RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017950
(363 letters)
>gnl|CDD|223131 COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic
ion transport and metabolism].
Length = 304
Score = 152 bits (387), Expect = 1e-43
Identities = 74/293 (25%), Positives = 143/293 (48%), Gaps = 13/293 (4%)
Query: 63 EEMKQLAKNERVAIYASNAANLVLFLAKVYASAESRSLAVIASTLDSLLDLLSGFILWFT 122
E ++L R A+ + A NL L L K+ A + S+A++A + SL D+++ I+
Sbjct: 3 MEEERLKLVRRAALISL-AVNLALALLKLIAGILTGSVALLADAIHSLSDIVASLIVLIG 61
Query: 123 AYAMKKPNQYQYPIGKNRMQPVGIVVFASIMATLGLQILFESGRELFTEAQPERDPEKEK 182
KP +P G + + + ++ + ++ G +IL E+ + L + E
Sbjct: 62 LRISSKPPDRDHPYGHGKAETLASLIVSILIFAAGFEILLEAIKRLISPQPVEPPL---- 117
Query: 183 WMIGIMVSVTVVKLALMMYCRR----FKNEIVRAYAQDHFFDVITNSIGLATALLAIKF- 237
+G+ + V+K AL Y RR ++ + A A H DV+T S+ + LL
Sbjct: 118 LALGVALISIVIKEALYRYLRRVGKKTNSQALIADALHHRSDVLT-SLAVLVGLLGSLLG 176
Query: 238 YWWIDPIGAILIALYTMGNWGNTVMENVWSLIGRTAPAEYLAKLTYLIWNHHEEIKYIET 297
+ W+DP+ A+LI+LY + E+V L+ E L K+ +I + +K +
Sbjct: 177 WPWLDPLAALLISLYILKTGFRLFKESVNELMDAALDPEDLEKIRAIILS-VPGVKGVHD 235
Query: 298 VRAYNFGCQYFVEADVVLPAEMSLSEAHNIGESLQEKL-EQLPEVERAFVHVD 349
+R G + F++ + + ++SL EAH I + +++++ ++ P+V +HV+
Sbjct: 236 LRTRKSGSRIFIDVHIEVDPDLSLEEAHEIADEVEKRIKKEFPKVADVTIHVE 288
>gnl|CDD|216561 pfam01545, Cation_efflux, Cation efflux family. Members of this
family are integral membrane proteins, that are found to
increase tolerance to divalent metal ions such as
cadmium, zinc, and cobalt. These proteins are thought to
be efflux pumps that remove these ions from cells.
Length = 273
Score = 145 bits (369), Expect = 2e-41
Identities = 68/274 (24%), Positives = 133/274 (48%), Gaps = 16/274 (5%)
Query: 85 VLFLAKVYASAESRSLAVIASTLDSLLDLLSGFILWFTAYAMKKPNQYQYPIGKNRMQPV 144
+L L K+ A + SLA++A L SL+DLLS + +P ++P G R++P+
Sbjct: 1 LLALVKLAAGLLTGSLALLADALHSLIDLLSSLLALLALRLSSRPPDKRHPFGHGRLEPL 60
Query: 145 GIVVFASIMATLGLQILFESGRELFTEAQPERDPEKEKWMIGIMVSVTVVKLALMMYCRR 204
++ + ++ +G+ IL+ES L + + E ++ + + VV L L +Y RR
Sbjct: 61 AALIVSLLLLGVGVFILYESIERLISPEEIEPG-----GILLVALISLVVNLLLALYLRR 115
Query: 205 ------FKNEIVRAYAQDHFFDVITNSIGLATALLAIKFYW--WIDPIGAILIALYTMGN 256
K+ +RA A DV+ S+ + LL I DP+ ++LIAL +
Sbjct: 116 AGRKIGKKSSALRADALHALVDVLG-SLAVLIGLLLILLTGLPIADPLASLLIALLILYT 174
Query: 257 WGNTVMENVWSLIGRTAPAEYLAKLTYLIWNHHEEIKYIETVRAYNFGCQYFVEADVVLP 316
+ E++ L+G + E + ++ + + + +R + G +YFV+ + +
Sbjct: 175 GLRLLKESLSELLGASPDPELVDEIRDAL-EKLPGVLGVHDLRVWKSGPKYFVDIHIEVD 233
Query: 317 AEMSLSEAHNIGESLQEKL-EQLPEVERAFVHVD 349
++++ EAH I + ++ L E+ P + +HV+
Sbjct: 234 PDLTVEEAHEIADEIERALKEKFPGIADVTIHVE 267
>gnl|CDD|233348 TIGR01297, CDF, cation diffusion facilitator family transporter.
