RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15517
(472 letters)
>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of transcription
factors; members include CAP (or cAMP receptor protein
(CRP)), which binds cAMP, FNR (fumarate and nitrate
reduction), which uses an iron-sulfur cluster to sense
oxygen) and CooA, a heme containing CO sensor. In all
cases binding of the effector leads to conformational
changes and the ability to activate transcription.
Cyclic nucleotide-binding domain similar to CAP are also
present in cAMP- and cGMP-dependent protein kinases
(cAPK and cGPK) and vertebrate cyclic nucleotide-gated
ion-channels. Cyclic nucleotide-monophosphate binding
domain; proteins that bind cyclic nucleotides (cAMP or
cGMP) share a structural domain of about 120 residues;
the best studied is the prokaryotic catabolite gene
activator, CAP, where such a domain is known to be
composed of three alpha-helices and a distinctive
eight-stranded, antiparallel beta-barrel structure;
three conserved glycine residues are thought to be
essential for maintenance of the structural integrity of
the beta-barrel; CooA is a homodimeric transcription
factor that belongs to CAP family; cAMP- and
cGMP-dependent protein kinases (cAPK and cGPK) contain
two tandem copies of the cyclic nucleotide-binding
domain; cAPK's are composed of two different subunits, a
catalytic chain and a regulatory chain, which contains
both copies of the domain; cGPK's are single chain
enzymes that include the two copies of the domain in
their N-terminal section; also found in vertebrate
cyclic nucleotide-gated ion-channels.
Length = 115
Score = 87.8 bits (218), Expect = 6e-21
Identities = 34/112 (30%), Positives = 53/112 (47%), Gaps = 7/112 (6%)
Query: 271 AFKGASPGCLRALSLKFKTTHAPPGDTLVHKGDVLTSLYFISRGSIEILRDD-----VVM 325
F G L L+ + P G+ ++ +GD SLY + GS+E+ + D ++
Sbjct: 1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIV 60
Query: 326 AILGKDDIYGENPCLHSTIGKSSSNVRALTYCDLHKIHRDDLLDVLDLYPEF 377
LG D++GE L + S+ VRALT +L + R D +L YPE
Sbjct: 61 GFLGPGDLFGELALLGNG--PRSATVRALTDSELLVLPRSDFRRLLQEYPEL 110
>gnl|CDD|197516 smart00100, cNMP, Cyclic nucleotide-monophosphate binding domain.
Catabolite gene activator protein (CAP) is a prokaryotic
homologue of eukaryotic cNMP-binding domains, present in
ion channels, and cNMP-dependent kinases.
Length = 120
Score = 81.7 bits (202), Expect = 8e-19
Identities = 31/119 (26%), Positives = 51/119 (42%), Gaps = 5/119 (4%)
Query: 272 FKGASPGCLRALSLKFKTTHAPPGDTLVHKGDVLTSLYFISRGSIEILRD-----DVVMA 326
FK LR L+ + P G+ ++ +GDV S Y I G +E+ + + ++
Sbjct: 2 FKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVG 61
Query: 327 ILGKDDIYGENPCLHSTIGKSSSNVRALTYCDLHKIHRDDLLDVLDLYPEFYNSFTENL 385
LG D +GE L ++ +S+ AL L +I D L +L P+ L
Sbjct: 62 TLGPGDFFGELALLTNSRRAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLEL 120
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 66.6 bits (163), Expect = 8e-14
Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 7/89 (7%)
Query: 293 PPGDTLVHKGDVLTSLYFISRGSIEILRDD-----VVMAILGKDDIYGENPCLHSTIGKS 347
G+ + +GD SLY + G +++ + D ++A LG D +GE L
Sbjct: 5 KKGEVIFREGDPADSLYIVLSGKVKVYKLDEDGREQILAFLGPGDFFGELALLGGE--PR 62
Query: 348 SSNVRALTYCDLHKIHRDDLLDVLDLYPE 376
S+ V ALT +L I R+D L++L+ PE
Sbjct: 63 SATVVALTDSELLVIPREDFLELLEQDPE 91
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 58.0 bits (140), Expect = 6e-09
Identities = 54/230 (23%), Positives = 97/230 (42%), Gaps = 25/230 (10%)
Query: 128 DRYSEYGAAGKGWGGF---NFKHLYLR--------------TSVGFGNVAPNTDNEKIFT 170
DRY GK W G NF+ L T+VG+G++ E IF
Sbjct: 225 DRYPH---QGKTWIGAVIPNFRETSLWIRYISAIYWSITTMTTVGYGDLHAVNTIEMIFI 281
Query: 171 ILVMLVGSLMYASIFGNVSAIIQRLYSGTARYHTQMLRVREFIRFHQIPNPLRQRLEEYF 230
I ML + A + GN++ ++ T + + F+ +++P L+ ++ Y
Sbjct: 282 IFYMLFNLGLTAYLIGNMTNLVVEGTRRTMEFRNSIEAASNFVGRNRLPPRLKDQILAYM 341
Query: 231 QHAWTYTNGIDMNSVLKGFPECLQADICLHLNRNLLSNCSAFKGASPGCLRALSLKFKTT 290
+ + ++ ++ P+ + IC HL ++ FKG S L L K K
Sbjct: 342 CLRFKAES-LNQQQLIDQLPKSICKSICQHLFLPVVEKVYLFKGVSREILLLLVTKMKAE 400
Query: 291 HAPPGDTLVHKGDVLTSLYFISRGSIEIL----RDDVVMAILGKDDIYGE 336
+ PP + ++ + + +Y + G +EI+ + V+ LG DI+GE
Sbjct: 401 YIPPREDVIMQNEAPDDVYIVVSGEVEIIDSEGEKERVVGTLGCGDIFGE 450
>gnl|CDD|223736 COG0664, Crp, cAMP-binding proteins - catabolite gene activator and
regulatory subunit of cAMP-dependent protein kinases
[Signal transduction mechanisms].
