RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18137
(320 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 = 112 bits (283), Expect = 5e-31
Identities = 48/115 (41%), Positives = 64/115 (55%), Gaps = 5/115 (4%)
Query: 76 LFSHLDENTRSDIFDAMFPVNCLPGESIITQGDEGDNFYVIDQGEVEVYVNNE-----LV 130
LFS LD+ ++ DA+ GE II QGD D+ Y++ G VEVY +E +V
Sbjct: 1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIV 60
Query: 131 TSVGEGGSFGELALIYGTPRAATVRAKTDVKLWGLDRDSYRRILMGSTIRKRKLY 185
+G G FGELAL+ PR+ATVRA TD +L L R +RR+L R+L
Sbjct: 61 GFLGPGDLFGELALLGNGPRSATVRALTDSELLVLPRSDFRRLLQEYPELARRLL 115
Score = 110 bits (277), Expect = 3e-30
Identities = 43/116 (37%), Positives = 64/116 (55%), Gaps = 1/116 (0%)
Query: 194 ILESLEKWERLTVADSLEPVSFQDKEAIVRQGQPGDDFYIIVEGTALVLQNTVEEESPVE 253
+ L+ E +AD+LE F E I+RQG P D YI++ G+ V + E+
Sbjct: 1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLD-EDGREQI 59
Query: 254 VGKLGPSDYFGEIALLLDRPRAATVVAKGPLKCVKLDRARFERVLGPCADILKRNI 309
VG LGP D FGE+ALL + PR+ATV A + + L R+ F R+L ++ +R +
Sbjct: 60 VGFLGPGDLFGELALLGNGPRSATVRALTDSELLVLPRSDFRRLLQEYPELARRLL 115
>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 = 100 bits (251), Expect = 2e-26
Identities = 48/121 (39%), Positives = 64/121 (52%), Gaps = 6/121 (4%)
Query: 76 LFSHLDENTRSDIFDAMFPVNCLPGESIITQGDEGDNFYVIDQGEVEVYVNNE-----LV 130
LF +LD ++ DA+ PV GE II QGD GD+FY+I GEVEVY E +V
Sbjct: 1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIV 60
Query: 131 TSVGEGGSFGELALIYGTPRAATVRAKTDVKLWGLDRDSYRRILMGSTIRKRKLYEEFLS 190
++G G FGELAL+ + RAA+ A ++L L R +R L + L E L
Sbjct: 61 GTLGPGDFFGELALLTNSRRAASAAAVA-LELATLLRIDFRDFLQLLPELPQLLLELLLE 119
Query: 191 R 191
Sbjct: 120 L 120
Score = 99.0 bits (247), Expect = 9e-26
Identities = 43/121 (35%), Positives = 65/121 (53%), Gaps = 3/121 (2%)
Query: 194 ILESLEKWERLTVADSLEPVSFQDKEAIVRQGQPGDDFYIIVEGTALVLQNTVEEESPVE 253
+ ++L+ E +AD+LEPV + E I+RQG GD FYIIV G V + + E
Sbjct: 1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEE-QI 59
Query: 254 VGKLGPSDYFGEIALLLD--RPRAATVVAKGPLKCVKLDRARFERVLGPCADILKRNITQ 311
VG LGP D+FGE+ALL + R +A VA +++D F ++L +L + +
