RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8735
(115 letters)
>gnl|CDD|148614 pfam07106, TBPIP, Tat binding protein 1(TBP-1)-interacting protein
(TBPIP). This family consists of several eukaryotic
TBP-1 interacting protein (TBPIP) sequences. TBP-1 has
been demonstrated to interact with the human
immunodeficiency virus type 1 (HIV-1) viral protein Tat,
then modulate the essential replication process of HIV.
In addition, TBP-1 has been shown to be a component of
the 26S proteasome, a basic multiprotein complex that
degrades ubiquitinated proteins in an ATP-dependent
fashion. Human TBPIP interacts with human TBP-1 then
modulates the inhibitory action of human TBP-1 on
HIV-Tat-mediated transactivation.
Length = 169
Score = 33.8 bits (78), Expect = 0.009
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 2 DDKEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTI 61
D ++ +LK L+ +T E +++ EL+ E+ E + KLE L ++ E + +
Sbjct: 93 QDCSTLEIELKSLTSDLTTEELQEEIQELKKEVREIEEKLESLEEGWKPVTPEE--MEKV 150
Query: 62 TDTKEKMVKEYNKRKRMCT 80
+ + KE+ KRK++C
Sbjct: 151 KKEYKDLHKEWKKRKKLCN 169
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 32.6 bits (75), Expect = 0.035
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 2 DDKEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSR 46
D ++ K + +QL QQ+ +A AK ++A QAELE K ++ +R
Sbjct: 73 DKIDRQKEETEQLKQQLAQAPAKLRQA--QAELEALKDDNDEETR 115
>gnl|CDD|236277 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
Length = 819
Score = 29.7 bits (67), Expect = 0.29
Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 7/89 (7%)
Query: 26 KKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITDTKEKMVKEYNKRKRMCTEMLEA 85
++ + LEE K + K + +S E ++ + + E+ + + K+ + ++
Sbjct: 444 EEEAILKSLEEFKQSIVKEAA----LSILEEIREKVLEQAEQGCENQEEVKKEVPKKVKK 499
Query: 86 ILENYPKSKKILLEEVGIETDEMVSMEKL 114
I E +LLEE+GI + +E L
Sbjct: 500 IPE---VDTYLLLEELGINEETYEKLEAL 525
>gnl|CDD|172588 PRK14098, PRK14098, glycogen synthase; Provisional.
Length = 489
Score = 29.7 bits (67), Expect = 0.31
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 9/52 (17%)
Query: 56 VDKKTITDTKEKMVKEYNKRKRMCTEMLEAILENYPKSKKILLEEVGIETDE 107
+D + + +K++K KR E L+ LEN KK LLEEVG+ DE
Sbjct: 263 IDTRQWNPSTDKLIK-----KRYSIERLDGKLEN----KKALLEEVGLPFDE 305
>gnl|CDD|221268 pfam11853, DUF3373, Protein of unknown function (DUF3373). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 472 to 574 amino acids in
length.
Length = 485
Score = 29.4 bits (66), Expect = 0.34
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 20 EAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITD 63
+ + QK L+ EL E K++L+ L + V+ + +KK+ D
Sbjct: 26 DIDLLQKIEALKKELAELKAQLKDLQKRVD-----KTEKKSAGD 64
Score = 29.0 bits (65), Expect = 0.56
Identities = 10/44 (22%), Positives = 23/44 (52%)
Query: 1 MDDKEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKL 44
+ K++ L +++ E +A+ K + + + EKKS ++L
Sbjct: 23 AAADIDLLQKIEALKKELAELKAQLKDLQKRVDKTEKKSAGDRL 66
>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 = 29.3 bits (66), Expect = 0.39
Identities = 22/101 (21%), Positives = 44/101 (43%), Gaps = 5/101 (4%)
Query: 4 KEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITD 63
E+++ +LK+ +++ E A+ EL+ +LEE + ++ +L + + +
Sbjct: 241 LEELQEELKEAEEELEELTAE--LQELEEKLEELRLEVSELEEEIEELQKELYALANEIS 298
Query: 64 TKEKMVKEYNKRKRMCT---EMLEAILENYPKSKKILLEEV 101
E+ + +R E LEA LE L EE+
Sbjct: 299 RLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEEL 339
>gnl|CDD|236745 PRK10722, PRK10722, hypothetical protein; Provisional.
