RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy480
(283 letters)
>gnl|CDD|216028 pfam00621, RhoGEF, RhoGEF domain. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that pfam00169
domains invariably occur C-terminal to RhoGEF/DH
domains.
Length = 179
Score = 89.6 bits (223), Expect = 8e-22
Identities = 37/175 (21%), Positives = 64/175 (36%), Gaps = 58/175 (33%)
Query: 43 VANWDRDHKIGDVFVASFSKSIVLEIYSEPWPIGTGIIRLVMCFKSIVLEIYSEFINNFS 102
+ W +IGD+F+ ++YS + +N+
Sbjct: 63 LEEWPDIQRIGDIFLKFAPF----------------------------FKVYSTYCSNYP 94
Query: 103 AAMDVARGESKKKPALAEFFKSRQNSSMDRLSFFGLMVKPVQRFPQFILFLQSRQNSSMD 162
A+++ + KK P A+F K + +
Sbjct: 95 RALELLKKLRKKNPRFAKFLK------------------------------ECEASPLCR 124
Query: 163 RLSFFGLMVKPVQRFPQFILFLQDLLNHTGHGHPDRMSLQLALTQLESLAELLNE 217
L ++KPVQR P++ L L++LL HT HPD L+ AL ++ +A +NE
Sbjct: 125 GLDLNSFLIKPVQRIPRYPLLLKELLKHTPPDHPDYEDLKKALEAIKEVASQINE 179
>gnl|CDD|238091 cd00160, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous
(DH) domain. It appears that PH domains invariably occur
C-terminal to RhoGEF/DH domains.
Length = 181
Score = 69.6 bits (171), Expect = 2e-14
Identities = 40/158 (25%), Positives = 62/158 (39%), Gaps = 34/158 (21%)
Query: 59 SFSKSIVLEIYSEPWPIGTGIIRLVMCFKSIVLEIYSEFINNFSAAMDVARGESKKKPAL 118
F KS+ E E G I + + +IYSE+ +N A+++ + K
Sbjct: 58 IFLKSL-EERVEEWDKSGPRIGDVFLKLAPF-FKIYSEYCSNHPDALELLKKLKKFNKFF 115
Query: 119 AEFFKSRQNSSMDRLSFFGLMVKPVQRFPQFILFLQSRQNSSMDRLSFFGLMVKPVQRFP 178
EF + S RL L++KPVQR
Sbjct: 116 QEF--------------------------------LEKAESECGRLKLESLLLKPVQRLT 143
Query: 179 QFILFLQDLLNHTGHGHPDRMSLQLALTQLESLAELLN 216
++ L L++LL HT GH DR L+ AL ++ +A +N
Sbjct: 144 KYPLLLKELLKHTPDGHEDREDLKKALEAIKEVASQVN 181
>gnl|CDD|214619 smart00325, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that PH domains
invariably occur C-terminal to RhoGEF/DH domains.
Improved coverage.
Length = 180
Score = 65.4 bits (160), Expect = 6e-13
Identities = 35/127 (27%), Positives = 58/127 (45%), Gaps = 31/127 (24%)
Query: 91 LEIYSEFINNFSAAMDVARGESKKKPALAEFFKSRQNSSMDRLSFFGLMVKPVQRFPQFI 150
+IYSE+ +N A+++ + + KK P +F K ++
Sbjct: 85 FKIYSEYCSNHPDALELLK-KLKKNPRFQKFLKEIES----------------------- 120
Query: 151 LFLQSRQNSSMDRLSFFGLMVKPVQRFPQFILFLQDLLNHTGHGHPDRMSLQLALTQLES 210
+ RL+ L++KPVQR ++ L L++LL HT H DR L+ AL ++
Sbjct: 121 -------SPQCRRLTLESLLLKPVQRLTKYPLLLKELLKHTPEDHEDREDLKKALKAIKE 173
Query: 211 LAELLNE 217
LA +NE
Sbjct: 174 LANQVNE 180
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 32.2 bits (73), Expect = 0.32
Identities = 52/267 (19%), Positives = 89/267 (33%), Gaps = 49/267 (18%)
Query: 40 NNPVANWDRDHKIGDVFVASFSKSIVLEIYSEPWPIGTGIIRLVMCFKSIVLEIYSEFIN 99
+ P R I +V LE + W I+ + I FI
Sbjct: 477 SLPKQEIKRQEAIYEVIYTERDFVKDLEYLRDTW------IKPLEESNIIPENARRNFIK 530
Query: 100 N-FSAAMDVARGESKKKPALAEFFKSRQNSSMDRLSFFGLMVKPVQRFPQFILFLQS--- 155
+ F+ ++ SK AL RQ S + + V +F FI + S
Sbjct: 531 HVFANINEIYAVNSKLLKALTN----RQCLSPIVNGIADIFLDYVPKFEPFIKYGASQPY 586
Query: 156 ------RQNSSMDRLSFF----------------GLMVKPVQRFPQFILFLQDLLNHTGH 193
R+ S + F G + KP R ++ L L+++L T
Sbjct: 587 AKYEFEREKSVNPNFARFDHEVERLDESRKLELDGYLTKPTTRLARYPLLLEEVLKFTDP 646
Query: 194 GHPDRMSLQLALTQLESLAELLNERKREAEQTQAFKDILKSISGKLSTRP------LADV 247
+PD + + L LN E+ + + D L ++ +L +P L D
Sbjct: 647 DNPDTEDIPKVIDMLREFLSRLN---FESGKAENRGD-LFHLNQQLLFKPEYVNLGLNDE 702
Query: 248 HRVLLRQDDVTQLVSALVARSSGKLEG 274
+R + V + + ++ G L G
Sbjct: 703 YR-KIIFKGVLKRKAKS--KTDGSLRG 726
>gnl|CDD|151671 pfam11229, DUF3028, Protein of unknown function (DUF3028). This
eukaryotic family of proteins has no known function.
