RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1512
(679 letters)
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 79.5 bits (196), Expect = 2e-15
Identities = 71/283 (25%), Positives = 130/283 (45%), Gaps = 21/283 (7%)
Query: 100 YWSMIVSLAFLYNFWVIIYRFAFQEIN-RESLVIWFCLDYMADLMYVIDILIHFRTGYLE 158
+W ++ + Y+ WV + AF + + L I D + DL + +DI++ F Y++
Sbjct: 63 WWETLMVVLVAYSAWVYPFEVAFLNASPKRGLEI---ADNVVDLFFAVDIVLTFFVAYID 119
Query: 159 D--GVLQTDSTKLRDHYMNSTTFYIDCLCLLPLDFL-YLSIGFN------SILRLFRLVK 209
+L D K+ Y+ ST F +D +P L YL G S+L L R +
Sbjct: 120 PRTQLLVRDRKKIAVRYL-STWFLMDVASTIPFQALAYLITGTVKLNLSYSLLGLLRFWR 178
Query: 210 IYRFWAFMDRTERHTNYPNLF-RSSSLIHYLLVIFHWNGCLYHIIYKNDGFGSRNW---V 265
+ R R E+ + + R + L+ L + H GCLY++I + W V
Sbjct: 179 LRRVKQLFTRLEKDIRFSYFWIRCARLLSVTLFLVHCAGCLYYLIADRYPHQGKTWIGAV 238
Query: 266 YGDSDTTDVVKQYLQSYYWCTLALTTIG--DLPRPRSKGEYFFVIVQLLFGLLLFATVLG 323
+ T + +Y+ + YW +TT+G DL + E F+I +LF L L A ++G
Sbjct: 239 IPNFRETSLWIRYISAIYWSITTMTTVGYGDL-HAVNTIEMIFIIFYMLFNLGLTAYLIG 297
Query: 324 HVANIVTSVSAARKEFQAKLDGVKTYMRMRRVPNALQVKVIKW 366
++ N+V + EF+ ++ ++ R+P L+ +++ +
Sbjct: 298 NMTNLVVEGTRRTMEFRNSIEAASNFVGRNRLPPRLKDQILAY 340
Score = 31.4 bits (71), Expect = 2.0
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 610 EVGKEMYIVNRGRLQVVADNG--KTVLATLRAGSYFGEISIL 649
E ++YIV G ++++ G + V+ TL G FGE+ L
Sbjct: 413 EAPDDVYIVVSGEVEIIDSEGEKERVVGTLGCGDIFGEVGAL 454
>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 = 70.4 bits (173), Expect = 7e-14
Identities = 45/210 (21%), Positives = 81/210 (38%), Gaps = 35/210 (16%)
Query: 135 CLDYMADLMYVIDILIHFRTGYLEDGVLQTDSTKLRDHYMNSTTFYIDCLCLLPLDFLYL 194
LDY+ +++ +++L+ F + Y S +D L +LP +
Sbjct: 1 ILDYVFTVIFTLEMLLKFIALGF------------KRKYFRSPWNILDFLVVLPSLVSLI 48
Query: 195 ---------SIGFNSILRLFRLVKIYRFWAFMDRTERH--TNYPNLFRSSSLIHYLLVIF 243
+ +LRL RL+++ R + + + + +L L+ LL IF
Sbjct: 49 LFLLGEDSGLLRVLRLLRLLRLLRLLRRFPGLRTLLQSLGRSLKSLLNLLLLLLLLLFIF 108
Query: 244 HWNGC-LYHIIYKNDGFGSRNWVYGDSDTTDVVKQYLQSYYWCTLALTTIG------DLP 296
G L+ + N + G+S+ Y ++ W LTT G D
Sbjct: 109 AIIGVQLFGGELDKCCDKNENPINGNSNFDS----YGEALLWLFRTLTTEGWGDVMYDTL 164
Query: 297 RPRSKGEY-FFVIVQLLFGLLLFATVLGHV 325
P + FFVI +L G+LL ++G +
Sbjct: 165 VPGTVLGKIFFVIFIILGGVLLLNLLIGVI 194
>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 = 50.1 bits (120), Expect = 1e-07
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 606 LEKGEVGKEMYIVNRGRLQVVA---DNGKTVLATLRAGSYFGEISILNM 651
+ +G+VG YI+ G ++V D + ++ TL G +FGE+++L
Sbjct: 29 IRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTN 77
Score = 33.9 bits (78), Expect = 0.058
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 458 IFQNTEAGFLCELVLRLRPVLFSPGDYICRKG 489
+F+N +A L EL L PV + G+ I R+G
Sbjct: 1 LFKNLDAEELRELADALEPVRYPAGEVIIRQG 32
>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 = 46.9 bits (112), Expect = 2e-06
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 606 LEKGEVGKEMYIVNRGRLQVV---ADNGKTVLATLRAGSYFGEISILN 650
+ +G+ +YIV G ++V D + ++ L G FGE+++L
Sbjct: 29 IRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLG 76
