RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14379
(120 letters)
>gnl|CDD|217962 pfam04201, TPD52, Tumour protein D52 family. The hD52 gene was
originally identified through its elevated expression
level in human breast carcinoma. Cloning of D52
homologues from other species has indicated that D52 may
play roles in calcium-mediated signal transduction and
cell proliferation. Two human homologues of hD52, hD53
and hD54, have also been identified, demonstrating the
existence of a novel gene/protein family. These proteins
have an amino terminal coiled-coil that allows members
to form homo- and heterodimers with each other.
Length = 162
Score = 54.2 bits (130), Expect = 3e-10
Identities = 28/67 (41%), Positives = 43/67 (64%), Gaps = 4/67 (5%)
Query: 52 LSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDDLTQS 111
LS E+E+ + E LA++EEEI+TL+ VLA+K K +LK+KLG T E ++++S
Sbjct: 26 LSEAEKEELRTE----LAKLEEEISTLRQVLAAKEKHLAELKRKLGLTPLSELKQNISKS 81
Query: 112 IKNVKET 118
+V T
Sbjct: 82 WHDVTAT 88
>gnl|CDD|223266 COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), A subunit [DNA replication,
recombination, and repair].
Length = 804
Score = 30.3 bits (69), Expect = 0.21
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 5/59 (8%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 107
L+ L+ E+EK + E +EL E+EI L+ +LAS+ + +KK+L K F D+
Sbjct: 428 LRRLTGLEEEKIEKEL-KEL---EKEIADLEKILASEERLLDIIKKELLEIKKK-FGDE 481
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 29.3 bits (66), Expect = 0.41
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 50 QNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKK 95
EQ+ Q+A+ ++L +E EI +L+ L +TA DLKK
Sbjct: 50 LEKKIREQQDQRAKLEKQLKSLETEIASLEAQL---IETADDLKKL 92
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 29.3 bits (66), Expect = 0.51
Identities = 13/88 (14%), Positives = 32/88 (36%), Gaps = 5/88 (5%)
Query: 12 PKCCLEMQDVLTIIRSFHVVGEEANNLDLSPDSGINDLQNLSPEEQEKQKAEWTQELAR- 70
+ C E++ L + S + + L G D+ +++ + +
Sbjct: 30 VRRCDEVERKLRKLESK----IKKLGIPLKDTGGKPDVPPSKEFLDLEEEILDLEAEIKE 85
Query: 71 VEEEINTLKHVLASKTKTAQDLKKKLGF 98
VEE + +L+ + + L ++ F
Sbjct: 86 VEENLESLEKEINELEEWLNVLDEEKSF 113
>gnl|CDD|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell
envelope biogenesis, outer membrane].
Length = 835
Score = 28.5 bits (64), Expect = 0.77
Identities = 10/64 (15%), Positives = 22/64 (34%), Gaps = 16/64 (25%)
Query: 55 EEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDDLTQSIKN 114
+++ + +Q L + E +N L + D + L QS +
Sbjct: 61 QQELAINDQLSQALNQQTERLNAL---------ASDDRQL-------ANLLLQLLQSSRT 104
Query: 115 VKET 118
++E
Sbjct: 105 IREQ 108
>gnl|CDD|145928 pfam03040, CemA, CemA family. Members of this family are probable
integral membrane proteins. Their molecular function is
unknown. CemA proteins are found in the inner envelope
membrane of chloroplasts but not in the thylakoid
membrane. A cyanobacterial member of this family has
been implicated in CO2 transport, but is probably not a
CO2 transporter itself. They are predicted to be
haem-binding however this has not been proven
experimentally.
