RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 000053
(2576 letters)
>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 = 241 bits (618), Expect = 6e-73
Identities = 86/197 (43%), Positives = 114/197 (57%), Gaps = 6/197 (3%)
Query: 630 FGRSLFERLSHL-RHSKHLLSIQYRMHPSISFFPNSYFYENKIHDSPTVEKRSYEKRFLP 688
RSLFERL + +L QYRMHP IS FP+ FY K+ D +V +R F
Sbjct: 1 LDRSLFERLQEAGPEAVVMLDTQYRMHPDISEFPSELFYGGKLKDGESVAERPLPWDFHL 60
Query: 689 GPMYGPYSFINVFGGREEF-IEHSCRNMVEVSVVMKILLNLYKGWINSKEKLSIGIVSPY 747
GP FI+V G EE S N E +V++++ L K + IGI++PY
Sbjct: 61 PDPLGPLVFIDVDGSEEEEEKSTSYSNEAEAELVVQLVEKLLKSGPEKNKD--IGIITPY 118
Query: 748 IAQVAAIQEKLGSKYVNSAGFAVKVMSVDGFQGGEEDIIIISTVRSNNGGSIGFISNPRR 807
AQV I++ L K+ ++V +VDGFQG E+D+II STVRSN G IGF+S+PRR
Sbjct: 119 RAQVRLIKKLLKRKFGGEPD--IEVNTVDGFQGREKDVIIFSTVRSNEKGGIGFLSDPRR 176
Query: 808 VNVALTRARHCLWILGN 824
+NVALTRA+ L I+GN
Sbjct: 177 LNVALTRAKRGLIIVGN 193
>gnl|CDD|224037 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase
subunits [DNA replication, recombination, and repair].
Length = 767
Score = 160 bits (407), Expect = 6e-40
Identities = 114/338 (33%), Positives = 163/338 (48%), Gaps = 17/338 (5%)
Query: 519 SECHFVLRKLLSSFNELNLPSAVEKDLLEDLLKRFCLKRASLFFSTASSSYMLHSVAMKP 578
L S E E L+ L+ A + ST S + +
Sbjct: 430 LPALNKSEALWISLEEKQKKILKELRRLKKKAVTKILEAADVVLSTLSIAGFSILKKYE- 488
Query: 579 LNFLVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLPAMVESKVSDEACFGRSLFERL 638
++++IDEA+Q E + I L S K +L GD QLP V K S SLFERL
Sbjct: 489 FDYVIIDEASQATEPSALIAL--SRAKKVILVGDHKQLPPTVFFKESSPEGLSASLFERL 546
Query: 639 -SHLRHSKHLLSIQYRMHPSISFFPNSYFYENK--IHDSPTVEKRSYEKRFLPGPMYGPY 695
+ +LL +QYRMHP I F + FY + +H S + P
Sbjct: 547 IDNGPEVVYLLRVQYRMHPDIIAFSSKVFYNGRLEVHTSFLAFTLLDGEIPEVVISN-PL 605
Query: 696 SFINVFGGREEFIEHSCRNMVEVSVVMKILLNLYKGWINSKEKLSIGIVSPYIAQVAAIQ 755
F + G E F S N +E +V I+ L K + E+ IG++SPY AQV+ I+
Sbjct: 606 EFYDTLGAEEFFESKSKLNELEAEIVKVIVDELLK---DGLEENDIGVISPYRAQVSLIR 662
Query: 756 EKLGSKYVNSAGFAVKVMSVDGFQGGEEDIIIISTVRSN-NGGSIGFISNPRRVNVALTR 814
L N AG V+V +VDGFQG E+D+II+S VRSN + G IGF+ +PRR+NVALTR
Sbjct: 663 RLL-----NEAGKGVEVGTVDGFQGREKDVIILSLVRSNDDKGEIGFLGDPRRLNVALTR 717
Query: 815 ARHCLWILGNERTLTRNRSVWKALVDDAKARQCFFNAD 852
A+ L ++G+ TL + ++K L++D K + +
Sbjct: 718 AKRKLIVVGSSSTL-ESDPLYKRLINDLKRKGLLAELN 754
>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 = 158 bits (402), Expect = 1e-39
Identities = 99/290 (34%), Positives = 147/290 (50%), Gaps = 34/290 (11%)
Query: 582 LVIDEAAQLKESESTIPLQLSGIKHA--VLFGDECQLPAMVESKVSDEACFGRSLFERLS 639
VIDEA+Q E IPL +K +L GD QLP + S D +LFERL
Sbjct: 365 AVIDEASQAMEPSCLIPL----LKARKLILAGDHKQLPPTILSH--DAEELELTLFERLI 418
Query: 640 HLRHSK-HLLSIQYRMHPSISFFPNSYFYENKIHDSPTVEKRSYEKRFLPGPMYG----- 693
+ L++QYRM+ I FP+ FY K+ +V R LP
Sbjct: 419 KEYPERSRTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANILL--RDLPKVEATESEDD 476
Query: 694 -----PYSFINVFG----GREEFIEHSCRNMVEVSVVMKILLNLYKGWINSKEKLSIGIV 744
P FI+ G +E S N E +V +I+ L K + + + IG++
Sbjct: 477 LETGIPLLFIDTSGCELFELKEADSTSKYNPGEAELVSEIIQALVKMGVPAND---IGVI 533
Query: 745 SPYIAQVAAIQEKLGSKYVNSAGFAVKVMSVDGFQGGEEDIIIISTVRSNNGGSIGFISN 804
+PY AQV +++ L ++++ ++V SVDGFQG E+++IIIS VRSN G +GF+ +
Sbjct: 534 TPYDAQVDLLRQLLEHRHID-----IEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKD 588
Query: 805 PRRVNVALTRARHCLWILGNERTLTRNRSVWKALVDDAKARQCFFNADDD 854
RR+NVALTRAR L ++G+ RTL+ ++ +K L++ K A D
