RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17442
(90 letters)
>gnl|CDD|197504 smart00079, PBPe, Eukaryotic homologues of bacterial periplasmic
substrate binding proteins. Prokaryotic homologues are
represented by a separate alignment: PBPb.
Length = 133
Score = 83.9 bits (208), Expect = 2e-22
Identities = 29/64 (45%), Positives = 39/64 (60%)
Query: 13 VRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIGLQKGSPWADAVTLAILD 72
V+ AFI +S LD+E +++C+L+T GE FGR GY I KGSP D ++ AIL
Sbjct: 57 VQRVRVSNYAFIMESPYLDYELSRNCDLMTVGEEFGRKGYGIAFPKGSPLRDDLSRAILK 116
Query: 73 FHES 76
ES
Sbjct: 117 LSES 120
>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 = 80.4 bits (199), Expect = 5e-20
Identities = 28/60 (46%), Positives = 39/60 (65%), Gaps = 1/60 (1%)
Query: 18 KKLMAFIWDSSRLDFEAAQD-CELVTAGELFGRSGYAIGLQKGSPWADAVTLAILDFHES 76
L AF+ +S+ L++E A+D C+L T GE+FG GY I KGSP D ++ AIL+ ES
Sbjct: 164 NGLYAFLMESAYLEYEVARDPCKLTTVGEVFGTKGYGIAFPKGSPLRDKLSRAILELRES 223
>gnl|CDD|236847 PRK11101, glpA, sn-glycerol-3-phosphate dehydrogenase subunit A;
Provisional.
Length = 546
Score = 29.2 bits (66), Expect = 0.21
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 10 STVVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAI 54
S V RHG + A++ RLD +CE VTAGE+ YA+
Sbjct: 408 SAVYRHG-DRAPAWL-SEGRLDRSLVCECEAVTAGEV----RYAV 446
>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional.
Length = 143
Score = 28.6 bits (64), Expect = 0.25
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 3/38 (7%)
Query: 18 KKLMAFIWDSSRLDFEAAQDCELVTAGELFGRSGYAIG 55
KK+ AF+ + L+F D E++ +G FGRSG+A+G
Sbjct: 79 KKITAFVPNDGCLNFINEND-EVLVSG--FGRSGHAVG 113
>gnl|CDD|151230 pfam10758, DUF2586, Protein of unknown function (DUF2586). This
bacterial family of proteins has no known function.
Length = 363
Score = 26.1 bits (58), Expect = 2.7
Identities = 7/20 (35%), Positives = 8/20 (40%)
Query: 50 SGYAIGLQKGSPWADAVTLA 69
+ AI L W AV A
Sbjct: 73 TAAAIPLAADDDWQAAVDKA 92
>gnl|CDD|226850 COG4427, COG4427, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 350
Score = 26.0 bits (57), Expect = 3.2
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 35 AQDCELVTAG-ELFGRSGYAIGLQKGSPWADAVTLAIL 71
A+ ELV A +L G G +I +G+P DAV L +
Sbjct: 27 ARLLELVAARLDLSGGVGESILGWRGAPEGDAVPLRLA 64
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 25.7 bits (57), Expect = 3.3
Identities = 10/38 (26%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 40 LVTAGELFGRSGYAIGLQKGSP-WADAVTLAILDFHES 76
LV E Y I ++KG P A+ A+ +
Sbjct: 170 LVVVDEPLSGEPYGIAVRKGDPELLAALNKALAELKAD 207
>gnl|CDD|217582 pfam03472, Autoind_bind, Autoinducer binding domain. This domain
is found a a large family of transcriptional regulators.
This domain specifically binds to autoinducer molecules.
Length = 146
Score = 25.4 bits (56), Expect = 3.9
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 12 VVRHGTKKLMAFIWDSSRLDFEAAQDCELVTAGELFG-RSGYAIGL 56
VVRH + F W S LD + + + FG R+GY + +
Sbjct: 61 VVRHALRSSTPFSW--SDLDLASPRARRVFEEARDFGLRAGYTVPV 104
>gnl|CDD|183061 PRK11260, PRK11260, cystine transporter subunit; Provisional.
Length = 266
Score = 25.5 bits (56), Expect = 4.9
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 30 LDFEAAQDCELVTAGELFGRSGYAIGLQKGSP 61
LD + L AGE F R + L+KG+P
Sbjct: 202 LDLVKKTNDTLAVAGEAFSRQESGVALRKGNP 233
>gnl|CDD|212754 cd11820, SH3_STAM, Src homology 3 domain of Signal Transducing
Adaptor Molecules. STAMs were discovered as proteins
that are highly phosphorylated following cytokine and
growth factor stimulation. They function in cytokine
signaling and surface receptor degradation, as well as
regulate Golgi morphology. They associate with many
proteins including Jak2 and Jak3 tyrosine kinases, Hrs,
AMSH, and UBPY. STAM adaptor proteins contain VHS
(Vps27, Hrs, STAM homology), ubiquitin interacting
(UIM), and SH3 domains. There are two vertebrate STAMs,
STAM1 and STAM2, which may be functionally redundant;
vertebrate STAMs contain ITAM motifs. They are part of
the endosomal sorting complex required for transport
(ESCRT-0). STAM2 deficiency in mice did not cause any
obvious abnormality, while STAM1 deficiency resulted in
growth retardation. Loss of both STAM1 and STAM2 in
mice proved lethal, indicating that STAMs are important
for embryonic development. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles
in the cell including the regulation of enzymes,
changing the subcellular localization of signaling
pathway components, and mediating the formation of
multiprotein complex assemblies.
Length = 54
Score = 23.6 bits (51), Expect = 7.0
Identities = 11/17 (64%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 31 DFEAAQDCELV-TAGEL 46
DFEAA+D EL AGE+
Sbjct: 8 DFEAAEDNELTFKAGEI 24
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
0.325 0.136 0.424
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,429,279
Number of extensions: 344988
Number of successful extensions: 312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 311
Number of HSP's successfully gapped: 12
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
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: 53 (24.2 bits)