Length = 214
Score = 52.1 bits (125), Expect = 9e-08
Identities = 31/126 (24%), Positives = 53/126 (42%), Gaps = 7/126 (5%)
Query: 265 LLSNCSAFKGASPGCLRALSLKFKTTHAPPGDTLVHKGDVLTSLYFISRGSIEILRDD-- 322
L L L+LK + P G+ L +G+ SLY I G +++ +
Sbjct: 1 ALKENPLLNLLPSELLELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYANTED 60
Query: 323 ---VVMAILGKDDIYGENPCLHSTIGKSSSNVRALTYCDLHKIHRDDLLDVLDLYPEFYN 379
+++ LG D +GE L S++ ALT ++ +I R D L++L P+
Sbjct: 61 GREIILGFLGPGDFFGELALLGGD--PRSASAVALTDVEVLEIPRKDFLELLAESPKLAL 118
Query: 380 SFTENL 385
+ L
Sbjct: 119 ALLRLL 124
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator Crp;
Provisional.
Length = 211
Score = 46.5 bits (111), Expect = 7e-06
Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 6/90 (6%)
Query: 293 PPGDTLVHKGDVLTSLYFISRGSIEILRDD-----VVMAILGKDDIYGENPCLHSTIGKS 347
P TL+H G+ +LY+I +GS+ +L D ++++ L + D GE L +
Sbjct: 26 PAKSTLIHAGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELG-LFEEGQER 84
Query: 348 SSNVRALTYCDLHKIHRDDLLDVLDLYPEF 377
S+ VRA T C++ +I ++ + P+
Sbjct: 85 SAWVRAKTACEVAEISYKKFRQLIQVNPDI 114
>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel. This family includes the two
membrane helix type ion channels found in bacteria.
Length = 74
Score = 39.5 bits (93), Expect = 2e-04
Identities = 11/38 (28%), Positives = 24/38 (63%)
Query: 152 TSVGFGNVAPNTDNEKIFTILVMLVGSLMYASIFGNVS 189
T++G+G++ P TD ++FTI+ +L+G ++ +
Sbjct: 37 TTIGYGDIVPLTDAGRLFTIIYILIGIPLFLLFLAVLG 74
>gnl|CDD|215968 pfam00520, Ion_trans, Ion transport protein. This family contains
Sodium, Potassium, Calcium ion channels. This family is
6 transmembrane helices in which the last two helices
flank a loop which determines ion selectivity. In some
sub-families (e.g. Na channels) the domain is repeated
four times, whereas in others (e.g. K channels) the
protein forms as a tetramer in the membrane. A bacterial
structure of the protein is known for the last two
helices but is not the Pfam family due to it lacking the
first four helices.
