVDEVLFRCHLPKHF-SAPNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIV 540
VDE L R L F + D Q A A+ R +S+I G PGTGKT T A ++
Sbjct: 132 IEVDEALLRQTLDALFGPVTDEVDW---QKVAAAVALTRRISVISGGPGTGKTTTVAKLL 188
Query: 541 YQLVKQTGSPVLV---CAPSNIAVDQLTE 566
L++ AP+ A +LTE
Sbjct: 189 AALIQLADGERCRIRLAAPTGKAAARLTE 217
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 39.8 bits (93), Expect = 0.007
Identities = 20/81 (24%), Positives = 30/81 (37%), Gaps = 10/81 (12%)
Query: 512 AVKHAI-QRPLSLIQGPPGTGKTVT--SATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKI 568
AV A+ LI+ P GTGKT+ + Y + G V++ + +QL E+
Sbjct: 26 AVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAR--EEGKKVIISTRTKALQEQLLEED 83
Query: 569 -----HRTGLKVVRVCAKSRE 584
L K R
Sbjct: 84 LPIHKLLKKLGGKFALLKGRS 104
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 37.7 bits (87), Expect = 0.008
Identities = 13/52 (25%), Positives = 21/52 (40%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLK 574
LI GPPG+GKT + + +L G + + + + G K
Sbjct: 6 LIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGK 57
>gnl|CDD|232804 TIGR00064, ftsY, signal recognition particle-docking protein FtsY.
There is a weak division between FtsY and SRP54; both
are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein [Protein fate,
Protein and peptide secretion and trafficking].
Length = 272
Score = 38.4 bits (90), Expect = 0.011
Identities = 34/114 (29%), Positives = 49/114 (42%), Gaps = 31/114 (27%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAP--SNIAVDQLTEKIHRTGLKVVR--- 577
L G G GKT T A + +L KQ S +L A++QL E R G+ V++
Sbjct: 76 LFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFRAAAIEQLEEWAKRLGVDVIKQKE 135
Query: 578 ------VC------AKSREA----IDSPVSFLA--LHNQIRNMEMNSELKKLLQ 613
V AK+R ID+ A L N++ M+ ELKK+ +
Sbjct: 136 GADPAAVAFDAIQKAKARNIDVVLIDT-----AGRLQNKVNLMD---ELKKIKR 181
>gnl|CDD|233210 TIGR00959, ffh, signal recognition particle protein. This model
represents Ffh (Fifty-Four Homolog), the protein
component that forms the bacterial (and organellar)
signal recognition particle together with a 4.5S RNA.
Ffh is a GTPase homologous to eukaryotic SRP54 and also
to the GTPase FtsY (TIGR00064) that is the receptor for
the signal recognition particle [Protein fate, Protein
and peptide secretion and trafficking].
Length = 428
Score = 38.4 bits (90), Expect = 0.015
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 16/75 (21%)
Query: 518 QRPLSLIQGPP---------GTGKTVTSATIVYQLVKQTGSPVLVCA-----PSNIAVDQ 563
L+L + PP G+GKT T + Y L K+ G VL+ A P+ A++Q
Sbjct: 89 NASLNLAKKPPTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYRPA--AIEQ 146
Query: 564 LTEKIHRTGLKVVRV 578
L + G+ V +
Sbjct: 147 LKVLGQQVGVPVFAL 161
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 37.9 bits (89), Expect = 0.022
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 4/51 (7%)
Query: 507 RSQVYAVKHAIQ--RPL-SLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVC 554
+A++ A++ RPL LI GPPGTGKT T V++ +++ V+
Sbjct: 40 EELAFALRPALRGSRPLNVLIYGPPGTGKTTT-VKKVFEELEEIAVKVVYV 89
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 36.4 bits (85), Expect = 0.030
Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 11/74 (14%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQLTEKIHRTGLKVVRV 578
L+ G G+GKT T A + L KQ +LV A + A++QL + R G V V
Sbjct: 5 LLVGLQGSGKTTTIAKLAAYLKKQGKKVLLVAADTFRAA--AIEQLKQLAERLG---VPV 59
Query: 579 CAKSREAIDSPVSF 592
P +
Sbjct: 60 FGSGTG--SDPAAV 71
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 36.2 bits (84), Expect = 0.078
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 529 GTGKTVTSATIVYQLVKQTGS-PVLVCAPSNIAVDQLTEKIHRTGLKVVR 577
GTGKT+T+ +L ++ G +LV P VDQ + + GL +
Sbjct: 34 GTGKTLTALAAASKLYEKIGLLVLLVVCPYQHLVDQWAREAEKFGLNPIL 83
>gnl|CDD|218958 pfam06252, DUF1018, Protein of unknown function (DUF1018). This
family consists of several bacterial and phage proteins
of unknown function.