Sbjct: 589 LRRLNVALTRARRKLIVIGDSRTLSNHK-FYKRLIEWCKQHGEVREAFKD 637
Score = 44.8 bits (106), Expect = 7e-04
Identities = 45/177 (25%), Positives = 77/177 (43%), Gaps = 21/177 (11%)
Query: 120 REPYKTL--PGDILVLADAKPETASDLQ----RVGRMWTFVSVA---NVTE---DENEID 167
R+ T GDI++++ P SDL RVG+ F++VA +V + ID
Sbjct: 51 RKAIATEISVGDIVLVSRGNPLQ-SDLTGVVTRVGK--RFITVALEESVPQWSLKRVRID 107
Query: 168 TSPTYFKVNATKEIQIDVSKKSLFVI-FLINRTSNRRIWNSLHMKG-----NLKIIKELL 221
KE +++ ++ F++ R + + + N + +L
Sbjct: 108 LYANDVTFKRMKEALRALTENHSRLLEFILGREAPSKASEIHDFQFFDPNLNESQKEAVL 167
Query: 222 CTDSGATVQLIWGPPGTGKTKTVSMLLVILLQMKFRTLVCTPTIVAIKELASRVVKL 278
S + LI GPPGTGKT+T+ L+ L++ R LV P+ +A+ L R+
Sbjct: 168 FALSSKDLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALC 224
>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 = 68.5 bits (168), Expect = 2e-12
Identities = 39/135 (28%), Positives = 60/135 (44%), Gaps = 5/135 (3%)
Query: 492 EELLSHSVDEDLSESIVDIKYLLHKRRSECHFVLRKLLSSFNELNLPSAV---EKDLLED 548
E++L +S++ L + + K +S KL +L E + L
Sbjct: 88 EDVLQYSLEYLLEAKFEQLLKRIRKLKSLLEE-KSKLKRERRKLRSEIKKLKKELERLRK 146
Query: 549 LLKRFCLKRASLFFSTASSSYMLHSVAMKPLNFLVIDEAAQLKESESTIPLQLSGIKHAV 608
+++ L A + +T S + +K + ++IDEAAQ E E+ IPL L G K V
Sbjct: 147 SIRKEILDEADVVCTTLSGAGSSLLEGLKKFDVVIIDEAAQATEPETLIPLLL-GCKKVV 205
Query: 609 LFGDECQLPAMVESK 623
L GD QLP V S
Sbjct: 206 LVGDHKQLPPTVLSP 220
Score = 64.7 bits (158), Expect = 5e-11
Identities = 25/99 (25%), Positives = 45/99 (45%), Gaps = 17/99 (17%)
Query: 229 VQLIWGPPGTGKTKTVSMLLVILL--QMKFRTLVCTPTIVAIKELASRVVKLVKESVERD 286
+ LI GPPGTGKT T+ ++ LL + LVC P+ A+ + R+++
Sbjct: 19 ITLIQGPPGTGKTTTIVEIIKQLLSNAPGKKVLVCAPSNSAVDNILERLLEQKFGL---- 74
Query: 287 CRDALFFPLGEILLLGNNERLKVDSGVEEIYLDYRVKRL 325
+I+ +G+ R + V + L+Y ++
Sbjct: 75 ----------KIVRIGSPARE-IHEDVLQYSLEYLLEAK 102
>gnl|CDD|223288 COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA replication,
recombination, and repair].
Length = 655
Score = 53.7 bits (129), Expect = 1e-06
Identities = 68/346 (19%), Positives = 112/346 (32%), Gaps = 62/346 (17%)
Query: 1194 NSFIDIPAKSYPLVITFHKFLMMLDGTLCNSYFERFHNIWKNYGQLQNSKSVFIETIIRK 1253
+ +PA V TFH F + ++ +L +
Sbjct: 68 LKLLGLPAAEGLTVGTFHSFA--------------LRILRRHGERLGLNA---------- 103
Query: 1254 KEVNYERFSSSYWPHFNAQLARKLDPSRVFTEIISHIKGGLQSIEVVNGKLNREDYVNLS 1313
N+ S +L R+ + + E N L+ + L
Sbjct: 104 ---NFTILDSDDQLALIKELLRRELNLDDKELLPREALRYIS--EAKNALLSPLEASALL 158
Query: 1314 ETRNSSLSRQKRERIYDIFESYEQMKMRNGEFDLADLVNDLHHRLKEESYKGDE----FH 1369
S + +K +Y E Y+++ N D DL+ L+E + F
Sbjct: 159 LAAIKSEAEKKLAELY---EEYQELLRLNNALDFDDLLLLALRLLEENPEVLEALQARFR 215
Query: 1370 FVYIDEVQDLTMSQVALFKYVCKNIEEGFVFSGDTAQTIARGIDFRFQDIRSL--FYKKF 1427
++ +DE QD Q L K + N FV GD Q+I FR D ++ F K F
Sbjct: 216 YILVDEFQDTNPLQYELLKLLAGNAANLFV-VGDDDQSI---YGFRGADPENILDFEKDF 271
Query: 1428 VLESRNNGNDGRQEKRQLSDIFNLRQNFRTHVGVLNLAQSIIELLYRFFPHSVDILKPET 1487
+ L QN+R+ +L A +I + + L+ E
Sbjct: 272 -----PAAK-----------VIKLEQNYRSTPNILAAANKVIANNKKRQAKT---LRTE- 311
Query: 1488 SLIYGEPPILLESGDEENAILKIFGNTGEVGGNMVGFGAEQVILVR 1533
GE +LL + DEE+ I + ++ IL R
Sbjct: 312 VEGSGEKVVLLLANDEEDEARWIASEIDALIEIGKVNYSDIAILYR 357
Score = 37.9 bits (88), Expect = 0.082
Identities = 48/236 (20%), Positives = 85/236 (36%), Gaps = 43/236 (18%)
Query: 1441 EKRQLSDIFNLRQNFRTHVGVLNLAQSIIELLYRFFPHSVDILKPETSLIYGEPPILLES 1500
L D L + R + + + I ELL ++ L SL+ E LE+
