RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11738
(323 letters)
>gnl|CDD|226590 COG4105, ComL, DNA uptake lipoprotein [General function prediction
only].
Length = 254
Score = 43.1 bits (102), Expect = 8e-05
Identities = 44/185 (23%), Positives = 73/185 (39%), Gaps = 30/185 (16%)
Query: 155 WYQRKIANAIFDTLPTSSYEEALKYFLEAEKQHPL--FYSQNVLMLGKTYMRLENYEQAA 212
Y + L +YEEA+KYF + +HP + Q L L Y + Y+ A
Sbjct: 37 LYNEGLTE-----LQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLAL 91
Query: 213 YYLEM-TKNYPVKQDKDQCFEITDMPWY---------QRKIANAI--FDTL----PTSSY 256
Y++ + YP + D + + + ++ Q A F L P S Y
Sbjct: 92 AYIDRFIRLYPTHPNADYAYYLKGLSYFFQIDDVTRDQSAARAAFAAFKELVQRYPNSRY 151
Query: 257 EEALKYFLEAEKQHPLFYSQNVLMLGKTYMRLENYEQAA-YYLEMTKNYP---AVQEATK 312
K + L + + + + Y++ Y A + E+ +NYP AV+EA
Sbjct: 152 APDAKARIVKLNDA-LAGHE--MAIARYYLKRGAYVAAINRFEEVLENYPDTSAVREALA 208
Query: 313 LLEKA 317
LE+A
Sbjct: 209 RLEEA 213
>gnl|CDD|234164 TIGR03302, OM_YfiO, outer membrane assembly lipoprotein YfiO.
Members of this protein family include YfiO, a
near-essential protein of the outer membrane, part of a
complex involved in protein insertion into the bacterial
outer membrane. Many proteins in this family are
annotated as ComL, based on the involvement of this
protein in natural transformation with exogenous DNA in
Neisseria gonorrhoeae. This protein family shows
sequence similarity to, but is distinct from, the
tol-pal system protein YbgF (TIGR02795) [Protein fate,
Protein and peptide secretion and trafficking].
Length = 235
Score = 37.9 bits (89), Expect = 0.003
Identities = 39/180 (21%), Positives = 71/180 (39%), Gaps = 43/180 (23%)
Query: 173 YEEALKYFLEAEKQHPLFYS----QNVLMLGKTYMRLENYEQA-AYYLEMTKNYPVKQDK 227
Y EA+KYF E ++P +S Q L L Y + +Y +A A + +P
Sbjct: 49 YTEAIKYFEALESRYP--FSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHP--NHP 104
Query: 228 DQCFEITDMPWYQRKIANAIFDTLP-----TSSYEEALKYFLEAEKQHP----------- 271
D + + ++ + ++ EA + F E +++P
Sbjct: 105 -------DADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKR 157
Query: 272 LFYSQNVL-----MLGKTYMRLENYEQAA-YYLEMTKNYP---AVQEATKLLEKAKSYLK 322
+ Y +N L + + Y++ Y A + + +NYP A +EA L ++YLK
Sbjct: 158 MDYLRNRLAGKELYVARFYLKRGAYVAAINRFQTVVENYPDTPATEEALARL--VEAYLK 215
>gnl|CDD|234419 TIGR03965, mycofact_glyco, mycofactocin system glycosyltransferase.
Members of this protein family are putative
glycosyltransferases, members of pfam00535 (glycosyl
transferase family 2). Members appear mostly in the
Actinobacteria, where they appear to be part of a system
for converting a precursor peptide (TIGR03969) into a
novel redox carrier designated mycofactocin. A radical
SAM enzyme, TIGR03962, is a proposed to be a key
maturase for mycofactocin.
