RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1887
(653 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 = 90.5 bits (225), Expect = 7e-22
Identities = 40/99 (40%), Positives = 55/99 (55%), Gaps = 2/99 (2%)
Query: 432 YTAKIPENATAGEKVVQVKATDVDTNLGGEILYTAILGYKNSSLELDAHTGDITIANGQQ 491
Y +PENA G V+ V ATD D+ GE+ Y+ + G ++ +D TG+IT A +
Sbjct: 2 YEVSVPENAPPGTVVLTVSATDPDSGENGEVTYSIVSGNEDGLFSIDPSTGEITTA--KP 59
Query: 492 FDREEASEYKFQVEARDMQGLGLRTVVPLQLTILDVNDN 530
DREE S Y V A D G L + + +T+LDVNDN
Sbjct: 60 LDREEQSSYTLTVTATDGGGPPLSSTATVTITVLDVNDN 98
Score = 56.9 bits (138), Expect = 3e-10
Identities = 35/115 (30%), Positives = 51/115 (44%), Gaps = 19/115 (16%)
Query: 311 QYITHLDENSPQGTALIFAESFHTQVTDDNMGKNG--IFSLTLENNNGTFEIWPSVVERK 368
Y + EN+P GT ++ TD + G+NG +S+ N +G F I PS E
Sbjct: 1 SYEVSVPENAPPGTVVL-----TVSATDPDSGENGEVTYSIVSGNEDGLFSIDPSTGE-- 53
Query: 369 AQFTIRVRNNKNLDYERTRTLSFVIVAKEISSDSSSNLLSSQAPVLVYINDVNDN 423
+ K LD E + + + A +D LSS A V + + DVNDN
Sbjct: 54 ------ITTAKPLDREEQSSYTLTVTA----TDGGGPPLSSTATVTITVLDVNDN 98
Score = 43.1 bits (102), Expect = 2e-05
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 538 PFEFVLASDSRNFSERTFIKATDQDAEAPNNIVRYEIISGNYDNKFSLHPETGV 591
+E + ++ + + ATD D+ N V Y I+SGN D FS+ P TG
Sbjct: 1 SYEVSVPENAPPGTVVLTVSATDPDSG-ENGEVTYSIVSGNEDGLFSIDPSTGE 53
Score = 35.0 bits (81), Expect = 0.019
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 31 VIQLAPNLTMNDVLTKITAIDGDKGHPRTIKYGLVSEGHPMTVFFTINELTG 82
+ + N V+ ++A D D G + Y +VS F+I+ TG
Sbjct: 3 EVSVPENAPPGTVVLTVSATDPDSGENGEVTYSIVSGNEDG--LFSIDPSTG 52
>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 = 70.5 bits (173), Expect = 4e-15
Identities = 33/83 (39%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 450 KATDVDTNLGGEILYTAILGYKNSSLELDAHTGDITIANGQQFDREEASEYKFQVEARDM 509
ATD D+ G++ Y+ + G + +D TG+IT + DREE EY VEA D
Sbjct: 1 SATDADSGENGKVTYSILSGNDDGLFSIDPETGEITTT--KPLDREEQPEYTLTVEATDG 58
Query: 510 QGLGLRTVVPLQLTILDVNDNAP 532
G L + + +T+LDVNDNAP
Sbjct: 59 GGPPLSSTATVTITVLDVNDNAP 81
Score = 56.2 bits (136), Expect = 4e-10
Identities = 29/93 (31%), Positives = 41/93 (44%), Gaps = 14/93 (15%)
Query: 335 QVTDDNMGKNG--IFSLTLENNNGTFEIWPSVVERKAQFTIRVRNNKNLDYERTRTLSFV 392
TD + G+NG +S+ N++G F I P T + K LD E +
Sbjct: 1 SATDADSGENGKVTYSILSGNDDGLFSIDPE--------TGEITTTKPLDREEQPEYTLT 52
Query: 393 IVAKEISSDSSSNLLSSQAPVLVYINDVNDNPP 425
+ A +D LSS A V + + DVNDN P
Sbjct: 53 VEA----TDGGGPPLSSTATVTITVLDVNDNAP 81