Sbjct: 457 GLALLLDFAELIEELREAILLSTALELIRELLEALG--YLEALLEAGSLVAAEDR--LEN 512
Query: 1501 GDEENAILKIFGNTGEVGGNMVGFGAEQVILVRDDCVRKEISNYVGKQALVLTIVESKGL 1560
+E +LK + E ++ F +E + L+ +D +E Q ++TI +KGL
Sbjct: 513 LEELLDVLKRYAEPRE---SLRAFLSE-LSLLANDEEEEEPDE--DGQVNLMTIHAAKGL 566
Query: 1561 EFQDVLLYKFFSASPLKNQWRVVYEYMKEQDLLDSTSPGSFPSFNEVKHNILCS--ELKQ 1618
EF V L G FP+ + E +
Sbjct: 567 EFPYVFLV--------------------------GLEEGLFPADRSLDEGDEPLEEERRL 600
Query: 1619 LYVAITRTRQRLWIWENKEEFSKPMFDYWKKRFLVQVRRLDDSLAQAMQVASSPEE 1674
LYVAITR +++L++ + + R + + A+ + + +E
Sbjct: 601 LYVAITRAKKKLYLTYAASRKL---WGKEVEE--EPSRFVSELPAEDLLLLGEAQE 651
>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 = 48.6 bits (116), Expect = 5e-05
Identities = 42/207 (20%), Positives = 71/207 (34%), Gaps = 35/207 (16%)
Query: 1328 IYDIFESYEQMKMRNGEFDLADLVNDLHHRLKEE------SYKGDEFHFVYIDEVQDLTM 1381
+ ++ E Y+ K + D DL++ L L E S + ++ + IDE QD
Sbjct: 334 LEELIERYDAEKRQRNALDFDDLIHRLAKLLTSEGEELAESLRE-QYPHILIDEFQDTDP 392
Query: 1382 SQVALFKYVCKNIEEG---FVFSGDTAQTIARGIDFRFQDIRSLFYKKFVLESRNNGNDG 1438
Q + + + G GD Q+I R FR DI + LE+ ++
Sbjct: 393 QQWRILSRLFAGFKAGNRTLFLVGDPKQSIYR---FRGADIFTF------LEAASSEKAF 443
Query: 1439 RQEKRQLSDIFNLRQNFRTHVGVLN-------LAQSIIELLYRFFP-HSVDILKPETSLI 1490
+ L N+R+ +LN A + P + +
Sbjct: 444 AR--------ITLETNYRSTPELLNAVNALFKQAMFAYPGEIDYDPVAELGARNGSPGSV 495
Query: 1491 YGEPPILLESGDEENAILKIFGNTGEV 1517
GEP L+ +EE+ E
Sbjct: 496 NGEPLPALKFWEEEDDWTAPENEEDER 522
Score = 36.7 bits (85), Expect = 0.23
Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 5/88 (5%)
Query: 1551 VLTIVESKGLEFQDVLLYKFFSASPLKNQWRVVYEYMKEQ-DLLDSTSPGSFPSFNEVKH 1609
++TI +SKGLEF V L S + ++ Y + +L D P K
Sbjct: 746 IMTIHKSKGLEFPIVFLPFILSKRFNDSDVPLLVYYDGLRFELFDDLKSYPTPESQANKE 805
Query: 1610 NI----LCSELKQLYVAITRTRQRLWIW 1633
L EL+ LYVA+TR +++L +
Sbjct: 806 LAEEEALAEELRLLYVALTRAKEQLILI 833
>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 = 46.5 bits (111), Expect = 8e-05
Identities = 30/123 (24%), Positives = 49/123 (39%), Gaps = 12/123 (9%)
Query: 1312 LSETRNSSLSRQKRERIYDIFESYEQMKMRNGEFDLADLVNDLHHRLKE-----ESYKGD 1366
E + + + + ++ Y++ N D DL+ L+ E+Y+ +
Sbjct: 149 SPEELQQGAATPRDKLAAEFYQEYQERLKENNALDFDDLLLLTLELLRSDPELLEAYR-E 207
Query: 1367 EFHFVYIDEVQDLTMSQVALFKYVCKNIEEGFVFSGDTAQTIARGIDFRFQDIR--SLFY 1424
F ++ +DE QD Q L K + E F+ GD Q+I FR DI F
Sbjct: 208 RFKYILVDEFQDTNPIQYRLLKLLAGGHENLFLV-GDPDQSIYG---FRGADIENILKFE 263
Query: 1425 KKF 1427
K F
Sbjct: 264 KDF 266
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 42.7 bits (101), Expect = 8e-05
Identities = 20/57 (35%), Positives = 29/57 (50%)
Query: 225 SGATVQLIWGPPGTGKTKTVSMLLVILLQMKFRTLVCTPTIVAIKELASRVVKLVKE 281
SG ++ ++ G PGTGKT T + ++ LL LV PT A + L R+ L
Sbjct: 8 SGRSLFVVDGGPGTGKTATAAAIIARLLAAGRSVLVVAPTGRAARRLRERLAALDLA 64
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 43.2 bits (102), Expect = 6e-04
Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 5/76 (6%)
Query: 214 LKIIKELLCTDSGATVQLIWGPPGTGKTKTV--SMLLVILLQMKFRTLVCTPTIVAIKEL 271
+ I+ LL SG ++ P G+GKT L + R LV PT ++
Sbjct: 14 KEAIEALL---SGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQW 70
Query: 272 ASRVVKLVKESVERDC 287
A + KL +
Sbjct: 71 AEELKKLGPSLGLKVV 86
>gnl|CDD|233261 TIGR01073, pcrA, ATP-dependent DNA helicase PcrA. Designed to
identify pcrA members of the uvrD/rep subfamily [DNA
metabolism, DNA replication, recombination, and repair].
