RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 038674
(343 letters)
>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 = 66.1 bits (162), Expect = 5e-14
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 60 LLLVGYLGVGALCFFLIRHQIKGEKTNGVLDSIYFCIVTMTTVGYGDLVPHSTLAKLLAC 119
+LL+ L G + + L + LD++YF VT+TT+GYGD+VP + +L
Sbjct: 1 ILLLLVLIFGTVYYSLEEEGWGWD----FLDALYFSFVTLTTIGYGDIVPLTDAGRLFTI 56
Query: 120 VYVFSGMALVGLILGKAA 137
+Y+ G+ L L L
Sbjct: 57 IYILIGIPLFLLFLAVLG 74
Score = 64.5 bits (158), Expect = 2e-13
Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 186 FILLVLIIAGIVFLSVVEDLK---FVDALYCVCSTITTLGYGDMSFSTRGGRFFAVFWIL 242
+LL+++I G V+ S+ E+ F+DALY T+TT+GYGD+ T GR F + +IL
Sbjct: 1 ILLLLVLIFGTVYYSLEEEGWGWDFLDALYFSFVTLTTIGYGDIVPLTDAGRLFTIIYIL 60
Query: 243 SGTICLAQFFLYLT 256
G F L
Sbjct: 61 IGIPLFLLFLAVLG 74
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 49.2 bits (118), Expect = 1e-06
Identities = 17/25 (68%), Positives = 20/25 (80%)
Query: 92 IYFCIVTMTTVGYGDLVPHSTLAKL 116
YF IVTM+TVGYGD+VP S A+L
Sbjct: 173 FYFSIVTMSTVGYGDIVPVSESARL 197
Score = 31.1 bits (71), Expect = 0.77
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 181 LVTATFILLVLIIAGIVFLSVVEDLKFVDALYCVCSTITTLGYGDMSFSTRGGRFFAVFW 240
L +TF L L G F +E L A Y T++T+GYGD+ + R F +
Sbjct: 148 LFYSTFGALYL---GDGFSPPIESL--STAFYFSIVTMSTVGYGDIVPVSESARLFTISV 202
Query: 241 ILSG 244
I+ G
Sbjct: 203 IILG 206
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 44.5 bits (105), Expect = 6e-05
Identities = 19/52 (36%), Positives = 30/52 (57%)
Query: 91 SIYFCIVTMTTVGYGDLVPHSTLAKLLACVYVFSGMALVGLILGKAADYLVE 142
+IY+ I TMTTVGYGDL +T+ + Y+ + L ++G + +VE
Sbjct: 254 AIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE 305
Score = 31.4 bits (71), Expect = 0.79
Identities = 12/38 (31%), Positives = 24/38 (63%)
Query: 205 LKFVDALYCVCSTITTLGYGDMSFSTRGGRFFAVFWIL 242
++++ A+Y +T+TT+GYGD+ F +F++L
Sbjct: 249 IRYISAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYML 286
>gnl|CDD|233196 TIGR00933, 2a38, potassium uptake protein, TrkH family. The
proteins of the Trk family are derived from
Gram-negative and Gram-positive bacteria, yeast and
wheat. The proteins of E. coli K12 TrkH and TrkG as well
as several yeast proteins have been functionally
characterized.The E. coli TrkH and TrkG proteins are
complexed to two peripheral membrane proteins, TrkA, an
NAD-binding protein, and TrkE, an ATP-binding protein.
This complex forms the potassium uptake system
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 390
Score = 38.8 bits (91), Expect = 0.003
Identities = 33/178 (18%), Positives = 62/178 (34%), Gaps = 27/178 (15%)
Query: 58 VLLLLVGYLGVGALCFFLIRHQIKGEKTNG-VLDSIYFCIVTMTTVGYG--DLVPHSTLA 114
LLL +G++ L R + G +L S +F T+ T G+ D T
Sbjct: 205 FLLLAIGFILF----LLLERGNTLYSYSFGALLLSAFFQSSTLRTAGFSTIDFAALPTAT 260
Query: 115 KLLACVYVFSGMALVGLILGKAADYLVEKQQLLLVKAMYNYENASAGSVSAAEVLKDVET 174
+L + +F G G A + +L+K +Y + +
Sbjct: 261 LVLLLLLMFIGGC-----SGSTAGGIKTTTFAILLKQVYREIRRGIHPRI-------IFS 308
Query: 175 HKVKYKLVT--------ATFILLVLIIAGIVFLSVVEDLKFVDALYCVCSTITTLGYG 224
++ K + + F++ LI + + F+ +L+ V S T+G
Sbjct: 309 RRIGGKTIDKAILISVWSFFLVFALIFLLSILELISSGYDFLTSLFEVVSAFGTVGLS 366
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 30.0 bits (68), Expect = 0.21
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 282 EAADLDHDKLVSVAEFVIYKLKEMGKINEEDISVLMER-FRTLDADQSGNLT 332
+ D D D + V E K+ +E++ L+E F +D D G ++
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRIS 52
>gnl|CDD|217009 pfam02386, TrkH, Cation transport protein. This family consists of
various cation transport proteins (Trk) and V-type
sodium ATP synthase subunit J or translocating ATPase J
EC:3.6.1.34. These proteins are involved in active
sodium up-take utilising ATP in the process. TrkH a
member of the family from E. coli is a hydrophobic
membrane protein and determines the specificity and
kinetics of cation transport by the TrK system in E.
coli.