Length = 247
Score = 28.8 bits (65), Expect = 0.56
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 16 QQMTEAEA---KQKKAELQAELEEKKSKLEKL 44
QQ +++E +Q++ LQ +LE KLE L
Sbjct: 171 QQSSDSELDALRQQQQRLQYQLELTTRKLENL 202
>gnl|CDD|177025 CHL00093, groEL, chaperonin GroEL.
Length = 529
Score = 28.9 bits (65), Expect = 0.57
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 10/64 (15%)
Query: 4 KEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITD 63
+E+VK++ +QL +Q+ A++ +K +LQ +L KLS V VI G T T+
Sbjct: 338 EEQVKARCEQLRKQIEIADSSYEKEKLQ-------ERLAKLSGGVAVIKVGAA---TETE 387
Query: 64 TKEK 67
K+K
Sbjct: 388 MKDK 391
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 28.9 bits (66), Expect = 0.58
Identities = 13/35 (37%), Positives = 24/35 (68%), Gaps = 2/35 (5%)
Query: 2 DDKEKVKSKLKQLSQQMTEAEAKQKKAELQAELEE 36
+D E + +++K+L +++ EA+ EL+AELEE
Sbjct: 66 EDAEALIAEVKELKEEIKALEAELD--ELEAELEE 98
Score = 26.2 bits (59), Expect = 4.9
Identities = 13/51 (25%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 6 KVKSKLKQLSQQMTEAEA-KQKKAELQAELEEKKSKLEKLSRNV-NVISEG 54
+ K K + + E + K++ L+AEL+E +++LE+L + N+ +
Sbjct: 60 QAKRKGEDAEALIAEVKELKEEIKALEAELDELEAELEELLLRIPNLPHDS 110
>gnl|CDD|163441 TIGR03729, acc_ester, putative phosphoesterase. Members of this
protein family belong to the larger family pfam00149
(calcineurin-like phosphoesterase), a family largely
defined by small motifs of metal-chelating residues. The
subfamily in this model shows a good but imperfect
co-occurrence in species with domain TIGR03715 that
defines a novel class of signal peptide typical of the
accessory secretory system.
Length = 239
Score = 28.4 bits (64), Expect = 0.59
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 1 MDDKEKVKSKLKQLSQQMTEAEAKQ 25
M D E+ LKQL +Q+ + + KQ
Sbjct: 142 MSDPERTAIVLKQLKKQLNQLDNKQ 166
>gnl|CDD|234375 TIGR03860, FMN_nitrolo, FMN-dependent oxidoreductase,
nitrilotriacetate monooxygenase family. This model
represents a distinctive clade, in which all
characterized members are FMN-binding, within the larger
family of luciferase-like monooxygenases (LLM), among
which there are both FMN- and F420-binding enzymes. A
well-characterized member is nitrilotriacetate
monooxygenase from Aminobacter aminovorans
(Chelatobacter heintzii), where nitrilotriacetate is a
chelating agent used in detergents [Unknown function,
Enzymes of unknown specificity].
