RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4730
(1513 letters)
>gnl|CDD|219818 pfam08393, DHC_N2, Dynein heavy chain, N-terminal region 2.
Dyneins are described as motor proteins of eukaryotic
cells, as they can convert energy derived from the
hydrolysis of ATP to force and movement along
cytoskeletal polymers, such as microtubules. This region
is found C-terminal to the dynein heavy chain N-terminal
region 1 (pfam08385) in many members of this family. No
functions seem to have been attributed specifically to
this region.
Length = 408
Score = 463 bits (1194), Expect = e-150
Identities = 172/412 (41%), Positives = 276/412 (66%), Gaps = 8/412 (1%)
Query: 97 VDEMLERLEPFDQLWSIILEFRESSDLWMEGPFKGLNADEIKDKTDFMFRELNQLARKMT 156
+ E+ + L+P +LW + E+ ES + W P+ ++ +E++ + + ++L +L + +
Sbjct: 3 LQELEKELKPLKKLWDLYSEWSESIEEWKNTPWSTIDPEELESEIEKFLKQLRKLPKNL- 61
Query: 157 RAPGCKMVNDLTRSKLESFRKEVPILQCISNPGMEERHWKILSDELGQDITPNDQTSLKN 216
++ +L + K++ F+K +P+++ + NP ++ERHW+ + LG P++ +L +
Sbjct: 62 --RQYEVAEEL-KKKIDDFKKSLPLIEDLKNPALKERHWEQIFKLLGFKDFPDEDFTLGD 118
Query: 217 MLDLGIRNILPKLEEVSLSASKEAELSQSLNKMVTEWSDIKLDVVPYRDTGTYIIQGTDE 276
+LDLG+ N ++EE+S A KE + ++L K+ W +++ ++VPY+DTGTY+++G DE
Sbjct: 119 LLDLGLLNYEEEIEEISEQAQKEYSIEKALKKIKDTWEELEFELVPYKDTGTYLLKGWDE 178
Query: 277 IQVMLDDHILRAQTMRGSPYIKPFETEMEAWESKLINMQDILDIWLQVQGTWMYLEPIFS 336
I +LDD+++ Q+M+ SPY+KPFE E + WE KL +Q++L++WL+VQ W+YLEPIFS
Sbjct: 179 IIELLDDNLVTLQSMKASPYVKPFEEEADEWEKKLNLIQEVLELWLKVQRKWVYLEPIFS 238
Query: 337 SEDIMRQMPEESRNFKTVDQIWKTIMLFVNKDPHILQATEMEDMLKNFNKCNLMLELIQK 396
S DI +Q+PEES+ F VD+ WK +M NKDP++L+ + +L+ K N LE IQK
Sbjct: 239 SSDIKKQLPEESKRFSNVDKEWKKLMKKANKDPNVLEVCNIPGLLEKLEKLNEQLEKIQK 298
Query: 397 GLNDYLEKKRLFFPRFFFLSNDELLEILSETKDPLRVQPHLKKIFEGINLLEYSD-SLEI 455
LN+YLE KR FPRF+FLSND+LLEILS++KDP VQPHLKK+FEGI+ LE+ + + I
Sbjct: 299 SLNEYLESKRSAFPRFYFLSNDDLLEILSQSKDPTAVQPHLKKLFEGISSLEFDEENNNI 358
Query: 456 IGMISLEGEKVALSGLIRPNDAKGLVEKWLQQVEDLMIKSLQDICMMALGAY 507
GMIS EGE+V L +P +G VE WL ++E M ++L+ + AL Y
Sbjct: 359 TGMISSEGEEVP---LSKPVSVEGNVEDWLNELEKEMKETLKKLLKEALQDY 407
>gnl|CDD|193250 pfam12774, AAA_6, Hydrolytic ATP binding site of dynein motor region
D1. the 380 kDa motor unit of dynein belongs to the AAA
class of chaperone-like ATPases. The core of the 380 kDa
motor unit contains a concatenated chain of six AAA
modules, of which four correspond to the ATP binding
sites with P-loop signatures described previously, and
two are modules in which the P loop has been lost in
evolution. This particular family is the D1 unit of the
motor and contains the hydrolytic ATP binding site.
Length = 231
Score = 195 bits (498), Expect = 1e-56
Identities = 90/143 (62%), Positives = 106/143 (74%)
Query: 1123 GAWACFDEFNRIELEVLSVVAQQVQSIQLATIAKLKKFMFEGTEISLNPTSMIFITMNPG 1182
GAW CFDEFNRI +EVLSVVA QV+ +Q A K + F F G EISL P+ IFITMNPG
Sbjct: 85 GAWGCFDEFNRISVEVLSVVAVQVKCVQDAIRDKKQWFNFLGEEISLIPSVGIFITMNPG 144
Query: 1183 YAGRTELPDNLKVLFRSVAMMVPDYAMIGEISLYSMGFQNAKILAEKIVYTYKLCSEQLS 1242
YAGRTELP+NLK LFR AM+VPD+ +I EI L + GF A++LA K + Y LC E LS
Sbjct: 145 YAGRTELPENLKALFRPCAMVVPDFELICEIMLVAEGFLEARLLARKFITLYTLCKELLS 204
Query: 1243 SQSHYDYGMRAVKSVLNAAGSLK 1265
Q HYD+G+RA+KSVL AGSLK
Sbjct: 205 KQDHYDWGLRAIKSVLVVAGSLK 227
Score = 104 bits (260), Expect = 8e-25
Identities = 45/68 (66%), Positives = 53/68 (77%)
Query: 629 YGYEYLGNSDRLVITPLTDRCYRTLMSALKLHLGGAPEGPAGTGKTETSKDLAKAVAKQC 688
Y YEYLGN+ RLVITPLTDRCY TL +L L + GAP GPAGTGKTET+KDL +A+
Sbjct: 1 YSYEYLGNTPRLVITPLTDRCYITLTQSLHLTMSGAPAGPAGTGKTETTKDLGRALGIMV 60
Query: 689 IVFNCSDR 696
VFNCS++
Sbjct: 61 YVFNCSEQ 68
>gnl|CDD|193251 pfam12775, AAA_7, P-loop containing dynein motor region D3. the 380
kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules, of
which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D3 and is an ATP binding
site.