Score = 37.7 bits (88), Expect = 0.001
Identities = 18/35 (51%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 557 KATDQDAEAPNNIVRYEIISGNYDNKFSLHPETGV 591
ATD D N V Y I+SGN D FS+ PETG
Sbjct: 1 SATDAD-SGENGKVTYSILSGNDDGLFSIDPETGE 34
Score = 28.9 bits (65), Expect = 1.8
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 48 TAIDGDKGHPRTIKYGLVSEGHPMTVFFTINELTG 82
+A D D G + Y ++S F+I+ TG
Sbjct: 1 SATDADSGENGKVTYSILSGNDD--GLFSIDPETG 33
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 67.7 bits (166), Expect = 4e-14
Identities = 33/94 (35%), Positives = 48/94 (51%), Gaps = 2/94 (2%)
Query: 432 YTAKIPENATAGEKVVQVKATDVDTNLGGEILYTAILGYKNSSLELDAHTGDITIANGQQ 491
Y+A +PENA G +V+ V ATD D G I Y+ + G +D TGD++ +
Sbjct: 1 YSASVPENAPVGTEVLTVTATDADLGPNGRIFYSILGGGPGGWFRIDPDTGDLSTT--KP 58
Query: 492 FDREEASEYKFQVEARDMQGLGLRTVVPLQLTIL 525
DRE EY+ V A D G L + + +T+L
Sbjct: 59 LDRESIGEYELTVLATDSGGPPLSSTTTVTITVL 92
Score = 36.9 bits (86), Expect = 0.003
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 539 FEFVLASDSRNFSERTFIKATDQDAEAPNNIVRYEIISGNYDNKFSLHPETGV 591
+ + ++ +E + ATD D PN + Y I+ G F + P+TG
Sbjct: 1 YSASVPENAPVGTEVLTVTATDAD-LGPNGRIFYSILGGGPGGWFRIDPDTGD 52
Score = 33.8 bits (78), Expect = 0.046
Identities = 29/108 (26%), Positives = 41/108 (37%), Gaps = 19/108 (17%)
Query: 312 YITHLDENSPQGTALIFAESFHTQVTDDNMGKNG--IFSLTLENNNGTFEIWPSVVERKA 369
Y + EN+P GT E TD ++G NG +S+ G F I P
Sbjct: 1 YSASVPENAPVGT-----EVLTVTATDADLGPNGRIFYSILGGGPGGWFRIDPD------ 49
Query: 370 QFTIRVRNNKNLDYERTRTLSFVIVAKEISSDSSSNLLSSQAPVLVYI 417
T + K LD E ++A +DS LSS V + +
Sbjct: 50 --TGDLSTTKPLDRESIGEYELTVLA----TDSGGPPLSSTTTVTITV 91
>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 = 32.7 bits (74), Expect = 0.11
Identities = 20/103 (19%), Positives = 34/103 (33%), Gaps = 12/103 (11%)
Query: 433 TAKIPENATAGEKVVQVKATDVDTNLGGEI-LYTAILGYKN----SSLELDAHTGDITIA 487
E + G V + T+L I S L + H+G +
Sbjct: 3 DGSAVEGRSRGSFRVSIP-----TDLIASSGEIIKISAAGKEALPSWLHWEPHSGILEGL 57
Query: 488 NGQQFDREEASEYKFQVEARDMQGLGLRTVVPLQLTILDVNDN 530
++ DRE+ + V A + +T + + D NDN
Sbjct: 58 --EKLDREDKGVHYISVSAASLGANVPQTSSVFSIEVYDENDN 98
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 33.5 bits (78), Expect = 0.38
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 443 GEKVVQVKATDVDTNLGGE 461
G+ V +V +T+ DT+LGG+
Sbjct: 205 GDGVFEVLSTNGDTHLGGD 223
>gnl|CDD|217537 pfam03404, Mo-co_dimer, Mo-co oxidoreductase dimerisation domain.