Length = 422
Score = 28.6 bits (65), Expect = 0.62
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 19 TEAEAKQKKAELQAELEEKKSKLEKLSRNVNV 50
TEAEA+ K AELQ L + L LS +
Sbjct: 275 TEAEARAKYAELQ-SLISPEGGLALLSGWTGI 305
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of this
protein are restricted to the Gram-positive lineages,
including the Mycoplasmas. This protein is designated
alpha chain and given the gene symbol polC, but is not a
full-length homolog of other polC genes. The N-terminal
region of about 200 amino acids is rich in low-complexity
sequence, poorly alignable, and not included n this model
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1213
Score = 28.5 bits (64), Expect = 0.72
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 3 DKEKVKSKLKQLSQQMTEAEAKQKKAELQAELE 35
KE +K KL++++ + +A K+ +L LE
Sbjct: 1084 GKEFIKQKLEEINTRRKINKASPKEKDLLTVLE 1116
>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 = 28.4 bits (64), Expect = 0.78
Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 22 EAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDK--KTITDTKEKMVKEYNKRKRMC 79
E K++ EL+ EL+E + +LEK+ + + + + + + EK+++ K
Sbjct: 331 ELKEELKELEEELKELEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETKEKLSEEL 390
Query: 80 TEM------LEAILENYPKSKKI 96
E+ L+ LE+ KI
Sbjct: 391 EELEEELKELKEELESLYSEGKI 413
>gnl|CDD|234780 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Validated.
Length = 339
Score = 27.8 bits (63), Expect = 1.1
Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 10/46 (21%)
Query: 8 KSKLKQLSQQMTEAEAKQKKA----------ELQAELEEKKSKLEK 43
K +L +L + + + +++K ++A LEE+K +LE
Sbjct: 36 KGELTELLKGLGKLPPEERKEAGALINELKQAIEAALEERKEELEA 81
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 28.0 bits (63), Expect = 1.1
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 4 KEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITD 63
+V K+ + ++ E K + E Q E +EKK + +K R E ++ K + +
Sbjct: 254 SPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEER------EAKLAKLSPEE 307
Query: 64 TKEKMVKEYNKRKR 77
++ KE K+ R
Sbjct: 308 QRKLEEKERKKQAR 321
>gnl|CDD|237205 PRK12792, flhA, flagellar biosynthesis protein FlhA; Reviewed.
Length = 694
Score = 28.2 bits (63), Expect = 1.1
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 12 KQLSQQMTEAEAKQKKAELQAELEEKKSKLEKL 44
++ + + AK K+ E A+ E K S E+L
Sbjct: 325 RRRAARAAAEAAKVKREEESAQAEAKDSVKEQL 357
>gnl|CDD|182225 PRK10077, xylE, D-xylose transporter XylE; Provisional.
Length = 479
Score = 27.3 bits (61), Expect = 1.7
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 14 LSQQMTEAEAKQKKAELQAELEEKKSKLEKL-SRNVNVISEG 54
L + M A Q E++ L+ + KL V VI G
Sbjct: 234 LRKIMGNTLATQALQEIKHSLDHGRKTGGKLLMFGVGVIVIG 275
>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 = 27.3 bits (61), Expect = 1.9
Identities = 12/67 (17%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 10 KLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITDTKEKMV 69
KL+ ++ + + + ++L+ E+E+K+ ++E+L R +++ D + + EK
Sbjct: 63 KLEVARKKERLNQIRARISQLKEEIEQKRERIEELKRA---LAQRRSDLSSASYQLEKRR 119
Query: 70 KEYNKRK 76
++
Sbjct: 120 ASQLEKL 126
>gnl|CDD|234090 TIGR03021, pilP_fam, type IV pilus biogenesis protein PilP.
Members of this protein family are found in type IV
pilus biogenesis loci and include proteins designated
PilP [Cell envelope, Surface structures].
Length = 119
Score = 26.6 bits (59), Expect = 2.0
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 11 LKQLSQQMTEAEAKQKKAELQAELEEKK 38
L+ L + EA+ +A+ Q ELEE +
Sbjct: 7 LEALQSETALLEAQLARAKAQNELEEAE 34
>gnl|CDD|233828 TIGR02348, GroEL, chaperonin GroL. This family consists of GroEL,
the larger subunit of the GroEL/GroES cytosolic
chaperonin. It is found in bacteria, organelles derived
from bacteria, and occasionally in the Archaea. The
bacterial GroEL/GroES group I chaperonin is replaced a
group II chaperonin, usually called the thermosome in
the Archaeota and CCT (chaperone-containing TCP) in the
Eukaryota. GroEL, thermosome subunits, and CCT subunits
all fall under the scope of pfam00118 [Protein fate,
Protein folding and stabilization].
