RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6930
(162 letters)
>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 = 66.5 bits (163), Expect = 3e-14
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 1 MAKGIRALLDTVMQALPQVGNLGLLFFLLFFIFAALGVELFGRLECSDELPCQG-LGEHA 59
G+R LL ++ ++L + NL LL LL FIFA +GV+LFG + + ++
Sbjct: 76 RFPGLRTLLQSLGRSLKSLLNLLLLLLLLLFIFAIIGVQLFGGELDKCCDKNENPINGNS 135
Query: 60 HFSNFGMAFLTLFRV 74
+F ++G A L LFR
Sbjct: 136 NFDSYGEALLWLFRT 150
>gnl|CDD|219699 pfam08016, PKD_channel, Polycystin cation channel. This family
contains the cation channel region of PKD1 and PKD2
proteins.
Length = 423
Score = 36.2 bits (84), Expect = 0.004
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 13/63 (20%)
Query: 11 TVMQALPQVGNLGLLFFLLFFIFAALGVELFGRLECSDELPCQGLGEHAHFSNFGMAFLT 70
T+ +AL ++ ++F +LF +A LG LFG + +FSNF + LT
Sbjct: 325 TLSRALKELLGFAVMFVILFLAYAQLGYLLFGS-------------QVDNFSNFVKSILT 371
Query: 71 LFR 73
LFR
Sbjct: 372 LFR 374
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 32.1 bits (73), Expect = 0.12
Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 14/89 (15%)
Query: 71 LFRVDMDMDKSSHMDKSSHMDKSSHKDTHLHSIEGRDNSSYHTSSLKDNSSLKDKSSKDK 130
LF ++ D+ S S+K++ D+S + + SS +DK+ K
Sbjct: 126 LFNLNSDISDYEQPRNSEKSTNDSNKNS--------DSSIKNDTD--TQSSKQDKADNQK 175
Query: 131 ----SSRKLKTNGRQQSMSDPSSINVNHK 155
++ K T+ +Q + P+ N ++
Sbjct: 176 APSSNNTKPSTSNKQPNSPKPTQPNQSNS 204
Score = 29.4 bits (66), Expect = 1.0
Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 6/87 (6%)
Query: 77 DMDKSSHMDKSSHMDKSSHKD--THLHSIEGRDNSSYHTSSLKDNS----SLKDKSSKDK 130
D K S +SH K S+ D + S + D + + +S +DN+ S D S+ D
Sbjct: 29 DPQKDSTAKTTSHDSKKSNDDETSKDTSSKDTDKADNNNTSNQDNNDKKFSTIDSSTSDS 88
Query: 131 SSRKLKTNGRQQSMSDPSSINVNHKNN 157
++ + + N ++
Sbjct: 89 NNIIDFIYKNLPQTNINQLLTKNKYDD 115
>gnl|CDD|227665 COG5373, COG5373, Predicted membrane protein [Function unknown].
Length = 931
Score = 29.8 bits (67), Expect = 0.63
Identities = 12/50 (24%), Positives = 16/50 (32%)
Query: 17 PQVGNLGLLFFLLFFIFAALGVELFGRLECSDELPCQGLGEHAHFSNFGM 66
P + LGL L F +A L V E + E +S
Sbjct: 802 PYLAMLGLAAAALLFAWATLSVRRTWHGEAQADWLGFSQLEQYSYSLAWT 851
>gnl|CDD|227703 COG5416, COG5416, Uncharacterized integral membrane protein
[Function unknown].
Length = 98
Score = 28.5 bits (64), Expect = 0.63
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 2 AKGIRALLDTVMQALPQVGNLGLLFFLLFFIFAALGVE------LFGRLE 45
A G A++ M+ V +G+L LL IFA + + LFG+ E
Sbjct: 9 APGEPAVVRKRMKGQWTVIIVGILILLLLLIFAVINTDSVEFNYLFGQWE 58
>gnl|CDD|212043 cd10336, SLC6sbd_Tyt1-Like, solute carrier 6 subfamily,
Fusobacterium nucleatum Tyt1-like; solute-binding
domain. SLC6 proteins (also called the sodium- and
chloride-dependent neurotransmitter transporter family
or Na+/Cl--dependent transporter family) include
neurotransmitter transporters (NTTs): these are sodium-
and chloride-dependent plasma membrane transporters for
the monoamine neurotransmitters serotonin
(5-hydroxytryptamine), dopamine, and norepinephrine, and
the amino acid neurotransmitters GABA and glycine. These
NTTs are widely expressed in the mammalian brain,
involved in regulating neurotransmitter signaling and
homeostasis, and the target of a range of therapeutic
drugs for the treatment of psychiatric diseases.
Bacterial members of the SLC6 family include the LeuT
amino acid transporter. An arrangement of 12
transmembrane (TM) helices appears to be as a common
topological motif for eukaryotic and some prokaryotic
and archaeal NTTs. However, this subfamily which
contains the majority of bacterial members and some
archaeal members, appears to contain only 11 TMs; for
example the functional Fusobacterium nucleatum tyrosine
transporter Tyt1.
