RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16169
(139 letters)
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial 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. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 35.4 bits (82), Expect = 0.006
Identities = 21/103 (20%), Positives = 48/103 (46%), Gaps = 2/103 (1%)
Query: 24 DVDLLKSDVALARDRVSRLKRELEQI--RTEMNYTQRGLVPMGTRLAEMARMRLEYDETR 81
V L+ +A + + RL+ LE++ R E + + AE+ ++ E +E
Sbjct: 387 KVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAELEELE 446
Query: 82 KRIQIIQTQLADLEEKVTPGQAESDKDRLILFQEKEQLLRSRS 124
+ ++ +Q +L LEE + + E ++ L + +L + ++
Sbjct: 447 EELEELQEELERLEEALEELREELEEAEQALDAAERELAQLQA 489
Score = 26.6 bits (59), Expect = 5.4
Identities = 15/66 (22%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 31 DVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQ 90
+AL R + L EL ++ ++ + +R L + +LA++ L + RI +Q +
Sbjct: 888 ALALLRSELEELSEELRELESKRSELRRELEELREKLAQL---ELRLEGLEVRIDNLQER 944
Query: 91 LADLEE 96
L++
Sbjct: 945 LSEEYS 950
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 30.9 bits (70), Expect = 0.20
Identities = 15/101 (14%), Positives = 27/101 (26%), Gaps = 6/101 (5%)
Query: 24 DVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKR 83
D D A AR L + + + A +A R +
Sbjct: 890 DAREAAEDAAEARAEAEEASLRLRTLEESVGAMVDEIR------ARLAETRAALASGGRE 943
Query: 84 IQIIQTQLADLEEKVTPGQAESDKDRLILFQEKEQLLRSRS 124
+ + LA EE + + + L + E +
Sbjct: 944 LPRLAEALATAEEARGRAEEKRAEADATLDERAEARDHAIG 984
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 30.3 bits (69), Expect = 0.25
Identities = 10/79 (12%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 36 RDRVSRLKRELEQIRTEMNYTQRGLV--------PMGTRLAEM-ARMRLEYDETRKRIQI 86
++ + L+ EL+++ E+ ++ L + E ++ ++ + ++
Sbjct: 333 KEELKELEEELKELEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETKEKLSEELEE 392
Query: 87 IQTQLADLEEKVTPGQAES 105
++ +L +L+E++ +E
Sbjct: 393 LEEELKELKEELESLYSEG 411
>gnl|CDD|220879 pfam10805, DUF2730, Protein of unknown function (DUF2730). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 106
Score = 29.3 bits (66), Expect = 0.29
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 8/82 (9%)
Query: 16 SSSASTKYDVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRL 75
S + + + DV+ L +A R++ ++ +LE + T + + E+ +R
Sbjct: 28 SKTYAKREDVEKLIDIIASNDKRLTEMETKLESLPTAKDVHALKI--------EITELRG 79
Query: 76 EYDETRKRIQIIQTQLADLEEK 97
E E +IQ I QL L E
Sbjct: 80 ELKELSAQIQSISHQLELLLEN 101
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 29.3 bits (66), Expect = 0.64
Identities = 26/106 (24%), Positives = 56/106 (52%), Gaps = 5/106 (4%)
Query: 19 ASTKYDVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEM----ARMR 74
+ + +++ L+ ++ A + LK ELE++R E+ Q L+ + + E+ + +R
Sbjct: 249 SRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLR 308
Query: 75 LEYDETRKRIQIIQTQLADLEEKVTPGQAESDKDRLILFQEKEQLL 120
+E ++ ++ +L +L+EK+ E ++R L +E EQLL
Sbjct: 309 ERLEELENELEELEERLEELKEKIE-ALKEELEERETLLEELEQLL 353
Score = 28.5 bits (64), Expect = 1.3
Identities = 23/109 (21%), Positives = 54/109 (49%), Gaps = 4/109 (3%)
Query: 19 ASTKYDVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRL----AEMARMR 74
S K ++ L+ + R ++ L+R+LE+++ E+ + L + +RL E+ +
