RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6129
(383 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 = 301 bits (773), Expect = e-102
Identities = 145/229 (63%), Positives = 170/229 (74%), Gaps = 1/229 (0%)
Query: 57 YQNEYLGCTERLVITPLTDRCYITLAQALTMSMGGSPCGPAGTGKTETVKDMGKTLAKYV 116
Y EYLG T RLVITPLTDRCYITL Q+L ++M G+P GPAGTGKTET KD+G+ L V
Sbjct: 1 YSYEYLGNTPRLVITPLTDRCYITLTQSLHLTMSGAPAGPAGTGKTETTKDLGRALGIMV 60
Query: 117 VVFNCSDQMDYRGLGRIYKGLAQSGSWGCFDEFNRIELPVLSVAAQQVAVVLAAKKEKKK 176
VFNCS+QMDY+ G IYKGLAQ+G+WGCFDEFNRI + VLSV A QV V A ++KK+
Sbjct: 61 YVFNCSEQMDYKSCGNIYKGLAQTGAWGCFDEFNRISVEVLSVVAVQVKCVQDAIRDKKQ 120
Query: 177 SFVFTDGDSIEMCPEFGIFITMNPGYAGRKELPENLKIQFRTVAMMVPDRQIIIRVKLAS 236
F F G+ I + P GIFITMNPGYAGR ELPENLK FR AM+VPD ++I + L +
Sbjct: 121 WFNFL-GEEISLIPSVGIFITMNPGYAGRTELPENLKALFRPCAMVVPDFELICEIMLVA 179
Query: 237 CGFLENITLARKFYTLYKLCEEQLTKQVHYDFGLRNILSVLRSLGAAKR 285
GFLE LARKF TLY LC+E L+KQ HYD+GLR I SVL G+ KR
Sbjct: 180 EGFLEARLLARKFITLYTLCKELLSKQDHYDWGLRAIKSVLVVAGSLKR 228
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 72.3 bits (177), Expect = 1e-13
Identities = 24/251 (9%), Positives = 61/251 (24%), Gaps = 36/251 (14%)
Query: 31 WLKQCRFYFKDDLDKTWINITDVTFTYQNEYLGCTERLVITPLTDRCYITLAQALTMSMG 90
+ + + + + + L +A+ +
Sbjct: 891 SVSISELPQGLY-KRFIKVRSSYRSAEMFAKNTIPFFVFEHSMDTSQHQKLFEAVCDEV- 948
Query: 91 GSPCGPAGTGKTETVKDMGKTLAKYVVVFNCSDQMDYRGLGRIYKGLAQSGSWGCFDEFN 150
C T + + + D + R RI G G +E
Sbjct: 949 ---CRFVDTENSRVYGMLVAGKGRIY------DGTEPR--SRIEAGPICEEERG-TEESA 996
Query: 151 RIELPVLSVAA--QQVAVVLAAKKEKKKSFVFTDGDSIEMCPEFGIFITMNPGYAGRKEL 208
++ ++ + +E + V + P + + +N R +
Sbjct: 997 LLDEISRTILVDEYLNSDEFRMLEELNSAVV----EHGLKSPSTPVEMIINE----RNIV 1048
Query: 209 PENLKIQFRTVAMMVPDRQIIIRVKLASCGFLENITLARKFYTLYKLCEEQLTKQVHYDF 268
E + +P I R + +L R+ + ++ F
Sbjct: 1049 LEIGRRALDMFLSNIPFGAIKSRRE----------SLDREIGAFNNEVDGIAREEDELMF 1098
Query: 269 GLRNILSVLRS 279
+ L++
Sbjct: 1099 --YPMFKSLKA 1107
Score = 49.2 bits (117), Expect = 3e-06
Identities = 56/240 (23%), Positives = 84/240 (35%), Gaps = 32/240 (13%)
Query: 36 RFYFKDDLDKTWINITDVTFTYQNEYLGCTERLVITPLTDRCYI--TLAQALTMSMGGSP 93
R Y K + + ++ Y EY T + + PL +R ++A + G
Sbjct: 1555 RLYPKPVVKDLVLFCDEINLPYGFEYYPPTVIVFLRPLVERQGFWSSIAVSWVTICGIIL 1614
Query: 94 CGPAGTGKTETVKDMGKTLAKYVVVFNCSDQMDYRGLGRIYKGLAQSGSWGCFDEFNRIE 153
G G E + + V C L IY+ + GS+ CFDEFNR+
Sbjct: 1615 YGACNPGTDEGRVKYYERFIRKPVFVFCCYPELA-SLRNIYEAVLM-GSYLCFDEFNRLS 1672
Query: 154 LPVLSVAAQQVAVVLAAKKEKKKSFVFTDGDSIEMCPEFGIFITMNPGYAGRKELPENLK 213
