RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7191
(413 letters)
>gnl|CDD|234597 PRK00050, PRK00050, 16S rRNA m(4)C1402 methyltranserfase;
Provisional.
Length = 296
Score = 181 bits (461), Expect = 4e-54
Identities = 106/344 (30%), Positives = 153/344 (44%), Gaps = 78/344 (22%)
Query: 79 GLNDSSDDVTMIDMTYGDGNHTRLILENIG-NVKVICLDRDKESFEKAKTLAANDPRLVP 137
L D + +D T+G G H+R ILE +G ++I +DRD ++ AK R
Sbjct: 14 ALAIKPDGI-YVDGTFGGGGHSRAILERLGPKGRLIAIDRDPDAIAAAKDRLKPFGRFTL 72
Query: 138 VYGKFSDLPNILKNMNNNFNSIDGIIMDVGISDSQ-ANSTRGFKPDSNSLLDMRMSQE-G 195
V+G FS+L +L +DGI++D+G+S Q ++ RGF + LDMRM Q G
Sbjct: 73 VHGNFSNLKEVLAE---GLGKVDGILLDLGVSSPQLDDAERGFSFRKDGPLDMRMDQSQG 129
Query: 196 ITGYQVLSAIDEVSLAKILKTYGEEKRSRQIARAIIETRYTFKKLERTRDLNELVASVSR 255
+T +V++ E LA+I K YGEE+ +R+IARAI+E R K + T +L E++ S
Sbjct: 130 LTAAEVVNTYSEEELARIFKEYGEERFARRIARAIVEARPK-KPITTTGELAEIIKSAV- 187
Query: 256 PSQTWKRACRTESLQWIATASVVGTEVRVDPRKHGSEHVAQKVYNGLRRFVNNELNELNY 315
P + H A + + LR VN+EL EL
Sbjct: 188 ------------------------------PPRRKGIHPATRTFQALRIEVNDELEELER 217
Query: 316 AMIIAEKYLKPEGLLLTKCNSIV-----EDKIVKRHLTGNVIEHCANDLALKFVNHNLTV 370
A+ A LKP G L +++ ED+IVKR C N LK
Sbjct: 218 ALEAALDLLKPGGRL-----AVISFHSLEDRIVKRFFRELSKGCCGNKPKLK-------- 264
Query: 371 NPLDMSSLTSSPWTILDKIIPSDSDL---------KLRVAMKKE 405
LT P I PS+ ++ KLRVA + E
Sbjct: 265 ------LLTKKP------IKPSEEEIAANPRARSAKLRVAERLE 296
>gnl|CDD|223352 COG0275, COG0275, Predicted S-adenosylmethionine-dependent
methyltransferase involved in cell envelope biogenesis
[Cell envelope biogenesis, outer membrane].
Length = 314
Score = 179 bits (457), Expect = 3e-53
Identities = 102/339 (30%), Positives = 155/339 (45%), Gaps = 66/339 (19%)
Query: 85 DDVTMIDMTYGDGNHTRLILENIGNVK-VICLDRDKESFEKAKT-LAANDPRLVPVYGKF 142
D ID T G G H+R ILE + ++ +I +DRD ++ AK L D R+ V+G F
Sbjct: 23 PDGIYIDGTLGAGGHSRAILEKLPDLGRLIGIDRDPQAIAIAKERLKEFDGRVTLVHGNF 82
Query: 143 SDLPNILKNMNNNFNSIDGIIMDVGISDSQAN-STRGFKPDSNSLLDMRMSQE-GITGYQ 200
++L LK + +DGI++D+G+S Q + + RGF + LDMRM Q G++ +
Sbjct: 83 ANLAEALKELGIG--KVDGILLDLGVSSPQLDDAERGFSFRKDGPLDMRMDQTQGLSAAE 140
Query: 201 VLSAIDEVSLAKILKTYGEEKRSRQIARAIIETRYTFKKLERTRDLNELVASVSRPSQTW 260
V++ E LA+I K YGEE+ +++IARAI+E R K +E T++L E++ S
Sbjct: 141 VVNTYSEEDLARIFKEYGEERFAKRIARAIVERRKK-KPIETTKELAEIIKSAIPA---- 195
Query: 261 KRACRTESLQWIATASVVGTEVRVDPRKHGSEHVAQKVYNGLRRFVNNELNELNYAMIIA 320
K H A + + +R +VN+EL EL A+ A
Sbjct: 196 -------------------------KEKRKKIHPATRTFQAIRIYVNDELEELEEALEAA 230
Query: 321 EKYLKPEGLLLTKCNSIV-----EDKIVKRHLTGNVIEHCANDLALKFVNHNLTVNPLDM 375
LKP G L +++ ED+IVK L + L
Sbjct: 231 LDLLKPGGRL-----AVISFHSLEDRIVKNFFKELSKPGVPKGLPVT-----EEGPALKF 280
Query: 376 SSLTSSPWTILDKIIPSDSDL---------KLRVAMKKE 405
+T P I+PS+ ++ KLRVA K E
Sbjct: 281 KLITKKP------IMPSEEEIEANPRARSAKLRVAEKIE 313
>gnl|CDD|216706 pfam01795, Methyltransf_5, MraW methylase family. Members of this
family are probably SAM dependent methyltransferases
based on Escherichia coli rsmH. This family appears to
be related to pfam01596.