Sbjct: 691 KSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELE 750
Query: 75 LEYDETRKRIQIIQTQLADLEEKVTPGQAESDKDRLILFQEKEQLLRSR 123
E +E ++R++ ++ +L LEE + + E ++ +E+L
Sbjct: 751 EELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELE 799
Score = 27.0 bits (60), Expect = 4.2
Identities = 20/98 (20%), Positives = 47/98 (47%), Gaps = 5/98 (5%)
Query: 28 LKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQII 87
L+ ++A ++ ++ ELE+++ E+ + L + RL ++ E + + +
Sbjct: 381 LREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEE---L 437
Query: 88 QTQLADLEEKVTPGQA--ESDKDRLILFQEKEQLLRSR 123
QT+L +L E++ + E +DRL + + L+
Sbjct: 438 QTELEELNEELEELEEQLEELRDRLKELERELAELQEE 475
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 29.1 bits (65), Expect = 0.67
Identities = 19/89 (21%), Positives = 43/89 (48%), Gaps = 5/89 (5%)
Query: 40 SRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQLADLEEKVT 99
LK + E+++ ++ Q+ + L E+ + EY+E ++R++ ++ + + LEE +
Sbjct: 131 MDLKEDYEELKEKLEELQKEKEEL---LKELEELEAEYEEVQERLKRLEVENSRLEEMLK 187
Query: 100 --PGQAESDKDRLILFQEKEQLLRSRSMS 126
PG+ K R + +L +S
Sbjct: 188 KLPGEVYDLKKRWDELEPGVELPEEELIS 216
>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 = 28.5 bits (64), Expect = 1.1
Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 3/87 (3%)
Query: 33 ALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQLA 92
A RD + + +LE+++ E+N +R L + L L + I I+ ++
Sbjct: 381 AETRDELKDYREKLEKLKREINELKRELDRLQEELQR-LSEELA--DLNAAIAGIEAKIN 437
Query: 93 DLEEKVTPGQAESDKDRLILFQEKEQL 119
+LEE+ E K L Q L
Sbjct: 438 ELEEEKEDKALEIKKQEWKLEQLAADL 464
Score = 27.0 bits (60), Expect = 4.0
Identities = 12/100 (12%), Positives = 49/100 (49%), Gaps = 4/100 (4%)
Query: 24 DVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRL----AEMARMRLEYDE 79
++ LK +++ + + R++ L+++ E++ R + + + E +++ +E
Sbjct: 682 RLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEE 741
Query: 80 TRKRIQIIQTQLADLEEKVTPGQAESDKDRLILFQEKEQL 119
+ + ++ ++ +++ ++ +A ++ L + +E L
Sbjct: 742 LEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEAL 781
>gnl|CDD|182611 PRK10642, PRK10642, proline/glycine betaine transporter;
Provisional.
Length = 490
Score = 28.5 bits (64), Expect = 1.2
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 58 RGLVPMGTRLAEMARMRLE--YDETRKRIQIIQTQLADLEEK 97
+G P + + E A+ L YD ++I I ++A+L+ K
Sbjct: 438 KGATPAASDIQE-AKEILVEHYDNIEQKIDDIDQEIAELQAK 478
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 28.6 bits (64), Expect = 1.3
Identities = 16/61 (26%), Positives = 33/61 (54%)
Query: 36 RDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQLADLE 95
+ + +L+ ELEQ+R E+ + L + + E+ + E +E +K ++ ++ L LE
Sbjct: 687 LEELEQLEEELEQLREELEELLKKLGEIEQLIEELESRKAELEELKKELEKLEKALELLE 746
Query: 96 E 96
E
Sbjct: 747 E 747
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 28.1 bits (63), Expect = 1.4
Identities = 19/122 (15%), Positives = 49/122 (40%), Gaps = 24/122 (19%)
Query: 6 KGICLRLCSSSSSASTKYDVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGT 65
K +++ K DLLK +VA ++R+++++ + Q++ E+
Sbjct: 40 KQKVEEALEGATNEDGKLAADLLKLEVARKKERLNQIRARISQLKEEI------------ 87
Query: 66 RLAEMARMRLEYDETRKRIQIIQTQLADLEEKVTPGQAESDKDRLILFQEKEQLLRSRSM 125