Length = 119
Score = 34.2 bits (79), Expect = 0.083
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 2/64 (3%)
Query: 195 QNSLKDMNWDQEQWKPLIADRSFLSWLVKVPTEQEQQRGRQVTSAQIAKLEEVWKDNAEA 254
+ S KD+ + Q ++ + + P ++ R SAQ+ K+ +W + +A
Sbjct: 16 KTSAKDLTDAELQ--KVLDHLKAKGFKPRSPAKKPGTRPPMARSAQLRKIRALWIELGKA 73
Query: 255 TFQD 258
Sbjct: 74 GAVR 77
>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 = 34.4 bits (79), Expect = 0.097
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 512 AVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQ 546
A++ + L L+ GPPGTGKT + I +L +
Sbjct: 13 ALELPPPKNL-LLYGPPGTGKTTLARAIANELFRP 46
>gnl|CDD|215649 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 = 34.1 bits (79), Expect = 0.11
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 4/30 (13%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
L+ GPPGTGKT T+ + K+ G+P +
Sbjct: 2 LLYGPPGTGKT----TLAKAVAKELGAPFI 27
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible oxidation
of CO to CO2. CODH contains a nickel-iron-sulfur cluster
(C-center) and an iron-sulfur cluster (B-center). CO
oxidation occurs at the C-center. Three accessory
proteins encoded by cooCTJ genes are involved in nickel
incorporation into a nickel site. CooC functions as a
nickel insertase that mobilizes nickel to apoCODH using
energy released from ATP hydrolysis. CooC is a homodimer
and has NTPase activities. Mutation at the P-loop
abolishs its function.
Length = 116
Score = 33.0 bits (76), Expect = 0.21
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 524 IQGPPGTGKTVTSATIVYQLVKQTGSPVLV--CAPSNIAVDQLTEKI 568
I G G GKT +A + L ++ G PVL P ++ ++L+ ++
Sbjct: 4 ITGKGGVGKTTIAALLARYLAEK-GKPVLAIDADPDDL-PERLSVEV 48
>gnl|CDD|223581 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha
subunit - helicase superfamily I member [DNA
replication, recombination, and repair].
Length = 696
Score = 35.2 bits (81), Expect = 0.21
Identities = 37/147 (25%), Positives = 55/147 (37%), Gaps = 27/147 (18%)
Query: 456 RMQLALRKFAVDDQSVSAYI----YHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVY 511
R+ +D V+ I HRLLG +V R L+ Q
Sbjct: 281 RLIARAELRILDSLFVALKIRAGTVHRLLGEVPAKVKLR--------------LSLEQKE 326
Query: 512 AVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEK---- 567
A+ + +S++ G PGTGKT I +L+K+ L+ AP+ A +L E
Sbjct: 327 ALDVLVVDEVSMLTGGPGTGKTTAIKAIA-RLIKEGDGDQLLAAPTGKAAKRLNESTGLE 385
Query: 568 ---IHRT-GLKVVRVCAKSREAIDSPV 590
IHR GL + D +
Sbjct: 386 ARTIHRLLGLWEKTGNNEEPLDGDLLI 412
>gnl|CDD|236694 PRK10436, PRK10436, hypothetical protein; Provisional.
Length = 462
Score = 34.5 bits (80), Expect = 0.26
Identities = 14/30 (46%), Positives = 21/30 (70%), Gaps = 2/30 (6%)
Query: 508 SQVYAVKHAIQRP--LSLIQGPPGTGKTVT 535
+Q+ + A+Q+P L L+ GP G+GKTVT
Sbjct: 205 AQLAQFRQALQQPQGLILVTGPTGSGKTVT 234
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with the
signal sequence when it emerges from the ribosome. SRP54
of the signal recognition particle has a three-domain
structure: an N-terminal helical bundle domain, a GTPase
domain, and the M-domain that binds the 7s RNA and also
binds the signal sequence. The extreme C-terminal region
is glycine-rich and lower in complexity and poorly
conserved between species. The GTPase domain is
evolutionary related to P-loop NTPase domains found in a
variety of other proteins.
Length = 197
Score = 33.5 bits (78), Expect = 0.29
Identities = 34/112 (30%), Positives = 44/112 (39%), Gaps = 32/112 (28%)
Query: 526 GPPGTGKTVTSATIVYQLVKQTG-SPVLVCA----PSNIAVDQL---------TEKIHRT 571
GP G GKT T A + +L + G +LV A + AV+QL
Sbjct: 8 GPNGVGKTTTIAKLAARLKLKGGKKVLLVAADTFRAA--AVEQLKTYAEILGVVPVAGGE 65
Query: 572 GLKVVRVC------AKSREA----IDSPVSFLALHNQIRNMEMNSELKKLLQ 613
G V V AK+R ID+ LHN ME ELKK+ +
Sbjct: 66 GADPVAVAKDAVELAKARGYDVVLIDTAGR---LHNDENLME---ELKKIKR 111
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 34.2 bits (79), Expect = 0.30
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 526 GPPGTGKTVTSATIVYQLVKQTGSPVLVCAPS--NIAVDQLTEKIHRTGLKVVR 577
G GTGKT T A + Y L K S V+ + A++QL E R G+KV++
Sbjct: 147 GVNGTGKTTTIAKLAYYLKKNGFSVVIAAGDTFRAGAIEQLEEHAERLGVKVIK 200
>gnl|CDD|238540 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 = 32.9 bits (75), Expect = 0.39
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLV 553
L+ GP G+GKT + + + + G V V
Sbjct: 3 LVFGPTGSGKTTLALQLALNIATKGGKVVYV 33
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 31.9 bits (72), Expect = 0.40
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 4/30 (13%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
LI GPPG+GK+ T+ +L ++ G PV+
Sbjct: 3 LITGPPGSGKS----TLAKKLAEKLGIPVI 28
>gnl|CDD|218535 pfam05281, Secretogranin_V, Neuroendocrine protein 7B2 precursor
(Secretogranin V). The neuroendocrine protein 7B2 has a
critical role in the proteolytic conversion and
activation of proPC2, the enzyme responsible for the
proteolytic conversion of many peptide hormone
precursors. The 7B2 protein acts as an intracellular
binding protein for proPC2, facilitates its maturation,
and is required for its enzymatic activity. Processing
of many important peptide precursors does not occur in
7B2 nulls. 7B2 null mice exhibit a unique form of
Cushing's disease with many atypical symptoms, such as
hypoglycemia.