Length = 467
Score = 35.5 bits (82), Expect = 0.037
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 7/67 (10%)
Query: 1 MSSDEAA-KTVSKVSEEFLKKSDDLFEEQQFEEVNKMLESSEYKEDVEIIWRLV----RV 55
+ +EA + VS ++ + L + EV E E EDV++ WRL RV
Sbjct: 213 LGPEEAVVRPRGPVS--YVPSAALLVRRRALLEVGGFDERLEVGEDVDLCWRLCEAGGRV 270
Query: 56 KYNLATH 62
+Y A
Sbjct: 271 RYEPAAV 277
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 35.1 bits (81), Expect = 0.048
Identities = 51/215 (23%), Positives = 80/215 (37%), Gaps = 41/215 (19%)
Query: 103 LNEKATLEGTKARIQQLETIKHHMNKAIELKPDDSTTLFMLGMWCFEITDMPWYQRKIAN 162
L K L + I+ KAI L+P++ L L E + K A+
Sbjct: 196 LLLKGDLLLSLGNIELALAA---YRKAIALRPNNIAVLLALATILIEAGEFE-EAEKHAD 251
Query: 163 AIFDTLPTSS---------------YEEALKYFLEAEKQHPLFYSQNVLMLGKTYMRLEN 207
A+ P S YE+A + +A K P + +L+ G + +L N
Sbjct: 252 ALLKKAPNSPLAHYLKALVDFQKKNYEDARETLQDALKSAPEYLP-ALLLAGASEYQLGN 310
Query: 208 YEQAAYYLEMTKNYPVKQDKDQCFEITDMPWYQRKIANAIFDTLPTSSYEEA---LKYFL 264
EQA YL +K + R++ +I L +EA L L
Sbjct: 311 LEQAYQYLNQI----LKYAPNSH--------QARRLLASIQ--LRLGRVDEAIATLSPAL 356
Query: 265 EAEKQHPLFYSQNVLMLGKTYMRLENYEQAAYYLE 299
+ P S +LG+ Y+ L ++E+AA YL
Sbjct: 357 GLDPDDPAALS----LLGEAYLALGDFEKAAEYLA 387
Score = 32.4 bits (74), Expect = 0.35
Identities = 34/147 (23%), Positives = 57/147 (38%), Gaps = 17/147 (11%)
Query: 168 LPTSSYEEALKYFLEAEKQHPLFYSQNVLMLGKTYMRLENYEQAAYYLEMTKNYPVKQDK 227
L +A+ F + P + +L+L Y ++NY +A L+ ++
Sbjct: 612 LAAGDLNKAVSSFKKLLALQP-DSALALLLLADAYAVMKNYAKAITSLKRA----LELKP 666
Query: 228 DQCFEITDMPWYQRKIANAIFDTLPTSSYEEALKYFLEAEKQHPLFYSQNVLMLGKTYMR 287
D T+ ++ A T E A K +KQHP + + G Y+R
Sbjct: 667 DN----TEAQIGLAQLLLAAKRT------ESAKKIAKSLQKQHPK-AALGFELEGDLYLR 715
Query: 288 LENYEQAA-YYLEMTKNYPAVQEATKL 313
++Y A Y + K P+ Q A KL
Sbjct: 716 QKDYPAAIQAYRKALKRAPSSQNAIKL 742
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 30.7 bits (70), Expect = 0.14
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 173 YEEALKYFLEAEKQHPLFYSQNVLMLGKTYMRLENYEQAA-YYLEMTKNYP 222
Y+EAL A ++PL L+LG+ +R +AA P
Sbjct: 13 YDEALAALEAALARYPLAAEAL-LLLGEALLRQGRLAEAAALLRAALAADP 62
Score = 30.7 bits (70), Expect = 0.14
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 256 YEEALKYFLEAEKQHPLFYSQNVLMLGKTYMRLENYEQAA-YYLEMTKNYP 305
Y+EAL A ++PL L+LG+ +R +AA P
Sbjct: 13 YDEALAALEAALARYPLAAEAL-LLLGEALLRQGRLAEAAALLRAALAADP 62
>gnl|CDD|236983 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional.