Length = 272
Score = 118 bits (298), Expect = 2e-29
Identities = 55/167 (32%), Positives = 87/167 (52%), Gaps = 3/167 (1%)
Query: 891 LDDLNMPQKETYGAQPAVELLRQIIDHKHLYDFQTVTRVDLVDIIYITAMIPTMN--TIT 948
+DD+NMP+ + YG L+RQ +D+ H YD +T ++ + Y++ M PT TI
Sbjct: 106 IDDMNMPEVDAYGTVQPHTLIRQHMDYGHWYDRSKLTLKEIHNCQYVSCMNPTAGSFTIN 165
Query: 949 GRLLRHMNIISIDSFNEATLSKIFTSVLDWHFSKG-FADSIVKLSKNIVAATFHVYSEST 1007
RL RH + ++ + LS I+ +L H + G + ++ K S +V A ++ +
Sbjct: 166 SRLQRHFCVFALSFPGQDALSTIYNIILTQHLALGSVSAALQKSSPPLVDAALALHQKIA 225
Query: 1008 KVFLPIPSKSHYVFNLRDFAKVIMGLTQLPASHCKAPDKMYKLWTHE 1054
FLP K HYVFNLRD + + GL K+P + +LW HE
Sbjct: 226 TTFLPTAIKFHYVFNLRDLSNIFQGLLFSSVECLKSPWDLIRLWLHE 272
Score = 60.3 bits (146), Expect = 1e-09
Identities = 36/121 (29%), Positives = 61/121 (50%), Gaps = 3/121 (2%)
Query: 699 FPPNLRPSDLIIPTNVTCMQNFFINLYLQNDVPMMFVGPTGTGKSTIVLNLLLNLSKDKY 758
P + ++ T+ T +F++L ++ P+M VG GTGKS +V + L +L D Y
Sbjct: 3 LDPEMPLQACLVHTSETIRVRYFMDLLMERQRPVMLVGNAGTGKSVLVGDKLASLDPDAY 62
Query: 759 LPNIINFSARTSSNITQEMIMAKLDRRRKGVYGPAMGKKYIVFIAGSLKIKYPEKDEFVI 818
L + F+ T+S + Q ++ L+++ YGP KK + FI + PE D +
Sbjct: 63 LVKNVPFNYYTTSAMLQAVLEKPLEKKAGRNYGPPGTKKLVYFID---DMNMPEVDAYGT 119
Query: 819 V 819
V
Sbjct: 120 V 120
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 70.0 bits (171), Expect = 1e-11
Identities = 48/386 (12%), Positives = 105/386 (27%), Gaps = 74/386 (19%)
Query: 1119 IIFPGAWACFDEFNRIELEVLSVVA-QQVQSIQLATIAKLKKFMFEGTEISLNPTSMIFI 1177
I +E ++ +++ + + S + + +L + E S P++ + +
Sbjct: 984 PICEEERG-TEESALLDEISRTILVDEYLNSDEFRMLEELNSAVVEHGLKS--PSTPVEM 1040
Query: 1178 TMNPGYAGRTELPDNLKVLFRSVAMMVPDYAMIGEISLYSMGFQNAKILAEKIVYTYKLC 1237
+N R + + + +P + I + L +I
Sbjct: 1041 IINE----RNIVLEIGRRALDMFLSNIP-FGAIKSRR---------ESLDREIGAFNNEV 1086
Query: 1238 SEQLSSQSHYDYGMRAVKSVLNAAGSLKIKYPEKDEFVIVLRAIIDVNMPKFLVQDLPLF 1297
+ + + SLK K+ +E L I+ + LPL
Sbjct: 1087 DGIAREEDELMF--YPMF------KSLKAKHRMLEEKTEYLNKILSIT-------GLPLI 1131
Query: 1298 IGIYKDLFPGIELPPTDRDELIEQIKINLAKRNAQATDWYIEKIIQVYEMILVRHGLMVV 1357
++ I+ + D + + Q + + + + +
Sbjct: 1132 SDTLRER---IDTLDAEWDSFCRISESLKKYESQQVSGLDVAQFVSFLRSVDTGAFHAEY 1188
Query: 1358 GESFGGKTTAYQTLADSLTDIAAKKSATMKEFKTGYKIINPKSITMGQLYGEFDSASHEW 1417
F K Y D L + KS +K+ ++ A E
Sbjct: 1189 FRVFLCKIKHYTDACDYLWHV---KSPYVKK--------------------KYFDADMEL 1225
Query: 1418 RDGILAKTFREMAVSTTPDRKWIMFDGPIDAVWIENMNTVLDDNKKLCLINGEIIKMSNT 1477
R L +M + + ++E + K GE
Sbjct: 1226 RQFFLMFNREDMEARLADSKMEYEVER-----YVEKTKAEVSSLKLELSSVGE------- 1273
Query: 1478 MNLIFECENLEFASPATVSRVGMIYF 1503
++ NL + V R + Y
Sbjct: 1274 GQVVV--SNLG-SIGDKVGRCLVEYD 1296
Score = 69.6 bits (170), Expect = 1e-11
Identities = 48/280 (17%), Positives = 99/280 (35%), Gaps = 19/280 (6%)
Query: 871 RNAQATDWYIEKIIQVYEMILDDLNMPQKETYGAQPAVELLRQIIDHKHLYDFQTVTRVD 930
N Y + +++ + D++N+P Y + LR +++ + + V+ V
Sbjct: 1549 PNTGVVRLYPKPVVKDLVLFCDEINLPYGFEYYPPTVIVFLRPLVERQGFWSSIAVSWVT 1608
Query: 931 LVDIIYI----TAMIPTMNTITGRLLRHMNIISIDSFNEATLSKIFTSVLDWHFSKGFAD 986
+ II R +R + A+L I+ +VL + D
Sbjct: 1609 ICGIILYGACNPGTDEGRVKYYERFIRKPVFVFCCYPELASLRNIYEAVLMGSYL--CFD 1666
Query: 987 SIVKLSKNIVAATFHVYSES---TKVFLPIPSKSHYVFNLRDFAKVIMGLTQLPASHCKA 1043
+LS+ ++A+ +Y S TK FL + +Y + R+ + + + +
Sbjct: 1667 EFNRLSEETMSASVELYLSSKDKTKFFL----QMNYGYKPRELTRSLRAIFGYAETRIDT 1722
Query: 1044 PD-KMYKLWTHEILRVFSDRLVDEADKQSLLDMMKYACQNIIGTKMDEFLKNKITDKTIS 1102
PD + W E +R DRLV + + + + + + E + I + I+
Sbjct: 1723 PDVSLIIDWYCEAIREKIDRLVQQKESSTSRQDL----YDFGLRAIREMIAGHIGEAEIT 1778
Query: 1103 ADDLRSLFFGNFLGNTIIFPGAWACFDEFNRIELEVLSVV 1142
+ L + F L+V +V
Sbjct: 1779 FSMILFFGM-ACLLKKDLAVFVEEVRKIFGSSHLDVEAVA 1817
Score = 62.3 bits (151), Expect = 2e-09
Identities = 37/354 (10%), Positives = 95/354 (26%), Gaps = 23/354 (6%)
Query: 336 SSEDIMRQMPEESRNFKTVDQIWKTIMLFVNKDPHILQATEME--DMLKNFNKCNLMLEL 393