Length = 310
Score = 157 bits (398), Expect = 1e-44
Identities = 99/341 (29%), Positives = 150/341 (43%), Gaps = 58/341 (17%)
Query: 78 SGLNDSSDDVTMIDMTYGDGNHTRLILENIG-NVKVICLDRDKESFEKAKT-LAANDPRL 135
LN D + ID T G G H+ ILE + ++I +DRD ++ AK L R+
Sbjct: 14 ELLNIKPDGI-YIDCTLGGGGHSEAILEQLPEEGRLIGIDRDPQAIANAKERLKPFKGRV 72
Query: 136 VPVYGKFSDLPNILKNMNNNFNSIDGIIMDVGISDSQAN-STRGFKPDSNSLLDMRMSQE 194
++ F++L LK +DGI+ D+G+S Q + + RGF ++ LDMRM Q
Sbjct: 73 TLIHSNFANLFAYLKE--LGVGKVDGILFDLGVSSPQLDGAERGFSFKHDAPLDMRMDQS 130
Query: 195 -GITGYQVLSAIDEVSLAKILKTYGEEKRSRQIARAIIETRYTFKKLERTRDLNELVASV 253
G+T +VL+ E LA+I K YGEE+ S++IARAI+E R K +E T++L E++
Sbjct: 131 AGLTAAEVLNTYSEEDLARIFKKYGEERFSKRIARAIVERRKK-KPIETTKELAEIIKKA 189
Query: 254 SRPSQTWKRACRTESLQWIATASVVGTEVRVDPRKHGSEHVAQKVYNGLRRFVNNELNEL 313
K H A + + +R +VN+EL L
Sbjct: 190 VPA-----------------------------KAKRKKIHPATRTFQAIRIYVNDELESL 220
Query: 314 NYAMIIAEKYLKPEGLLLTKCNSIVEDKIVKRHLTGNVIEHCANDLAL-KFVNHNLTVNP 372
A+ A L P G L +ED+IVK N + + + L
Sbjct: 221 KEALEQAPDLLAPGGRLSVISFHSLEDRIVK-----NFFREYSKGCQVPAGLPVILEGLE 275
Query: 373 LDMSSLTSSPWTILDKIIPSDSDL---------KLRVAMKK 404
+ +T P I+PS+ ++ KLRVA K
Sbjct: 276 PLLKIITKKP------ILPSEEEIEENPRSRSAKLRVAEKI 310
>gnl|CDD|232778 TIGR00006, TIGR00006, 16S rRNA
(cytosine(1402)-N(4))-methyltransferase. This model
describes RsmH, a 16S rRNA methyltransferase.
Previously, this gene was designated MraW, known to be
essential in E. coli and widely conserved in bacteria
[Cell envelope, Biosynthesis and degradation of murein
sacculus and peptidoglycan].
