RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2654
(1949 letters)
>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 = 442 bits (1137), Expect = e-143
Identities = 195/227 (85%), Positives = 212/227 (93%)
Query: 1013 FDHEYLGCTPRLVITPLTDRCYITLSQSLHLNMGGAPAGPAGTGKTETTKDLGKAIGIMV 1072
+ +EYLG TPRLVITPLTDRCYITL+QSLHL M GAPAGPAGTGKTETTKDLG+A+GIMV
Sbjct: 1 YSYEYLGNTPRLVITPLTDRCYITLTQSLHLTMSGAPAGPAGTGKTETTKDLGRALGIMV 60
Query: 1073 YVFNCSEQMDYRSCGNIYKGLAQTGAWGCFDEFNRISVEVLSVVAVQVKSVLDSVKMRKS 1132
YVFNCSEQMDY+SCGNIYKGLAQTGAWGCFDEFNRISVEVLSVVAVQVK V D+++ +K
Sbjct: 61 YVFNCSEQMDYKSCGNIYKGLAQTGAWGCFDEFNRISVEVLSVVAVQVKCVQDAIRDKKQ 120
Query: 1133 RFNFMGENIKLVTTVGMFITMNPGYAGRAELPENLKALFRPCAMVVPDFALICEIMLVSE 1192
FNF+GE I L+ +VG+FITMNPGYAGR ELPENLKALFRPCAMVVPDF LICEIMLV+E
Sbjct: 121 WFNFLGEEISLIPSVGIFITMNPGYAGRTELPENLKALFRPCAMVVPDFELICEIMLVAE 180
Query: 1193 GFQEARLLSRKFITLYSLCKELLSKQDHYDWGLRAIKSVLVVAGSLK 1239
GF EARLL+RKFITLY+LCKELLSKQDHYDWGLRAIKSVLVVAGSLK
Sbjct: 181 GFLEARLLARKFITLYTLCKELLSKQDHYDWGLRAIKSVLVVAGSLK 227
Score = 425 bits (1093), Expect = e-137
Identities = 198/282 (70%), Positives = 215/282 (76%), Gaps = 52/282 (18%)
Query: 1400 FDHEYLGCTPRLVITPLTDRCYITLSQSLHLNMGGAPAGPAGTGKTETTKDLGKAIGIMV 1459
+ +EYLG TPRLVITPLTDRCYITL+QSLHL M GAPAGPAGTGKTETTKDLG+A+GIMV
Sbjct: 1 YSYEYLGNTPRLVITPLTDRCYITLTQSLHLTMSGAPAGPAGTGKTETTKDLGRALGIMV 60
Query: 1460 YVFNCSEQMDYRSCGNIYKGLAQTGAWGCFDEFNRISVEVLSVVAVQVKSVLDSVKMRKS 1519
YVFNCSEQMDY+SCGNIYKGLAQTGAWGCFDEFNRISVEVLSVVAVQVK V D+++ +K
Sbjct: 61 YVFNCSEQMDYKSCGNIYKGLAQTGAWGCFDEFNRISVEVLSVVAVQVKCVQDAIRDKKQ 120
Query: 1520 RFNFMGESSLAGLAQTGAWGCFDEFNRISVEVLSVVAVQVKSVLDSVKMRKSRFNFMGEN 1579
FNF+GE
Sbjct: 121 WFNFLGEE---------------------------------------------------- 128
Query: 1580 IKLVTTVGMFITMNPGYAGRAELPENLKALFRPCAMVVPDFALICEIMLVSEGFQEARLL 1639
I L+ +VG+FITMNPGYAGR ELPENLKALFRPCAMVVPDF LICEIMLV+EGF EARLL
Sbjct: 129 ISLIPSVGIFITMNPGYAGRTELPENLKALFRPCAMVVPDFELICEIMLVAEGFLEARLL 188
Query: 1640 SRKFITLYSLCKELLSKQDHYDWGLRAIKSVLVVAGSLKRGD 1681
+RKFITLY+LCKELLSKQDHYDWGLRAIKSVLVVAGSLKRGD
Sbjct: 189 ARKFITLYTLCKELLSKQDHYDWGLRAIKSVLVVAGSLKRGD 230
>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 = 244 bits (624), Expect = 6e-71
Identities = 104/277 (37%), Positives = 166/277 (59%), Gaps = 12/277 (4%)
Query: 472 KEIIEDITDMGVKIKRVAKRTENTYKVWSTLEFEYDIHARTKTPLLRCSEELIEMLEENQ 531
+E IE+I++ K + K + W LEFE + T T LL+ +E+IE+L++N
Sbjct: 128 EEEIEEISEQAQKEYSIEKALKKIKDTWEELEFELVPYKDTGTYLLKGWDEIIELLDDNL 187
Query: 532 VQLQNMASSKFVGYFQKEVNEWQIKLSNADAVISIWIEVQRTWQHLESIFIGSDDIRQQL 591
V LQ+M +S +V F++E +EW+ KL+ V+ +W++VQR W +LE IF SD I++QL
Sbjct: 188 VTLQSMKASPYVKPFEEEADEWEKKLNLIQEVLELWLKVQRKWVYLEPIFSSSD-IKKQL 246
Query: 592 PEDSRRFDATDKAFRALAQDMHKTPNVVIGTNKPGLYEKLETIQKDLTKCEKALAQYLET 651
PE+S+RF DK ++ L + +K PNV+ N PGL EKLE + + L K +K+L +YLE+
Sbjct: 247 PEESKRFSNVDKEWKKLMKKANKDPNVLEVCNIPGLLEKLEKLNEQLEKIQKSLNEYLES 306
Query: 652 KKLTYPRFYFVSSSDLLDILANGNNPEAFRP--GK--DGKINVKI------AQGMYAKDG 701
K+ +PRFYF+S+ DLL+IL+ +P A +P K +G +++ GM + +G
Sbjct: 307 KRSAFPRFYFLSNDDLLEILSQSKDPTAVQPHLKKLFEGISSLEFDEENNNITGMISSEG 366
Query: 702 EYVEFNGDCDCSGQANKASTEMI-EMEDVLNKLMEQA 737
E V + G E+ EM++ L KL+++A
Sbjct: 367 EEVPLSKPVSVEGNVEDWLNELEKEMKETLKKLLKEA 403
Score = 175 bits (445), Expect = 4e-47
Identities = 70/192 (36%), Positives = 114/192 (59%), Gaps = 1/192 (0%)
Query: 750 LANARKDLKMAKLIWDYILVIQGWMLDWKETLWKKIDSEAMDMELKKFTKELRTLDKDLR 809
L K+LK K +WD + +WK T W ID E ++ E++KF K+LR L K+LR
