RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1366
(345 letters)
>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 274 bits (702), Expect = 1e-86
Identities = 130/331 (39%), Positives = 181/331 (54%), Gaps = 25/331 (7%)
Query: 14 NNEDIGSLLQISGTVVRITVAKMLEFRREYVCTKCKQCFYVKADFEQFYSIANPLSCGSP 73
+E IG L+ + G V R + + + + C KC + V + + + P C
Sbjct: 101 RSEHIGKLVSVEGIVTRASEVRPRLKKAVFECPKCGREVEV---EQSEFRVEPPREC--E 155
Query: 74 SSCDGTNFSPVTSVDQDNYKDYQEIKIQERAAGV--GSVPKSIWVTLEDDLVDLARPGDD 131
+ + + D+Q++KIQE V G +P+SI V LEDDLVD RPGD
Sbjct: 156 NCGKFGKGPLKLVPRKSEFIDFQKVKIQELPELVPGGELPRSIEVILEDDLVDSVRPGDR 215
Query: 132 VIVCGAVLRRWRPVVKGVRSDI--ELCLSANYLTVCNDQSSSLVITPELRAEVTQFWEDH 189
V + G V + G R E+ L AN D+ + IT E E+ +
Sbjct: 216 VKITGVVRIVPSRSLSGRRKGPVFEIYLEANS-VEKLDKREEVEITEEDEEEIKE----- 269
Query: 190 KYDGLAARNHIL----ASICPAIYGLYLVKLCLAVVLAGGVGRGGEDGSKVRAESHLLLV 245
LA R I SI P+IYG VK + + L GGV + DG+++R + H+LLV
Sbjct: 270 ----LAKRPDIYDILIKSIAPSIYGHEDVKKAILLQLFGGVKKNLPDGTRIRGDIHILLV 325
Query: 246 GDPGTGKSEILKFAKRMSPRSVLTTGVGTTTAGLTVSALRE--NGEWHLEAGALVLSDGG 303
GDPGT KS++LK+ +++PR V T+G G++ AGLT + +R+ GEW LEAGALVL+DGG
Sbjct: 326 GDPGTAKSQLLKYVAKLAPRGVYTSGKGSSAAGLTAAVVRDKVTGEWVLEAGALVLADGG 385
Query: 304 VCCIDEFSSIKEHDRTSIHEAMEQQTISVAK 334
VCCIDEF + E DR +IHEAMEQQTIS+AK
Sbjct: 386 VCCIDEFDKMNEEDRVAIHEAMEQQTISIAK 416
>gnl|CDD|214631 smart00350, MCM, minichromosome maintenance proteins.
Length = 509
Score = 261 bits (669), Expect = 2e-83
Identities = 119/338 (35%), Positives = 181/338 (53%), Gaps = 30/338 (8%)
Query: 14 NNEDIGSLLQISGTVVRITV--AKMLEFRREYVCTKCKQCFYVKADFEQFYSIANPLSCG 71
+ +G L++ISG V R + K+ + C++C Q P C
Sbjct: 9 RADHLGKLVRISGIVTRTSGVRPKL-----KRASFTCEKCGATLGPEIQSGRETEPTVCP 63
Query: 72 SPSSCDGTNFSPVTSVDQDNYKDYQEIKIQERAAGV--GSVPKSIWVTLEDDLVDLARPG 129
P C + + ++ + D+Q+IK+QE V G +P+S+ V L+ DLVD A+PG
Sbjct: 64 -PREC-QSPTPFSLNHERSTFIDFQKIKLQESPEEVPVGQLPRSVDVILDGDLVDKAKPG 121
Query: 130 DDVIVCG---AVLRRWRPVVKGVRSDIELCLSANYLTVCNDQSSSLV-------ITPELR 179
D V V G V ++ + AN++ + + S ++ E
Sbjct: 122 DRVEVTGIYRNVPYGFKLNTVKGLPVFATYIEANHVRKLDYKRSFEDSSFSVQSLSDEEE 181
Query: 180 AEVTQFWED-HKYDGLAARNHILASICPAIYGLYLVKLCLAVVLAGGVGRGGEDGSKVRA 238
E+ + +D Y+ LA S+ P+IYG +K + ++L GGV + DG K+R
Sbjct: 182 EEIRKLSKDPDIYERLAR------SLAPSIYGHEDIKKAILLLLFGGVHKNLPDGMKIRG 235
Query: 239 ESHLLLVGDPGTGKSEILKFAKRMSPRSVLTTGVGTTTAGLTVSALR--ENGEWHLEAGA 296
+ ++LL GDPGT KS++LK+ ++ +PR+V TTG G++ GLT + R E E+ LEAGA
Sbjct: 236 DINILLCGDPGTAKSQLLKYVEKTAPRAVYTTGKGSSAVGLTAAVTRDPETREFTLEAGA 295
Query: 297 LVLSDGGVCCIDEFSSIKEHDRTSIHEAMEQQTISVAK 334
