RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy936
(344 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 = 106 bits (266), Expect = 1e-26
Identities = 42/108 (38%), Positives = 62/108 (57%), Gaps = 3/108 (2%)
Query: 206 EVWFLILISLVLIGPIMHAIMRV--RRW-LSGTQSELYPISACTWFVYGALMKQGSTLNP 262
EVW IL + +L+G ++ + R W + + +S WF +GAL++QG P
Sbjct: 1 EVWLCILAAYLLVGVVLFLLERFSPYEWRGPPEEPNQFTLSNSLWFSFGALVQQGHRELP 60
Query: 263 RTDSTRIMFASWWIFIMILTAFYTANLTAFLTLSQFTLPIHSVEDIAN 310
R+ S RI+ WW F +IL + YTANL AFLT+ + PI S+ED+A
Sbjct: 61 RSLSGRILVGVWWFFALILLSSYTANLAAFLTVERMQSPIQSLEDLAK 108
>gnl|CDD|214911 smart00918, 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.
Length = 62
Score = 30.3 bits (69), Expect = 0.20
Identities = 12/41 (29%), Positives = 18/41 (43%)
Query: 72 PMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPS 112
P + + G G ++L L+ K F+YEIIL
Sbjct: 1 PYVMLKESPDGGNDRFEGYCIDLLKELAKKLGFTYEIILVP 41
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 30.7 bits (70), Expect = 0.84
Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 12/66 (18%)
Query: 72 PMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGE 131
P S+V ++ GKL G + ++ ++ + E + S L+ LK+G+
Sbjct: 11 PFSYV---DENGKLVGFDV--DLAKAIAKRLGVKVEFVPVSWDGLIPA-------LKSGK 58
Query: 132 VDMVAA 137
VD++ A
Sbjct: 59 VDIIIA 64
>gnl|CDD|236637 PRK09970, PRK09970, xanthine dehydrogenase subunit XdhA;
Provisional.
Length = 759
Score = 30.4 bits (69), Expect = 1.4
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 133 DMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMK 171
D VAA V + K L+K E EEL + E A+
Sbjct: 105 DAVAAVVARDELTAEKALKLIKVEYEELPVITDPEAALA 143
>gnl|CDD|148314 pfam06632, XRCC4, DNA double-strand break repair and V(D)J
recombination protein XRCC4. This family consists of
several eukaryotic DNA double-strand break repair and
V(D)J recombination protein XRCC4 sequences. In the
non-homologous end joining pathway of DNA double-strand
break repair, the ligation step is catalyzed by a
complex of XRCC4 and DNA ligase IV. It is thought that
XRCC4 and ligase IV are essential for alignment-based
gap filling, as well as for final ligation of the
breaks.
Length = 331
Score = 29.9 bits (67), Expect = 2.2
Identities = 16/41 (39%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 131 EVDMVAAFVPVLNIKKNKMAALVK--SEEEELKLQLQQEEA 169
E D+ F+ VLN KK K+ +L K SE +EL+ ++Q++
Sbjct: 173 ETDLYKRFILVLNEKKAKIRSLHKLLSEAQELEKSIKQKKE 213
>gnl|CDD|182613 PRK10644, PRK10644, arginine:agmatin antiporter; Provisional.
Length = 445
Score = 29.8 bits (67), Expect = 2.6
Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 18/78 (23%)
Query: 213 ISLVLIGPIMHAIMRVRRWLSGTQSELYPISACTWFVYGALMKQGSTLNPRTDSTRIMFA 272
+L+L+G R + +Y C W V G + + +M++
Sbjct: 370 AALLLLGHGHFGKARPAYLAVTLIAFVY----CIWAVVG------------SGAKEVMWS 413
Query: 273 SWWIFIMILTAFYTANLT 290
++ +M++TAFY N
Sbjct: 414 --FVTLMVITAFYALNYN 429
>gnl|CDD|172637 PRK14148, PRK14148, heat shock protein GrpE; Provisional.