Sbjct: 3 LQELEKELKPLKKLWDLYSEWSESIEEWKNTPWSTIDPEELESEIEKFLKQLRKLPKNLR 62
Query: 810 NWDIFLQLESEIKNMIAALKAVTELQNPAIRDRHWEELMSVTKVKFSIDDSTTLKDLLDL 869
+++ +L+ +I + +L + +L+NPA+++RHWE++ + K D+ TL DLLDL
Sbjct: 63 QYEVAEELKKKIDDFKKSLPLIEDLKNPALKERHWEQIFKLLGFKDFPDEDFTLGDLLDL 122
Query: 870 ELYKFEEEVKTIVDKSVKEQQMEKVLKDFDKVWSTLEFEYDIHARTKTPLLRCSEELIEM 929
L +EEE++ I +++ KE +EK LK W LEFE + T T LL+ +E+IE+
Sbjct: 123 GLLNYEEEIEEISEQAQKEYSIEKALKKIKDTWEELEFELVPYKDTGTYLLKGWDEIIEL 182
Query: 930 LEENQINQLNAL 941
L++N L ++
Sbjct: 183 LDDNL-VTLQSM 193
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 70.4 bits (172), Expect = 9e-12
Identities = 105/441 (23%), Positives = 183/441 (41%), Gaps = 90/441 (20%)
Query: 1516 MRKSRFNFMGESSLAGLAQT------GAWGCFDEFNRISVEVLSVVAVQVKSVLDSVKMR 1569
+RK F F LA L G++ CFDEFNR+S E +S +V++
Sbjct: 1634 IRKPVFVFCCYPELASLRNIYEAVLMGSYLCFDEFNRLSEETMSA-SVELYLSS------ 1686
Query: 1570 KSRFNFMGENIKLVTTVGMFITMNPGYAGRAELPENLKALFRPCAMVV--PDFALICEIM 1627
K + F F+ MN GY R EL +L+A+F + PD +LI I
Sbjct: 1687 KDKTKF-------------FLQMNYGYKPR-ELTRSLRAIFGYAETRIDTPDVSLI--ID 1730
Query: 1628 LVSEGFQEA--RLLSRKFITLYSLCKELLSKQDHYDWGLRAIKSVLVVAGSLKRGDRQRP 1685
E +E RL+ +K + S+QD YD+GLRAI+ ++
Sbjct: 1731 WYCEAIREKIDRLVQQK--------ESSTSRQDLYDFGLRAIREMIAGHIG--------- 1773
Query: 1686 EDQVLMRALRDFNIPKIITEDLQVFMGLIGDLFPALDVPRKRDIDFEKQVRQATIDMKLQ 1745
E ++ + F + ++ +DL VF+ + +F + +D E + + L+
Sbjct: 1774 EAEITFSMILFFGMACLLKKDLAVFVEEVRKIFGS------SHLDVEAVAYKDALLHILR 1827
Query: 1746 PEDSFILKVVQLVELFAVRHSVFIIGFAGTGKSCVWKTLYKTYVNAKKKPMYNDLEPKAV 1805
L VV H V + G G + ++N + M
Sbjct: 1828 SRR--GLLVVGG-------HGV-LKGVLIRGACDA--REFVCWLNPRN--MR-------- 1865
Query: 1806 TNDELFGIINPSTREWKDGLFSCLIREQAQSTGDGPKWMVMDGDI-DPMWIESLNTVMDD 1864
E+FG + T +++D L +R G + + + ++E N ++D+
Sbjct: 1866 ---EIFGHRDELTGDFRDSLKVQDLR--RNIHGGRECLFIFESIPVESSFLEDFNPLLDN 1920
Query: 1865 NKVLTLAS-NERIALTPSMRLLFEISNLRTATPATVSRAGILYINPQDLGWNPYVLSWTD 1923
N+ L L S NERI + ++R +FE ++L T AT++R ++Y+ ++L P V S
Sbjct: 1921 NRFLCLFSGNERIRIPENLRFVFESTSLEKDTEATLTRVFLVYME-ENL---PVVFSACC 1976
Query: 1924 TRESESEKNILM-GLFDKLTP 1943
++++ I L ++
Sbjct: 1977 SQDTSVLAGIRSPALKNRCFI 1997
Score = 68.5 bits (167), Expect = 4e-11
Identities = 57/385 (14%), Positives = 113/385 (29%), Gaps = 77/385 (20%)
Query: 1529 LAGLAQTGAWGCFDEFNRISVEVLSVVAVQVKSVLDSVKMRKSRFNFMGENIKLVTTVGM 1588
AG G +E + E+ + V D +M + + + E+ + +
Sbjct: 981 EAGPICEEERG-TEESALLD-EISRTILVDEYLNSDEFRMLEELNSAVVEHGLKSPSTPV 1038
Query: 1589 FITMNPGYAGRAELPENLKALFRPCAMVVPDFALICEIMLVSEGFQEARLLSRKFITLYS 1648
+ +N R + E + +P F I +E+ L R+ +
Sbjct: 1039 EMIINE----RNIVLEIGRRALDMFLSNIP-FGAIKSR-------RES--LDREIGAFNN 1084
Query: 1649 LCKELLSKQDHYDWGLRAIKSVLVVAGSLKRGDRQRPE-DQVLMRALRDFNIPKIITEDL 1707
+ ++D + + SLK R E + L + L +P
Sbjct: 1085 EVDGIAREEDELMF--YPMF------KSLKAKHRMLEEKTEYLNKILSITGLP------- 1129
Query: 1708 QVFMGLIGDLFPALDVPRKRDIDFEKQVRQATIDMKLQPEDSFILKVVQLVE-LFAVRHS 1766
LI D + D +++ R + K + + L V Q V L +V
Sbjct: 1130 -----LISDTL--RERIDTLDAEWDSFCRISESLKKYESQQVSGLDVAQFVSFLRSVDTG 1182
Query: 1767 VFII--GFAGTGKSCVWKTL--YKTYVNAKKKPMYNDLEPKAVTNDELFGIINPSTREWK 1822
F K + Y +V + + F + E +
Sbjct: 1183 AFHAEYFRVFLCKIKHYTDACDYLWHVKS------------PYVKKKYF----DADMELR 1226
Query: 1823 DGLFSCLIREQAQST-GDGPKWMVMDGDIDPMWIESLNTVMDDNKVLTLASNERIALTPS 1881
F RE ++ D ++ ++E + K+ + E
Sbjct: 1227 -QFFLMFNREDMEARLADSKMEYEVER-----YVEKTKAEVSSLKLELSSVGEG------ 1274
Query: 1882 MRLLFEISNLRTATPATVSRAGILY 1906
+++ NL + V R + Y
Sbjct: 1275 -QVVVS--NLGS-IGDKVGRCLVEY 1295
Score = 65.4 bits (159), Expect = 3e-10