LVL+D GVCCIDEF + + DRT+IHEAMEQQTIS+AK
Sbjct: 296 LVLADNGVCCIDEFDKMDDSDRTAIHEAMEQQTISIAK 333
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 219 bits (560), Expect = 3e-69
Identities = 75/137 (54%), Positives = 103/137 (75%), Gaps = 2/137 (1%)
Query: 200 ILASICPAIYGLYLVKLCLAVVLAGGVGRGGEDGSKVRAESHLLLVGDPGTGKSEILKFA 259
+ SI P+IYG VK + + L GGV + DG+++R + ++LLVGDPGT KS++LK+
Sbjct: 18 LARSIAPSIYGHEDVKKAILLQLFGGVKKNLPDGTRLRGDINVLLVGDPGTAKSQLLKYV 77
Query: 260 KRMSPRSVLTTGVGTTTAGLTVSALREN--GEWHLEAGALVLSDGGVCCIDEFSSIKEHD 317
+++PR+V T+G G++ AGLT + +R+ GEW LEAGALVL+DGGVCCIDEF + E D
Sbjct: 78 AKLAPRAVYTSGKGSSAAGLTAAVVRDPDTGEWTLEAGALVLADGGVCCIDEFDKMNEED 137
Query: 318 RTSIHEAMEQQTISVAK 334
R +IHEAMEQQTIS+AK
Sbjct: 138 RVAIHEAMEQQTISIAK 154
>gnl|CDD|173403 PTZ00111, PTZ00111, DNA replication licensing factor MCM4;
Provisional.
Length = 915
Score = 124 bits (313), Expect = 2e-31
Identities = 77/256 (30%), Positives = 114/256 (44%), Gaps = 44/256 (17%)
Query: 112 KSIWVTLEDDLVDLARPGDDVIVCGAVLRRWRPVVKGVRSDIELCLSANYLTVCNDQSSS 171
+ I + L DDL+D + GD V V G + + P+ L + Y N
Sbjct: 346 EVINLNLYDDLIDSVKTGDRVTVVGIL--KVTPIRTSTTRR---TLKSLYTYFVN----- 395
Query: 172 LVITPEL--RAEVTQFWEDHKYDGLA--------------ARN-----HILASICPAIYG 210
VI ++ Q + KY G +RN +L S P+I
Sbjct: 396 -VIHVKVINSTNANQPEKGLKYLGNENDFSDLQVYKILELSRNPMIYRILLDSFAPSIKA 454
Query: 211 LYLVKLCLAVVLAGG---------VGRGGEDGSKVRAESHLLLVGDPGTGKSEILKFAKR 261
VK+ L L G R ++LL GDPGT KS++L +
Sbjct: 455 RNNVKIGLLCQLFSGNKNSSDFNKSPDACYKVDNFRGIINVLLCGDPGTAKSQLLHYTHL 514
Query: 262 MSPRSVLTTGVGTTTAGLTVSAL---RENGEWHLEAGALVLSDGGVCCIDEFSSIKEHDR 318
+SPRS+ T+G +++ GLT S +NG ++ GA+VL++GGVCCIDE R
Sbjct: 515 LSPRSIYTSGKSSSSVGLTASIKFNESDNGRAMIQPGAVVLANGGVCCIDELDKCHNESR 574
Query: 319 TSIHEAMEQQTISVAK 334
S++E MEQQT+++AK
Sbjct: 575 LSLYEVMEQQTVTIAK 590
>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 = 50.0 bits (120), Expect = 1e-07
Identities = 24/80 (30%), Positives = 34/80 (42%), Gaps = 15/80 (18%)
Query: 241 HLLLVGDPGTGKSEILK-FAKRMSPRSVLTTGVGTTTAGLTVSALRENGEWHLEAGALVL 299
+LLVG PGTGKSE+ + A +S R V T T L+ G +++ G
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYV---QLTRDTTEEDLK--GRRNIDPGGASW 55
Query: 300 SD---------GGVCCIDEF 310
D G + +DE
Sbjct: 56 VDGPLVRAAREGEIAVLDEI 75
>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 = 45.2 bits (107), Expect = 7e-06
Identities = 23/91 (25%), Positives = 35/91 (38%), Gaps = 3/91 (3%)
Query: 240 SHLLLVGDPGTGKSEILK-FAKR--MSPRSVLTTGVGTTTAGLTVSALRENGEWHLEAGA 296
+LLL G PGTGK+ + + A L GL V+ L + L
Sbjct: 20 KNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFEL 79