Length = 389
Score = 31.3 bits (72), Expect = 0.65
Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 7/52 (13%)
Query: 168 LPTSSYEEALKYFLEAEKQHPLFYSQNV---LMLGKTYMRLENYEQAAYYLE 216
L + A +A P Q V ++LG + +Y A LE
Sbjct: 191 LARGDLDAARALLKKALAADP----QCVRASILLGDLALAQGDYAAAIEALE 238
Score = 31.3 bits (72), Expect = 0.65
Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 7/52 (13%)
Query: 251 LPTSSYEEALKYFLEAEKQHPLFYSQNV---LMLGKTYMRLENYEQAAYYLE 299
L + A +A P Q V ++LG + +Y A LE
Sbjct: 191 LARGDLDAARALLKKALAADP----QCVRASILLGDLALAQGDYAAAIEALE 238
>gnl|CDD|188247 TIGR02795, tol_pal_ybgF, tol-pal system protein YbgF. Members of
this protein family are the product of one of seven
genes regularly clustered in operons to encode the
proteins of the tol-pal system, which is critical for
maintaining the integrity of the bacterial outer
membrane. The gene for this periplasmic protein has been
designated orf2 and ybgF. All members of the seed
alignment were from unique tol-pal gene regions from
completed bacterial genomes. The architecture of this
protein is a signal sequence, a low-complexity region
usually rich in Asn and Gln, a well-conserved region
with tandem repeats that resemble the tetratricopeptide
(TPR) repeat, involved in protein-protein interaction.
Length = 117
Score = 29.6 bits (67), Expect = 0.78
Identities = 24/95 (25%), Positives = 39/95 (41%), Gaps = 16/95 (16%)
Query: 245 NAIFDTLPTSSYEEALKYFLEAEKQHPLF-YSQNVLM-LGKTYMRLENYEQAA-YYLEMT 301
+A L Y +A++ F K++P Y+ N LG+ Y +Y AA +L +
Sbjct: 5 DAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGDYADAAKAFLAVV 64
Query: 302 KNYP-------------AVQEATKLLEKAKSYLKK 323
K YP + EKAK+ L++
Sbjct: 65 KKYPKSPKAPDALLKLGMSLQELGDKEKAKATLQQ 99
Score = 28.0 bits (63), Expect = 2.6
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 162 NAIFDTLPTSSYEEALKYFLEAEKQHPLF-YSQNVLM-LGKTYMRLENYEQAA-YYLEMT 218
+A L Y +A++ F K++P Y+ N LG+ Y +Y AA +L +
Sbjct: 5 DAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGDYADAAKAFLAVV 64
Query: 219 KNYP 222
K YP
Sbjct: 65 KKYP 68
>gnl|CDD|131573 TIGR02521, type_IV_pilW, type IV pilus biogenesis/stability protein
PilW. Members of this family are designated PilF in ref
(PMID:8973346) and PilW in ref (PMID:15612916). This
outer membrane protein is required both for pilus
stability and for pilus function such as adherence to
human cells. Members of this family contain copies of
the TPR (tetratricopeptide repeat) domain.
Length = 234
Score = 30.0 bits (68), Expect = 1.3
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 4/70 (5%)
Query: 256 YEEALKYFLEAEKQHPLFYSQ--NVLMLGKTYMRLENYEQAAYYLEMTKNYPAVQEATKL 313
YE+A++ F +A + PL+ ++ G ++ ++++A YL Q L
Sbjct: 115 YEQAMQQFEQAIED-PLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDP-QRPESL 172
Query: 314 LEKAKSYLKK 323
LE A+ Y +
Sbjct: 173 LELAELYYLR 182
>gnl|CDD|182548 PRK10559, PRK10559, p-hydroxybenzoic acid efflux subunit AaeA;
Provisional.