Length = 726
Score = 41.7 bits (98), Expect = 0.007
Identities = 45/204 (22%), Positives = 84/204 (41%), Gaps = 45/204 (22%)
Query: 1274 ARKLDPSRVFTEIISHIKGGLQSIEVVNGKLNREDYVNLSETRNSSLSRQKRERIYDIFE 1333
+K +P R IS+ K L ED+ ++ + + ++++
Sbjct: 129 PKKFEP-RSILGTISNAKNELLP---------PEDF----AKEATNY---FEKVVAEVYQ 171
Query: 1334 SYEQMKMRNGEFDLADLV---NDLHHRLKE--ESYKGDEFHFVYIDEVQDLTMSQVALFK 1388
Y++ +RN D DL+ +L R+ + E Y+ +F ++++DE QD +Q L +
Sbjct: 172 EYQKRLLRNNALDFDDLIMTTINLFQRVPDVLEYYQ-RKFQYIHVDEYQDTNRAQYTLVR 230
Query: 1389 YVCKNIEEGFVFSGDTAQTIARGIDFRFQDIRSL--FYKKFVLESRNNGNDGRQEKRQLS 1446
+ V GD Q+I +R DI+++ F K + N +
Sbjct: 231 LLASRFRNLCVV-GDADQSIYG---WRGADIQNILSFEKDY-------PN---------A 270
Query: 1447 DIFNLRQNFRTHVGVLNLAQSIIE 1470
L QN+R+ +L A +IE
Sbjct: 271 TTILLEQNYRSTKNILQAANEVIE 294
>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 = 41.3 bits (97), Expect = 0.008
Identities = 31/154 (20%), Positives = 53/154 (34%), Gaps = 26/154 (16%)
Query: 1330 DIFESYEQMKMRNGEFDLADLVNDLHHRLKEESYKG------DEFHFVYIDEVQDLTMSQ 1383
++ E ++ K R E DL++ L LK + +++ IDE QD Q
Sbjct: 253 EVQEELKKEKKRRREIGFDDLLSRLETALKSAEGEKLAQAIREQYPIALIDEFQDTDPQQ 312
Query: 1384 VALFKYV-CKNIEEGFVFSGDTAQTIARGIDFRFQDIRSLFYKKFVLESRNNGNDGRQEK 1442
+F + GD Q I FR DI + K ++R
Sbjct: 313 YRIFSKLFIAQKTTSLFLIGDPKQAI---YSFRGADIFTYLQAKSKADAR---------- 359
Query: 1443 RQLSDIFNLRQNFRTHVGVLNLAQSIIELLYRFF 1476
+ L N+R+ ++ + L+ F
Sbjct: 360 ------YTLGTNWRSTPALVGSLNKLFSLISNPF 387
Score = 37.0 bits (86), Expect = 0.16
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 3/83 (3%)
Query: 1551 VLTIVESKGLEFQDVLLYKFFSASPLKNQWRVVYEYMKEQDLLDSTSPGSFPSFNEVKHN 1610
++TI +SKGLE+ V L F + + N + ++ E L D V+
Sbjct: 655 IVTIHKSKGLEYPIVFL-PFITDAKKSNFASLHDQHSHEYQLYDFNQSEENQKLARVE-- 711
Query: 1611 ILCSELKQLYVAITRTRQRLWIW 1633
L +L+ LYVA+TR +++L+I
Sbjct: 712 RLAEDLRLLYVALTRAKKQLFIG 734
>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 = 37.7 bits (88), Expect = 0.021
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 229 VQLIWGPPGTGKTKTVSMLLVILLQM--KFRTLVCTPTIVAIKELASRVVKLVKESVE 284
L+ P G+GKT + ++ LL + LV PT ++A R+ +L E ++
Sbjct: 2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIK 59
>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
Firmicutes type. AddAB, also called RexAB, substitutes
for RecBCD in several bacterial lineages. These DNA
recombination proteins act before synapse and are
particularly important for DNA repair of double-stranded
breaks by homologous recombination. The term AddAB is
used broadly, with AddA homologous between the Firmicutes
(as modeled here) and the alphaproteobacteria, while the
partner AddB proteins show no strong homology across the
two groups of species [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1230
Score = 39.7 bits (93), Expect = 0.025
Identities = 40/153 (26%), Positives = 65/153 (42%), Gaps = 22/153 (14%)
Query: 1330 DIFESYEQMKMRNGEFDLAD--------LVNDLHHRLKEESYKGDEFHFVYIDEVQDLTM 1381
D E + K D +D L N+ + + ++FH V +DE QD +
Sbjct: 343 DFIERFGAEKREKNILDFSDLEHYALQILTNENESPSEAAEFYREKFHEVLVDEYQDTNL 402
Query: 1382 SQVALFKYVCKNIE-EGFVFS-GDTAQTIARGIDFRFQDIRSLFYKKFVLESRNNGNDGR 1439
Q ++ + V + E EG +F GD Q+I R FR D LF +K+ +
Sbjct: 403 VQESILQLVKRGPEEEGNLFMVGDVKQSIYR---FRQAD-PLLFLEKY--------HRFA 450
Query: 1440 QEKRQLSDIFNLRQNFRTHVGVLNLAQSIIELL 1472
QE + +L +NFR+ VL+ + + L
Sbjct: 451 QEGEEHGKRIDLAENFRSRAEVLDTTNFLFKQL 483
Score = 35.8 bits (83), Expect = 0.44
Identities = 26/89 (29%), Positives = 46/89 (51%), Gaps = 9/89 (10%)
Query: 1551 VLTIVESKGLEFQDVL---LYKFFSASPLKNQWRVVYEYMKEQDLLDSTSPGSFPSF--- 1604
++TI +SKGLEF V + K F+ L + + + + +D S+PS
Sbjct: 784 LMTIHKSKGLEFPVVFVLGMGKQFNKQDLNSSYLLDRQLGLGIKYIDPQERLSYPSLPKV 843
Query: 1605 ---NEVKHNILCSELKQLYVAITRTRQRL 1630
++K +L E++ LYVA+TR +++L
Sbjct: 844 AIKQKMKRELLSEEMRVLYVALTRAKEKL 872
>gnl|CDD|222209 pfam13538, UvrD_C_2, Family description. This domain is found at the
C-terminus of a wide variety of helicase enzymes. This
domain has a AAA-like structural fold.
