RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7562
(582 letters)
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain. Cadherins
are glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium. They
play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing proteins
exist as monomers, homodimers, or heterodimers.
Length = 98
Score = 100 bits (252), Expect = 9e-26
Identities = 41/100 (41%), Positives = 58/100 (58%), Gaps = 5/100 (5%)
Query: 324 YETNISESVPVGSEILKVAASDSDQE--SKVLYSIHHAQSPLSAALFRIDFHSGALSVAQ 381
YE ++ E+ P G+ +L V+A+D D +V YSI S LF ID +G ++ A+
Sbjct: 2 YEVSVPENAPPGTVVLTVSATDPDSGENGEVTYSI---VSGNEDGLFSIDPSTGEITTAK 58
Query: 382 PLDRESLSHHLLTIMARDQGTPAKRNFARVSINVLDSNDH 421
PLDRE S + LT+ A D G P + A V+I VLD ND+
Sbjct: 59 PLDREEQSSYTLTVTATDGGGPPLSSTATVTITVLDVNDN 98
Score = 98.2 bits (245), Expect = 8e-25
Identities = 46/89 (51%), Positives = 56/89 (62%)
Query: 433 RVFETSAVGTNIVQVVATDRDHGENGVVTYSIASGNIGNVFTMDPILGTIQTARPLDLSL 492
V E + GT ++ V ATD D GENG VTYSI SGN +F++DP G I TA+PLD
Sbjct: 5 SVPENAPPGTVVLTVSATDPDSGENGEVTYSIVSGNEDGLFSIDPSTGEITTAKPLDREE 64
Query: 493 MSEYMLLVKATDQGAPPLAATVPVQIIVV 521
S Y L V ATD G PPL++T V I V+
Sbjct: 65 QSSYTLTVTATDGGGPPLSSTATVTITVL 93
Score = 72.3 bits (178), Expect = 1e-15
Identities = 37/133 (27%), Positives = 52/133 (39%), Gaps = 41/133 (30%)
Query: 110 RVEVTENDAVGFLVALIQASDPDGD---TLWYRIVDGDPNSTFSIGNDKGNVLLARRVDW 166
V V EN G +V + A+DPD + Y IV G+ + FSI G + A+ +D
Sbjct: 3 EVSVPENAPPGTVVLTVSATDPDSGENGEVTYSIVSGNEDGLFSIDPSTGEITTAKPLDR 62
Query: 167 ETQAQYTLNISVSDGIHEWTGRHRPSAIRTVVNLDHESLPRIEFHVQVTDLGRPRLTSDT 226
E Q+ YTL ++ +DG G P L+S
Sbjct: 63 EEQSSYTLTVTATDG------------------------------------GGPPLSS-- 84
Query: 227 LAKVIVEVTDTND 239
A V + V D ND
Sbjct: 85 TATVTITVLDVND 97
Score = 35.8 bits (83), Expect = 0.008
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 537 AELFENEPPGTVVRHIEAR-----STSSLVFEIIRGDSDDMFSINK 577
+ EN PPGTVV + A + + I+ G+ D +FSI+
Sbjct: 4 VSVPENAPPGTVVLTVSATDPDSGENGEVTYSIVSGNEDGLFSIDP 49
Score = 35.8 bits (83), Expect = 0.008
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 11 QEFDLLVRATDHGSPNQSSTARVSIQVV 38
+ L V ATD G P SSTA V+I V+
Sbjct: 66 SSYTLTVTATDGGGPPLSSTATVTITVL 93
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 89.3 bits (222), Expect = 1e-21
Identities = 41/89 (46%), Positives = 51/89 (57%)
Query: 432 GRVFETSAVGTNIVQVVATDRDHGENGVVTYSIASGNIGNVFTMDPILGTIQTARPLDLS 491
V E + VGT ++ V ATD D G NG + YSI G G F +DP G + T +PLD
Sbjct: 3 ASVPENAPVGTEVLTVTATDADLGPNGRIFYSILGGGPGGWFRIDPDTGDLSTTKPLDRE 62
Query: 492 LMSEYMLLVKATDQGAPPLAATVPVQIIV 520
+ EY L V ATD G PPL++T V I V
Sbjct: 63 SIGEYELTVLATDSGGPPLSSTTTVTITV 91
Score = 74.3 bits (183), Expect = 2e-16
Identities = 37/95 (38%), Positives = 54/95 (56%), Gaps = 5/95 (5%)
Query: 324 YETNISESVPVGSEILKVAASDSD--QESKVLYSIHHAQSPLSAALFRIDFHSGALSVAQ 381
Y ++ E+ PVG+E+L V A+D+D ++ YSI FRID +G LS +
Sbjct: 1 YSASVPENAPVGTEVLTVTATDADLGPNGRIFYSI---LGGGPGGWFRIDPDTGDLSTTK 57
Query: 382 PLDRESLSHHLLTIMARDQGTPAKRNFARVSINVL 416