S ED+M +P ++ + I V + + D L F K ++
Sbjct: 636 SLEDLMPLIPHAVHRKMSLVSGVRGIYKRVVSGCEAINTILEDVGDDLDLFYK---EMDQ 692
Query: 394 IQKGLNDYLEKKRLFFPRFFFLSNDELLEILSETKDPLRVQPHLKKIFEGINLLEYSDSL 453
+ + L + R +EL++ + E ++ + K + S
Sbjct: 693 VFMSIEKVLGLRWREVERA--SEVEELMDRVRELENRVYSYRFFVKKIAKEEMKTVFSSR 750
Query: 454 EIIGMISLEGEKVALSGLIRPNDAKGLVEKWLQQVEDLMIKSLQDICMMALGAYYKSERV 513
I + A G R + K +V + + + ++ + ++ + E
Sbjct: 751 -IQKKEPFSLDSEAYVGFFRLYE-KSIVIRGINRSMGRVLSQYLE----SVQEALEIEDG 804
Query: 514 VWVTKWPGMVVICVSSITWTAEVEKAIQGRKLDAMLDKSVKQIDIMVIKVRGKLLMSERI 573
+ + + E D L + + ++ + G
Sbjct: 805 SFFVSRHRVRDGGLEKGRGCDAWENC-----FDPPLSEYFRILEKIFPSEEGYFFDEVLK 859
Query: 574 TICALIVIDVHAKEVVASLVESKVTQVEDFAWMSQLRYYN-VNNLVNVCMITTTVQYGYE 632
+ I +E++ + +E +S + + +
Sbjct: 860 RLDPGHEIKSRIEEIIRMVTVKYDFCLEVLGSVSISELPQGLYKRFIKVRSSYRSAEMFA 919
Query: 633 YLGNSDRLVITPLTDRCYRTLMSALKLHLGGAPEGPAGTGKTETSKDLAKAVAK 686
+ + ++ L A+ + T + L +
Sbjct: 920 KNTIPFFVFEHSMDTSQHQKLFEAVCDEVCRF----VDTENSRVYGMLVAGKGR 969
Score = 61.5 bits (149), Expect = 4e-09
Identities = 86/389 (22%), Positives = 151/389 (38%), Gaps = 82/389 (21%)
Query: 1119 IIFPGAWACFDEFNRIELEVLSVVAQQVQSIQLATIAKLKKFMFEGTEISLNPTSMIFIT 1178
+ G++ CFDEFNR+ E +S + S + K F F+
Sbjct: 1656 AVLMGSYLCFDEFNRLSEETMSASVELYLSSK-------DKTKF-------------FLQ 1695
Query: 1179 MNPGYAGRTELPDNLKVLFRSVAMMVPDYAMIGEISLYSMGFQNAKILAEKIVYTYKLCS 1238
MN GY R EL +L+ +F A D + I + + +++V K S
Sbjct: 1696 MNYGYKPR-ELTRSLRAIF-GYAETRIDTPDVSLIIDWYCE--AIREKIDRLV-QQKESS 1750
Query: 1239 EQLSSQSHYDYGMRAVKSVLNAAGSLKIKYPEKDEFVIVLRAIIDVNMPKFLVQDLPLFI 1298
S Q YD+G+RA+ E I I F
Sbjct: 1751 T--SRQDLYDFGLRAI--------------REMIAGHIGEAEIT--------------FS 1780
Query: 1299 GIYKDLFPGIELPPTDRDELIEQIKINLAKRNAQATDWYIEKIIQVYEMILVRHGLMVVG 1358
I L D +E+++ + + + ++ R GL+VVG
Sbjct: 1781 MILFFGMA--CLLKKDLAVFVEEVRKIFGSSHLDVEAVAYKDALL--HILRSRRGLLVVG 1836
Query: 1359 ESFGGKTTAYQTLADSLTDIAAKKSATMKEFKTGYKIINPKSITMGQLYGEFDSASHEWR 1418
K I A EF NP+++ +++G D + ++R
Sbjct: 1837 GHGVLKGVL----------IRGACDAR--EFVCWL---NPRNMR--EIFGHRDELTGDFR 1879
Query: 1419 DGILAKTFREMAVSTTPDRK-WIMFDG-PIDAVWIENMNTVLDDNKKLCLING-EIIKMS 1475
D + + R + R+ +F+ P+++ ++E+ N +LD+N+ LCL +G E I++
Sbjct: 1880 DSLKVQDLR---RNIHGGRECLFIFESIPVESSFLEDFNPLLDNNRFLCLFSGNERIRIP 1936
Query: 1476 NTMNLIFECENLEFASPATVSRVGMIYFE 1504
+ +FE +LE + AT++RV ++Y E
Sbjct: 1937 ENLRFVFESTSLEKDTEATLTRVFLVYME 1965
Score = 36.1 bits (83), Expect = 0.18
Identities = 29/141 (20%), Positives = 56/141 (39%), Gaps = 22/141 (15%)
Query: 703 LRPSDLIIPTNVTCMQNFFINLYLQNDVPMMFVGPTGTGKSTIVLNLLLNLSKDKYLPNI 762
+ +++IPT+ T + F N L ++ GP G+GK ++ L + +
Sbjct: 1468 MLRKEVVIPTSDTGFVDSFSNEALNTLRSYIYCGPPGSGKEMLMCPSLRSELITEVKY-- 1525
Query: 763 INFSARTSSNITQEMIMAKLDRRRKGVYGPAMGKKYIVFIAGSLKIKYPEKDEFVIVLRA 822
NFS T + ++ L+R Y P G + YP+ +VL
Sbjct: 1526 FNFSTCTMT----PSKLSVLERET--EYYPNTG----------VVRLYPKPVVKDLVL-F 1568
Query: 823 IIDVNMPK---FLVQDLPLFI 840
++N+P + + +F+
Sbjct: 1569 CDEINLPYGFEYYPPTVIVFL 1589
>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 = 48.4 bits (116), Expect = 2e-06
Identities = 18/98 (18%), Positives = 31/98 (31%), Gaps = 15/98 (15%)
Query: 731 PMMFVGPTGTGKSTIVLNLLLNLSKDKYLPNIINFSARTS-SNITQEM-IMAKLDRRRKG 788
++ VGP GTGKS + L LS + + T+ ++ I G
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVF--YVQLTRDTTEEDLKGRRNIDPGGASWVDG 58
Query: 789 VYGPAMGKKYIVFIAGSLKIKYPEKDEFVIVLRAIIDV 826
A + I + DE +++
Sbjct: 59 PLVRAAREGEIAVL-----------DEINRANPDVLNS 85
Score = 39.2 bits (92), Expect = 0.003
Identities = 33/155 (21%), Positives = 55/155 (35%), Gaps = 31/155 (20%)
Query: 1353 GLMVVGESFGGKTTAYQTLADSLTDIAAKKSATMKEFKTGYKIINPKSITMGQLYGEFDS 1412
G+++VG GK+ LA+ L + + + + T L G +
Sbjct: 1 GVLLVGPPGTGKS----ELAERLAAALSNRPVFY--------VQLTRDTTEEDLKGRRNI 48
Query: 1413 A--SHEWRDGILAKTFREMAVSTTPDRKWIMFDGPID---AVWIENMNTVLDDNKKLCLI 1467