Length = 524
Score = 26.9 bits (60), Expect = 2.5
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 2 DDKEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTI 61
DK +K+++ Q+ Q+ E + + +LQ +L KL+ V VI G T
Sbjct: 335 GDKAAIKARVAQIKAQIEETTSDYDREKLQ-------ERLAKLAGGVAVIKVGAA---TE 384
Query: 62 TDTKEK 67
T+ KEK
Sbjct: 385 TEMKEK 390
>gnl|CDD|132062 TIGR03017, EpsF, chain length determinant protein EpsF. Sequences
in this family of proteins are members of the chain
length determinant family (pfam02706) which includes the
wzc protein from E.coli. This family of proteins are
homologous to the EpsF protein of the methanolan
biosynthesis operon of Methylobacillus species strain
12S. The distribution of this protein appears to be
restricted to a subset of exopolysaccharide operons
containing a syntenic grouping of genes including a
variant of the EpsH exosortase protein. Exosortase has
been proposed to be involved in the targetting and
processing of proteins containing the PEP-CTERM domain
to the exopolysaccharide layer.
Length = 444
Score = 26.7 bits (59), Expect = 3.0
Identities = 16/54 (29%), Positives = 32/54 (59%), Gaps = 6/54 (11%)
Query: 5 EKVKSKLKQLSQQMTEA------EAKQKKAELQAELEEKKSKLEKLSRNVNVIS 52
+KS+L +++T + KQ++AEL+ LE +K+K+ +L+R + +S
Sbjct: 292 NSLKSQLNAEIKKVTSSVGTNSRILKQREAELREALENQKAKVLELNRQRDEMS 345
>gnl|CDD|221180 pfam11712, Vma12, Endoplasmic reticulum-based factor for assembly
of V-ATPase. The yeast vacuolar proton-translocating
ATPase (V-ATPase) is the best characterized member of
the V-ATPase family. A total of thirteen genes are
required for encoding the subunits of the enzyme
complex itself and an additional three for providing
factors necessary for the assembly of the whole. Vma12
is one of these latter, all three of which are
localised to the endoplasmic reticulum.
Length = 137
Score = 26.1 bits (58), Expect = 3.0
Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 22 EAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITDTKEKMVKEYNK 74
E + L+A EE++ ++++RNV+ + + + DT + KE +
Sbjct: 23 EFLARLERLRAAQEERE--YQRMTRNVDPQTNSKGPSEDDEDTFGQEYKEVKR 73
>gnl|CDD|216110 pfam00771, FHIPEP, FHIPEP family.
Length = 658
Score = 26.6 bits (60), Expect = 3.2
Identities = 6/15 (40%), Positives = 11/15 (73%)
Query: 19 TEAEAKQKKAELQAE 33
E EA++++ EL+ E
Sbjct: 145 DEEEARRRREELERE 159
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 26.7 bits (59), Expect = 3.6
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 7 VKSKLKQLSQQMTEAEAKQK----KAELQAELEEKKSKLEKLSRN 47
VK L L +Q+ E E K+ KA++Q LE K+ LEKL+
Sbjct: 367 VKVTLDNLFEQIKEGELKELNIILKADVQGSLEAIKNSLEKLNNE 411
>gnl|CDD|218186 pfam04636, PA26, PA26 p53-induced protein (sestrin). PA26 is a
p53-inducible protein. Its function is unknown. It has
similarity to pfam04636 in its N-terminus.
