RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6534
(309 letters)
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1
subunit/Transcription initiation factor TFIIB
[Transcription].
Length = 285
Score = 268 bits (687), Expect = 1e-89
Identities = 104/269 (38%), Positives = 163/269 (60%), Gaps = 8/269 (2%)
Query: 16 LIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLST 75
+I DY G+ +C++CGLV+ D +ID G EWR F RVG P P ++ LST
Sbjct: 12 IITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDER----HERRVGAPLTPSIHDKGLST 67
Query: 76 MIGPGRGDASFDGFGMSKYQNR-RTMNSSDRALLNAIREINSMADRINLTKTIVDRANNL 134
+IG G D + + K+Q R R ++ +R L+ A+ E+ +A + L +++ + A +
Sbjct: 68 IIGWGDKDKMYR---LRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARI 124
Query: 135 FKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKA 194
+++ D L+GRS +++A+AC+Y ACR GVPRT EI +SKKEIGR ++L+++
Sbjct: 125 YRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEIGRTYRLLVRE 184
Query: 195 LETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMA 254
L+ + + D++ RF S L L + V++ A I +KA + G+SP +AAAAIY+A
Sbjct: 185 LKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLA 244
Query: 255 SQASSDKRSQKEIGDIAGVAEVTIRQSYK 283
S ++R+QKE+ +AGV EVTIR YK
Sbjct: 245 SLLLGERRTQKEVAKVAGVTEVTIRNRYK 273
Score = 62.3 bits (152), Expect = 3e-11
Identities = 34/85 (40%), Positives = 50/85 (58%)
Query: 201 LITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSD 260
LIT + + R S L LP V++ A I RKAV+ ++ GRS SVAAA IY A + +
Sbjct: 97 LITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGV 156
Query: 261 KRSQKEIGDIAGVAEVTIRQSYKLM 285
R+ EI GV++ I ++Y+L+
Sbjct: 157 PRTLDEIAKALGVSKKEIGRTYRLL 181
Score = 52.3 bits (126), Expect = 8e-08
Identities = 22/86 (25%), Positives = 42/86 (48%)
Query: 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEI 173
I A ++ L+ + +A + K+ G+S +A+A +Y+A G RT KE+
Sbjct: 198 IPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEV 257
Query: 174 CAVSKISKKEIGRCFKLILKALETSV 199
V+ +++ I +K + AL+ V
Sbjct: 258 AKVAGVTEVTIRNRYKELADALDIEV 283
>gnl|CDD|234758 PRK00423, tfb, transcription initiation factor IIB; Reviewed.
Length = 310
Score = 249 bits (637), Expect = 1e-81
Identities = 106/286 (37%), Positives = 167/286 (58%), Gaps = 11/286 (3%)
Query: 8 CYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPL 67
C E LI DY G+ +C++CGLV+ + +ID G EWR F E+ SRVG P
Sbjct: 14 CPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQRE-KRSRVGAPMTYT 72
Query: 68 LNGSDLSTMIGPGRGDA---SFDG------FGMSKYQNR-RTMNSSDRALLNAIREINSM 117
++ LST I D+ S G + + K+Q R R N+++R L A+ E++ +
Sbjct: 73 IHDKGLSTDIDWRNKDSYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRI 132
Query: 118 ADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVS 177
A ++ L +++ + A ++++ + ++GRS + + +A LY ACR+ VPRT EI VS
Sbjct: 133 ASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVS 192
Query: 178 KISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDI 237
++S+KEIGRC++ +L+ L + D++ RF S L L VQK A I +KA E +
Sbjct: 193 RVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGL 252
Query: 238 VPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYK 283
G+ P +AAAAIY+AS ++R+Q+E+ ++AGV EVT+R YK
Sbjct: 253 TSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYK 298
Score = 56.2 bits (136), Expect = 4e-09
Identities = 28/76 (36%), Positives = 42/76 (55%)
Query: 210 RFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGD 269
R S L LP V++ A I RKAVE ++ GRS V AAA+Y A + R+ EI +
Sbjct: 131 RIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAE 190
Query: 270 IAGVAEVTIRQSYKLM 285
++ V+ I + Y+ +
Sbjct: 191 VSRVSRKEIGRCYRFL 206
Score = 37.3 bits (87), Expect = 0.006
Identities = 17/88 (19%), Positives = 42/88 (47%)
Query: 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEI 173
+ A + L+ + +A + ++ + G+ +A+A +YIA G RT +E+
Sbjct: 223 VPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREV 282
Query: 174 CAVSKISKKEIGRCFKLILKALETSVDL 201
V+ +++ + +K + + L+ + L
Sbjct: 283 AEVAGVTEVTVRNRYKELAEKLDIKIPL 310
>gnl|CDD|109440 pfam00382, TFIIB, Transcription factor TFIIB repeat.
