RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3235
(149 letters)
>gnl|CDD|234815 PRK00701, PRK00701, manganese transport protein MntH; Reviewed.
Length = 439
Score = 61.0 bits (149), Expect = 9e-12
Identities = 18/56 (32%), Positives = 33/56 (58%)
Query: 14 VMSLQLPFAVLPTIAFTSNPNIMGDFVNSTGTKVVTLCLSAVIITINSTFFYDLLS 69
V+S LPFA++P + FTS+ +MG+ VN K++ ++ +I+ +N Y +
Sbjct: 382 VLSFGLPFALIPLLLFTSDRKLMGELVNPRWVKIIAWIIAVLIVALNIYLLYQTFT 437
>gnl|CDD|162246 TIGR01197, nramp, NRAMP (natural resistance-associated macrophage
protein) metal ion transporters. This model describes
the Nramp metal ion transporter family. Historically, in
mammals these proteins have been functionally
characterized as proteins involved in the host pathogen
resistance, hence the name - NRAMP. At least two
isoforms Nramp1 and Nramp2 have been identified. However
the exact mechanism of pathogen resistance was unclear,
until it was demonstrated by expression cloning and
electrophysiological techniques that this protein was a
metal ion transporter. It was also independently
demonstrated that a microcytic anemia (mk) locus in
mouse, encodes a metal ion transporter (DCT1 or Nramp2).
The transporter has a broad range of substrate
specificity that include Fe+2, Zn+2, Mn+2, Co+2, Cd+2,
Cu+2, Ni+2 and Pb+2. The uptake of these metal ions is
coupled to proton symport. Metal ions are essential
cofactors in a number of biological process including,
oxidative phosphorylation, gene regulation and metal ion
homeostasis. Nramp1 could confer resistance to infection
in one of the two ways. (1) The uptake of Fe+2 can
produce toxic hydroxyl radicals via Fenton reaction
killing the pathogens in phagosomes or (2) Deplete the
metal ion pools in the phagosome and deprive the
pathogens of metal ions, which is critical for its
survival [Transport and binding proteins, Cations and
iron carrying compounds].
Length = 390
Score = 54.7 bits (132), Expect = 1e-09
Identities = 17/36 (47%), Positives = 22/36 (61%)
Query: 1 MEDLTSMNDILNTVMSLQLPFAVLPTIAFTSNPNIM 36
E LT + V+SL LPFA++P I FTS+ IM
Sbjct: 355 REGLTGALNASQVVLSLLLPFALIPLIMFTSSKKIM 390
>gnl|CDD|224826 COG1914, MntH, Mn2+ and Fe2+ transporters of the NRAMP family
[Inorganic ion transport and metabolism].
Length = 416
Score = 47.7 bits (114), Expect = 4e-07
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 13 TVMSLQLPFAVLPTIAFTSNPNIMGDFVNSTGTKVVTLCLSAVIITINSTFFYDLLS 69
++S+ LPFA++P + TS+ +MGD+ N V+ + +I+ +N L
Sbjct: 357 VLLSVILPFALIPLLLLTSDKKLMGDYKNPRWLTVLGWIVVILIVALNIILLVGTLG 413
>gnl|CDD|216575 pfam01566, Nramp, Natural resistance-associated macrophage protein.
The natural resistance-associated macrophage protein
(NRAMP) family consists of Nramp1, Nramp2, and yeast
proteins Smf1 and Smf2. The NRAMP family is a novel
family of functional related proteins defined by a
conserved hydrophobic core of ten transmembrane domains.
This family of membrane proteins are divalent cation
transporters. Nramp1 is an integral membrane protein
expressed exclusively in cells of the immune system and
is recruited to the membrane of a phagosome upon
phagocytosis. By controlling divalent cation
concentrations Nramp1 may regulate the interphagosomal
replication of bacteria. Mutations in Nramp1 may
genetically predispose an individual to susceptibility
to diseases including leprosy and tuberculosis
conversely this might however provide protection form
rheumatoid arthritis. Nramp2 is a multiple divalent
cation transporter for Fe2+, Mn2+ and Zn2+ amongst
others it is expressed at high levels in the intestine;
and is major transferrin-independent iron uptake system
in mammals. The yeast proteins Smf1 and Smf2 may also
transport divalent cations.