Length = 105
Score = 35.1 bits (81), Expect = 0.079
Identities = 28/144 (19%), Positives = 53/144 (36%), Gaps = 40/144 (27%)
Query: 1489 LIYGEPPILLESGDEENAILKIFGNTGEVGGNMVGFGAEQVILVRDDCVRKEISNYVGKQ 1548
L G+ +LL + ++ A+L G+ G++ ++ Q L R + Y
Sbjct: 1 LRPGDIVVLLRNDYDKAALLN--GDLGDIE--ILARILGQDELGRTVRADPYFNAYQVGL 56
Query: 1549 ALVLTIVESKGLEFQDVLLYKFFSASPLKNQWRVVYEYMKEQDLLDSTSPGSFPSFNEVK 1608
A LTI ++KG E + V+ + D + F
Sbjct: 57 AYALTIHKAKGSE------------------FPAVF-------VPDPDAHAYDMLFR--- 88
Query: 1609 HNILCSELKQLYVAITRTRQRLWI 1632
+ LY A+TR +++L++
Sbjct: 89 --------RLLYTAVTRAKKKLYL 104
Score = 29.3 bits (66), Expect = 8.4
Identities = 8/51 (15%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 772 VMSVDGFQGGEEDIIIISTVRSNNGGSIGFISNPRRVNVALTRARHCLWIL 822
+++ +G E + + + + R + A+TRA+ L+++
Sbjct: 59 ALTIHKAKGSEFPAVFVP----DPDAHAYDMLFRRLLYTAVTRAKKKLYLV 105
>gnl|CDD|236783 PRK10875, recD, exonuclease V subunit alpha; Provisional.
Length = 615
Score = 37.2 bits (87), Expect = 0.12
Identities = 14/26 (53%), Positives = 19/26 (73%)
Query: 229 VQLIWGPPGTGKTKTVSMLLVILLQM 254
+ +I G PGTGKT TV+ LL L+Q+
Sbjct: 169 ISVISGGPGTGKTTTVAKLLAALIQL 194
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 36.3 bits (84), Expect = 0.18
Identities = 19/73 (26%), Positives = 24/73 (32%), Gaps = 11/73 (15%)
Query: 231 LIWGPPGTGKTKTVSMLLVILLQMKFRTLVCTPT----------IVAIKELASRVVKLVK 280
L+ GPPG GKT L L + F + CTP A L + V
Sbjct: 47 LLEGPPGVGKTLLA-RALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVP 105
Query: 281 ESVERDCRDALFF 293
+ R L
Sbjct: 106 GPLFAAVRVILLL 118
>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 = 36.3 bits (84), Expect = 0.24
Identities = 45/204 (22%), Positives = 71/204 (34%), Gaps = 64/204 (31%)
Query: 1460 GVLNLAQSIIELLYRFFPHSVDILKPETSLIYGEPPILLESGDEENAILKIF-GNTGEVG 1518
GVL L + I + L + P+ Y PI++ D L +F G+ G +
Sbjct: 441 GVLGLNRRIEQELQEKY------FDPDEEGWYIGRPIMVTENDYT---LGLFNGDIGVLL 491
Query: 1519 GNMVGFGAEQVILVRDDCVR----KEISNYVGKQALVLTIVESKGLEFQDVLLYKFFSAS 1574
+ G V D + + NY + A +T+ +S+G EF V+L
Sbjct: 492 RDPDGL---TVWFHFADGSKAVLPSRLPNY--ETAFAMTVHKSQGSEFDHVILI------ 540
Query: 1575 PLKNQWRVVYEYMKEQDLLDSTSPGSFPSFNEVKHNILCSELKQLYVAITRTRQRLWIWE 1634
L + SP +L EL LY ITR + +L +W
Sbjct: 541 -----------------LPNGNSP------------VLTREL--LYTGITRAKDQLSVWS 569
Query: 1635 NKEEFSKPMFDYWKKRFLVQVRRL 1658
+KE + +RL
Sbjct: 570 DKE--------TLNAAIKRKNKRL 585
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 35.7 bits (83), Expect = 0.32
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 209 HMKGNLKIIKELLCTDSGATVQLI-WGPPGTGKTKTVSMLLVILLQMKFRTLVCTPTIVA 267
H+ G K ++ + ++G +I WGPPGTGKT T++ L+ F L +
Sbjct: 31 HLLGEGKPLRRAV--EAGHLHSMILWGPPGTGKT-TLARLIAGTTNAAFEAL--SAVTSG 85
Query: 268 IKEL 271
+K+L
Sbjct: 86 VKDL 89
>gnl|CDD|216506 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
Helicase activity for this family has been demonstrated
and NTPase activity. This helicase has multiple roles at
different stages of viral RNA replication, as dissected
by mutational analysis.
Length = 226
Score = 35.0 bits (81), Expect = 0.32
Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 17/99 (17%)
Query: 523 FVLRKLLSSFNELNLPSAVEKDLLEDLLKRFCLKRASLFFSTASSSYMLHSVAMKPL--- 579
++RKLL + + P+ L+ + + + M L
Sbjct: 13 TLIRKLLRTDLTVIRPT-------------AELRTEGKPDLPNLNVRTVDTFLMALLKPT 59
Query: 580 -NFLVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLP 617
L++DE L + +SG K +LFGD Q+P
Sbjct: 60 GKILILDEYTLLPPGYILLLAAISGAKLVILFGDPLQIP 98
>gnl|CDD|177271 PHA00360, II, replication initiation protein.
