RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5317
(101 letters)
>gnl|CDD|233194 TIGR00930, 2a30, K-Cl cotransporter. [Transport and binding
proteins, Other].
Length = 953
Score = 67.0 bits (164), Expect = 1e-14
Identities = 34/94 (36%), Positives = 53/94 (56%), Gaps = 5/94 (5%)
Query: 11 KYGLREYFESLELISAFSPLFYSAVLTSGLTCAFSSLQEAPRVFRHLSKDGLYPYIGWFG 70
YGL + + L+S F PL + + ++ L+ A +SL APR+F+ L KD +YP++ +FG
Sbjct: 370 SYGLMNNLQVMSLVSPFPPLITAGIFSATLSSALASLVSAPRLFQALCKDNIYPFLQFFG 429
Query: 71 R--GKTSRPH---VLTTGIAAAFILMSAAKLTKP 99
+ GK P +LT IA FIL++ P
Sbjct: 430 KGYGKNGEPLRAYLLTAFIAEGFILIAELNTIAP 463
>gnl|CDD|215858 pfam00324, AA_permease, Amino acid permease.
Length = 473
Score = 47.3 bits (113), Expect = 1e-07
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 6/89 (6%)
Query: 12 YGLREYFESLELISAFSPLFYSAVLTSGLTCAFSSLQEAPRVFRHLSKDGLYPYIG-WFG 70
F IS +PL + +LT+ L+ A SSL RV L++DGL P
Sbjct: 269 ASPFVIFFKSLGISGLAPLINAVILTAALSAANSSLYSGSRVLYALARDGLAPKFLKKVD 328
Query: 71 RGKTSRPH---VLTTGIAAAFILMSAAKL 96
+ P +L+T I+ +L+++
Sbjct: 329 KSG--VPLRAILLSTAISLLAVLLASLNP 355
>gnl|CDD|227342 COG5009, MrcA, Membrane carboxypeptidase/penicillin-binding protein
[Cell envelope biogenesis, outer membrane].
Length = 797
Score = 31.1 bits (71), Expect = 0.065
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 25 SAFSPLFYSAVLTSGLTCAFSSLQEAPRVFRHLSKDGLY 63
S+F P YSA L GLT A S + +AP F G++
Sbjct: 459 SSFKPFVYSAALDKGLTPA-SVINDAPISFWDGGGGGVW 496
>gnl|CDD|185770 cd09247, BRO1_Alix_like_2, Protein-interacting Bro1-like domain of
an Uncharacterized family of the BRO1_Alix_like
superfamily. This domain family is comprised of
uncharacterized proteins. It belongs to the
BRO1_Alix_like superfamily which includes the Bro1-like
domains of mammalian Alix (apoptosis-linked gene-2
interacting protein X), His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and
Rim23 interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. HD-PTP and Bro1 function in
endosomal trafficking, with HD-PTP having additional
functions in cell migration. Rim20 and Rim23 play roles
in the response to the external pH via the Rim101
pathway. Bro1-like domains are boomerang-shaped, and
part of the domain is a tetratricopeptide repeat
(TPR)-like structure. These domains bind components of
the ESCRT-III complex: CHMP4 (in the case of Alix, Brox
and HD-PTP) and Snf7 (in the case of yeast Bro1 and
Rim20). The Bro1-like domains of Alix, HD-PTP, Brox, and
Rhophilin can bind human immunodeficiency virus type 1
(HIV-1) nucleocapsid. This family lacks the V-shaped (V)
domain found in many members of the BRO1_Alix_like
superfamily.