Query: 297 LVLSDGGVCCIDEFSSIKEHDRTSIHEAMEQ 327
+ GV IDE S+ + ++ +E
Sbjct: 80 AEKAKPGVLFIDEIDSLSRGAQNALLRVLET 110
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 37.8 bits (88), Expect = 0.006
Identities = 29/123 (23%), Positives = 50/123 (40%), Gaps = 26/123 (21%)
Query: 213 LVKLCLAVVLAGGVGRGGEDGSKVRAESHLLLVGDPGTGKSEILK-FAKRMSPRSV---L 268
+++L L +LAGG H+LL G PG GK+ + + A+ + V
Sbjct: 32 VIELALLALLAGG---------------HVLLEGPPGVGKTLLARALARALGLPFVRIQC 76
Query: 269 TTGVGTTTAGLT-----VSALRENGEWHLEAGALVLSDGGVCCIDEFSSIKEHDRTSIHE 323
T + L + L E GE+ G L + + +DE + + ++ E
Sbjct: 77 T--PDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEINRAPPEVQNALLE 134
Query: 324 AME 326
A+E
Sbjct: 135 ALE 137
>gnl|CDD|215459 PLN02854, PLN02854, 3-ketoacyl-CoA synthase.
Length = 521
Score = 34.5 bits (79), Expect = 0.066
Identities = 26/114 (22%), Positives = 45/114 (39%), Gaps = 6/114 (5%)
Query: 182 VTQFWEDHKYDGLAARNHILASICPAIYGLYLVKLCLAVVLAGGVGRGGEDGSKVRAESH 241
V++ W + A ++ + GLY K V L ED K+ +S
Sbjct: 76 VSELWSNQALHLDTATRLTGSAFLLFLLGLYWAKRSKPVYLVDFACYKPEDERKISVDSF 135
Query: 242 LLLVGDPGTGKSEILKFAKRMSPRS------VLTTGVGTTTAGLTVSALRENGE 289
L + + G+ + E ++F +R+S RS L G+ + L + R E
Sbjct: 136 LTMTEENGSFEDETVQFQRRISTRSGLGDETYLPRGITSRPPNLCMEEARAEAE 189
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 33.4 bits (77), Expect = 0.19
Identities = 11/23 (47%), Positives = 17/23 (73%), Gaps = 3/23 (13%)
Query: 241 HLLLVGDPGTGKSEILKFAKRMS 263
H++++G PGTGKS + AK M+
Sbjct: 52 HVMMIGSPGTGKSML---AKAMA 71
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 32.9 bits (75), Expect = 0.24
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 234 SKVRAESHLLLVGDPGTGKSEILKFAKRMSPRSVLT 269
+ + ++LL+G+PG GKS + K + P L
Sbjct: 32 KAAKQKRNVLLIGEPGVGKSMLAKAMAELLPDEELE 67
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 32.1 bits (74), Expect = 0.29
Identities = 10/22 (45%), Positives = 17/22 (77%), Gaps = 3/22 (13%)
Query: 241 HLLLVGDPGTGKSEILKFAKRM 262
+LL++G PG+GK+ + AKR+
Sbjct: 24 NLLMIGPPGSGKTML---AKRL 42
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 32.2 bits (74), Expect = 0.36
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 226 VGRGGEDGSKV----RAESHLLLVGDPGTGKSEILK 257
+G G D + V HLL+ GD +GK+ +L+
Sbjct: 346 LGIGESDLAPVYLDFAESPHLLVFGDSESGKTTLLR 381
>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 = 31.2 bits (70), Expect = 0.41
Identities = 7/17 (41%), Positives = 13/17 (76%)
Query: 241 HLLLVGDPGTGKSEILK 257
+L+VG PG+GK+ + +
Sbjct: 4 VILIVGPPGSGKTTLAR 20
>gnl|CDD|224930 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport and
metabolism].
