RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8715
(164 letters)
>gnl|CDD|216554 pfam01529, zf-DHHC, DHHC palmitoyltransferase. This family
includes the well known DHHC zinc binding domain as well
as three of the four conserved transmembrane regions
found in this family of palmitoyltransferase enzymes.
Length = 167
Score = 29.8 bits (67), Expect = 0.44
Identities = 9/33 (27%), Positives = 16/33 (48%)
Query: 15 LLAIVGVVIAVGMLFYFQVKAILKNQTNIEDWI 47
L+ + ++ + L +F + ILKN T E
Sbjct: 133 LVLSLFFLLFLSFLLFFHLYLILKNITTYEYIK 165
>gnl|CDD|234252 TIGR03545, TIGR03545, TIGR03545 family protein. This model
represents a relatively rare but broadly distributed
uncharacterized protein family, distributed in 1-2
percent of bacterial genomes, all of which have outer
membranes. In many of these genomes, it is part of a
two-gene pair.
Length = 555
Score = 30.1 bits (68), Expect = 0.48
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 12 WGPLLAIVGVVIAVGMLFYFQVKAILKNQTNIEDWIVEKATKRK 55
W LL + +V + L YF + K + +EKA K
Sbjct: 4 WSGLLGFLIIVAVILALLYFFFDPLAKKAI---ERSLEKAFGAK 44
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 30.0 bits (68), Expect = 0.51
Identities = 27/108 (25%), Positives = 46/108 (42%), Gaps = 11/108 (10%)
Query: 18 IVGVVIAVGMLFYFQVKAILKNQTNIEDWIVEKATKRKRQDKFVYPYNLGWKKNIHL--- 74
IV + +Y V+ LK+ N D + KA+ R +F+ ++GW K + L
Sbjct: 16 IVEKFTVWDVFYYSSVEDGLKSPNNP-DVVQNKASSRMTYGRFLEYLDMGWIKKVDLYDN 74
Query: 75 ----VFGSSS--ISNGITWPVVEGCHQYSLTMEQLEQKNIK-KAHSQP 115
+ +SS + N VE S +++L++ NI AH
Sbjct: 75 GRTAIVEASSPELGNRPQRIRVELPVGASELIQKLKEANIDFDAHPPV 122
>gnl|CDD|225419 COG2864, FdnI, Cytochrome b subunit of formate dehydrogenase
[Energy production and conversion].
Length = 218
Score = 29.6 bits (67), Expect = 0.57
Identities = 18/89 (20%), Positives = 27/89 (30%), Gaps = 15/89 (16%)
Query: 4 SPGKRLFHWGP-----LLAIVGVVIAVGMLFY---------FQVKAILKNQTNI-EDWIV 48
+ +R+ HW +LA+ G+ + QV IL I
Sbjct: 11 TALERINHWIVAICFFILALSGLAFFFPDFMWLTHIFGGPVLQVARILHPFFGIVFFISF 70
Query: 49 EKATKRKRQDKFVYPYNLGWKKNIHLVFG 77
R ++ W KNI V G
Sbjct: 71 IIMFLRFWHHNLPNKEDIQWLKNIGGVLG 99
>gnl|CDD|213362 cd12828, TmCorA-like_1, Thermotoga maritima CorA_like subfamily.
This subfamily belongs to the Thermotoga maritima CorA
(TmCorA)-family of the MIT superfamily of essential
membrane proteins involved in transporting divalent
cations (uptake or efflux) across membranes. Members of
this subfamily are found in all three kingdoms of life.
It is functionally diverse subfamily, in addition to the
CorA Co2+ transporter from the hyperthermophilic
Thermotoga maritima, it includes Methanosarcina mazei
CorA which may be involved in transport of copper and/or
other divalent metal ions. Thermotoga maritima CorA
forms funnel-shaped homopentamers, the tip of the funnel
is formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport by a related protein, Saccharomyces cerevisiae
Alr1p. Natural variants in this signature sequence may
be associated with the transport of different divalent
cations. The functional diversity of the MIT superfamily
may also be due to minor structural differences
regulating gating, substrate selection, and transport.