Length = 195
Score = 29.0 bits (64), Expect = 2.8
Identities = 20/65 (30%), Positives = 34/65 (52%)
Query: 125 NILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYV 184
NI K E D+ A + ++ ++ S E+ LK +++ EEA+ K GIEL V
Sbjct: 72 NIRKRAERDVSNARKFGIEKFAKELLPVIDSIEQALKHEVKLEEAIAMKEGIELTAKMLV 131
Query: 185 VMMKR 189
++K+
Sbjct: 132 DILKK 136
>gnl|CDD|234092 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. This family of proteins encompasses
the E. coli WcaJ protein involved in colanic acid
biosynthesis , the Methylobacillus EpsB protein involved
in methanolan biosynthesis , as well as the GumD protein
involved in the biosynthesis of xanthan. All of these
are closely related to the well-characterized WbaP
(formerly RfbP) protein which is the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose (NOTE: not
glucose) to a polyprenyl carrier (utilizing the highly
conserved C-terminal sugar transferase domain,
pfam02397) a reaction which takes place at the
cytoplasmic face of the inner membrane. The N-terminal
hydrophobic domain is then believed to facilitate the
"flippase" function of transferring the liposaccharide
unit from the cytoplasmic face to the periplasmic face
of the inner membrane. Most of these genes are found
within large operons dedicated to the production of
complex exopolysaccharides such as the enterobacterial
O-antigen. Colanic acid biosynthesis utilizes a
glucose-undecaprenyl carrier , knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 29.1 bits (66), Expect = 3.5
Identities = 19/92 (20%), Positives = 33/92 (35%), Gaps = 3/92 (3%)
Query: 196 GSGLLAPFEIEVWFLILISLV--LIGPIMHAIMRVRRWLSGTQSELYPISACTWFVYGAL 253
GS + E + L+L L+ LI + + R R S + L I + L
Sbjct: 20 GSRGIPDIESYLALLLLAVLLFLLIFALFG-LYRSWRRRSRLREMLLRILLAWTLTFLIL 78
Query: 254 MKQGSTLNPRTDSTRIMFASWWIFIMILTAFY 285
L T+ +R+ W++ + L
Sbjct: 79 ALLAFLLKYGTEFSRLWLLLWFLLALALLLLG 110
>gnl|CDD|226451 COG3942, COG3942, Surface antigen [General function prediction
only].
Length = 173
Score = 27.8 bits (62), Expect = 5.3
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 233 SGTQSELYPISACTWFVYGALMKQGSTLNP 262
S S Y + CTW+V + G + P
Sbjct: 61 SVDASNTYYVGQCTWYVANRRGQAGGYVGP 90
>gnl|CDD|179334 PRK01770, PRK01770, sec-independent translocase; Provisional.
Length = 171
Score = 27.9 bits (62), Expect = 5.4
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 203 FEIEVWFLILIS---LVLIGP--IMHAIMRVRRWLSGTQS 237
F+I L+L+ LV++GP + A+ V W+ +S
Sbjct: 2 FDIGFSELLLVFVIGLVVLGPQRLPVAVKTVAGWIRALRS 41
>gnl|CDD|234093 TIGR03025, EPS_sugtrans, exopolysaccharide biosynthesis polyprenyl
glycosylphosphotransferase. Members of this family are
generally found near other genes involved in the
biosynthesis of a variety of exopolysaccharides. These
proteins consist of two fused domains, an N-terminal
hydrophobic domain of generally low conservation and a
highly conserved C-terminal sugar transferase domain
(pfam02397). Characterized and partially characterized
members of this subfamily include Salmonella WbaP
(originally RfbP) , E. coli WcaJ , Methylobacillus EpsB,
Xanthomonas GumD, Vibrio CpsA, Erwinia AmsG, Group B
Streptococcus CpsE (originally CpsD), and Streptococcus
suis Cps2E. Each of these is believed to act in
transferring the sugar from, for instance, UDP-glucose
or UDP-galactose, to a lipid carrier such as
undecaprenyl phosphate as the first (priming) step in
the synthesis of an oligosaccharide "block". This
function is encoded in the C-terminal domain. The
liposaccharide is believed to be subsequently
transferred through a "flippase" function from the
cytoplasmic to the periplasmic face of the inner
membrane by the N-terminal domain. Certain closely
related transferase enzymes such as Sinorhizobium ExoY
and Lactococcus EpsD lack the N-terminal domain and are
not found by this model.
Length = 445
Score = 28.3 bits (64), Expect = 6.5
Identities = 18/86 (20%), Positives = 33/86 (38%)
Query: 197 SGLLAPFEIEVWFLILISLVLIGPIMHAIMRVRRWLSGTQSELYPISACTWFVYGALMKQ 256
G L P L+L+ L+L + A R W + E W + L+
Sbjct: 19 GGGLLPPPSFYSLLLLLILLLFLILFAASGLYRSWRGRSLLEELARVLLAWLLVFLLLLA 78
Query: 257 GSTLNPRTDSTRIMFASWWIFIMILT 282
+ L D +R++ W++ ++L
Sbjct: 79 LAFLLKGFDFSRLVLLLWFVLALVLL 104
>gnl|CDD|224488 COG1572, COG1572, Uncharacterized conserved protein [Function
unknown].
Length = 606
Score = 28.3 bits (63), Expect = 7.6
Identities = 13/89 (14%), Positives = 22/89 (24%), Gaps = 2/89 (2%)
Query: 56 LPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKT 115
I + N G + +G F L+ Y++ E
Sbjct: 176 AEINGGNVYLIIYCDYTNYQEEYNEINGAKDPNGG-FVGLSYAPTLYDYLVESSTQLADV 234
Query: 116 LLDQDGSIMNILKTGEVDMVAAFVPVLNI 144
+ + G VD A + N
Sbjct: 235 VNLLSI-ANSSPYFGFVDEDTASILEEND 262
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
0.322 0.135 0.415
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,737,853
Number of extensions: 1705339
Number of successful extensions: 1629
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1626
Number of HSP's successfully gapped: 43
Length of query: 344
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 246
Effective length of database: 6,590,910
Effective search space: 1621363860
Effective search space used: 1621363860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.4 bits)