+S + + K+K K F+ MN GY R EL +L
Sbjct: 1673 EETMSASVELYLSS----KDKTKF-----------------FLQMNYGYKPR-ELTRSL- 1709
Query: 214 IQFRTVAMMVPDRQIIIRVKLASCGFLENITLARKFYTLYKLCEEQLTKQVHYDFGLRNI 273
A D + + C + K L + E ++Q YDFGLR I
Sbjct: 1710 RAIFGYAETRIDTPDVSLIIDWYCE-----AIREKIDRLVQQKESSTSRQDLYDFGLRAI 1764
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 41.9 bits (98), Expect = 6e-04
Identities = 53/242 (21%), Positives = 95/242 (39%), Gaps = 47/242 (19%)
Query: 66 ERLVITPLTDRCYITLAQALTMSMGGSPC---GPAGTGKTETVKDMGKTLAKYVVVFNC- 121
E +ITP + Y+ +A ++S P GP +GKT + + + V N
Sbjct: 865 EHYIITPFVQKNYLNTMRAASLSN--FPLLIQGPTSSGKTSMILYLARETGHKFVRINNH 922
Query: 122 --SDQMDYRGL------GRI-YK-----GLAQSGSWGCFDEFNRIELPVLSVAAQQVAVV 167
+D +Y G G + +K + G W DE N VL + +
Sbjct: 923 EHTDLQEYIGTYVTDDDGSLSFKEGVLVEALRRGYWIVLDELNLAPTDVLEALNRLL--- 979
Query: 168 LAAKKEKKKSFVFTDGDSIEMCPEFGIFITMNP--GYAGRKELPENLKIQFRTVAMM--- 222
+ ++ F+ + + P F +F T NP GY GRK L + +F + M
Sbjct: 980 ----DDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRNRF--LEMHFDD 1033
Query: 223 VPDRQIII----RVKLASCGFLENITLARKFYTLYKLCEEQLTKQVHYDFGLRNILSVLR 278
+P+ ++ R ++A + A+K +Y+ + ++ F +N + LR
Sbjct: 1034 IPEDELEEILHGRCEIAP-------SYAKKIVEVYR--GLSSRRSINRIFEQKNSFATLR 1084
Query: 279 SL 280
L
Sbjct: 1085 DL 1086
Score = 38.8 bits (90), Expect = 0.005
Identities = 56/255 (21%), Positives = 99/255 (38%), Gaps = 27/255 (10%)
Query: 91 GSPCGPAGTGKTETVKDMGKTLAKYVVVFNCSDQMDYRGLGRIYKGLAQSGSWGCFD-EF 149
GSP G GKT + + + K ++ N S+Q D L + + G + D F
Sbjct: 1550 GSP----GVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAPF 1605
Query: 150 NR-------IELPVLSVAAQQVAVVL-AAKKEKKKSFVFTDGDSIEMCPEFGIFITMNPG 201
+ L +++A+Q V L A ++++++ + ++ P F +F NP
Sbjct: 1606 LHAMRDGGWVLLDEINLASQSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQ 1665
Query: 202 YA--GRKELPENLKIQFRTVAM-MVPDRQIIIRVKLASCGFLE-NITLARKFYTLYKLCE 257
GRK LP++ +F V M + I +A+ + + N K +
Sbjct: 1666 DQGGGRKGLPKSFLNRFSVVKMDGLTTDDIT---HIANKMYPQVNEDWRLKIIKFMSRLQ 1722
Query: 258 EQLTKQVHY-------DFGLRNILSVLRSLGAAKRVNSRDTESTIVMRVLRDMNLSKLID 310
+ + K + + +F LR+ L L L + DT I V+R M +
Sbjct: 1723 DNIEKDISFGSFGSPWEFNLRDTLRWLILLNQVGTLEDVDTSDFIDESVVRRMRTVEDRV 1782
Query: 311 EDEPLFISLVADLFP 325
LF + D P
Sbjct: 1783 RTCELFKEVFGDYEP 1797
Score = 37.7 bits (87), Expect = 0.012
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 9/92 (9%)
Query: 140 SGSWGCFDEFNRIELPVLSVAAQQVAVVLAAKKEKKKSFVFTDGDS--IEMCPEFGIFIT 197
+G W DE N L + L KKE + GD I + P F +F