Identities = 26/217 (11%), Positives = 62/217 (28%), Gaps = 30/217 (13%)
Query: 1016 EYLGCTPRLVITPLTDRCYITLSQSLHLNMGGAPAGPAGTGKTETTKDLGKAIGIMVYVF 1075
+ + + L +++ + T + L G +
Sbjct: 919 AKNTIPFFVFEHSMDTSQHQKLFEAVCDEV----CRFVDTENSRVYGMLVAGKGRIY--- 971
Query: 1076 NCSEQMDYRSCGNIYKGLAQTGAWGCFDEFNRISVEVLSVVAVQVKSVLDSVKMRKSRFN 1135
+ + RS I G G +E + E+ + V D +M + +
Sbjct: 972 ---DGTEPRS--RIEAGPICEEERG-TEESALLD-EISRTILVDEYLNSDEFRMLEELNS 1024
Query: 1136 FMGENIKLVTTVGMFITMNPGYAGRAELPENLKALFRPCAMVVPDFALICEIMLVSEGFQ 1195
+ E+ + + + +N R + E + +P F I +
Sbjct: 1025 AVVEHGLKSPSTPVEMIINE----RNIVLEIGRRALDMFLSNIP-FGAIKSR-------R 1072
Query: 1196 EARLLSRKFITLYSLCKELLSKQDHYDWGLRAIKSVL 1232
E+ L R+ + + ++D + + L
Sbjct: 1073 ES--LDREIGAFNNEVDGIAREEDELMF--YPMFKSL 1105
Score = 37.7 bits (87), Expect = 0.077
Identities = 57/192 (29%), Positives = 86/192 (44%), Gaps = 39/192 (20%)
Query: 1051 GPAGTGKTETTKDLG-KAIGIMVYVFNCSEQMDYRSCGNIYKGLAQTGAWGCFDEFNRIS 1109
G G E + I V+VF C ++ S NIY+ + G++ CFDEFNR+S
Sbjct: 1616 GACNPGTDEGRVKYYERFIRKPVFVFCCYPEL--ASLRNIYEAVLM-GSYLCFDEFNRLS 1672
Query: 1110 VEVLSVVAVQVKSVLDSVKMRKSRFNFMGENIKLVTTVGMFITMNPGYAGRAELPENLKA 1169
E +S +V++ K + F F+ MN GY R EL +L+A
Sbjct: 1673 EETMS-ASVELYLSS------KDKTKF-------------FLQMNYGYKPR-ELTRSLRA 1711
Query: 1170 LFRPCAMVV--PDFALICEIMLVSEGFQEA--RLLSRKFITLYSLCKELLSKQDHYDWGL 1225
+F + PD +LI I E +E RL+ +K + S+QD YD+GL
Sbjct: 1712 IFGYAETRIDTPDVSLI--IDWYCEAIREKIDRLVQQK--------ESSTSRQDLYDFGL 1761
Query: 1226 RAIKSVLVVAGS 1237
RAI+ ++
Sbjct: 1762 RAIREMIAGHIG 1773
>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 = 53.5 bits (129), Expect = 4e-08
Identities = 34/147 (23%), Positives = 58/147 (39%), Gaps = 24/147 (16%)
Query: 1766 SVFIIGFAGTGKSCVWKTLYKTYVNAKKKPMYNDLEPKAVTNDELFGIINPSTR--EWKD 1823
V ++G GTGKS + + L N + + T ++L G N W D
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQL---TRDTTEEDLKGRRNIDPGGASWVD 57
Query: 1824 GLFSCLIREQAQSTGDGPKWMVMDGDID---PMWIESLNTVMDDNKVLTLASNERI-ALT 1879
G L+R A+ + + +I+ P + SL +++D+ ++L E + A
Sbjct: 58 G---PLVRA-ARE-----GEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKAAP 108
Query: 1880 PSMRLLFEISNLR-----TATPATVSR 1901
RL+ N +PA SR
Sbjct: 109 DGFRLIAT-MNPLDRGLNELSPALRSR 134
Score = 38.4 bits (90), Expect = 0.008
Identities = 36/138 (26%), Positives = 53/138 (38%), Gaps = 25/138 (18%)
Query: 1051 GPAGTGKTETTKDLGKAI-GIMVYVFNCSEQM---------------DYRSCGNIYKGLA 1094
GP GTGK+E + L A+ V+ + G + + A
Sbjct: 6 GPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPLVRA-A 64
Query: 1095 QTGAWGCFDEFNRISVEVLSVVAVQVKSVLDSVKMRKSRFNFMGENIKLVTTVGMFI-TM 1153
+ G DE NR + +VL+ + S+LD R+ GE +K I TM
Sbjct: 65 REGEIAVLDEINRANPDVLNS----LLSLLDE---RRLLLPEGGELVKAAPDGFRLIATM 117
Query: 1154 NPGYAGRAELPENLKALF 1171
NP G EL L++ F
Sbjct: 118 NPLDRGLNELSPALRSRF 135
Score = 33.0 bits (76), Expect = 0.45
Identities = 40/175 (22%), Positives = 59/175 (33%), Gaps = 47/175 (26%)
Query: 1438 GPAGTGKTETTKDLGKAI-GIMVYVFNCSEQMDYRSCGNIYKGLAQTGAWGCFDEFNRIS 1496
GP GTGK+E + L A+ V+ + D R +
Sbjct: 6 GPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEE------------------DLKGRRN 47
Query: 1497 VEVLSVVAVQVKSVLDSVKMRKSRFNFMGESSLAGLAQTGAWGCFDEFNRISVEVLSVVA 1556
+ S +D +R A+ G DE NR + +VL+
Sbjct: 48 I------DPGGASWVDGPLVRA--------------AREGEIAVLDEINRANPDVLNS-- 85
Query: 1557 VQVKSVLDSVKMRKSRFNFMGENIKLVTTVGMFI-TMNPGYAGRAELPENLKALF 1610
+ S+LD R+ GE +K I TMNP G EL L++ F
Sbjct: 86 --LLSLLDE---RRLLLPEGGELVKAAPDGFRLIATMNPLDRGLNELSPALRSRF 135
Score = 33.0 bits (76), Expect = 0.46
