RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12486
(148 letters)
>gnl|CDD|148567 pfam07019, Rab5ip, Rab5-interacting protein (Rab5ip). This family
consists of several Rab5-interacting protein (RIP5 or
Rab5ip) sequences. The ras-related GTPase rab5 is
rate-limiting for homotypic early endosome fusion.
Rab5ip represents a novel rab5 interacting protein that
may function on endocytic vesicles as a receptor for
rab5-GDP and participate in the activation of rab5.
Length = 81
Score = 82.6 bits (205), Expect = 9e-22
Identities = 34/69 (49%), Positives = 39/69 (56%)
Query: 38 LSGCTAGILGLTGFYGFGFYVLAVIGLWVLLLMRAGSKWNRYFLNRKSLLTNGFVGGLCT 97
L+G AGILGLTGF GF FY L +G L + G YF R L T G + GL T
Sbjct: 13 LAGVIAGILGLTGFLGFIFYFLISLGTSYLYYAKVGKIDEEYFGGRWELFTEGLLTGLAT 72
Query: 98 YVLFWTFFY 106
+VL WT FY
Sbjct: 73 FVLTWTLFY 81
>gnl|CDD|234721 PRK00302, lnt, apolipoprotein N-acyltransferase; Reviewed.
Length = 505
Score = 31.0 bits (71), Expect = 0.20
Identities = 21/88 (23%), Positives = 31/88 (35%), Gaps = 16/88 (18%)
Query: 32 AHLWLP-LSGCTAGILGLTGFYGFGFYVLAVIGLWVLLLMRAGSKWNRYFLNRKSLLTNG 90
WL L AG LG F F + LA++ L LL + G+ + L
Sbjct: 3 LRGWLRLLLALLAGALGTLAFAPFDLWPLALLSLAGLLWLLLGASPKQAAL--------- 53
Query: 91 FVGGLCTYVLFWTFFYTMGDKWIASHMT 118
+G L + F + WI +
Sbjct: 54 -IGFLWGFGYFGSGLS-----WIYVSIH 75
>gnl|CDD|219117 pfam06638, Strabismus, Strabismus protein. This family consists of
several strabismus (STB) or Van Gogh-like (VANGL)
proteins 1 and 2. The exact function of this family is
unknown. It is thought, however that STB1 gene and STB2
may be potent tumour suppressor gene candidates.
Length = 507
Score = 30.5 bits (69), Expect = 0.34
Identities = 23/78 (29%), Positives = 29/78 (37%), Gaps = 6/78 (7%)
Query: 29 VLPAHLW-LPLSGCTAGILGLTGFYGFGFYVLAVIGLWVLLLMRAGSKWNRYFLNRKSLL 87
VLP W L C GL F +L +I W L L + R F+ R LL
Sbjct: 115 VLPQVGWRDRLEPCGTACEGLLISLAFKLLIL-LIASWALFLRPPRADMPRIFVFRALLL 173
Query: 88 TNGFVGGLCTYVLFWTFF 105
F L +W F+
Sbjct: 174 VLVF---LFL-FSYWLFY 187
>gnl|CDD|130543 TIGR01478, STEVOR, variant surface antigen, stevor family. This
model represents the stevor branch of the rifin/stevor
family (pfam02009) of predicted variant surface antigens
as found in Plasmodium falciparum. This model is based
on a set of stevor sequences kindly provided by Matt
Berriman from the Sanger Center. This is a global model
and assesses a penalty for incomplete sequence.
Additional fragmentary sequences may be found with the
fragment model and a cutoff of 8 bits.
Length = 295
Score = 29.8 bits (67), Expect = 0.51
Identities = 19/78 (24%), Positives = 25/78 (32%), Gaps = 12/78 (15%)
Query: 39 SGCTAGI----LG--LTGFYGFGFYVLAVI----GLWVLLLMRAGSK--WNRYFLNRKSL 86
GCTAG+ L L G G A I G + L + +K F S+
Sbjct: 170 KGCTAGVGTCALSSALLGNIGIAAAKTAAIEVITGSYSLDIANKCTKALAGINFFFSSSI 229
Query: 87 LTNGFVGGLCTYVLFWTF 104
+ G G Y
Sbjct: 230 ESAGKTGVGIFYGASDDA 247
>gnl|CDD|177916 PLN02277, PLN02277, H(+) -translocating inorganic pyrophosphatase.
Length = 730
Score = 29.8 bits (67), Expect = 0.53
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 13/56 (23%)
Query: 58 VLAVIGL-----WVLLLMRAGSKWNRYFLNRKSLLTNGFVGGLCTYVLFW-TFFYT 107
+LAV+ W+L +A S W + L G VG + Y W + +YT
Sbjct: 326 ILAVVTFGASTRWLLYTEQAPSAWFNFALC-------GLVGIITAYAFVWISQYYT 374
>gnl|CDD|183207 PRK11570, PRK11570, peptidyl-prolyl cis-trans isomerase;
Provisional.
Length = 206
Score = 27.5 bits (61), Expect = 2.1
Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 56 FYVLAVIGLWV--LLLMRAGSKWNRY 79
F V VI W+ L LM GSKW
Sbjct: 149 FPVNGVIPGWIEALTLMPVGSKWELT 174
>gnl|CDD|220515 pfam10003, DUF2244, Integral membrane protein (DUF2244). This
domain, found in various bacterial hypothetical and
putative membrane proteins, has no known function.