Length = 189
Score = 30.8 bits (70), Expect = 0.77
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 244 LVGDPGTGKSEILKFAKRMSPR 265
+ G PG GK+ +LK A + +
Sbjct: 9 ITGVPGVGKTTVLKIALKELVK 30
>gnl|CDD|131701 TIGR02653, Lon_rel_chp, conserved hypothetical protein. This model
describes a protein family of unknown function, about
690 residues in length, in which some members show
C-terminal sequence similarity to pfam05362, which is
the Lon protease C-terminal proteolytic domain, from
MEROPS family S16. However, the annotated catalytic
sites of E. coli Lon protease are not conserved in
members of this family. Members have a motif
GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif
GxxGxGK[ST] [Hypothetical proteins, Conserved].
Length = 675
Score = 31.0 bits (70), Expect = 0.96
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 236 VRAESHLLLVGDPGTGKSEILKFAKRMSPRSVLTTGVGTTTAGL 279
V +L +G GTGKS + K SP S+L +G TT A L
Sbjct: 213 VENNYNLCELGPRGTGKSHVYK---ECSPNSILMSGGQTTVANL 253
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 29.8 bits (68), Expect = 1.4
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 242 LLLVGDPGTGKSEILK-FA-KRMSPRSVLTTGV 272
++L+GD G GKS +L F + S + T GV
Sbjct: 3 IILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGV 35
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 30.2 bits (69), Expect = 1.4
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 233 GSKVRAES--HLLLVGDPGTGK 252
+K R E+ H+LL G PG GK
Sbjct: 44 AAKKRGEALDHVLLFGPPGLGK 65
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 29.2 bits (66), Expect = 1.6
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 236 VRAESHLLLVGDPGTGKSEILKFAKRMSPRS 266
R +L G+ G+GK+ +L+ R P
Sbjct: 1 RRGAGIGVLTGESGSGKTTLLRRLARQLPNR 31
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 30.3 bits (69), Expect = 1.6
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 239 ESHLLLVGDPGTGKSE-----ILKFAKRMSP 264
+ HL + G PG GKS I+ A++ SP
Sbjct: 810 DGHLAIFGSPGYGKSTFLQTLIMSLARQHSP 840
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.4 bits (68), Expect = 1.8
Identities = 9/41 (21%), Positives = 18/41 (43%)
Query: 236 VRAESHLLLVGDPGTGKSEILKFAKRMSPRSVLTTGVGTTT 276
++ LLVG+ GTGK+ ++++ + T
Sbjct: 461 IQNNEPTLLVGETGTGKTTMIQYLALKLHFKLTVINKSQQT 501
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form (CCALD),
the milder adult form, adrenomyeloneuropathy (AMN), and
variants without neurologic involvement (i.e.
asymptomatic).
Length = 166
Score = 29.4 bits (67), Expect = 1.8
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 236 VRAESHLLLVGDPGTGKSEILK 257
++ LL+ G GTGKS + +
Sbjct: 24 IKPGDRLLITGPSGTGKSSLFR 45
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 30.3 bits (69), Expect = 1.8
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 15/47 (31%)
Query: 221 VLAGGVGRGGEDGSKVRAESHLLLVGDPGTGKSEIL-----KFAKRM 262
VL GG+ G S +L+ GDPG GKS +L + AKR
Sbjct: 85 VLGGGLVPG----------SVILIGGDPGIGKSTLLLQVAARLAKRG 121
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 29.9 bits (68), Expect = 1.9
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 244 LVGDPGTGKSEILK 257
L G PGTGKS +LK
Sbjct: 219 LKGRPGTGKSTMLK 232
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 29.9 bits (67), Expect = 2.6
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 221 VLAGGVGRGGEDGSKVRAESHLLLVGDPGTGKSEILKFAK 260
VL G G +D + V + +LL G GK++ F+K
Sbjct: 65 VLDSGDGLSDKDEADVAGDMKVLLNGSKLVGKAQAEVFSK 104
>gnl|CDD|234914 PRK01184, PRK01184, hypothetical protein; Provisional.
Length = 184
Score = 29.1 bits (66), Expect = 2.6
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 242 LLLVGDPGTGKSEILKFAKRM 262
+ +VG PG+GK E K A+ M
Sbjct: 4 IGVVGMPGSGKGEFSKIAREM 24
>gnl|CDD|224588 COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related
proteins [Cell division and chromosome partitioning].