Length = 294
Score = 28.9 bits (66), Expect = 0.96
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 11 HWG-PLLAIVGVVIAVGMLFYFQVK 34
+G P + V ++IA+GML YF+ K
Sbjct: 267 KYGYPAVLGVMLLIALGMLLYFKRK 291
>gnl|CDD|118327 pfam09796, QCR10, Ubiquinol-cytochrome-c reductase complex
subunit (QCR10). The QCR10 family of proteins are a
component of the ubiquinol-cytochrome c reductase
complex (also known as complex III or cytochrome b-c1
complex). This complex is located on the inner
mitochondrial membrane and it couples electron transfer
from ubiquinol to cytochrome. This subunit (QCR10) is
required for stable association of the iron-sulfur
protein with the complex.
Length = 64
Score = 27.2 bits (61), Expect = 1.1
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 7 KRLFHWGPLLAIVGVVIAVGMLFYF 31
K L +GP LA+ G G+LF+F
Sbjct: 8 KTLTKYGPNLALWGGAAGAGVLFFF 32
>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma. The second
LIM domain of Enigma: Enigma was initially characterized
in humans as a protein containing three LIM domains at
the C-terminus and a PDZ domain at N-terminus. The
third LIM domain specifically interacts with the insulin
receptor and the second LIM domain interacts with the
receptor tyrosine kinase Ret and the adaptor protein
APS. Thus Enigma is implicated in signal transduction
processes, such as mitogenic activity, insulin related
actin organization, and glucose metabolism. Enigma is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 26.9 bits (59), Expect = 1.2
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 129 LMFGLKVSWHTPCFDIA 145
+M LK++WH CF A
Sbjct: 12 IMHALKMTWHVHCFTCA 28
>gnl|CDD|224099 COG1178, ThiP, ABC-type Fe3+ transport system, permease component
[Inorganic ion transport and metabolism].
Length = 540
Score = 28.8 bits (65), Expect = 1.5
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 4 SPGKRLFHWGPLL--AIVGVVIAVGMLFYFQVKAILKNQTNIEDWIV 48
S RL +L A+ GVV+A+G+L F+ L Q I+
Sbjct: 365 SRLSRLLERLSMLPLAVPGVVLALGLLLLFRAPDGLLYQPLYTLLIL 411
>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 = 28.7 bits (65), Expect = 1.6
Identities = 19/100 (19%), Positives = 35/100 (35%), Gaps = 9/100 (9%)
Query: 29 FYFQVKAILKNQTNIEDWIVEKATKRKRQDKFVYPYNLGW---KKNIHLVFGSSSISNGI 85
Y ++ +I + N + R NLG+ + I + F + G
Sbjct: 672 LYLELPSINLDDKNFSITVNGYTLNRTFNYYRTQVINLGYRVKGQTITITF---QLPKGQ 728
Query: 86 TWPVVEGCHQYSLTMEQLEQKNIKKAHSQPVLVVKNYNGR 125
++ Y L L++ IKK Q + V K + +
Sbjct: 729 LS--LDDLQLYGLNYTTLKKA-IKKLKEQQLKVTKYSDNK 765
>gnl|CDD|173803 cd07477, Peptidases_S8_Subtilisin_subset, Peptidase S8 family
domain in Subtilisin proteins. This group is composed
of many different subtilisins: Pro-TK-subtilisin,
subtilisin Carlsberg, serine protease Pb92 subtilisin,
and BPN subtilisins just to name a few.