Length = 310
Score = 30.1 bits (68), Expect = 1.4
Identities = 28/97 (28%), Positives = 39/97 (40%), Gaps = 13/97 (13%)
Query: 220 NYPVKQDKDQCFEITDMPWYQRKIANAIFDTLPTSSYEEALKYFLEAEKQHPLFYSQNVL 279
N VK K Q D P YQ+ +A A D +Y + L EK+ +
Sbjct: 66 NQLVK--KGQVLFTIDQPRYQKALAEAEADV----AYYQVLA----QEKRRE---AGRRN 112
Query: 280 MLGKTYMRLENYEQAAYYLEMTKNYPAVQEATKLLEK 316
LG M E +QA L+ + A +AT+ L K
Sbjct: 113 RLGVQAMSREEIDQANNVLQTVLHQLAKAQATRDLAK 149
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 28.1 bits (63), Expect = 1.5
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 173 YEEALKYFLEAEKQ------HPLFYSQNVLMLGKTYMRLENYEQAAYYLE 216
Y+EAL+ +A + ++ + L + Y+ L +Y++A YLE
Sbjct: 21 YDEALELLEKALELARELGEDHPETARALNNLARLYLALGDYDEALEYLE 70
Score = 28.1 bits (63), Expect = 1.5
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 256 YEEALKYFLEAEKQ------HPLFYSQNVLMLGKTYMRLENYEQAAYYLE 299
Y+EAL+ +A + ++ + L + Y+ L +Y++A YLE
Sbjct: 21 YDEALELLEKALELARELGEDHPETARALNNLARLYLALGDYDEALEYLE 70
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 29.8 bits (68), Expect = 2.0
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 7/45 (15%)
Query: 15 EEFLKKSDDLFEEQQFEEVNKMLESSEYKEDVEIIWRLVRV--KY 57
E + +++ LF+E V ++LE+ E+K+ +E I L R KY
Sbjct: 419 RELIAEAEALFKE-----VGELLEAGEFKKALEEIMELAREANKY 458
>gnl|CDD|107278 cd06283, PBP1_RegR_EndR_KdgR_like, Ligand-binding domain of DNA
transcription repressor RegR and other putative
regulators such as KdgR and EndR. Ligand-binding domain
of DNA transcription repressor RegR and other putative
regulators such as KdgR and EndR, all of which are
members of the LacI-GalR family of bacterial
transcription regulators. RegR regulates bacterial
competence and the expression of virulence factors,
including hyaluronidase. The LacI-GalR family repressors
are composed of two functional domains: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
ligand-binding domain, which is homologous to the
sugar-binding domain of ABC-type transport systems that
contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 267
Score = 29.5 bits (67), Expect = 2.3
Identities = 25/127 (19%), Positives = 49/127 (38%), Gaps = 25/127 (19%)
Query: 158 RKIANAIFDTLPTSSYE---EALKYFLEAEKQHPLFYSQNVLMLGKTYMRLENYEQAAYY 214
RKI DT+ +YE EA+ + +E + LF ++ + + R E +++A
Sbjct: 86 RKIPELGVDTVTLDNYEAAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEAL-- 143
Query: 215 LEMTKNYPVKQDKDQCFEITDMPWYQRKIANAIFDTLPTSSYEEALKYFLEAEKQHPLFY 274
+ + +++ EI D +E L+ L K+ +
Sbjct: 144 ----AEHGIGVNEEL-IEIDDED---------------ADELDERLRQLLNKPKKKTAIF 183
Query: 275 SQNVLML 281
+ N L+L
Sbjct: 184 AANGLIL 190
>gnl|CDD|188072 TIGR00683, nanA, N-acetylneuraminate lyase. N-acetylneuraminate
lyase is also known as N-acetylneuraminic acid aldolase,
sialic acid aldolase, or sialate lyase. It is an
intracellular enzyme. The structure of this
homotetrameric enzyme related to dihydrodipicolinate
synthase is known. In Clostridium tertium, the enzyme
appears to be in an operon with a secreted sialidase
that releases sialic acid from host
sialoglycoconjugates. In several E. coli strains,
however, this enzyme is responsible for
N-acetyl-D-neuraminic acid synthesis for capsule
production by condensing N-acetyl-D-mannosamine and
pyruvate [Cell envelope, Biosynthesis and degradation of
surface polysaccharides and lipopolysaccharides, Central
intermediary metabolism, Amino sugars].
