RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14454
(117 letters)
>gnl|CDD|236798 PRK10929, PRK10929, putative mechanosensitive channel protein;
Provisional.
Length = 1109
Score = 38.1 bits (89), Expect = 4e-04
Identities = 29/104 (27%), Positives = 52/104 (50%), Gaps = 9/104 (8%)
Query: 8 ENNSERESLEQELSNAKLLIERLERTQ-----RQEAARSQAELGSYKQRLDRADADL--L 60
++ +L+ E + K L++ LE Q RQE AR ++EL K+R + DA L L
Sbjct: 170 LAQAQLTALQAESAALKALVDELELAQLSANNRQELARLRSEL--AKKRSQQLDAYLQAL 227
Query: 61 HSRKENIRLTEQIANIEKELQMAKLSADDREDLLQDPKKDKELT 104
++ + R E +E +A+ S D + ++ K ++EL+
Sbjct: 228 RNQLNSQRQREAERALESTELLAEQSGDLPKSIVAQFKINRELS 271
>gnl|CDD|130187 TIGR01117, mmdA, methylmalonyl-CoA decarboxylase alpha subunit.
This model describes methymalonyl-CoA decarboxylase
aplha subunit in archaea and bacteria. Metylmalonyl-CoA
decarboxylase Na+ pump is a representative of a class of
Na+ transport decarboxylases that couples the energy
derived by decarboxylation of carboxylic acid substrates
to drive the extrusion of Na+ ion across the membrane
[Energy metabolism, ATP-proton motive force
interconversion, Energy metabolism, Fermentation,
Transport and binding proteins, Cations and iron
carrying compounds].
Length = 512
Score = 34.0 bits (78), Expect = 0.009
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 58 DLLHSRKENIRLTEQIANIEKELQMAKLSADDREDLLQDPKKDKELTSLIMDMDAKH 114
+ LH +KE I+ IEK+ K++A +R LL DP E +D KH
Sbjct: 4 EELHEKKEKIKQGGGEKRIEKQHAQGKMTARERLALLFDPGSFVE-----IDQFVKH 55
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 34.1 bits (79), Expect = 0.010
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 12 ERESLEQELSNAKLLIERLERTQR--QEAARSQAELGSYKQRLDRADADLLHSRKENIRL 69
+++ LE E KL+ + LE+T + R + E KQ+L +A A L ++ E L
Sbjct: 50 KQKLLEAE---DKLVQQDLEQTLALLDKIDRQKEETEQLKQQLAQAPAKLRQAQAELEAL 106
Query: 70 TEQIANIEKELQMAKLSADDREDLL 94
+ +E ++ LS E L
Sbjct: 107 KDDNDEETRE-TLSTLSLRQLESRL 130
>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 = 32.3 bits (74), Expect = 0.031
Identities = 19/101 (18%), Positives = 44/101 (43%), Gaps = 2/101 (1%)
Query: 16 LEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLHSRKENIRLTEQIAN 75
E L A+LL+E E Q+ E A A K D ++ ++ ++ +I+
Sbjct: 23 YELRLDLARLLLENEELKQKVEEALEGATNEDGKLAADLLKLEVARKKERLNQIRARISQ 82
Query: 76 IEKELQMAKLSADDREDLLQDPKKDKELTSLIMDMDAKHGR 116
+++E++ + ++ + L + D L+S ++ +
Sbjct: 83 LKEEIEQKRERIEELKRALAQRRSD--LSSASYQLEKRRAS 121
>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 = 29.2 bits (66), Expect = 0.33
Identities = 14/86 (16%), Positives = 37/86 (43%), Gaps = 1/86 (1%)
Query: 7 NENNSERESLEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLHSRKEN 66
E E L+++L+ + + L + + L R+ + A+ + +EN
Sbjct: 76 AELQEELAELQEQLAELQQENQEL-KQELSTLEAELERLQKELARIKQLSANAIELDEEN 134
Query: 67 IRLTEQIANIEKELQMAKLSADDRED 92
L E++A +++E + + + ++
Sbjct: 135 RELREELAELKQENEALEAENERLQE 160
Score = 26.1 bits (58), Expect = 4.7
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 1/81 (1%)
Query: 16 LEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLHSRKENIRLTEQIAN 75
L + LS+ ERL Q QE A Q EL +++L + ++E L ++
Sbjct: 54 LSRYLSDTPSARERLPELQ-QELAELQEELAELQEQLAELQQENQELKQELSTLEAELER 112
Query: 76 IEKELQMAKLSADDREDLLQD 96
++KEL K + + +L ++
Sbjct: 113 LQKELARIKQLSANAIELDEE 133
>gnl|CDD|217135 pfam02601, Exonuc_VII_L, Exonuclease VII, large subunit. This
family consist of exonuclease VII, large subunit
EC:3.1.11.6 This enzyme catalyzes exonucleolytic
cleavage in either 5'->3' or 3'->5' direction to yield
5'-phosphomononucleotides. This exonuclease VII enzyme
is composed of one large subunit and 4 small ones.