Length = 439
Score = 29.3 bits (67), Expect = 0.76
Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 8/32 (25%)
Query: 12 VMQALPQV------GNL-GLLFFLLFFIFAAL 36
+ LP V G L G+LFFLL FAAL
Sbjct: 283 LFITLPAVFAQMPGGRLFGILFFLLLL-FAAL 313
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 29.5 bits (66), Expect = 0.84
Identities = 27/130 (20%), Positives = 40/130 (30%), Gaps = 18/130 (13%)
Query: 42 GRLECSDELPCQGLGEHAHFSNFGMAFLTLFRVDMDMDKSSHMDKSSHMDK---SSHKDT 98
L + EL H + T + K H + ++H
Sbjct: 222 KGLTSTKELVPVQNSGGNHSLSKSSNSQTPELEYSEKGKDHHHSHNHQHHSIGINNHHSK 281
Query: 99 HL-------HSIEGRDNSSYHTSSL--------KDNSSLKDKSSKDKSSRKLKTNGRQQS 143
H IE N S +SS ++SS S KSS+ K + R +S
Sbjct: 282 HADSKLQTIEVIENHSNKSRPSSSSTNGSKETTSNSSSAAAGSIGSKSSKSAKHSNRNKS 341
Query: 144 MSDPSSINVN 153
S P S +
Sbjct: 342 NSSPKSHSSA 351
>gnl|CDD|220477 pfam09933, DUF2165, Predicted small integral membrane protein
(DUF2165). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 160
Score = 28.0 bits (63), Expect = 1.6
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 5/50 (10%)
Query: 22 LGLLFFLLFFIFAALGVELFGRLECSDELPCQGLGEHAHFSNFGMAFLTL 71
L L F + F F +G E FG + + G+ + F F L L
Sbjct: 109 LTLGFLVWFVGFMVVGGEWFGMWQSK-----EWNGQDSAFRFFVFILLVL 153
>gnl|CDD|193227 pfam12751, Vac7, Vacuolar segregation subunit 7. Vac7 is localised
at the vacuole membrane, a location which is consistent
with its involvement in vacuole morphology and
inheritance. Vac7 has been shown to function as an
upstream regulator of the Fab1 lipid kinase pathway. The
Fab1 lipid kinase pathway is important for correct
regulation of membrane trafficking events.
Length = 386
Score = 28.3 bits (63), Expect = 2.1
Identities = 26/86 (30%), Positives = 34/86 (39%), Gaps = 5/86 (5%)
Query: 74 VDMDMDKSSHMDKSSHMDKSSHKDTHLH-SIEGRDNSSYHTSSLKDNSSLKDKSSK-DKS 131
+D D D+ S +H H H GR N + SL DN S +S K KS
Sbjct: 156 LDGDGDEDGGRGSSRSNGHGTHTPRHHHIGRHGR-NGGH--PSLFDNDSPFPQSQKSPKS 212
Query: 132 SRKLKTNGRQQSMSDPSSINVNHKNN 157
R NG +QS N N++
Sbjct: 213 PRHFIGNGSRQSRRGTPRSNPNYRTI 238
>gnl|CDD|225754 COG3213, NnrS, Uncharacterized protein involved in response to NO
[Inorganic ion transport and metabolism].
Length = 396
Score = 28.1 bits (63), Expect = 2.1
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 17 PQVGNLGL-LFFLLFFIFAALGVELF-----GRLECSDELPCQGLGEHAHFSNFGMA 67
P + +LG FFLL ++A L + L+ G L + + P L HAH FG A
Sbjct: 13 PPIWSLGFRPFFLLAALWAVLAMLLWIAALTGFLPLAGDYP--ALNWHAHEMLFGFA 67
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 27.9 bits (62), Expect = 2.5
Identities = 21/89 (23%), Positives = 36/89 (40%), Gaps = 12/89 (13%)
Query: 75 DMDMDKSSHMDKSSHMDKSSHKDTHLHSIEG--------RDNSSYHT---SSLKDNSSLK 123
D D+SS + D+S +D H S E RD Y + SL+ +S +
Sbjct: 14 GRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRR 73
Query: 124 DKSSKDKSSRKLKTNGRQQSMS-DPSSIN 151
+ + SR +++ + + D S N
Sbjct: 74 SRDRPRRRSRSVRSIEQHRRRLRDRSPSN 102
>gnl|CDD|204398 pfam10110, GPDPase_memb, Membrane domain of glycerophosphoryl
diester phosphodiesterase. Members of this family
comprise the membrane domain of the prokaryotic enzyme
glycerophosphoryl diester phosphodiesterase.