Sbjct: 60 VGTLGPGDFFGELALLTNSRRAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLE 119
Query: 312 Y 312
Sbjct: 120 L 120
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 82.0 bits (203), Expect = 8e-20
Identities = 32/87 (36%), Positives = 50/87 (57%), Gaps = 5/87 (5%)
Query: 94 PVNCLPGESIITQGDEGDNFYVIDQGEVEVYVNNE-----LVTSVGEGGSFGELALIYGT 148
+ GE I +GD D+ Y++ G+V+VY +E ++ +G G FGELAL+ G
Sbjct: 1 LRSFKKGEVIFREGDPADSLYIVLSGKVKVYKLDEDGREQILAFLGPGDFFGELALLGGE 60
Query: 149 PRAATVRAKTDVKLWGLDRDSYRRILM 175
PR+ATV A TD +L + R+ + +L
Sbjct: 61 PRSATVVALTDSELLVIPREDFLELLE 87
Score = 80.8 bits (200), Expect = 3e-19
Identities = 33/87 (37%), Positives = 47/87 (54%), Gaps = 1/87 (1%)
Query: 212 PVSFQDKEAIVRQGQPGDDFYIIVEGTALVLQNTVEEESPVEVGKLGPSDYFGEIALLLD 271
SF+ E I R+G P D YI++ G V + E+ + LGP D+FGE+ALL
Sbjct: 1 LRSFKKGEVIFREGDPADSLYIVLSGKVKVYKLD-EDGREQILAFLGPGDFFGELALLGG 59
Query: 272 RPRAATVVAKGPLKCVKLDRARFERVL 298
PR+ATVVA + + + R F +L
Sbjct: 60 EPRSATVVALTDSELLVIPREDFLELL 86
>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 = 74.1 bits (182), Expect = 1e-15
Identities = 35/111 (31%), Positives = 55/111 (49%), Gaps = 1/111 (0%)
Query: 188 FLSRVSILESLEKWERLTVADSLEPVSFQDKEAIVRQGQPGDDFYIIVEGTALVLQNTVE 247
L +L L +A LE E + +G+ D YII+ G + NT E
Sbjct: 1 ALKENPLLNLLPSELLELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYANT-E 59
Query: 248 EESPVEVGKLGPSDYFGEIALLLDRPRAATVVAKGPLKCVKLDRARFERVL 298
+ + +G LGP D+FGE+ALL PR+A+ VA ++ +++ R F +L
Sbjct: 60 DGREIILGFLGPGDFFGELALLGGDPRSASAVALTDVEVLEIPRKDFLELL 110
Score = 73.7 bits (181), Expect = 2e-15
Identities = 38/132 (28%), Positives = 62/132 (46%), Gaps = 5/132 (3%)
Query: 70 AIAKNVLFSHLDENTRSDIFDAMFPVNCLPGESIITQGDEGDNFYVIDQGEVEVYVNNE- 128
A+ +N L + L + + GE + T+G+E D+ Y+I G V++Y N E
Sbjct: 1 ALKENPLLNLLPSELLELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYANTED 60
Query: 129 ----LVTSVGEGGSFGELALIYGTPRAATVRAKTDVKLWGLDRDSYRRILMGSTIRKRKL 184
++ +G G FGELAL+ G PR+A+ A TDV++ + R + +L S L
Sbjct: 61 GREIILGFLGPGDFFGELALLGGDPRSASAVALTDVEVLEIPRKDFLELLAESPKLALAL 120
Query: 185 YEEFLSRVSILE 196
R+
Sbjct: 121 LRLLARRLRQAL 132
>gnl|CDD|178459 PLN02868, PLN02868, acyl-CoA thioesterase family protein.