Length = 71
Score = 101 bits (253), Expect = 2e-27
Identities = 37/71 (52%), Positives = 47/71 (66%)
Query: 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEI 173
I AD + L K + D AN L K D LKGRS ++IA+ACLYIACR E V RT KEI
Sbjct: 1 IKRFADALELPKKVADAANELAKLALDDNLLKGRSPESIAAACLYIACRLEEVKRTLKEI 60
Query: 174 CAVSKISKKEI 184
+V+++S+K I
Sbjct: 61 SSVAQVSEKTI 71
Score = 95.8 bits (239), Expect = 3e-25
Identities = 30/71 (42%), Positives = 45/71 (63%)
Query: 208 MSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEI 267
+ RF L LP V AA +A+ A++ +++ GRSP S+AAA +Y+A + KR+ KEI
Sbjct: 1 IKRFADALELPKKVADAANELAKLALDDNLLKGRSPESIAAACLYIACRLEEVKRTLKEI 60
Query: 268 GDIAGVAEVTI 278
+A V+E TI
Sbjct: 61 SSVAQVSEKTI 71
>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold. Protein binding domain
functioning in cell-cycle and transcription control.
Present in cyclins, TFIIB and Retinoblastoma (RB).The
cyclins consist of 8 classes of cell cycle regulators
that regulate cyclin dependent kinases (CDKs). TFIIB is
a transcription factor that binds the TATA box. Cyclins,
TFIIB and RB contain 2 copies of the domain.
Length = 88
Score = 68.4 bits (168), Expect = 7e-15
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 1/84 (1%)
Query: 110 AIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRT 169
+ + +A + L+ + A NL + ++ GRS +A+A LY+A + E +P
Sbjct: 5 PLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPW 64
Query: 170 FKEICAVSKI-SKKEIGRCFKLIL 192
K++ V+ +++EI R KL+L
Sbjct: 65 LKDLVHVTGYATEEEILRMEKLLL 88
Score = 64.6 bits (158), Expect = 2e-13
Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 206 DFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQK 265
DF+ R L L A ++ + + V GRSP VAAAA+Y+A++ K
Sbjct: 7 DFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLK 66
Query: 266 EIGDIAGVA-EVTIRQSYKLMY 286
++ + G A E I + KL+
Sbjct: 67 DLVHVTGYATEEEILRMEKLLL 88
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and
Retinoblastoma. A helical domain present in cyclins and
TFIIB (twice) and Retinoblastoma (once). A protein
recognition domain functioning in cell-cycle and
transcription control.
Length = 83
Score = 63.0 bits (154), Expect = 5e-13
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 1/81 (1%)
Query: 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEI 173
+ + +NL ++ A NL + S IA+A LY+A + E P KE+
Sbjct: 3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKEL 62
Query: 174 CAVSKI-SKKEIGRCFKLILK 193
+ +++EI R +L+L+
Sbjct: 63 VHYTGYFTEEEILRMERLLLE 83
Score = 56.1 bits (136), Expect = 2e-10
Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 1/82 (1%)
Query: 206 DFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQK 265
DF+ R C L+L A ++ + + SP +AAAA+Y+AS+ K
Sbjct: 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTK 60
Query: 266 EIGDIAGVA-EVTIRQSYKLMY 286
E+ G E I + +L+
Sbjct: 61 ELVHYTGYFTEEEILRMERLLL 82
>gnl|CDD|203895 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding. The transcription
factor TFIIB contains a zinc-binding motif near the
N-terminus. This domain is involved in the interaction
with RNA pol II and TFIIF and plays a crucial role in
selecting the transcription initiation site. The domain
adopts a zinc ribbon like structure.
Length = 40
Score = 51.5 bits (124), Expect = 3e-09
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 8 CYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEW 45
C ++ DY G+ +C+ECGLV+ D +ID G EW
Sbjct: 3 CPNCGSTEIVFDYERGEYVCTECGLVLEDNIIDEGPEW 40
>gnl|CDD|227640 COG5333, CCL1, Cdk activating kinase (CAK)/RNA polymerase II
transcription initiation/nucleotide excision repair
factor TFIIH/TFIIK, cyclin H subunit [Cell division and
chromosome partitioning / Transcription / DNA
replication, recombination, and repair].