Score = 46.2 bits (110), Expect = 3e-06
Identities = 29/136 (21%), Positives = 52/136 (38%), Gaps = 25/136 (18%)
Query: 458 IFQNTEAGFLCELVLRLRPVLFSPGDYICRKGNRRTASVRSVGYSDLFVLSKTDMWDVLK 517
+F + L EL L F G+ I R+G+ + L+++
Sbjct: 1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADS---------LYIVLS-------- 43
Query: 518 EYPAARVRLESIAVKRLQKYKRTPLEKG---ISPSPFPGNRRTASVRSVGYSDLFVLSKT 574
V + + ++ L G + R+A+VR++ S+L VL ++
Sbjct: 44 ----GSVEVYKLDEDGREQIVGF-LGPGDLFGELALLGNGPRSATVRALTDSELLVLPRS 98
Query: 575 DMWDVLKEYPAARVRL 590
D +L+EYP RL
Sbjct: 99 DFRRLLQEYPELARRL 114
Score = 42.7 bits (101), Expect = 5e-05
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 10/76 (13%)
Query: 455 RVEIFQNTEAGFLCELVLRLRPVLFSPGDYICR----KGNRRTASVRSVGYSDLFVLSKT 510
VE+++ E G E ++ PGD R+A+VR++ S+L VL ++
Sbjct: 45 SVEVYKLDEDGR--EQIVGF----LGPGDLFGELALLGNGPRSATVRALTDSELLVLPRS 98
Query: 511 DMWDVLKEYPAARVRL 526
D +L+EYP RL
Sbjct: 99 DFRRLLQEYPELARRL 114
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 41.5 bits (98), Expect = 7e-05
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 3/48 (6%)
Query: 606 LEKGEVGKEMYIVNRGRLQVV--ADNGK-TVLATLRAGSYFGEISILN 650
+G+ +YIV G+++V ++G+ +LA L G +FGE+++L
Sbjct: 11 FREGDPADSLYIVLSGKVKVYKLDEDGREQILAFLGPGDFFGELALLG 58
Score = 36.1 bits (84), Expect = 0.007
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 10/71 (14%)
Query: 455 RVEIFQNTEAGFLCELVLRLRPVLFSPGDYICR----KGNRRTASVRSVGYSDLFVLSKT 510
+V++++ E G E +L PGD+ G R+A+V ++ S+L V+ +
Sbjct: 27 KVKVYKLDEDGR--EQILAF----LGPGDFFGELALLGGEPRSATVVALTDSELLVIPRE 80
Query: 511 DMWDVLKEYPA 521
D ++L++ P
Sbjct: 81 DFLELLEQDPE 91
Score = 32.7 bits (75), Expect = 0.090
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 551 FPGNRRTASVRSVGYSDLFVLSKTDMWDVLKEYPA 585
G R+A+V ++ S+L V+ + D ++L++ P
Sbjct: 57 LGGEPRSATVVALTDSELLVIPREDFLELLEQDPE 91
>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 = 34.1 bits (79), Expect = 0.024
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 278 YLQSYYWCTLALTTIG--DLPRPRSKGEYFFVIVQLLFGLLLFATVLG 323
+L + Y+ + LTTIG D+ P + F I+ +L G+ LF L
Sbjct: 25 FLDALYFSFVTLTTIGYGDI-VPLTDAGRLFTIIYILIGIPLFLLFLA 71
>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 = 34.4 bits (79), Expect = 0.13
Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 590 LESIAVKRLQKYKR--TPLEKGEVGKEMYIVNRGRLQVVA--DNGKT-VLATLRAGSYFG 644
++K + +GE +YI+ G +++ A ++G+ +L L G +FG
Sbjct: 17 ELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYANTEDGREIILGFLGPGDFFG 76
Query: 645 EISIL 649
E+++L
Sbjct: 77 ELALL 81
Score = 30.2 bits (68), Expect = 2.9
Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 10/86 (11%)
Query: 455 RVEIFQNTEAGFLCELVLRLRPVLFSPGDYICR----KGNRRTASVRSVGYSDLFVLSKT 510
V+++ NTE G E++L PGD+ G+ R+AS ++ ++ + +
Sbjct: 51 IVKLYANTEDG--REIILGF----LGPGDFFGELALLGGDPRSASAVALTDVEVLEIPRK 104
Query: 511 DMWDVLKEYPAARVRLESIAVKRLQK 536
D ++L E P + L + +RL++
Sbjct: 105 DFLELLAESPKLALALLRLLARRLRQ 130
>gnl|CDD|165381 PHA03099, PHA03099, epidermal growth factor-like protein (EGF-like
protein); Provisional.
