RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6810
(168 letters)
>gnl|CDD|191268 pfam05405, Mt_ATP-synt_B, Mitochondrial ATP synthase B chain
precursor (ATP-synt_B). The Fo sector of the ATP
synthase is a membrane bound complex which mediates
proton transport. It is composed of nine different
polypeptide subunits (a, b, c, d, e, f, g F6, A6L).
Length = 163
Score = 86.2 bits (214), Expect = 6e-22
Identities = 35/106 (33%), Positives = 61/106 (57%), Gaps = 1/106 (0%)
Query: 58 NDKLASLKGAIENELWNQERSKAQAVLYEAKRENIQMQLEAVFRERALFAYQQVKNRLEY 117
N +LK IE Q + VL+E +E + ++ EA RE Y+++K++L+
Sbjct: 58 NLHEKALKERIEYVKKLQSLVEETKVLFEVSKETVALEAEAFERELQAALYREIKSKLDT 117
Query: 118 QAALESIQRRISQKHMVSWVVSHVLKSITPDQ-DKQSIKKCISDLK 162
ES R+ Q H+V+WV+S VLK ++P Q K+++++ I+DL+
Sbjct: 118 LVRKESSVRQREQDHLVNWVISSVLKELSPPQFQKKTLQESIADLE 163
>gnl|CDD|224128 COG1207, GlmU, N-acetylglucosamine-1-phosphate uridyltransferase
(contains nucleotidyltransferase and I-patch
acetyltransferase domains) [Cell envelope biogenesis,
outer membrane].
Length = 460
Score = 29.1 bits (66), Expect = 1.1
Identities = 12/28 (42%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 111 VKNRLEYQAALESI-QRRISQKHMVSWV 137
V +R++ A E I QRRI++K M++ V
Sbjct: 229 VNDRVQ-LAEAERIMQRRIAEKLMLAGV 255
>gnl|CDD|180537 PRK06348, PRK06348, aspartate aminotransferase; Provisional.
Length = 384
Score = 28.5 bits (64), Expect = 1.8
Identities = 9/33 (27%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 81 QAVLYEAK-RENIQMQLEAVFRERALFAYQQVK 112
+A +Y K R+ I ++ F++R +AY++++
Sbjct: 273 RAAIYALKHRDTIVPLIKEEFQKRLEYAYKRIE 305
>gnl|CDD|233897 TIGR02499, HrpE_YscL_not, type III secretion apparatus protein,
HrpE/YscL family. This model is related to pfam06188,
but is broader. pfam06188 describes HrpE-like proteins,
components of bacterial type III secretion systems
primarily in bacteria that infect plants. This model
includes also the homologous proteins of animal
pathogens, such as YscL of Yersinia pestis. This model
excludes the related protein FliH of the bacterial
flagellar apparatus (see pfam02108) [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 166
Score = 27.3 bits (61), Expect = 3.7
Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 8/75 (10%)
Query: 79 KAQAVLYEAKR--ENIQMQLEAVFRERALFAYQQVKNRLEYQAALESIQRRISQ-----K 131
+AQA+L A++ E I E Y+Q + Q A + +
Sbjct: 14 QAQAILAAARQRAEAILADAEEEAEASRQLGYEQGLEQFW-QEAAAQLAEWQQEAEQLEA 72
Query: 132 HMVSWVVSHVLKSIT 146
+ + VL+++
Sbjct: 73 SLEERLAELVLQALE 87
>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 = 27.7 bits (62), Expect = 4.1
Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 6/84 (7%)
Query: 48 QSHRAGKIRTNDKLASLKGAIENELWNQERSKAQAVLYEAKRENIQMQLEAVFRERALFA 107
S R +L L+ E QE + L EA+ + +Q +LE + E
Sbjct: 396 ASLNNEIERLEARLERLEDRRER--LQQEIEELLKKLEEAELKELQAELEELEEELE--- 450
Query: 108 YQQVKNRLEYQAALESIQRRISQK 131
+ + + ALE ++ + +
Sbjct: 451 -ELQEELERLEEALEELREELEEA 473
>gnl|CDD|217606 pfam03543, Peptidase_C58, Yersinia/Haemophilus virulence surface
antigen.
Length = 203
Score = 27.1 bits (60), Expect = 4.5
Identities = 18/100 (18%), Positives = 30/100 (30%), Gaps = 11/100 (11%)
Query: 74 NQERSKAQAVLYEAKRENIQMQLEAVFRERALFAYQQVKNRLEYQAALESIQRRISQKHM 133
R+ + LY K ++QL + F +Q L+ S +
Sbjct: 51 GHARAAERQSLYSIK----KLQLLSRGAGAQFFQFQATDTWLQEAGLEPSGE--EKGLGS 104
Query: 134 VSWVVSH-----VLKSITPDQDKQSIKKCISDLKALAARA 168
V+ VS +LK+I + S A
Sbjct: 105 VAGTVSASNVSRLLKAILDTGSDHLLSLKFSINGEGGGHA 144
>gnl|CDD|236799 PRK10930, PRK10930, FtsH protease regulator HflK; Provisional.
