RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16308
(371 letters)
>gnl|CDD|219699 pfam08016, PKD_channel, Polycystin cation channel. This family
contains the cation channel region of PKD1 and PKD2
proteins.
Length = 423
Score = 55.0 bits (133), Expect = 3e-08
Identities = 27/126 (21%), Positives = 59/126 (46%), Gaps = 6/126 (4%)
Query: 55 LVWFGVLRYLGFFKTYNVVILTLKKAFPKVARFLLCAVLIYAGFTFCGWLVLGPYHMKFR 114
L W + + L F +T ++ TL +A ++ F + V+++ + G+L+ G F
Sbjct: 304 LTWLKLFKVLRFNRTMSLFTKTLSRALKELLGFAVMFVILFLAYAQLGYLLFGSQVDNFS 363
Query: 115 SLSTTSECLFALINGDDMFATFSIMPKKSAMLWWYLRIYLYSFISLYIYVILSLFISVIM 174
+ + LF + GD + + + +F+ L I+++L+LF+++I
Sbjct: 364 NFVKSILTLFRTLCGDFGYTEIFSGNR------VLGPLLFLTFVFLVIFILLNLFLAIIN 417
Query: 175 DAYETI 180
D+Y +
Sbjct: 418 DSYVEV 423
>gnl|CDD|215637 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
Length = 1634
Score = 49.2 bits (117), Expect = 2e-06
Identities = 30/151 (19%), Positives = 64/151 (42%), Gaps = 4/151 (2%)
Query: 33 ERKQFIGDQWNLCSVFLGTGNLLVWFGVLRYLGFFKTYNVVILTLKKAFPKVARFLLCAV 92
E K + D + G +L+ +L+ + F V+ TL A + F +
Sbjct: 1280 EMKNLV-DYFQWYMTLSGINIILLLGRILKLMDFQPRLGVITRTLWLAGADLMHFFVIFG 1338
Query: 93 LIYAGFTFCGWLVLGPYHMKFRSLSTTSECLFALINGD-DMFATFSIMPKKSAMLWWYLR 151
+++ G+ F G ++ G + F ++ + LF + GD F + + + +
Sbjct: 1339 MVFVGYAFIGHVIFGNASVHFSDMTDSINSLFENLLGDITYF--NEDLKNLTGLQFVVGM 1396
Query: 152 IYLYSFISLYIYVILSLFISVIMDAYETIKQ 182
IY YS+ ++ + +++I DA+ +K
Sbjct: 1397 IYFYSYNIFVFMILFNFLLAIICDAFGEVKA 1427
>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 = 46.1 bits (110), Expect = 7e-06
Identities = 36/181 (19%), Positives = 61/181 (33%), Gaps = 28/181 (15%)
Query: 7 FLNLWYVMIIANDVLLILGSSIKEQIERKQFIGDQWNLCSVFLGTGNLLVWFGVLRYLGF 66
F + W ++ D L++L S + I S L LL +LR L
Sbjct: 28 FRSPWNIL----DFLVVLPSLV-------SLILFLLGEDSGLLRVLRLLRLLRLLRLLRR 76
Query: 67 FKTYNVVILTLKKAFPKVARFLLCAVLIYAGFTFCGWLVLGPY--------------HMK 112
F ++ +L ++ + LL +L+ F G + G +
Sbjct: 77 FPGLRTLLQSLGRSLKSLLNLLLLLLLLLFIFAIIGVQLFGGELDKCCDKNENPINGNSN 136
Query: 113 FRSLSTTSECLFALINGDDMFATFSIMPKKSAMLWWYLRIYLYSFISLYIYVILSLFISV 172
F S LF + + +M +I+ FI L ++L+L I V
Sbjct: 137 FDSYGEALLWLFRTLTTEGW---GDVMYDTLVPGTVLGKIFFVIFIILGGVLLLNLLIGV 193
Query: 173 I 173
I
Sbjct: 194 I 194
>gnl|CDD|212061 cd11492, SLC5sbd_NIS-SMVT, Na(+)/iodide (NIS) and
Na(+)/multivitamin (SMVT) cotransporters, and related
proteins; solute binding domain. NIS (encoded by the
SLC5A5 gene) transports I-, and other anions including
ClO4-, SCN-, and Br-. SMVT (encoded by the SLC5A6 gene)
transports biotin, pantothenic acid and lipoate. This
subfamily also includes SMCT1 and -2. SMCT1(encoded by
the SLC5A8 gene) is a high-affinity transporter of
various monocarboxylates including lactate and pyruvate,
short-chain fatty acids, ketone bodies, nicotinate and
its structural analogs, pyroglutamate, benzoate and its
derivatives, and iodide. SMCT2 (encoded by the SLC5A12
gene) is a low-affinity transporter for short-chain
fatty acids, lactate, pyruvate, and nicotinate. This
subgroup belongs to the solute carrier 5 (SLC5)
transporter family.
