RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8408
(393 letters)
>gnl|CDD|216168 pfam00876, Innexin, Innexin. This family includes the drosophila
proteins Ogre and shaking-B, and the C. elegans proteins
Unc-7 and Unc-9. Members of this family are integral
membrane proteins which are involved in the formation of
gap junctions. This family has been named the Innexins.
Length = 341
Score = 356 bits (915), Expect = e-122
Identities = 130/350 (37%), Positives = 194/350 (55%), Gaps = 24/350 (6%)
Query: 26 DNLVFRCHYRITSAMLFVSCVLVTANNLIGDPINCIADGAVPG---HVINTYCWITSTFT 82
D+ V R HY+ T +L +LV+A GDPI C PG N YCW+ +T+
Sbjct: 1 DDFVDRLHYKYTVIILLAFSLLVSAKQYFGDPIECWVPAEFPGSWEEYANNYCWVQNTYF 60
Query: 83 LPHQAHKPVGSHVIHPAVGSYVEGEDEKRYHTYYQWVPFMLFFQGILFYVPHWIWKNL-- 140
LP P + E E++Y TYYQWVPF+LF Q +LFY+PH+IWK L
Sbjct: 61 LPLGEEVPGTDPE--------EDRERERKYITYYQWVPFVLFLQALLFYIPHYIWKLLSS 112
Query: 141 -EENKVRMITDGMRGAIVTSKEDRRERQKRLVQYIIDTLHMHNV-----YAAGYFFCEFL 194
E +++ + D + AI++ ++R++R K L +Y+ D LH HN A YFFC+ L
Sbjct: 113 WEGGRLKALVDELNSAILSEPDERKKRIKPLARYLDDNLHSHNRYYGNYLAYLYFFCKLL 172
Query: 195 NFVNVVGNMILIDSFLGGTFFTYGTEVLKFTQLNQENRTDPMVEVFPRVTKCTFHKYGSS 254
N +NV+G + L++ FLGG F YG +VL LN E+ TD V FPRVTKC F
Sbjct: 173 NLINVIGQIFLLNRFLGGDFHFYGIDVLAD-LLNGEDWTDSGV--FPRVTKCDFEIRKLG 229
Query: 255 GSIQDHDALCILALNILNEKIYILLWFWFYALAIMSFGAICYSLSVITLPSIRETILIRR 314
GS+Q++ C+L +NI NEKI+I LWFWF LAI+S ++ Y ++ + PS R + +
Sbjct: 230 GSVQNYTVQCVLPINIFNEKIFIFLWFWFVFLAIISVLSLLYWIATLLSPSRRVSFRKKL 289
Query: 315 FRF-GTPAGVSALIRR-TQVGDFLLLHLLGQNMNNMFFGEILDELSTNLH 362
R + +R ++ + LL +L +N+ ++ + E+++EL
Sbjct: 290 LRASSKLNPLDKFVRDYLRIDGWFLLRMLAKNLGDLVYKELIEELWQRFR 339
>gnl|CDD|165115 PHA02748, PHA02748, viral inexin-like protein; Provisional.
Length = 360
Score = 300 bits (771), Expect = e-100
Identities = 137/358 (38%), Positives = 205/358 (57%), Gaps = 15/358 (4%)
Query: 8 SAMAGFVKVRYLMDKAIIDNLVFRCHYRITSAMLFVSCVLVTANNLIGDPINCIADGAVP 67
SA+ G +KV+ IDN FR HY+IT +L +LVT+ GDPI+C P
Sbjct: 6 SALRGLLKVQ----SVSIDNNFFRLHYKITVIILLAFSLLVTSRQYFGDPIDCDFPD-YP 60
Query: 68 GHVINTYCWITSTFTLPHQAHKPVGSHVIHPAVGSYVEGEDEKRYHTYYQWVPFMLFFQG 127
+NTYC++ STF + + V S V P V S EDE RY+ YYQWV LF Q
Sbjct: 61 NGSLNTYCYVQSTFLVERKVTHTVNSTVPDPGV-SGDTEEDELRYYGYYQWVFITLFLQA 119
Query: 128 ILFYVPHWIWKNLEENKVRMITDGMRGAIVTSKEDRRERQKRLVQYIIDTLHMHNVYAAG 187
+ FY+PH+IWK E K++M+ + + V SK+ + + LV Y LH HN YA
Sbjct: 120 VFFYIPHYIWKAWEGGKMKMLAVEL-ASPVLSKDCIEKNTQPLVDYFFMNLHSHNAYAYK 178
Query: 188 YFFCEFLNFVNVVGNMILIDSFLGGTFFTYGTEVLKFTQLNQENRTDPMVEVFPRVTKCT 247
YF CE LN +N+VG + ++ F+G F YG V+ F Q ++ T+PM +FP VTKCT
Sbjct: 179 YFTCELLNLINIVGQIQFMNIFIGEDFQLYGIYVIFFNQEAGKSMTNPMERLFPTVTKCT 238
Query: 248 FHKYGSSGSIQDHDALCILALNILNEKIYILLWFWFYALAIMSFGAICYSLSVITLPSIR 307
+ KYG SG+ ++ + +C+L N LNEKIY+ LWFWF+ LA++S + Y ++ + S+R
Sbjct: 239 YEKYGPSGTPENIEGICLLTQNSLNEKIYVFLWFWFHILAVISAFVVIYRIATLLSSSLR 298
Query: 308 ETILIRRFRF----GTPAGVSALIRRTQVGDFLLLHLLGQNMNNMFFGEILDELSTNL 361
+ FR ++ + + Q+GD+ LLH+L +N+N + + E++ L+ +
Sbjct: 299 ----LYMFRSSSSLNRADDIAVVYNKLQIGDWFLLHMLRKNINPLAYKELISRLAQHF 352
>gnl|CDD|163630 cd07387, MPP_PolD2_C, PolD2 (DNA polymerase delta, subunit 2),
C-terminal domain. PolD2 (DNA polymerase delta, subunit
2) is an auxiliary subunit of the eukaryotic DNA
polymerase delta (PolD) complex thought to play a
regulatory role and to serve as a scaffold for PolD
assembly by interacting simultaneously with all of the
other three subunits. PolD2 is catalytically inactive