Pro-TK-subtilisin is a serine protease from the
hyperthermophilic archaeon Thermococcus kodakaraensis
and consists of a signal peptide, a propeptide, and a
mature domain. TK-subtilisin is matured from
pro-TK-subtilisin upon autoprocessing and degradation of
the propeptide. Unlike other subtilisins though, the
folding of the unprocessed form of pro-TK-subtilisin is
induced by Ca2+ binding which is almost completed prior
to autoprocessing. Ca2+ is required for activity unlike
the bacterial subtilisins. The propeptide is not
required for folding of the mature domain unlike the
bacterial subtilases because of the stability produced
from Ca2+ binding. Subtilisin Carlsberg is extremely
similar in structure to subtilisin BPN'/Novo thought it
has a 30% difference in amino acid sequence. The
substrate binding regions are also similar and 2
possible Ca2+ binding sites have been identified
recently. Subtilisin Carlsberg possesses the highest
commercial importance as a proteolytic additive for
detergents. Serine protease Pb92, the serine protease
from the alkalophilic Bacillus strain PB92, also
contains two calcium ions and the overall folding of
the polypeptide chain closely resembles that of the
subtilisins. Members of the peptidases S8 and S35 clan
include endopeptidases, exopeptidases and also a
tripeptidyl-peptidase. The S8 family has an Asp/His/Ser
catalytic triad similar to that found in trypsin-like
proteases, but do not share their three-dimensional
structure and are not homologous to trypsin. The S53
family contains a catalytic triad Glu/Asp/Ser. The
stability of these enzymes may be enhanced by calcium,
some members have been shown to bind up to 4 ions via
binding sites with different affinity. Some members of
this clan contain disulfide bonds. These enzymes can be
intra- and extracellular, some function at extreme
temperatures and pH values.
Length = 229
Score = 28.3 bits (64), Expect = 1.9
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 78 SSSISNGITWPVVEGCH--QYSLTME---QLEQKNIKKAHSQPVLVV 119
S I GI W + G SL ++ IKKA++ +LVV
Sbjct: 82 YSDIIAGIEWAIENGMDIINMSLGGPSDSPALREAIKKAYAAGILVV 128
>gnl|CDD|238344 cd00625, ArsB_NhaD_permease, Anion permease ArsB/NhaD. These
permeases have been shown to translocate sodium,
arsenate, antimonite, sulfate and organic anions across
biological membranes in all three kingdoms of life. A
typical anion permease contains 8-13 transmembrane
helices and can function either independently as a
chemiosmotic transporter or as a channel-forming subunit
of an ATP-driven anion pump.
Length = 396
Score = 28.0 bits (63), Expect = 2.3
Identities = 9/47 (19%), Positives = 20/47 (42%)
Query: 15 LLAIVGVVIAVGMLFYFQVKAILKNQTNIEDWIVEKATKRKRQDKFV 61
A+ +++ +G+L+ K +L + + E R KF+
Sbjct: 163 PPALGLLLLLLGLLYLLFRKKLLLPDEDKLTVLAEPLPARPLLKKFL 209
>gnl|CDD|226118 COG3590, PepO, Predicted metalloendopeptidase [Posttranslational
modification, protein turnover, chaperones].
Length = 654
Score = 27.8 bits (62), Expect = 3.1
Identities = 18/56 (32%), Positives = 22/56 (39%), Gaps = 7/56 (12%)
Query: 3 LSPGKRLFHWGPLLAIVGV----VIAVGMLFYFQVKAILKNQTNIEDWIVEKATKR 54
L P W L + +G VI V FY + A L + N DW KA R
Sbjct: 236 LQPELPGDDWSLLFSALGQLPDKVIVVENPFYLKEFASLLAEENWADW---KAWLR 288
>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like
family. The second LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes, such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. The second member, ENH protein, was
first identified in rat brain. It has been shown that
ENH interacts with protein kinase D1 (PKD1) via its LIM
domains and forms a complex with PKD1 and the alpha1C
subunit of cardiac L-type voltage-gated calcium channel
in rat neonatal cardiomyocytes. The N-terminal PDZ
domain interacts with alpha-actinin at the Z-line.