PLDRES+ + LT++A D G P + V+I VL
Sbjct: 58 PLDRESIGEYELTVLATDSGGPPLSSTTTVTITVL 92
Score = 55.4 bits (134), Expect = 9e-10
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 111 VEVTENDAVGFLVALIQASDPDGDTLW---YRIVDGDPNSTFSIGNDKGNVLLARRVDWE 167
V EN VG V + A+D D Y I+ G P F I D G++ + +D E
Sbjct: 3 ASVPENAPVGTEVLTVTATDADLGPNGRIFYSILGGGPGGWFRIDPDTGDLSTTKPLDRE 62
Query: 168 TQAQYTLNISVSDG 181
+ +Y L + +D
Sbjct: 63 SIGEYELTVLATDS 76
Score = 34.2 bits (79), Expect = 0.023
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 11 QEFDLLVRATDHGSPNQSSTARVSIQV 37
E++L V ATD G P SST V+I V
Sbjct: 65 GEYELTVLATDSGGPPLSSTTTVTITV 91
Score = 32.3 bits (74), Expect = 0.13
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 5/46 (10%)
Query: 537 AELFENEPPGTVVRHIEARST-----SSLVFEIIRGDSDDMFSINK 577
A + EN P GT V + A + + I+ G F I+
Sbjct: 3 ASVPENAPVGTEVLTVTATDADLGPNGRIFYSILGGGPGGWFRIDP 48
>gnl|CDD|214520 smart00112, CA, Cadherin repeats. Cadherins are glycoproteins
involved in Ca2+-mediated cell-cell adhesion. Cadherin
domains occur as repeats in the extracellular regions
which are thought to mediate cell-cell contact when
bound to calcium.
Length = 81
Score = 81.2 bits (201), Expect = 5e-19
Identities = 43/81 (53%), Positives = 52/81 (64%), Gaps = 1/81 (1%)
Query: 448 VATDRDHGENGVVTYSIASGNIGNVFTMDPILGTIQTARPLDLSLMSEYMLLVKATDQGA 507
ATD D GENG VTYSI SGN +F++DP G I T +PLD EY L V+ATD G
Sbjct: 1 SATDADSGENGKVTYSILSGNDDGLFSIDPETGEITTTKPLDREEQPEYTLTVEATDGGG 60
Query: 508 PPLAATVPVQIIVV-MADNDP 527
PPL++T V I V+ + DN P
Sbjct: 61 PPLSSTATVTITVLDVNDNAP 81
Score = 76.6 bits (189), Expect = 2e-17
Identities = 33/80 (41%), Positives = 44/80 (55%), Gaps = 3/80 (3%)
Query: 344 SDSDQESKVLYSIHHAQSPLSAALFRIDFHSGALSVAQPLDRESLSHHLLTIMARDQGTP 403
+DS + KV YSI S LF ID +G ++ +PLDRE + LT+ A D G P
Sbjct: 5 ADSGENGKVTYSIL---SGNDDGLFSIDPETGEITTTKPLDREEQPEYTLTVEATDGGGP 61
Query: 404 AKRNFARVSINVLDSNDHPP 423
+ A V+I VLD ND+ P
Sbjct: 62 PLSSTATVTITVLDVNDNAP 81
Score = 55.0 bits (133), Expect = 9e-10
Identities = 30/119 (25%), Positives = 42/119 (35%), Gaps = 41/119 (34%)
Query: 127 QASDPDGDTLW---YRIVDGDPNSTFSIGNDKGNVLLARRVDWETQAQYTLNISVSDGIH 183
A+D D Y I+ G+ + FSI + G + + +D E Q +YTL
Sbjct: 1 SATDADSGENGKVTYSILSGNDDGLFSIDPETGEITTTKPLDREEQPEYTLT-------- 52
Query: 184 EWTGRHRPSAIRTVVNLDHESLPRIEFHVQVTDLGRPRLTSDTLAKVIVEVTDTNDCPP 242
V+ TD G P L+S A V + V D ND P
Sbjct: 53 ----------------------------VEATDGGGPPLSS--TATVTITVLDVNDNAP 81
Score = 38.1 bits (89), Expect = 8e-04
Identities = 18/40 (45%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 9 AGQEFDLLVRATDHGSPNQSSTARVSIQVVRLPDESKNPP 48
E+ L V ATD G P SSTA V+I V+ D + N P
Sbjct: 45 EQPEYTLTVEATDGGGPPLSSTATVTITVL---DVNDNAP 81
>gnl|CDD|206635 cd00031, CA_like, Cadherin repeat-like domain. Cadherins are
glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium. They
play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing proteins
exist as monomers, homodimers, or heterodimers. This
family also includes the cadherin-like repeats of
extracellular alpha-dystroglycan.