W DG L + RE I I+ + ++ ++LD+ + L
Sbjct: 49 DPGGASWVDGPLVRAARE---------GEIAVLDEINRANPDVLNSLLSLLDERRLLLPE 99
Query: 1468 NGEIIKMSNT-MNLIFECENL----EFASPATVSR 1497
GE++K + LI L SPA SR
Sbjct: 100 GGELVKAAPDGFRLIATMNPLDRGLNELSPALRSR 134
Score = 36.1 bits (84), Expect = 0.036
Identities = 21/78 (26%), Positives = 30/78 (38%), Gaps = 12/78 (15%)
Query: 1123 GAWACFDEFNRIELEVLSVVAQQVQSIQLATIAKLKKFMFE--GTEISLNPTSMIFI-TM 1179
G A DE NR +VL+ L ++ ++ + G + P I TM
Sbjct: 67 GEIAVLDEINRANPDVLNS---------LLSLLDERRLLLPEGGELVKAAPDGFRLIATM 117
Query: 1180 NPGYAGRTELPDNLKVLF 1197
NP G EL L+ F
Sbjct: 118 NPLDRGLNELSPALRSRF 135
>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 = 39.8 bits (93), Expect = 0.002
Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 2/79 (2%)
Query: 724 LYLQNDVPMMFVGPTGTGKSTIVLNLLLNLSKDKYLPNIINFSARTSSNITQEMIMAKLD 783
L L ++ GP GTGK+T+ + L + +N S + E+ L
Sbjct: 14 LELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLV 73
Query: 784 RRRKGVYGPAMGKKYIVFI 802
R + K ++FI
Sbjct: 74 RLLFEL--AEKAKPGVLFI 90
Score = 30.2 bits (68), Expect = 4.4
Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 13/58 (22%)
Query: 647 DRCYRTLMSALKLHLGGAP--EGPAGTGKTETSKDLAKAVAKQC-------IVFNCSD 695
+ L AL+L GP GTGKT LA+A+A + + N SD
Sbjct: 4 EEAIEALREALELPPPKNLLLYGPPGTGKTT----LARAIANELFRPGAPFLYLNASD 57
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 37.7 bits (88), Expect = 0.049
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 718 QNFFINLYLQNDVPMMFV-GPTGTGKSTIVLNLLLNLSKDKYLPNIINFS 766
F+ N ++ DV + GPTG GK+ + L+ LL + P I+ F
Sbjct: 424 SPFYFNFHVGEDVGHTLIIGPTGAGKTVL-LSFLLAQALKYGNPQIVAFD 472
>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 = 35.0 bits (80), Expect = 0.10
Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 2/64 (3%)
Query: 731 PMMFVGPTGTGKSTIVLNLLLNLSKDKYLPNIINFSARTSSNITQEMIMAKLDRRRKGVY 790
++ VGP G+GK+T+ L L +I + ++ + +K
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGG--GVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 791 GPAM 794
+
Sbjct: 62 SGEL 65
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 34.4 bits (79), Expect = 0.33
Identities = 27/69 (39%), Positives = 30/69 (43%), Gaps = 18/69 (26%)
Query: 645 LTDRCYRTLMSALKLHLGGAPEGPAGTGKTETSKDLAKAVAKQCIVFNCSDRPTFPPN-- 702
+T R R L S +HL GPAGTGKT LA VA DRP N
Sbjct: 10 VTSRALRYLKSGYPVHL----RGPAGTGKTT----LAMHVA------RKRDRPVMLINGD 55
Query: 703 --LRPSDLI 709
L SDL+
Sbjct: 56 AELTTSDLV 64
Score = 32.1 bits (73), Expect = 2.2
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 725 YLQNDVPMMFVGPTGTGKSTIVLNL 749
YL++ P+ GP GTGK+T+ +++
Sbjct: 17 YLKSGYPVHLRGPAGTGKTTLAMHV 41
>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 = 33.1 bits (77), Expect = 0.50
Identities = 13/20 (65%), Positives = 16/20 (80%), Gaps = 1/20 (5%)
Query: 734 FVGPTGTGKSTIVLNLLLNL 753
VGP+G+GKST+ L LLL L
Sbjct: 33 IVGPSGSGKSTL-LKLLLRL 51
>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 = 33.0 bits (76), Expect = 0.51
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 733 MFVGPTGTGKSTIVLNLLLNLSKDK 757
+ G GTGKST+ L+L ++ +
Sbjct: 37 LLAGAPGTGKSTLALDLAAAVATGR 61
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 33.9 bits (78), Expect = 0.52
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 666 EGPAGTGKTETSKDLAKAVAKQCIVFNCSDRPTFPPNLRPSDLI 709
EGP G GKT ++ LA+A+ + C+ P+L PSDL+
Sbjct: 49 EGPPGVGKTLLARALARALGLPFVRIQCT------PDLLPSDLL 86
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 33.7 bits (78), Expect = 0.68
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 10/54 (18%)
Query: 651 RTLMSAL---KLHLGGAPEGPAGTGKTETSKDLAKAVAKQCIVFNCSDRPTFPP 701
+TL +A+ ++ GP GTGKT ++ AKA+ NC + P P
Sbjct: 24 QTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKAL-------NCQNGPDGEP 70
>gnl|CDD|169028 PRK07588, PRK07588, hypothetical protein; Provisional.