Length = 139
Score = 30.0 bits (67), Expect = 2.2
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 60 KCFHGNTGADCAVHRVAERYPRSSGPNLTFVFDPA 94
+C HG TG C H V Y RS PN T + P+
Sbjct: 70 RCSHGYTGIRCQ-HVVLVDYQRSEKPNTTTSYIPS 103
>gnl|CDD|234323 TIGR03710, OAFO_sf, 2-oxoacid:acceptor oxidoreductase, alpha
subunit. This family of proteins contains a C-terminal
thiamine diphosphate (TPP) binding domain typical of
flavodoxin/ferredoxin oxidoreductases (pfam01855) as
well as an N-terminal domain similar to the gamma
subunit of the same group of oxidoreductases
(pfam01558). The genes represented by this model are
always found in association with a neighboring gene for
a beta subunit (TIGR02177) which also occurs in a
4-subunit (alpha/beta/gamma/ferredoxin) version of the
system. This alpha/gamma plus beta structure was used to
define the set of sequences to include in this model.
This pair of genes is not consistantly observed in
proximity to any electron acceptor genes, but is found
next to putative ferredoxins or ferredoxin-domain
proteins in Azoarcus sp. EbN1, Bradyrhizobium japonicum
USDA 110, Frankia sp. CcI3, Rhodoferax ferrireducens DSM
15236, Rhodopseudomonas palustris BisB5, Os,
Sphingomonas wittichii RW1 and Streptomyces
clavuligerus. Other potential acceptors are also
sporadically observed in close proximity including
ferritin-like proteins, reberythrin, peroxiredoxin and a
variety of other flavin and iron-sulfur
cluster-containing proteins. The phylogenetic
distribution of this family encompasses archaea, a
number of deeply-branching bacterial clades and only a
small number of firmicutes and proteobacteria. The
enzyme from Sulfolobus has been characterized with
respect to its substrate specificity which is described
as wide, encompassing various 2-oxoacids such as
2-oxoglutarate, 2-oxobutyrate and pyruvate. The enzyme
from Hydrogenobacter thermophilus has been shown to have
a high specificity towards 2-oxoglutarate and is one of
the key enzymes in the reverse TCA cycle in this
organism. Furthermore, considering its binding of
coenzyme A, it can be reasonably inferred that the
product of the reaction is succinyl-CoA. The genes for
this enzyme in Prevotella intermedia 17, Persephonella
marina EX-H1 and Picrophilus torridus DSM 9790 are in
close proximity to a variety of TCA cycle genes.
Persephonella marina and P. torridus are believed to
encode complete TCA cycles, and none of these contains
the lipoate-based 2-oxoglutarate dehydrogenase
(E1/E2/E3) system. That system is presumed to be
replaced by this one. In fact, the lipoate system is
absent in most organisms possessing a member of this
family, providing additional circumstantial evidence
that many of these enzymes are capable of acting as
2-oxoglutarate dehydrogenases and.
Length = 562
Score = 30.2 bits (69), Expect = 3.9
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 502 SDLFVLSKTDMWDV--LKEYPAARVRLESIAVKRLQKYKRTPLEKGISPSPFPG 553
SD ++ + L + PA + ++Y+ T E GISP PG
Sbjct: 358 SDQYLANSYATVPPPDLDDLPAIDRGKVLEPEEEYKRYELT--EDGISPRAIPG 409
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator Crp;
Provisional.