++ R+RI+ ++ LA ++ + +K R ++ + ++
Sbjct: 88 ------------EQKRERIEELKRALAQRRSDLSSASYQLEKRRASQLEKLQDEIKRTRS 135
Query: 126 SL 127
L
Sbjct: 136 KL 137
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 28.1 bits (63), Expect = 1.5
Identities = 15/103 (14%), Positives = 43/103 (41%), Gaps = 3/103 (2%)
Query: 17 SSASTKYDVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLE 76
+ K + L E++ + +N + L + + ++ + E
Sbjct: 69 QEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDELAELMEEIEKLEK---E 125
Query: 77 YDETRKRIQIIQTQLADLEEKVTPGQAESDKDRLILFQEKEQL 119
++ ++R++ ++ LA+ E ++ AE ++ L ++E+L
Sbjct: 126 IEDLKERLERLEKNLAEAEARLEEEVAEIREEGQELSSKREEL 168
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 27.7 bits (62), Expect = 1.8
Identities = 15/83 (18%), Positives = 48/83 (57%), Gaps = 2/83 (2%)
Query: 28 LKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQII 87
L+ ++A +++++ L++E ++++ E++ + L + LA + ++ E + + +
Sbjct: 78 LQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEENREL 137
Query: 88 QTQLADLEEKVTPGQAESDKDRL 110
+ +LA+L+++ E++ +RL
Sbjct: 138 REELAELKQENE--ALEAENERL 158
Score = 25.7 bits (57), Expect = 7.3
Identities = 14/98 (14%), Positives = 42/98 (42%), Gaps = 4/98 (4%)
Query: 28 LKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQII 87
L+ ++A ++ ++ L+ +L +++ E ++ L + L + + + +
Sbjct: 71 LQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIEL 130
Query: 88 QTQLADLEEKVTPGQAESDKDRLILFQEKEQLLRSRSM 125
+ +L E++ + E++ L E E+L +
Sbjct: 131 DEENRELREELAELKQENEA----LEAENERLQENEQR 164
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 27.4 bits (61), Expect = 1.9
Identities = 20/113 (17%), Positives = 49/113 (43%), Gaps = 10/113 (8%)
Query: 7 GICLRLCSSSSSASTKYDVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTR 66
G+ L + + ++ L+ +++ + ++S L+ ELE + + + L
Sbjct: 56 GLLCLLLKAPVQSVRPQKLEELQGELSELKQQLSELQEELEDLEERIAELESEL------ 109
Query: 67 LAEMARMRLEYDETRKRIQIIQTQLADLEEKVTPGQAESDKDRLILFQEKEQL 119
++ + R+ ++ ++ +L LEE + E + R L +E E+L
Sbjct: 110 ----EDLKEDLQLLRELLKSLEERLESLEESIKELAKELRELRQDLREEVEEL 158
>gnl|CDD|178101 PLN02483, PLN02483, serine palmitoyltransferase.
Length = 489
Score = 27.8 bits (62), Expect = 1.9
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 32 VALARDRVSRLKRELEQIRTEMNYTQRGLVPMG 64
V L D +R ++L QIR N+ + L MG
Sbjct: 357 VILGEDGTNRGAQKLAQIRENSNFFRSELQKMG 389
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 28.0 bits (63), Expect = 1.9
Identities = 16/61 (26%), Positives = 37/61 (60%), Gaps = 8/61 (13%)
Query: 40 SRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRL--EYDE-TRKRIQIIQTQLADLEE 96
+R++ E++ E++ R ++ + E+ R L E DE +++R++ ++ +LA+LEE
Sbjct: 394 ARIRMEIDSKPEELDELDRRIIQL-----EIEREALKKEKDEASKERLEDLEKELAELEE 448
Query: 97 K 97
+
Sbjct: 449 E 449
Score = 25.7 bits (57), Expect = 10.0
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 18/74 (24%)
Query: 37 DRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARM-RLEYD---ETRKRIQIIQTQLA 92
+ ++K E+EQ+R E+ +R ++A+ L+Y E KR+Q + +L
Sbjct: 465 QGIQQIKEEIEQVRLELEQAERE--------GDLAKAAELQYGKLPELEKRLQAAEAKLG 516
Query: 93 D------LEEKVTP 100
+ L E+VT
Sbjct: 517 EETKPRLLREEVTA 530
>gnl|CDD|184370 PRK13886, PRK13886, conjugal transfer protein TraL; Provisional.