Length = 210
Score = 33.3 bits (76), Expect = 0.41
Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 5/67 (7%)
Query: 37 DFTLPSQSQTQASQLDSVNQIQVNGKQNLDNSNLNLVSQKLHELQFEEEEDDGNEFFNKE 96
F P++SQT +S+ +S+ I K + L+++K H + N + E
Sbjct: 142 MFPCPAKSQTDSSKQESLQPILEESKWHK-----TLLAKKFHVKKSSRRSRSVNPYLQGE 196
Query: 97 LPPHACK 103
K
Sbjct: 197 RLDVVAK 203
>gnl|CDD|239389 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the membrane
by an interaction between SRP and its cognated receptor
(SR). In mammals, SRP consists of six protein subunits
and a 7SL RNA. One of these subunits is a 54 kd protein
(SRP54), which is a GTP-binding protein that interacts
with the signal sequence when it emerges from the
ribosome. SRP54 is a multidomain protein that consists
of an N-terminal domain, followed by a central G
(GTPase) domain and a C-terminal M domain.
Length = 173
Score = 32.9 bits (76), Expect = 0.42
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQLTEKIHRTGLKVV 576
G GKT T+A + L K+ +LV A P+ A++QL + G+ V
Sbjct: 10 GVGKTTTAAKLALYLKKKGKKVLLVAADTYRPA--AIEQLRVLGEQVGVPVF 59
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 33.8 bits (78), Expect = 0.46
Identities = 33/112 (29%), Positives = 46/112 (41%), Gaps = 31/112 (27%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPS--NIAVDQLTEKIHRTGLKVVR--- 577
L G G GKT T A + L +Q S +L + A++QL R G+ V+
Sbjct: 143 LFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAAGDTFRAAAIEQLEVWGERLGVPVISGKE 202
Query: 578 ------VC------AKSREA----IDSPVSFLA--LHNQIRNMEMNSELKKL 611
V AK+R ID+ A LHN+ M+ ELKK+
Sbjct: 203 GADPAAVAFDAIQAAKARGIDVVLIDT-----AGRLHNKKNLMD---ELKKI 246
>gnl|CDD|236686 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 33.5 bits (78), Expect = 0.47
Identities = 35/141 (24%), Positives = 56/141 (39%), Gaps = 50/141 (35%)
Query: 507 RSQVYAVKHAIQRPLSLIQGPP---------GTGKTVTSATIVYQLVKQTGSPVLVCAPS 557
+ ++ + +++PL++ + P G GKT T + ++ Q G VL+ A
Sbjct: 93 KEELAEILEPVEKPLNIEEKKPFVILVVGVNGVGKTTTIGKLAHKYKAQ-GKKVLLAA-- 149
Query: 558 NI-------AVDQLTEKIHRTGLKVVR---------VC------AKSREA----IDSPVS 591
A++QL R G+ V+ V AK+R ID+
Sbjct: 150 --GDTFRAAAIEQLQVWGERVGVPVIAQKEGADPASVAFDAIQAAKARGIDVLIIDT--- 204
Query: 592 FLA--LHNQIRNMEMNSELKK 610
A LHN+ ME ELKK
Sbjct: 205 --AGRLHNKTNLME---ELKK 220
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains contain
a P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 316
Score = 33.6 bits (77), Expect = 0.48
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 520 PLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLV 553
P LI GP G+GK+ + +L+ + G V+V
Sbjct: 2 PNMLIVGPSGSGKSTLLKLLALRLLAR-GGRVIV 34
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 33.8 bits (78), Expect = 0.56
Identities = 35/135 (25%), Positives = 47/135 (34%), Gaps = 39/135 (28%)
Query: 494 PKHFSAPNLPDLNRSQVYAVKHAIQRPL----SLIQGPPGTGKTVTSATIVY-QLVKQT- 547
P S LN+ Q AV+ + L+ G G+GKT VY + + +
Sbjct: 188 PPDPSLSEWLALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTE-----VYLEAIAKVL 242
Query: 548 --GSPVLVCAPSNIAV-DQLTEKIH-RTGLKV-----------------------VRVCA 580
G VLV P IA+ QL + R G KV RV
Sbjct: 243 AQGKQVLVLVPE-IALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVI 301
Query: 581 KSREAIDSPVSFLAL 595
+R A+ P L L
Sbjct: 302 GTRSALFLPFKNLGL 316
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 33.2 bits (76), Expect = 0.56
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 6/49 (12%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRT 571
LI GPPGTGKT+ + +Y+ ++ G PVL ++ ++ E++
Sbjct: 27 LITGPPGTGKTIFALQFLYEGARE-GEPVLY-----VSTEESPEELLEN 69
>gnl|CDD|216004 pfam00580, UvrD-helicase, UvrD/REP helicase N-terminal domain. The
Rep family helicases are composed of four structural
domains. The Rep family function as dimers. REP
helicases catalyze ATP dependent unwinding of double
stranded DNA to single stranded DNA. Some members have
large insertions near to the carboxy-terminus relative
to other members of the family.