Length = 364
Score = 40.2 bits (95), Expect = 2e-04
Identities = 15/29 (51%), Positives = 23/29 (79%)
Query: 14 VMSLQLPFAVLPTIAFTSNPNIMGDFVNS 42
++SL LPFA++P + TS+ +MG+FVNS
Sbjct: 335 LLSLLLPFALIPLLLLTSSRKLMGEFVNS 363
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 29.1 bits (66), Expect = 0.75
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 19 LPFAVLPTIAFTSNPNIMGDFVNSTGTKVVTLCLSAVIITINSTFF 64
+PFA+ AF + ++G+ V S+G KV+ L AVI+ I ST F
Sbjct: 181 IPFALFGKTAFLAE-RVLGNVV-SSGIKVLVL---AVIVGIGSTLF 221
>gnl|CDD|216630 pfam01654, Bac_Ubq_Cox, Bacterial Cytochrome Ubiquinol Oxidase.
This family are the alternative oxidases found in many
bacteria which oxidise ubiquinol and reduce oxygen as
part of the electron transport chain. This family is the
subunit I of the oxidase E. coli has two copies of the
oxidase, bo and bd', both of which are represented here
In some nitrogen fixing bacteria, e.g. Klebsiella
pneumoniae this oxidase is responsible for removing
oxygen in microaerobic conditions, making the oxidase
required for nitrogen fixation. This subunit binds a
single b-haem, through ligands at His186 and Met393
(using SW:P11026 numbering). In addition His19 is a
ligand for the haem b found in subunit II.
Length = 432
Score = 27.8 bits (63), Expect = 2.6
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 73 EELSWIIIGFLLVYGIFYVIMVLYLLLHLI 102
++ + +IGF L+Y + +V V YLLL
Sbjct: 398 GQVLFSLIGFTLLYAVLFVAEV-YLLLRYA 426
>gnl|CDD|215637 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
Length = 1634
Score = 27.2 bits (60), Expect = 4.4
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 76 SWIIIGFLLVYGIFYVIMVLY-LLLHLIVSMGGDFKFNRSEFVSKY--IGSQLRD 127
+ + + Y IF V M+L+ LL +I G+ K N +E VS + + LRD
Sbjct: 1392 FVVGMIYFYSYNIF-VFMILFNFLLAIICDAFGEVKANAAETVSVHTELFPMLRD 1445
>gnl|CDD|239588 cd03511, Rhizopine-oxygenase-like, This CD includes the putative
hydrocarbon oxygenase, MocD, a bacterial rhizopine
(3-O-methyl-scyllo-inosamine, 3-O-MSI) oxygenase, and
other related proteins. It has been proposed that MocD,
MocE (Rieske-like ferredoxin), and MocF (ferredoxin
reductase) under the regulation of MocR, act in concert
to form a ferredoxin oxygenase system that demethylates
3-O-MSI to form scyllo-inosamine. This domain family
appears to be structurally related to the membrane
fatty acid desaturases and the alkane hydroxylases.
They all share in common extensive hydrophobic regions
that would be capable of spanning the membrane bilayer
at least twice. Comparison of sequences also reveals
the existence of three regions of conserved histidine
cluster motifs that contain eight histidine residues:
HXXXH, HXXHH, and HXXHH. These histidine residues are
reported to be catalytically essential and proposed to
be the ligands for the iron atoms contained within
homologs, stearoyl CoA desaturase and alkane
hydroxylase.
Length = 285
Score = 26.6 bits (59), Expect = 4.9
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 76 SWIIIGFLLVYGIFYVIM 93
SW + LVYG+ Y +
Sbjct: 41 SWWALPAFLVYGVLYAAL 58
>gnl|CDD|233307 TIGR01195, oadG_fam, sodium pump decarboxylases, gamma subunit.
This model finds the subfamily of distantly related, low
complexity, hydrophobic small subunits of several
related sodium ion-pumping decarboxylases. These include
oxaloacetate decarboxylase gamma subunit and
methylmalonyl-CoA decarboxylase delta subunit. Most
sequences scoring between the noise and trusted cutoffs
are eukaryotic sodium channel proteins.
Length = 82
Score = 25.5 bits (56), Expect = 5.2
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 76 SWIIIGFLL-VYGIFYVIMVLYLLLHLIVSMG 106
S ++ G L V G+ V + L LL++ + MG
Sbjct: 2 SLLLEGATLTVLGMGIVFLFLSLLIYAVRGMG 33
>gnl|CDD|179504 PRK02935, PRK02935, hypothetical protein; Provisional.