Length = 450
Score = 26.6 bits (59), Expect = 3.6
Identities = 10/38 (26%), Positives = 23/38 (60%)
Query: 2 DDKEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKS 39
+ E + ++K+L ++ + EA Q++ + E E+K+S
Sbjct: 227 TEVEALMERMKKLQEERDDDEASQEEMTTRFEKEKKES 264
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 26.5 bits (59), Expect = 3.7
Identities = 9/36 (25%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 3 DKEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKK 38
++ ++++ L +L+ AE + EL EL+ +K
Sbjct: 96 ERSRLQALLAELAGAGAAAE--GRAGELAQELDSEK 129
>gnl|CDD|234540 TIGR04318, lacto_ODC_hypo, putative ornithine decarboxylase. In at
least ten species of Lactobacillus, this close homolog
to known ornithine decarboxylase occurs in a three-gene
neighborhood, along with an amino acid permease family
transporter and pyridoxal phosphate-dependent enyzme
from the cystathionine gamma-lyase family. Species
include L. acidophilus, L. amylovorus, L. crispatus, L.
delbrueckii, L. farciminis, L. helveticus, L. johnsonii,
etc. The combination of a decarboxylase with an
antiporter in a two-gene system suggests a
decarboxylation/antiport proton-motive cycle for
transient resistance to acidic conditions. The substrate
for this decarboxylase might be ornithine but is
unknown.
Length = 695
Score = 26.3 bits (58), Expect = 4.3
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 11 LKQLSQQMTEAEAKQKKAELQAELEEKKS 39
LKQL Q+M E A+ + +LQ L K
Sbjct: 569 LKQLCQEMHEYYAENEIFKLQQALFIKPD 597
>gnl|CDD|193253 pfam12777, MT, Microtubule-binding stalk of dynein motor. the
380 kDa motor unit of dynein belongs to the AAA class
of chaperone-like ATPases. The core of the 380 kDa
motor unit contains a concatenated chain of six AAA
modules, of which four correspond to the ATP binding
sites with P-loop signatures described previously, and
two are modules in which the P loop has been lost in
evolution. This family is the region between D4 and D5
and is the two predicted alpha-helical coiled coil
segments that form the stalk supporting the
ATP-sensitive microtubule binding component.
Length = 344
Score = 26.2 bits (57), Expect = 4.9
Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 10 KLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITDTKEKMV 69
KL+ + Q+ + +AK A + EL++K +KL + V V +E +K I D +E V
Sbjct: 9 KLQSTASQVDDLKAKL--AIQEVELKQKNEDADKLIQVVGVETEKVSKEKAIADQEEVKV 66
Query: 70 ----KEYNKRKRMCTEML 83
KE ++++ C E L
Sbjct: 67 AVINKEVTEKQKDCEEDL 84
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 26.2 bits (58), Expect = 4.9
Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 3/58 (5%)
Query: 24 KQKKAELQAELEEKKSKLEKL-SRNVNVISEGEVDK--KTITDTKEKMVKEYNKRKRM 78
K+K +L AELE+K+ +LEKL + + ++DK + + + +E KE K +R+
Sbjct: 1101 KEKVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRL 1158
>gnl|CDD|235596 PRK05764, PRK05764, aspartate aminotransferase; Provisional.