Length = 297
Score = 37.4 bits (87), Expect = 0.006
Identities = 16/87 (18%), Positives = 40/87 (45%)
Query: 92 SKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDA 151
+ T+ ++ ++ I + R+NL +T++ A F + + +++ S +
Sbjct: 30 LVLEPELTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYS 89
Query: 152 IASACLYIACRQEGVPRTFKEICAVSK 178
+ + C+Y+AC+ E PR ++
Sbjct: 90 VVTTCVYLACKVEDTPRDISIESFEAR 116
>gnl|CDD|198101 smart01033, BING4CT, BING4CT (NUC141) domain. This C terminal
domain is found in the BING4 family of nucleolar WD40
repeat proteins.
Length = 80
Score = 29.5 bits (67), Expect = 0.43
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 74 STMIGPGRGDASFDGFGMSKYQNRRTMNSSD-RALLNAIR 112
S++I PG G+ +FD + ++ R+ + R+LL +
Sbjct: 33 SSIIVPGAGEPNFDSLEANPFETRKQRREREVRSLLEKLP 72
>gnl|CDD|216744 pfam01857, RB_B, Retinoblastoma-associated protein B domain. The
crystal structure of the Rb pocket bound to a
nine-residue E7 peptide containing the LxCxE motif,
shared by other Rb-binding viral and cellular proteins,
shows that the LxCxE peptide binds a highly conserved
groove on the B domain. The B domain has a cyclin fold.
Length = 130
Score = 30.4 bits (69), Expect = 0.54
Identities = 15/69 (21%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 107 LLNAIREINSMADRINLTKTIVDRANNLFKQ--VHDGKNLKGRSNDAIASACLYIACRQE 164
L A+R + + +R++L++ + ++ LF+ + + + R D I +Y + +
Sbjct: 12 KLAAVR-LRDLCERLSLSEELREKIWTLFEHTLQQETELMMDRHLDQILLCAIYGIAKVK 70
Query: 165 GVPRTFKEI 173
FKEI
Sbjct: 71 QEDLKFKEI 79
>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain. Cyclins regulate
cyclin dependent kinases (CDKs). Human cyclin-O is a
Uracil-DNA glycosylase that is related to other cyclins.
Cyclins contain two domains of similar all-alpha fold,
of which this family corresponds with the N-terminal
domain.
Length = 127
Score = 29.0 bits (66), Expect = 1.3
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 123 LTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGV-PRTFKEICAVSK--I 179
L +DR L KQ L+ + CL IA + E + P + ++ ++
Sbjct: 54 LAVNYLDRF--LSKQPVPRTKLQ-----LVGVTCLLIAAKYEEIYPPSVEDFVYITDNAY 106
Query: 180 SKKEIGRCFKLILKALE 196
+K+EI R LIL L
Sbjct: 107 TKEEILRMELLILSTLN 123
>gnl|CDD|217307 pfam02984, Cyclin_C, Cyclin, C-terminal domain. Cyclins regulate
cyclin dependent kinases (CDKs). Human CCNO is a
Uracil-DNA glycosylase that is related to other cyclins.
Cyclins contain two domains of similar all-alpha fold,
of which this family corresponds with the C-terminal
domain.
Length = 117
Score = 28.7 bits (65), Expect = 1.4
Identities = 13/44 (29%), Positives = 26/44 (59%)
Query: 152 IASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKAL 195
IA+A +Y+A + G P + + + S++++ C KL+L+ L
Sbjct: 45 IAAAAVYLARKTLGSPPWTETLEHYTGYSEEDLKPCVKLLLELL 88
>gnl|CDD|129461 TIGR00364, TIGR00364, queuosine biosynthesis protein QueC. Members
of this protein family are QueC, involved in
synthesizing pre-Q0 from GTP en route to tRNA
modification with queuosine. This protein family is
represented by a single member in nearly every completed
large (> 1000 genes) prokaryotic genome. In Rhizobium
meliloti, the gene was designated exsB, possibly because
of polar effects on exsA expression in a shared
polycistronic mRNA. In Arthrobacter viscosus, the
homologous gene was designated ALU1 and was associated
with an aluminum tolerance phenotype [Unknown function,
General].
