RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4009
(391 letters)
>gnl|CDD|216239 pfam01007, IRK, Inward rectifier potassium channel.
Length = 336
Score = 398 bits (1026), Expect = e-139
Identities = 163/325 (50%), Positives = 204/325 (62%), Gaps = 56/325 (17%)
Query: 54 VFKHGDCNVVQENVAKRRRRYLQDIFTTLVDAQWRWTLLVFALNFLLSWLMFAIVWWLIV 113
V K G CNV +NV R RYLQDIFTTLVD +WR+ LL+F+L FLLSWL F +WWLI
Sbjct: 1 VSKDGRCNVYFKNVRGERGRYLQDIFTTLVDLKWRYMLLIFSLAFLLSWLFFGTIWWLIA 60
Query: 114 YTHGDLDKVNLGNATWTPCVTSIHSFTSCFLFSVETQHTIGYGAKQVTEECPEAIFILCL 173
+ HGDL+ +A TPCV ++HSFTS FLFS+ETQ TIGYG + +TEECP AIF+L L
Sbjct: 61 FAHGDLEP--APDANHTPCVMNVHSFTSAFLFSIETQTTIGYGFRCITEECPLAIFLLIL 118
Query: 174 QSIVGVMIQAFMVGIVFAKLSRPKKRTQTLLFS--------------------------- 206
QSI+G +I AFM+G +FAK++RPKKR +TL+FS
Sbjct: 119 QSILGCIINAFMIGCIFAKMARPKKRAETLIFSHHAVIALRDGKLCLMFRVGDLRKSHLV 178
Query: 207 ----RINCLQTSV---------------------EDKIFFIWPTTIVHKINPMSPLYTLS 241
R L++ V D+IF + P TI H I+ SPLY LS
Sbjct: 179 EAHVRAQLLKSRVTPEGEFIPLHQIDIKVGFDTGSDRIFLVSPLTICHVIDERSPLYDLS 238
Query: 242 AADMLRERFEIVVILEGVIESTGMTTQARSSYLPNEILWGHRFETLVSFKKETGEHEVNY 301
A D+ FEIVVILEG +ESTGMT QAR+SYLP EILWGHRFE +VS + G+++V+Y
Sbjct: 239 AQDLKSADFEIVVILEGTVESTGMTCQARTSYLPEEILWGHRFEPVVSLEN--GKYKVDY 296
Query: 302 GLFNNTYEVHTPLCSAQALDQLLAI 326
F+ TYEV TP CSA+ LD+ +I
Sbjct: 297 SQFHKTYEVPTPDCSARELDEEKSI 321
>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 = 35.7 bits (83), Expect = 0.020
Identities = 29/128 (22%), Positives = 48/128 (37%), Gaps = 12/128 (9%)
Query: 66 NVAKRRRRYLQDIFTTLVDAQWRWTLLVFALNFLLSWLMFAIVWWLIVYTHGDLDKVNLG 125
R LQ + +L LL L LL +FAI+ + G+LDK
Sbjct: 75 RRFPGLRTLLQSLGRSLKS------LLNLLLLLLLLLFIFAIIGVQLFG--GELDKCCDK 126
Query: 126 NATWTPCVTSIHSFTSCFLFSVETQHTIGYGAKQVTEECP----EAIFILCLQSIVGVMI 181
N ++ S+ L+ T T G+G P IF + + GV++
Sbjct: 127 NENPINGNSNFDSYGEALLWLFRTLTTEGWGDVMYDTLVPGTVLGKIFFVIFIILGGVLL 186
Query: 182 QAFMVGIV 189
++G++
Sbjct: 187 LNLLIGVI 194
>gnl|CDD|129856 TIGR00774, NhaB, Na+/H+ antiporter NhaB. These proteins are
members of the NhaB Na+:H+ Antiporter (NhaB) Family (TC
2.A.34). The only characterised member of this family is
the Escherichia coli NhaB protein, which has 12 GES
predicted transmembrane regions, and catalyses
sodium/proton exchange. Unlike NhaA this activity is not
pH dependent [Transport and binding proteins, Cations
and iron carrying compounds].