Length = 522
Score = 36.3 bits (85), Expect = 0.023
Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 10/87 (11%)
Query: 96 AGFTFCGWLVLG------PYHMKFRSLSTTSE-CLFALINGDDMFATFSIMPKKSAMLWW 148
G F W+ +G P + L ++E C + T + +S +
Sbjct: 437 VGLAFSLWIGIGGQPAYPPGPLSTPPLPLSTEGCNYTNNTTTTTSTTTTTTEDESELFSL 496
Query: 149 YLRI-YL-YSFISLYIYVILSLFISVI 173
Y RI YL YS I I V++ L +S++
Sbjct: 497 Y-RISYLYYSLIGTLITVVVGLIVSLL 522
>gnl|CDD|180570 PRK06457, PRK06457, pyruvate dehydrogenase; Provisional.
Length = 549
Score = 34.4 bits (79), Expect = 0.094
Identities = 24/108 (22%), Positives = 43/108 (39%), Gaps = 11/108 (10%)
Query: 193 VIKFMGEIQEDETNHDFWSSIETASF-----SFREQIHKMHKSIALATRADREANGKRR- 246
VI G+++ D HD++ + F + + + + RA REA KR
Sbjct: 93 VIALTGQVESDMIGHDYFQEVNLTKLFDDVAVFNQILINPENAEYIIRRAIREAISKRGV 152
Query: 247 PHLNT-----RKGEEEEENRKFPDYNLSYRVILVLNQSTITRSERPFV 289
H+N RK E + ++ + Y + + I SE+P +
Sbjct: 153 AHINLPVDILRKSSEYKGSKNTEVGKVKYSIDFSRAKELIKESEKPVL 200
>gnl|CDD|212149 cd11542, NTP-PPase_u5, Nucleoside Triphosphate Pyrophosphohydrolase
(EC 3.6.1.8) MazG-like domain found in a group of
uncharacterized proteins from bacteria and archaea.
This family corresponds to a group of uncharacterized
hypothetical proteins from bacteria, showing a high
sequence similarity to the dimeric 2-deoxyuridine
5'-triphosphate nucleotidohydrolase (dUTP
pyrophosphatase or dUTPase) and NTP-PPase MazG proteins.
However, unlike typical tandem-domain MazG proteins,
members in this family consist of a single MazG-like
domain that contains a well conserved divalent
ion-binding motif EXX[E/D].
Length = 99
Score = 31.9 bits (73), Expect = 0.12
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 197 MGEIQEDETNHDFWSSIETASFSFREQIHKMHKSIALATRADREANGKRRPHLNTRKGEE 256
+ E E+ H +W T + +F E + +H ++ A R G L R E
Sbjct: 5 VDEAHENAVAHGWWDDPRTGNNNFGELLMLIHSEVSEALEGLR--KGLMDDKLPHRPMIE 62
Query: 257 EE 258
E
Sbjct: 63 VE 64
>gnl|CDD|233445 TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type
ATPase. This model describes the P-type ATPase
primarily responsible for translocating copper ions
accross biological membranes. These transporters are
found in prokaryotes and eukaryotes. This model
encompasses those species which pump copper ions out of
cells or organelles (efflux pumps such as CopA of
Escherichia coli ) as well as those which pump the ion
into cells or organelles either for the purpose of
supporting life in extremely low-copper environments
(for example CopA of Enterococcus hirae ) or for the
specific delivery of copper to a biological complex for
which it is a necessary component (for example FixI of
Bradyrhizobium japonicum, or CtaA and PacS of
Synechocystis). The substrate specificity of these
transporters may, to a varying degree, include silver
ions (for example, CopA from Archaeoglobus fulgidus).