Sbjct: 635 NGEWLLLDEINLASEETLELIDG-----LLGKKESG-ILLSESGDLRPIRIHPGFRLFGC 688
Query: 198 MNPGY-AGRKELPENLKIQFRTVAMMVPDRQI 228
MNPG G+++L + + +F + + P +
Sbjct: 689 MNPGTDVGKRKLEGSFRSRFTEIYVHSPSTSL 720
Score = 30.0 bits (67), Expect = 2.6
Identities = 25/118 (21%), Positives = 45/118 (38%), Gaps = 23/118 (19%)
Query: 95 GPAGTGKTETVKDMGKTLAKYVVVFNCSDQMDYRGLGRIY-----------KGL----AQ 139
G G+GK+ + ++ + +V + + D + L Y KG+
Sbjct: 156 GGRGSGKSFLISELCDEGGQRIVEIHLREITDAKVLIGTYTSPKPGDFEWMKGVLIEAVV 215
Query: 140 SGSWGCFDEFNRIELPVLSVAAQQVAVVLAAKKEKKKSFVFTDGDSIEMCPEFGIFIT 197
SG W F ++ VLS L EK++ + + G+++ F IF T
Sbjct: 216 SGDWILFKRIDKAPHGVLS--------YLLTLLEKRRLLIPSRGETVLAHDNFQIFFT 265
Score = 29.6 bits (66), Expect = 3.6
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 93 PC---GPAGTGKTETVKDMGKTLAKYVVVFNC---SDQMDYRG 129
P G G GKT ++ + + + +FNC +D MD G
Sbjct: 1852 PLILVGDTGVGKTSLLRFLASIFGQEMTLFNCNSDTDVMDLLG 1894
Score = 29.2 bits (65), Expect = 4.9
Identities = 24/76 (31%), Positives = 31/76 (40%), Gaps = 15/76 (19%)
Query: 147 DEFNRIELPVL----SVAAQQVAVVLAAKKEKKKSFVFTDGDSIEMCPEFGIFITMNPG- 201
DE + + VL SV Q + L + DG F F TMNPG
Sbjct: 1300 DEISLADDSVLERLNSVLESQRTLYLTETGNAAEEVTAHDG--------FRFFATMNPGG 1351
Query: 202 -YAGRKELPENLKIQF 216
Y G+KEL L+ +F
Sbjct: 1352 DY-GKKELSPALRNRF 1366
Score = 29.2 bits (65), Expect = 5.4
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 95 GPAGTGKTETVKDMGKTLAKYVVVFNCSDQMD 126
G GTGKT ++ + L + V N S Q +
Sbjct: 471 GETGTGKTTMIQYLALKLHFKLTVINKSQQTE 502
>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 = 37.3 bits (87), Expect = 0.003
Identities = 32/139 (23%), Positives = 48/139 (34%), Gaps = 26/139 (18%)
Query: 95 GPAGTGKTETVKDMGKTLAKY-VVVFNCSDQMDYRGL--GRIYKGL------------AQ 139
GP GTGK+E + + L+ V + L R A+
Sbjct: 6 GPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPLVRAAR 65
Query: 140 SGSWGCFDEFNRIELPVLSVAAQQVAVVLAAKKEKKKSFVFTDGDSIEMCPEFG--IFIT 197
G DE NR VL +L+ E++ + +G + G + T
Sbjct: 66 EGEIAVLDEINRANPDVL-------NSLLSLLDERR--LLLPEGGELVKAAPDGFRLIAT 116
Query: 198 MNPGYAGRKELPENLKIQF 216
MNP G EL L+ +F
Sbjct: 117 MNPLDRGLNELSPALRSRF 135
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 35.9 bits (83), Expect = 0.030
Identities = 33/140 (23%), Positives = 45/140 (32%), Gaps = 33/140 (23%)
Query: 95 GPAGTGKTETVKDMGKTL-AKYVVVFNCSDQMD-------------YRGLG--RIYKG-- 136
GP G GKT + + + L +V + C+ + G R G
Sbjct: 50 GPPGVGKTLLARALARALGLPFVRI-QCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPL 108
Query: 137 LAQSGSWGCFDEFNRIELPVLSVAAQQVAVVLAAKKEKKKSFVFTDGDSIEMCPE--FGI 194