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 1316 FIIGFAGTGKSCVWKTLYKTYVNAKKKPMYNDLEPKAVTNDELFGIINPSTR--EWKDG 1372
++G GTGKS + + L N + + T ++L G N W DG
Sbjct: 3 LLVGPPGTGKSELAERLAAALSNRPVFYVQL---TRDTTEEDLKGRRNIDPGGASWVDG 58
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 39.4 bits (92), Expect = 0.023
Identities = 18/33 (54%), Positives = 22/33 (66%)
Query: 1050 AGPAGTGKTETTKDLGKAIGIMVYVFNCSEQMD 1082
AGP G GKTE T L KA+GI + F+ SE M+
Sbjct: 494 AGPTGVGKTEVTVQLSKALGIELLRFDMSEYME 526
Score = 39.4 bits (92), Expect = 0.023
Identities = 18/33 (54%), Positives = 22/33 (66%)
Query: 1437 AGPAGTGKTETTKDLGKAIGIMVYVFNCSEQMD 1469
AGP G GKTE T L KA+GI + F+ SE M+
Sbjct: 494 AGPTGVGKTEVTVQLSKALGIELLRFDMSEYME 526
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit clpA.
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 730
Score = 36.2 bits (84), Expect = 0.24
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 1050 AGPAGTGKTETTKDLGKAIGIMVYVFNCSEQMD 1082
GP G GKTE K L + +G+ + F+ SE M+
Sbjct: 489 VGPTGVGKTELAKQLAEELGVHLLRFDMSEYME 521
Score = 36.2 bits (84), Expect = 0.24
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 1437 AGPAGTGKTETTKDLGKAIGIMVYVFNCSEQMD 1469
GP G GKTE K L + +G+ + F+ SE M+
Sbjct: 489 VGPTGVGKTELAKQLAEELGVHLLRFDMSEYME 521
>gnl|CDD|218681 pfam05667, DUF812, Protein of unknown function (DUF812). This
family consists of several eukaryotic proteins of
unknown function.
Length = 536
Score = 34.3 bits (79), Expect = 0.65
Identities = 29/158 (18%), Positives = 64/158 (40%), Gaps = 15/158 (9%)
Query: 465 ESLCSQLKEIIEDITDMGVKIKRVAKRTENTYKVWSTLEFEYDIHARTKTPLLRCSEELI 524
+ L S ++E++ +I + KIK+V + + LE EY I RT EL+
Sbjct: 280 DELESSIEEVLSEIKALASKIKQVNEELTTVRQENEELEEEYKIKKRT--------VELL 331
Query: 525 EMLEENQVQLQNM--ASSKFVGYFQKEVNEWQIKLSNA-----DAVISIWIEVQRTWQHL 577
E N +LQ + ASS+ + ++ + L + + + E QR +
Sbjct: 332 PDAENNVAKLQALVVASSERLLELAQQWEAHRTPLIDEYRSLKEKNRNKEDETQRQLDEI 391
Query: 578 ESIFIGSDDIRQQLPEDSRRFDATDKAFRALAQDMHKT 615
+ + +++ +L + + + + + ++
Sbjct: 392 KKLRNKIEELESELQTKEQLYKQLLDEYENAPKSVSRS 429
>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 = 32.5 bits (74), Expect = 0.92
Identities = 19/97 (19%), Positives = 35/97 (36%), Gaps = 13/97 (13%)
Query: 1051 GPAGTGKTETTKDLGKAI---GIMVYVFNCS---EQMDYRSCGNIY-----KGLAQTGAW 1099
GP GTGKT + + + G N S E + + LA+
Sbjct: 26 GPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKP 85
Query: 1100 GC--FDEFNRISVEVLSVVAVQVKSVLDSVKMRKSRF 1134
G DE + +S + + ++++ D R++
Sbjct: 86 GVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVR 122
Score = 32.5 bits (74), Expect = 0.92
Identities = 19/97 (19%), Positives = 35/97 (36%), Gaps = 13/97 (13%)
Query: 1438 GPAGTGKTETTKDLGKAI---GIMVYVFNCS---EQMDYRSCGNIY-----KGLAQTGAW 1486
GP GTGKT + + + G N S E + + LA+
Sbjct: 26 GPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKP 85
Query: 1487 GC--FDEFNRISVEVLSVVAVQVKSVLDSVKMRKSRF 1521
G DE + +S + + ++++ D R++
Sbjct: 86 GVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVR 122
>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional.
Length = 211
Score = 33.2 bits (76), Expect = 1.0
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 288 EDSVHENMEEEQTMVEEKESVAPTAEQEEDDGGDNFDRDESVDLDMDKKSDEDDERKKLL 347
+D+ HENMEE+ +E E+ +EED + +++E ++ + + +E K
Sbjct: 6 KDAKHENMEED--CCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDEN 63
Query: 348 KPPSDE 353
+E
Sbjct: 64 NKLKEE 69
>gnl|CDD|234726 PRK00321, rdgC, recombination associated protein; Reviewed.