Length = 421
Score = 35.4 bits (81), Expect = 0.38
Identities = 26/119 (21%), Positives = 49/119 (41%), Gaps = 3/119 (2%)
Query: 1887 SMDLIRNFLNSKGCFDELLVLEEESESFMDAANIARLRGDIL--RTVDLLQKVGNFKEAC 1944
F + C +L + + +DA A+ D + + +D L+ V N +
Sbjct: 115 GEAFFGAFAAALPCLYDLCDVNATTIGRIDATFSAKAANDHIAKQVIDFLRNVSNGQTKK 174
Query: 1945 NLTLNYVLSNSLWSSGSKGWPLKQFTQKKELLEKAKLLAKNESNKFYNFVCTEADILSN 2003
L++ S +W+ GS+ L + + EL + K L K +S + ++LSN
Sbjct: 175 TRALDWE-STVMWNEGSRHRTLVAYLKHHELQAQIKQLQKKKSAHLTIYEKECLEVLSN 232
>gnl|CDD|222073 pfam13361, UvrD_C, UvrD-like helicase C-terminal domain. This domain
is found at the C-terminus of a wide variety of helicase
enzymes. This domain has a AAA-like structural fold.
Length = 342
Score = 35.4 bits (82), Expect = 0.40
Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 27/88 (30%)
Query: 1551 VLTIVESKGLEFQDVLLYKFFSASPLKNQWRVVYEYMKEQDLLDSTSPGSFPSFNEV-KH 1609
++TI +KGLEF V L G+FP +
Sbjct: 281 LMTIHSAKGLEFPVVFLPGLEE--------------------------GTFPHQRSLEDE 314
Query: 1610 NILCSELKQLYVAITRTRQRLWIWENKE 1637
+ L E + YVAITR +++L++ K
Sbjct: 315 DRLEEERRLFYVAITRAKKQLYLTYAKT 342
>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 = 33.5 bits (76), Expect = 0.53
Identities = 13/52 (25%), Positives = 20/52 (38%)
Query: 231 LIWGPPGTGKTKTVSMLLVILLQMKFRTLVCTPTIVAIKELASRVVKLVKES 282
LI GPPG+GKT L L + + + L ++ +V
Sbjct: 6 LIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGK 57
Score = 31.6 bits (71), Expect = 3.0
Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 2/29 (6%)
Query: 1081 PRSTFILGRSGTGKTTVL--IMKLFQKEK 1107
I+G G+GKTT+ + +
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPG 30
>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 = 35.1 bits (81), Expect = 0.56
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 218 KELLCTDSGATVQLIWGPPGTGKTKTVSMLLVI--LLQMKFRTLVCTPTIVAIKELA 272
K+ L T V ++ G PGTGKT ++ + L + PT A K L
Sbjct: 329 KQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLG 385
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 34.7 bits (81), Expect = 0.59
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 209 HMKGNLKIIKELLCTDSGATVQLI-WGPPGTGKTKTVSMLLVILLQMKFRTL 259
H+ G K ++ ++ ++G +I WGPPGTGKT T++ ++ F L
Sbjct: 19 HLLGPGKPLRRMI--EAGRLSSMILWGPPGTGKT-TLARIIAGATDAPFEAL 67
>gnl|CDD|178266 PLN02660, PLN02660, pantoate--beta-alanine ligase.
Length = 284
Score = 34.6 bits (80), Expect = 0.61
Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 7/88 (7%)
Query: 1296 SIEVVNGKLNRE-DYVNLSETRNSSLSRQKRERIYDIFESYEQMK--MRNGEFDLADLVN 1352
IEVV + RE D + +S +RN LS ++RE+ I S + + + GE D +L
Sbjct: 173 DIEVVGSPIVREADGLAMS-SRNVRLSAEEREKALSISRSLARAEELVEEGETDADELKE 231
Query: 1353 DLHHRLKEESYKGDEFHFVYIDEVQDLT 1380
+ + E G E +V I + + L
Sbjct: 232 QVRQAIAEA---GGEVDYVEIVDQETLQ 256
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 32.7 bits (75), Expect = 0.79
Identities = 23/103 (22%), Positives = 35/103 (33%), Gaps = 16/103 (15%)
Query: 231 LIWGPPGTGKTKTVSMLLVILLQMKFRTLVCTP-----TIVAIKELASRVVKLVKESVER 285
L+ GPPGTGK++ L L + T + + + V + R
Sbjct: 3 LLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPLVR 62
Query: 286 DCRDALFFPLGEI-----------LLLGNNERLKVDSGVEEIY 317
R+ L EI L L + RL + G E +
Sbjct: 63 AAREGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVK 105
>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 = 33.3 bits (77), Expect = 0.88
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 223 TDSGATVQLIWGPPGTGKTKTVSMLLVILLQMK-FRTLVCTPTIVAIKELAS 273
SG V ++ GP GTGKT ++ + +R + PT A K L
Sbjct: 14 LTSGDRVAVVQGPAGTGKTTSLK-AAREAWEAAGYRVIGLAPTGKAAKVLGE 64
>gnl|CDD|203709 pfam07652, Flavi_DEAD, Flavivirus DEAD domain.
Length = 146
Score = 32.7 bits (75), Expect = 0.98
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 7/41 (17%)
Query: 236 PGTGKTKTVSMLLVILL----QMKFRTLVCTPTIVAIKELA 272
PG GKT+ V L L+ + RTLV PT V + E+
Sbjct: 11 PGAGKTRKV---LPELVRECIDRRLRTLVLAPTRVVLAEME 48
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 31.8 bits (73), Expect = 1.1
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 231 LIWGPPGTGKTKTVSMLLVILLQMKFRTLVCTPTI 265
LI G+GKT T + L+ L + K + L P
Sbjct: 22 LIVMATGSGKTLTAAALIARLAKGKKKVLFVVPRK 56
>gnl|CDD|226368 COG3850, NarQ, Signal transduction histidine kinase,
nitrate/nitrite-specific [Signal transduction
mechanisms].