A DE NR V + L A +E+ T + F +
Sbjct: 109 FAAVRVILLLDEINRAPPEVQNAL-------LEALEER----QVTVPGLTTIRLPPPFIV 157
Query: 195 FITMNPG-YAGRKELPENLK 213
T NPG Y G LPE L
Sbjct: 158 IATQNPGEYEGTYPLPEALL 177
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 35.2 bits (82), Expect = 0.050
Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 10/51 (19%)
Query: 95 GPAGTGKTETVK----DMGKTLAKYVVVF-NCSDQMD---YRGLGRIYKGL 137
GP GTGKT TVK ++ + K V V+ NC Q+D Y I + L
Sbjct: 62 GPPGTGKTTTVKKVFEELEEIAVKVVYVYINC--QIDRTRYAIFSEIARQL 110
>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 = 0.063
Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 6/78 (7%)
Query: 94 CGPAGTGKTETVKDMGKTLAKY---VVVFNCSDQMDYRGLGRIYKGLAQSGSWGCFDEFN 150
GP G+GKT + + + L V+ + D ++ + + + G +
Sbjct: 8 VGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRL 67
Query: 151 RIELPVLSVAAQQVAVVL 168
R+ L++A + VL
Sbjct: 68 RL---ALALARKLKPDVL 82
>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 = 33.7 bits (77), Expect = 0.068
Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 13/72 (18%)
Query: 94 CGPAGTGKTETVKDMGKTLAKY---VVVFNCSD---QMDYRGLGRIY-----KGLAQSGS 142
GP GTGKT + + L + + N SD + L + LA+
Sbjct: 25 YGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAK 84
Query: 143 WGC--FDEFNRI 152
G DE + +
Sbjct: 85 PGVLFIDEIDSL 96
>gnl|CDD|217922 pfam04139, Rad9, Rad9. Rad9 is required for transient cell-cycle
arrests and transcriptional induction of DNA repair in
response to DNA damage. It contains a Bcl-2 homology
domain 3 (BH3).
Length = 252
Score = 32.7 bits (75), Expect = 0.21
Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 15/96 (15%)
Query: 243 ITLARKFYTLYKLCEEQLTKQVHYDFGLRNILSVLRSLGAAKR------VNSRDTESTIV 296
+ F+ Y+ + Q+ ++++LSV RSL ++ ++ D +S ++
Sbjct: 39 FLFSPLFFQSYQG-TTDGSPQIRCKILMKSVLSVFRSLSTLEKSVEKCQISLDDLKSRLI 97
Query: 297 MR------VLRDMNLSKLIDEDEPLFISLVADLFPN 326
+ V + N+S ++ EPL + PN
Sbjct: 98 FQLLCKHGVTKTHNIS--YEDSEPLQAVFDKNTCPN 131
>gnl|CDD|211373 cd09262, AP_stonin-1_MHD, Mu homology domain (MHD) of
adaptor-like protein (AP-like), stonin-1 (also called
Stoned B-like factor). A small family of proteins
named stonins has been characterized as
clathrin-dependent AP-2 mu2 chain related factors,
which may act as cargo-specific sorting adaptors in
endocytosis. Stonins include stonin 1 and stonin 2,
which are the only mammalian homologs of Drosophila
stoned B, a presynaptic protein implicated in
neurotransmission and synaptic vesicle (SV) recycling.