Length = 201
Score = 29.7 bits (67), Expect = 1.7
Identities = 24/111 (21%), Positives = 45/111 (40%), Gaps = 28/111 (25%)
Query: 154 SACLYIACRQEGVPRTFKEICAVS----KISKKEIGRCFKLILKAL---ETSVDLITTGD 206
+ CL IA + E+ A++ + +E+ + I +AL +DL
Sbjct: 12 TTCLAIAKDE------GYEVHAITFDYGQRHSREL-ESARKIAEALGIEHHVIDL----S 60
Query: 207 FMSRFCSNLSLPNMVQKAATHIARKAVELDI-----VPGRSPISVAAAAIY 252
+ + + +L + +K+ E D VPGR+ I ++ AA Y
Sbjct: 61 LLKQLGGS-AL----TDESEIPPQKSNEEDTLPNTFVPGRNAIFLSIAASY 106
>gnl|CDD|218139 pfam04545, Sigma70_r4, Sigma-70, region 4. Region 4 of sigma-70
like sigma-factors are involved in binding to the -35
promoter element via a helix-turn-helix motif. Due to
the way Pfam works, the threshold has been set
artificially high to prevent overlaps with other
helix-turn-helix families. Therefore there are many
false negatives.
Length = 50
Score = 27.0 bits (61), Expect = 1.7
Identities = 6/19 (31%), Positives = 12/19 (63%)
Query: 262 RSQKEIGDIAGVAEVTIRQ 280
+ +EIG+ G++ +RQ
Sbjct: 21 LTLEEIGERLGISRERVRQ 39
>gnl|CDD|149288 pfam08149, BING4CT, BING4CT (NUC141) domain. This C terminal
domain is found in the BING4 family of nucleolar WD40
repeat proteins.
Length = 80
Score = 27.9 bits (63), Expect = 1.9
Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 73 LSTMIGPGRGDASFDGFGMSKYQNRRTMNSSD-RALLNAIR 112
S++I PG G+ +FD + ++ ++ + R+LL +
Sbjct: 32 FSSIIVPGSGEPNFDSLEANPFETKKQRREREVRSLLEKLP 72
>gnl|CDD|211425 cd11583, Orc6_mid, Middle domain of the origin recognition complex
subunit 6. Orc6 is a subunit of the origin recognition
complex in eukaryotes, and it may be involved in binding
to DNA. This model describes the central or middle
domain of Orc6, whose structure resembles that of TFIIB,
a DNA-binding transcription factor. Orc6 appears to form
distinct complexes with DNA, and a putative DNA-binding
site has been identified.
Length = 94
Score = 27.6 bits (62), Expect = 2.4
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 148 SNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALE 196
S +A Y+AC++ V ++ VS + F + ++E
Sbjct: 44 SLPQFTAAAFYLACKKLKVKVDKSKLLEVSGVDPSI----FDRLCASME 88
>gnl|CDD|173944 cd08185, Fe-ADH1, Iron-containing alcohol dehydrogenases-like.
Iron-containing alcohol dehydrogenases-like (ADH).
Alcohol dehydrogenase catalyzes the reduction of
acetaldehyde to alcohol with NADP as cofactor. Its
activity requires iron ions. The protein structure
represents a dehydroquinate synthase fold and is a
member of the iron-containing alcohol dehydrogenase-like
family. They are distinct from other alcohol
dehydrogenases which contain different protein domains.
Proteins of this family have not been characterized.
Their specific function is unknown. They are present in
bacteria and archaea.
Length = 380
Score = 29.5 bits (67), Expect = 2.6
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 131 ANNLFKQVHDGKNLKGRSNDAIAS--ACLYIAC 161
A L + V DG +L+ R A A+ + A
Sbjct: 224 AKYLPRAVKDGSDLEAREKMAWANTLGGMVEAN 256
>gnl|CDD|236989 PRK11809, putA, trifunctional transcriptional regulator/proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1318
Score = 29.2 bits (66), Expect = 3.4
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 217 LPNMVQKAATHIARKAVELDIVP-----GRSPISVAAAAIYMASQASSDKRSQKEIGDIA 271
LP V +AA A + E + VP R P +A AA +A Q + R+QK G A
Sbjct: 86 LPQSVLRAAITAAYRRPETEAVPMLLEQARLPAPLAEAAHKLAYQLAEKLRNQKSAGGRA 145
Query: 272 GVAE 275
G+ +
Sbjct: 146 GMVQ 149
>gnl|CDD|218305 pfam04877, Hairpins, HrpZ. HrpZ from the plant pathogen
Pseudomonas syringae binds to lipid bilayers and forms a
cation-conducting pore in vivo. This pore-forming
activity may allow nutrient release or delivery of
virulence factors during bacterial colonisation of host
plants. The family of hairpinN proteins, Harpin, has
been merged into this family. HrpN is a virulence
determinant which elicits lesion formation in
Arabidopsis and tobacco and triggers systemic resistance
in Arabidopsis.