Length = 334
Score = 33.0 bits (76), Expect = 0.21
Identities = 36/190 (18%), Positives = 71/190 (37%), Gaps = 16/190 (8%)
Query: 55 FRQVLLLLVGYLGVGALCFFLIRHQIKGEKTNGVLDSIYFCIVTMTTVGYG--DLVPHST 112
R LLLL G++ + L ++ + + + +F + + T G+ DL S
Sbjct: 127 RRTFLLLLPGFITI--LLLEVLVVLLASLPLGSRILNAFFQVSSTRTAGFSTIDLSQLSP 184
Query: 113 LAKLLACVYVFSGMALVGLILGKAADYLVEKQQLLLVKAMYNYENASA-GSVSAAEVLKD 171
K+L + +F G + G +++KA+ A G+V +
Sbjct: 185 ATKVLLMLLMFIGGSPGSTAGGIKTITF-----AVILKALNWINRAFLPGAVEPVKFGGR 239
Query: 172 VETHKVKYKLVTATFILLVLIIAGIVFLSVVEDLKFVDALYCVCSTITTLGYG------D 225
++ + ++ I + LS+ F D+L+ V S T+G +
Sbjct: 240 HLREQLIRDAWAFFLLYFLICIFEGLLLSLTGYDPFFDSLFEVVSAFGTVGLSLGITTPN 299
Query: 226 MSFSTRGGRF 235
+S S G+
Sbjct: 300 LSLSPDLGKL 309
>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 = 31.9 bits (73), Expect = 0.27
Identities = 17/86 (19%), Positives = 39/86 (45%), Gaps = 10/86 (11%)
Query: 58 VLLLLVGYLGVGALCFFLIRHQIKGEKTNGV---------LDSIYFCIVTMTTVGYGDLV 108
+LLLL + +G F + + N + +++ + T+TT G+GD++
Sbjct: 101 LLLLLFIFAIIGVQLFGGELDKCCDKNENPINGNSNFDSYGEALLWLFRTLTTEGWGDVM 160
Query: 109 PHSTLA-KLLACVYVFSGMALVGLIL 133
+ + +L ++ + L G++L
Sbjct: 161 YDTLVPGTVLGKIFFVIFIILGGVLL 186
>gnl|CDD|226547 COG4061, MtrC, Tetrahydromethanopterin S-methyltransferase, subunit
C [Coenzyme metabolism].
Length = 262
Score = 30.9 bits (70), Expect = 0.81
Identities = 26/115 (22%), Positives = 49/115 (42%), Gaps = 8/115 (6%)
Query: 91 SIYFCIVTMTTVG--YGDLVPHSTLAKLLACVYVFSGMALVGLILGKAADYLVEKQQLLL 148
SI + M V G +P+ TL L A + A++G ++G +V + ++
Sbjct: 73 SIGMMSLGMGIVAAVAGLAIPYFTLPALAAPIIGLIVAAVIGAVVGVLTVKVVGMKIPIM 132
Query: 149 VKAMYNYENASAGSVS----AAEVLKDVETHKVKYKLVTATFILLVLIIAGIVFL 199
+ M E + AG+++ + + V ++ I L+ IIAG+ L
Sbjct: 133 ERCM--TEISGAGALALLGFSVAIAGSFTPQAVIDYVIANGMIALLFIIAGMAIL 185
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 29.5 bits (67), Expect = 2.7
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 280 DLEAADLDHDKLVSVA----EFVIYKLKEMG-KINEEDISVLMERFRTLDADQSGN-LTT 333
D E ++ + V KL+E+G +++EE++ L R + L +T
Sbjct: 309 DPEDVGRRRRIVIGGKHSGRKAVKAKLEELGIELDEEELDKLFSRVKELADKGKKKEVTD 368
Query: 334 ADIMLL 339
AD+ L
Sbjct: 369 ADLEAL 374
>gnl|CDD|221595 pfam12479, DUF3698, Protein of unknown function (DUF3698). This
domain family is found in eukaryotes, and is typically
between 89 and 105 amino acids in length.
