RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13439
(261 letters)
>gnl|CDD|215685 pfam00060, Lig_chan, Ligand-gated ion channel. This family
includes the four transmembrane regions of the
ionotropic glutamate receptors and NMDA receptors.
Length = 268
Score = 97.7 bits (244), Expect = 2e-24
Identities = 25/108 (23%), Positives = 47/108 (43%), Gaps = 5/108 (4%)
Query: 151 WMLVGVVAIQASAFTIFFFEWLSPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHI 210
W+ + + +F E SP + ++F+L + W + L Q H
Sbjct: 3 WLCILAAYLL-VGVVLFLLERFSPYEWRGPPEE---PNQFTLSNSLWFSFGALVQQG-HR 57
Query: 211 DTPKGFTAKFMTNMWAMFAVVFLAIYTANLAAFMITREEFHEFTGVDD 258
+ P+ + + + +W FA++ L+ YTANLAAF+ ++D
Sbjct: 58 ELPRSLSGRILVGVWWFFALILLSSYTANLAAFLTVERMQSPIQSLED 105
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 53.4 bits (129), Expect = 1e-08
Identities = 18/60 (30%), Positives = 28/60 (46%)
Query: 29 LSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIIS 88
+ W+GLI L + K D+ + + I R+ VDF+ P +G +VV K I
Sbjct: 40 VEFVPVSWDGLIPALKSGKVDIIIAGMTITPERKKQVDFSDPYYYSGQVLVVRKDDSSIK 99
>gnl|CDD|238078 cd00134, PBPb, Bacterial periplasmic transport systems use
membrane-bound complexes and substrate-bound,
membrane-associated, periplasmic binding proteins
(PBPs) to transport a wide variety of substrates, such
as, amino acids, peptides, sugars, vitamins and
inorganic ions. PBPs have two cell-membrane
translocation functions: bind substrate, and interact
with the membrane bound complex. A diverse group of
periplasmic transport receptors for
lysine/arginine/ornithine (LAO), glutamine, histidine,
sulfate, phosphate, molybdate, and methanol are
included in the PBPb CD.
Length = 218
Score = 50.4 bits (121), Expect = 1e-07
Identities = 19/56 (33%), Positives = 28/56 (50%)
Query: 33 NGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIIS 88
W+GLI L + K D+ + I R VDF+ P ++G I+V K + I S
Sbjct: 44 EVDWDGLITALKSGKVDLIAAGMTITPERAKQVDFSDPYYKSGQVILVKKGSPIKS 99
>gnl|CDD|214497 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
bacterial proteins, eukaryotic ones are in PBPe.
Length = 219
Score = 44.2 bits (105), Expect = 2e-05
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 36 WNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISP 89
++ L+ L + K D+ + I R VDF+ P +G I+V K + I S
Sbjct: 48 FDSLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYRSGQVILVRKDSPIKSL 101
>gnl|CDD|233269 TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding
periplasmic protein. [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 250
Score = 43.9 bits (104), Expect = 2e-05
Identities = 17/59 (28%), Positives = 30/59 (50%)
Query: 36 WNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPTAFLE 94
++GLI L +K D + ++ I +R+ +DF+ P TG VV K + + L+
Sbjct: 72 FDGLIPSLKAKKVDAIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDLAKTLEDLD 130
>gnl|CDD|223904 COG0834, HisJ, ABC-type amino acid transport/signal transduction
systems, periplasmic component/domain [Amino acid
transport and metabolism / Signal transduction
mechanisms].
Length = 275
Score = 42.7 bits (100), Expect = 7e-05
Identities = 16/56 (28%), Positives = 27/56 (48%)
Query: 27 EVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAK 82
+ + W+GLI L K D+ + + I R+ VDF+ P +G ++V K
Sbjct: 77 KKVEFVPVAWDGLIPALKAGKVDIIIAGMTITPERKKKVDFSDPYYYSGQVLLVKK 132
>gnl|CDD|236540 PRK09495, glnH, glutamine ABC transporter periplasmic protein;
Reviewed.