Length = 413
Score = 53.6 bits (129), Expect = 4e-08
Identities = 36/103 (34%), Positives = 49/103 (47%), Gaps = 4/103 (3%)
Query: 187 EFLSRVSILESLEKWERLTVADSLEPVSFQDKEAIVRQGQPGDDFYIIVEGTALVLQNTV 246
EFL V +L+ L +A+ + P + E +VR+G+PGD Y I +G A V
Sbjct: 8 EFLGSVPLLQRLPSSSLKKIAEVVVPKRYGKGEYVVREGEPGDGLYFIWKGEAEVSGPAE 67
Query: 247 EEESPVEVGKLGPSDYFGEIALLLDRPRAATVVAKGPLKCVKL 289
EE P + L DYFG L +A VVA L C+ L
Sbjct: 68 EESRPEFL--LKRYDYFGY--GLSGSVHSADVVAVSELTCLVL 106
Score = 33.2 bits (76), Expect = 0.16
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 99 PGESIITQGDEGDNFYVIDQGEVEVYVNNE 128
GE ++ +G+ GD Y I +GE EV E
Sbjct: 38 KGEYVVREGEPGDGLYFIWKGEAEVSGPAE 67
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 45.2 bits (107), Expect = 3e-05
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 218 KEAIVRQGQPGDDFYIIVEGTALVLQNTVEEESPVEVGKLGPSDYFGEIALLLDRPRAAT 277
+E ++ Q + DD YI+V G ++ + E+E V G LG D FGE+ L RP++ T
Sbjct: 405 REDVIMQNEAPDDVYIVVSGEVEIIDSEGEKERVV--GTLGCGDIFGEVGALCCRPQSFT 462
Score = 40.6 bits (95), Expect = 9e-04
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 99 PGESIITQGDEGDNFYVIDQGEVEVY----VNNELVTSVGEGGSFGELALIYGTPRAATV 154
P E +I Q + D+ Y++ GEVE+ +V ++G G FGE+ + P++ T
Sbjct: 404 PREDVIMQNEAPDDVYIVVSGEVEIIDSEGEKERVVGTLGCGDIFGEVGALCCRPQSFTF 463
Query: 155 RAKT 158
R KT
Sbjct: 464 RTKT 467
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator Crp;
Provisional.
Length = 211
Score = 42.3 bits (100), Expect = 1e-04
Identities = 24/91 (26%), Positives = 46/91 (50%), Gaps = 6/91 (6%)
Query: 218 KEAIVRQGQPGDDFYIIVEGTALVLQNTVEEESPVE--VGKLGPSDYFGEIALLLD-RPR 274
K ++ G+ + Y IV+G+ VL +++E E + L D+ GE+ L + + R
Sbjct: 28 KSTLIHAGEKAETLYYIVKGSVAVL---IKDEEGKEMILSYLNQGDFIGELGLFEEGQER 84
Query: 275 AATVVAKGPLKCVKLDRARFERVLGPCADIL 305
+A V AK + ++ +F +++ DIL
Sbjct: 85 SAWVRAKTACEVAEISYKKFRQLIQVNPDIL 115
Score = 41.9 bits (99), Expect = 2e-04
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 102 SIITQGDEGDNFYVIDQGEVEVYVNNE-----LVTSVGEGGSFGELAL-IYGTPRAATVR 155
++I G++ + Y I +G V V + +E +++ + +G GEL L G R+A VR
Sbjct: 30 TLIHAGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVR 89
Query: 156 AKTD 159
AKT
Sbjct: 90 AKTA 93
>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 = 40.3 bits (94), Expect = 9e-04
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 221 IVRQGQPGDDFYIIVEGTALVLQNTVEEES---PVEVGKLGPSDYFGEIALLLDRPRAAT 277
++ +G+ D +I+++GT V E+ E+ +L + GE++LL RP AT
Sbjct: 19 LIEEGKAADFLFILLDGTFTVTTPQPEDNPLTRAFELARLSRGEIVGEMSLLETRPPVAT 78
Query: 278 VVA 280
+ A
Sbjct: 79 IKA 81
Score = 36.0 bits (83), Expect = 0.017
Identities = 25/105 (23%), Positives = 44/105 (41%), Gaps = 5/105 (4%)
Query: 75 VLFSHLDENTRSDIFDAMFPVNCLPGESIITQGDEGDNFYVIDQGEVEVYVN-NELVTSV 133
+F L E+ + + + P G +I +G D Y++ GE + ++ + V
Sbjct: 144 FIFGELHESDVAWMMASGTPQKLPAGTILIHEGGTVDALYILLYGEASLSISPDGPGREV 203
Query: 134 G---EGGSFGELALIYGT-PRAATVRAKTDVKLWGLDRDSYRRIL 174
G G GE + G+ P ATV+A + L +D+ L
Sbjct: 204 GSSRRGEILGETPFLNGSLPGTATVKAIENSVLLAIDKQQLAAKL 248
>gnl|CDD|225457 COG2905, COG2905, Predicted signal-transduction protein containing
cAMP-binding and CBS domains [Signal transduction
mechanisms].