Length = 393
Score = 25.9 bits (58), Expect = 5.0
Identities = 5/21 (23%), Positives = 12/21 (57%)
Query: 66 EKMVKEYNKRKRMCTEMLEAI 86
E+M + + +R+ + + L I
Sbjct: 291 EEMRQAFEERRDLMVDGLNEI 311
>gnl|CDD|176478 cd08641, DNA_pol_gammaA, Pol gammaA is a family A polymerase that
is responsible for DNA replication and repair in
mitochondria. DNA polymerase gamma (Pol gamma), 5'-3'
polymerase domain (Pol gammaA). Pol gammaA is a family A
polymerase that is responsible for DNA replication and
repair in mitochondria. Family A polymerase functions
primarily to fill DNA gaps that arise during DNA repair,
recombination and replication. DNA-dependent DNA
polymerases can be classified into six main groups based
upon phylogenetic relationships with E. coli polymerase
I (classA), E. coli polymerase II (class B), E.coli
polymerase III (class C), euryarchaeota polymerase II
(class D), human polymerase beta (class X), E. coli
UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum
variant (class Y). Family A polymerases are found
primarily in organisms related to prokaryotes and
include prokaryotic DNA polymerase I, mitochondrial
polymerase gammaA, and several bacteriophage polymerases
including those from odd-numbered phage (T3, T5, and
T7). The structure of these polymerases resembles in
overall morphology a cupped human right hand, with
fingers (which bind an incoming nucleotide and interact
with the single-stranded template), palm (which harbors
the catalytic amino acid residues and also binds an
incoming dNTP) and thumb (which binds double-stranded
DNA) subdomains. Pol gammaA has also the right hand
configuration. Pol gammaA has both polymerase and
proofreading exonuclease activities separated by a
spacer. Pol gamma holoenzyme is a heterotrimer
containing one Pol gammaA subunit and a dimeric Pol
gammaB subunit. Pol gamma is important for mitochondria
DNA maintenance and mutation of the catalytic subunit of
Pol gamma is implicated in more than 30 human diseases.
Length = 425
Score = 26.1 bits (58), Expect = 5.1
Identities = 8/44 (18%), Positives = 22/44 (50%)
Query: 11 LKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEG 54
L Q + ++T AEA +K ++ A + + +++ ++ +
Sbjct: 225 LMQFNPRLTPAEATEKAKQMYAATKGIRIAIQRSTKGKRLFKRP 268
>gnl|CDD|235672 PRK06012, flhA, flagellar biosynthesis protein FlhA; Validated.
Length = 697
Score = 25.9 bits (58), Expect = 5.3
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 19 TEAEAKQKKAELQAE 33
E EAK+++ ELQ E
Sbjct: 176 DEEEAKKRRKELQQE 190
>gnl|CDD|214479 smart00033, CH, Calponin homology domain. Actin binding domains
present in duplicate at the N-termini of spectrin-like
proteins (including dystrophin, alpha-actinin). These
domains cross-link actin filaments into bundles and
networks. A calponin homology domain is predicted in
yeasst Cdc24p.
Length = 101
Score = 25.4 bits (56), Expect = 5.5
Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 48 VNVISEGEVDKKTITDTKEKMVKEYNKRKRMCTEMLEAILENYPKSKKILLEEVGIETDE 107
+N +S G VDKK + + + K N L +K+ + V E ++
Sbjct: 36 LNSLSPGLVDKKKVAASLSRFKKIEN-----INLALSFA-------EKLGGKVVLFEPED 83
Query: 108 MVSMEKLQ 115
+V KL
Sbjct: 84 LVEGPKLI 91
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 26.0 bits (58), Expect = 5.5
Identities = 8/57 (14%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 2 DDKEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDK 58
+++ ++++ ++ E ++++ L EL+E K + + E E+++
Sbjct: 208 EEEGTPSELIREIKEE--LEEIEKERESLLEELKELAKKYLEELLALYEYLEIELER 262
>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III
C-methyltransferase; Provisional.
Length = 390
Score = 25.8 bits (57), Expect = 6.0
Identities = 11/45 (24%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 3 DKEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRN 47
K++++ LKQ ++ + +A +++A L +L+E + K+ +S +
Sbjct: 86 QKQELEGILKQQAKAL--DQANRQQAALAKQLDELQQKVATISGS 128
>gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase.
Length = 684
Score = 25.9 bits (57), Expect = 6.0
Identities = 13/48 (27%), Positives = 22/48 (45%)
Query: 55 EVDKKTITDTKEKMVKEYNKRKRMCTEMLEAILENYPKSKKILLEEVG 102
EV+ I K+++ + +++ E LEA+ E K LE G
Sbjct: 446 EVEVLVIVPNKKELGLAFKGDQKVVVEALEAMNEKEAMEMKAKLESKG 493
>gnl|CDD|223136 COG0058, GlgP, Glucan phosphorylase [Carbohydrate transport and
metabolism].