Length = 589
Score = 31.2 bits (70), Expect = 0.71
Identities = 17/38 (44%), Positives = 22/38 (57%)
Query: 198 RMSLQLALTQLESLAELLNERKREAEQTQAFKDILKSI 235
R++LQ LT L LL +++ EQTQ F D L SI
Sbjct: 511 RVTLQEVLTLLPRSMLLLLQKEPWKEQTQKFIDWLFSI 548
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 30.6 bits (70), Expect = 0.92
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 5/38 (13%)
Query: 205 LTQLESLAELLNERKREAEQTQAFKDILKSISGKLSTR 242
LTQ E++A+L++ A+ QA + L+ + G LS
Sbjct: 124 LTQAEAIADLID-----AKTEQAARIALRQLQGALSQL 156
>gnl|CDD|218440 pfam05110, AF-4, AF-4 proto-oncoprotein. This family consists of
AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental
retardation syndrome) nuclear proteins. These proteins
have been linked to human diseases such as acute
lymphoblastic leukaemia and mental retardation. The
family also contains a Drosophila AF4 protein homologue
Lilliputian which contains an AT-hook domain.
Lilliputian represents a novel pair-rule gene that acts
in cytoskeleton regulation, segmentation and
morphogenesis in Drosophila.
Length = 1154
Score = 30.7 bits (69), Expect = 1.2
Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 8/41 (19%)
Query: 2 SHGASTSSATSWEEECHQLHPSSGSEHEDLSSDVDSESNNP 42
S G+S+SS+ S SSGS+ E SS DSE N P
Sbjct: 397 SSGSSSSSSGS--------ESSSGSDSESESSSSDSEENEP 429
>gnl|CDD|224369 COG1452, Imp, Organic solvent tolerance protein OstA [Cell envelope
biogenesis, outer membrane].
Length = 784
Score = 29.3 bits (66), Expect = 2.4
Identities = 11/59 (18%), Positives = 20/59 (33%), Gaps = 2/59 (3%)
Query: 122 FKSRQNSSMDRLSFFGLMVKPVQRFPQFILFLQ--SRQNSSMDRLSFFGLMVKPVQRFP 178
++ +++ +L + + PV F L Q N L V+P R
Sbjct: 382 KDNKPYNALPQLDYNYYLNDPVLGELNFTLDSQFVRFSNDDDYMPERTRLHVEPSLRLS 440
>gnl|CDD|134050 PRK00036, PRK00036, primosomal replication protein N; Reviewed.
Length = 107
Score = 27.3 bits (60), Expect = 3.5
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 164 LSFFGLMVKPVQRFPQFILFLQDLLNHTGH----GHPDRMSLQLALTQLESLAELL 215
LS L ++ P + L+ LL H GHP R+ L ++ L LA LL
Sbjct: 6 LSARVLECGAMRHTPAGLPALELLLVHESEVVEAGHPRRVELTISAVALGDLALLL 61
>gnl|CDD|218120 pfam04511, DER1, Der1-like family. The endoplasmic reticulum (ER)
of the yeast Saccharomyces cerevisiae contains of
proteolytic system able to selectively degrade misfolded
lumenal secretory proteins. For examination of the
components involved in this degradation process, mutants
were isolated. They could be divided into four
complementation groups. The mutations led to
stabilisation of two different substrates for this
process. The mutant classes were called 'der' for
'degradation in the ER'. DER1 was cloned by
complementation of the der1-2 mutation. The DER1 gene
codes for a novel, hydrophobic protein, that is
localised to the ER. Deletion of DER1 abolished
degradation of the substrate proteins. The function of
the Der1 protein seems to be specifically required for
the degradation process associated with the ER.