Length = 610
Score = 32.7 bits (75), Expect = 0.30
Identities = 24/99 (24%), Positives = 40/99 (40%), Gaps = 1/99 (1%)
Query: 76 LFSHLDENTRSDIFDAMFPVNCLPGESIITQGDEGDNFYVIDQGEVEVYVNN-ELVTSVG 134
FS L + A+ GE II G YVI +G VEV + E++ +
Sbjct: 14 PFSQLPAEELEQLMGALEVKYYRKGEIIIYAGSPVHYLYVIRKGVVEVRSDGGEVLDRLA 73
Query: 135 EGGSFGELALIYGTPRAATVRAKTDVKLWGLDRDSYRRI 173
G FG +L + + A+ D + L + + ++
Sbjct: 74 AGDLFGFSSLFTELNKQRYMAAEEDSLCYLLPKSVFMQL 112
Score = 30.8 bits (70), Expect = 0.94
Identities = 24/110 (21%), Positives = 43/110 (39%), Gaps = 5/110 (4%)
Query: 187 EFLSRVSILESLEKWERLTVADSLEPVSFQDKEAIVRQGQPGDDFYIIVEGTALVLQNTV 246
+FL + L E + +LE ++ E I+ G P Y+I +G V +
Sbjct: 7 QFLQQHPPFSQLPAEELEQLMGALEVKYYRKGEIIIYAGSPVHYLYVIRKGVVEVRSDGG 66
Query: 247 EEESPVEVGKLGPSDYFGEIALLLDRPRAATVVAKGPLKCVKLDRARFER 296
E + G D FG +L + + + A+ C L ++ F +
Sbjct: 67 EVLDRLAAG-----DLFGFSSLFTELNKQRYMAAEEDSLCYLLPKSVFMQ 111
>gnl|CDD|181817 PRK09392, ftrB, transcriptional activator FtrB; Provisional.
Length = 236
Score = 30.4 bits (69), Expect = 1.1
Identities = 14/49 (28%), Positives = 24/49 (48%)
Query: 76 LFSHLDENTRSDIFDAMFPVNCLPGESIITQGDEGDNFYVIDQGEVEVY 124
LF+ + + T + F PG +IT+G+ D +V+ G VE+
Sbjct: 14 LFADMADATFERLMRGAFLQRFPPGTMLITEGEPADFLFVVLDGLVELS 62
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 29.8 bits (67), Expect = 2.0
Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 133 VGEGGSFGELALIYGTPRAATVRAKTDVKLWGLDRDSYRRILMGSTIRKRKLYEEFLSRV 192
GE +F E+A YG P +AKT G ++ ++ + +++L ++
Sbjct: 480 PGESYAF-EIAQRYGIPHFIIEQAKTFY---GEFKEEINVLIEKLSALEKELEQKNEHLE 535
Query: 193 SILESLEKWER 203
+L+ EK ++
Sbjct: 536 KLLKEQEKLKK 546
>gnl|CDD|204259 pfam09517, RE_Eco29kI, Eco29kI restriction endonuclease. This
family includes the Eco29kI (recognises and cleaves
CCGC^GG) restriction endonuclease.
Length = 170
Score = 28.6 bits (64), Expect = 2.8
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 52 YVKKVVPKDYKTMAALSKAIAKNVLFSHLDENTRS 86
YV K VPK ++ A N LF+ L E+ RS
Sbjct: 37 YVGKAVPKGWRQGRGSDNAPPGNELFNRLREHARS 71
>gnl|CDD|221472 pfam12228, DUF3604, Protein of unknown function (DUF3604). This
family of proteins is found in bacteria. Proteins in
this family are typically between 621 and 693 amino
acids in length.