Length = 267
Score = 33.0 bits (76), Expect = 0.56
Identities = 58/261 (22%), Positives = 90/261 (34%), Gaps = 87/261 (33%)
Query: 505 LNRSQVYAVKHAIQRPLSLIQGPPGTGKT-VTSATIVYQLVKQTGSPVLVCAPSNIAVDQ 563
LN Q AV H + PL L+ G+GKT V + I Y L+ + G P I
Sbjct: 1 LNPEQRKAVTH-LGGPL-LVLAGAGSGKTRVLTERIAY-LILEGG-----IDPEEILAVT 52
Query: 564 LTEK-------------------------IHRTGLKVVR--------------------- 577
T K H L+++R
Sbjct: 53 FTNKAAREMKERILKLLGKAELSELNISTFHSFCLRILRKYANRIGLLPNFSILDELDQL 112
Query: 578 -----VCAKSREAIDS----PVSFLALHNQIRNMEMNSELKKLLQLKEETGELSSADE-- 626
+ K R +D + L ++ +N L +L++
Sbjct: 113 ALLKELLEKDRLNLDPKLLRKLELKELISKAKN-----RLLSPEELQQGAATPRDKLAAE 167
Query: 627 --KRY--RMLKKNAEKSLLDNADVICCTC-VGAGDPRLLKI---KFHSILIDESMQATEP 678
+ Y R+ + NA LD D++ T + DP LL+ +F IL+DE Q T P
Sbjct: 168 FYQEYQERLKENNA----LDFDDLLLLTLELLRSDPELLEAYRERFKYILVDE-FQDTNP 222
Query: 679 --ECMVPVILGAKQ-LILVGD 696
++ ++ G + L LVGD
Sbjct: 223 IQYRLLKLLAGGHENLFLVGD 243
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase /
dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin that
induces shoot formation on host plants infected with the
Ti plasmid.
Length = 232
Score = 32.8 bits (75), Expect = 0.62
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 521 LSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLV 553
L LI G TGKT + L K+TG PV+V
Sbjct: 3 LYLIWGATCTGKTAEAI----ALAKETGWPVIV 31
>gnl|CDD|216631 pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain.
This family consists of various cobyrinic acid
a,c-diamide synthases. These include CbiA and CbiP from
S.typhimurium, and CobQ from R. capsulatus. These
amidases catalyze amidations to various side chains of
hydrogenobyrinic acid or cobyrinic acid a,c-diamide in
the biosynthesis of cobalamin (vitamin B12) from
uroporphyrinogen III. Vitamin B12 is an important
cofactor and an essential nutrient for many plants and
animals and is primarily produced by bacteria. The
family also contains dethiobiotin synthetases as well as
the plasmid partitioning proteins of the MinD/ParA
family.
Length = 217
Score = 32.8 bits (75), Expect = 0.63
Identities = 33/184 (17%), Positives = 58/184 (31%), Gaps = 41/184 (22%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLV--CAPSNIAVDQLTEKIHRTGLKVVRVCAKSREAI 586
G GKT +A + L K+ G VL+ P L + + V A++ +AI
Sbjct: 9 GVGKTTLAANLARALAKR-GYRVLLIDLDPQANNSSYLGKVEEVLPEGLEIVDAQALQAI 67
Query: 587 DSPVSFLALHNQIRNMEMNSELKKLLQLKEETGELSSAD------EKRYRMLKKNAEKSL 640
+ + S L L L + + KR L+ E +
Sbjct: 68 AAAIV-------------PSRNLDPLLLIPSNLSLENFESELIVEGKRESRLRAALESLI 114
Query: 641 LDNADVICCTCVGAGDPRLLKIKFHSILIDESMQA-------TEPECMVPVILGAKQLIL 693
D + L ++ A EPE + + GA++L+
Sbjct: 115 KLAYDYVIIDGPPG----------LGELTANALVAADILVVPIEPEGV--AVEGAQRLLE 162
Query: 694 VGDH 697
+ +
Sbjct: 163 LIED 166
>gnl|CDD|236780 PRK10867, PRK10867, signal recognition particle protein;
Provisional.
Length = 433
Score = 32.7 bits (76), Expect = 1.00
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 16/61 (26%)
Query: 518 QRPLSLIQGPP---------GTGKTVTSATIVYQLVKQTGSPVLVCA-----PSNIAVDQ 563
L+L PP G GKT T+ + L K+ VL+ A P+ A++Q
Sbjct: 90 NSELNLAAKPPTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPA--AIEQ 147
Query: 564 L 564
L
Sbjct: 148 L 148
>gnl|CDD|237554 PRK13909, PRK13909, putative recombination protein RecB;
Provisional.
Length = 910
Score = 33.0 bits (76), Expect = 1.0
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 9/73 (12%)
Query: 887 LNDPRRLN---VALTRAKYGIIVIGNPKVLSKQPLWNNLLNF--YKEQKVLVEGP-LNNL 940
L +N VA TRAK +IV+ + +L+ + ++ ++ P ++
Sbjct: 676 LKYEEEINVLYVAFTRAKNSLIVVKKDE---SSGSMFEILDLKPLERGEIEIKEPKISPK 732
Query: 941 KESLILFSKPKQY 953
KESLI K K +
Sbjct: 733 KESLITSVKLKPH 745
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is one
of the Kai proteins among which direct protein-protein
association may be a critical process in the generation
of circadian rhythms in cyanobacteria.
