RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16364
(276 letters)
>gnl|CDD|216598 pfam01602, Adaptin_N, Adaptin N terminal region. This family
consists of the N terminal region of various alpha, beta
and gamma subunits of the AP-1, AP-2 and AP-3 adaptor
protein complexes. The adaptor protein (AP) complexes
are involved in the formation of clathrin-coated pits
and vesicles. The N-terminal region of the various
adaptor proteins (APs) is constant by comparison to the
C-terminal which is variable within members of the AP-2
family; and it has been proposed that this constant
region interacts with another uniform component of the
coated vesicles.
Length = 522
Score = 114 bits (287), Expect = 6e-29
Identities = 46/139 (33%), Positives = 81/139 (58%), Gaps = 8/139 (5%)
Query: 1 MSKILKTHPKSVQSHRDLIMQCLD-DKDESIRLRALDLLYGMVSKKTLMEIVKKLMVHM- 58
++KIL+ HP +VQ H DLI+ CL D D SIRLRALDLLY +V + + EIVK+L+ ++
Sbjct: 289 LNKILEKHPPAVQ-HLDLIIFCLKTDDDISIRLRALDLLYKLVDESNVKEIVKELLKYVS 347
Query: 59 DKAEGTMYRDELLSKVIDICSQNNYQYITNFEWYMTVLVELTRMEGTRHGALVAAQMMDV 118
+ A+ ++ +L+ + + + + T+ EW + VL+EL + G+ + + D+
Sbjct: 348 EIADPE-FKIKLVKAIGRLAEK----FPTDAEWCIDVLLELLSLAGSYVVDEIVEVIRDI 402
Query: 119 AIRVSAVRAFAVAQMSSLL 137
+ +R + + + LL
Sbjct: 403 IRKYPELREYILEHLCELL 421
Score = 86.1 bits (214), Expect = 4e-19
Identities = 39/110 (35%), Positives = 67/110 (60%), Gaps = 8/110 (7%)
Query: 169 IKFSSRMPNHMKYLGLLAMSKILKTHPKSVQSHRDLIMQCLD-DKDESIRLRALDLLYGM 227
+ S +++Y+ L ++KIL+ HP +VQ H DLI+ CL D D SIRLRALDLLY +
Sbjct: 271 GRLLSSPDENLRYVALRNLNKILEKHPPAVQ-HLDLIIFCLKTDDDISIRLRALDLLYKL 329
Query: 228 VSKKTLMEIVKKLMVHM-DKAEGTMYRDELLSKVIDICSQNNYQYITNFE 276
V + + EIVK+L+ ++ + A+ ++ +L+ + + ++ T+ E
Sbjct: 330 VDESNVKEIVKELLKYVSEIADPE-FKIKLVKAIGRLAE----KFPTDAE 374
>gnl|CDD|227565 COG5240, SEC21, Vesicle coat complex COPI, gamma subunit
[Intracellular trafficking and secretion].
Length = 898
Score = 31.1 bits (70), Expect = 0.64
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 177 NHMKYLGLLAMSKIL--KTHPKSVQSHRDLIMQCLDDKDESIRLRALDLLYGMVSKKTLM 234
N ++ + A+SK + S QS + + +CL+D+D+ +R RA LL M
Sbjct: 501 NIVRSAAVQALSKFALNISDVVSPQSVENALKRCLNDQDDEVRDRASFLLRNMRLSDACE 560
Query: 235 EIVK 238
+
Sbjct: 561 PLFS 564
Score = 29.2 bits (65), Expect = 2.8
Identities = 13/47 (27%), Positives = 22/47 (46%)
Query: 6 KTHPKSVQSHRDLIMQCLDDKDESIRLRALDLLYGMVSKKTLMEIVK 52
+ S QS + + +CL+D+D+ +R RA LL M +
Sbjct: 518 ISDVVSPQSVENALKRCLNDQDDEVRDRASFLLRNMRLSDACEPLFS 564
>gnl|CDD|218854 pfam06012, DUF908, Domain of Unknown Function (DUF908).
Length = 309
Score = 30.0 bits (68), Expect = 1.1
Identities = 19/98 (19%), Positives = 34/98 (34%), Gaps = 8/98 (8%)
Query: 133 MSSLLASPSPPLSQPSSRMAEMMFDEYSDRSSKIFNIKFSSRMPNHMKYLGLLAMSKILK 192
+S LL S + + + R+ ++ Y + FS R+ + L + K+
Sbjct: 31 LSDLLNSTNLDVVLAALRVLLVLAQRYVISRRSSY---FSPRLLRKKYNILLEKLLKLAS 87
Query: 193 THPKSVQ-----SHRDLIMQCLDDKDESIRLRALDLLY 225
+ P S L+ DDK + L Y
Sbjct: 88 SWPSSPIPGGKSDGLSLVDCLFDDKKYPSKWGQLRFEY 125
>gnl|CDD|234945 PRK01346, PRK01346, hypothetical protein; Provisional.
Length = 411
Score = 28.7 bits (65), Expect = 3.0
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 6/40 (15%)
Query: 104 GTRHGALVAAQMMDVAIRVSAVRAFAVAQMSSLLASPSPP 143
G R L AA RV + A+A+ + A+ P
Sbjct: 372 GHRASTLAAAG------RVRELDPGALARADAAFATDRAP 405
>gnl|CDD|234152 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC transporter,
ATP-binding protein. This ABC transporter ATP-binding
protein is found in a number of genomes in operon-like
contexts strongly suggesting a substrate specificity for
2-aminoethylphosphonate (2-AEP). The characterized
PhnSTUV system is absent in the genomes in which this
system is found. These genomes encode systems for the
catabolism of 2-AEP, making the need for a
2-AEP-specific transporter likely [Transport and binding
proteins, Amino acids, peptides and amines].