Length = 750
Score = 25.7 bits (57), Expect = 6.2
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 11 LKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITDTKEKMVK 70
L L + + A+ K + + E K ++L+ + + EVD + D + + +
Sbjct: 441 LDILDELLWFADDKAFRELIAEIKRENK---KRLAEEIADRTGIEVDPNALFDGQARRIH 497
Query: 71 EYNKR 75
EY KR
Sbjct: 498 EY-KR 501
>gnl|CDD|153344 cd07660, BAR_Arfaptin, The Bin/Amphiphysin/Rvs (BAR) domain of
Arfaptin. The BAR domain of Arfaptin-like proteins,
also called the Arfaptin domain, is a dimerization and
lipid binding module that can detect and drive membrane
curvature. Arfaptins are ubiquitously expressed proteins
implicated in mediating cross-talk between Rac, a member
of the Rho family GTPases, and Arf (ADP-ribosylation
factor) small GTPases. Arfaptins bind to GTP-bound Arf1,
Arf5, and Arf6, with strongest binding to GTP-Arf1.
Arfaptins also bind to Rac-GTP and Rac-GDP with similar
affinities. The Arfs are thought to bind to the same
surface as Rac, and their binding is mutually exclusive.
Mammals contain at least two isoforms of Arfaptin.
Arfaptin 1 has been shown to inhibit the activation of
Arf-dependent phospholipase D (PLD) and the secretion of
matrix metalloproteinase-9 (MMP-9), an enzyme implicated
in cancer invasiveness and metastasis. Arfaptin 2
regulates the aggregation of the protein huntingtin,
which is implicated in Huntington disease. Arfaptins are
single-domain proteins with a BAR-like structure. BAR
domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 201
Score = 25.7 bits (57), Expect = 6.4
Identities = 12/43 (27%), Positives = 21/43 (48%)
Query: 8 KSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNV 50
++ L+ L+ +A + E Q + K K EKL +V+V
Sbjct: 117 RNDLEALNLGPRDAATSARLEEAQRRFQAHKDKYEKLRNDVSV 159
>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein. This family
consists of several Borrelia P83/P100 antigen proteins.
Length = 489
Score = 25.7 bits (56), Expect = 6.8
Identities = 18/82 (21%), Positives = 35/82 (42%)
Query: 4 KEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITD 63
KE++ K + +A+ Q A+ Q + +K + K S + DK+ +
Sbjct: 219 KEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKPADTSSPKEDKQVAEN 278
Query: 64 TKEKMVKEYNKRKRMCTEMLEA 85
K ++ K + K+ E L+A
Sbjct: 279 QKREIEKAQIEIKKNDEEALKA 300
>gnl|CDD|234829 PRK00750, lysK, lysyl-tRNA synthetase; Reviewed.
Length = 510
Score = 25.5 bits (57), Expect = 7.3
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 80 TEMLEAILENYPKSKKILLEEVGIETDE 107
E + LEN + +ILL +G E
Sbjct: 142 DEAILTALENRDEIMEILLPYLGEERQA 169
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein
TraB; Provisional.