This model describes a broadly distributed family of
transporters, a number of which have been shown to
transport divalent cations of cobalt, cadmium and/or
zinc. The family has six predicted transmembrane
domains. Members of the family are variable in length
because of variably sized inserts, often containing
low-complexity sequence [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 268
Score = 110 bits (278), Expect = 3e-28
Identities = 65/272 (23%), Positives = 123/272 (45%), Gaps = 13/272 (4%)
Query: 85 VLFLAKVYASAESRSLAVIASTLDSLLDLLSGFILWFTAYAMKKPNQYQYPIGKNRMQPV 144
+L L K+ S SLA++A + SL D+ + I ++P ++P G R + +
Sbjct: 1 LLMLIKIVGGLLSGSLALLADAIHSLSDVAASAIALLALRISRRPADERHPFGHGRAEIL 60
Query: 145 GIVVFASIMATLGLQILFESGRELFTEAQPERDPEKEKWMIGIMVSVTVVKLALMMYCRR 204
++ + + L IL+E+ L M+ + + +V L L +Y R
Sbjct: 61 AALLNGLFLVVVALFILYEAIERLINP----EPEIDGGTMLIVAIVGLIVNLILALYLHR 116
Query: 205 F----KNEIVRAYAQDHFFDVITNSIGLATALLAIKFYW-WIDPIGAILIALYTMGNWGN 259
+ +RA A D ++ S+G+ L I F W W DPI A+LI+L +
Sbjct: 117 VGHRLGSLALRAAALHVLSDALS-SVGVLIGALLIYFGWHWADPIAALLISLLILYTAFR 175
Query: 260 TVMENVWSLIGRTAPAEYLAKLTYLIWNHHEEIKYIETVRAYNFG-CQYFVEADVVLPAE 318
+ E++ L+ E L ++ I + +K + + + G + F++ VV+ +
Sbjct: 176 LLKESINVLLDAAPDEEDLEEIKKAILS-IPGVKGVHDLHIWRIGPGKLFLDVHVVVDPD 234
Query: 319 MSLSEAHNIG-ESLQEKLEQLPEVERAFVHVD 349
+ L +AH+I E +E L++ P +E + V+
Sbjct: 235 LDLKQAHDIALEIEREILKRHPGIEHVTIQVE 266
Score = 28.7 bits (65), Expect = 4.1
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 81 AANLVLFLAKVYASAESRSLAVIASTLDSLLDLLS-------GFILWFT 122
NL+L L SLA+ A+ L L D LS +++F
Sbjct: 105 IVNLILALYLHRVGHRLGSLALRAAALHVLSDALSSVGVLIGALLIYFG 153
>gnl|CDD|224151 COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion
transport and metabolism].
Length = 296
Score = 60.8 bits (148), Expect = 2e-10
Identities = 46/187 (24%), Positives = 85/187 (45%), Gaps = 11/187 (5%)
Query: 70 KNERVAIYASNAANLVLFLAKVYASAESRSLAVIASTLDSLLDLLSGFILWFTAYAMKKP 129
+NER + + NL L ++ + SLA++A L L D L+ + ++P
Sbjct: 19 RNER-RLLIALLLNLAFMLIEIIGGLLTGSLALLADALHMLSDALALLLALIAIKLARRP 77
Query: 130 NQYQYPIGKNRMQPVGIVVFASIMATLGLQILFESGRELFTEAQPERDPEKEKWMIGIMV 189
++ G R++ + + A ++ + L IL+E+ + L M+ + +
Sbjct: 78 ATKRFTFGYKRLEILAAFLNALLLIVVSLLILWEAIQRLLAPPPIH-----YSGMLVVAI 132
Query: 190 SVTVVKL--ALMMYCRRFKNEIVRAYAQDHFFDVITNSIGLATALLAIKFYWW--IDPIG 245
VV L AL+++ +N +R A H S+G+ A + I+F W +DPI
Sbjct: 133 IGLVVNLVSALLLHKGHEENLNMRG-AYLHVLGDALGSVGVIIAAIVIRFTGWSWLDPIL 191
Query: 246 AILIALY 252
+I+IAL
Sbjct: 192 SIVIALL 198
>gnl|CDD|181919 PRK09509, fieF, ferrous iron efflux protein F; Reviewed.