Length = 858
Score = 29.8 bits (67), Expect = 2.8
Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 239 ESHLLLVGDPGTGKSE-----ILKFAKRMSPRSVL 268
HLL+ G G+GKS IL SP V
Sbjct: 530 AGHLLIAGATGSGKSVALNTMILSLLYTHSPEEVR 564
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 29.1 bits (66), Expect = 3.2
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 242 LLLVGDPGTGKSEILK--FAKRMSPRSVLTTGVGTTTAGLTVSALRENG 288
+LL+G G+GKS + F+ SPR L G T + S +R G
Sbjct: 2 VLLMGLRGSGKSSMRSIIFSN-YSPRDTLRLGA---TIDVEQSHVRFLG 46
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit. All
proteins in this family for which functions are known
are 5'-3' DNA helicases that, as part of a complex with
RuvA homologs serve as a 5'-3' Holliday junction
helicase. RuvA specifically binds Holliday junctions as
a sandwich of two tetramers and maintains the
configuration of the junction. It forms a complex with
two hexameric rings of RuvB, the subunit that contains
helicase activity. The complex drives ATP-dependent
branch migration of the Holliday junction recombination
intermediate. The endonuclease RuvC resolves junctions
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 305
Score = 28.8 bits (65), Expect = 3.6
Identities = 34/123 (27%), Positives = 56/123 (45%), Gaps = 27/123 (21%)
Query: 232 DGSKVRAES--HLLLVGDPGTGKSEILKF-AKRMSPRSVLTTGVGTTTAGLTVSALRENG 288
+ +K+R E+ HLLL G PG GK+ + A M +T+G AL + G
Sbjct: 21 EAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSG----------PALEKPG 70
Query: 289 EWHLEAGALV-LSDGGVCCIDEF----SSIKEHDRTSIHEAME--QQTISVAKDKESKKV 341
+ A L L +G V IDE +++E ++ AME + I + K ++ V
Sbjct: 71 DL---AAILTNLEEGDVLFIDEIHRLSPAVEEL----LYPAMEDFRLDIVIGKGPSARSV 123
Query: 342 KVK 344
++
Sbjct: 124 RLD 126
>gnl|CDD|173959 cd08549, G1PDH_related, Glycerol-1-phosphate_dehydrogenase and
related proteins. Bacterial and archeal
glycerol-1-phosphate dehydrogenase-like oxidoreductases.
The proteins have similarity with glycerol-1-phosphate
dehydrogenase (G1PDH). G1PDH plays a role in the
synthesis of phosphoglycerolipids in gram-positive
bacterial species. It catalyzes the reversibly reduction
of dihydroxyacetone phosphate (DHAP) to
glycerol-1-phosphate (G1P) in a NADH-dependent manner.
Its activity requires Ni++ ion. It also contains
archaeal Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH)
that plays an important role in the formation of the
enantiomeric configuration of the glycerophosphate
backbone (sn-glycerol-1-phosphate) of archaeal ether
lipids.
Length = 332
Score = 29.1 bits (65), Expect = 3.6
Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 5/74 (6%)
Query: 263 SPRSVLTTGVGTTTAGLTVS-----ALRENGEWHLEAGALVLSDGGVCCIDEFSSIKEHD 317
+P +T G G + T + GE + + A ++ + ID + I D
Sbjct: 153 APYEFITAGFGDVISNYTALADWYISSVITGETYSDDIAAMVKESINKVIDASTGILGRD 212
Query: 318 RTSIHEAMEQQTIS 331
SI E +E I+
Sbjct: 213 EKSIKELVEALIIN 226
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 29.2 bits (66), Expect = 3.7
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 242 LLLVGDPGTGKSEILKFAKR 261
L L+G G GKS +++ KR
Sbjct: 81 LYLLGPVGGGKSSLVECLKR 100
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 29.0 bits (65), Expect = 3.8
Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 231 EDGSKVRAES-HLLLVGDPGTGKSEILK-FAK 260
E G V S H+L G PGTGK+ I + AK
Sbjct: 303 ERGLPVAQTSNHMLFAGPPGTGKTTIARVVAK 334
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 28.9 bits (66), Expect = 4.3
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 232 DGSKVRAES--HLLLVGDPGTGK 252
+ +K R E+ H+LL G PG GK
Sbjct: 42 EAAKKRGEALDHVLLYGPPGLGK 64
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 28.7 bits (65), Expect = 4.6
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 17/56 (30%)
Query: 208 IYGLYLVKLCLAVVLAGGVGRGGEDGSKVRAESHLLLVGDPGTGKSEILKFAKRMS 263
+ G K L + AGG +LLLVG PGTGK+ + A R+
Sbjct: 181 VKGQEQAKRALEIAAAGG--------------HNLLLVGPPGTGKTML---ASRLP 219
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 28.7 bits (65), Expect = 4.6
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 10/39 (25%)
Query: 218 LAVVLAGGVGRGGEDGSKVRAESHLLLVGDPGTGKSEIL 256
L VL GG+ G S +L+ GDPG GKS +L
Sbjct: 71 LDRVLGGGLVPG----------SVILIGGDPGIGKSTLL 99
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 27.9 bits (62), Expect = 4.9
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 240 SHLLLVGDPGTGKSEILK-FAKRMSPRSVLTTGVGTTTAGLTVSALRE 286
+LL G GTGK+ +L+ + + + ALRE
Sbjct: 25 PSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRE 72
>gnl|CDD|236769 PRK10820, PRK10820, DNA-binding transcriptional regulator TyrR;
Provisional.