Copper transporters from this family are well known as
the genes which are mutated in two human disorders of
copper metabolism, Wilson's and Menkes' diseases. The
sequences contributing to the seed of this model are all
experimentally characterized. The copper P-type ATPases
have been characterized as Type IB based on a
phylogenetic analysis which combines the
copper-translocating ATPases with the
cadmium-translocating species. This model and that
describing the cadmium-ATPases (TIGR01512) are well
separated, and thus we further type the copper-ATPases
as IB1 (and the cadmium-ATPases as IB2). Several
sequences which have not been characterized
experimentally fall just below the cutoffs for both of
these models. A sequence from Enterococcus faecalis
scores very high against this model, but yet is
annotated as an "H+/K+ exchanging ATPase". BLAST of this
sequence does not hit anything else annotated in this
way. This error may come from the characterization paper
published in 1987. Accession GP|7415611 from
Saccharomyces cerevisiae appears to be mis-annotated as
a cadmium resistance protein. Accession
OMNI|NTL01HS00542 from Halobacterium which scores above
trusted for this model is annotated as
"molybdenum-binding protein" although no evidence can be
found for this classification [Cellular processes,
Detoxification, Transport and binding proteins, Cations
and iron carrying compounds].
Length = 572
Score = 30.7 bits (70), Expect = 1.3
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 83 KVARFLLCAVLIYAGFTFCGWLVLGP 108
KVA + + V+ A TF WL+LG
Sbjct: 204 KVAGYFVPVVIAIALITFVIWLILGA 229
>gnl|CDD|218835 pfam05975, EcsB, Bacterial ABC transporter protein EcsB. This
family consists of several bacterial ABC transporter
proteins which are homologous to the EcsB protein of
Bacillus subtilis. EcsB is thought to encode a
hydrophobic protein with six membrane-spanning helices
in a pattern found in other hydrophobic components of
ABC transporters.
Length = 385
Score = 30.3 bits (69), Expect = 1.9
Identities = 16/123 (13%), Positives = 44/123 (35%), Gaps = 5/123 (4%)
Query: 93 LIYAGFTFCGWLVLGPYHMKFRSLSTTSECLFAL----INGDDMFATFSIMPKKSAMLWW 148
++ ++L P +K LS L L + ++ + I+ W
Sbjct: 106 ILQLILQVLLAILLLPLLLKILGLSILQYVLLLLFLLLLKAWNLLLKWRILYLVEGKRWD 165
Query: 149 YLRIYLYSFISLYIYVILSLFISVIMDAYETIKQY-YINGFPKSDVIKFMGEIQEDETNH 207
L + + + LY+ +L+ ++ I+ + + K ++ + I+ ++
Sbjct: 166 LLIRLILNLLLLYLLFLLAPLLAAILFLILLVVLLLLLRKLKKKKLLDWEKLIELEQRRK 225
Query: 208 DFW 210
+
Sbjct: 226 QRF 228
>gnl|CDD|217705 pfam03739, YjgP_YjgQ, Predicted permease YjgP/YjgQ family. Members
of this family are predicted integral membrane proteins
of unknown function. They are about 350 amino acids long
and contain about 6 transmembrane regions. They are
predicted to be permeases although there is no
verification of this.
Length = 354
Score = 29.2 bits (66), Expect = 3.9
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 122 CLFALINGDDMFATFSIMPKKSAMLWWYLRIYLYSFISLYIYVI-LSLFISVIM 174
L L D+ + K L LR+ L S+ ++ L+L ++V++
Sbjct: 17 VLLLLFLLVDLLRLLDDILSKGLPLADILRLLLLLLPSILELILPLALLLAVLL 70
>gnl|CDD|234609 PRK00068, PRK00068, hypothetical protein; Validated.