Length = 515
Score = 33.3 bits (76), Expect = 0.21
Identities = 37/120 (30%), Positives = 50/120 (41%), Gaps = 13/120 (10%)
Query: 102 WLMFAIVWWLIVYTHGDLDKVNLGNATWTPCVTSIHSFTSCFLFSVETQHTIGYGAKQVT 161
W+ I WLIV L V L + TS FT V +H+IG K
Sbjct: 302 WVQALIAVWLIVALALHLAAVGLIGLSVIILATS---FTG-----VTDEHSIG---KAFE 350
Query: 162 EECPEAIFILCLQSIVGVMI-QAFMVGIVFAKLSRPKKRTQTLLFSRINCLQTSVEDKIF 220
E P + S+V V+I Q I+ L+ +K TQ LF N L +S+ D +F
Sbjct: 351 ESLPFTALLAVFFSVVAVIIDQELFSPIIDFVLAAEEK-TQLALFYVFNGLLSSISDNVF 409
>gnl|CDD|217681 pfam03706, UPF0104, Uncharacterized protein family (UPF0104). This
family of proteins are integral membrane proteins. These
proteins are uncharacterized but contain a conserved PG
motif. Some members of this family are annotated as
dolichol-P-glucose synthetase and contain a pfam00535
domain.
Length = 292
Score = 32.3 bits (74), Expect = 0.40
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 75 LQDIFTTLVDAQWRWTLLVFALNFLLSWLMFAIVWWLIV 113
L ++ L A W LL L LLS+L+ A+ W L++
Sbjct: 14 LSELAAALRSANPWWLLLALLL-ALLSYLLRALRWRLLL 51
>gnl|CDD|206187 pfam14017, DUF4233, Protein of unknown function (DUF4233). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 122 and 147 amino
acids in length. Proteins in this family are integral
membrane proteins.
Length = 105
Score = 29.8 bits (68), Expect = 0.81
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 103 LMFAIVWWLIVYTHGDLDK 121
++FA+VWW +Y +D+
Sbjct: 82 IVFALVWWYALYLGRRIDR 100
>gnl|CDD|148201 pfam06450, NhaB, Bacterial Na+/H+ antiporter B (NhaB). This family
consists of several bacterial Na+/H+ antiporter B (NhaB)
proteins. The exact function of this family is unknown.
Length = 515
Score = 30.6 bits (69), Expect = 1.5
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 147 VETQHTIGYGAKQVTEECPEAIFILCLQSIVGVMI-QAFMVGIVFAKLSRPKKRTQTLLF 205
V +H IG K E P + S+V V+I Q I+ LS + TQ LF
Sbjct: 340 VTDEHAIG---KAFEESLPFTALLAVFFSVVAVIIDQQLFSPIIQFVLSAEEN-TQLALF 395
Query: 206 SRINCLQTSVEDKIF 220
N L +S+ D +F
Sbjct: 396 YIFNGLLSSISDNVF 410
>gnl|CDD|177151 MTH00086, CYTB, cytochrome b; Provisional.
Length = 355
Score = 30.3 bits (69), Expect = 1.7
Identities = 21/64 (32%), Positives = 28/64 (43%), Gaps = 20/64 (31%)
Query: 86 QWRW--------TL-LVFALNFLLSW-LMFAIVWWLI----------VYTHGDLDKVNLG 125
W W TL F L+FLL W L+ +++ LI +Y HGD DK+ G
Sbjct: 151 MWIWGGFGVSSATLKFFFVLHFLLPWGLLVLVLFHLIFLHSTGSTSSLYCHGDYDKICFG 210
Query: 126 NATW 129
W
Sbjct: 211 PEYW 214
>gnl|CDD|240538 cd13133, MATE_like_7, Uncharacterized subfamily of the multidrug
and toxic compound extrusion (MATE) proteins. The
integral membrane proteins from the MATE family are
involved in exporting metabolites across the cell
membrane and are responsible for multidrug resistance
(MDR) in many bacteria and animals. A number of family
members are involved in the synthesis of peptidoglycan
components in bacteria.