Length = 299
Score = 53.1 bits (128), Expect = 7e-08
Identities = 64/282 (22%), Positives = 124/282 (43%), Gaps = 43/282 (15%)
Query: 75 AIYASNAANLVLFLAKVYASAESRSLAVIASTLDSLLDLLSGFI-LWFTAYAMKKPN-QY 132
A A+ A +L L K++A + S++++A+ +DSL+D+ + L Y+++ + ++
Sbjct: 12 AAIAATAMASLLLLIKIFAWWYTGSVSLLAALVDSLVDIAASLTNLLVVRYSLQPADDEH 71
Query: 133 QYPIGKNRMQPVGIVVFASIMATLGLQILFESGRELF---------TEAQPERDPEKEKW 183
+ GK A +A L Q +F SG LF P DP
Sbjct: 72 TFGHGK-----------AESLAALA-QSMFISGSALFLFLTGIQHLISPTPMNDPG---- 115
Query: 184 MIGIMVSVT--VVKLALMMY----CRRFKNEIVRAYAQDHFFDVITNSIGLATALLAIKF 237
+GI+V++ + L L+ + R+ +++ VRA + DV+ N LLA+
Sbjct: 116 -VGIIVTLVALICTLILVTFQRWVVRKTQSQAVRADMLHYQSDVMMN----GAILLALGL 170
Query: 238 YW----WIDPIGAILIALYTMGNWGNTVMENVWSLIGRTAPAEYLAKLTYLIWNHHEEIK 293
W D + A+ I +Y + + E V SL+ R P E ++ ++ + +
Sbjct: 171 SWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTS-WPGVS 229
Query: 294 YIETVRAYNFGCQYFVEADVVLPAEMSLSEAHNIGESLQEKL 335
+R G F++ + + + L +AH I + +++ L
Sbjct: 230 GAHDLRTRQSGPTRFIQLHLEMEDNLPLVQAHMIADQVEQAL 271
>gnl|CDD|226474 COG3965, COG3965, Predicted Co/Zn/Cd cation transporters [Inorganic
ion transport and metabolism].
Length = 314
Score = 39.4 bits (92), Expect = 0.002
Identities = 50/283 (17%), Positives = 99/283 (34%), Gaps = 43/283 (15%)
Query: 71 NERVAIYASNAANLVLFLAKVYASAESRSLAVIASTLDSLLDL-LSGFILWFTAYAMKKP 129
NE++ + S A ++ + S S+++I + SL+D ++ L + K P
Sbjct: 17 NEQLYLRISIAGTVIFAAFGIIWGLLSGSMSIIFDGVYSLIDAGMTLLSLLVSRLIAKDP 76
Query: 130 NQYQYPIGKNRMQPV----------GIVVFASIMATLGLQILFESGRELFTEAQPERDPE 179
++P G ++P+ + ++A I A L L + GRE+ +P
Sbjct: 77 RDARFPYGFWHLEPLVLAINGTLLALLCLYALINA---LGSLLDGGREV--------EPG 125
Query: 180 KEKWMIGIMVSVTVVKLALMMY------CRRFKNEIVRAYAQDHFFDVITNS---IGLAT 230
I ++ V + RR K+ ++ + ++ + A
Sbjct: 126 -----HAIAYTLVSVTGCAAIAWKLRRLNRRLKSPLIALDTKQWLMSTCLSAALFVAFAA 180
Query: 231 ALL--AIKFYW---WIDPIGAILIALYTMGNWGNTVMENVWSLIGRTAPAEYLAKLTYLI 285
A L KF + DP+ L+ L + TV + ++ P E +
Sbjct: 181 AWLLAGTKFAHLVVYADPMVLALVCLVFIPLPLGTVKSALREIL-LMTPNELQQSIESHA 239
Query: 286 WNHHEEIKYIET-VRAYNFGCQYFVEADVVLPAEMSLSEAHNI 327
E+ + V G F+E ++P E +
Sbjct: 240 HEIVEKYGFPSYHVYVARVGRGLFIEIHFIIPRESDARNVEDW 282
>gnl|CDD|222292 pfam13656, RNA_pol_L_2, RNA polymerase Rpb3/Rpb11 dimerisation
domain. The two eukaryotic subunits Rpb3 and Rpb11
dimerise to from a platform onto which the other
subunits of the RNA polymerase assemble (D/L in
archaea). The prokaryotic equivalent of the Rpb3/Rpb11
platform is the alpha-alpha dimer. The dimerisation
domain of the alpha subunit/Rpb3 is interrupted by an
insert domain (pfam01000). Some of the alpha subunits
also contain iron-sulphur binding domains (pfam00037).