Length = 475
Score = 25.6 bits (56), Expect = 7.6
Identities = 9/41 (21%), Positives = 20/41 (48%)
Query: 7 VKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRN 47
V + +Q E + A++Q + EE + +L+ L++
Sbjct: 58 VDTTFDDKVRQHATTEMQVTAAQMQKQYEEIRRELDVLNKQ 98
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 25.5 bits (56), Expect = 7.7
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 16 QQMTEAEAKQKKAELQAELEEKKSKLEKLSRN 47
E K+ A+L +EL + KLE+L N
Sbjct: 201 LAQLLEERKKTLAQLNSELSADQKKLEELRAN 232
>gnl|CDD|226966 COG4607, CeuA, ABC-type enterochelin transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 320
Score = 25.4 bits (56), Expect = 7.8
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 20 EAEAKQKKAELQAELEEKKSKLEKLSRNVNVI--SEGEV 56
E EAK+ A++ A + K K + VI + G++
Sbjct: 169 EEEAKELLADIDASIAAAKEKAAGKGKTALVILVNGGKI 207
>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 = 25.7 bits (57), Expect = 8.2
Identities = 13/41 (31%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 5 EKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLS 45
E ++ K K+LS + E +K+ EL+ + E++ +LE++S
Sbjct: 104 ENLEKKEKELSNK--EKNLDEKEEELEELIAEQREELERIS 142
>gnl|CDD|221059 pfam11285, DUF3086, Protein of unknown function (DUF3086). This
family of proteins with unknown function appears to be
restricted to Cyanobacteria.
Length = 283
Score = 25.4 bits (56), Expect = 8.6
Identities = 7/26 (26%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 21 AEAKQKKAELQAE---LEEKKSKLEK 43
+ +Q++ L+ E LE +K ++E+
Sbjct: 7 KDLEQRRQALEIEIEKLERRKEQIEQ 32
>gnl|CDD|222465 pfam13942, Lipoprotein_20, YfhG lipoprotein. This family includes
the YfhG protein from E. coli. Members of this family
have an N-terminal lipoprotein attachment site. The
members of this family are functionally uncharacterized.
Length = 180
Score = 24.9 bits (55), Expect = 8.7
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 3/32 (9%)
Query: 16 QQMTEAE---AKQKKAELQAELEEKKSKLEKL 44
QQ +++E ++++A LQ ELE KLE L
Sbjct: 125 QQSSDSELDRLREQQARLQYELETTTRKLENL 156
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 25.6 bits (57), Expect = 8.8
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 2 DDKEKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSR 46
+DKEK+ + L + E E +QK E +A L+E + E+L
Sbjct: 513 EDKEKLNELIASLEEL--ERELEQKAEEAEALLKEAEKLKEELEE 555
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 25.2 bits (56), Expect = 8.8
Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 1 MDDKEKVKSKLKQ-LSQQMTEAEAKQKKAELQAELEEKKS 39
+ DK+ + +LK+ LS Q A A++++ E + E EE+ S
Sbjct: 278 LADKDALDEELKEVLSAQAQAAAAEEEEEEEEEEEEEEPS 317
>gnl|CDD|221952 pfam13166, AAA_13, 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. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 25.4 bits (56), Expect = 9.5
Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 25 QKKAELQAELEEKKSKLEKLSRNVNVISEGEVDKKTITDTKEKMVKEYNKR 75
++ E++A++EE K +L+KL I + E + + + EK ++ +
Sbjct: 88 EENIEIEAQIEELKKELKKLEEK---IEQLEAEIEKKEEELEKAKNKFLDK 135
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 25.4 bits (56), Expect = 9.6
Identities = 14/52 (26%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 2 DDKEKVKSKL--KQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVI 51
++ + + KL K L ++ E ++++AE Q EL +++LE L R ++ +
Sbjct: 178 SEELEARRKLKEKGLVSRLELLELERERAEAQGELGRLEAELEVLKRQIDEL 229
>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 = 25.0 bits (55), Expect = 9.8
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 5 EKVKSKLKQLSQQMTEAEAKQKKAELQAELEEKKSKLEKLSRNVNVISEGE 55
+K +++KQLS E + ++ EL+ EL E K + E L + E E
Sbjct: 114 QKELARIKQLSANAIELD--EENRELREELAELKQENEALEAENERLQENE 162
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
0.302 0.120 0.290
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,437,458
Number of extensions: 481812
Number of successful extensions: 2372
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2008
Number of HSP's successfully gapped: 820
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.8 bits)
S2: 53 (24.3 bits)