Length = 391
Score = 33.9 bits (78), Expect = 0.71
Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 5/82 (6%)
Query: 784 RRRKGVYGPAMGKKY---IVFIAGSLKIKYPEKDEFVIVLRAIIDVNMPKF-LVQDLPLF 839
R+ V+GP ++ A + Y +DE VL + + + L D LF
Sbjct: 159 HVRRLVFGPERDFEHYLGCKVAACVVD-GYRPRDERTYVLYNEVGRQVARVALRGDRTLF 217
Query: 840 IGIYKDLFPGIELPPTDRDELI 861
+ I++ L P + +L+
Sbjct: 218 LFIFRAEHDNPPLTPAEEKQLL 239
Score = 32.0 bits (73), Expect = 2.9
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 2/61 (3%)
Query: 1260 AAGSLKIKYPEKDEFVIVLRAIIDVNMPKF-LVQDLPLFIGIYKDLFPGIELPPTDRDEL 1318
AA + Y +DE VL + + + L D LF+ I++ L P + +L
Sbjct: 180 AACVVD-GYRPRDERTYVLYNEVGRQVARVALRGDRTLFLFIFRAEHDNPPLTPAEEKQL 238
Query: 1319 I 1319
+
Sbjct: 239 L 239
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 33.7 bits (78), Expect = 0.77
Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 7/32 (21%)
Query: 667 GPAGTGKTETSKDLAKAVAKQCIVFNCSDRPT 698
GP GTGKT +K AKAV NC + P
Sbjct: 45 GPRGTGKTSAAKIFAKAV-------NCLNPPD 69
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 33.8 bits (78), Expect = 0.85
Identities = 31/141 (21%), Positives = 50/141 (35%), Gaps = 10/141 (7%)
Query: 65 TLLDLLQKDR---TTARQINEEQELLKMVRTNYE--TVDEMLERLEPFDQLWSIILEFRE 119
TL D L K+ R + +E K V YE D L P + L+ E E
Sbjct: 264 TLFDYLPKNTLIVVDERVLEAAEEFEKEVADFYEARLSDGEYPPLPP-EALYLSAEELFE 322
Query: 120 SSDLWMEGPFKGLNADEIKDKTDFMFRELNQLARKMTRAPGCKMVNDLTRSKLESFRKEV 179
P L + + + + L+ L K D R ++E FR
Sbjct: 323 LLKPV---PRISLFPEHLPELSAEEIINLDPLPDLAFFGQH-KEPLDALRKEIERFRGGY 378
Query: 180 PILQCISNPGMEERHWKILSD 200
++ + G ER ++L++
Sbjct: 379 KVIILAESEGRRERLLELLAE 399
>gnl|CDD|114259 pfam05527, DUF758, Domain of unknown function (DUF758). Family of
eukaryotic proteins with unknown function, which are
induced by tumour necrosis factor.
Length = 186
Score = 32.7 bits (75), Expect = 0.86
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 380 MLKNFNKC-NLMLELIQKGLND-YLEKKRLFFPRFFFLSNDELLEILSETKDPLRVQPHL 437
+ K +C +L+ +L+Q+ L + F F ++ ELL L + P R PHL
Sbjct: 116 LSKLLTECRDLLHQLVQRHLTPKSHGRINHVFNHF---ADPELLTALYGPEGPYR--PHL 170
Query: 438 KKIFEGIN-LLE 448
KKI G+N LL+
Sbjct: 171 KKICAGLNKLLD 182
>gnl|CDD|203693 pfam07599, DUF1563, Protein of unknown function (DUF1563). A small
family of short hypothetical proteins in Leptospira
interrogans.
Length = 43
Score = 29.6 bits (66), Expect = 1.1
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 955 MNIISIDSFNEATLSKIFTSVLDWHFSKGFADSIVKLSK 993
MNII ID F TL ++ + ++ + F D I K+ K
Sbjct: 1 MNIILIDFFLLETLENLYATYVECFLKQIFLDKIQKIFK 39
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain of
glucan transporter and related proteins, subfamily C.
Glucan exporter ATP-binding protein. In A. tumefaciens
cyclic beta-1, 2-glucan must be transported into the
periplasmic space to exert its action as a virulence
factor. This subfamily belongs to the MRP-like family
and is involved in drug, peptide, and lipid export. 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 = 229
Score = 32.6 bits (75), Expect = 1.1
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 722 INLYLQNDVPMMFVGPTGTGKSTIVLNLLL 751
IN ++ + VGPTG GK+T++ NLL+
Sbjct: 22 INFSIKPGETVAIVGPTGAGKTTLI-NLLM 50
>gnl|CDD|233209 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein.
[Transport and binding proteins, Other].
Length = 711
Score = 33.2 bits (76), Expect = 1.2
Identities = 28/100 (28%), Positives = 43/100 (43%), Gaps = 25/100 (25%)
Query: 679 DLAKAVAKQCIVFNCSDRPTFPPNLRPSDLIIPTNVTCM---QNFFINLYLQNDVPMM-- 733
+ +AV VF DR PN+ + + P N+ + Q+ + + DVP++
Sbjct: 443 GMMQAVGASEKVFEYLDRK---PNIPLTGTLAPLNLEGLIEFQDVSFSYPNRPDVPVLKG 499
Query: 734 ------------FVGPTGTGKSTIVLNLLLNLSKDKYLPN 761
VGP+G+GKST+ LL NL Y P
Sbjct: 500 LTFTLHPGEVVALVGPSGSGKSTVAA-LLQNL----YQPT 534
>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 = 31.4 bits (72), Expect = 1.2
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 666 EGPAGTGKTETSKDLAKAVAKQCIVFNCSDRPTFPPNLRPSDLI 709
EG G KT ++ LA+++ F R F P+L PSD+
Sbjct: 5 EGVPGLAKTLLARTLARSLGLD---FR---RIQFTPDLLPSDIT 42
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 33.0 bits (75), Expect = 1.5
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 643 TPLTDRCYRTLMSALKLHLGGAPEGPAGTGKTETSKDLAKAVAKQCIVFNCSDR 696
+P T R ++ A+++ EG G GKT LA+ K+ I N S++
Sbjct: 1526 SPTTTVNLRRVLRAMQVGKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQ 1579
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 31.3 bits (71), Expect = 1.5
Identities = 21/98 (21%), Positives = 41/98 (41%), Gaps = 8/98 (8%)
Query: 733 MFVGPTGTGKSTIVLNL-------LLNLSKDKYLPNIINFSARTSSNITQEMIMAKLDRR 785
+ G G+GK+T+ L L +L+K+ L ++ S E +AKL +
Sbjct: 2 LITGTPGSGKTTLAKELAERLGDVLRDLAKENGLVLELDEEITDESKRLDEDKLAKLLDK 61
Query: 786 RKGVYGPAMGKKYIVFIAGSLKIKYPE-KDEFVIVLRA 822
+ + + ++ +++ KD +VLRA
Sbjct: 62 LEKIIEELAEGENVIIDGHLAELELERFKDLVFVVLRA 99
>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 = 32.4 bits (74), Expect = 1.7
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 732 MMFVGPTGTGKSTIVLNLLLNLSK 755
M+ VGP+G+GKST++ L L L
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLLA 27
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 32.5 bits (74), Expect = 1.9
Identities = 18/39 (46%), Positives = 21/39 (53%), Gaps = 10/39 (25%)
Query: 667 GPAGTGKTETSKDLAKAVAKQCIVFNCSDRPTFPPNLRP 705
GP G GKT T++ LAKAV NC+ T P RP
Sbjct: 45 GPRGVGKTSTARILAKAV-------NCT---TNDPKGRP 73
>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 = 30.6 bits (70), Expect = 2.4
Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 8/33 (24%)
Query: 667 GPAGTGKTETSKDLAKAVAKQC----IVFNCSD 695
GP GTGKT LAKAVAK+ I + S+
Sbjct: 5 GPPGTGKTT----LAKAVAKELGAPFIEISGSE 33
>gnl|CDD|233041 TIGR00596, rad1, DNA repair protein (rad1). All proteins in this
family for which functions are known are components in a
multiprotein endonuclease complex (usually made up of
Rad1 and Rad10 homologs). This complex is used primarily
for nucleotide excision repair but also for some aspects
of recombinational repair in some species. Most Archaeal
species also have homologs of these genes, but the
function of these Archaeal genes is not known, so we
have set our cutoff to only pick up the eukaryotic
genes.This family is based on the phylogenomic analysis
of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 814
Score = 32.1 bits (73), Expect = 2.6
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 923 FQTVTRVDLVDIIYITAMIPTMNTITGRLLRHMNIISIDSFNEATLSKIFTSVLDWHFSK 982
F +R+ +VD++ T +IP ITG L+ + I I+S EA + +++ F K
Sbjct: 11 FSITSRILVVDLL--TGIIPP-ELITGILVLRADRI-IESSQEAFILRLYRQKNKTGFIK 66
Query: 983 GFADS 987
F+D+
Sbjct: 67 AFSDN 71
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 31.7 bits (73), Expect = 2.6
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 732 MMFVGPTGTGKSTIVLNLLL-NLSKDKYLPNIINFSART 769
+M VG +G GKST + L L KY P +T
Sbjct: 7 IMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKT 45
>gnl|CDD|213216 cd03249, ABC_MTABC3_MDL1_MDL2, ATP-binding cassette domain of a
mitochondrial protein MTABC3 and related proteins.