Length = 574
Score = 34.2 bits (79), Expect = 1.2
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 494 LLSHSVDEDLSESIVDIKYLLHKRRSECHFVLRKLLSSF----NELNLPSAVEKDLLEDL 549
LL ++ E+L E +I + + ++ + LR+LL++F E LP A+E +L +
Sbjct: 397 LLKTAIPEELPEKAREIIAQIRQGLNDAYRQLRELLTTFRLTLQEAELPPALE-QMLAEF 455
Query: 550 LKRF 553
+
Sbjct: 456 SNQT 459
>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 = 31.8 bits (73), Expect = 1.5
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 231 LIWGPPGTGKTKTVSML 247
L++GPPGTGKT +
Sbjct: 2 LLYGPPGTGKTTLAKAV 18
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 32.9 bits (76), Expect = 2.1
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 8/38 (21%)
Query: 1073 EQLDMIL-------FPRSTFILGRSGTGKTTVLIMKLF 1103
E+L L P + I G GTGKTT + K+F
Sbjct: 40 EELAFALRPALRGSRPLNVLIYGPPGTGKTTT-VKKVF 76
>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 = 31.7 bits (72), Expect = 2.1
Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 214 LKIIKELLCTDSGATVQLIWGPPGTGKT 241
++ ++E L + L++GPPGTGKT
Sbjct: 7 IEALREALELPPPKNL-LLYGPPGTGKT 33
>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 = 30.8 bits (70), Expect = 2.5
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 237 GTGKTKTVSMLLVILLQMKFRTLVCTPTIV 266
G GKT + L L + R L+ ++
Sbjct: 9 GVGKTTLAANLAAALAKRGKRVLLIDDYVL 38
>gnl|CDD|226482 COG3973, COG3973, Superfamily I DNA and RNA helicases [General
function prediction only].
Length = 747
Score = 32.9 bits (75), Expect = 2.7
Identities = 47/270 (17%), Positives = 84/270 (31%), Gaps = 59/270 (21%)
Query: 1367 EFHFVYIDEVQDLTMSQVALFKYVCKNIEEGFVFSGDTAQTIARGIDFRFQDIRSLFYKK 1426
IDE QD + Q + + + GD Q I Q++ +
Sbjct: 528 RLKHTVIDEAQDYSRFQFTDNRTLAERA--SMTIVGDYGQ----VIYDEAQELSPMERMD 581
Query: 1427 FVLESRNNGNDGRQEKRQLSDIFNLRQNFRTHVGVLNLAQSIIELLYRFFPHSVDILKPE 1486
E + + L ++R+ + A S++ +R P + KP
Sbjct: 582 VFFEDPS------------FEYVGLIASYRSTAEIDEFANSLLPDRFRIHPLTRSGEKPA 629
Query: 1487 TSLIYGEPPILLESGDEENAILKIFG--NTGEVGGNMVGFGAEQVILVRDDCVR--KEIS 1542
+ L++ + +K G + A L D R + +
Sbjct: 630 VIMSVAN-EELVQRNPDIIPRMKKRGSETIAVICKTDHDCKAVMDSLREKDSQRTIAKEN 688
Query: 1543 NYVGKQALVLTIVESKGLEFQDVLLYKFFSASPLKNQWRVVYEYMKEQDLLDSTSPGSFP 1602
+ V+ + ++KGLEF V++ S ++ EQD
Sbjct: 689 QRFHHGSDVIPVYDAKGLEFDHVIVV---DPSIVEE---------TEQD----------- 725
Query: 1603 SFNEVKHNILCSELKQLYVAITRTRQRLWI 1632
L+ LYVA+TR L+I
Sbjct: 726 -------------LRDLYVAVTRALHSLYI 742
>gnl|CDD|182930 PRK11054, helD, DNA helicase IV; Provisional.
Length = 684
Score = 32.6 bits (75), Expect = 3.3
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 9/41 (21%)
Query: 1619 LYVAITRTRQRLWIWENKEEFSKPMFDYWKKRFLVQVRRLD 1659
LYVA+TR + R+W+ NK S F+ +++ LD
Sbjct: 646 LYVALTRAKHRVWLLFNKGNPS---------PFVEELKNLD 677
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 31.0 bits (71), Expect = 3.4
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 231 LIWGPPGTGKTKTVSMLLVILLQMKFRTLVCTP 263
L+ G PG KT L L + FR + TP
Sbjct: 3 LLEGVPGLAKTLLAR-TLARSLGLDFRRIQFTP 34
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all species
from bacteria to human, and the function was determined
first in a hyperthermophilic bacterium to be an NTPase.
The structure of one member-sequence represents a
variation of the RecA fold, and implies that the function
might be that of a DNA/RNA modifying enzyme. The sequence
carries both a Walker A and Walker B motif which together
are characteristic of ATPases or GTPases. The protein
exhibits an increased expression profile in human liver
cholangiocarcinoma when compared to normal tissue.
Length = 168
Score = 31.0 bits (71), Expect = 4.1
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 1085 FILGRSGTGKTTVLIMKLFQKEKLHNMALEGF 1116
FI G G GKTT L+ K+ + K + + GF
Sbjct: 3 FITGPPGVGKTT-LVKKVIELLKSEGVKVGGF 33
>gnl|CDD|182732 PRK10789, PRK10789, putative multidrug transporter
membrane\ATP-binding components; Provisional.