Length = 303
Score = 33.3 bits (77), Expect = 1.1
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 17/79 (21%)
Query: 820 EIKNMIAALKAVTELQNPAIRDRHWEELMSVTKVKFSIDDSTTLKDLLDLELYKFEEEVK 879
EI+ I A K VT+L A+ W++ ++ F + D T+K L KF + ++
Sbjct: 217 EIRQHIEAGKQVTKL---AL---TWQD-----RLSFVLTDDLTIKRL------KFLDVLR 259
Query: 880 TIVDKSVKEQQMEKVLKDF 898
D E + DF
Sbjct: 260 EQNDDIDGEDAAARFDADF 278
>gnl|CDD|191413 pfam05970, PIF1, PIF1-like helicase. This family includes homologues
of the PIF1 helicase, which inhibits telomerase activity
and is cell cycle regulated. This family includes a large
number of largely uncharacterized plant proteins. This
family includes a P-loop motif that is involved in
nucleotide binding.
Length = 364
Score = 33.1 bits (76), Expect = 1.3
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 1765 HSVFIIGFAGTGKSCVWKTLYKT 1787
F+ G+ GTGK+ +WK L +
Sbjct: 23 GVFFVYGYGGTGKTYLWKALSAS 45
Score = 31.9 bits (73), Expect = 3.7
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 1316 FIIGFAGTGKSCVWKTLYKT 1335
F+ G+ GTGK+ +WK L +
Sbjct: 26 FVYGYGGTGKTYLWKALSAS 45
>gnl|CDD|200572 cd10948, CE4_BsPdaA_like, Catalytic NodB homology domain of
Bacillus subtilis polysaccharide deacetylase PdaA, and
its bacterial homologs. The Bacillus subtilis genome
contains six polysaccharide deacetylase gene homologs:
pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH
and ylxY. This family is represented by Bacillus
subtilis pdaA gene encoding polysaccharide deacetylase
BsPdaA, which is a member of the carbohydrate esterase 4
(CE4) superfamily. BsPdaA deacetylates peptidoglycan
N-acetylmuramic acid (MurNAc) residues to facilitate the
formation of muramic delta-lactam, which is required for
recognition of germination lytic enzymes. BsPdaA
deficiency leads to the absence of muramic delta-lactam
residues in the spore cortex. Like other CE4 esterases,
BsPdaA consists of a single catalytic NodB homology
domain that appears to adopt a deformed (beta/alpha)8
barrel fold with a putative substrate binding groove
harboring the majority of the conserved residues. It
utilizes a general acid/base catalytic mechanism
involving a tetrahedral transition intermediate, where a
water molecule functions as the nucleophile tightly
associated to the zinc cofactor.
Length = 223
Score = 32.6 bits (75), Expect = 1.4
Identities = 30/109 (27%), Positives = 43/109 (39%), Gaps = 14/109 (12%)
Query: 80 DAFRQKIDQYEALYKTVNEIEESK-------VFDEWLLVDLKPFKYSLLNVVCKWSMLFK 132
+ F+++I E YK V E K F E L K Y+ V WS ++
Sbjct: 111 EKFKKEITGVEEEYKEVTGKEMMKYFRPPRGEFSERSLKITKDLGYT--TVF--WSFAYR 166
Query: 133 KHLMDSVINSLNELKDFIEEADKGLATPLH---KGDYEALVKIITYLKK 178
+D+ LK + + G LH K + EAL II L+K
Sbjct: 167 DWEVDNQPGPEEALKKIMNQLHPGAIYLLHAVSKTNAEALDDIIKDLRK 215
>gnl|CDD|143469 cd07151, ALDH_HBenzADH, NADP+-dependent p-hydroxybenzaldehyde
dehydrogenase-like. NADP+-dependent,
p-hydroxybenzaldehyde dehydrogenase (PchA, HBenzADH)
which catalyzes oxidation of p-hydroxybenzaldehyde to
p-hydroxybenzoic acid and other related sequences are
included in this CD.
Length = 465
Score = 33.0 bits (76), Expect = 1.9
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 139 VINS--LNELKDFIEEADKGLATPLHKGDYEALVKIITYLKKVRDRTPTTDN-MFEPLAA 195
+IN ++ L D IE+A + AT L G+ E V T L V + +F P+A
Sbjct: 316 LINESQVDGLLDKIEQAVEEGATLLVGGEAEGNVLEPTVLSDVTNDMEIAREEIFGPVAP 375
Query: 196 II 197
II
Sbjct: 376 II 377
>gnl|CDD|217373 pfam03115, Astro_capsid, Astrovirus capsid protein precursor. This
product is encoded by astrovirus ORF2, one of the three
astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein
undergoes an intracellular cleavage to form a 79kD
protein. Subsequently, extracellular trypsin cleavage
yields the three proteins forming the infectious virion.
Length = 787
Score = 32.8 bits (75), Expect = 2.0
Identities = 24/110 (21%), Positives = 41/110 (37%), Gaps = 17/110 (15%)
Query: 279 QNYKLYFHIEDSVHENMEEEQTMVEEKESVAPTAEQ-----EEDDGGDNFDRDESVDLD- 332
++YF + S+ ++ E + E AP + EE D D DE +LD
Sbjct: 632 AASQIYFEMRTSLPQSRAELSGLEERAVEDAPDPYEDLISLEETDTEDESTEDEDDELDR 691
Query: 333 -----MDKKSDEDDE---RKKLLKPPSDEPIDMDVYGAASEMGSEAAPLP 374
EDD+ R LL ++ + ++ A+ + A P
Sbjct: 692 FDLHDSSGSEPEDDDENNRVTLLSTLINQGMSVE---RATRITKRAFPTL 738
>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional.