Length = 353
Score = 28.8 bits (65), Expect = 3.1
Identities = 9/36 (25%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 94 TVLVELTRMEGTRHGALVAAQMMDVAIRVSAVRAFA 129
++ +++ E R G + A Q + + + +RAFA
Sbjct: 319 ALVADVSASEVERLG-IRAGQPIWIELPAERLRAFA 353
>gnl|CDD|217228 pfam02781, G6PD_C, Glucose-6-phosphate dehydrogenase, C-terminal
domain.
Length = 294
Score = 28.1 bits (63), Expect = 4.8
Identities = 11/42 (26%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 175 MPNH-MKYLGLLAMSKILKTHPKSVQSHRDLIMQCLDDKDES 215
M NH ++ L L+AM K + + ++ + +++ L DE
Sbjct: 49 MQNHLLQILCLVAMEKPVSFSAEDIRDEKVKVLKALRPIDED 90
>gnl|CDD|237787 PRK14681, PRK14681, hypothetical protein; Provisional.
Length = 158
Score = 27.2 bits (60), Expect = 6.4
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 134 SSLLASPSPPLSQPSSRMAEMMFD 157
+L SP+PP QP +A M+ D
Sbjct: 14 QPMLPSPTPPAEQPLESLAAMLGD 37
>gnl|CDD|177277 PHA00432, PHA00432, internal virion protein A.
Length = 137
Score = 26.9 bits (60), Expect = 6.6
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 18/49 (36%)
Query: 43 SKKTLMEIVKKLMVHMDKAEGTMYRDELLSKVIDICSQNNYQYITNFEW 91
+KK E K +M YRD +L + Y + N+ W
Sbjct: 71 TKKEKREFRKLIM---------EYRDMMLDQ---------YPSLWNYVW 101
>gnl|CDD|107287 cd06292, PBP1_LacI_like_10, Ligand-binding domain of
uncharacterized DNA-binding regulatory proteins that are
members of the LacI-GalR family of bacterial
transcription repressors. This group includes the
ligand-binding domain of uncharacterized DNA-binding
regulatory proteins that are members of the LacI-GalR
family of bacterial transcription repressors. The
LacI-GalR family repressors are composed of two
functional domains: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal ligand-binding domain,
which is homologous to the sugar-binding domain of
ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. As also observed
in the periplasmic binding proteins, the C-terminal
domain of the bacterial transcription repressor
undergoes a conformational change upon ligand binding
which in turn changes the DNA binding affinity of the
repressor.
Length = 273
Score = 27.7 bits (62), Expect = 6.9
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 134 SSLLASPSPPLS---QPSSRMAEMMFDEYSDR 162
S+L+A PPL+ QP MA D R
Sbjct: 219 SALMAFTDPPLTTVRQPVEEMAAAAVDRLMAR 250
>gnl|CDD|219944 pfam08633, Rox3, Rox3 mediator complex subunit. The mediator
complex is part of the RNA polymerase II holoenzyme.
Rox3 is a subunit of the mediator complex.
Length = 210
Score = 27.5 bits (61), Expect = 7.2
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 6/85 (7%)
Query: 177 NHMKYLGLLAMSKILKTHPKSVQSHRDLIMQCLDDKDESIRLRALDLLYGMVSKKTLMEI 236
+K LG+ +KT P LI+ ++ D +++ D++ GM S E+
Sbjct: 44 GQIKDLGVAGKFDAVKTRPNGPGGLISLILWPQEEWDN-FQVQGKDIMVGMSS-----EL 97
Query: 237 VKKLMVHMDKAEGTMYRDELLSKVI 261
+ +L A GT+ + S V+
Sbjct: 98 LSELSRARTMARGTVPNMDWCSSVL 122
>gnl|CDD|233162 TIGR00871, zwf, glucose-6-phosphate 1-dehydrogenase. This enzyme
(EC 1.1.1.49) acts on glucose 6-phospate and reduces
NADP(+). An alternate name appearing in the literature
for the human enzyme, based on a slower activity with
beta-D-glucose, is glucose 1-dehydrogenase (EC
1.1.1.47), but that name more properly describes a
subfamily of the short chain dehydrogenases/reductases
family. This is a well-studied enzyme family, with
sequences available from well over 50 species. The
trusted cutoff is set above the score for the Drosophila
melanogaster CG7140 gene product, a homolog of unknown
function. G6PD homologs from the bacteria Aquifex
aeolicus and Helicobacter pylori lack several motifs
well conserved most other members, were omitted from the
seed alignment, and score well below the trusted cutoff
[Energy metabolism, Pentose phosphate pathway].
Length = 482
Score = 27.7 bits (62), Expect = 8.2
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 175 MPNH-MKYLGLLAMSKILKTHPKSVQSHRDLIMQCLDDKDES 215
+ NH ++ L L+AM S++ + +++ L D
Sbjct: 235 VQNHLLQLLCLVAMEPPASFDADSIRDEKVKVLKALRPIDPD 276
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
0.321 0.132 0.368
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,465,097
Number of extensions: 1258236
Number of successful extensions: 1298
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1294
Number of HSP's successfully gapped: 40
Length of query: 276
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 180
Effective length of database: 6,679,618
Effective search space: 1202331240
Effective search space used: 1202331240
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: 58 (26.0 bits)