Length = 98
Score = 50.4 bits (120), Expect = 5e-08
Identities = 21/79 (26%), Positives = 32/79 (40%)
Query: 343 ASDSDQESKVLYSIHHAQSPLSAALFRIDFHSGALSVAQPLDRESLSHHLLTIMARDQGT 402
+D S + I A + + HSG L + LDRE H +++ A G
Sbjct: 20 PTDLIASSGEIIKISAAGKEALPSWLHWEPHSGILEGLEKLDREDKGVHYISVSAASLGA 79
Query: 403 PAKRNFARVSINVLDSNDH 421
+ + SI V D ND+
Sbjct: 80 NVPQTSSVFSIEVYDENDN 98
>gnl|CDD|165099 PHA02732, PHA02732, hypothetical protein; Provisional.
Length = 1467
Score = 35.9 bits (82), Expect = 0.074
Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 6/94 (6%)
Query: 28 SSTARVSIQVVRLPDESKNPP--TIKSPDQRVEVTENDAVGFLVALIQASDPDGDTLWYR 85
S+T V+I + P+ ++ P +I SP+ + ++N GFL L+ D +WY
Sbjct: 925 SNTLNVTIHITSFPEGAQYNPGISIYSPNIGDQPSDNAISGFLAILVDFYD---GNIWYH 981
Query: 86 IYVLHWECLPDESKNPPTIKSPDQ-RVEVTENDA 118
+W+ L + P P V TEN A
Sbjct: 982 GPNANWQELRSSALPQPNPAYPFTFSVIFTENGA 1015
>gnl|CDD|221114 pfam11454, DUF3016, Protein of unknown function (DUF3016). This is
a bacterial family of uncharacterized proteins.
Length = 141
Score = 32.2 bits (74), Expect = 0.27
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 172 YTLNISVSD----GIHEWTGRHRPSAIRTVVNLDHESLPRIEFHVQVTD 216
L I V+D G E T + +R V ++ PRI ++ D
Sbjct: 51 QKLEIEVTDVDLAGDVEPTWGSGANDVRVVRDIY---PPRINLSYKLLD 96
>gnl|CDD|143207 cd05730, Ig3_NCAM-1_like, Third immunoglobulin (Ig)-like domain of
Neural Cell Adhesion Molecule NCAM-1 (NCAM).
Ig3_NCAM-1_like: domain similar to the third
immunoglobulin (Ig)-like domain of Neural Cell Adhesion
Molecule NCAM-1 (NCAM). NCAM plays important roles in
the development and regeneration of the central nervous
system, in synaptogenesis and neural migration. NCAM
mediates cell-cell and cell-substratum recognition and
adhesion via homophilic (NCAM-NCAM), and heterophilic
(NCAM-non-NCAM), interactions. NCAM is expressed as
three major isoforms having different intracellular
extensions. The extracellular portion of NCAM has five
N-terminal Ig-like domains and two fibronectin type III
domains. The double zipper adhesion complex model for
NCAM homophilic binding involves Ig1, Ig2, and Ig3. By
this model, Ig1,and Ig2 mediate dimerization of NCAM
molecules situated on the same cell surface (cis
interactions), and Ig3 domains mediate interactions
between NCAM molecules expressed on the surface of
opposing cells (trans interactions), through binding to
the Ig1 and Ig2 domains. The adhesive ability of NCAM is
modulated by the addition of polysialic acid chains to
the fifth Ig-like domain.
Length = 95
Score = 31.4 bits (71), Expect = 0.30
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 15/81 (18%)
Query: 101 PPTIKSPDQRVEVTENDAVGFLVALIQASDPDG----DTLWYR----IVDGDPNSTFSIG 152
PPTI++ V T N +G V L A D DG W + I G+ +F
Sbjct: 1 PPTIRARQSEVNATAN--LGQSVTL--ACDADGFPEPTMTWTKDGEPIESGEEKYSF--- 53
Query: 153 NDKGNVLLARRVDWETQAQYT 173
N+ G+ + VD +A+YT
Sbjct: 54 NEDGSEMTILDVDKLDEAEYT 74
>gnl|CDD|183425 PRK12308, PRK12308, bifunctional argininosuccinate
lyase/N-acetylglutamate synthase; Provisional.
Length = 614
Score = 32.4 bits (74), Expect = 0.71
Identities = 26/68 (38%), Positives = 33/68 (48%), Gaps = 21/68 (30%)
Query: 361 SPLSAALFRIDF---HSGALS-VAQPLDRESLSHHLLTIMARDQGTPAKRNFARVSINVL 416
S L AL R+D SGAL+ A P+DRE+L+H+L F R + N L
Sbjct: 181 SRLEDALTRLDTCPLGSGALAGTAYPIDREALAHNL--------------GFRRATRNSL 226
Query: 417 DS---NDH 421
DS DH
Sbjct: 227 DSVSDRDH 234
>gnl|CDD|203892 pfam08266, Cadherin_2, Cadherin-like. This cadherin domain is
usually the most N-terminal copy of the domain.