Length = 230
Score = 28.3 bits (64), Expect = 0.80
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 43 DSGINDLQNLSPEEQEKQKAEWTQELARV--EEEINTLKHVLA 83
D I + S +E + + ELA++ EE I + ++L
Sbjct: 71 DELIKESPPTSLQELRIEIHKKAIELAKIYNEESIQAILNLLT 113
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 27.0 bits (61), Expect = 2.5
Identities = 10/25 (40%), Positives = 20/25 (80%), Gaps = 1/25 (4%)
Query: 56 EQEKQK-AEWTQELARVEEEINTLK 79
E+E++K AE+ ++LA+++E + LK
Sbjct: 849 EKEREKLAEYEEKLAKLKERLARLK 873
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 27.1 bits (61), Expect = 2.6
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTK 87
L+ L+ EE EK + E + +E+EI L+ +LAS+ K
Sbjct: 386 LRRLTKEEIEKLEKE----IEELEKEIAELEKILASEKK 420
>gnl|CDD|182904 PRK11020, PRK11020, hypothetical protein; Provisional.
Length = 118
Score = 26.1 bits (58), Expect = 3.2
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 62 AEWTQELARVEEEINTLKHVLASKT-KTAQDLKK 94
A++ +E A +E EI LK V + K K AQ L K
Sbjct: 34 AQFEKEKATLEAEIARLKEVQSQKLSKEAQKLMK 67
>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 = 26.6 bits (59), Expect = 3.7
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 55 EEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKL 96
EE+ K++ + T+E A ++EE+ L+ L K + + +L
Sbjct: 346 EEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDEL 387
>gnl|CDD|147038 pfam04682, Herpes_BTRF1, Herpesvirus BTRF1 protein conserved
region. Herpesvirus protein.
Length = 256
Score = 26.5 bits (59), Expect = 4.0
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 36 NNLDLSPDSGINDLQNL 52
N+L PD IN LQ+L
Sbjct: 96 NSLRFLPDLDINPLQHL 112
>gnl|CDD|237054 PRK12316, PRK12316, peptide synthase; Provisional.
Length = 5163
Score = 26.5 bits (58), Expect = 4.1
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 42 PDSGINDLQNLSPEEQEKQKAEWTQELAR 70
P + +LQ L EQ++ A W + A
Sbjct: 4518 PQRRLGELQLLEKAEQQRIVALWNRTDAG 4546
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 26.2 bits (58), Expect = 4.6
Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 55 EEQEKQKAEWTQELARVEEEINTLKHVLASKTK-----TAQDLKKKLGFTVWKEFNDDLT 109
+ E Q E + L+ E E+ L+ L ++ T + +K L + E ++
Sbjct: 101 DNLENQLEEREKALSARELELEELEKQLDNELYRVAGLTPEQARKLLLKLLDAELEEEKA 160
Query: 110 QSIKNVKE 117
Q +K ++E
Sbjct: 161 QRVKKIEE 168
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 26.4 bits (59), Expect = 5.0
Identities = 16/92 (17%), Positives = 34/92 (36%), Gaps = 17/92 (18%)
Query: 17 EMQDVLTIIRSFHVVGEEANNLDLSPDSGINDLQNLSPEEQEKQKAEWTQELARVEEEIN 76
+VL + VV +++L E ++ + L ++ E ++
Sbjct: 17 YKDEVLEALHELGVV----------------HIEDLKEELSNERLRKLRSLLTKLSEALD 60
Query: 77 TLKHVLASKTKTAQDLKKKLGFTVWKEFNDDL 108
L+ L K ++ KKK+ +E D+
Sbjct: 61 KLRSYL-PKLNPLREEKKKVSVKSLEELIKDV 91
>gnl|CDD|219690 pfam07996, T4SS, Type IV secretion system proteins. Members of
this family are components of the type IV secretion
system. They mediate intracellular transfer of
macromolecules via a mechanism ancestrally related to
that of bacterial conjugation machineries.