MTABC3 (also known as ABCB6) is a mitochondrial
ATP-binding cassette protein involved in iron
homeostasis and one of four ABC transporters expressed
in the mitochondrial inner membrane, the other three
being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast
MDL1 (multidrug resistance-like protein 1) and MDL2
(multidrug resistance-like protein 2) transporters are
also included in this CD. MDL1 is an ATP-dependent
permease that acts as a high-copy suppressor of ATM1 and
is thought to have a role in resistance to oxidative
stress. Interestingly, subfamily B is more closely
related to the carboxyl-terminal component of subfamily
C than the two halves of ABCC molecules are with one
another.
Length = 238
Score = 31.4 bits (72), Expect = 2.8
Identities = 10/18 (55%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 734 FVGPTGTGKSTIVLNLLL 751
VG +G GKST+V +LL
Sbjct: 34 LVGSSGCGKSTVV-SLLE 50
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 31.5 bits (72), Expect = 3.0
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 6/47 (12%)
Query: 667 GPAGTGKTETSKDLAKAVAKQCIVFNCSD--RPTFPPNLRPSDLIIP 711
GPA TGKT +LA+A+A ++ C + FP N P+ L+I
Sbjct: 120 GPASTGKT----NLAQAIAHAVPLYGCVNWTNENFPFNDCPNKLLIW 162
>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 = 29.7 bits (67), Expect = 3.1
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 733 MFVGPTGTGKSTIVLNLLLNLSKDKY 758
+ G G GK+T+ NL L+K
Sbjct: 3 VVTGKGGVGKTTLAANLAAALAKRGK 28
>gnl|CDD|237918 PRK15172, PRK15172, putative aldose-1-epimerase; Provisional.
Length = 300
Score = 31.3 bits (71), Expect = 3.3
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 300 FETEMEAWESKLINMQDILDIWLQVQGTWMYLEPIFSSEDIMRQ 343
F+T + WE ++ + Q L + L W+ I+S E + RQ
Sbjct: 220 FKTANDLWEVRITHPQQALSVSLCSDQPWL---QIYSGEKLQRQ 260
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 31.2 bits (72), Expect = 3.4
Identities = 11/18 (61%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 734 FVGPTGTGKSTIVLNLLL 751
VG +G GKST+ LN LL
Sbjct: 90 LVGQSGVGKSTL-LNALL 106
>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 = 30.5 bits (69), Expect = 3.4
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 733 MFVGPTGTGKSTIVLNLLLNLSK 755
+ GPTG+GK+T+ L L LN++
Sbjct: 3 LVFGPTGSGKTTLALQLALNIAT 25
>gnl|CDD|218199 pfam04665, Pox_A32, Poxvirus A32 protein. The A32 protein is
thought to be involved in viral DNA packaging.
Length = 241
Score = 31.2 bits (71), Expect = 3.5
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 717 MQNFFINLYLQNDVPMMFVGPTGTGKSTIVLNLLLNLSKDKY 758
+ F + L M VG +G+GK+T +L+LL L K+
Sbjct: 1 EKRFDRDSLLAAPFRMAIVGGSGSGKTTYLLSLLRTL-VRKF 41
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 30.2 bits (69), Expect = 4.3
Identities = 10/18 (55%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 734 FVGPTGTGKSTIVLNLLL 751
G +G GKST+ LN LL
Sbjct: 40 LAGQSGVGKSTL-LNALL 56
>gnl|CDD|215003 smart01060, Catalase, Catalases are antioxidant enzymes that catalyse
the conversion of hydrogen peroxide to water and
molecular oxygen, serving to protect cells from its toxic
effects. Hydrogen peroxide is produced as a consequence
of oxidative cellular metabolism and can be converted to
the highly reactive hydroxyl radical via transition
metals, this radical being able to damage a wide variety
of molecules within a cell, leading to oxidative stress
and cell death. Catalases act to neutralise hydrogen
peroxide toxicity, and are produced by all aerobic
organisms ranging from bacteria to man. Most catalases
are mono-functional, haem-containing enzymes, although
there are also bifunctional haem-containing
peroxidase/catalases that are closely related to plant
peroxidases, and non-haem, manganese-containing catalases
that are found in bacteria.
Length = 373
Score = 31.3 bits (72), Expect = 4.5
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 1020 VFNLRD---FAKVIMGLTQLPASHCKAPDKMYKLWT------HEILRVFSDR 1062
VF +RD F I + P ++ D + W+ H++ + SDR
Sbjct: 122 VFFIRDPIKFPDFIHAQKRDPRTNLPDHDMFWDFWSLNPESLHQVTWLMSDR 173
>gnl|CDD|163712 cd08156, catalase_clade_3, Clade 3 of the heme-binding enzyme
catalase. Catalase is a ubiquitous enzyme found in both
prokaryotes and eukaryotes, which is involved in the
protection of cells from the toxic effects of peroxides.
It catalyzes the conversion of hydrogen peroxide to water
and molecular oxygen. Catalases also utilize hydrogen
peroxide to oxidize various substrates such as alcohol or
phenols. Clade 3 catalases are the most abundant
subfamily and are found in all three kingdoms of life;
they have a relatively small subunit size of 43 to 75
kDa, and bind a protoheme IX (heme b) group buried deep
inside the structure. Clade 3 catalases also bind NADPH
as a second redox-active cofactor. They form tetramers,
and in eukaryotic cells, catalases are located in
peroxisomes.