Length = 80
Score = 30.1 bits (68), Expect = 2.2
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 282 KLYFHIEDSVHENMEEEQTMVEEKESVAPTAEQEEDDGGDNFDRDESVDLDMDKKSDEDD 341
K + I ++ E + EE+ VE SV E+ EDD D D D+ D D D+DD
Sbjct: 18 KEFASIMEARTEALIEEEK-VEIARSVMIEGEEPEDDDDDEDDDDDDDKDDKDDDDDDDD 76
Query: 342 E 342
E
Sbjct: 77 E 77
Score = 29.0 bits (65), Expect = 4.3
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 311 TAEQEEDDGGDNFDRDESVDLDMDKKSDEDDE 342
E ++DD D+ D D+ D D DEDDE
Sbjct: 49 EPEDDDDDEDDDDDDDKDDKDDDDDDDDEDDE 80
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 32.5 bits (74), Expect = 2.5
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 287 IEDSVHENMEEEQT---MVEEKESVAPTAEQEEDDGGDNFDRDESVDLDMDKKSDEDDER 343
E +V E EEE ++ E ES PT E++D + E D + + + E ++R
Sbjct: 236 SESTVKEESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSGERSDSEEETEEKEKEKR 295
Query: 344 KKLLKPPSDE 353
K+L K DE
Sbjct: 296 KRLKKMMEDE 305
>gnl|CDD|217132 pfam02597, ThiS, ThiS family. ThiS (thiaminS) is a 66 aa protein
involved in sulphur transfer. ThiS is coded in the
thiCEFSGH operon in E. coli. This family of proteins
have two conserved Glycines at the COOH terminus.
Thiocarboxylate is formed at the last G in the
activation process. Sulphur is transferred from ThiI to
ThiS in a reaction catalyzed by IscS. MoaD, a protein
involved sulphur transfer in molybdopterin synthesis, is
about the same length and shows limited sequence
similarity to ThiS. Both have the conserved GG at the
COOH end.
Length = 70
Score = 29.5 bits (67), Expect = 2.5
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 846 ELMSVTKVKFSIDDSTTLKDLLDLELYKFEEEVKTIVDKS-VKEQQMEKVLKDFDKV 901
EL + + + + T+ +LL+ L E V V+ V Q + LKD D+V
Sbjct: 6 ELRELAGKELELPEGATVAELLE-ALGLNPERVAVAVNGEIVPRSQADTPLKDGDEV 61
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 32.3 bits (73), Expect = 2.8
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 303 EEKESVAPTAEQEEDDGGDNFDRDESVDLDMDKKSDEDDE 342
+E E A E ++++ D+ D ++ D D D D++DE
Sbjct: 43 KEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDE 82
Score = 31.5 bits (71), Expect = 5.2
Identities = 20/76 (26%), Positives = 39/76 (51%)
Query: 267 EEAGDEIHDLLWQNYKLYFHIEDSVHENMEEEQTMVEEKESVAPTAEQEEDDGGDNFDRD 326
E A E+ D W L + + ++++ M++E + + + A +EEDD ++ D D
Sbjct: 4 EFASSELEDDDWVRGSLDYKEKLTLNDTMKKENAIRKLGKEAEEEAMEEEDDDEEDDDDD 63
Query: 327 ESVDLDMDKKSDEDDE 342
+ D D D D++D+
Sbjct: 64 DDEDEDDDDDDDDEDD 79
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 32.1 bits (74), Expect = 3.0
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 12/52 (23%)
Query: 1051 GPAGTGKTETTKDLGKAIG------IMVYVFNCSEQMD---YRSCGNIYKGL 1093
GP GTGKT T K + + + + VY+ NC Q+D Y I + L
Sbjct: 62 GPPGTGKTTTVKKVFEELEEIAVKVVYVYI-NC--QIDRTRYAIFSEIARQL 110
Score = 32.1 bits (74), Expect = 3.0
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 12/52 (23%)
Query: 1438 GPAGTGKTETTKDLGKAIG------IMVYVFNCSEQMD---YRSCGNIYKGL 1480
GP GTGKT T K + + + + VY+ NC Q+D Y I + L
Sbjct: 62 GPPGTGKTTTVKKVFEELEEIAVKVVYVYI-NC--QIDRTRYAIFSEIARQL 110
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 32.3 bits (74), Expect = 3.0
Identities = 22/119 (18%), Positives = 42/119 (35%), Gaps = 16/119 (13%)
Query: 784 KIDSEAMDMELKKFTKELRTLDKDLRNWDIFLQLESEIKNMIAALKAVTELQNPAIRDRH 843
E ++ EL++ LR L+ L + L+ E + A L+ +
Sbjct: 860 NGKKEELEEELEELEAALRDLESRLGD------LKKERDELEAQLRELERKIEELEAQIE 913
Query: 844 -WEELMSVTKVKFSIDDSTTLKDLLDLELYKFEEEVKTIVDKSVKEQQMEKVLKDFDKV 901
+ +S K K L+ EL + E+ + +E +E V + +V
Sbjct: 914 KKRKRLSELKAKLEA---------LEEELSEIEDPKGEDEEIPEEELSLEDVQAELQRV 963
>gnl|CDD|225015 COG2104, ThiS, Sulfur transfer protein involved in thiamine
biosynthesis [Coenzyme metabolism].