Length = 277
Score = 28.7 bits (64), Expect = 4.0
Identities = 7/41 (17%), Positives = 15/41 (36%)
Query: 71 SDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAI 111
DL + G G ++ + + + + D +L I
Sbjct: 130 PDLGNQVLNGLGKSALNDLLTHSDSSGTSFSKDDMPMLKEI 170
>gnl|CDD|236526 PRK09458, pspB, phage shock protein B; Provisional.
Length = 75
Score = 26.8 bits (60), Expect = 4.0
Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 92 SKYQNRRTMNSSDRALLN-AIREINSMADRINLTKTIVD 129
SK Q + ++ ++ L + M +RI + I+D
Sbjct: 28 SKRQGSQGLSQEEQQRLAQLTEKAERMRERIQALEAILD 66
>gnl|CDD|162579 TIGR01883, PepT-like, peptidase T-like protein. This model
represents a clade of enzymes closely related to
Peptidase T, an aminotripeptidase found in bacteria.
This clade consists of gram positive bacteria of which
several additionally contain a Peptidase T gene.
Length = 361
Score = 28.4 bits (63), Expect = 4.9
Identities = 23/79 (29%), Positives = 31/79 (39%), Gaps = 2/79 (2%)
Query: 219 NMVQKAATHIARKAVELDIVP--GRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEV 276
K IA K +VP G S ISVA AI+ D+ + IG +G
Sbjct: 170 PTQVKVDATIAGKDAHAGLVPEDGISAISVARMAIHAMRLGRIDEETTANIGSFSGGVNT 229
Query: 277 TIRQSYKLMYPHASKLFPQ 295
I Q +L+ A L +
Sbjct: 230 NIVQDEQLIVAEARSLSFR 248
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 28.0 bits (63), Expect = 6.6
Identities = 23/103 (22%), Positives = 46/103 (44%), Gaps = 23/103 (22%)
Query: 191 ILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKA-VELDIVPGRSPISVAAA 249
IL ++ + L + L N + + A + ++ E I R +S+++A
Sbjct: 113 ILGQVKNAYKLAKEAGTSGK------LLNRLFQKAIKVGKRVRTETGI--SRGAVSISSA 164
Query: 250 AIYMASQASSDKRSQK-------EIGDIA-------GVAEVTI 278
A+ +A + + + +K E+G++A GVAE+TI
Sbjct: 165 AVELAEKIFGNLKGKKVLVIGAGEMGELAAKHLAAKGVAEITI 207
>gnl|CDD|225870 COG3333, COG3333, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 504
Score = 27.6 bits (62), Expect = 8.6
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 237 IVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVA 274
++PG ++A+ Y + S K + G I GVA
Sbjct: 266 VLPGGGA-TIASFLSYSTEKRLSKKPEEFGKGSIEGVA 302
>gnl|CDD|216988 pfam02353, CMAS, Mycolic acid cyclopropane synthetase. This
family consist of Cyclopropane-fatty-acyl-phospholipid
synthase or CFA synthase EC:2.1.1.79 this enzyme
catalyze the reaction: S-adenosyl-L-methionine +
phospholipid olefinic fatty acid <=>
S-adenosyl-L-homocysteine + phospholipid cyclopropane
fatty acid.
Length = 273
Score = 27.7 bits (62), Expect = 8.6
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 7 CCY-EHPDAPLIEDYRAG-DQICSECGLVVGDRVIDVGSEW 45
C Y E PD L E +A D I + GL G ++D+G W
Sbjct: 33 CAYFERPDMTLEEAQQAKLDLILDKLGLKPGMTLLDIGCGW 73
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
0.319 0.134 0.392
Gapped
Lambda K H
0.267 0.0773 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,338,723
Number of extensions: 1425335
Number of successful extensions: 1361
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1355
Number of HSP's successfully gapped: 40
Length of query: 309
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 212
Effective length of database: 6,635,264
Effective search space: 1406675968
Effective search space used: 1406675968
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: 59 (26.4 bits)