This domain is found in molybdopterin cofactor (Mo-co)
oxidoreductases. It is involved in dimer formation, and
has an Ig-fold structure.
Length = 130
Score = 31.1 bits (71), Expect = 0.61
Identities = 12/47 (25%), Positives = 22/47 (46%)
Query: 427 FTATLYTAKIPENATAGEKVVQVKATDVDTNLGGEILYTAILGYKNS 473
F ++ +P + G K + V+A D N+ E +Y + G N+
Sbjct: 74 FCWCFWSLDVPVSELLGAKEIMVRAVDESGNVQPEDMYWNVRGMMNN 120
>gnl|CDD|146960 pfam04572, Gb3_synth, Alpha 1,4-glycosyltransferase conserved
region. The glycosphingolipids (GSL) form part of
eukaryotic cell membranes. They consist of a hydrophilic
carbohydrate moiety linked to a hydrophobic ceramide
tail embedded within the lipid bilayer of the membrane.
Lactosylceramide, Gal1,4Glc1Cer (LacCer), is the common
synthetic precursor to the majority of GSL found in
vertebrates. Alpha 1.4-glycosyltransferases utilise UDP
donors and transfer the sugar to a beta-linked acceptor.
This region appears to be confined to higher eukaryotes.
No function has been yet assigned to this region.
Length = 135
Score = 29.6 bits (67), Expect = 2.4
Identities = 8/45 (17%), Positives = 13/45 (28%), Gaps = 6/45 (13%)
Query: 351 LENNNGTFEIW----PSVVERKAQFTIRVRNNKNLDYERTRTLSF 391
N NG W P +V R + + + R +
Sbjct: 18 AANFNGN--KWGHNGPGLVTRVLRKWCNTGDFAGMTRLRCGGFTV 60
>gnl|CDD|171842 PRK13023, PRK13023, bifunctional preprotein translocase subunit
SecD/SecF; Reviewed.
Length = 758
Score = 30.4 bits (68), Expect = 3.9
Identities = 13/44 (29%), Positives = 23/44 (52%)
Query: 265 GQPVILMVLAEEERKDLNEPSPQSSTATIALVFDQAINTPPYFD 308
GQPVI + L + R+ L + + Q + + A+V D + + P
Sbjct: 182 GQPVITLTLDDNGRRRLADLTAQGNENSFAIVVDNQVVSAPTVS 225
>gnl|CDD|185246 PRK15348, PRK15348, type III secretion system lipoprotein SsaJ;
Provisional.
Length = 249
Score = 29.5 bits (66), Expect = 4.5
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 13/61 (21%)
Query: 590 GVPHKWSTTQVRIYPPDSAVRNIKFLVPHSQAQ----LERKQLEDILSEMSGGRVSVVNT 645
G PH+ TT +++P + V + P + Q L+ +++E +LS+M G V+N
Sbjct: 75 GYPHRQFTTADKMFPANQLV-----VSPQEEQQKINFLKEQRIEGMLSQMEG----VINA 125
Query: 646 R 646
+
Sbjct: 126 K 126
>gnl|CDD|212676 cd10234, HSPA9-Ssq1-like_NBD, Nucleotide-binding domain of human
HSPA9 and similar proteins. This subfamily includes
human mitochondrial HSPA9 (also known as 70-kDa heat
shock protein 9, CSA; MOT; MOT2; GRP75; PBP74; GRP-75;
HSPA9B; MTHSP75; the gene encoding HSPA9 maps to
5q31.1), Escherichia coli DnaK, Saccharomyces cerevisiae
Stress-seventy subfamily Q protein 1/Ssq1p (also called
Ssc2p, Ssh1p, mtHSP70 homolog), and S. cerevisiae
Stress-Seventy subfamily C/Ssc1p (also called mtHSP70,
Endonuclease SceI 75 kDa subunit). It belongs to the
heat shock protein 70 (HSP70) family of chaperones that
assist in protein folding and assembly, and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs); for Escherichia coli DnaK, these are the
DnaJ and GrpE, respectively.