Length = 195
Score = 25.8 bits (57), Expect = 5.1
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 56 EQEKQKAEWTQELARVEEEINTLKHVLASKTKT 88
+ +Q A+W Q+L +++++I K S T +
Sbjct: 16 QSLQQLAQWAQQLDQLKQQIQQAKQQYNSITGS 48
>gnl|CDD|193529 cd05652, M20_ArgE_DapE_like_fungal, M20 Peptidases with similarity
to acetylornithine deacetylases and
succinyl-diaminopimelate desuccinylases. Peptidase M20
family, Uncharacterized protein subfamily with
similarity to acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze
analogous reactions and share a common activator, the
metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad
range of substrates, including N-acetylornithine,
alpha-N-acetylmethionine and alpha-N-formylmethionine,
while DapE catalyzes the hydrolysis of
N-succinyl-L,L-diaminopimelate (L,L-SDAP) to
L,L-diaminopimelate and succinate. Proteins in this
subfamily are mostly fungal, and have been inferred by
homology as being related to both ArgE and DapE.
Length = 335
Score = 26.0 bits (58), Expect = 5.4
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 8/26 (30%)
Query: 30 VVGEE--------ANNLDLSPDSGIN 47
VVGEE AN+L L ++ I
Sbjct: 121 VVGEETGGDGMKAANDLGLGWEAVIF 146
>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 = 26.0 bits (58), Expect = 6.1
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 4/48 (8%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKL 96
L+ L+ E+EK +EL +E EI L+ +LAS+ + K++L
Sbjct: 399 LRRLTKLEREK----LLKELKELEAEIEDLEKILASEERPKDLWKEEL 442
>gnl|CDD|223001 PHA03148, PHA03148, hypothetical protein; Provisional.
Length = 289
Score = 25.8 bits (57), Expect = 6.3
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 3 NIHIKHPIIPKCCLEMQDVLTIIRSFHVVGEEANNLDLSPDSGINDLQNL 52
I +K P + C + +TI+ H N+L L P IN LQ+L
Sbjct: 102 AISLKTPKLGNCPAAPYNTVTIMNRSH------NSLRLVPSLDINPLQHL 145
>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 = 25.8 bits (57), Expect = 6.6
Identities = 16/64 (25%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 33 EEANNLDLSPDSGINDLQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDL 92
+ N+ L I +L+ EE E++ AE + LA + +E+ L+ L K ++L
Sbjct: 666 AKTNSSILERRREIEELEEKI-EELEEKIAELEKALAELRKELEELEEELEQLRKELEEL 724
Query: 93 KKKL 96
+++
Sbjct: 725 SRQI 728
>gnl|CDD|233256 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV [DNA metabolism, DNA
replication, recombination, and repair].
Length = 800
Score = 25.7 bits (57), Expect = 6.6
Identities = 16/59 (27%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 107
LQ L+ E+EK + +E + E I L+ +LAS+ + + ++++L + ++F D
Sbjct: 421 LQRLTGLEREKLQ----EEYKELLELIADLEDILASEERVLEIIREEL-EEIKEQFGDP 474
>gnl|CDD|150365 pfam09677, TrbI_Ftype, Type-F conjugative transfer system protein
(TrbI_Ftype). This entry represents TrbI, an essential
component of the F-type conjugative transfer system for
plasmid DNA transfer that has been shown to be
localized to the periplasm.
Length = 111
Score = 25.2 bits (55), Expect = 6.6
Identities = 3/34 (8%), Positives = 10/34 (29%)
Query: 50 QNLSPEEQEKQKAEWTQELARVEEEINTLKHVLA 83
+ L +++ + L + H +
Sbjct: 52 KELDEAQRKALSTRFNTALEDSLQAYQQQHHAVI 85
>gnl|CDD|218827 pfam05960, DUF885, Bacterial protein of unknown function
(DUF885). This family consists of several hypothetical
bacterial proteins several of which are putative
membrane proteins.
Length = 539
Score = 25.8 bits (57), Expect = 7.4
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEE 73
L +LSPE + A LA +E
Sbjct: 17 LDDLSPEALAARLAALRALLAELEA 41
>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 = 25.4 bits (56), Expect = 7.5
Identities = 10/42 (23%), Positives = 22/42 (52%)
Query: 55 EEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKL 96
E +++ AE +ELA ++E++ L+ + L+ +L
Sbjct: 69 PELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAEL 110
>gnl|CDD|219186 pfam06810, Phage_GP20, Phage minor structural protein GP20. This
family consists of several phage minor structural
protein GP20 sequences of around 180 residues in length.