Length = 429
Score = 31.0 bits (71), Expect = 5.0
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 9/52 (17%)
Query: 1020 VFNLRD---FAKVIMGLTQLPASHCKAPDKMYKLWT------HEILRVFSDR 1062
VF +RD F I + P ++ K PD + W+ H++ +FSDR
Sbjct: 85 VFFIRDPIKFPDFIHTQKRNPQTNLKDPDMFWDFWSLSPESLHQVTILFSDR 136
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 31.1 bits (71), Expect = 5.0
Identities = 17/37 (45%), Positives = 23/37 (62%), Gaps = 9/37 (24%)
Query: 667 GPAGTGKTETSKDLAKAVAKQCIVFNC--SDRPTFPP 701
GP GTGKT +++ LAK++ NC SD+PT P
Sbjct: 45 GPRGTGKTSSARILAKSL-------NCLNSDKPTPEP 74
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of
the nitrate and sulfonate transporters. NrtD and SsuB
are the ATP-binding subunits of the bacterial ABC-type
nitrate and sulfonate transport systems, respectively.
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules. The nucleotide binding domain shows
the highest similarity between all members of the
family. 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 = 220
Score = 30.5 bits (70), Expect = 5.5
Identities = 10/22 (45%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 734 FVGPTGTGKSTIVLNLLLNLSK 755
VGP+G GKST+ L ++ L +
Sbjct: 35 LVGPSGCGKSTL-LRIIAGLER 55
>gnl|CDD|215783 pfam00199, Catalase, Catalase.
Length = 383
Score = 30.7 bits (70), Expect = 5.7
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 9/52 (17%)
Query: 1020 VFNLRD---FAKVIMGLTQLPASHCKAPDKMYKLWT------HEILRVFSDR 1062
VF +RD F I PA++ P + H++ +FSDR
Sbjct: 125 VFFIRDPIKFPDFIHAQKPDPATNLPDPTMFWDFLALHPESLHQVTWLFSDR 176
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is also
a nucleotide binding domain (NBD).
Length = 227
Score = 30.6 bits (70), Expect = 5.7
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 2/22 (9%)
Query: 734 FVGPTGTGKSTI--VLNLLLNL 753
+GP+G GKST+ +LN L +L
Sbjct: 31 LIGPSGCGKSTLLRLLNRLNDL 52
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein
DNA-binding domain. The plasmid conjugative coupling
protein TrwB forms hexamers from six structurally very
similar protomers. This hexamer contains a central
channel running from the cytosolic pole (made up by the
AADs) to the membrane pole ending at the transmembrane
pore shaped by 12 transmembrane helices, rendering an
overall mushroom-like structure. The TrwB_AAD (all-alpha
domain) domain appears to be the DNA-binding domain of
the structure. TrwB, a basic integral inner-membrane
nucleoside-triphosphate-binding protein, is the
structural prototype for the type IV secretion system
coupling proteins, a family of proteins essential for
macromolecular transport between cells and export.
Length = 386
Score = 31.0 bits (71), Expect = 5.7
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 732 MMFVGPTGTGKSTIVLNLL 750
++ VG TGTGK+ + LL
Sbjct: 18 ILIVGTTGTGKTQALRELL 36
>gnl|CDD|213215 cd03248, ABCC_TAP, ATP-binding cassette domain of the Transporter
Associated with Antigen Processing, subfamily C. TAP
(Transporter Associated with Antigen Processing) is
essential for peptide delivery from the cytosol into the
lumen of the endoplasmic reticulum (ER), where these
peptides are loaded on major histocompatibility complex
(MHC) I molecules. Loaded MHC I leave the ER and display
their antigenic cargo on the cell surface to cytotoxic T
cells. Subsequently, virus-infected or malignantly
transformed cells can be eliminated. TAP belongs to the
large family of ATP-binding cassette (ABC) transporters,
which translocate a vast variety of solutes across
membranes.
Length = 226
Score = 30.1 bits (68), Expect = 6.4
Identities = 12/19 (63%), Positives = 15/19 (78%), Gaps = 1/19 (5%)
Query: 735 VGPTGTGKSTIVLNLLLNL 753
VGP+G+GKST+V LL N
Sbjct: 46 VGPSGSGKSTVV-ALLENF 63
>gnl|CDD|190347 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic protein
and predicted ATPase that is induced by phosphate
starvation.
Length = 205
Score = 30.1 bits (69), Expect = 6.5
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 715 TCMQNFFINLYLQNDVPMMFVGPTGTGKS 743
T Q ++ +ND+ GP GTGK+
Sbjct: 6 TLGQKRYVEAIRKNDIVFGI-GPAGTGKT 33
>gnl|CDD|213244 cd03277, ABC_SMC5_euk, ATP-binding cassette domain of eukaryotic
SMC5 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 213
Score = 30.3 bits (69), Expect = 6.5
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 733 MFVGPTGTGKSTIV 746
M +GP G+GKS+IV
Sbjct: 27 MIIGPNGSGKSSIV 40
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 29.3 bits (66), Expect = 6.8
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 733 MFVGPTGTGKST---IVLNLLLN 752
+ VGP +GK+T +LN L
Sbjct: 4 LVVGPKDSGKTTLIRKLLNYLKR 26
>gnl|CDD|225913 COG3378, COG3378, Phage associated DNA primase [General function
prediction only].