Length = 295
Score = 29.2 bits (66), Expect = 0.47
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 12 ERESLEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLHSRKENIRLTE 71
+R L Q+L + +RL R + + Q L ++RL LL +E +
Sbjct: 144 DRTELLQKLEGLE---QRLSRALKNRLEKEQDRLNLLRERLKSLSRRLLEQHEERLAELR 200
Query: 72 Q--IANIEKELQMAK 84
I++I+ L +
Sbjct: 201 DRLISSIQNLLSRKQ 215
>gnl|CDD|224482 COG1566, EmrA, Multidrug resistance efflux pump [Defense
mechanisms].
Length = 352
Score = 28.8 bits (65), Expect = 0.51
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 48 YKQRLDRADADLLHSRKENIRL----TEQIANIEK----ELQMAKLSADDREDLLQ 95
Y+ L++A+A L + + L A I + +L A+ + R +L Q
Sbjct: 89 YRAALEQAEAALAAAEAQLRNLRAQLASAQALIAQAEAQDLDQAQNELERRAELAQ 144
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 28.1 bits (63), Expect = 1.1
Identities = 22/92 (23%), Positives = 47/92 (51%)
Query: 5 LKNENNSERESLEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLHSRK 64
L E +E LE++LS +E L R+E A +AEL + L+ ++ +
Sbjct: 352 LLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEE 411
Query: 65 ENIRLTEQIANIEKELQMAKLSADDREDLLQD 96
RL+E++ ++++EL+ + ++ + L++
Sbjct: 412 RLERLSERLEDLKEELKELEAELEELQTELEE 443
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 27.7 bits (62), Expect = 1.4
Identities = 18/118 (15%), Positives = 49/118 (41%), Gaps = 3/118 (2%)
Query: 1 MSKLLKN---ENNSERESLEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADA 57
M KL K+ E N + ++L+ ++ + + I+ + ++ ++ + + + D
Sbjct: 168 MDKLNKDKIRELNQQIQTLDMKIDHIQQQIKTYNKNIEEQRKKNGENIARKQNKYDELVE 227
Query: 58 DLLHSRKENIRLTEQIANIEKELQMAKLSADDREDLLQDPKKDKELTSLIMDMDAKHG 115
+ + E LT+++ N+ +++ + + K E ++ M K G
Sbjct: 228 EAKTIKAEIEELTDELLNLVMDIEDPSAALNKLNTAAAKIKSKIEQFQKVIKMYEKGG 285
>gnl|CDD|237103 PRK12447, PRK12447, histidinol dehydrogenase; Reviewed.
Length = 426
Score = 27.6 bits (62), Expect = 1.6
Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 11/56 (19%)
Query: 38 AARSQAELGSYKQRLDRADADLLHSRKENIRLTEQIANIEKELQMAKLSADDREDL 93
AR A + Y ++ D+ + RL+ E + +AK+ +ED+
Sbjct: 34 EARGDAAVREYSRKFDKWS-------PGSFRLSAA----EIDAAVAKVPEQVKEDI 78
>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 = 27.7 bits (62), Expect = 1.7
Identities = 28/106 (26%), Positives = 42/106 (39%), Gaps = 12/106 (11%)
Query: 11 SERESLEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLHSRKENIRLT 70
+ SLE L + + E +E Q +Q+L + L +R E
Sbjct: 256 EQLLSLELRLQHLHGELVADEERLAEEQEERQEAKNRLRQQLRTLEDQLKEARDE----- 310
Query: 71 EQIANIEKELQMAKLSADDRE-DLLQDPKK---DKELTSLIMDMDA 112
N E AKL+AD E +LL+D K D ++ L D+D
Sbjct: 311 ---LNQELSAANAKLAADRSELELLEDQKGAFEDADIEQLQADLDQ 353
>gnl|CDD|172952 PRK14477, PRK14477, bifunctional nitrogenase molybdenum-cofactor
biosynthesis protein NifE/NifN; Provisional.