Length = 84
Score = 29.4 bits (67), Expect = 1.1
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 367 LFRIDFHSGALSVAQPLDRESL 388
F+++ +G L V + +DRE L
Sbjct: 46 YFQLNPETGDLLVNERIDREEL 67
>gnl|CDD|238308 cd00552, RaiA, RaiA ("ribosome-associated inhibitor A", also known
as Protein Y (PY), YfiA, and SpotY, is a
stress-response protein that binds the ribosomal subunit
interface and arrests translation by interfering with
aminoacyl-tRNA binding to the ribosomal A site. RaiA is
also thought to counteract miscoding at the A site thus
reducing translation errors. The RaiA fold structurally
resembles the double-stranded RNA-binding domain
(dsRBD).
Length = 93
Score = 29.0 bits (66), Expect = 1.5
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 7/48 (14%)
Query: 175 NISVSDGIHEWT-------GRHRPSAIRTVVNLDHESLPRIEFHVQVT 215
NI V+D + E+ ++ I V L E F V++T
Sbjct: 8 NIEVTDALREYVEEKLEKLEKYFDRIISVDVVLSVEKNHGKRFKVEIT 55
>gnl|CDD|131981 TIGR02935, TIGR02935, probable nitrogen fixation protein. Members
of this protein family, called DUF269 by pfam03270, are
strictly limited to nitrogen-fixing species, although
not universal among them. The gene typically is found
next to the nifX gene (see TIGRFAMs model TIGR02663)
[Central intermediary metabolism, Nitrogen fixation].
Length = 140
Score = 29.6 bits (67), Expect = 2.2
Identities = 20/70 (28%), Positives = 27/70 (38%), Gaps = 22/70 (31%)
Query: 68 LVALIQASDPDGDTLWYRIYVLHWECLPDESKNPPTIKSPDQRVEVTENDAVGFLVALIQ 127
LV I+A D G WE D P I + ++R E+ +I
Sbjct: 8 LVRQIRAQDTYG----------AWEGKSDAELLAPYIVTKEERREI----------PII- 46
Query: 128 ASDPDGDTLW 137
DPD +TLW
Sbjct: 47 -GDPDPETLW 55
>gnl|CDD|224367 COG1450, PulD, Type II secretory pathway, component PulD [Cell
motility and secretion / Intracellular trafficking and
secretion].
Length = 587
Score = 30.8 bits (70), Expect = 2.6
Identities = 20/90 (22%), Positives = 31/90 (34%), Gaps = 3/90 (3%)
Query: 394 TIMARDQGTPAKRNFARVSINVLDSNDHPPEFATSLVKGRVFETSAVGTNIVQVVATDRD 453
T RD + A + +LDS D P + + R A+ ++ +V
Sbjct: 200 TYQYRDDEVSSPGALAAILSQLLDSLDVPSSPSGNSYDLRSANAKALAVSLKSLVE--GL 257
Query: 454 HGENGVVTYSIASGNIGNV-FTMDPILGTI 482
E G I SG G + DP +
Sbjct: 258 KDEGGSSGEGIGSGASGAITIIADPQTNAL 287
>gnl|CDD|149118 pfam07872, DUF1659, Protein of unknown function (DUF1659). This
family consists of hypothetical bacterial proteins of
unknown function.
Length = 47
Score = 26.8 bits (60), Expect = 3.7
Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 9/45 (20%)
Query: 207 RIEFHVQVTDLGRPRLTSDTLAKVIVEVTDTNDCPPQFSQDVYNV 251
+++ + + G+P + T + V + TD +D+Y+V
Sbjct: 9 VLKYQDGLDESGKPIYKNKTFSNVKPDATD---------EDLYDV 44
>gnl|CDD|233991 TIGR02743, TraW, type-F conjugative transfer system protein TraW.
This protein is an essential component of the F-type
conjugative transfer sytem for plasmid DNA transfer and
has been shown to be localized to the periplasm.
Length = 202
Score = 28.5 bits (64), Expect = 8.9
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 382 PLDRESLSHHLLTIMARDQGTPAKRNFAR 410
PLDR SLS LL A D P + +A+
Sbjct: 115 PLDRVSLSKTLLFFDADD---PEQLAWAQ 140
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
0.316 0.132 0.383
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,207,229
Number of extensions: 2848325
Number of successful extensions: 2178
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2171
Number of HSP's successfully gapped: 33
Length of query: 582
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 480
Effective length of database: 6,413,494
Effective search space: 3078477120
Effective search space used: 3078477120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 62 (27.7 bits)