Length = 517
Score = 30.9 bits (70), Expect = 6.8
Identities = 38/181 (20%), Positives = 56/181 (30%), Gaps = 45/181 (24%)
Query: 733 MFVGPTGTGKSTIVLNLLLNLSKDKYLPNIINFSARTSSNITQEMIMAKLDRRRKG---- 788
GP G GKST V +L+ NL TS+ +T + DR G
Sbjct: 234 WLYGPGGNGKSTFV-DLISNLLGRY---------NVTSAPLT---DLEADDRHPFGLAAL 280
Query: 789 -----VYGPAMGKKYI-------VFIAG-SLKIKYPEKDEFVIVLRAIIDVN---MPKFL 832
V K + G + + KD F A + P+
Sbjct: 281 VGKRLVTVSETEKGRLDDEGKLKALTGGDVISAERKRKDFFSFTPNAKLIQATNHPPRIR 340
Query: 833 VQDLPLF----IGIYKDLFPGIELPPTDRDELIEQIKIN----LAKRNAQATDWYIEKII 884
D ++ I ++ FP E D+L E++ L A D E +
Sbjct: 341 GDDEAIWRRLLIVPFEKQFPPAE----RDDKLDEKLAAERPGILNWLVAGFLDLQREGLD 396
Query: 885 Q 885
Q
Sbjct: 397 Q 397
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 30.6 bits (70), Expect = 6.8
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 733 MFVGPTGTGKSTIVLNLLL 751
+ G +G GKST+ LN L
Sbjct: 168 VLAGQSGVGKSTL-LNALA 185
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 30.2 bits (68), Expect = 7.1
Identities = 26/173 (15%), Positives = 66/173 (38%), Gaps = 16/173 (9%)
Query: 734 FVGPTGTGKSTIV--LNLLL----NLSKDKYLPNIINFSARTSSNITQEMIMAKLDRRRK 787
GP G+GK+TI+ + L + K I+ + ++ ++
Sbjct: 24 IYGPNGSGKTTILDAIRWALYGKTSRLKKSKGRGIVKGDIEIEKDEGKKKTYVEITFENN 83
Query: 788 GVYGPAMGKKYIVFIAGSLKIKYPEKDEFVIVLRAIIDVNMPKFLVQDLPLFIGIYKDLF 847
GK + I S ++ K + V ++I+++ L + + + K++
Sbjct: 84 K------GKLKLRLIEESRELT---KKKGKKVKKSILEIVEIDELQEFIDELLKSDKEIL 134
Query: 848 PGIELPPTDRDELIEQIKINLAKRNAQATDWYIEKIIQVYEMILDDLNMPQKE 900
P + +R E ++ + +R + +E++ +++ L +K+
Sbjct: 135 PLLLYLGQERLEELKFKRKEKKERLEELEK-ELEELEDEKDLLEKLLEEKEKK 186
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 30.6 bits (70), Expect = 7.1
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 732 MMFVGPTGTGKST 744
+ VGPTG GK+T
Sbjct: 224 VALVGPTGVGKTT 236
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 30.4 bits (69), Expect = 7.1
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 732 MMFVGPTGTGKST 744
+ VGPTG GK+T
Sbjct: 198 IALVGPTGVGKTT 210
>gnl|CDD|203379 pfam06028, DUF915, Alpha/beta hydrolase of unknown function (DUF915).
This family consists of several bacterial proteins of
unknown function. Members of this family have an
alpha/beta hydrolase fold.
Length = 255
Score = 30.4 bits (69), Expect = 7.2
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 1369 QTLADSLTDIAAKKSATMKEFKTGYKIINPKSITMGQLYGEFDSASHEWRDGI 1421
QTLA L D K+ YK P + + + G+ D+ DGI
Sbjct: 153 QTLAIVLKDGPKNKTPMYDYLIDNYKKKIPSDLEVLNIAGDLDNGKQS--DGI 203
>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 = 30.1 bits (69), Expect = 7.4
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 732 MMFVGPTGTGKST 744
++ VGP G GK+T
Sbjct: 4 ILLVGPNGVGKTT 16
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 30.4 bits (70), Expect = 7.6
Identities = 17/73 (23%), Positives = 37/73 (50%), Gaps = 15/73 (20%)
Query: 732 MMFVGPTGTGKSTIVLNLLLNLSKDKYLPNIINFSARTSSNITQEM--IMAKLDRRRKGV 789
M+ GP GTGK+T+ ++ + + SA +S + +++ ++ + +RR
Sbjct: 39 MILWGPPGTGKTTLA-RIIAGATDAPF----EALSA-VTSGV-KDLREVIEEARQRR--- 88
Query: 790 YGPAMGKKYIVFI 802
+ G++ I+FI
Sbjct: 89 ---SAGRRTILFI 98
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 30.6 bits (70), Expect = 7.9
Identities = 13/21 (61%), Positives = 14/21 (66%), Gaps = 4/21 (19%)
Query: 667 GPAGTGKTETSKDLAKAVAKQ 687
GP GTGKT LAKAVA +
Sbjct: 172 GPPGTGKTL----LAKAVAHE 188
>gnl|CDD|188649 cd09817, linoleate_diol_synthase_like, Linoleate (8R)-dioxygenase
and related enzymes. These fungal enzymes, related to
animal heme peroxidases, catalyze the oxygenation of
linoleate and similar targets. Linoleate
(8R)-dioxygenase, also called linoleate:oxygen
7S,8S-oxidoreductase, generates
(9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate as a
product. Other members are 5,8-linoleate dioxygenase
(LDS, ppoA) and linoleate 10R-dioxygenase (ppoC),
involved in the biosynthesis of oxylipins.
Length = 550
Score = 30.4 bits (69), Expect = 8.2
Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 5/75 (6%)
Query: 119 ESSDLWMEGPFKGL--NADEIKDKTDFMFRELNQLARKMTRAPGCKMVNDLTRSKLESFR 176
+ W E F+ L + + L + + + P + L R FR
Sbjct: 285 ARDEKWTEDLFESLFGGKSPDEVTLKEFMQALGRFEALIPKDPSQRTFGGLKRGPDGRFR 344
Query: 177 KE--VPILQ-CISNP 188
E V IL+ I +P
Sbjct: 345 DEDLVRILKDSIEDP 359
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family are
found in a variety of single stranded RNA viruses.
Length = 105
Score = 28.4 bits (64), Expect = 9.1
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 667 GPAGTGKTETSKDLAKAVAKQ 687
GP G GK+ +K LA+A+ K
Sbjct: 5 GPPGCGKSTLAKYLARALLKH 25
>gnl|CDD|218788 pfam05872, DUF853, Bacterial protein of unknown function (DUF853).
This family consists of several bacterial proteins of
unknown function. BMEI1370 is thought to be an ATPase.
Length = 504
Score = 30.5 bits (69), Expect = 9.2
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 1351 RHGLMVVGESFGGKTTAYQTLADSLTDI 1378
RHGL + G + GKT Q LA+S +D
Sbjct: 22 RHGL-IAGATGTGKTVTLQVLAESFSDA 48
>gnl|CDD|216584 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE, which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block in
cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 201
Score = 29.7 bits (67), Expect = 9.4
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 732 MMFVGPTGTGKSTIVLNLLLNL 753
++ G TG+GKST + L+L+L
Sbjct: 41 LLIAGATGSGKSTFLNTLILSL 62
>gnl|CDD|172735 PRK14247, PRK14247, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 250
Score = 29.9 bits (67), Expect = 9.5
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 722 INLYLQNDVPMMFVGPTGTGKSTI--VLNLLLNL 753
+NL + ++ +GP+G+GKST+ V N L+ L
Sbjct: 22 VNLEIPDNTITALMGPSGSGKSTLLRVFNRLIEL 55
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 0.136 0.396
Gapped
Lambda K H
0.267 0.0853 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 77,545,513
Number of extensions: 7898287
Number of successful extensions: 8535
Number of sequences better than 10.0: 1
Number of HSP's gapped: 8511
Number of HSP's successfully gapped: 144
Length of query: 1513
Length of database: 10,937,602
Length adjustment: 109
Effective length of query: 1404
Effective length of database: 6,103,016
Effective search space: 8568634464
Effective search space used: 8568634464
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 (21.8 bits)
S2: 66 (29.0 bits)