Interestingly this family seems distantly related to the
Rhomboid family of membrane peptidases. Suggesting that
this family may also mediate degradation of misfolded
proteins (Bateman A pers. obs.).
Length = 192
Score = 28.4 bits (64), Expect = 3.5
Identities = 20/114 (17%), Positives = 41/114 (35%), Gaps = 13/114 (11%)
Query: 76 GTGIIRLVMCFKSIVLEIYSEFINNFSAAMDVARGESKKKPALAEFFKSRQNSSMDRLSF 135
TG L + F+ +S+ ++ G + + A + +
Sbjct: 54 NTGFHFLFNLY----------FLYRYSSMLE--NGSFRGRAADYLYMLIFGAVLITIFGL 101
Query: 136 FGLMVKPVQRFPQFILFLQSRQNSSMDRLSFFGLMVKPVQRFPQFILFLQDLLN 189
Q I+++ SR+N+ + +++FFGL+ P +L LL
Sbjct: 102 IVNAYFLGQGLTAMIVYVWSRKNADV-QVNFFGLIRFKASYLPWVLLGFSFLLG 154
>gnl|CDD|226615 COG4130, COG4130, Predicted sugar epimerase [Carbohydrate transport
and metabolism].
Length = 272
Score = 28.6 bits (64), Expect = 3.9
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 222 AEQTQAFKDI--LKSISG----KLSTRPLADVHRVLLRQDDVTQ 259
A +T+ F D+ L ISG +L + D HRVL+ + D
Sbjct: 181 AGETEFFPDLTGLVHISGVEDPRLDVEDMRDPHRVLVGEKDRLD 224
>gnl|CDD|216261 pfam01041, DegT_DnrJ_EryC1, DegT/DnrJ/EryC1/StrS aminotransferase
family. The members of this family are probably all
pyridoxal-phosphate-dependent aminotransferase enzymes
with a variety of molecular functions. The family
includes StsA, StsC and StsS. The aminotransferase
activity was demonstrated for purified StsC protein as
the L-glutamine:scyllo-inosose aminotransferase
EC:2.6.1.50, which catalyzes the first amino transfer in
the biosynthesis of the streptidine subunit of
streptomycin.
Length = 362
Score = 28.4 bits (64), Expect = 4.0
Identities = 20/116 (17%), Positives = 39/116 (33%), Gaps = 22/116 (18%)
Query: 161 MDRLSFFGLMVKPVQRFPQFILFLQDLLNHTGHGHPDRMS-LQ--LALTQLESLAELLNE 217
L G +R+ + G+ R++ LQ + L QLE L +
Sbjct: 195 ARCLRNHGCGRPAFRRY----------RHEVPLGYNYRLTELQAAIGLAQLERL-DEFIA 243
Query: 218 RKREAEQTQAFKDILKSISGKLSTRPLADVHR------VLLRQDDVTQLVSALVAR 267
R+RE + + ++L + G + + +L ++ LV
Sbjct: 244 RRREIAEL--YSELLAELPGFVPLTLPTEEDDHAWHLFPILVPEERAISRDRLVEA 297
>gnl|CDD|214511 smart00090, RIO, RIO-like kinase.
Length = 237
Score = 28.4 bits (64), Expect = 4.0
Identities = 14/45 (31%), Positives = 22/45 (48%)
Query: 212 AELLNERKREAEQTQAFKDILKSISGKLSTRPLADVHRVLLRQDD 256
E+L+ R R A + + IL +I G +ST A+V+ L
Sbjct: 9 EEVLDGRTRLALYSLLNRGILSAIGGCISTGKEANVYHALDFDGS 53
>gnl|CDD|234003 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
This protein contains domains distinctive of a single
strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
well as a helicase domain (central region, homologous to
the corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 28.6 bits (64), Expect = 4.2
Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 1/81 (1%)
Query: 188 LNHTGHGHPDRMSLQLALTQLESLAELLNERKREAEQTQAFKDI-LKSISGKLSTRPLAD 246
L T H +++ E L E L R+ AE+ ++ L ++ + S D
Sbjct: 209 LIPTKHIGVHAKAMERRGEAAERLPENLAIRQENAERILDNPELVLDLLTTEQSVFTRRD 268
Query: 247 VHRVLLRQDDVTQLVSALVAR 267
+ R+L R D Q L+AR
Sbjct: 269 IARLLHRYIDDPQQFQQLMAR 289
>gnl|CDD|99740 cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family
(AHBA_syn). AHBA_syn family belongs to pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The members of this CD are
involved in various biosynthetic pathways for secondary
metabolites. Some well studied proteins in this CD are
AHBA_synthase, protein product of pleiotropic regulatory
gene degT, Arnb aminotransferase and pilin
glycosylation protein. The prototype of this family, the
AHBA_synthase, is a dimeric PLP dependent enzyme.