Length = 569
Score = 32.0 bits (73), Expect = 4.9
Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 13/64 (20%)
Query: 103 LYDVKVDCWRNRFSNLGREPY---KTLPGDILVLADAKPE-TASDLQRVGRMWTFVSVAN 158
L +++D WR+R + + + P+ T+ +I A +P+ T +++ V R+ A+
Sbjct: 379 LTKLQLDSWRSRLAVVSQTPFLFSDTVANNI---ALGRPDATQQEIEHVARL------AS 429
Query: 159 VTED 162
V +D
Sbjct: 430 VHDD 433
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP (Multidrug
Resistance Protein)-like transporters are involved in
drug, peptide, and lipid export. They belong to the
subfamily C of the ATP-binding cassette (ABC) superfamily
of transport proteins. The ABCC subfamily contains
transporters with a diverse functional spectrum that
includes ion transport, cell surface receptor, and toxin
secretion activities. The MRP-like family, similar to all
ABC proteins, have a common four-domain core structure
constituted by two membrane-spanning domains, each
composed of six transmembrane (TM) helices, and two
nucleotide-binding domains (NBD). ABC transporters are a
subset of nucleotide hydrolases that contain a signature
motif, Q-loop, and H-loop/switch region, in addition to,
the Walker A motif/P-loop and Walker B motif commonly
found in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 30.8 bits (71), Expect = 5.2
Identities = 9/23 (39%), Positives = 17/23 (73%), Gaps = 2/23 (8%)
Query: 1084 TFILGRSGTGKTTV--LIMKLFQ 1104
I+G SG+GK+T+ L+++L+
Sbjct: 31 VAIVGPSGSGKSTLLKLLLRLYD 53
>gnl|CDD|201077 pfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase.
Length = 500
Score = 31.6 bits (72), Expect = 5.8
Identities = 9/34 (26%), Positives = 12/34 (35%), Gaps = 1/34 (2%)
Query: 2515 VIAEAFEKIGNPLVVASLGGKCPGFACPNAIVVD 2548
IA A +I V+ G P N +V
Sbjct: 297 EIASALAQIPQK-VLWRFDGTKPSTLGRNTRLVK 329
>gnl|CDD|236784 PRK10876, recB, exonuclease V subunit beta; Provisional.
Length = 1181
Score = 31.9 bits (73), Expect = 5.9
Identities = 30/102 (29%), Positives = 42/102 (41%), Gaps = 16/102 (15%)
Query: 1328 IYDIFESYEQMKMRNGEFDLADLVNDLHHRLKEESYKGD--------EFHFVYIDEVQDL 1379
+ +I E+ Q K R GE DL++ L L+ E G+ + IDE QD
Sbjct: 332 LAEIRETVAQEKRRRGELGFDDLLSRLDSALQSEG--GEALAAAIRTRYPVAMIDEFQDT 389
Query: 1380 TMSQVALFK--YVCKNIEEGFVFSGDTAQTIARGIDFRFQDI 1419
Q +F+ Y + E + GD Q I FR DI
Sbjct: 390 DPQQYRIFRRIYRHQP-ETALLLIGDPKQAI---YAFRGADI 427
>gnl|CDD|236261 PRK08412, flgL, flagellar hook-associated protein FlgL; Validated.
Length = 827
Score = 31.7 bits (72), Expect = 6.9
Identities = 13/32 (40%), Positives = 23/32 (71%)
Query: 1154 AVKQHISHMKSSTIGGKFATEGSLIDTDDIDD 1185
A+K+H+ ++ +++IGG+F GS +DT ID
Sbjct: 116 ALKEHMINLANTSIGGEFLFSGSKVDTKPIDS 147
>gnl|CDD|213736 TIGR02773, addB_Gpos, helicase-exonuclease AddAB, AddB subunit. DNA
repair is accomplished by several different systems in
prokaryotes. Recombinational repair of double-stranded
DNA breaks involves the RecBCD pathway in some lineages,
and AddAB (also called RexAB) in other. The AddA protein
is conserved between the firmicutes and the
alphaproteobacteria, while the partner protein is not.
Nevertheless, the partner is designated AddB in both
systems. This model describes the AddB protein as found
Bacillus subtilis and related species. Although the RexB
protein of Streptococcus and Lactococcus is considered to
be orthologous, functionally equivalent, and merely named
differently, all members of this protein family have a
P-loop nucleotide binding motif GxxGxGK[ST] at the
N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif
at the C-terminus, both of which may be relevant to
function [DNA metabolism, DNA replication, recombination,
and repair].
Length = 1160
Score = 31.6 bits (72), Expect = 7.2
Identities = 14/21 (66%), Positives = 17/21 (80%)
Query: 1085 FILGRSGTGKTTVLIMKLFQK 1105
FI GRSGTGKTT +I ++ QK
Sbjct: 5 FIYGRSGTGKTTFIINEIKQK 25
>gnl|CDD|237554 PRK13909, PRK13909, putative recombination protein RecB; Provisional.
Length = 910
Score = 31.5 bits (72), Expect = 8.6
Identities = 29/123 (23%), Positives = 51/123 (41%), Gaps = 24/123 (19%)
Query: 1539 KEISNYVGKQALVLTIVESKGLEFQDVLLYKFFSA-----SPL------KNQWRVVYEYM 1587
KEI++ K ++T+ +SKGLEF+ V++ S L W++ Y +
Sbjct: 598 KEIASEESKGVQIMTVHKSKGLEFEHVIVCDRLGKPNSDSSNLLFEYDGIELWQIYYR-I 656
Query: 1588 KEQDLLDSTSPGSFPSFNEVKHNILCSELKQ----LYVAITRTRQRLWIWENKEEFSKPM 1643
K ++ D + + ++ LYVA TR + L + + E S M
Sbjct: 657 KGRENFDKD-------YARALEKEKALKYEEEINVLYVAFTRAKNSLIVVKKDES-SGSM 708
Query: 1644 FDY 1646
F+
Sbjct: 709 FEI 711
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
0.321 0.137 0.405
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 131,516,087
Number of extensions: 13347151
Number of successful extensions: 12147
Number of sequences better than 10.0: 1
Number of HSP's gapped: 12112
Number of HSP's successfully gapped: 81
Length of query: 2576
Length of database: 10,937,602
Length adjustment: 113
Effective length of query: 2463
Effective length of database: 5,925,600
Effective search space: 14594752800
Effective search space used: 14594752800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 68 (30.2 bits)