Length = 231
Score = 32.2 bits (74), Expect = 1.0
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
LI G PGTGKT+ +Y + G P +
Sbjct: 23 LITGGPGTGKTIFGLQFLYNGALEYGEPGV 52
>gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated.
Length = 234
Score = 31.9 bits (73), Expect = 1.1
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 521 LSLIQGPPGTGKTVTSATIVYQLVKQ 546
L LI+G GTGK+V S VY +KQ
Sbjct: 27 LILIEGDHGTGKSVLSQQFVYGALKQ 52
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 32.5 bits (75), Expect = 1.1
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 519 RPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
RP +L+ G GTGKT+ + + +K+ P +
Sbjct: 32 RP-TLVSGTAGTGKTLFALQFLVNGIKRFDEPGV 64
>gnl|CDD|218449 pfam05127, Helicase_RecD, Helicase. This domain contains a P-loop
(Walker A) motif, suggesting that it has ATPase
activity, and a Walker B motif. In tRNA(Met) cytidine
acetyltransferase (TmcA) it may function as an RNA
helicase motor (driven by ATP hydrolysis) which delivers
the wobble base to the active centre of the GCN5-related
N-acetyltransferase (GNAT) domain. It is found in the
bacterial exodeoxyribonuclease V alpha chain (RecD),
which has 5'-3' helicase activity. It is structurally
similar to the motor domain 1A in other SF1 helicases.
Length = 160
Score = 31.4 bits (72), Expect = 1.2
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 542 QLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVCAKSREAIDSPVS 591
L+ Q S +LV APS V L E + GL + K RE I + +
Sbjct: 7 ALIAQGYSRILVTAPSPANVQTLFEFAIK-GLDALGYKPKKREGIIASLR 55
>gnl|CDD|223801 COG0729, COG0729, Outer membrane protein [Cell envelope biogenesis,
outer membrane].
Length = 594
Score = 32.3 bits (74), Expect = 1.3
Identities = 40/250 (16%), Positives = 63/250 (25%), Gaps = 60/250 (24%)
Query: 263 GVDEDPHQVLLRYEDGYQYQNIFGPLVKLEADY----------DKRLKESQTQENVTVRW 312
V E +E G Y G ++ + + S + + +
Sbjct: 271 SVSERKE---NTFELGVGYSTDVGAGLEAGWEKRNLFGRGHSLRIESEISAPLQTLEATY 327
Query: 313 DVGLNKKSIAY----------FSLAKTDGDGY--------QYQNIFGPLVKLEADYDKRL 354
L + L T+ D Y + G L +
Sbjct: 328 KAPLLFNPLGQYNPVSAGFDRLDLYDTESDAYTESLSASRGWDASLGWQRSLALRF---S 384
Query: 355 KESQTQENVTVRWDVGLNKKSIAYFSLAKT-DGDMRLM--QGDELKLRYSYDASKTWSGL 411
++ Q +++ G + T D D L GD L + S G
Sbjct: 385 YDNFRQGDIS-----GKTSLLTPGVEFSYTRDTDDGLFPTWGDRL--DLTIGPSYEALG- 436
Query: 412 GHVIKIPDNFGDEVGLELKSSAGAPTEAT-----TGFSVDFIWKSTSFDRMQLALRKFAV 466
D L S T + I D + +LR FA
Sbjct: 437 ------SDVD---FRLVQARSGYLRTGGADHRLAGRGELGAILTG-DLDDVPPSLRFFAG 486
Query: 467 DDQSVSAYIY 476
D+SV Y Y
Sbjct: 487 GDRSVRGYGY 496
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 30.7 bits (70), Expect = 2.0
Identities = 26/111 (23%), Positives = 42/111 (37%), Gaps = 17/111 (15%)
Query: 521 LSLIQGPPGTGKTVTSATIVYQLVKQ--TGSPVL---VCAPSNIAVDQLTEKIHRTGLKV 575
L+L+ G PGTGK+ T+ L TG P L P + + ++
Sbjct: 35 LTLLAGAPGTGKS----TLALDLAAAVATGRPFLGPFPVEPGRVLYLDGEDSEAGLRRRL 90
Query: 576 VRVCAKSREA-------IDSPVSFLALHNQIRNMEMNSELKKLLQLKEETG 619
+ E ID P++ L ++ N + + L L +L TG
Sbjct: 91 RALGEALEEIEGPDLVVID-PLASLLGGDENDNAAVGALLAALDRLARRTG 140
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 31.5 bits (72), Expect = 2.0
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
L+ G GTGKT +A I +L+++ G PV+
Sbjct: 118 LLWGSVGTGKTYLAACIANELIEK-GVPVI 146
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 31.3 bits (72), Expect = 2.4
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 5/34 (14%)
Query: 523 LIQGPPGTGKTVTSATIV-YQL---VKQTGSPVL 552
L+ GPPG GKT T A I+ ++ ++ T P L
Sbjct: 55 LLYGPPGLGKT-TLANIIANEMGVNIRITSGPAL 87
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 29.9 bits (68), Expect = 2.4
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 518 QRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHR 570
+ ++ G G+GKT + QL + V V APS L KI R
Sbjct: 3 GAGIGVLTGESGSGKTTLLRRLARQLPNRRV--VYVEAPSLGTPKDLLRKILR 53
>gnl|CDD|233914 TIGR02538, type_IV_pilB, type IV-A pilus assembly ATPase PilB.