Length = 520
Score = 28.9 bits (65), Expect = 5.0
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 242 LLLVGDPGTGKSEILKFAKRMSPR 265
LL+ GD GTGK + SPR
Sbjct: 230 LLITGDTGTGKDLLAYACHLRSPR 253
>gnl|CDD|223315 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
Length = 201
Score = 28.0 bits (63), Expect = 5.4
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 244 LVGDPGTGKSEILKFAKRM 262
L G G+GKS + K +
Sbjct: 7 LTGGIGSGKSTVAKILAEL 25
>gnl|CDD|188598 TIGR04083, rSAM_pep_methan, putative peptide-modifying radical SAM
enzyme, Mhun_1560 family. Members of this family are
radical SAM enzymes, homologous to a variety of other
peptide-modifying radical SAM, and found primarily in
methanogenic archaea.
Length = 376
Score = 28.5 bits (64), Expect = 5.5
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 34 AKMLEFRREYVCTKCKQCFYVK 55
ML F+ EYV T C +C ++K
Sbjct: 284 KLMLAFK-EYVDTHCAKCSHIK 304
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of unknown
function.
Length = 248
Score = 28.2 bits (64), Expect = 5.6
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 241 HLLLVGDPGTGKSEILKFA 259
++LL G GTGKS ++K
Sbjct: 55 NVLLWGARGTGKSSLVKAL 73
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 27.9 bits (63), Expect = 6.4
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 244 LVGDPGTGKSEILKFAKRMSP 264
+ G PG GK+ +L A
Sbjct: 7 VTGVPGVGKTTVLNKALEKLK 27
>gnl|CDD|100033 cd02197, HypE, HypE (Hydrogenase expression/formation protein).
HypE is involved in Ni-Fe hydrogenase biosynthesis.
HypE dehydrates its own carbamoyl moiety in an
ATP-dependent process to yield the enzyme thiocyanate.
The N-terminal domain of HypE is related to the
ATP-binding domains of the AIR synthases,
selenophosphate synthetase (SelD), and FGAM synthase and
is thought to bind ATP.
Length = 293
Score = 28.2 bits (64), Expect = 6.6
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 5/34 (14%)
Query: 105 AGVGSVPKSIWVTLEDDLVDLARPGDDVIVCGAV 138
G+G +P+ + RPGD +IV G +
Sbjct: 134 TGIGVIPRGV-----IISPSNIRPGDKIIVSGTI 162
>gnl|CDD|206659 cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13
(Rab8, Rab10, Rab13). Rab8/Sec4/Ypt2 are known or
suspected to be involved in post-Golgi transport to the
plasma membrane. It is likely that these Rabs have
functions that are specific to the mammalian lineage and
have no orthologs in plants. Rab8 modulates polarized
membrane transport through reorganization of actin and
microtubules, induces the formation of new surface
extensions, and has an important role in directed
membrane transport to cell surfaces. The Ypt2 gene of
the fission yeast Schizosaccharomyces pombe encodes a
member of the Ypt/Rab family of small GTP-binding
proteins, related in sequence to Sec4p of Saccharomyces
cerevisiae but closer to mammalian Rab8. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 167
Score = 27.6 bits (62), Expect = 6.9
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 242 LLLVGDPGTGKSEIL-KFAKRMSPRSVLTT 270
LLL+GD G GKS +L +F++ S ++T
Sbjct: 6 LLLIGDSGVGKSCLLLRFSEDSFNPSFIST 35
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 27.9 bits (63), Expect = 6.9
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 7/47 (14%)
Query: 243 LLVGDPGTGKSEILKFAK---RMSPRSVLTTGVGTTTAGLTVSALRE 286
++ G GTGK+ LK A+ + V +G G L E
Sbjct: 22 VVQGPAGTGKTTSLKAAREAWEAAGYRV----IGLAPTGKAAKVLGE 64
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 28.4 bits (64), Expect = 6.9
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 236 VRAESHLLLVGDPGTGKSEILK 257
VR LL+ G+ G GK+ +L+
Sbjct: 416 VRPGERLLITGESGAGKTSLLR 437
>gnl|CDD|134464 PRK01008, PRK01008, queuine tRNA-ribosyltransferase; Provisional.