Length = 917
Score = 27.4 bits (61), Expect = 1.7
Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 8/91 (8%)
Query: 23 AKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLHSRKENIRLTEQIANIEKELQM 82
++L +R+E+ +E A+ +A L Y+ RL+ L + T + N +EL +
Sbjct: 289 KRVLQDRVEKLIAEEEAKCRAALAPYRARLEGKRVVLFTGGVK----TWSMVNALRELGV 344
Query: 83 AKLSADDREDLLQDPKKDKELTSLIMDMDAK 113
L+A + L+D + K L M DA
Sbjct: 345 EVLAAGTQNSTLEDFARMKAL----MHKDAH 371
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 27.4 bits (61), Expect = 1.9
Identities = 15/70 (21%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 15 SLEQELSNAKLLIERLERT---QRQEAARSQAELGSYKQRLDRADADLLHSRKENIRLTE 71
+ +++L + I LE+ Q+ + A+ + +L S + + +A L+ + + +L +
Sbjct: 35 ADDKQLKQIQKEIAALEKKIREQQDQRAKLEKQLKSLETEIASLEAQLIETADDLKKLRK 94
Query: 72 QIANIEKELQ 81
QIA++ L
Sbjct: 95 QIADLNARLN 104
>gnl|CDD|181719 PRK09239, PRK09239, chorismate mutase; Provisional.
Length = 104
Score = 26.5 bits (59), Expect = 2.1
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 37 EAARSQAELGSYKQRLDRADADLLHSRKENIRLTEQI 73
E AR+ AEL + +Q +D DA L+H E + T+ +
Sbjct: 4 EQARAPAELAALRQSIDNIDAALIHMLAERFKCTQAV 40
>gnl|CDD|148759 pfam07334, IFP_35_N, Interferon-induced 35 kDa protein (IFP 35)
N-terminus. This family represents the N-terminus of
interferon-induced 35 kDa protein (IFP 35)
(approximately 80 residues long), which contains a
leucine zipper motif in an alpha helical configuration.
This family also includes N-myc-interactor (Nmi), a
homologous interferon-induced protein.
Length = 76
Score = 26.0 bits (57), Expect = 2.5
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 64 KENIRLTEQIANIEKELQMAKLSADDRED 92
KENI+L E+I +E ELQ +ED
Sbjct: 7 KENIQLKEEIQKLEAELQQLTREFQIKED 35
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 26.4 bits (59), Expect = 4.1
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 4/83 (4%)
Query: 6 KNENNSERESLEQELSNAKLLIERLER--TQRQEAARSQAELGSYKQR-LDRADADLLHS 62
K E + R LE+EL + ++RLER QR+E + E K+ L++ + +L +
Sbjct: 57 KEEVHKLRAELERELKERRNELQRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNK 116
Query: 63 RKENIRLTEQIANIEKELQMAKL 85
K E++ + E Q +L
Sbjct: 117 EKNLDEKEEELEELIAE-QREEL 138
>gnl|CDD|181657 PRK09116, PRK09116, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 405
Score = 26.5 bits (59), Expect = 4.1
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 25 LLIERLERTQRQEAARSQAELGSYKQRLDRADADLLHSRKENIRLTEQIANIEKELQMAK 84
L++E LE + + A AE+ + ++D H + T QIA +E L+ A
Sbjct: 238 LVLEELEHAKAR-GATIYAEIVGFG-----TNSDGAHVTQPQ-AETMQIA-MELALKDAG 289
Query: 85 LSADD 89
L+ +D
Sbjct: 290 LAPED 294
>gnl|CDD|189014 cd09607, M3B_PepF_2, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 581
Score = 26.3 bits (59), Expect = 4.3
Identities = 26/102 (25%), Positives = 43/102 (42%), Gaps = 7/102 (6%)
Query: 3 KLLKNENNSERESLEQELSNAKLLIERLER--TQRQEAARSQAELGSYKQRLDRADAD-- 58
K LK + + L+ L + + +E LE T QE LG++ L AD
Sbjct: 20 KKLKQLIDELKSLLDALLPSDEDAVETLEALITLLQELLELLRTLGAFVSCLLSADTTDE 79
Query: 59 ---LLHSRKENIRLTEQIANIEKELQMAKLSADDREDLLQDP 97
L S+ + + + + ++A LS +D + LL DP
Sbjct: 80 EAQALLSQLNQLSASLEQLLTLLDKKLAALSEEDLDALLADP 121