Length = 438
Score = 30.2 bits (69), Expect = 2.3
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 90 TLLVFALNFLLSWLMFAIVWWLIVYTHGDL 119
T V +++WL +L+V L
Sbjct: 382 TRFVMLAELIVAWLYLLPPAYLLVVLGAGL 411
>gnl|CDD|191703 pfam07219, HemY_N, HemY protein N-terminus. This family represents
the N-terminus (approximately 150 residues) of bacterial
HemY porphyrin biosynthesis proteins. This is a membrane
protein involved in a late step of protoheme IX
synthesis.
Length = 108
Score = 28.4 bits (64), Expect = 2.4
Identities = 5/23 (21%), Positives = 11/23 (47%)
Query: 90 TLLVFALNFLLSWLMFAIVWWLI 112
+L + LL + ++ WL+
Sbjct: 15 SLTFAVILLLLVLAVLFLLEWLL 37
>gnl|CDD|130279 TIGR01212, TIGR01212, radical SAM protein, TIGR01212 family. This
family has a cluster of conserved Cys residues
suggestive of Fe-S cluster binding. Members belong to
the radical-SAM family of putative This uncharacterized
protein family shows significant similarity to
TIGR01211, a longer protein that is a histone
acetyltransferase at its C-terminus and is a subunit of
RNA polymerase II (in yeast). This family lacks the GNAT
acetyltransferase domain [Unknown function, Enzymes of
unknown specificity].
Length = 302
Score = 29.3 bits (66), Expect = 3.2
Identities = 15/65 (23%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 239 TLSAADMLRERFEIVVILEGVIESTGMTTQARSSYLPNEILWGHRFETLVSFKKETGEHE 298
T + ++L+E +E + + V+ G++ R +P+E+L + L + + E
Sbjct: 89 TYAPVEVLKEMYEQALSYDDVV---GLSVGTRPDCVPDEVL-----DLLAEYVERGYEVW 140
Query: 299 VNYGL 303
V GL
Sbjct: 141 VELGL 145
>gnl|CDD|214890 smart00893, ETF, Electron transfer flavoprotein domain. Electron
transfer flavoproteins (ETFs) serve as specific electron
acceptors for primary dehydrogenases, transferring the
electrons to terminal respiratory systems. They can be
functionally classified into constitutive,
"housekeeping" ETFs, mainly involved in the oxidation of
fatty acids (Group I), and ETFs produced by some
prokaryotes under specific growth conditions, receiving
electrons only from the oxidation of specific substrates
(Group II). ETFs are heterodimeric proteins composed of
an alpha and beta subunit, and contain an FAD cofactor
and AMP. ETF consists of three domains: domains I and II
are formed by the N- and C-terminal portions of the
alpha subunit, respectively, while domain III is formed
by the beta subunit. Domains I and III share an almost
identical alpha-beta-alpha sandwich fold, while domain
II forms an alpha-beta-alpha sandwich similar to that of
bacterial flavodoxins. FAD is bound in a cleft between
domains II and III, while domain III binds the AMP
molecule. Interactions between domains I and III
stabilise the protein, forming a shallow bowl where
domain II resides. This entry represents the N-terminal
domain of both the alpha and beta subunits from Group I
and Group II ETFs.
Length = 185
Score = 28.4 bits (64), Expect = 4.7
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 229 HKINPMSPLYTLSAADMLRERFEIVVILEG 258
INP+ L L AA L+E+ E+ ++ G
Sbjct: 7 ALINPVD-LEALEAARRLKEKGEVTAVVVG 35
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 28.8 bits (65), Expect = 5.4
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 104 MFAIVWWLIVYTHGDLDKVNLGNATWTPCVTSIHSFTSCFLFSVETQHTIGYG 156
+FA++ + + + LG+ P I S ++ F FS+ T T+GYG
Sbjct: 138 LFAVISITSLLFYSTFGALYLGDGFSPP----IESLSTAFYFSIVTMSTVGYG 186
>gnl|CDD|222273 pfam13632, Glyco_trans_2_3, Glycosyl transferase family group 2.
Members of this family of prokaryotic proteins include
putative glucosyltransferases, which are involved in
bacterial capsule biosynthesis.