Length = 110
Score = 25.8 bits (57), Expect = 5.7
Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 5/37 (13%)
Query: 75 LSWIIIGFLLVY-GIF----YVIMVLYLLLHLIVSMG 106
LS + IGF+++Y GIF +IM +++LL + +
Sbjct: 17 LSLVFIGFIVMYLGIFFRESIIIMTIFMLLGFLAVIA 53
>gnl|CDD|239583 cd03506, Delta6-FADS-like, The Delta6 Fatty Acid Desaturase
(Delta6-FADS)-like CD includes the integral-membrane
enzymes: delta-4, delta-5, delta-6, delta-8,
delta-8-sphingolipid, and delta-11 desaturases found in
vertebrates, higher plants, fungi, and bacteria. These
desaturases are required for the synthesis of highly
unsaturated fatty acids (HUFAs), which are mainly
esterified into phospholipids and contribute to
maintaining membrane fluidity. While HUFAs may be
required for cold tolerance in bacteria, plants and
fish, the primary role of HUFAs in mammals is cell
signaling. These enzymes are described as front-end
desaturases because they introduce a double bond between
the pre-exiting double bond and the carboxyl (front) end
of the fatty acid. Various substrates are involved, with
both acyl-coenzyme A (CoA) and acyl-lipid desaturases
present in this CD. Acyl-lipid desaturases are localized
in the membranes of cyanobacterial thylakoid, plant
endoplasmic reticulum (ER), and plastid; and acyl-CoA
desaturases are present in ER membrane. ER-bound plant
acyl-lipid desaturases and acyl-CoA desaturases require
cytochrome b5 as an electron donor. Most of the
eukaryotic desaturase domains have an adjacent
N-terminal cytochrome b5-like domain. This domain family
has extensive hydrophobic regions that would be capable
of spanning the membrane bilayer at least twice.
Comparison of sequences also reveals the existence of
three regions of conserved histidine cluster motifs that
contain the residues: HXXXH, HXX(X)HH, and Q/HXXHH.
These histidine residues are reported to be
catalytically essential and proposed to be the ligands
for the iron atoms contained within the homolog,
stearoyl CoA desaturase.
Length = 204
Score = 26.1 bits (58), Expect = 6.6
Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 10/76 (13%)
Query: 75 LSWIIIGFLLVYGIFYVIMVLYLLL-HLIVSMGGDFKFNRSEFVSKYIGSQLRDNIVLTS 133
L+ +++ FL+V + + + L H + + ++++++ + Q VLT+
Sbjct: 105 LALLLLAFLVVQLAGGLWLAVVFQLNHFGMPVEDPPGESKNDWLER----Q-----VLTT 155
Query: 134 CDNVSSLPSTRLSGNL 149
+ S L G L
Sbjct: 156 RNITGSPFLDWLHGGL 171
>gnl|CDD|220299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is
a conserved membrane protein. The yfhO gene is
transcribed in Difco sporulation medium and the
transcription is affected by the YvrGHb two-component
system. Some members of this family have been annotated
as glycosyl transferases of the PMT family.
Length = 835
Score = 26.4 bits (59), Expect = 7.7
Identities = 11/72 (15%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 47 VVTLCLSAVIITINSTFFYDLLSRNHEELSW-------IIIGFLLVYGIFYVIMVLYLLL 99
++ + L ++ +N + Y L++ + L+ +++ L I ++++ LLL
Sbjct: 373 LLLVLLFILVFLLNLSKHYSFLTQTNLLLTLLFLLLYLLLLLLFLKKQIRKKLVIILLLL 432
Query: 100 HLIVSMGGDFKF 111
+++ +G +
Sbjct: 433 VVVLELGLNAYL 444
>gnl|CDD|225146 COG2237, COG2237, Predicted membrane protein [Function unknown].
Length = 364
Score = 26.2 bits (58), Expect = 7.8
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 58 TINSTFFY--DLLSRNHEELSWIIIGF----LLVYGIFYVIMVLYLLLHLIVSMG 106
I ST++ L + E S ++G LL+YGI + +LY +I +
Sbjct: 137 GIESTYYLIKRYLKKTDPEYSRTVLGPPGLVLLLYGILALANILYPAGAVIGILL 191
>gnl|CDD|181938 PRK09543, znuB, high-affinity zinc transporter membrane component;
Reviewed.
Length = 261
Score = 26.2 bits (58), Expect = 7.9
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 35 IMGDFVNSTGTKVVTLCLSAVIITINSTFFYDLLSRNHEELSWIIIGFLLVYGI 88
IM S G VV+L +S V + + + F DLL+ E+L I IG ++V I
Sbjct: 88 IMAHSALSLGLVVVSL-MSNVRVDLMAYLFGDLLAVTPEDLISIAIGVVIVLAI 140
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 0.140 0.404
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,485,744
Number of extensions: 688850
Number of successful extensions: 1743
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1719
Number of HSP's successfully gapped: 151
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
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: 54 (24.5 bits)