They are conserved from C. elegans to humans, but are
not found in prokaryotes or yeasts. This family
corresponds to the mu homology domain of stonin 1,
which is distantly related to the C-terminal domain of
mu chains among AP complexes. Due to the low degree of
sequence conservation of the corresponding binding
site, the mu homology domain of stonin-1 is unable to
recognize tyrosine-based endocytic sorting signals. To
data, little is known about the localization and
function of stonin-1.
Length = 309
Score = 32.9 bits (75), Expect = 0.25
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 17 LECRMNIKSVNDFEWLKQCRFYFKDDLDKTWINITDVTF 55
EC + ++ND E K+ YF+ + K WI I D F
Sbjct: 50 AECFL---TLNDLELQKRDEDYFEKEAGKLWIEILDYHF 85
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 31.1 bits (71), Expect = 0.37
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 94 CGPAGTGKTETVKDMGKTLAKYVVVF-NCSDQMDYRGLGR 132
G +G+GKT ++ + + L VV+ + L R
Sbjct: 10 TGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLR 49
>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 = 31.7 bits (72), Expect = 0.54
Identities = 42/167 (25%), Positives = 63/167 (37%), Gaps = 42/167 (25%)
Query: 95 GPAGTGKTETVKDMGKTLAKYVVVFNCSDQM-------DYRGLGRI----------YK-- 135
GPAGTGKT + + + V++ N ++ Y G R K
Sbjct: 28 GPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLE 87
Query: 136 ------------GLA-QSGSWGCFDEFNRIELPVLSVAAQQVAVVLAAKKEKKKSFVFTD 182
LA + G +DEF R + P + V+L+ +E
Sbjct: 88 DIVRQNWVDNRLTLAVREGFTLVYDEFTRSK-PETN------NVLLSVFEEGVLELPGKR 140
Query: 183 GDS--IEMCPEFGIFITMNPG-YAGRKELPENLKIQFRTVAMMVPDR 226
G S +++ PEF + T NP YAG E + L + T+ M PD
Sbjct: 141 GTSRYVDVHPEFRVIFTSNPVEYAGVHETQDALLDRLITIFMDYPDI 187
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 32.0 bits (73), Expect = 0.69
Identities = 14/32 (43%), Positives = 14/32 (43%), Gaps = 6/32 (18%)
Query: 94 CGPAGTGKTETVKDMGKTLAKYVVVFNCSDQM 125
GP G GKTE K LA Y F D M
Sbjct: 545 SGPTGVGKTELT----KALASY--FFGSEDAM 570
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 31.7 bits (72), Expect = 0.75
Identities = 13/33 (39%), Positives = 14/33 (42%), Gaps = 7/33 (21%)
Query: 94 CGPAGTGKTETVKDMGKTLAKYVVVFNCSDQMD 126
GP GTGKT K L NCS + D
Sbjct: 46 SGPRGTGKTSVAKIFANAL-------NCSHKTD 71
>gnl|CDD|131686 TIGR02638, lactal_redase, lactaldehyde reductase. This clade of
genes encoding iron-containing alcohol dehydrogenase
(pfam00465) proteins is generally found in apparent
operons for the catabolism of rhamnose or fucose.
Catabolism of both of these monosaccharides results in
lactaldehyde which is reduced by this enzyme to 1,2
propanediol. This protein is alternatively known by the
name 1,2 propanediol oxidoreductase. This enzyme is
active under anaerobic conditions in E. coli while being
inactivated by reactive oxygen species under aerobic
conditions. Under aerobic conditions the lactaldehyde
product of rhamnose and fucose catabolism is believed to
be oxidized to lactate by a separate enzyme,
lactaldehyde dehydrogenase [Energy metabolism, Sugars].