Length = 970
Score = 29.2 bits (66), Expect = 4.0
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 12/58 (20%)
Query: 47 VFLGTGNLLV-------WFGVLRYLGFFKTYNVVILTLKKAFPKVARFLLCAVLIYAG 97
+ L G LV WFG + Y F T ++T F + LL +++
Sbjct: 26 LLLLFGPRLVDFYIDWLWFGEVGYRSVFFT---KLVTRIVLF--IPVGLLVGGIVFIS 78
>gnl|CDD|225105 COG2194, COG2194, Predicted membrane-associated, metal-dependent
hydrolase [General function prediction only].
Length = 555
Score = 28.5 bits (64), Expect = 6.2
Identities = 14/130 (10%), Positives = 46/130 (35%), Gaps = 15/130 (11%)
Query: 66 FFKTYNVVILTLKKAFPKVARFLLCAVLI------YAGFTFCGWLVLGPYHMKFRSLSTT 119
+ +++L L FP++ + L + + Y + + ++ +M T
Sbjct: 53 LVFAFLLLLLLLS--FPRLLKPLAGVLSLVSAAASYFAYFYG---IIIDKNMLLNVFETN 107
Query: 120 SECLFALINGDDM--FATFSIMPKKSAMLWWYLRIYLYSFISLYIYVILSLFISVIMDAY 177
+ L+ + ++P + ++ + Y ++ ++S+ +S+++
Sbjct: 108 TAESSELLTLYFLLWLVLVGLLP--ALLIVLVIIRYYRVWLRRLWARLVSILLSLLVILA 165
Query: 178 ETIKQYYING 187
Y
Sbjct: 166 FAAPFYKNYA 175
>gnl|CDD|223445 COG0368, CobS, Cobalamin-5-phosphate synthase [Coenzyme
metabolism].
Length = 246
Score = 28.4 bits (64), Expect = 6.3
Identities = 19/120 (15%), Positives = 37/120 (30%), Gaps = 14/120 (11%)
Query: 88 LLCAVLIYAGFTFCGWLVLGPYHMKFRSLST--TSECLFALINGDDMFATFSIMPKKSAM 145
L ++L L L K R L S+ +A + F+ K
Sbjct: 122 ALASLLDLGAA---ALLALAEVLAKSRMLLVALLSKPPYA--GLGGLGKEFADPRKGLIG 176
Query: 146 LWWYLRIYLYSFISLY---IYVILSLFISVIMDAYETIKQYYINGFPKSDVIKFMGEIQE 202
L + L + + I V ++L + ++ + + G D + E+
Sbjct: 177 ALLLLVLLLLALLFGLSGAIAVAVALLAAALLGRLAKRRFGGVTG----DTLGAAIELSR 232
>gnl|CDD|237163 PRK12663, PRK12663, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 497
Score = 28.4 bits (64), Expect = 7.2
Identities = 12/27 (44%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 8 LNLWY-VMIIANDVLLILGSSIKEQIE 33
L +W+ VM+IA+ VL+ LG +EQ+
Sbjct: 133 LYVWFEVMLIASFVLITLGQE-REQLR 158
>gnl|CDD|177458 PHA02676, PHA02676, A-type inclusion protein; Provisional.
Length = 520
Score = 28.0 bits (62), Expect = 9.5
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 16/75 (21%)
Query: 273 ILVLNQSTITRSERPFVKKKKRLLGGKSPKTGLRTWEYRKRPPEVLCDVCFYWAQALNSS 332
+LV N++ + RP + + + G P PP VL + W
Sbjct: 453 VLVSNKTDVHTCNRPGAEVTRHAIDGSLP------------PPHVLGN----WGARSYCG 496
Query: 333 NNRKQRCVLSNQKTW 347
R V +K W
Sbjct: 497 RRRHYPRVSHGEKPW 511
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
0.326 0.139 0.435
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,081,178
Number of extensions: 1869283
Number of successful extensions: 2321
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2301
Number of HSP's successfully gapped: 61
Length of query: 371
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 273
Effective length of database: 6,590,910
Effective search space: 1799318430
Effective search space used: 1799318430
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 (21.6 bits)
S2: 60 (26.8 bits)