Length = 307
Score = 146 bits (369), Expect = 1e-40
Identities = 84/262 (32%), Positives = 130/262 (49%), Gaps = 35/262 (13%)
Query: 86 DVTMIDMTYGDGNHTRLILENIGNVKVICLDRDKESFEKAKTLAANDPRLVPVYGKFSDL 145
D ID T G G H++ IL +G ++I +DRD ++ AK + +D R V ++ F++
Sbjct: 21 DGIYIDGTLGRGGHSKAILSQLGEGRLIGIDRDPQAIAFAKEIL-SDLRFVIIHDNFANF 79
Query: 146 PNILKNMNNNFNSIDGIIMDVGISDSQAN-STRGFKPDSNSLLDMRMSQE-GITGYQVLS 203
LK + IDGI++D+G+S Q + RGF + LDMRM Q ++ ++L+
Sbjct: 80 FEYLKELLVT--KIDGILVDLGVSSPQLDDPERGFSFMHDGPLDMRMDQSQKLSAAEILN 137
Query: 204 AIDEVSLAKILKTYGEEKRSRQIARAIIETRYTFKKLERTRDLNELVASVSRPSQTWKRA 263
E L ILK YGEE+ S++IARAI+E R K ++ T++L E+++
Sbjct: 138 TYSEEDLEWILKKYGEERFSKRIARAIVERRKK-KPIQTTKELAEVISKAVPG------- 189
Query: 264 CRTESLQWIATASVVGTEVRVDPRKHGSEHVAQKVYNGLRRFVNNELNELNYAMIIAEKY 323
K+ S H A +V+ +R +VN+EL EL A+ A
Sbjct: 190 ----------------------FSKYKSIHPATRVFQAIRIYVNDELEELEEALQFAPNL 227
Query: 324 LKPEGLLLTKCNSIVEDKIVKR 345
L P G L +ED+IVK
Sbjct: 228 LAPGGRLSIISFHSLEDRIVKN 249
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 34.7 bits (80), Expect = 0.017
Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 9/84 (10%)
Query: 86 DVTMIDMTYGDGNHTRLILENIGNVKVICLDRDKESFEKAK---TLAANDPRLVPVYGKF 142
++D G G + +V+ ++ D E+ A+ LA PR+ V G
Sbjct: 1 GDRVLDPGAGSGAFLLAAARAGPDARVVGVELDPEAAALARRRLALAGLAPRVRVVVGDA 60
Query: 143 SDLPNILKNMNNNFNSIDGIIMDV 166
+L + S D ++ +
Sbjct: 61 RELLELPD------GSFDLVLGNP 78
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 34.3 bits (79), Expect = 0.044
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 83 SSDDVTMIDMTYGDGNHTRLILENIG-NVKVICLDRDKESFEKAKTLAAN 131
+ ++D+ G G T ++ E +G +V+ +D +E+ EKAK A
Sbjct: 1 LKSGIKVLDLGCGTGYLTFILAEKLGPGAEVVGIDISEEAIEKAKENAKK 50
>gnl|CDD|100107 cd02440, AdoMet_MTases, S-adenosylmethionine-dependent
methyltransferases (SAM or AdoMet-MTase), class I;
AdoMet-MTases are enzymes that use
S-adenosyl-L-methionine (SAM or AdoMet) as a substrate
for methyltransfer, creating the product
S-adenosyl-L-homocysteine (AdoHcy). There are at least
five structurally distinct families of AdoMet-MTases,
class I being the largest and most diverse. Within this
class enzymes can be classified by different substrate
specificities (small molecules, lipids, nucleic acids,
etc.) and different target atoms for methylation
(nitrogen, oxygen, carbon, sulfur, etc.).
Length = 107
Score = 30.9 bits (70), Expect = 0.31
Identities = 16/73 (21%), Positives = 24/73 (32%), Gaps = 9/73 (12%)
Query: 95 GDGNHTRLILENIGNVKVICLDRDKESFEKAKTLAAN--DPRLVPVYGKFSDLPNILKNM 152
G G + +V +D + E A+ AA + + G +LP
Sbjct: 8 GTGALALALASG-PGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPE---- 62
Query: 153 NNNFNSIDGIIMD 165
S D II D
Sbjct: 63 --ADESFDVIISD 73
>gnl|CDD|224729 COG1816, Add, Adenosine deaminase [Nucleotide transport and
metabolism].