Length = 194
Score = 37.7 bits (88), Expect = 0.006
Identities = 36/180 (20%), Positives = 61/180 (33%), Gaps = 37/180 (20%)
Query: 12 FFFLQRTTTLIGLLKTARLLRLVRVARKIDRYSEYGAAVLLLL--MATFALIAHWLACIW 69
F L + L+ +L+ RLLRL+R+ R+ ++ L + L+ L I+
Sbjct: 49 LFLLGEDSGLLRVLRLLRLLRLLRLLRRFPGLRTLLQSLGRSLKSLLNLLLLLLLLLFIF 108
Query: 70 YAIGNAEKSSVGWLDILANDTHQFYINGTGGPSIKTTTLIGLLKTARLLRLVRVARKIDR 129
IG + N G S + LL R L
Sbjct: 109 AIIGVQ------LFGGELDKCCDKNENPINGNSNFDSYGEALLWLFRTL----------- 151
Query: 130 YSEYGAAGKGWGGFNFKHLYLRTSVGFGNVAPNTDNEKIFTILVMLVGS-LMYASIFGNV 188
+GWG V + + P T KIF ++ +++G L+ + G +
Sbjct: 152 ------TTEGWGD-----------VMYDTLVPGTVLGKIFFVIFIILGGVLLLNLLIGVI 194
>gnl|CDD|225457 COG2905, COG2905, Predicted signal-transduction protein containing
cAMP-binding and CBS domains [Signal transduction
mechanisms].
Length = 610
Score = 35.0 bits (81), Expect = 0.093
Identities = 22/118 (18%), Positives = 46/118 (38%), Gaps = 7/118 (5%)
Query: 272 FKGASPGCLRALSLKFKTTHAPPGDTLVHKGDVLTSLYFISRGSIEILRDD-VVMAILGK 330
F L L + + G+ +++ G + LY I +G +E+ D V+ L
Sbjct: 15 FSQLPAEELEQLMGALEVKYYRKGEIIIYAGSPVHYLYVIRKGVVEVRSDGGEVLDRLAA 74
Query: 331 DDIYGENPCLHSTIGKSSSNVRALTYCD--LHKIHRDDLLDVLDLYPEFYNSFTENLE 386
D++G S + + D + + + + +++ PEF + F +L
Sbjct: 75 GDLFG----FSSLFTELNKQRYMAAEEDSLCYLLPKSVFMQLMEENPEFADFFLRSLA 128
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 33.1 bits (76), Expect = 0.27
Identities = 22/67 (32%), Positives = 40/67 (59%), Gaps = 8/67 (11%)
Query: 152 TSVGFGNVAPNTDNEKIFTILVMLVGSLMYA----SIFGNV-SAIIQRLYSGTARYHTQM 206
++VG+G++ P +++ ++FTI V+++G ++A +IFG V ++RL G R M
Sbjct: 181 STVGYGDIVPVSESARLFTISVIILGITVFATSISAIFGPVIRGNLKRLVKG--RISH-M 237
Query: 207 LRVREFI 213
R FI
Sbjct: 238 HRKDHFI 244
>gnl|CDD|178459 PLN02868, PLN02868, acyl-CoA thioesterase family protein.
Length = 413
Score = 32.8 bits (75), Expect = 0.41
Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 15/87 (17%)
Query: 279 CLRALSLK-----FKTTHAPPGDTLVHKGDVLTSLYFISRGSIEILR----DDVVMAILG 329
L + SLK G+ +V +G+ LYFI +G E+ + +L
Sbjct: 18 RLPSSSLKKIAEVVVPKRYGKGEYVVREGEPGDGLYFIWKGEAEVSGPAEEESRPEFLLK 77
Query: 330 KDDIYGENPCLHSTIGK-SSSNVRALT 355
+ D +G + G S++V A++
Sbjct: 78 RYDYFG-----YGLSGSVHSADVVAVS 99
>gnl|CDD|234384 TIGR03896, cyc_nuc_ocin, bacteriocin-type transport-associated
protein. Members of this protein family are
uncharacterized and contain two copies of the cyclic
nucleotide-binding domain pfam00027. Members are
restricted to select cyanobacteria but are found
regularly in association with a transport operon that,
in turn, is associated with the production of putative
bacteriocins. The models describing the transport operon
are TIGR03794, TIGR03796, and TIGR03797.
Length = 317
Score = 31.0 bits (70), Expect = 1.3
Identities = 35/149 (23%), Positives = 61/149 (40%), Gaps = 10/149 (6%)
Query: 293 PPGDTLVHKGDVLTSLYFISRG--SIEILRDDVVMAI--LGKDDIYGENPCLHSTIGKSS 348
P G L+H+G + +LY + G S+ I D + + +I GE P L+ ++ +
Sbjct: 167 PAGTILIHEGGTVDALYILLYGEASLSISPDGPGREVGSSRRGEILGETPFLNGSL-PGT 225
Query: 349 SNVRALTYCDLHKIHRDDLLDVLDLYPEFYNSFTENLEITFYMRDEEQAGVDPR-CGRHS 407
+ V+A+ L I + L L F + F + R +Q V R R
Sbjct: 226 ATVKAIENSVLLAIDKQQLAAKLQQDVGFASRFYRVIASLLSQRSRDQ--VSSRGYARRV 283
Query: 408 RRRSGSSSNDRPTVDVGGGGGLEIDIRRF 436
R G ++ +D+ + I +RF
Sbjct: 284 YLREGLEYDEE--LDLNTLDRMSIAGKRF 310
>gnl|CDD|222391 pfam13803, DUF4184, Domain of unknown function (DUF4184). This
domain of unknown function contains several highly
conserved histidines.