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 26.1 bits (58), Expect = 4.8
Identities = 25/104 (24%), Positives = 45/104 (43%), Gaps = 7/104 (6%)
Query: 2 SKLLKNENNSERESLEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLH 61
L+ + E + LE+EL+ ++ E LER Q ++ + E+ +L L
Sbjct: 392 RVRLEIDKPEELDELERELAQLEIEKEALEREQDEKEKKLIDEI----IKLKEGRIPELE 447
Query: 62 SRKENIRLTEQIANIEKELQ---MAKLSADDREDLLQDPKKDKE 102
E + IA + +AKL D++E LL ++ K+
Sbjct: 448 KELEAEVDEDDIAEVVARWTGIPVAKLLEDEKEKLLNLERRLKK 491
>gnl|CDD|234005 TIGR02774, rexB_recomb, ATP-dependent nuclease subunit B. DNA
repair is accomplished by several different systems in
prokaryotes. Recombinational repair of double-stranded
DNA breaks involves the RecBCD pathway in some lineages,
and AddAB (also called RecAB) in other. The AddA protein
is conserved between the firmicutes and the
alphaproteobacteria, while the partner protein is not.
The partner may be designated AddB, as in Bacillus and
in alphaproteobacteria, or RexB as in Streptococcus and
Lactococcus. Note, however, that RexB proteins lack an
N-terminal GxxGxGK[ST] ATP-binding motif found in
Bacillus subtilis and related species, and this
difference may be important; this model represents
specifically RexB proteins as found in Streptococcus and
Lactococcus [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1076
Score = 26.3 bits (58), Expect = 5.0
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 52 LDRADADLLHSRKENIRLTEQIANIEKELQMAKLSADDREDLLQDPKKDKELTSLI 107
L+ D + K++ + +Q+ + KELQ ++LS D E+ L P K ++L ++
Sbjct: 96 LEPGDLKVYGRLKQDPQFIQQLVELYKELQKSQLSILDLEN-LTSPDKREDLLAIF 150
>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed.
Length = 438
Score = 25.9 bits (58), Expect = 5.2
Identities = 13/69 (18%), Positives = 31/69 (44%), Gaps = 5/69 (7%)
Query: 15 SLEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLHSRKENIRLTEQIA 74
+ L + L +RL R R+ + + L +RL + L ++++ +++
Sbjct: 261 DRAELLQRLQQLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLLAQQQ-----QRLD 315
Query: 75 NIEKELQMA 83
+++ LQ A
Sbjct: 316 RLQQRLQRA 324
>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 = 25.9 bits (57), Expect = 5.7
Identities = 15/94 (15%), Positives = 29/94 (30%)
Query: 2 SKLLKNENNSERESLEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLH 61
++ E + E A L + LE + +A L + L +L
Sbjct: 887 AESDAREAAEDAAEARAEAEEASLRLRTLEESVGAMVDEIRARLAETRAALASGGRELPR 946
Query: 62 SRKENIRLTEQIANIEKELQMAKLSADDREDLLQ 95
+ E E++ A + D+R +
Sbjct: 947 LAEALATAEEARGRAEEKRAEADATLDERAEARD 980
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 25.8 bits (58), Expect = 5.8
Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 13/92 (14%)
Query: 4 LLKNENNSERESLEQELSNAKLLIERLERTQ--RQEAARSQAELGSYKQRLDRAD----- 56
LLK + +R LE + I+RL R + A +A G+ + A+
Sbjct: 748 LLKGADAEDRARLEANEA----YIKRLARLESLEILADDEEAPEGAASAVVGGAELFLPL 803
Query: 57 ADLLHSRKENIRLTEQIANIEKELQM--AKLS 86
L+ E RL +++A +EKE++ KLS
Sbjct: 804 EGLIDVEAELARLEKELAKLEKEIERVEKKLS 835
>gnl|CDD|184699 PRK14478, PRK14478, nitrogenase molybdenum-cofactor biosynthesis
protein NifE; Provisional.