Rpb11 is found as a continuous domain. Members of this
family include: alpha subunit from eubacteria, alpha
subunits from chloroplasts, Rpb3 subunits from
eukaryotes, Rpb11 subunits from eukaryotes, RpoD
subunits from archaeal spp, and RpoL subunits from
archaeal spp. Many of the members of this family carry
only the N-terminal region of Rpb11.
Length = 77
Score = 31.4 bits (72), Expect = 0.12
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 323 EAHNIGESLQEKLEQLPEVERAFVHVDFNATHQLEHKP 360
E H +G L+E+L + P+VE A V H LE K
Sbjct: 10 EDHTLGNLLREELLKDPDVEFAGYSVP----HPLEDKI 43
>gnl|CDD|223370 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 205
Score = 30.3 bits (69), Expect = 1.2
Identities = 25/78 (32%), Positives = 31/78 (39%), Gaps = 20/78 (25%)
Query: 8 ERRMDSHLSIGYYIKTLRRHRKIAGY-----YKRQE-----KLLK-GYNEVDTFTELGIL 56
+R + HL YY K K GY YK E KL K G VD LG
Sbjct: 5 QRWLAEHLRDPYYKKA-----KKEGYRSRAAYKLLELNEKFKLFKPGMVVVD----LGAA 55
Query: 57 PGSLTQEEMKQLAKNERV 74
PG +Q K+L ++
Sbjct: 56 PGGWSQVAAKKLGAGGKI 73
>gnl|CDD|223383 COG0306, PitA, Phosphate/sulphate permeases [Inorganic ion
transport and metabolism].
Length = 326
Score = 28.7 bits (65), Expect = 5.0
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 222 ITNSIG-LATALLAIKFYWWIDPIGAILIALYTMGNWGNTVMENVWSLIGRTAPAEYLA 279
+ N+IG L L++ +W+ +G I +AL T+ G V+E V I P+ +
Sbjct: 194 VANAIGPLVAVLISSLPPFWVLVLGGIALALGTL-TGGPRVIETVGKKITELTPSRGFS 251
>gnl|CDD|176370 cd01775, CYR1_RA, Ubiquitin domain of CYR1 adenylate cyclase.
CYR1 is a fungal adenylate cyclase with at least four
domains, an N-terminal RA (Ras association) domain, a
middle leucine-rich repeat domain, a catalytic domain.
The N-terminal RA domain of CYR1 post-translationally
modifies a small GTPase called Ras. The Ras-CYR1
pathway has been implicated in the transduction of a
glucose-triggered signal to an intracellular
environment where a protein phosphorylation cascade is
initiated by cyclic AMP.
Length = 97
Score = 26.6 bits (59), Expect = 6.9
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 44 YNEVDTFTELGILPGSLTQEEMKQLAK 70
+ TFT L + E + QLAK
Sbjct: 8 FRSDGTFTTLSCPLNTTVSELIPQLAK 34
>gnl|CDD|107282 cd06287, PBP1_LacI_like_8, Ligand-binding domain of uncharacterized
DNA-binding regulatory proteins that are members of the
LacI-GalR family of bacterial transcription repressors.
This group includes the ligand-binding domain of
uncharacterized DNA-binding regulatory proteins that are
members of the LacI-GalR family of bacterial
transcription repressors. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 269
Score = 27.7 bits (62), Expect = 8.4
Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 3/66 (4%)
Query: 294 YIETVRAYNFGCQYFVEADVVLPAEMSLSEAHNIGES-LQEKLEQLPEVERAFVHVDFNA 352
Y+E AY VVL + + E G + + L Q P+++ V VD A
Sbjct: 133 YLEAEAAYRAFAAEHGMPPVVLRVDEAGGE--EAGYAACAQLLAQHPDLDALCVPVDAFA 190
Query: 353 THQLEH 358
+
Sbjct: 191 VGAVRA 196
>gnl|CDD|237167 PRK12667, PRK12667, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 520
Score = 28.0 bits (63), Expect = 8.6
Identities = 7/40 (17%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 218 FFDVITNSIGLATALLAIKFYWWIDPIGAILIALYTMGNW 257
+ + L T +L+I + + ++ Y G W
Sbjct: 33 IQKIYALLVSLITLILSILLFIQVYSSNKPIV--YLFGGW 70
>gnl|CDD|131289 TIGR02235, menA_cyano-plnt, 1,4-dihydroxy-2-naphthoate
phytyltransferase. This family of phytyltransferases,
found in plants and cyanobacteria, are involved in the
biosythesis of phylloquinone (Vitamin K1). Phylloquinone
is a critical component of photosystem I. The closely
related MenA enzyme from bacteria transfers a prenyl
group (which only differs in the saturation of the
isoprenyl groups) in the biosynthesis of menaquinone.