Length = 194
Score = 28.1 bits (63), Expect = 6.0
Identities = 8/55 (14%), Positives = 19/55 (34%), Gaps = 8/55 (14%)
Query: 69 KRRRRYLQDIFTTLVDA--QWRWTLLVFALNFLLSWL------MFAIVWWLIVYT 115
++R R+ I + + W L+ L L + ++ L++
Sbjct: 133 RQRLRWAYGILEQGILLVRRLGWLRLLLWSYLPLRLLLLLLSSLSSLALLLLLLA 187
>gnl|CDD|227865 COG5578, COG5578, Predicted integral membrane protein [Function
unknown].
Length = 208
Score = 28.0 bits (63), Expect = 6.3
Identities = 8/35 (22%), Positives = 13/35 (37%)
Query: 85 AQWRWTLLVFALNFLLSWLMFAIVWWLIVYTHGDL 119
+L F F L + A ++ V H +L
Sbjct: 103 PGLLLFILTFVFVFALFLYVIAFLYVFPVLVHFEL 137
>gnl|CDD|236251 PRK08375, PRK08375, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 487
Score = 28.7 bits (65), Expect = 6.4
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 88 RWTLLVFALNFLLSWLMFAIVWWLIVYT 115
+ L +AL L++ L FA+ L+
Sbjct: 25 KRRRLRWALALLVAALTFALAISLLPQV 52
>gnl|CDD|200504 cd11243, Sema_7A, The Sema domain, a protein interacting module, of
semaphorin 7A (Sema7A, also called CD108). Sema7A plays
regulatory roles in both immune and nervous systems.
Unlike other semaphorins, which act as repulsive
guidance cues, Sema7A enhances central and peripheral
axon growth and is required for proper axon tract
formation during embryonic development. Sema7A also
plays a critical role in the negative regulation of T
cell activation and function. Sema7A is a
membrane-anchored member of the semaphorin family of
proteins. Semaphorins are regulatory molecules in the
development of the nervous system and in axonal
guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 414
Score = 28.7 bits (64), Expect = 6.8
Identities = 23/106 (21%), Positives = 41/106 (38%), Gaps = 3/106 (2%)
Query: 216 EDKIFFIWPTTIVHKINPMSPLYTLSAADMLRERFEIVVILEGVIESTGMTTQARSSYLP 275
+DKI++ + K P + A + +E L ST + + P
Sbjct: 166 QDKIYYFFREDNEDK-GPEAEPNISRVARLCKEDQGGTSSLSTSKWSTFLKARLVCGD-P 223
Query: 276 NEILWGHRFETLVSFKKETGEHEVNYGLFNNTYEVHTPLCSAQALD 321
+ +R + + KE V YG+F+NT+ + +CS D
Sbjct: 224 ATPMNFNRLQDVFLLPKEEWREAVVYGVFSNTWG-SSAVCSYSLGD 268
>gnl|CDD|129428 TIGR00328, flhB, flagellar biosynthetic protein FlhB. FlhB and its
functionally equivalent orthologs, from among a larger
superfamily of proteins involved in type III protein
export systems, are specifically involved in flagellar
protein export. The seed members are restricted and the
trusted cutoff is set high such that the proteins
gathered by this model play roles specifically related
to flagellar structures. Full-length homologs scoring
below the trusted cutoff are involved in peptide export
but not necessarily in the creation of flagella
[Cellular processes, Chemotaxis and motility].
Length = 347
Score = 28.4 bits (64), Expect = 6.8
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 10/43 (23%)
Query: 168 IFILCLQSIVGVMIQAFMVGIVFA-KLSRPKKRTQTLLFSRIN 209
IF+L L +VGV+ G +F K +PK FS+IN
Sbjct: 89 IFVLLL--VVGVLSNIAQFGFLFTTKPLKPK-------FSKIN 122
>gnl|CDD|219354 pfam07264, EI24, Etoposide-induced protein 2.4 (EI24). This family
contains a number of eukaryotic etoposide-induced 2.4
(EI24) proteins approximately 350 residues long as well
as bacterial CysZ proteins (formerly known as DUF540).