Length = 241
Score = 27.4 bits (61), Expect = 2.4
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 10/38 (26%)
Query: 64 GTRLAEMARMRLEYDE----------TRKRIQIIQTQL 91
G +EM + RL +DE TR+R++I++ QL
Sbjct: 194 GRDFSEMLQDRLTFDEALADSSLTIMTRQRLKIVKDQL 231
>gnl|CDD|218037 pfam04348, LppC, LppC putative lipoprotein. This family includes
several bacterial outer membrane antigens, whose
molecular function is unknown.
Length = 535
Score = 27.5 bits (61), Expect = 2.5
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 14 SSSSSASTKYDVDLLK-----SDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMG 64
S S+S +T + DL SD+ +D VS +++ + + L MG
Sbjct: 432 SRSNSGNTGPEQDLDLNGIQFSDIPFFKDPVSSQYQKVAVKWPNGDGSLMRLYAMG 487
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 27.5 bits (62), Expect = 2.7
Identities = 7/30 (23%), Positives = 17/30 (56%)
Query: 25 VDLLKSDVALARDRVSRLKRELEQIRTEMN 54
+ L+ + +L+RELE++++E+
Sbjct: 17 IRQLELKLRDLEAENEKLERELERLKSELE 46
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 27.4 bits (61), Expect = 2.9
Identities = 18/68 (26%), Positives = 37/68 (54%)
Query: 28 LKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQII 87
LK ++ + + +L+ ELE+ R E+ R + R + R+ E +E +KR++ +
Sbjct: 441 LKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEEL 500
Query: 88 QTQLADLE 95
+ +LA+L
Sbjct: 501 ERKLAELR 508
Score = 26.2 bits (58), Expect = 7.2
Identities = 15/63 (23%), Positives = 32/63 (50%)
Query: 36 RDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQLADLE 95
+ S LKRELE+++ E+ + L + + R E +RI+ ++ +L + +
Sbjct: 435 EEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKK 494
Query: 96 EKV 98
++V
Sbjct: 495 KRV 497
>gnl|CDD|215656 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold
many proteins. Hsp70 assisted folding involves repeated
cycles of substrate binding and release. Hsp70 activity
is ATP dependent. Hsp70 proteins are made up of two
regions: the amino terminus is the ATPase domain and the
carboxyl terminus is the substrate binding region.
Length = 598
Score = 26.8 bits (60), Expect = 3.9
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 21 TKYDVDLLKSDVALAR--DRVSRLKRELEQIRTEMN 54
KY +DL K AL R + + K EL +TE+N
Sbjct: 240 KKYGIDLSKDPRALQRLREAAEKAKIELSSNQTEIN 275
>gnl|CDD|227061 COG4717, COG4717, Uncharacterized conserved protein [Function
unknown].
Length = 984
Score = 27.1 bits (60), Expect = 4.1
Identities = 23/107 (21%), Positives = 44/107 (41%), Gaps = 11/107 (10%)
Query: 36 RDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQ------T 89
R++ L+ EL R + R V + RL E +LE + TR+R ++
Sbjct: 218 HARLAELRSELRADRDHIR-ALRDAVELWPRLQEWK--QLEQELTRRREELATFPRDGVL 274
Query: 90 QLADLEEKVTPGQAESDKDRLILFQEKEQLLRSRSMSLIRWPIKDTI 136
+L E + +AE D + L + K+ S+ + ++ +
Sbjct: 275 RLEKREAHLQKTEAEIDALLVRLAELKDL--ASQLIPAKEAVLQALV 319
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 26.7 bits (60), Expect = 4.2
Identities = 9/23 (39%), Positives = 20/23 (86%)
Query: 28 LKSDVALARDRVSRLKRELEQIR 50
L++D L R+R+++L++ELE+++
Sbjct: 4 LETDRRLIRERIAKLRKELEKVK 26
>gnl|CDD|220968 pfam11074, DUF2779, Domain of unknown function(DUF2779). This
domain is conserved in bacteria. The function is not
known.