This model describes a protein of type IV pilus
biogenesis designated PilB in Pseudomonas aeruginosa but
PilF in Neisseria gonorrhoeae; the more common usage,
reflected here, is PilB. This protein is an ATPase
involved in protein export for pilin assembly and is
closely related to GspE (TIGR02533) of type II
secretion, also called the main terminal branch of the
general secretion pathway. Note that type IV pilus
systems are often divided into type IV-A and IV-B, with
the latter group including bundle-forming pilus,
mannose-sensitive hemagglutinin, etc. Members of this
family are found in type IV-A systems [Cell envelope,
Surface structures, Protein fate, Protein and peptide
secretion and trafficking].
Length = 564
Score = 31.5 bits (72), Expect = 2.6
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 514 KHAIQRP--LSLIQGPPGTGKTVT 535
AI +P + L+ GP G+GKTV+
Sbjct: 309 LEAIHKPQGMVLVTGPTGSGKTVS 332
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 31.0 bits (71), Expect = 2.6
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVK 545
L+ G PGTGKTV + + +L
Sbjct: 5 LVTGGPGTGKTVVALNLFAELSD 27
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 31.1 bits (71), Expect = 2.8
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 493 LPKHFSAPNLPDL--NRSQVYAVKHAIQRP--LSLIQGPPGTGKTVT 535
L K +L L + Q+ + + RP L L+ GP G+GKT T
Sbjct: 228 LDKDQVILDLEKLGMSPFQLARLLRLLNRPQGLILVTGPTGSGKTTT 274
>gnl|CDD|226581 COG4096, HsdR, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 875
Score = 31.3 bits (71), Expect = 2.9
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 519 RPLSLIQGPPGTGKTVTSATIVYQLVK-QTGSPVLVCAPSNIAVDQ 563
+ +L+ GTGKT T+ I+ +L+K VL A N VDQ
Sbjct: 185 QNRALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQ 230
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 31.0 bits (71), Expect = 2.9
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 517 IQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
++ L L+ GPPG GKT ++ + L G V+
Sbjct: 38 PKKAL-LLYGPPGVGKT----SLAHALANDYGWEVI 68
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 31.3 bits (71), Expect = 3.0
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 503 PDLNRSQVYAVKHAIQRPLS----LIQGPPGTGKTVTSATIVYQL 543
++ R Y + +I+RP LI G G GK+V ++ + Y+L
Sbjct: 237 EEVARR--YRLLRSIRRPPRPLHVLIGGVSGVGKSVLASALAYRL 279
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 31.0 bits (71), Expect = 3.0
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 523 LIQGPPGTGKTVTSATIVYQL---VKQTGSPVL 552
L+ GPPG GKT + I +L +K T P L
Sbjct: 56 LLFGPPGLGKTTLAHIIANELGVNLKITSGPAL 88
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 31.3 bits (72), Expect = 3.0
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 15/59 (25%)
Query: 519 RPLSLIQGPP---------GTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQL 564
L+L + PP G+GKT T+ + L K+ +LV A P+ A++QL
Sbjct: 91 SELNLAKKPPTVILMVGLQGSGKTTTAGKLAKYLKKKGKKVLLVAADTYRPA--AIEQL 147
>gnl|CDD|234277 TIGR03604, TOMM_cyclo_SagD, thiazole/oxazole-forming peptide
maturase, SagD family component. Members of this
protein family include enzymes related to SagD,
previously referred to as a scaffold or docking protein
involved in the biosynthesis of streptolysin S in
Streptococcus pyogenes from the protoxin polypeptide
(product of the sagA gene). Newer evidence describes an
enzymatic activity, an ATP-dependent cyclodehydration
reaction, previously ascribed to the SagC component.
This protein family serves as a marker for widely
distributed prokaryotic systems for making a general
class of heterocycle-containing bacteriocins.
Length = 377
Score = 31.1 bits (71), Expect = 3.1
Identities = 10/20 (50%), Positives = 10/20 (50%)
Query: 559 IAVDQLTEKIHRTGLKVVRV 578
I VD I GL VVRV
Sbjct: 312 IVVDITPPDIRALGLYVVRV 331
>gnl|CDD|239241 cd02931, ER_like_FMN, Enoate reductase (ER)-like FMN-binding
domain. Enoate reductase catalyzes the NADH-dependent
reduction of carbon-carbon double bonds of several
molecules, including nonactivated 2-enoates,
alpha,beta-unsaturated aldehydes, cyclic ketones, and
methylketones. ERs are similar to 2,4-dienoyl-CoA
reductase from E. coli and to the old yellow enzyme from
Saccharomyces cerevisiae.