In cells treated with the cytotoxic drug etoposide, EI24
is induced by p53. It has been suggested to play an
important role in negative cell growth control.
Length = 205
Score = 27.9 bits (63), Expect = 7.2
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 87 WRWTLLVFALNFLLSWLMFAIVWWLIV 113
R LL LN LL + ++ L+
Sbjct: 14 RRLVLLPLLLNLLLFAGLLYFLFSLLG 40
>gnl|CDD|216137 pfam00822, PMP22_Claudin, PMP-22/EMP/MP20/Claudin family.
Length = 161
Score = 27.7 bits (62), Expect = 7.7
Identities = 22/113 (19%), Positives = 33/113 (29%), Gaps = 28/113 (24%)
Query: 98 FLLSWLMFAIVW------------WLIVYTHGDLDKVNLGNATWTPCVTSIHSF-TSCFL 144
LL +++ I W W + G L W C T + SC +
Sbjct: 4 LLLGFIVSHIAWVILLFVATIPDQWKVSRYVGAAASAGL----WRNCTTQSCTGQISCKV 59
Query: 145 FSVETQHTIGYGAKQVTEECPEAIFILCLQSIVGVMIQAFMVGIVFAKLSRPK 197
A Q + A+ IL + + +I F K R K
Sbjct: 60 LE-------LNDALQAVQ----ALMILSIILGIISLIVFFFQLFTMRKGGRFK 101
>gnl|CDD|100084 cd06163, S2P-M50_PDZ_RseP-like, RseP-like Site-2 proteases (S2P),
zinc metalloproteases (MEROPS family M50A), cleave
transmembrane domains of substrate proteins, regulating
intramembrane proteolysis (RIP) of diverse signal
transduction mechanisms. In Escherichia coli, the S2P
homolog RseP is involved in the sigmaE pathway of
extracytoplasmic stress responses. Also included in this
group are such homologs as Bacillus subtilis YluC,
Mycobacterium tuberculosis Rv2869c S2P, and Bordetella
bronchiseptica HurP. Rv2869c S2P appears to have a role
in the regulation of prokaryotic lipid biosynthesis and
membrane composition and YluC of Bacillus has a role in
transducing membrane stress. This group includes
bacterial and eukaryotic S2P/M50s homologs with either
one or two PDZ domains present. PDZ domains are believed
to have a regulatory role. The RseP PDZ domain is
required for the inhibitory reaction that prevents
cleavage of its substrate, RseA.
Length = 182
Score = 27.8 bits (63), Expect = 7.7
Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 87 WRWTLLVFA---LNFLLSWLMFAIVWWLIV 113
W+ L+VFA NFLL+ ++FA++ +
Sbjct: 88 WQRILIVFAGPLANFLLAIVLFAVLLSFLA 117
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 28.4 bits (64), Expect = 8.0
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 87 WRWTLLVFALNFLLSWLMFAIV 108
W+WT N +L++++ IV
Sbjct: 623 WKWTAFSVLYNLVLAYVLAFIV 644
>gnl|CDD|227836 COG5549, COG5549, Predicted Zn-dependent protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 236
Score = 28.0 bits (62), Expect = 9.1
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 85 AQWRWTLLVFALNFLLSWLMFAIVWWLIV 113
A W L +F +LL L I ++V
Sbjct: 6 AGEDWQLKLFDKPWLLVPLTVYIDDGIVV 34
>gnl|CDD|214404 MTH00025, ATP8, ATP synthase F0 subunit 8; Validated.
Length = 70
Score = 25.8 bits (57), Expect = 9.9
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 80 TTLVDAQWRWTLLV-FALNFLLSWLMFAIV---WWL 111
TT Q+RWTL+V F L F L + + + W +
Sbjct: 6 TTTYLTQYRWTLIVLFLLLFFLVFFVLPTIKRNWLI 41
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
0.321 0.134 0.410
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,487,884
Number of extensions: 1849254
Number of successful extensions: 1981
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1972
Number of HSP's successfully gapped: 43
Length of query: 391
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 292
Effective length of database: 6,546,556
Effective search space: 1911594352
Effective search space used: 1911594352
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 (21.9 bits)
S2: 60 (26.8 bits)