Length = 372
Score = 28.2 bits (63), Expect = 7.2
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 174 ITPELRAEVTQFWEDHKYDGLA 195
I P+ R +F ED +DG A
Sbjct: 208 IDPDQRKIGCKFVEDLPFDGSA 229
>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast homolog
Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in every
eukaryote and is a key regulatory component for the
transport of vesicles from the ER to the Golgi
apparatus. Studies on mutations of Ypt1, the yeast
homolog of Rab1, showed that this protein is necessary
for the budding of vesicles of the ER as well as for
their transport to, and fusion with, the Golgi
apparatus. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 166
Score = 27.7 bits (62), Expect = 7.3
Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 242 LLLVGDPGTGKSEIL-KFAKRMSPRSVLTT-GV 272
LLL+GD G GKS +L +FA S ++T GV
Sbjct: 5 LLLIGDSGVGKSCLLLRFADDTYTESYISTIGV 37
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 27.0 bits (60), Expect = 7.4
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 243 LLVGDPGTGKSEILKFAKRM 262
L+ G PG+GK+ + K
Sbjct: 2 LITGTPGSGKTTLAKELAER 21
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed in
a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 201
Score = 27.7 bits (62), Expect = 8.6
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 242 LLLVGDPGTGKSEILK 257
+L++GD G GK+ I+K
Sbjct: 3 VLVIGDLGVGKTSIIK 18
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 27.7 bits (62), Expect = 8.7
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 10/41 (24%)
Query: 238 AESHLLLVGDPGTGKSEILK------FAKRMSPRSVLTTGV 272
E L+LVGD G GK+ +K F K+ P T GV
Sbjct: 8 PEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIP----TLGV 44
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 27.8 bits (62), Expect = 9.6
Identities = 10/27 (37%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 240 SHLLLVGDPGTGKSEIL-KFAKRMSPR 265
+ LL++G PG+GK+ L + A ++ R
Sbjct: 223 AKLLILGAPGSGKTTFLQRLALWLAQR 249
>gnl|CDD|206658 cd01866, Rab2, Rab GTPase family 2 (Rab2). Rab2 is localized on
cis-Golgi membranes and interacts with Golgi matrix
proteins. Rab2 is also implicated in the maturation of
vesicular tubular clusters (VTCs), which are
microtubule-associated intermediates in transport
between the ER and Golgi apparatus. In plants, Rab2
regulates vesicle trafficking between the ER and the
Golgi bodies and is important to pollen tube growth.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 168
Score = 27.0 bits (60), Expect = 9.8
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 243 LLVGDPGTGKS-EILKFA-KRMSPRSVLTTGV 272
+++GD G GKS +L+F KR P LT GV
Sbjct: 8 IIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGV 39
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 27.4 bits (61), Expect = 9.8
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 10/37 (27%)
Query: 242 LLLVGDPGTGKSEILK------FAKRMSPRSVLTTGV 272
L++VGD GTGK+ +K F K+ P T GV
Sbjct: 16 LVIVGDGGTGKTTFVKRHLTGEFEKKYEP----TIGV 48
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.135 0.403
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,281,887
Number of extensions: 1657990
Number of successful extensions: 2100
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2085
Number of HSP's successfully gapped: 77
Length of query: 345
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 247
Effective length of database: 6,590,910
Effective search space: 1627954770
Effective search space used: 1627954770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.5 bits)