Length = 382
Score = 30.9 bits (70), Expect = 3.2
Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 13/76 (17%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLVCAPSN-----IAVDQLTEKIHRTGLKVV------- 576
GTG +T T+V ++Q P L C N ++TE++H G K+
Sbjct: 48 GTGLIITGVTMVDNEIEQFPMPSLPCPTYNPTAFIRTAKEMTERVHAYGTKIFLQLTAGF 107
Query: 577 -RVCAKSREAIDSPVS 591
RVC D PV+
Sbjct: 108 GRVCIPGFLGEDKPVA 123
>gnl|CDD|238941 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 = 28.9 bits (65), Expect = 3.6
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVC 554
++ G G GKT +A + L K+ G VL+
Sbjct: 3 VVTGKGGVGKTTLAANLAAALAKR-GKRVLLI 33
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 30.3 bits (69), Expect = 3.9
Identities = 9/52 (17%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 503 PDLNRSQVYAVKHAIQRPLS-LIQGPPGTGKTVTSATIVYQLVKQTGSPVLV 553
+ ++ A+Q + L+ G G+GKT ++ ++ V +
Sbjct: 112 GAFDADIAEFLRQAVQARGNILVSGGTGSGKTTLLYALLNEINTDDERIVTI 163
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 30.5 bits (69), Expect = 3.9
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 7/47 (14%)
Query: 507 RSQVYAVKHAI--QRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPV 551
+ A+ + L++GPPG GKT + L + G P
Sbjct: 30 EEVIELALLALLAGGHV-LLEGPPGVGKT----LLARALARALGLPF 71
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 30.6 bits (70), Expect = 4.0
Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 9/48 (18%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQL---TEKIH 569
G+GKT T+A + K+ LV A P+ A DQL EKI
Sbjct: 105 GSGKTTTAAKLARYFKKKGLKVGLVAADTYRPA--AYDQLKQLAEKIG 150
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 30.8 bits (70), Expect = 4.7
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 10/77 (12%)
Query: 502 LP-DLNRSQVYAVKHAIQRPLS-------LIQGPPGTGKTVTSATIVYQLVKQTGSPVLV 553
LP L R+Q VK I + L L+QG G+GKT+ +A + ++ G V +
Sbjct: 232 LPFKLTRAQKRVVKE-ILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA-GYQVAL 289
Query: 554 CAPSNIAVDQLTEKIHR 570
AP+ I +Q +
Sbjct: 290 MAPTEILAEQHYNSLRN 306
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 30.4 bits (70), Expect = 4.8
Identities = 14/23 (60%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 519 RPLSLI-QGPPGTGKTVTSATIV 540
R S+I GPPGTGKT T A I+
Sbjct: 35 RLSSMILWGPPGTGKT-TLARII 56
>gnl|CDD|216554 pfam01529, zf-DHHC, DHHC palmitoyltransferase. This family
includes the well known DHHC zinc binding domain as well
as three of the four conserved transmembrane regions
found in this family of palmitoyltransferase enzymes.
Length = 167
Score = 29.4 bits (66), Expect = 5.4
Identities = 12/49 (24%), Positives = 22/49 (44%)
Query: 73 VSQKLHELQFEEEEDDGNEFFNKELPPHACKYCGIHDPAYVIMCNICKK 121
V + E + E++ D+ +E ++E C C I P C +C +
Sbjct: 15 VPKNPTEKEQEKQPDEESEEGDEEDELKFCSTCNIIKPPRSHHCRVCNR 63
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 29.5 bits (67), Expect = 5.8
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQ 546
L+ GPPG GKT + + +Q +
Sbjct: 51 LLLGPPGVGKTHLACALGHQACRA 74
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 30.0 bits (68), Expect = 5.9
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 519 RPLS-LIQGPPGTGKTVTSATIVYQLVKQTGSP--VLVCAPSNIAVDQLTEKIHRTGLKV 575
RP + +I GP GTGKT T ++ +L + + + V + Q+ KI KV
Sbjct: 41 RPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKV 100
>gnl|CDD|176230 cd08269, Zn_ADH9, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 312
Score = 29.6 bits (67), Expect = 7.1
Identities = 16/88 (18%), Positives = 27/88 (30%), Gaps = 23/88 (26%)
Query: 668 LIDESMQATEPECMVPVILGAKQL-----------ILVGDHC------QLGPVVMCKKAA 710
L D P + + L I G +G + + + AA
Sbjct: 92 LADADHAVPLPSLLDGQAFPGEPLGCALNVFRRGWIRAGKTVAVIGAGFIGLLFL-QLAA 150
Query: 711 RAGLSQSLFERLVVLGIRPFRLEVQYRM 738
AG R++ + RP RL + +
Sbjct: 151 AAG-----ARRVIAIDRRPARLALAREL 173
>gnl|CDD|224000 COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit
(contains helicase and exonuclease domains) [DNA
replication, recombination, and repair].