AHBA_syn is the terminal enzyme of
3-amino-5-hydroxybenzoic acid (AHBA) formation which is
involved in the biosynthesis of ansamycin antibiotics,
including rifamycin B. Some members of this CD are
involved in 4-amino-6-deoxy-monosaccharide D-perosamine
synthesis. Perosamine is an important element in the
glycosylation of several cell products, such as
antibiotics and lipopolysaccharides of gram-positive and
gram-negative bacteria. The pilin glycosylation protein
encoded by gene pglA, is a galactosyltransferase
involved in pilin glycosylation. Additionally, this CD
consists of ArnB (PmrH) aminotransferase, a
4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying
enzyme. This CD also consists of several predicted
pyridoxal phosphate-dependent enzymes apparently
involved in regulation of cell wall biogenesis. The
catalytic lysine which is present in all characterized
PLP dependent enzymes is replaced by histidine in some
members of this CD.
Length = 352
Score = 28.3 bits (64), Expect = 4.8
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 6/43 (13%)
Query: 198 RMS-LQ--LALTQLESLAELLNERKREAEQTQAFKDILKSISG 237
R+S +Q + L QLE L E++ R+ AE +K++L + G
Sbjct: 214 RLSEIQAAIGLAQLEKLDEIIARRREIAE---RYKELLADLPG 253
>gnl|CDD|132622 TIGR03583, EF_0837, probable amidohydrolase EF_0837/AHA_3915.
Members of this family of relatively uncommon proteins
are found in both Gram-positive (e.g. Enterococcus
faecalis) and Gram-negative (e.g. Aeromonas hydrophila)
bacteria, as part of a cluster of conserved proteins.
These proteins resemble aminohydrolases (see pfam01979),
including dihydroorotases. The function is unknown
[Hypothetical proteins, Conserved].
Length = 365
Score = 27.4 bits (61), Expect = 8.5
Identities = 10/38 (26%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 125 RQN--SSMDRLSFFGLMVKPVQRFPQFILFLQSRQNSS 160
Q+ + + L + + V+R+P FI+ L++R + S
Sbjct: 120 AQDELADLSNLDAS-AVKQAVERYPDFIVGLKARMSKS 156
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 27.4 bits (62), Expect = 9.1
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 205 LTQLESLAELLNERKREAEQTQAFKDILKSISGKLSTR 242
LTQ E++A+L++ A+ A + L+ + G LS
Sbjct: 122 LTQAEAIADLID-----AKTEAAARLALRQLQGALSKL 154
>gnl|CDD|200432 TIGR04181, NHT_00031, aminotransferase, LLPSF_NHT_00031 family.
This clade of aminotransferases is a member of the
pfam01041 (DegT/DnrJ/EryC1/StrS) superfamily. The family
is named after the instance in Leptospira interrogans
serovar Lai, str. 56601, where it is the 31st gene in
the 91-gene lipopolysaccharide biosynthesis locus.
Members of this family are generally found within a
subcluster of seven or more genes including an
epimerase/dehydratase, four genes homologous to the
elements of the neuraminic (sialic) acid biosynthesis
cluster (NeuABCD) and a nucleotidyl transferase.
Together it is very likely that these enzymes direct the
biosynthesis of a nine-carbon sugar analogous to
CMP-neuraminic acid. These seven genes form the core of
the cassette, although they are often accompanied by
additional genes that may further modify the product
sugar.
Length = 359
Score = 27.1 bits (61), Expect = 9.9
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 194 GHPDRMS-LQLAL--TQLESLAELLNERKREAEQTQAFKDILKSISG 237
G+ RM + AL QLE L E L RKRE + +K+ I G
Sbjct: 238 GYNYRMPNINAALGCAQLEQLEEFL-ARKREL--AEIYKEFFSGIPG 281
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
0.318 0.132 0.378
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,065,809
Number of extensions: 1344214
Number of successful extensions: 1354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1349
Number of HSP's successfully gapped: 38
Length of query: 283
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 187
Effective length of database: 6,679,618
Effective search space: 1249088566
Effective search space used: 1249088566
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 (21.8 bits)
S2: 58 (26.1 bits)