Length = 149
Score = 27.1 bits (61), Expect = 2.8
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 4 GIRALLDTVMQALPQVGNLGLLFFLLFFIF 33
++AL + L ++ GLLFFL++F+
Sbjct: 23 SLKALFKQTFKRLKKLRPGGLLFFLIYFLL 52
>gnl|CDD|212053 cd11484, SLC-NCS1sbd_CobB-like, nucleobase-cation-symport-1 (NCS1)
transporter CobB-like; solute-binding domain. This NCS1
subfamily includes Escherichia coli CodB (cytosine
permease), and the Saccharomyces cerevisiae
transporters: Fcy21p (Purine-cytosine permease), and
vitamin B6 transporter Tpn1. NCS1s are essential
components of salvage pathways for nucleobases and
related metabolites; their known substrates include
allantoin, uracil, thiamine, and nicotinamide riboside.
NCS1s belong to a superfamily which also contains the
solute carrier 5 family sodium/glucose transporters
(SLC5s), and solute carrier 6 family neurotransmitter
transporters (SLC6s).
Length = 403
Score = 27.6 bits (62), Expect = 3.4
Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 26 FFL---LFFIFAALGVELFGRLECSDELPCQGLG 56
FFL L FIF A+G G + SD + QGLG
Sbjct: 230 FFLGNSLMFIFGAVGAMATGGADISDVMIAQGLG 263
>gnl|CDD|215858 pfam00324, AA_permease, Amino acid permease.
Length = 473
Score = 27.3 bits (61), Expect = 3.9
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 15 ALPQVGNLGLLFFLLFFIFAALGVELFGRLE 45
+P + G +F +L I +GV+ +G E
Sbjct: 109 DIPYLWVWGAVFIVLLLIINLVGVKGYGEAE 139
>gnl|CDD|225866 COG3329, COG3329, Predicted permease [General function prediction
only].
Length = 372
Score = 27.1 bits (60), Expect = 4.5
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 8 LLDTVMQALPQVGNLGLLFFLLFFIFAALGVEL 40
L + +M + + + LLFF+L + AA +L
Sbjct: 4 LSEFLMDFVGNLLSPTLLFFILGMLIAAFKSDL 36
>gnl|CDD|224185 COG1266, COG1266, Predicted metal-dependent membrane protease
[General function prediction only].
Length = 226
Score = 26.8 bits (59), Expect = 4.9
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 7 ALLDTVMQALPQVGNLGLLFFLLFFIFAALGVELF 41
LL+ + L LLFFL+ I A L EL
Sbjct: 106 LLLNQLPLLLTLAVLWLLLFFLVLLILAPLAEELL 140
>gnl|CDD|240539 cd13134, MATE_like_8, 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 = 27.1 bits (61), Expect = 5.3
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 22 LGLLFFLLFFIFAALGVELFG 42
LGL+F LL F A + L G
Sbjct: 92 LGLVFSLLLLFFGAELLRLMG 112
>gnl|CDD|216236 pfam01003, Flavi_capsid, Flavivirus capsid protein C.
Flaviviruses are small enveloped viruses with virions
comprised of 3 proteins called C, M and E. Multiple
copies of the C protein form the nucleocapsid, which
contains the ssRNA molecule.
Length = 117
Score = 25.7 bits (57), Expect = 7.7
Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 4/36 (11%)
Query: 2 AKGIRALLDTVMQALPQVGNLGL-LFFLLFFIFAAL 36
K + Q L G L L L FL FF F A+
Sbjct: 21 LKKTKRK---TGQLLDGRGPLRLVLAFLAFFRFTAI 53
>gnl|CDD|225272 COG2409, COG2409, Predicted drug exporters of the RND superfamily
[General function prediction only].
Length = 937
Score = 26.6 bits (59), Expect = 8.3
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 54 GLGEHAHFSNFGMAFLTLFRVDMD 77
LG H+ ++F+ L V D
Sbjct: 809 ILGIELHWLVPALSFVVLLAVGSD 832
>gnl|CDD|148737 pfam07301, DUF1453, Protein of unknown function (DUF1453). This
family consists of several hypothetical bacterial
proteins of around 150 residues in length. The function
of this family is unknown. Members of this family seem
to be found exclusively in the Order Bacillales.
Length = 149
Score = 25.7 bits (57), Expect = 8.8
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 5 IRALLDTVMQALPQVGNLGLLFFLLFF 31
IR L + G L +F+LL F
Sbjct: 106 IRIALKIYLSNSIDPGELSGMFYLLAF 132
>gnl|CDD|235865 PRK06814, PRK06814, acylglycerophosphoethanolamine
acyltransferase; Provisional.
Length = 1140
Score = 26.5 bits (59), Expect = 8.8
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 23 GLLFFLLFFIFAALGVEL 40
G +F L FFIF+AL +L
Sbjct: 58 GAVFILPFFIFSALAGQL 75
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
0.317 0.131 0.371
Gapped
Lambda K H
0.267 0.0615 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,579,310
Number of extensions: 651238
Number of successful extensions: 1065
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1051
Number of HSP's successfully gapped: 36
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
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 (21.7 bits)
S2: 55 (25.2 bits)