Length = 379
Score = 31.3 bits (71), Expect = 0.88
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 150 NRIELPVLS---VAAQQVAVVLAAKKEKKKSFVFTDGDSIEMCPEFGI 194
NR+ L S A + V ++ KK+ V TD D I +FG+
Sbjct: 2 NRLILNETSYFGAGAIEDIVDEVKRRGFKKALVVTDKDLI----KFGV 45
>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 = 29.9 bits (68), Expect = 0.97
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 95 GPAGTGKTETVKDMGKTLAKYVVVFNCSDQMD-YRGLG 131
GP GTGKT K + K L + + S+ + Y G
Sbjct: 5 GPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGES 42
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 30.2 bits (68), Expect = 2.3
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 7/28 (25%)
Query: 94 CGPAGTGKTETVKDMGKTLAKYVVVFNC 121
GP G GKT + LAK V NC
Sbjct: 44 TGPRGVGKTS----TARILAKAV---NC 64
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 29.8 bits (68), Expect = 2.5
Identities = 14/33 (42%), Positives = 15/33 (45%), Gaps = 7/33 (21%)
Query: 94 CGPAGTGKTETVKDMGKTLAKYVVVFNCSDQMD 126
GP GTGKT K AK V NC + D
Sbjct: 44 SGPRGTGKTSA----AKIFAKAV---NCLNPPD 69
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 29.8 bits (67), Expect = 2.8
Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 17/78 (21%)
Query: 81 LAQALTMSMGG-----SP------CGPAGTGKTETVKDMGKTLAKYVVVFNCSDQMDYRG 129
L +A+ MS G P GP G GKTE + K L ++ F+ S+ M+
Sbjct: 470 LTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHT 529
Query: 130 LGRI------YKGLAQSG 141
+ R+ Y G Q G
Sbjct: 530 VSRLIGAPPGYVGFDQGG 547
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 29.9 bits (68), Expect = 2.8
Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 14/52 (26%)
Query: 79 ITLAQALTMSMGGSP----CGPAGTGKTETVKDMGKTLAKYVVVFNC--SDQ 124
TL AL S +P GP GTGKT + + + K+L NC SD+
Sbjct: 26 TTLKNALI-SNRIAPAYLFTGPRGTGKTSSARILAKSL-------NCLNSDK 69
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 29.1 bits (66), Expect = 3.9
Identities = 16/48 (33%), Positives = 20/48 (41%)
Query: 95 GPAGTGKTETVKDMGKTLAKYVVVFNCSDQMDYRGLGRIYKGLAQSGS 142
GP G GKT + V+ N SDQ + R+ A SGS
Sbjct: 46 GPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGS 93
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 28.9 bits (65), Expect = 5.0
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 95 GPAGTGKTETVKDMGK-----TLAKYVVVFNCSDQMDYRGLGRIYKGLAQS 140
GP GTGKT TVK + + + VV NC ++ R ++ +
Sbjct: 49 GPTGTGKTATVKFVMEELEESSANVEVVYINC---LELRTPYQVLSKILNK 96
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 28.9 bits (64), Expect = 5.1
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 94 CGPAGTGKTETVKDMGKTL 112
GP+G GK+ TVK + K L
Sbjct: 51 TGPSGCGKSTTVKVLSKEL 69
>gnl|CDD|220758 pfam10443, RNA12, RNA12 protein. This family includes RNA12 from
S. cerevisiae. That protein contains an RRM domain. This
region is C-terminal to that and includes a P-loop motif
suggesting this region binds to NTP. The RNA12 proteins
is involved in pre-rRNA maturation.
Length = 428
Score = 28.8 bits (65), Expect = 5.4
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 95 GPAGTGKTETVKDMGKTLA--KYVVVFNCSDQMDYRG 129
GP G+GK E V D + L K V+V +C + R
Sbjct: 24 GPRGSGKRELVMD--RVLKDRKNVLVIDCDQLVKARN 58
>gnl|CDD|233167 TIGR00881, 2A0104, phosphoglycerate transporter family protein.