Length = 127
Score = 26.0 bits (58), Expect = 4.8
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 65 TRLAEMARMRLEYDETRKRIQIIQTQLADLEE 96
TRL E+A++ E +I+ I + DL +
Sbjct: 82 TRLKELAQLFPEL---ADKIKAIIERTVDLLD 110
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 27.0 bits (60), Expect = 4.9
Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 8/97 (8%)
Query: 26 DLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQ 85
+ + A + + + +L Q E+ +R AE + +R+Q
Sbjct: 610 QQAEEALQSAVAKQKQAEEQLVQANAELEEQKRA-------EAEARTALKQARLDLQRLQ 662
Query: 86 IIQTQLAD-LEEKVTPGQAESDKDRLILFQEKEQLLR 121
Q L D LE + + +++ L + +QLL
Sbjct: 663 NEQQSLKDKLELAIAERKQQAETQLRQLDAQLKQLLE 699
>gnl|CDD|234084 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
protein, PEP-CTERM locus subfamily. Members of this
protein family belong to the family of polysaccharide
chain length determinant proteins (pfam02706). All are
found in species that encode the PEP-CTERM/exosortase
system predicted to act in protein sorting in a number
of Gram-negative bacteria, and are found near the epsH
homolog that is the putative exosortase gene [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 498
Score = 26.6 bits (59), Expect = 5.4
Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 15/80 (18%)
Query: 25 VDLLKSDVALARDRVSRLKRELEQIRTEMNYTQ----------RGLVPMGTRLAEMARMR 74
+L +S + ELE R E+N G P+ + +A
Sbjct: 192 GGILPDQEGDYYSEISEAQEELEAARLELNEAIAQRDALKRQLGGEEPVLLAGSSVAN-- 249
Query: 75 LEYDETRKRIQIIQTQLADL 94
E RI+ ++ QL L
Sbjct: 250 ---SELDGRIEALEKQLDAL 266
>gnl|CDD|234342 TIGR03752, conj_TIGR03752, integrating conjugative element protein,
PFL_4705 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida toluene catabolic TOL plasmid pWWO_p085. Usually,
however, they are found on the bacterial main chromosome
in regions flanked by markers of conjugative transfer
and/or transposition [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 472
Score = 26.5 bits (59), Expect = 5.8
Identities = 12/67 (17%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 36 RDRVSRLKRELEQIRTEMNYTQRGLVPMGTRL-----AEMARMRLEYDETRKRIQIIQTQ 90
R R+++L E E ++ E Q+ + ++ +E + E ++ + Q +Q
Sbjct: 72 RKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGL 131
Query: 91 LADLEEK 97
+ L+ +
Sbjct: 132 IDQLQRR 138
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 26.5 bits (59), Expect = 5.9
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 3/74 (4%)
Query: 36 RDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQLADLE 95
+ V LK++LE E +Q L + + E +E ++ ++ QL L+
Sbjct: 148 QQEVLTLKQQLELQAREKAQSQALAEAQQQELVALEGLAAELEEKQQE---LEAQLEQLQ 204
Query: 96 EKVTPGQAESDKDR 109
EK E + R
Sbjct: 205 EKAAETSQERKQKR 218
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 26.1 bits (57), Expect = 6.7
Identities = 20/125 (16%), Positives = 42/125 (33%), Gaps = 18/125 (14%)
Query: 15 SSSSASTKYDVDLLKSDVALARDRVSRLKRELEQIRTEMNYTQRGLVPMGTR-------- 66
+ + S + +D ++ + R + + E TE + L
Sbjct: 66 NRNLRSGVFQLDDIRPQLRALRTELGTAQGEKRAAETEREAARSELQKARQEREAVRQEL 125
Query: 67 ----------LAEMARMRLEYDETRKRIQIIQTQLADLEEKVTPGQAESDKDRLILFQEK 116
E+AR+ + + + R++ + Q LE + QA + + Q K
Sbjct: 126 AAARQNLAKAQQELARLTKQAQDLQTRLKTLAEQRRQLEAQAQSLQASQKQLQASATQLK 185
Query: 117 EQLLR 121
Q+L
Sbjct: 186 SQVLD 190
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 26.1 bits (58), Expect = 7.4
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 28 LKSDVALARDRVSRLKRELEQIR 50
L++D R R+++LKRELE +
Sbjct: 155 LETDRRRIRRRIAKLKRELENVE 177
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 26.3 bits (58), Expect = 8.0
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 66 RLAEMARMRLEYDETRKRIQIIQTQLADLEEKVT 99
L + D+ R+RI ++ LA EE+V