The function of this family is unknown.
Length = 156
Score = 25.4 bits (56), Expect = 7.5
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 66 QELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDDLTQSIKNVKE 117
+L + EE ++LK L ++ K +DLKKK+ N++L + I+ +K+
Sbjct: 20 SKLDKANEERDSLKKQLKNRDKQIEDLKKKVK------DNEELQKKIEKLKQ 65
>gnl|CDD|222469 pfam13949, ALIX_LYPXL_bnd, ALIX V-shaped domain binding to HIV.
The binding of the LYPxL motif of late HIV p6Gag and
EIAV p9Gag to this domain is necessary for viral
budding.This domain is generally central between an
N-terminal Bro1 domain, pfam03097 and a C-terminal
proline-rich domain. The retroviruses thus used this
domain to hijack the ESCRT system of the cell.
Length = 292
Score = 25.7 bits (57), Expect = 7.9
Identities = 15/77 (19%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 43 DSGINDLQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWK 102
+L+ L P + E +++++R+ E +N L + A + K ++LK+K
Sbjct: 118 SGPEEELEALLPSSSPSKTPEVSEQISRLRELLNKLNELKAEREKLLEELKEKAQ----- 172
Query: 103 EFNDDLTQSIKNVKETQ 119
+DD+++ + + +
Sbjct: 173 --DDDISKLLIALNKLG 187
>gnl|CDD|222997 PHA03132, PHA03132, thymidine kinase; Provisional.
Length = 580
Score = 25.5 bits (56), Expect = 8.0
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 11/58 (18%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTL---KHVLASKTKTAQDLKKKLGFTVWKE 103
LQ +PE+ + T I T+ +A K TA+ L K F ++
Sbjct: 452 LQYFTPEDIVQVCLGTTT--------ITTVCHSSGTVAIKHLTAEKLWKNSIFNTLRD 501
>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in
cell division proteins which are required for
kinetochore-spindle association.
Length = 321
Score = 25.4 bits (56), Expect = 9.0
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 3/54 (5%)
Query: 46 INDLQNLSPEEQEKQKAEWT---QELARVEEEINTLKHVLASKTKTAQDLKKKL 96
I L+ L+ E E QEL + +I+ + L + Q+L +
Sbjct: 191 IASLRQLADELNLCDPLELEKARQELRSLSVKISEKRKQLEELQQELQELTIAI 244
>gnl|CDD|181731 PRK09257, PRK09257, aromatic amino acid aminotransferase;
Provisional.
Length = 396
Score = 25.5 bits (57), Expect = 9.1
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 61 KAEWTQELARVEEEINTLKHVLASKTKTA 89
+AEW EL + E I ++ +L K
Sbjct: 304 RAEWEAELEEMRERIKAMRQLLVEALKAK 332
>gnl|CDD|235503 PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
Length = 742
Score = 25.5 bits (57), Expect = 9.2
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 66 QELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 107
+E + +EI L+ +LAS+ K + +KK+L K+F D
Sbjct: 444 KEQDELRKEIAELEAILASERKLRKLIKKELK-ADAKKFGDP 484
>gnl|CDD|237192 PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
Length = 869
Score = 25.3 bits (56), Expect = 9.4
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 59 KQKAEWTQELARVEEEINTLKHVLASKTKTA----QDLKKKLG 97
KA+ + +AR+E EI +KH LA T A +LKKK G
Sbjct: 427 SDKAD--ELIARLEAEIAEVKHHLAHLTDYAIAYFTNLKKKYG 467
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
0.312 0.129 0.364
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,943,041
Number of extensions: 507503
Number of successful extensions: 809
Number of sequences better than 10.0: 1
Number of HSP's gapped: 800
Number of HSP's successfully gapped: 141
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)