ZASP/Cypher is required for maintenance of Z-line
structure during muscle contraction, but not required
for Z-line assembly. In heart, Cypher/ZASP plays a
structural role through its interaction with
cytoskeletal Z-line proteins. In addition, there is
increasing evidence that Cypher/ZASP also performs
signaling functions. Studies reveal that Cypher/ZASP
interacts with and directs PKC to the Z-line, where PKC
phosphorylates downstream signaling targets. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 25.5 bits (56), Expect = 4.0
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 129 LMFGLKVSWHTPCF 142
+M LK +WH CF
Sbjct: 12 VMHALKQTWHVSCF 25
>gnl|CDD|239506 cd03413, CbiK_C, Anaerobic cobalamin biosynthetic cobalt chelatase
(CbiK), C-terminal domain. CbiK is part of the
cobalt-early path for cobalamin biosynthesis. It
catalyzes the insertion of cobalt into the oxidized form
of precorrin-2, factor II (sirohydrochlorin), the second
step of the anaerobic branch of vitamin B12
biosynthesis. CbiK belongs to the class II family of
chelatases, and is a homomeric enzyme that does not
require ATP for its enzymatic activity.
Length = 103
Score = 25.7 bits (57), Expect = 5.9
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 89 VVEGCHQYSLTMEQLEQKNIKKAHSQPVLVV 119
VEG + +L++ IKK P+++V
Sbjct: 37 TVEGYPGLDDVLAKLKKAGIKKVTLMPLMLV 67
>gnl|CDD|179568 PRK03356, PRK03356, L-carnitine/gamma-butyrobetaine antiporter;
Provisional.
Length = 504
Score = 26.6 bits (59), Expect = 6.4
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 9 LFHWGPLLAIVGVVIAVGMLFYFQVK 34
LFHWGPL ++V ++F V+
Sbjct: 139 LFHWGPLPWATYSFLSVAFGYFFFVR 164
>gnl|CDD|233168 TIGR00883, 2A0106, metabolite-proton symporter. This model
represents the metabolite:H+ symport subfamily of the
major facilitator superfamily (pfam00083), including
citrate-H+ symporters, dicarboxylate:H+ symporters, the
proline/glycine-betaine transporter ProP, etc [Transport
and binding proteins, Unknown substrate].
Length = 394
Score = 26.5 bits (59), Expect = 7.1
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 11 HWGPLLAIVGVVIAVGMLFYF 31
H P L +G+VIA FY
Sbjct: 217 HRKPFLLGLGLVIATTTTFYL 237
>gnl|CDD|227609 COG5285, COG5285, Protein involved in biosynthesis of mitomycin
antibiotics/polyketide fumonisin [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 299
Score = 26.3 bits (58), Expect = 8.0
Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 83 NGITWPVVEGCHQYSLTMEQLEQKNIKKAHSQPVLVVK 120
NG T VV G H++ + E+ + + + ++ PV + K
Sbjct: 163 NGATL-VVPGSHKWDVIPERPDHETYLERNAVPVELEK 199
>gnl|CDD|225092 COG2181, NarI, Nitrate reductase gamma subunit [Energy production
and conversion].
Length = 228
Score = 26.1 bits (58), Expect = 8.0
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 3 LSPGKRLFHWGPLLAIVGVVIAVGML 28
L G LFH G LL ++G I G+L
Sbjct: 46 LWIGSNLFHIGILLVLLGHAI--GLL 69
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
0.324 0.138 0.441
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,241,971
Number of extensions: 717753
Number of successful extensions: 1276
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1273
Number of HSP's successfully gapped: 42
Length of query: 164
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 74
Effective length of database: 6,945,742
Effective search space: 513984908
Effective search space used: 513984908
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 (21.5 bits)
S2: 55 (25.1 bits)