Length = 247
Score = 35.5 bits (82), Expect = 0.018
Identities = 12/46 (26%), Positives = 26/46 (56%)
Query: 36 WNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVA 81
++G+I L + D+AL + I R+ +DF+ ++G+ ++V
Sbjct: 72 FSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVK 117
>gnl|CDD|183061 PRK11260, PRK11260, cystine transporter subunit; Provisional.
Length = 266
Score = 34.3 bits (79), Expect = 0.048
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 35 KWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGI-AIVVAKRTGIIS 88
KW+G++A L +++ D+ + + I+ R+ DF+ P +GI A+V G I
Sbjct: 88 KWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTVSGIQALVKKGNEGTIK 142
>gnl|CDD|223550 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 917
Score = 33.8 bits (78), Expect = 0.085
Identities = 17/154 (11%), Positives = 38/154 (24%), Gaps = 22/154 (14%)
Query: 101 WMLVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPFDTASWMLVGVVAIQ 160
W + ++ + ++ I F + F L + + V V+
Sbjct: 780 WRFILIIGLLSAILFILTFLL-------YLLGFIANTLGLDLFQALLQTTAFTVLVLIQL 832
Query: 161 ASAFTIFFFEWLSPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHIDTPK-GFTAK 219
+ +P LF +L A+L + +
Sbjct: 833 LLTLAVRSRG--------------RPFLSSLLFSNKYLWLALLVIIILQLLIIFLPPLNL 878
Query: 220 FMTNMWAMFAVVFLAIYTANLAAFMITREEFHEF 253
+ + +L L I E ++
Sbjct: 879 KIFQPTPLSLFEWLIAIAVALLLLYIVVSELYKL 912
>gnl|CDD|219123 pfam06653, Claudin_3, Tight junction protein, Claudin-like. This
is a family of probable membrane tight junction,
Claudin-like, proteins.
Length = 165
Score = 31.6 bits (72), Expect = 0.20
Identities = 12/64 (18%), Positives = 24/64 (37%)
Query: 106 VVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPFDTASWMLVGVVAIQASAFT 165
V++ + +F W++ +G ++ S P ASWM+ A+
Sbjct: 14 VISFILNIVGVFTPGWITDTGGFLEPSIGIVPFYSTEGGWLVAASWMMYISFALFLVLIL 73
Query: 166 IFFF 169
I+
Sbjct: 74 IYIV 77
>gnl|CDD|236778 PRK10859, PRK10859, membrane-bound lytic transglycosylase F;
Provisional.
Length = 482
Score = 32.5 bits (75), Expect = 0.22
Identities = 14/54 (25%), Positives = 18/54 (33%), Gaps = 2/54 (3%)
Query: 21 YLHSKNEVLSVENGKWNGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMET 74
YL K E+ +N + L L K D+A L R F P
Sbjct: 77 YLGVKLEIKVRDN--ISQLFDALDKGKADLAAAGLTYTPERLKQFRFGPPYYSV 128
>gnl|CDD|145978 pfam03120, DNA_ligase_OB, NAD-dependent DNA ligase OB-fold domain.
DNA ligases catalyze the crucial step of joining the
breaks in duplex DNA during DNA replication, repair and
recombination, utilising either ATP or NAD(+) as a
cofactor. This family is a small domain found after the
adenylation domain pfam01653 in NAD dependent ligases.
OB-fold domains generally are involved in nucleic acid
binding.
Length = 82
Score = 28.3 bits (64), Expect = 1.0
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 83 RTGIISPTAFLEPFDTASWMLVGVVAIQAS 112
RTG+I+P A LEP L G +A+
Sbjct: 14 RTGVITPVAILEPV-----ELAGTTVSRAT 38
>gnl|CDD|182697 PRK10749, PRK10749, lysophospholipase L2; Provisional.