Length = 107
Score = 28.0 bits (62), Expect = 2.7
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 4 HKNNDDATGSGQPLLSSKPVDYSNLNEPMEQND-KKSLLPLESALMSQEEIR 54
+KN DA + + L + Y N +EQ D ++ P S++ +R
Sbjct: 17 YKNEADAIDTKEKLEICFGIAYKTGNYYLEQGDPFFNVAPRPFEQSSRKSLR 68
>gnl|CDD|217327 pfam03030, H_PPase, Inorganic H+ pyrophosphatase. The H+
pyrophosphatase is an transmembrane proton pump involved
in establishing the H+ electrochemical potential
difference between the vacuole lumen and the cell
cytosol. Vacuolar-type H(+)-translocating inorganic
pyrophosphatases have long been considered to be
restricted to plants and to a few species of
photo-trophic bacteria. However, in recent
investigations, these pyrophosphatases have been found
in organisms as disparate as thermophilic Archaea and
parasitic protists.
Length = 669
Score = 29.0 bits (66), Expect = 4.2
Identities = 22/102 (21%), Positives = 37/102 (36%), Gaps = 12/102 (11%)
Query: 177 VKYKLVTATFILLVLIIAGIVFLSVVEDLKFVDALY------CVCSTITTLGYGDMSFST 230
V + L+ A ++ II G F+ + + AL + S + T
Sbjct: 250 VLFPLLVAAVGIIASII-GTFFVRTGKGANPMKALNRGLIVSAILSIVATYFATYWLLPA 308
Query: 231 RGGRF--FAVFW-ILSGTICLAQFFLYLTELYTQSRQNSFVK 269
G F + +F +L G + +TE YT S V+
Sbjct: 309 AGKGFLWWNLFLAVLIGLV-AGALIGLITEYYT-STSYRPVR 348
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 28.0 bits (63), Expect = 4.3
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 310 EEDISVLMERFRTLDADQSGNLTTADIM 337
EE I L E F+ D D G + ++
Sbjct: 16 EEQIQELKEAFQLFDRDSDGLIDRNELG 43
>gnl|CDD|180361 PRK06035, PRK06035, 3-hydroxyacyl-CoA dehydrogenase; Validated.
Length = 291
Score = 28.3 bits (63), Expect = 5.3
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 290 KLVSVAEFVIYKLKEMGKINEEDISVLMERFRTLDADQSGNLTTADIML 338
+L+ + + L E GK++E++ +M R RT + +L+ AD ++
Sbjct: 44 ELIESGPYGLRNLVEKGKMSEDEAKAIMARIRT--STSYESLSDADFIV 90
>gnl|CDD|234336 TIGR03734, PRTRC_parB, PRTRC system ParB family protein. A novel
genetic system characterized by six major proteins,
included a ParB homolog and a ThiF homolog, is
designated PRTRC, or ParB-Related,ThiF-Related Cassette.
It is often found on plasmids. This protein family the
member related to ParB, and is designated PRTRC system
ParB family protein.
Length = 554
Score = 28.1 bits (63), Expect = 7.5
Identities = 17/78 (21%), Positives = 23/78 (29%), Gaps = 9/78 (11%)
Query: 257 ELYTQSRQNSFVKWVLTRQLTFSDLEAADLDHDKLVSVAEFVIYKLKEMGKINEEDISVL 316
EL QN V L SD A + +K KL D+
Sbjct: 392 ELALNPEQNRRVLIALAL---ASD--ARVIKDEKFGKAFG----KLTGEKSAAAADLGTA 442
Query: 317 MERFRTLDADQSGNLTTA 334
+ + LD + L A
Sbjct: 443 LTQAMALDDEHLAKLLQA 460
>gnl|CDD|214713 smart00543, MIF4G, Middle domain of eukaryotic initiation factor 4G
(eIF4G). Also occurs in NMD2p and CBP80. The domain is
rich in alpha-helices and may contain multiple
alpha-helical repeats. In eIF4G, this domain binds
eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G
domain homologues (in press).
Length = 200
Score = 27.3 bits (61), Expect = 9.2
Identities = 9/47 (19%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 177 VKYKLVTATFILLVLIIAGIVFLSVVEDLKFVDALYCVCSTITTLGY 223
++++T + I+L L+ + L+ ++ + ++ C+ S + T G
Sbjct: 107 YNFQVLT-SKIILELLKELLNDLTKLDPPRSDFSVECLLSLLPTCGK 152
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
0.323 0.137 0.389
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,207,233
Number of extensions: 1687650
Number of successful extensions: 2033
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2027
Number of HSP's successfully gapped: 60
Length of query: 343
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 245
Effective length of database: 6,590,910
Effective search space: 1614772950
Effective search space used: 1614772950
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 (22.0 bits)
S2: 59 (26.6 bits)