Length = 290
Score = 29.1 bits (65), Expect = 2.9
Identities = 23/105 (21%), Positives = 38/105 (36%), Gaps = 16/105 (15%)
Query: 34 NKMLESSEYKEDVEIIWRLVRVKYNLATHSSSLSDADKKQLILSAYFLVYNAL------- 86
N ML + E KE I + + L S++ + +L A L Y+ L
Sbjct: 48 NFMLSTEEKKEIFRIAKDEAKDQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFY 107
Query: 87 -----PQHEDHY----AIHKWLAVILNEKATLEGTKARIQQLETI 122
P+ + +Y A L +I+ L G I+Q +
Sbjct: 108 YKFSFPEIKHYYDTIIAETGGLNMIVYSIPFLTGVNMGIEQFGEL 152
>gnl|CDD|224643 COG1729, COG1729, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 262
Score = 29.0 bits (65), Expect = 3.5
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 162 NAIFDTLPTSSYEEALKYFLEAEKQHPL-FYSQNVLM-LGKTYMRLENYEQAAY-YLEMT 218
NA D + Y EA + F K++P Y+ N LG++ +YE AAY + +
Sbjct: 146 NAALDLYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVV 205
Query: 219 KNYP 222
K+YP
Sbjct: 206 KDYP 209
Score = 29.0 bits (65), Expect = 3.5
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 245 NAIFDTLPTSSYEEALKYFLEAEKQHPL-FYSQNVLM-LGKTYMRLENYEQAAY-YLEMT 301
NA D + Y EA + F K++P Y+ N LG++ +YE AAY + +
Sbjct: 146 NAALDLYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVV 205
Query: 302 KNYP 305
K+YP
Sbjct: 206 KDYP 209
>gnl|CDD|232936 TIGR00355, purH, phosphoribosylaminoimidazolecarboxamide
formyltransferase/IMP cyclohydrolase. PurH is
bifunctional: IMP cyclohydrolase (EC 3.5.4.10);
phosphoribosylaminoimidazolecarboxamide
formyltransferase (EC 2.1.2.3) Involved in purine
ribonucleotide biosynthesis. The IMP cyclohydrolase
activity is in the N-terminal region [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 511
Score = 28.6 bits (64), Expect = 4.5
Identities = 26/114 (22%), Positives = 41/114 (35%), Gaps = 22/114 (19%)
Query: 212 AYYLEMTKNYPVKQDKDQ-----CFEITDMPWYQRKIANAIFDTLPTSSYEEALKYFLEA 266
A E+ + + FE T Y IAN F L +E ++ L
Sbjct: 149 AILSELDEQGSISLALRFDLAIKAFEHTAA--YDAAIAN-YFGKL--VGEKEPRQFNLNF 203
Query: 267 EKQHPLFYSQNVLMLGKTYMRLENYEQAAYYLEMTKNYPAVQEATKLLEKAKSY 320
K+ L Y +N +++AA+Y+ +V A +L K SY
Sbjct: 204 TKKQTLRYGEN------------PHQKAAFYVTQNVKEGSVATAEQLQGKELSY 245
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate
transport and metabolism].