Length = 68
Score = 29.1 bits (66), Expect = 3.1
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 857 IDDSTTLKDLLDLELYKFEEEVKTIVDKSV--KEQQMEKVLKDFDKV 901
I + TT+ DLL E V V+ + + Q + +LK+ D++
Sbjct: 14 IAEGTTVADLLAQLGLN-PEGVAVAVNGEIVPRSQWADTILKEGDRI 59
>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 = 3.2
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 1051 GPAGTGKTETTKDLGKAIGIMVYVFNCSEQMD 1082
GP GTGKT K + K +G + SE +
Sbjct: 5 GPPGTGKTTLAKAVAKELGAPFIEISGSELVS 36
Score = 30.6 bits (70), Expect = 3.2
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 1438 GPAGTGKTETTKDLGKAIGIMVYVFNCSEQMD 1469
GP GTGKT K + K +G + SE +
Sbjct: 5 GPPGTGKTTLAKAVAKELGAPFIEISGSELVS 36
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 32.3 bits (74), Expect = 3.5
Identities = 34/141 (24%), Positives = 64/141 (45%), Gaps = 12/141 (8%)
Query: 793 ELKKFTKELRTLDKDLRNWDIFLQLESEIKNMIAALKAVTELQNPAIRDRHWEELMSVTK 852
ELK+ ++ R L K+LR + L+ ESE+ + + + EL+ E+L
Sbjct: 467 ELKEIEEKERKLRKELRELEKVLKKESELIKLKELAEQLKELE---------EKLKKYNL 517
Query: 853 VKFSIDDSTTLKDLLDLELYKFEEEVKTIVDKSVKEQQMEKVLKDFDKVWSTLEFEY-DI 911
+ + L +L K + E+K++ + K ++++K L + +K LE E ++
Sbjct: 518 EELEKK--AEEYEKLKEKLIKLKGEIKSLKKELEKLEELKKKLAELEKKLDELEEELAEL 575
Query: 912 HARTKTPLLRCSEELIEMLEE 932
+ EEL E L+E
Sbjct: 576 LKELEELGFESVEELEERLKE 596
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 32.2 bits (73), Expect = 3.5
Identities = 40/169 (23%), Positives = 59/169 (34%), Gaps = 14/169 (8%)
Query: 288 EDSVHENMEEEQTMVEEKESVAPTAEQEEDDGGDNFDRDESVDLDMDKKSDEDDERKKLL 347
E+ E EEEQ EE+ E+ E D G + + S + D D + E+D ++
Sbjct: 449 EEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERRNS 508
Query: 348 KPPSDEPIDMDVYGAASEMGSEAAP-LPDILEHTEVADIGENEDDALSAVPGMPDEFDQE 406
+ + S + E+ P E + +GE D+ L A +E
Sbjct: 509 EMAGISRMSEGQQPRGSSVQPESPQEEPLQPESMDAESVGEESDEELLA---------EE 559
Query: 407 SSSQNLKLTSRVHLVYITDEMCHTDFSNKAPLFRVSFSLEEPDLVFTPT 455
S + V T S K P VS SLE T T
Sbjct: 560 SPLSSHTELEGVATPVETK----ISSSRKLPPPPVSTSLENDSATVTST 604
>gnl|CDD|225669 COG3127, COG3127, Predicted ABC-type transport system involved in
lysophospholipase L1 biosynthesis, permease component
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 829
Score = 32.0 bits (73), Expect = 3.8
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 11/69 (15%)
Query: 1637 RLLSRKFITLYSLCKELLSKQ-----DHYDWGLRA------IKSVLVVAGSLKRGDRQRP 1685
R L+R F T+ + Q D + VLV+A +L G+R R
Sbjct: 676 RQLTRAFPTVTLVDVGAALDQVNQLLDQVATAVEVAAVLALAAGVLVLAAALAAGNRARV 735
Query: 1686 EDQVLMRAL 1694
++ V++R L
Sbjct: 736 QEAVVLRTL 744
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 31.5 bits (72), Expect = 5.2
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 1050 AGPAGTGKTETTKDLGKAIG---IMVYVFNCSEQMD 1082
GP G GKTE K L +A+ + + SE M+
Sbjct: 527 LGPTGVGKTELAKALAEALFGDEQALIRIDMSEYME 562
Score = 31.5 bits (72), Expect = 5.2
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 1437 AGPAGTGKTETTKDLGKAIG---IMVYVFNCSEQMD 1469
GP G GKTE K L +A+ + + SE M+
Sbjct: 527 LGPTGVGKTELAKALAEALFGDEQALIRIDMSEYME 562
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 31.5 bits (72), Expect = 5.6
Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 1/84 (1%)
Query: 303 EEKESVAPTAEQEEDDGGDNFDRDESVDLDMDKKSDEDDERKKLLKPPSDEPI-DMDVYG 361
+ + + + DD + D D+ D + D D DDE ++ + E + D D +
Sbjct: 129 QADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFV 188
Query: 362 AASEMGSEAAPLPDILEHTEVADI 385
+ + T AD
Sbjct: 189 WDEDDSEALRQARKDAKLTATADP 212
>gnl|CDD|217442 pfam03233, Cauli_AT, Aphid transmission protein. This protein is
found in various caulimoviruses. It codes for an 18 kDa
protein (PII), which is dispensable for infection but
which is required for aphid transmission of the virus.
This protein interacts with the PIII protein.
Length = 163
Score = 30.2 bits (68), Expect = 6.1
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 873 KFEEEVKTIVDKSVKEQQMEKVLKDFDK 900
K E + K + DK V E ++ +KDFD+
Sbjct: 122 KIENQTKKLADKIVTEPLTKEEVKDFDE 149
>gnl|CDD|143616 cd07355, HN_L-delphilin-R2_like, Second harmonin_N_like domain
(repeat 2) of L-delphilin, and related domains. This
subgroup contains the second of two harmonin_N_like
domains of an alternatively spliced longer variant of
mouse delphilin (L-delphilin), and related domains.
Delphilin is a postsynaptic density-95/discs-large/ZO-1
(PDZ) domain-containing scaffold protein which binds the
glutamate receptor delta-2 (GRID2) subunit and the
monocarboxylate transporter 2 at the cerebellar parallel
fiber-Purkinje cell synapses. This harmonin_N_like domain
in L-delphilin follows the second PDZ protein-binding
domain, PDZ2; it is also found in the shorter C-terminal
isoforms (S-delphilin/delphilin alpha and delphilin
beta). It is a putative protein-binding module based on
its sequence similarity to the harmonin N-domain. The
first harmonin_N_like domain of L-delphilin belongs to a
different subgroup and is missing from S-delphilin.