Length = 345
Score = 32.7 bits (75), Expect = 0.32
Identities = 23/106 (21%), Positives = 38/106 (35%), Gaps = 10/106 (9%)
Query: 212 KILKTYGEEKRSRQIARAIIETRYT----FKKLERTRDLNELVASVSRPSQTWKRACRTE 267
++ + YG + I+E F L+ + ASV R + + R E
Sbjct: 31 ELARRYGIALPPAEFDETILEELRAEYNKFNDLQEFLEKYYRGASVLRTEEDFYRLAY-E 89
Query: 268 SLQWIATASVVGTEVRVDPRKHGSEHVAQKVY-----NGLRRFVNN 308
L+ A +VV E+R DP H ++ G R +
Sbjct: 90 YLEDAAADNVVYAEIRFDPYLHTKRGLSVDTVVEGLIAGFRPAERD 135
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 30.4 bits (69), Expect = 0.45
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 2/57 (3%)
Query: 95 GDGNHTRLILENIGNVKVICLDRDKESFEKAKTLA--ANDPRLVPVYGKFSDLPNIL 149
G G+ + +V +D E E A+ A A PR+ V G D ++L
Sbjct: 11 GTGSLAIELARLFPGARVTGVDLSPEMLELARENAKLALGPRITFVQGDAPDALDLL 67
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 32.6 bits (75), Expect = 0.49
Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 4/79 (5%)
Query: 270 QWIATASVVGTEVRVDPRK-HGSEHVAQKVYNGLRRFVNNELNELNYAMIIAEKYLKPEG 328
+A+ + G ++ D ++ G + K++N RFV L++L + +
Sbjct: 550 FTLASLASPGRDINFDEKRVEGYRNFLNKLWN-ATRFVLMNLDDLGPDDLDLLALSLADR 608
Query: 329 LLLTKCNSIVEDKIVKRHL 347
+L++ N V++ V L
Sbjct: 609 WILSRLNETVKE--VTEAL 625
>gnl|CDD|222287 pfam13649, Methyltransf_25, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 97
Score = 30.4 bits (69), Expect = 0.50
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 95 GDGNHTRLILENIGNVKVICLDRDKESFEKAK-TLAANDPRLVPVYGKFSDLP 146
G G R + G V +D KE+ E AK L P++ V DLP
Sbjct: 7 GTGRVLRALAR-AGPSSVTGVDISKEALELAKERLRDKGPKVRFVVADARDLP 58
>gnl|CDD|236453 PRK09287, PRK09287, 6-phosphogluconate dehydrogenase; Validated.
Length = 459
Score = 30.1 bits (69), Expect = 2.3
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 222 RSRQIARAIIETRYTFKKLERTRDLNELVASVSRP 256
R+ + + KK+ L E VAS+ +P
Sbjct: 21 RTPEKTDEFLAEEGKGKKIVPAYTLEEFVASLEKP 55
>gnl|CDD|232896 TIGR00260, thrC, threonine synthase. Involved in threonine
biosynthesis it catalyses the reaction
O-PHOSPHO-L-HOMOSERINE + H(2)O = L-THREONINE +
ORTHOPHOSPHATE using pyridoxal phosphate as a cofactor.
the enzyme is distantly related to the serine/threonine
dehydratases which are also pyridoxal-phosphate
dependent enzymes. the pyridoxal-phosphate binding site
is a Lys (K) residues present at residue 70 of the model
[Amino acid biosynthesis, Aspartate family].
Length = 328
Score = 29.7 bits (67), Expect = 2.8
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 109 NVKVICL-DRDKESFEKAKTLAANDPRLVPVYGKFSDLPNILKNM-----NNNFNSIDGI 162
VKV+ L K S K + +V + G F D ++K + NS++ I
Sbjct: 94 GVKVVILYPAGKISLGKLAQALGYNAEVVAIDGNFDDAQRLVKQLFGDKEALGLNSVNSI 153
Query: 163 I 163
Sbjct: 154 P 154
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 28.8 bits (65), Expect = 5.9
Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 5/51 (9%)
Query: 103 ILENIGNVKVICLDRDKESFEKAKTLAA----NDPRLVPVYGKFSDLPNIL 149
I + +G VI +D +E E AK L A N P K + L
Sbjct: 184 IAKAMG-AAVIAVDIKEEKLELAKELGADEVLNSLDDSPKDKKAAGLGGGF 233
>gnl|CDD|220491 pfam09958, DUF2192, Uncharacterized protein conserved in archaea
(DUF2192). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 231
Score = 28.4 bits (64), Expect = 5.9
Identities = 25/104 (24%), Positives = 39/104 (37%), Gaps = 11/104 (10%)
Query: 135 LVPVYGK--FSDLPNILKNM---NNNFNSIDGIIMDVGISDSQANSTRGFKPDSNSLLDM 189
+V YG D P + + N + II++ +++ T S+
Sbjct: 65 VVGKYGLGLDEDYPGVFDKLFYIENRYEEALEIILEKEPEEAREKVTGELGGKSDENKVA 124
Query: 190 RMSQEGITGYQVLSAIDEVSLAKILKTYGE-----EKRSRQIAR 228
R+ + TG VL E L K LKT E + +R AR
Sbjct: 125 RVLRLVFTG-VVLGFKPEELLVKALKTLEEAFPELKHTARNYAR 167
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
0.314 0.130 0.362
Gapped
Lambda K H
0.267 0.0668 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,458,387
Number of extensions: 1974318
Number of successful extensions: 1545
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1523
Number of HSP's successfully gapped: 28
Length of query: 413
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 314
Effective length of database: 6,546,556
Effective search space: 2055618584
Effective search space used: 2055618584
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: 42 (22.0 bits)
S2: 60 (27.0 bits)