Length = 299
Score = 28.5 bits (64), Expect = 4.6
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 1 MSSDEAAKTVSKVSEEFLKKSDDLFEEQQFEEVNKMLESSEYKEDVE--IIWRLVR 54
+ D A ++ EE K+ L + + EV + L E + ++WR +R
Sbjct: 29 VDPDLAYSIAIEIQEELKKEGIRLVTKDEIREVYQKLLEKGDPEVAKRYLLWRRIR 84
>gnl|CDD|233224 TIGR00993, 3a0901s04IAP86, chloroplast protein import component
Toc86/159, G and M domains. The long precursor of the
86K protein originally described is proposed to have
three domains. The N-terminal A-domain is acidic,
repetitive, weakly conserved, readily removed by
proteolysis during chloroplast isolation, and not
required for protein translocation. The other domains
are designated G (GTPase) and M (membrane anchor); this
family includes most of the G domain and all of M
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 763
Score = 28.4 bits (63), Expect = 5.6
Identities = 13/21 (61%), Positives = 17/21 (80%)
Query: 181 LEAEKQHPLFYSQNVLMLGKT 201
LEAE Q PL +S N+L+LGK+
Sbjct: 107 LEAEGQDPLDFSLNILVLGKS 127
Score = 28.4 bits (63), Expect = 5.6
Identities = 13/21 (61%), Positives = 17/21 (80%)
Query: 264 LEAEKQHPLFYSQNVLMLGKT 284
LEAE Q PL +S N+L+LGK+
Sbjct: 107 LEAEGQDPLDFSLNILVLGKS 127
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like 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.
Length = 316
Score = 27.8 bits (62), Expect = 8.7
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 30 FEEVNKMLESSEYKEDVEIIWRLVRVKYN----LATHSSS--LSDADKKQLI-LSAYFLV 82
+E ++L S E + ++ + R R KY LAT S S L+ K ++ S ++
Sbjct: 238 IDEAWRLLSSPEGADFLDELAREGR-KYGAGVILATQSPSDLLASGIAKGILNNSTTKII 296
Query: 83 YN 84
Sbjct: 297 LR 298
>gnl|CDD|233253 TIGR01057, topA_arch, DNA topoisomerase I, archaeal. This model
describes topoisomerase I from archaea. These enzymes
are involved in the control of DNA topology. DNA
topoisomerase I belongs to the type I topoisomerases,
which are ATP-independent [DNA metabolism, DNA
replication, recombination, and repair].
Length = 618
Score = 27.9 bits (62), Expect = 9.4
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 4 DEAAKTVSKVSEEFLKKSDDLFEE 27
DEA K + K+ EEF K+ DD+ E
Sbjct: 555 DEAKKRLRKILEEFKKRLDDIGIE 578
>gnl|CDD|241405 cd13251, PH_ASAP, ArfGAP with SH3 domain, ankyrin repeat and PH
domain Pleckstrin homology (PH) domain. ASAPs (ASAP1,
ASAP2, and ASAP3) function as an Arf-specific GAPs,
participates in rhodopsin trafficking, is associated
with tumor cell metastasis, modulates phagocytosis,
promotes cell proliferation, facilitates vesicle
budding, Golgi exocytosis, and regulates vesicle coat
assembly via a Bin/Amphiphysin/Rvs domain. ASAPs contain
an NH2-terminal BAR domain, a tandem PH domain/GAP
domain, three ankyrin repeats, two proline-rich regions,
and a COOH-terminal Src homology 3 (SH3) domain. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 108
Score = 26.6 bits (59), Expect = 9.8
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 55 VKYNLATHSSSLSDADKKQLILSAYFLVYNALPQHEDHYAIHKWLAVILNEK 106
VK NL T + DKK L ++ Y+ Q ED W++V+ N K
Sbjct: 52 VKLNLLTCQVKPNPEDKKCFDLISHNRTYHF--QAEDEQEAEAWISVLQNSK 101
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
0.316 0.130 0.372
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,176,022
Number of extensions: 1552605
Number of successful extensions: 1927
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1882
Number of HSP's successfully gapped: 80
Length of query: 323
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 226
Effective length of database: 6,635,264
Effective search space: 1499569664
Effective search space used: 1499569664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.5 bits)