Length = 330
Score = 29.6 bits (67), Expect = 1.7
Identities = 16/41 (39%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 221 MTNMWAMFAVVFLAIYTANLAAFMITREEFHEFTGVDDVRI 261
W F A L F REE EFTGVDD+ I
Sbjct: 4 QQKDWLTRENAFAAFTMGPLLDFWRQREE-AEFTGVDDIPI 43
>gnl|CDD|185334 PRK15437, PRK15437, histidine ABC transporter substrate-binding
protein HisJ; Provisional.
Length = 259
Score = 29.2 bits (65), Expect = 1.9
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 37 NGLIADLVNRKTDMALTSLVINSRRESVVDFTVPIMETGIAIVVAKRTGIISPT 90
+ LI L +K D ++SL I +R+ + FT + +VVAK + I PT
Sbjct: 75 DALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSD-IQPT 127
>gnl|CDD|239288 cd02990, UAS_FAF1, UAS family, FAS-associated factor 1 (FAF1)
subfamily; FAF1 contains a UAS domain of unknown
function N-terminal to a ubiquitin-associated UBX
domain. FAF1 also contains ubiquitin-associated UBA and
nuclear targeting domains, N-terminal to the UAS
domain. FAF1 is an apoptotic signaling molecule that
acts downstream in the Fas signal transduction pathway.
It interacts with the cytoplasmic domain of Fas, but
not to a Fas mutant that is deficient in signal
transduction. It is widely expressed in adult and
embryonic tissues, and in tumor cell lines, and is
localized not only in the cytoplasm where it interacts
with Fas, but also in the nucleus. FAF1 contains
phosphorylation sites for protein kinase CK2 within the
nuclear targeting domain. Phosphorylation influences
nuclear localization of FAF1 but does not affect its
potentiation of Fas-induced apoptosis. Other functions
have also been attributed to FAF1. It inhibits nuclear
factor-kB (NF-kB) by interfering with the nuclear
translocation of the p65 subunit. FAF1 also interacts
with valosin-containing protein (VCP), which is
involved in the ubiquitin-proteosome pathway.
Length = 136
Score = 28.2 bits (63), Expect = 2.2
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 13 KKRKLLTVYLHSKNEVLS 30
+ RKLL +YLH VLS
Sbjct: 19 RDRKLLAIYLHHDESVLS 36
>gnl|CDD|204533 pfam10613, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
glycine-binding site. This region, sometimes called
the S1 domain, is the luminal domain just upstream of
the first, M1, transmembrane region of transmembrane
ion-channel proteins, and it binds L-glutamate and
glycine. It is found in association with Lig_chan,
pfam00060.
Length = 65
Score = 26.8 bits (60), Expect = 2.4
Identities = 6/14 (42%), Positives = 11/14 (78%)
Query: 32 ENGKWNGLIADLVN 45
+ G+WNG+I +L+
Sbjct: 52 KTGEWNGMIGELIR 65
>gnl|CDD|239256 cd02958, UAS, UAS family; UAS is a domain of unknown function.
Most members of this family are uncharacterized
proteins with similarity to FAS-associated factor 1
(FAF1) and ETEA because of the presence of a UAS domain
N-terminal to a ubiquitin-associated UBX domain. FAF1
is a longer protein, compared to the other members of
this family, having additional N-terminal domains, a
ubiquitin-associated UBA domain and a nuclear targeting
domain. FAF1 is an apoptotic signaling molecule that
acts downstream in the Fas signal transduction pathway.
It interacts with the cytoplasmic domain of Fas, but
not to a Fas mutant that is deficient in signal
transduction. ETEA is the protein product of a highly
expressed gene in T-cells and eosinophils of atopic
dermatitis patients. The presence of the
ubiquitin-associated UBX domain in the proteins of this
family suggests the possibility of their involvement in
ubiquitination. Recently, FAF1 has been shown to
interact with valosin-containing protein (VCP), which
is involved in the ubiquitin-proteosome pathway. Some
members of this family are uncharacterized proteins
containing only a UAS domain.