Length = 1139
Score = 30.1 bits (68), Expect = 7.1
Identities = 20/70 (28%), Positives = 27/70 (38%), Gaps = 4/70 (5%)
Query: 891 RRLNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFYKEQKVLVEGPLNNLKESLILFSKP 950
R L VALTRAK +I+IG P K + L Q+V V G + I
Sbjct: 817 RLLYVALTRAKEQLILIGAPSKREK---SSALAPLDLGQRVQVGGTQDWEGLLAIALKLS 873
Query: 951 -KQYFKKNNM 959
++
Sbjct: 874 DPVLEEEALG 883
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 30.2 bits (68), Expect = 7.4
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 43 QSQTQASQLDSVNQIQVNGKQNLDNSNLNLVSQKLHELQFEEEEDD 88
+S ++S ++ ++ +QNLD NLV + LHE FE E D
Sbjct: 138 RSHEGRPFMESFSKQEIQVQQNLDTKVYNLVIK-LHEEGFEAERFD 182
>gnl|CDD|225429 COG2874, FlaH, Predicted ATPases involved in biogenesis of archaeal
flagella [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 235
Score = 29.2 bits (66), Expect = 8.0
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 521 LSLIQGPPGTGKTVTSATIVYQLVKQ 546
L LI+G GTGK+V S Y +
Sbjct: 30 LILIEGDNGTGKSVLSQRFAYGFLMN 55
>gnl|CDD|233050 TIGR00609, recB, exodeoxyribonuclease V, beta subunit. The RecBCD
holoenzyme is a multifunctional nuclease with potent
ATP-dependent exodeoxyribonuclease activity. Ejection of
RecD, as occurs at chi recombinational hotspots,
cripples exonuclease activity in favor of recombinagenic
helicase activity. All proteins in this family for which
functions are known are DNA-DNA helicases that are used
as part of an exonuclease-helicase complex (made up of
RecBCD homologs) that function to generate substrates
for the initiation of recombination and recombinational
repair. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1087
Score = 30.1 bits (68), Expect = 8.5
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 5/77 (6%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTG----SPVLVCAPSNIAVDQLTEKIHRTGLKVVRV 578
LI+ GTGKT T A + +L+ + G +LV +N A ++L +I R +
Sbjct: 13 LIEASAGTGKTFTIAQLYLRLLLEGGPLTVEEILVVTFTNAATEELKTRI-RGRIHQALR 71
Query: 579 CAKSREAIDSPVSFLAL 595
K+ L
Sbjct: 72 ALKAALTSQELPEPLKE 88
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 29.1 bits (66), Expect = 8.5
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 518 QRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAP 556
+R + I GPPG GK+ T A + L++Q G + P
Sbjct: 32 RRTIVGIAGPPGAGKS-TLAEFLEALLQQDGELPAIQVP 69
>gnl|CDD|222178 pfam13500, AAA_26, AAA domain. This domain is found in a number of
proteins involved in cofactor biosynthesis such as
dethiobiotin synthase and cobyric acid synthase. This
domain contains a P-loop motif.
Length = 197
Score = 29.1 bits (66), Expect = 8.5
Identities = 6/35 (17%), Positives = 14/35 (40%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPS 557
+++G G + + + G PV++ A
Sbjct: 102 VVEGAGGLMVPLNENLLNIDIAANLGLPVILVARG 136
>gnl|CDD|234566 PRK00004, rplX, 50S ribosomal protein L24; Reviewed.
Length = 105
Score = 27.8 bits (63), Expect = 9.3
Identities = 18/38 (47%), Positives = 19/38 (50%), Gaps = 7/38 (18%)
Query: 557 SNIA-VDQLTEKIHRTGLKV------VRVCAKSREAID 587
SN+A VD T K R G K VRV KS E ID
Sbjct: 68 SNVALVDPKTGKATRVGFKFLEDGKKVRVAKKSGEVID 105
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus.
The RuvB protein makes up part of the RuvABC revolvasome
which catalyzes the resolution of Holliday junctions
that arise during genetic recombination and DNA repair.
Branch migration is catalyzed 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 = 231
Score = 29.0 bits (66), Expect = 9.4
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 9/49 (18%)
Query: 512 AVKHAIQR--PLS--LIQGPPGTGKTVTSATIVYQ----LVKQTGSPVL 552
++ A +R L L+ GPPG GKT T A I+ ++ T P L
Sbjct: 39 FIEAAKKRGEALDHVLLYGPPGLGKT-TLANIIANEMGVNIRITSGPAL 86
>gnl|CDD|216306 pfam01117, Aerolysin, Aerolysin toxin. This family represents the
pore forming lobe of aerolysin.
Length = 359
Score = 29.3 bits (66), Expect = 9.4
Identities = 15/64 (23%), Positives = 22/64 (34%), Gaps = 8/64 (12%)
Query: 398 LRYSYDASKTWS-----GLGHVIKIPDNFGDEVGLELKSSAGAPTEATTGFSVDFIWKST 452
+ YD S WS G + I + F + L K+ EA +S ST
Sbjct: 121 VTLRYDQSTNWSKTDTYGFAEKVGIKNKF--KWPLVGKTELSIEFEANQSWS-STNGGST 177
Query: 453 SFDR 456
+
Sbjct: 178 TKSV 181
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 28.8 bits (65), Expect = 9.9
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 8/61 (13%)
Query: 523 LIQGPPGTGKTVTSA-TIVYQLVKQTGSP-VLVCAPS-----NIAVDQLTEKIHRTGLKV 575
L+Q P G+GKT+ I+ L+ + G P LV AP+ I ++L + GL+V
Sbjct: 18 LVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQI-YEELKKLFKILGLRV 76
Query: 576 V 576
Sbjct: 77 A 77
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
0.318 0.135 0.400
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 48,137,221
Number of extensions: 4734338
Number of successful extensions: 4370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4334
Number of HSP's successfully gapped: 97
Length of query: 959
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 853
Effective length of database: 6,236,078
Effective search space: 5319374534
Effective search space used: 5319374534
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: 64 (28.1 bits)