Length = 475
Score = 25.8 bits (57), Expect = 6.6
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 26 LIERLERTQRQEAARSQAELGSYKQRL 52
L+ER E +E A++ A L Y+ RL
Sbjct: 296 LVERTEALIAEEEAKAWAALEPYRPRL 322
>gnl|CDD|233894 TIGR02492, flgK_ends, flagellar hook-associated protein FlgK. The
flagellar hook-associated protein FlgK of bacterial
flagella has conserved N- and C-terminal domains. The
central region is highly variable in length and
sequence, and often contains substantial runs of
low-complexity sequence. This model is built from an
alignment of FlgK sequences with the central region
excised. Note that several other proteins of the
flagellar apparatus also are homologous in the N- and
C-terminal regions to FlgK, but are excluded from this
model [Cellular processes, Chemotaxis and motility].
Length = 324
Score = 25.8 bits (57), Expect = 6.8
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 68 RLTEQIANIEKELQMAKLSADDREDLL-QDPKKDKELTSLI 107
L +QIA++ KE++ + S D DLL Q KEL+ LI
Sbjct: 170 SLLKQIASLNKEIKQVEASGQDANDLLDQRDLLLKELSQLI 210
>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional.
Length = 428
Score = 25.4 bits (56), Expect = 8.1
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 10 NSERESLEQELSNAK-LLIERLERTQRQEAARS--QAELGSYKQRLDRADADLLHSRKEN 66
+++ LE++ S K LL E+ + Q+ E AR+ + L + L + L R
Sbjct: 183 AAQKAELEEKQSQQKTLLYEQQAQQQKLEQARNERKKTLTGLESSLQKDQQQLSELRANE 242
Query: 67 IRLTEQIANIEKE 79
RL + IA E+E
Sbjct: 243 SRLRDSIARAERE 255
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 25.5 bits (57), Expect = 8.1
Identities = 16/87 (18%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 6 KNENNSERESLEQELSNAKLLIERLERTQRQEAARSQAELGSYKQRLDRADADLLHSRKE 65
K E + R E+EL + +++LE+ Q+ ++ LDR L +E
Sbjct: 63 KEEIHKLRNEFEKELRERRNELQKLEKRLLQK-----------EENLDRKLELLEKREEE 111
Query: 66 NIRLTEQIANIEKELQMAKLSADDRED 92
+ +++ ++EL+ + ++ +
Sbjct: 112 LEKKEKELEQKQQELEKKEEELEELIE 138
>gnl|CDD|225148 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain)
[Inorganic ion transport and metabolism].
Length = 451
Score = 25.3 bits (56), Expect = 9.2
Identities = 23/113 (20%), Positives = 47/113 (41%), Gaps = 16/113 (14%)
Query: 1 MSKLLKNENNSERESLEQELSNAKL--LIERLERTQRQEAARSQAELGSYKQRLDRADAD 58
+ LL++++ S L L A + ++E L +R ++ A+
Sbjct: 12 LIDLLEDKDLSVLRKLLARLHPADVAEILEELPGRERVVV---------WRLLPKEDAAE 62
Query: 59 LLHSRKENIRLT--EQIANIEKELQMAKLSADDREDLLQD---PKKDKELTSL 106
+L + +R E +++ E + +L DD DLL + +D+ L+ L
Sbjct: 63 VLGELDDEVREEIIEALSDEELAAAIEELDIDDAADLLDELPDEVRDELLSLL 115
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 25.3 bits (56), Expect = 9.4
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 57 ADLLHSRKENIRLTEQIANIEKELQMA--KLS 86
A L+ E RL +++ +EKE+ KLS
Sbjct: 807 AGLIDLAAELARLEKELEKLEKEIDRIEKKLS 838
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
0.308 0.125 0.312
Gapped
Lambda K H
0.267 0.0865 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,669,341
Number of extensions: 504638
Number of successful extensions: 1267
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1176
Number of HSP's successfully gapped: 412
Length of query: 117
Length of database: 10,937,602
Length adjustment: 80
Effective length of query: 37
Effective length of database: 7,389,282
Effective search space: 273403434
Effective search space used: 273403434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (23.9 bits)