Activity towards both substrates in certain organisms
should be considered a possibility [Biosynthesis of
cofactors, prosthetic groups, and carriers, Menaquinone
and ubiquinone].
Length = 285
Score = 27.8 bits (62), Expect = 9.4
Identities = 24/112 (21%), Positives = 38/112 (33%), Gaps = 14/112 (12%)
Query: 183 WMIGIMVSVTVVKLALMMYCRRFKNEIVRAYAQDHFFDVITNSIGLATALLAIKFYWWID 242
W I+V + L+++C F D + + L T L A W I
Sbjct: 164 WKASILVGLAT---TLILFCSHFHQ-----VEDDLAHGKRSPVVRLGTKLAAKIVPWVIS 215
Query: 243 PIGAILIALYTMGNWGNTVMENVWSLIGRTAP-AEYLAKLTYLIWNHHEEIK 293
+L+ G T + L + P A L +L N+ E+I
Sbjct: 216 LSYVVLLIAVIGGFLPWTTL-----LALASIPWAVKLIRLVRQNHNNPEQIS 262
>gnl|CDD|236800 PRK10935, PRK10935, nitrate/nitrite sensor protein NarQ;
Provisional.
Length = 565
Score = 27.9 bits (63), Expect = 9.4
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 63 EEMKQLAKNERVAIYASNAANLV----LFLAKVYASAESRSLAVIASTLDSLLD--LLSG 116
EMK + Y +N AN V LF+ + AE + + + A +L L+ L
Sbjct: 107 LEMKSYLEQGDSRWYQANIANYVDQIDLFVLALQHFAERKLILLAAISLLGLILILTLVF 166
Query: 117 FILWFT 122
F + FT
Sbjct: 167 FTVRFT 172
>gnl|CDD|239249 cd02951, SoxW, SoxW family; SoxW is a bacterial periplasmic TRX,
containing a redox active CXXC motif, encoded by a
genetic locus (sox operon) involved in thiosulfate
oxidation. Sulfur bacteria oxidize sulfur compounds to
provide reducing equivalents for carbon dioxide fixation
during autotrophic growth and the respiratory electron
transport chain. It is unclear what the role of SoxW is,
since it has been found to be dispensable in the
oxidation of thiosulfate to sulfate. SoxW is
specifically kept in the reduced state by SoxV, which is
essential in thiosulfate oxidation.
Length = 125
Score = 26.9 bits (60), Expect = 9.7
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 5/32 (15%)
Query: 201 YCRRFKNEI-----VRAYAQDHFFDVITNSIG 227
YC + K + V+AY + HF V N G
Sbjct: 28 YCDKLKRDYLNDPAVQAYIRAHFVVVYINIDG 59
>gnl|CDD|238176 cd00284, Cytochrome_b_N, Cytochrome b (N-terminus)/b6/petB:
Cytochrome b is a subunit of cytochrome bc1, an
11-subunit mitochondrial respiratory enzyme. Cytochrome
b spans the mitochondrial membrane with 8 transmembrane
helices (A-H) in eukaryotes. In plants and
cyanobacteria, cytochrome b6 is analogous to eukaryote
cytochrome b, containing two chains: helices A-D are
encoded by the petB gene and helices E-H are encoded by
the petD gene in these organisms. Cytochrome b/b6
contains two bound hemes and two ubiquinol/ubiquinone
binding sites. The C-terminal portion of cytochrome b
is described in a separate CD.
Length = 200
Score = 27.3 bits (61), Expect = 10.0
Identities = 7/27 (25%), Positives = 15/27 (55%)
Query: 176 RDPEKEKWMIGIMVSVTVVKLALMMYC 202
+ P + W+IG+++ + + A M Y
Sbjct: 100 KKPRELTWVIGVILLLLTMATAFMGYV 126
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
0.322 0.136 0.405
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,936,546
Number of extensions: 1858474
Number of successful extensions: 2231
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2206
Number of HSP's successfully gapped: 45
Length of query: 363
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 265
Effective length of database: 6,590,910
Effective search space: 1746591150
Effective search space used: 1746591150
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 (26.9 bits)