Sbjct: 741 LLQNIKEKLQAADDLRQRIAAMERDLARFEEEVE 774
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 26.2 bits (58), Expect = 8.5
Identities = 14/74 (18%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 37 DRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQLADLEE 96
+R++ L+ EL ++ E+ + E + E++E R+ ++ ++ ++ DL E
Sbjct: 206 ERLNGLESELAELDEEIERYEEQREQARETRDEADEVLEEHEERREELETLEAEIEDLRE 265
Query: 97 KVTPGQAESDKDRL 110
+ + E +++ L
Sbjct: 266 TIA--ETEREREEL 277
>gnl|CDD|234345 TIGR03755, conj_TIGR03755, integrating conjugative element protein,
PFL_4711 family. Members of this protein family are
found in genomic regions associated with conjugative
transfer and integrated TOL-like plasmids. The specific
function is unknown [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 418
Score = 25.7 bits (57), Expect = 8.6
Identities = 11/62 (17%), Positives = 25/62 (40%), Gaps = 10/62 (16%)
Query: 38 RVSRLKRELEQIRTEMNYTQRGLV---PM------GTRLAEMARMRLEYDETRKRIQIIQ 88
+ +L RE+ ++TE+ ++ L + R A + + D KR+ ++
Sbjct: 358 AIDKLDREINNLKTELE-LRKELASNTALTILQRHHARRASSSPGIEQQDPDPKRLNDLR 416
Query: 89 TQ 90
Sbjct: 417 VP 418
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 25.8 bits (57), Expect = 9.3
Identities = 13/63 (20%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 36 RDRVSRLKRELEQIRTEMNYTQRGLVPMGTRLAEMARMRLEYDETRKRIQIIQTQLADLE 95
+++ + +ELE+++ E+ ++ L + ++ + E +RI+ ++ ++ +LE
Sbjct: 223 LEKLEKEVKELEELKEEIEELEKEL---ESLEGSKRKLEEKIRELEERIEELKKEIEELE 279
Query: 96 EKV 98
EKV
Sbjct: 280 EKV 282
>gnl|CDD|191851 pfam07798, DUF1640, Protein of unknown function (DUF1640). This
family consists of sequences derived from hypothetical
eukaryotic proteins. A region approximately 100 residues
in length is featured.
Length = 177
Score = 25.7 bits (57), Expect = 9.5
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 27 LLKSDVALARDRVSRLKRELEQIRTEMNY-TQRGLVPMGTRL---AEMARMRLEYDETRK 82
L KS+ A + +LK +LE+++ + + V G RL E R+R E E
Sbjct: 70 LEKSEFANLQAENEKLKNDLEKLKNRLRDEITK--VTAGVRLDLNLEKGRIREESAEQEL 127
Query: 83 RIQIIQTQL 91
+I+ T++
Sbjct: 128 KIKETDTKI 136
>gnl|CDD|179566 PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated.
Length = 380
Score = 25.9 bits (57), Expect = 9.6
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 68 AEMARMRLEYDETRKRIQIIQTQLADLEEKVT 99
A A R+++ E R Q+IQ + A + K+
Sbjct: 260 ARYANQRVQFGEAIGRFQLIQEKFAHMAIKLN 291
>gnl|CDD|238111 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A';
bacterial DNA topoisomerase IV (C subunit, ParC),
bacterial DNA gyrases (A subunit, GyrA),mammalian DNA
toposiomerases II. DNA topoisomerases are essential
enzymes that regulate the conformational changes in DNA
topology by catalysing the concerted breakage and
rejoining of DNA strands during normal cellular growth.
Length = 445
Score = 25.6 bits (57), Expect = 9.9
Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 13/73 (17%)
Query: 37 DRVSRLKRELEQIRTEM--NYTQRGLVPMG---------TRLAEMARMRL--EYDETRKR 83
D V L R ++ + + + G + RL ++ R +L E E
Sbjct: 361 DEVINLIRSSDEAKKALIEELEKLGFSEIQADAILDMRLRRLTKLEREKLLKELKELEAE 420
Query: 84 IQIIQTQLADLEE 96
I+ ++ LA E
Sbjct: 421 IEDLEKILASEER 433
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 25.5 bits (57), Expect = 10.0
Identities = 8/17 (47%), Positives = 15/17 (88%)
Query: 34 LARDRVSRLKRELEQIR 50
L R+R+++LK+ELE++
Sbjct: 158 LIRERIAQLKKELEKVE 174
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 0.132 0.360
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,886,475
Number of extensions: 619666
Number of successful extensions: 1213
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1163
Number of HSP's successfully gapped: 202
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.7 bits)