Length = 346
Score = 27.4 bits (61), Expect = 1.4
Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 2/48 (4%)
Query: 47 LQEAPRVFRHLSKDGLYPYIGWFGRGKTSRPHVLTTGIAAAFILMSAA 94
L+ A VF L+ D L G RP T +A A L+ A
Sbjct: 143 LRRAAGVFEFLAHDELPRLRG--ALSADERPPECTPSLALAMSLLCLA 188
>gnl|CDD|212665 cd07793, FGGY_GK5_metazoa, metazoan glycerol kinase 5-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a group of
metazoan putative glycerol kinases (GK), which may be
coded by the GK-like gene, GK5. Sequence comparison
shows members of this group are homologs of bacterial
GKs, and they retain all functionally important
residues. However, GK-like proteins in this family do
not have detectable GK activity. The reason remains
unclear. It has been suggested tha the conserved
catalytic residues might facilitate them performing a
distinct function. GKs belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 504
Score = 26.9 bits (60), Expect = 2.1
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 56 HLSKDGLYPYIGW 68
H S GLYP +GW
Sbjct: 291 HASVKGLYPLVGW 303
>gnl|CDD|185692 cd02183, GH16_fungal_CRH1_transglycosylase,
glycosylphosphatidylinositol-glucanosyltransferase.
Group of fungal GH16 members related to Saccharomyces
cerevisiae Crh1p. Chr1p and Crh2p are transglycosylases
that are required for the linkage of chitin to
beta(1-3)glucose branches of beta(1-6)glucan, an
important step in the assembly of new cell wall. Both
have been shown to be glycosylphosphatidylinositol
(GPI)-anchored. A third homologous protein, Crr1p,
functions in the formation of the spore wall. They
belongs to the family 16 of glycosyl hydrolases that
includes lichenase, xyloglucan endotransglycosylase
(XET), beta-agarase, kappa-carrageenase,
endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase,
and endo-beta-galactosidase, all of which have a
conserved jelly roll fold with a deep active site
channel harboring the catalytic residues.
Length = 203
Score = 26.4 bits (59), Expect = 2.2
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 9/35 (25%)
Query: 65 YIGWFGRG----KTSRPHVLTTGIAAAFILMSAAK 95
YI ++G+ K + GI ++F+L S
Sbjct: 44 YI-FYGKVEVTMKAAP----GQGIVSSFVLQSDDL 73
>gnl|CDD|233710 TIGR02074, PBP_1a_fam, penicillin-binding protein, 1A family.
Bacterial that synthesize a cell wall of peptidoglycan
(murein) generally have several transglycosylases and
transpeptidases for the task. This family consists of
bifunctional transglycosylase/transpeptidase
penicillin-binding proteins (PBP). In the
Proteobacteria, this family includes PBP 1A but not the
paralogous PBP 1B (TIGR02071). This family also includes
related proteins, often designated PBP 1A, from other
bacterial lineages [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan].
Length = 531
Score = 26.8 bits (60), Expect = 2.3
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 25 SAFSPLFYSAVLTSGLTCAFSSLQEAPRVF 54
S F P Y+A L GLT A + + + P +
Sbjct: 295 STFKPFVYAAALEKGLTPA-TIVNDEPITY 323
>gnl|CDD|217478 pfam03294, Pox_Rap94, RNA polymerase-associated transcription
specificity factor, Rap94.
Length = 796
Score = 26.2 bits (58), Expect = 3.1
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 5 SYTLLPKYGLREYFESLELISAFSPLFYSAVLTS 38
SY L Y L + F ELI+ S +FY +L+
Sbjct: 275 SYIFLSNYFLCDLF--PELINEKSAVFYDLILSD 306
>gnl|CDD|129984 TIGR00906, 2A0303, cationic amino acid transport permease.
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 557
Score = 25.9 bits (57), Expect = 4.7
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 10/60 (16%)
Query: 34 AVLTSGLTCAFSSLQEAPRVFRHLSKDGLYPYIGWFGR--GKTSRP--HVLTTGIAAAFI 89
+ TS L F PRV +++DGL W + KT P + +G AA +
Sbjct: 324 GMSTSLLGGMFP----LPRVIYAMARDGLLF--KWLAQINSKTKTPINATVVSGAIAALM 377
>gnl|CDD|218943 pfam06219, DUF1005, Protein of unknown function (DUF1005). Family
of plant proteins with undetermined function.