Length = 246
Score = 29.5 bits (67), Expect = 2.9
Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 2/71 (2%)
Query: 12 FFFLQRTTTLIGLLKTARLLRLVRVARKIDRYSEYGAAVLLLLMATFALIAHWLACIWYA 71
+ LQ ++L+GLL + R R+ + + A + L L+ ++
Sbjct: 153 YKILQHGSSLLGLL--LLAWMIWRYLRRHPQKPQVPAKIKLFYWIVVILLGLLGFLLYAL 210
Query: 72 IGNAEKSSVGW 82
E S +
Sbjct: 211 YFPLEVWSELY 221
>gnl|CDD|222225 pfam13564, DoxX_2, DoxX-like family. This family of
uncharacterized proteins are related to DoxX pfam07681.
Length = 102
Score = 27.9 bits (63), Expect = 4.4
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 20 TLIGLLKTARLLRLVRVARKIDRYSEYGAAVLLLLMATFALIAHWLA 66
L+G+L+ L L+ R E AA L LLM A+ AH
Sbjct: 39 RLLGILELLGALGLLLPLVGAPRLKELAAAGLALLM-IGAIAAHLRV 84
>gnl|CDD|235414 PRK05331, PRK05331, putative phosphate acyltransferase;
Provisional.
Length = 334
Score = 29.3 bits (67), Expect = 4.4
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 3/27 (11%)
Query: 28 ARLLR--LVRVARKIDRYSEYGAAVLL 52
A LL+ L R+ +K+D EYG AVLL
Sbjct: 265 ALLLKPALKRLKKKLD-PREYGGAVLL 290
>gnl|CDD|237522 PRK13822, PRK13822, conjugal transfer coupling protein TraG;
Provisional.
Length = 641
Score = 29.5 bits (67), Expect = 5.0
Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 5/25 (20%)
Query: 386 EITFYMRDEEQ----AGVDP-RCGR 405
EI MR +EQ G P RCGR
Sbjct: 593 EILQSMRADEQIIFVQGNPPLRCGR 617
>gnl|CDD|236958 PRK11709, PRK11709, putative L-ascorbate 6-phosphate lactonase;
Provisional.
Length = 355
Score = 29.2 bits (66), Expect = 5.6
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 14/59 (23%)
Query: 281 RALSLKFKTTHAPPGDTLVHKGDVLTSLYFISRGSIEILRD-DVVMAILGKDDIYGENP 338
RA++ FKT PG + H GD S YF G D + +A+ YGENP
Sbjct: 209 RAVNYLFKT----PGGNIYHSGDSHYSNYFAKHG-----NDHQIDVALGS----YGENP 254
>gnl|CDD|183004 PRK11161, PRK11161, fumarate/nitrate reduction transcriptional
regulator; Provisional.
Length = 235
Score = 28.5 bits (64), Expect = 6.4
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 295 GDTLVHKGDVLTSLYFISRGSI 316
G TL GD L SLY I G+I
Sbjct: 45 GQTLFKAGDELKSLYAIRSGTI 66
>gnl|CDD|237620 PRK14136, recX, recombination regulator RecX; Provisional.
Length = 309
Score = 28.4 bits (63), Expect = 9.3
Identities = 23/74 (31%), Positives = 30/74 (40%), Gaps = 13/74 (17%)
Query: 393 DEEQAGVDPRCGRHSRRRSGSSSNDRPTVDVGGGGGLEIDIRRFPSRPARTRAFNQDSME 452
D ++A R R + R S DR V G G R R A TRA + D++
Sbjct: 9 DPQEADHPARAAR-AGRPHASRETDRT---VSGEG-------RPAGRTA-TRA-SDDALV 55
Query: 453 SAAAAMFQDVMDDD 466
S A + DDD
Sbjct: 56 SFEIAAPDEPFDDD 69
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
0.324 0.139 0.421
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,662,996
Number of extensions: 2457255
Number of successful extensions: 3056
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3046
Number of HSP's successfully gapped: 30
Length of query: 472
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 372
Effective length of database: 6,502,202
Effective search space: 2418819144
Effective search space used: 2418819144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 61 (27.4 bits)