Length = 211
Score = 29.2 bits (66), Expect = 5.4
Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 602 KRTPLEKGEVGKEMYIVNRGRLQVVA--DNGK-TVLATLRAGSYFGEISILNMGTAGTNL 658
K T + GE + +Y + +G + V+ + GK +L+ L G + GE+ + G +
Sbjct: 28 KSTLIHAGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAW 87
Query: 659 IQ---ECE 663
++ CE
Sbjct: 88 VRAKTACE 95
>gnl|CDD|214790 smart00725, NEAT, NEAr Transporter domain.
Length = 123
Score = 28.1 bits (63), Expect = 7.1
Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 7/71 (9%)
Query: 606 LEKGEVGKEM---YIVNRGRLQVVADNGKTVLATLRAGSYFGEISILNMGTAG-TNLIQE 661
L+ + M Y+ +L +V + V TL S++ + + GT ++ +
Sbjct: 12 LKDNSNEESMMDDYVNKPAKL-IVKNGKTYVTLTLNNSSFWKDFEVEVNGTKVDVEVVSK 70
Query: 662 --CEDHISIRF 670
D +IRF
Sbjct: 71 DKDNDTRTIRF 81
>gnl|CDD|224251 COG1332, COG1332, CRISPR system related protein, RAMP superfamily
[Defense mechanisms].
Length = 369
Score = 29.3 bits (66), Expect = 7.6
Identities = 20/109 (18%), Positives = 36/109 (33%), Gaps = 19/109 (17%)
Query: 512 MWDVLKEYPAARVRLESIAVKRLQKYKR----TPLEKGISPSPFPGNRRTASVRSVGYSD 567
+++ LK+ R+E + L+ Y L K + P + R++ SD
Sbjct: 129 LYNYLKKNTDEPTRVEGNQNRELRNYGEAFERKELRKDGKKNIRPKDAVNDIFRAIRVSD 188
Query: 568 LFVLSKTDMWDVLKEYPAARVRLESIAVKRLQKYKR--TPLEKGEVGKE 614
L V + I K+L PL+ + +E
Sbjct: 189 SPALRT-------------SVSDKRIEYKKLMNVHEKGIPLDNLPIERE 224
>gnl|CDD|183183 PRK11537, PRK11537, putative GTP-binding protein YjiA; Provisional.
Length = 318
Score = 28.9 bits (65), Expect = 7.9
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 490 NRRTASVRSVGYSDLFVLSKTDMWDVLKEYPAARVRLESI 529
N+ T + VGY+D +L+KT DV E R RL I
Sbjct: 140 NQFTIAQSQVGYADRILLTKT---DVAGEAEKLRERLARI 176
Score = 28.9 bits (65), Expect = 7.9
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 554 NRRTASVRSVGYSDLFVLSKTDMWDVLKEYPAARVRLESI 593
N+ T + VGY+D +L+KT DV E R RL I
Sbjct: 140 NQFTIAQSQVGYADRILLTKT---DVAGEAEKLRERLARI 176
>gnl|CDD|218392 pfam05031, NEAT, Iron Transport-associated domain. This domain is
involved in the transport of iron, possibly as a
siderophore.
Length = 118
Score = 28.0 bits (63), Expect = 7.9
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 616 YIVNRGRLQVVADNGKTVLATLRAGSYFGEISILNMGT-AGTNLIQEC--EDHISIRF 670
Y+V +L V D K V TL S+ + + G ++ E ++ +RF
Sbjct: 26 YLVKPAKL-TVKDGKKYVTLTLNNSSWIKDFKVEVNGKFVDAEVVSEDKGKNTRVVRF 82
>gnl|CDD|215106 PLN00212, PLN00212, glutelin; Provisional.
Length = 493
Score = 29.0 bits (65), Expect = 9.3
Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 615 MYIVN-RGRLQVVADNGKTVL-ATLRAG 640
+YI R R+QVV++NGKTV LR G
Sbjct: 373 VYITQGRARVQVVSNNGKTVFNGVLRPG 400
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 0.138 0.424
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,477,368
Number of extensions: 3407389
Number of successful extensions: 3595
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3575
Number of HSP's successfully gapped: 41
Length of query: 679
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 576
Effective length of database: 6,369,140
Effective search space: 3668624640
Effective search space used: 3668624640
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: 62 (27.7 bits)