and lacks the active site residues required for
phosphoesterase activity in other members of this
superfamily. PolD2 is also involved in the recruitment
of several proteins regulating DNA metabolism, including
p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists
of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3),
and p12(PolD4). PolD is one of three major replicases
in eukaryotes. PolD also plays an essential role in
translesion DNA synthesis, homologous recombination, and
DNA repair. Within the PolD complex, PolD2 tightly
associates with PolD3. PolD2 belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but share a conserved domain with
an active site consisting of two metal ions (usually
manganese, iron, or zinc) coordinated with octahedral
geometry by a cage of histidine, aspartate, and
asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 257
Score = 29.5 bits (67), Expect = 2.6
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 7/44 (15%)
Query: 342 GQNMNNMF----FGEILDELSTNLHLGNNIPTAPSTLELSPIYP 381
GQN++++ LD L L + PTAP TL YP
Sbjct: 151 GQNVDDILKYSSLESRLDILERTLKWRHIAPTAPDTL---WCYP 191
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 29.9 bits (68), Expect = 2.9
Identities = 10/17 (58%), Positives = 15/17 (88%), Gaps = 2/17 (11%)
Query: 376 LSPIYPSDKLRLHKETE 392
L+P+YP+++LRL ETE
Sbjct: 384 LTPLYPNERLRL--ETE 398
>gnl|CDD|212128 cd11663, GH119_BcIgtZ-like, putative catalytic domain of glycoside
hydrolase family 119 (GH119). The prokaryotic subgroup
is represented by IgtZ, an alpha-amylase from a Bacillus
circulans strain. The GH119 family is related to GH57, a
chiefly prokaryotic family with the majority of
thermostable enzymes coming from extremophiles (many of
these are archaeal hyperthermophiles), which exhibit the
enzyme specificities of alpha-amylase (EC 3.2.1.1),
4-alpha-glucanotransferase (EC 2.4.1.25),
amylopullulanase (EC 3.2.1.1/41), and
alpha-galactosidase (EC 3.2.1.22). GH57s cleave
alpha-glycosidic bonds by employing a retaining
mechanism, which involves a glycosyl-enzyme
intermediate, allowing transglycosylation.
Length = 363
Score = 29.1 bits (65), Expect = 4.0
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 62 ADGAVPGHVINTYCWITSTFTLPHQAHKPVGSHVIHPAVGSYVEGEDEKRYHTYYQW-VP 120
AD V G I+ Y + + P S V+H GS+++ D ++ W +P
Sbjct: 308 ADSGVKGMGIDEYL----------RTNTPAASDVVHVQDGSWIDTRDSSSDPQWHHWKLP 357
Query: 121 F 121
F
Sbjct: 358 F 358
>gnl|CDD|220659 pfam10260, SAYSvFN, Uncharacterized conserved domain (SAYSvFN).
This domain of approximately 75 residues contains a
highly conserved SATSv/iFN motif. The function is
unknown but the domain is conserved from plants to
humans.
Length = 71
Score = 26.5 bits (59), Expect = 5.9
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 275 IYILLWFWFYALAIM-SFGAICYSLSVITL 303
+YILLW +AI SFG + + LS L
Sbjct: 1 VYILLWLILLPIAIELSFGLVFFILSGFLL 30
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
0.328 0.141 0.443
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,512,297
Number of extensions: 2028268
Number of successful extensions: 2376
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2365
Number of HSP's successfully gapped: 27
Length of query: 393
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 294
Effective length of database: 6,546,556
Effective search space: 1924687464
Effective search space used: 1924687464
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: 60 (26.8 bits)