Length = 420
Score = 26.0 bits (57), Expect = 4.7
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 7/32 (21%)
Query: 70 GRGKTSRP-------HVLTTGIAAAFILMSAA 94
G GK S+P HV AAAF+ ++AA
Sbjct: 368 GEGKCSKPLVEVGVRHVTCMEDAAAFVALAAA 399
>gnl|CDD|223903 COG0833, LysP, Amino acid transporters [Amino acid transport and
metabolism].
Length = 541
Score = 25.7 bits (57), Expect = 4.8
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 26 AFSPLFYSAV-LTSGLTCAFSSLQEAPRVFRHLSKDGLYPYIGWFGR-GKTSRPH--VLT 81
+ +AV LTS L+ A S L + R+ L+K G P F + + P +L
Sbjct: 323 PVAASIMNAVILTSVLSAANSGLYASSRMLYSLAKQGKAP--KIFAKVDRRGVPLVALLV 380
Query: 82 TGIAAAFILMSAAK 95
T + ++++
Sbjct: 381 TLLFGLLAFLNSSF 394
>gnl|CDD|224038 COG1113, AnsP, Gamma-aminobutyrate permease and related permeases
[Amino acid transport and metabolism].
Length = 462
Score = 25.3 bits (56), Expect = 6.4
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 4/60 (6%)
Query: 35 VLTSGLTCAFSSLQEAPRVFRHLSKDGLYPYIGWFGRGKTSRPHVLTTGIAAAFILMSAA 94
VLT+ L+ S L R+ L+K G P K S+ V I + +++
Sbjct: 294 VLTAALSALNSGLYSTSRMLYSLAKQGDAPKA----FAKLSKRGVPVNAILLSAVVLLLG 349
>gnl|CDD|234752 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 638
Score = 25.0 bits (56), Expect = 7.4
Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 4/24 (16%)
Query: 71 RGKTSRPHVLTTGIAAAFILMSAA 94
RG PHV +TG AF L+ A
Sbjct: 182 RG----PHVPSTGKIKAFKLLKVA 201
>gnl|CDD|233530 TIGR01686, FkbH, FkbH-like domain. This model describes a domain
of a family of proteins of unknown overall function. One
of these, however, is a modular polyketide synthase 4800
amino acids in length from Streptomyces avermilitis in
which this domain is the C-terminal segment. By
contrast, the FkbH protein from Streptomyces
hygroscopicus aparently contains only this domain. The
remaining members of the family all contain an
additional N-terminal domain of between 200 and 275
amino acids which show less than 20% identity to one
another. It seems likely then that these proteins are
involved in disparate functions, probably the
biosynthesis of different natural products. For
instance, the FkbH gene is found in a gene cluster
believed to be responsible for the biosynthesis of
unususal "PKS extender units" in the ascomycin pathway.
This domain is composed of two parts, the first of which
is a member of subfamily IIIC (TIGR01681) of the
haloacid dehalogenase (HAD) superfamily of
aspartate-nucleophile hydrolases. All of the
characterized enzymes within subfamily III are
phosphatases, and all of the active site residues
characteristic of HAD-superfamily phosphatases are
present in this domain. The C-terminal portion of this
domain is unique to this family (by BLAST).
Length = 320
Score = 24.8 bits (54), Expect = 8.6
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 12 YGLREYFESLELISAFSPL 30
EY ++LEL S
Sbjct: 174 SDDEEYLQNLELSLNISKN 192
>gnl|CDD|237050 PRK12305, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 575
Score = 24.7 bits (55), Expect = 10.0
Identities = 9/18 (50%), Positives = 9/18 (50%)
Query: 77 PHVLTTGIAAAFILMSAA 94
PHV T AF L S A
Sbjct: 119 PHVPNTKFIKAFKLTSVA 136
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 0.136 0.406
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,018,877
Number of extensions: 406640
Number of successful extensions: 403
Number of sequences better than 10.0: 1
Number of HSP's gapped: 403
Number of HSP's successfully gapped: 38
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.0 bits)