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 379
Score = 28.5 bits (64), Expect = 5.6
Identities = 17/88 (19%), Positives = 30/88 (34%), Gaps = 11/88 (12%)
Query: 293 STIVMRVLRDMNLSKLIDEDEPLFISLVADLFPNQALEKTAYPALEGAIQEQCEAAGLIF 352
S I +LRD S + E + + E T + +Q ++
Sbjct: 164 SLICFLLLRDSPQSCGLPPAEEMPNEEPDGDAEKKEEELT---KKQIFLQY------VLL 214
Query: 353 HPP-WVLKLIQLYETQRVRHGIMTLGPT 379
+ W + L ++ VR GI+ P
Sbjct: 215 NKVLWYISLGYVF-VYVVRTGILDWSPL 241
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 27.9 bits (63), Expect = 6.0
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 11/39 (28%)
Query: 94 CGPAGTGKTETVKDMGKTLAKY-------VVVFNCSDQM 125
GP G GKTE + K LA+ ++ + S+ M
Sbjct: 9 LGPTGVGKTE----LAKALAELLFGDERALIRIDMSEYM 43
>gnl|CDD|183584 PRK12545, PRK12545, RNA polymerase sigma factor; Provisional.
Length = 201
Score = 28.0 bits (62), Expect = 7.1
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 241 ENITLARKFYTLYKLCEEQLTKQVHYDFGLRNILSV 276
E I ++F+TL++ C + L +Q+ F +R L
Sbjct: 121 ETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDF 156
>gnl|CDD|130679 TIGR01618, phage_P_loop, phage nucleotide-binding protein. This
model represents an uncharacterized family of proteins
from a number of phage of Gram-positive bacteria. This
protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near
its amino end. The function of this protein is unknown
[Mobile and extrachromosomal element functions, Prophage
functions].
Length = 220
Score = 27.8 bits (62), Expect = 8.1
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 6/28 (21%)
Query: 95 GPAGTGKTETVKDM-GKTLAKYVVVFNC 121
G GTGKT T+K + GKTL V +
Sbjct: 19 GKPGTGKTSTIKYLPGKTL-----VLSF 41
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 28.4 bits (64), Expect = 8.2
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 11/39 (28%)
Query: 95 GPAGTGKTETVKDMGKTLAKYV-------VVFNCSDQMD 126
GP G GKTE K LA+ + + + S+ M+
Sbjct: 528 GPTGVGKTELA----KALAEALFGDEQALIRIDMSEYME 562
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 28.4 bits (64), Expect = 8.8
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 94 CGPAGTGKTETV 105
GP+G GKTET
Sbjct: 602 VGPSGVGKTETA 613
>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA
polymerase I and homologs. The 5'-3' exonuclease
(53EXO) PIN (PilT N terminus) domain of multi-domain DNA
polymerase I and single domain protein homologs are
included in this family. Taq contains a polymerase
domain for synthesizing a new DNA strand and a 53EXO PIN
domain for cleaving RNA primers or damaged DNA strands.
Taq's 53EXO PIN domain recognizes and
endonucleolytically cleaves a structure-specific DNA
substrate that has a bifurcated downstream duplex and an
upstream template-primer duplex that overlaps the
downstream duplex by 1 bp. The 53EXO PIN domain cleaves
the unpaired 5'-arm of the overlap flap DNA substrate.
5'-3' exonucleases are members of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN domain with
a helical arch/clamp region (I domain) of variable
length (approximately 16 residues in 53EXO PIN domains)
and a H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA/RNA binding. The active site
includes a set of conserved acidic residues that are
essential for binding divalent metal ions required for
nuclease activity.
Length = 174
Score = 27.4 bits (62), Expect = 9.1
Identities = 8/18 (44%), Positives = 10/18 (55%), Gaps = 1/18 (5%)
Query: 200 PGY-AGRKELPENLKIQF 216
P Y A R +PE L+ Q
Sbjct: 68 PEYKANRPPMPEELRPQL 85
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
0.323 0.138 0.421
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: 19,650,969
Number of extensions: 1911153
Number of successful extensions: 1768
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1758
Number of HSP's successfully gapped: 45
Length of query: 383
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 284
Effective length of database: 6,546,556
Effective search space: 1859221904
Effective search space used: 1859221904
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 60 (27.3 bits)