Length = 114
Score = 27.6 bits (62), Expect = 2.7
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 12 KKKRKLLTVYLHSKNEVLS 30
K ++K L VYL S++E S
Sbjct: 14 KSEKKWLLVYLQSEDEFDS 32
>gnl|CDD|214709 smart00532, LIGANc, Ligase N family.
Length = 441
Score = 28.4 bits (64), Expect = 3.8
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 83 RTGIISPTAFLEP 95
RTG I+P A LEP
Sbjct: 327 RTGKITPVAELEP 339
>gnl|CDD|236137 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 28.6 bits (65), Expect = 4.1
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 83 RTGIISPTAFLEP 95
RTG ++P A LEP
Sbjct: 332 RTGAVTPVARLEP 344
>gnl|CDD|220662 pfam10265, DUF2217, Uncharacterized conserved protein (DUF2217).
This is a family of conserved proteins of from 500 - 600
residues found from worms to humans. Its function is not
known.
Length = 515
Score = 27.8 bits (62), Expect = 5.9
Identities = 16/50 (32%), Positives = 19/50 (38%), Gaps = 14/50 (28%)
Query: 171 WLSPSGFDMKTTALQPSHRFSLFRTYWLVWAVLFQAAVHIDTPKGFTAKF 220
WLS S K TAL + W+VL + P GF A F
Sbjct: 407 WLSNS---FKETALATA-----------CWSVLKAKRRMLKVPDGFIAHF 442
>gnl|CDD|181074 PRK07668, PRK07668, hypothetical protein; Validated.
Length = 254
Score = 27.7 bits (62), Expect = 5.9
Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 14/88 (15%)
Query: 89 PTAFLEPFDTASWMLVGVVAIQASAFTIFFFEWLSPSGFDMKISFSYRPLPFLPPEPF-- 146
T L+ S++L G++ + I+F W Y +P F
Sbjct: 167 GTPMLQFTQMQSYILAGLIFLITVIINIYFLGW---------FGLLYLIIPLSIMFLFKY 217
Query: 147 ---DTASWMLVGVVAIQASAFTIFFFEW 171
+ M+ ++ + S + + F E
Sbjct: 218 FNSEDVVPMIFQIIILYGSLYVLMFIEI 245
>gnl|CDD|233030 TIGR00575, dnlj, DNA ligase, NAD-dependent. All proteins in this
family with known functions are NAD-dependent DNA
ligases. Functions of these proteins include DNA repair,
DNA replication, and DNA recombination. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). The member of this
family from Treponema pallidum differs in having three
rather than just one copy of the BRCT (BRCA1 C Terminus)
domain (pfam00533) at the C-terminus. It is included in
the seed [DNA metabolism, DNA replication,
recombination, and repair].
Length = 652
Score = 28.0 bits (63), Expect = 6.2
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 83 RTGIISPTAFLEP 95
RTG I+P A LEP
Sbjct: 320 RTGAITPVAKLEP 332
>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 27.9 bits (63), Expect = 6.2
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 83 RTGIISPTAFLEP 95
RTG I+P A LEP
Sbjct: 332 RTGAITPVARLEP 344
>gnl|CDD|200468 cd11329, AmyAc_maltase-like, Alpha amylase catalytic domain family
found in maltase. Maltase (EC 3.2.1.20) hydrolyzes the
terminal, non-reducing (1->4)-linked alpha-D-glucose
residues in maltose, releasing alpha-D-glucose. The
catalytic triad (DED) which is highly conserved in the
other maltase group is not present in this subfamily.
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 477
Score = 27.7 bits (62), Expect = 7.3
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 189 RFSLFRTYWLVWAVLFQAAVHI--DTPK 214
R+ LF +WL+W + AV I PK
Sbjct: 29 RWLLFVLFWLLWVAMLLGAVAIIVLAPK 56
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 0.136 0.423
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,843,227
Number of extensions: 1347303
Number of successful extensions: 1815
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1800
Number of HSP's successfully gapped: 79
Length of query: 261
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 166
Effective length of database: 6,723,972
Effective search space: 1116179352
Effective search space used: 1116179352
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: 58 (26.0 bits)