Length = 419
Score = 27.1 bits (60), Expect = 4.9
Identities = 28/83 (33%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 67 AIENELWNQERSKAQAVLYEAKRENIQMQLEAVFRERALFAYQQVKNRLEYQAALESIQR 126
A NE+ + +AQ +L EA+ Q LEA E A FA K EY+AA E +
Sbjct: 270 AYTNEVQPRANGQAQRILEEARAYKAQTILEAQ-GEVARFA----KLLPEYKAAPEITRE 324
Query: 127 RISQKHMVSWVVSHVLKSITPDQ 149
R+ + M V+ H K + D+
Sbjct: 325 RLYIETMEK-VLGHTRKVLVNDK 346
>gnl|CDD|204512 pfam10557, Cullin_Nedd8, Cullin protein neddylation domain. This
is the neddylation site of cullin proteins which are a
family of structurally related proteins containing an
evolutionarily conserved cullin domain. With the
exception of APC2, each member of the cullin family is
modified by Nedd8 and several cullins function in
Ubiquitin-dependent proteolysis, a process in which the
26S proteasome recognises and subsequently degrades a
target protein tagged with K48-linked poly-ubiquitin
chains. Cullins are molecular scaffolds responsible for
assembling the ROC1/Rbx1 RING-based E3 ubiquitin
ligases, of which several play a direct role in
tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like
protein, which was originally found to be conjugated to
Cdc53, a cullin component of the SCF
(Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in
Saccharomyces cerevisiae, and Nedd8 modification has now
emerged as a regulatory pathway of fundamental
importance for cell cycle control and for embryogenesis
in metazoans. The only identified Nedd8 substrates are
cullins. Neddylation results in covalent conjugation of
a Nedd8 moiety onto a conserved cullin lysine residue.
Length = 68
Score = 24.8 bits (55), Expect = 8.2
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 113 NRLEYQAALESI---QRRISQKHMVSWVVSHVLKSITPDQDKQSIKKCISDL 161
+LE QAA+ I ++ +S +V+ V+ + K P IKK I L
Sbjct: 5 RKLEIQAAIVRIMKSRKTLSHNELVAEVIEQLKKRFPPS--VADIKKRIESL 54
>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal
domain. This domain is found in a number of different
types of plant proteins including NAM-like proteins.
Length = 147
Score = 25.8 bits (57), Expect = 8.5
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 51 RAGKIRTNDKLASLKGAIENELWNQERSKAQAVLYEAKRENIQM-QLEA 98
+A + DKL + K E E +ER E +R ++ + EA
Sbjct: 67 KAKEKLRRDKLKAKKEEAEKEKEKEERFMKALAEAEKERAELEKKKAEA 115
>gnl|CDD|99916 cd05533, POLBc_delta, DNA polymerase type-B delta subfamily
catalytic domain. Three DNA-dependent DNA polymerases
type B (alpha, delta, and epsilon) have been identified
as essential for nuclear DNA replication in eukaryotes.
Presently, no direct data is available regarding the
strand specificity of DNA polymerase during DNA
replication in vivo. However, mutation analysis supports
the hypothesis that DNA polymerase delta is the enzyme
responsible for both elongation and maturation of
Okazaki fragments on the lagging strand.
Length = 393
Score = 26.5 bits (59), Expect = 9.0
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 133 MVSWVVSHVLKSITPDQDKQS----IKKCISDL 161
+V VV L I ++D + +K ISDL
Sbjct: 258 LVQNVVETCLNKILIERDVEGAIEFVKGVISDL 290
>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 = 9.0
Identities = 13/77 (16%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 60 KLASLKGAIENELWNQERSKAQAVLYEAKRENIQMQLEAVFRERALFAYQ----QVKNRL 115
++ASL+ +I + E ++ + EA+ + + ++E + ER + + ++
Sbjct: 302 EIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEEL--EREIEEERKRRDKLTEEY 359
Query: 116 -EYQAALESIQRRISQK 131
E + LE ++ + +
Sbjct: 360 AELKEELEDLRAELEEV 376
>gnl|CDD|221188 pfam11725, AvrE, Pathogenicity factor. This family is secreted by
gram-negative Gammaproteobacteria such as Pseudomonas
syringae of tomato and the fire blight plant pathogen
Erwinia amylovora, amongst others. It is an essential
pathogenicity factor of approximately 198 kDa. Its
injection into the host-plant is dependent upon the
bacterial type III or Hrp secretion system. The family is
long and carries a number of predicted functional
regions, including an ERMS or endoplasmic reticulum
membrane retention signal at both the C- and the
N-termini, a leucine-zipper motif from residues 539-560,
and a nuclear localisation signal at 1358-1361. this
conserved AvrE-family of effectors is among the few that
are required for full virulence of many phytopathogenic
pseudomonads, erwinias and pantoeas.
Length = 1771
Score = 26.3 bits (58), Expect = 10.0
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 81 QAVLYEAKRENIQMQLEAVFRERALFAYQQVKNRLEYQAALESIQRRISQ------KHMV 134
A + E IQ QL+ + FA + V+N +Y+ AL S++R + + KH V
Sbjct: 1528 NAEYAKTPDEKIQAQLDGL---NEHFADKTVQNDDQYE-ALRSLKRLVVRQEAAVSKHSV 1583
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
0.320 0.128 0.368
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,198,531
Number of extensions: 711549
Number of successful extensions: 769
Number of sequences better than 10.0: 1
Number of HSP's gapped: 765
Number of HSP's successfully gapped: 44
Length of query: 168
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 78
Effective length of database: 6,945,742
Effective search space: 541767876
Effective search space used: 541767876
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 (21.9 bits)
S2: 55 (25.0 bits)