Length = 80
Score = 28.6 bits (64), Expect = 6.1
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 1685 PEDQVLMRALRDFNIPKIITEDLQVFMGLIGDLFPALDVPRKRDI 1729
PE + +AL D+ + I LI D++P LD P K+ I
Sbjct: 19 PERYGIKKALEDYFQHRNID-------TLIVDVYPVLDTPAKQVI 56
>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 = 31.0 bits (71), Expect = 6.4
Identities = 13/39 (33%), Positives = 16/39 (41%), Gaps = 7/39 (17%)
Query: 1050 AGPAGTGKTETTKDLGKAIGIMVYVFNCSEQMDYRSCGN 1088
+GP GTGKT + KA+ NC D C
Sbjct: 42 SGPRGTGKTSIARIFAKAL-------NCQNGPDGEPCNE 73
Score = 31.0 bits (71), Expect = 6.4
Identities = 13/39 (33%), Positives = 16/39 (41%), Gaps = 7/39 (17%)
Query: 1437 AGPAGTGKTETTKDLGKAIGIMVYVFNCSEQMDYRSCGN 1475
+GP GTGKT + KA+ NC D C
Sbjct: 42 SGPRGTGKTSIARIFAKAL-------NCQNGPDGEPCNE 73
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 31.5 bits (71), Expect = 7.1
Identities = 17/93 (18%), Positives = 31/93 (33%), Gaps = 2/93 (2%)
Query: 1051 GPAGTGKTETTKDLGKAIGIMVYVFNCSEQMDYRSCGNIYKGLAQT-GAWGCFDEFNRIS 1109
G G GKT + L G + +FNC+ D Y+ + + +
Sbjct: 1857 GDTGVGKTSLLRFLASIFGQEMTLFNCNSDTDVMDLLGQYEQMDNGRFESCDSEVVTSVK 1916
Query: 1110 VEVLSVVAVQVKSVLDSVKMRKSRFNFMGENIK 1142
+ V A +V+ S+ R + +
Sbjct: 1917 EGKMVVFA-KVEFNEKSIFDRLNLLFESERTLN 1948
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 31.2 bits (71), Expect = 7.2
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 1050 AGPAGTGKTETTKDLGKAIGIMVYVFNCSEQM 1081
+GP G GKTE TK L Y F + M
Sbjct: 545 SGPTGVGKTELTKALAS------YFFGSEDAM 570
Score = 31.2 bits (71), Expect = 7.2
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 1437 AGPAGTGKTETTKDLGKAIGIMVYVFNCSEQM 1468
+GP G GKTE TK L Y F + M
Sbjct: 545 SGPTGVGKTELTKALAS------YFFGSEDAM 570
>gnl|CDD|130884 TIGR01825, gly_Cac_T_rel, pyridoxal phosphate-dependent
acyltransferase, putative. This model represents an
enzyme subfamily related to three known enzymes; it
appears closest to glycine C-acteyltransferase, shows no
overlap with it in species distribution, and may share
that function. The three closely related enzymes are
glycine C-acetyltransferase (2-amino-3-ketobutyrate
coenzyme A ligase), 5-aminolevulinic acid synthase, and
8-amino-7-oxononanoate synthase. All transfer the
R-group (acetyl, succinyl, or 6-carboxyhexanoyl) from
coenzyme A to an amino acid (Gly, Gly, Ala,
respectively), with release of CO2 for the latter two
reactions.
Length = 385
Score = 30.6 bits (69), Expect = 8.5
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 335 KKSDEDDERKKLLKPPSDEPIDMDVYGAASEMGSEAAPLPDILEHTEVADIGENEDDA 392
K +D DD + L + P + V M + APLP+I+E E DDA
Sbjct: 145 KHADMDDLDRVLRENP-SYGKKLIVTDGVFSMDGDVAPLPEIVELAERYGAVTYVDDA 201
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 30.8 bits (70), Expect = 9.0
Identities = 22/117 (18%), Positives = 38/117 (32%), Gaps = 18/117 (15%)
Query: 296 EEEQTMVEEKES----VAPTAEQEEDDGGDNFDRDESVD-LDMDKKSDEDDERKKLLKPP 350
E + EE+ ++ E+ D N D E+ D + K E +
Sbjct: 24 ERKAATAEEESLKNIDISDLFERSVDM---NKDPKEATDQVKAVDKHSEIESL------- 73
Query: 351 SDEPIDMDVYGAASEMGSEAAPLPDILEHTEVADIGENEDDALSAVPGMPDEFDQES 407
+S+ S+ A +PD + A+ + P D F QE+
Sbjct: 74 --NVGMRLDVRLSSKELSDVA-VPDDYDMVPDAESPFDLAPPAREYPFELDPFQQEA 127
>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein.
Genome duplication is precisely regulated by
cyclin-dependent kinases CDKs, which bring about the
onset of S phase by activating replication origins and
then prevent relicensing of origins until mitosis is
completed. The optimum sequence motif for CDK
phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found
to have at least 11 potential phosphorylation sites.
Drc1 is required for DNA synthesis and S-M replication
checkpoint control. Drc1 associates with Cdc2 and is
phosphorylated at the onset of S phase when Cdc2 is
activated. Thus Cdc2 promotes DNA replication by
phosphorylating Drc1 and regulating its association with
Cut5. Sld2 and Sld3 represent the minimal set of S-CDK
substrates required for DNA replication.
Length = 397
Score = 30.5 bits (69), Expect = 9.5
Identities = 22/125 (17%), Positives = 44/125 (35%), Gaps = 18/125 (14%)
Query: 292 HENMEEEQTMVEEKESVAPTAEQEEDDGGDNFDRDESVDLDMDKKSDEDDERKKLLKPPS 351
E++++E ++ E E+ E++ D+ ++ KK + R+ ++P
Sbjct: 243 EESIDDELDVLREIEAEEAGIGPIEEEVVDSQAANDEPRRVFKKKGQKRTTRRVKMRPVR 302
Query: 352 DEPIDMDVYGAASEMGSEAAPLPDILEHTEVADIGENE-----DDALSAVPGMPDEFDQE 406
+P D LP+ H E+ + E DE D+E
Sbjct: 303 AKPSDEPS-------------LPESDIHEEIPKLDEKSLSEFLGYMGGIDEDDEDEDDEE 349
Query: 407 SSSQN 411
S +
Sbjct: 350 SKEEV 354
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 28.8 bits (64), Expect = 9.8
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 1051 GPAGTGKTETTKDLGKAIGIMVY 1073
GP G+GK+ K L + +GI V
Sbjct: 6 GPPGSGKSTLAKKLAEKLGIPVI 28
Score = 28.8 bits (64), Expect = 9.8
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 1438 GPAGTGKTETTKDLGKAIGIMVY 1460
GP G+GK+ K L + +GI V
Sbjct: 6 GPPGSGKSTLAKKLAEKLGIPVI 28
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
0.319 0.135 0.400
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 100,180,209
Number of extensions: 10139803
Number of successful extensions: 10441
Number of sequences better than 10.0: 1
Number of HSP's gapped: 10356
Number of HSP's successfully gapped: 115
Length of query: 1949
Length of database: 10,937,602
Length adjustment: 111
Effective length of query: 1838
Effective length of database: 6,014,308
Effective search space: 11054298104
Effective search space used: 11054298104
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 (21.7 bits)
S2: 67 (30.0 bits)