Length = 140
Score = 27.1 bits (61), Expect = 2.3
Identities = 9/41 (21%), Positives = 14/41 (34%), Gaps = 3/41 (7%)
Query: 38 LSGCTAGILGLTGFYG-FGFYVLAVIGLWVLLL--MRAGSK 75
+S A TG + F L ++ LW+ R
Sbjct: 22 VSLLIALAFLGTGAWPVLPFAGLELLALWLAFRRSYRHARD 62
>gnl|CDD|225669 COG3127, COG3127, Predicted ABC-type transport system involved in
lysophospholipase L1 biosynthesis, permease component
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 829
Score = 27.3 bits (61), Expect = 3.4
Identities = 11/71 (15%), Positives = 17/71 (23%), Gaps = 15/71 (21%)
Query: 18 LACAKQCSCGRVLPAHLWLPLSG-CTAGILGLTGFYG--------------FGFYVLAVI 62
LA +Q V P +L + + L F VL ++
Sbjct: 378 LAVLRQGVEAGVWPLLTYLAGAALLLVALAALAVLMAGDRLLWAILAGAVVLAFLVLRLV 437
Query: 63 GLWVLLLMRAG 73
L
Sbjct: 438 AGGGLWAALRS 448
>gnl|CDD|172699 PRK14211, PRK14211, camphor resistance protein CrcB; Provisional.
Length = 114
Score = 26.4 bits (58), Expect = 4.0
Identities = 24/72 (33%), Positives = 29/72 (40%), Gaps = 16/72 (22%)
Query: 44 GILGLTGFYGFGFYVLA------------VIGLWVLLLMRAGSKWNRYFLNRKSLLTNGF 91
G LG T Y G YV + V G +L L+ S + F +LL GF
Sbjct: 10 GALGATTRYLTGRYVDSYRSFPVATFLVNVAGCLILGLLSGASLSTQTF----ALLGTGF 65
Query: 92 VGGLCTYVLFWT 103
GGL TY F
Sbjct: 66 CGGLTTYSTFAV 77
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that catalyze the conversion
of a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
The NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal NAD
binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 26.8 bits (60), Expect = 4.3
Identities = 22/78 (28%), Positives = 26/78 (33%), Gaps = 26/78 (33%)
Query: 9 PGDHT-AYSELACAKQCSCGRVLPA----------HLWLP-----LSGCTAGILGLTG-- 50
PG + A +E A + R LP LW L G T GI+GL G
Sbjct: 93 PGANAEAVAEHALGLLLALLRRLPRADAAVRRGWGWLWAGFPGYELEGKTVGIVGL-GRI 151
Query: 51 -------FYGFGFYVLAV 61
FG VL
Sbjct: 152 GQRVAKRLQAFGMKVLYY 169
>gnl|CDD|240599 cd12916, VKOR_1, Vitamin K epoxide reductase family in bacteria
and plants. This family includes vitamin K epoxide
reductase (VKOR) present in bacteria and plant. VKOR
(also named VKORC1) is an integral membrane protein
that catalyzes the reduction of vitamin K 2,3-epoxide
and vitamin K to vitamin K hydroquinone, an essential
co-factor subsequently used in the gamma-carboxylation
of glutamic acid residues in blood coagulation enzymes.
All homologs of VKOR contain an active site CXXC motif,
which is switched between reduced and disulfide-bonded
states during the reaction cycle. In some plant and
bacterial homologs, the VKOR domain is fused with
domains of the thioredoxin family of oxidoreductases
which may function as redox partners in initiating the
reduction cascade.
Length = 133
Score = 26.4 bits (59), Expect = 4.6
Identities = 19/70 (27%), Positives = 27/70 (38%), Gaps = 10/70 (14%)
Query: 12 HTAYSELACAKQCSCGRVLPAHLWLPLSGCTAGILGL-TGFYGFGFYVLAVIGLWVLLLM 70
S C C V L+ A +LG+ +GF Y LA++ L VL L+
Sbjct: 23 KLTGSSAVCPGGGGCDTV--------LNSPYATLLGIPLSLFGFLAY-LAILVLAVLPLL 73
Query: 71 RAGSKWNRYF 80
K R+
Sbjct: 74 LKSEKLERWT 83
>gnl|CDD|235978 PRK07234, PRK07234, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 470
Score = 26.8 bits (60), Expect = 4.8
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 30 LPAHLWLPLSGCTAGILGLTGFYGFGFYVLAVIGL--WVLLLM 70
L W+PL+ + I G GF VL + L W + +
Sbjct: 325 LGIGKWIPLTMASFSIAGFPLLAGFVSKVLTLKNLLPWQAIAL 367
>gnl|CDD|233104 TIGR00726, TIGR00726, uncharacterized protein, YfiH family.
PSI-BLAST converges on members of this family of
uncharacterized bacterial proteins and shows no
significant similarity to any characterized protein. No
completed genome to date has two members. Members of the
family have been crystallized but the function is
unknown [Unknown function, General].
Length = 221
Score = 26.2 bits (58), Expect = 5.9
Identities = 11/29 (37%), Positives = 12/29 (41%), Gaps = 4/29 (13%)
Query: 81 LNRKSLLTNG----FVGGLCTYVLFWTFF 105
+ R L G FV CTY TFF
Sbjct: 175 IARLQLRELGVKQIFVSDRCTYTEPETFF 203
>gnl|CDD|224204 COG1285, SapB, Uncharacterized membrane protein [Function unknown].
Length = 221
Score = 25.7 bits (57), Expect = 8.3
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 32 AHLWLPLSGCTAGILGLTGFYGFGFYVLAVIGLWVLLLMRAGSKWNRYFLNRKS 85
A +W TA I G+ G G YVLA+ ++L + + L RK
Sbjct: 100 ASIW-----ATAAI-GIA--AGSGLYVLALAATLIILAVLFLLRRLVRRLGRKD 145
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
0.327 0.142 0.497
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,583,673
Number of extensions: 671359
Number of successful extensions: 1163
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1149
Number of HSP's successfully gapped: 108
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (24.6 bits)