Length = 592
Score = 28.8 bits (65), Expect = 4.5
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 82 ENTRSDIFDAM 92
ENTR IFDAM
Sbjct: 385 ENTREAIFDAM 395
>gnl|CDD|240337 PTZ00261, PTZ00261, acyltransferase; Provisional.
Length = 355
Score = 28.3 bits (63), Expect = 5.1
Identities = 33/150 (22%), Positives = 57/150 (38%), Gaps = 14/150 (9%)
Query: 79 HLDENTRSDIFDAMFPVNCLPGESIITQGDEGDNFYVIDQGEVEVYVNNELVTSVGEGGS 138
+D + R A FP + + Q F I + +EVY + SVG +
Sbjct: 207 AIDAHLRLGGSLAFFPEGAINKHPQVLQTFRYGTFATIIKHRMEVY----YMVSVGSEKT 262
Query: 139 FGELALIYGTPRAATVRAKTDVKLWGLDRDSYRRILMGSTIRKRKLYEEFLSRVSILESL 198
+ +I G P A + + DRDS + + +G R +K+ +E + V+ E
Sbjct: 263 WPWWMMIGGLP--ADMHIRIGAYPIDYDRDSSKDVAVGLQQRMQKVRDEIAAEVAAAEEA 320
Query: 199 EKWERLTVADSLEPVSFQDKEAIVRQGQPG 228
+ R VA++ K + P
Sbjct: 321 RRRRRGIVAEA--------KASKTLDIAPP 342
>gnl|CDD|219618 pfam07883, Cupin_2, Cupin domain. This family represents the
conserved barrel domain of the 'cupin' superfamily
('cupa' is the Latin term for a small barrel).
Length = 70
Score = 26.4 bits (59), Expect = 5.3
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 99 PGESIITQGDEGD-NFYVIDQGEVEVYVNNELVTSVGEGGSF 139
PGES G+ FYV++ GE E+ V+ E V + G S
Sbjct: 7 PGESSPPHRHPGEEFFYVLE-GEGELTVDGEEVV-LKAGDSV 46
>gnl|CDD|219118 pfam06640, P_C, P protein C-terminus. This family represents the
C-terminus of plant P proteins. The maize P gene is a
transcriptional regulator of genes encoding enzymes for
flavonoid biosynthesis in the pathway leading to the
production of a red phlobaphene pigment, and P proteins
are homologous to the DNA-binding domain of myb-like
transcription factors. All members of this family
contain the pfam00249 domain.
Length = 209
Score = 27.7 bits (61), Expect = 7.0
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 5/52 (9%)
Query: 4 EQAHDAKLKATSPEETED-----LSPLPSQGQQSARRRGGISAEPVSEEDAT 50
+A A+SP ++ + P P+Q S+ G P S EDAT
Sbjct: 42 GEAAGDAAAASSPRHSDGARSAVVDPGPNQPNSSSGSTGTAEEGPCSSEDAT 93
>gnl|CDD|202886 pfam04096, Nucleoporin2, Nucleoporin autopeptidase.
Length = 137
Score = 26.8 bits (60), Expect = 9.9
Identities = 10/26 (38%), Positives = 12/26 (46%)
Query: 111 DNFYVIDQGEVEVYVNNELVTSVGEG 136
D VEVY ++E VGEG
Sbjct: 49 DKIVDFGPRSVEVYPDDENKPPVGEG 74
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
0.315 0.134 0.376
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: 16,378,371
Number of extensions: 1611811
Number of successful extensions: 1390
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1373
Number of HSP's successfully gapped: 37
Length of query: 320
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 223
Effective length of database: 6,635,264
Effective search space: 1479663872
Effective search space used: 1479663872
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 (21.5 bits)
S2: 59 (26.6 bits)