Length = 376
Score = 29.5 bits (67), Expect = 5.0
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 443 GEKVVQVKATDVDTNLGGE 461
G+ V +V AT+ DT+LGG+
Sbjct: 206 GDGVFEVLATNGDTHLGGD 224
>gnl|CDD|220006 pfam08758, Cadherin_pro, Cadherin prodomain like. Cadherins are a
family of proteins that mediate calcium dependent
cell-cell adhesion. They are activated through cleavage
of a prosequence in the late Golgi. This domain
corresponds to the folded region of the prosequence, and
is termed the prodomain. The prodomain shows structural
resemblance to the cadherin domain, but lacks all the
features known to be important for cadherin-cadherin
interactions.
Length = 90
Score = 27.6 bits (62), Expect = 5.3
Identities = 19/94 (20%), Positives = 34/94 (36%), Gaps = 12/94 (12%)
Query: 425 PVFTATLYTAKIPENATAGEKVVQVKATDVDTNLGGEILYTAILGYKNSSLELDAHT-GD 483
P F+ +YT +P G+ + +VK D + Y++S + + G
Sbjct: 4 PGFSEEVYTFLVPRRLEEGQPLGRVKFNDCKGRRR--------IQYESSDPDFKVNEDGT 55
Query: 484 ITIANGQQFDREEASEYKFQVEARDMQGLGLRTV 517
+ E+ S F V A D + + V
Sbjct: 56 VYAKRSVTLHSEQKS---FLVHAWDSETREMAEV 86
>gnl|CDD|197786 smart00553, SEP, Domain present in Saccharomyces cerevisiae Shp1,
Drosophila melanogaster eyes closed gene (eyc), and
vertebrate p47.
Length = 93
Score = 27.8 bits (62), Expect = 5.4
Identities = 19/72 (26%), Positives = 26/72 (36%), Gaps = 16/72 (22%)
Query: 236 RHLSGPKNMYLMREIRLSKPYRELHTVASGQPVILMVLAEEER----------------K 279
R P+N + IR + EL VA GQPV + V + +
Sbjct: 22 RTYDDPENAEFLESIRRGEAPLELLRVAKGQPVNVDVEDHRDEDYVAPPGAFKPFSGSGQ 81
Query: 280 DLNEPSPQSSTA 291
L P PQS +
Sbjct: 82 KLGSPGPQSLST 93
>gnl|CDD|153283 cd07599, BAR_Rvs167p, The Bin/Amphiphysin/Rvs (BAR) domain of
Saccharomyces cerevisiae Reduced viability upon
starvation protein 167 and similar proteins. BAR
domains are dimerization, lipid binding and curvature
sensing modules found in many different proteins with
diverse functions. This subfamily is composed of fungal
proteins with similarity to Saccharomyces cerevisiae
Reduced viability upon starvation protein 167 (Rvs167p)
and Schizosaccharomyces pombe Hob1 (homolog of Bin1). S.
cerevisiae Rvs167p plays a role in regulation of the
actin cytoskeleton, endocytosis, and sporulation. It
forms a heterodimer with another BAR domain protein
Rvs161p. Rvs161p and Rvs167p share common functions but
are not interchangeable. Their BAR domains cannot be
replaced with each other and the overexpression of one
cannot suppress the mutant phenotypes of the other.
Rvs167p also interacts with the GTPase activating
protein (GAP) Gyp5p, which is involved in ER to Golgi
vesicle trafficking. BAR domains form dimers that bind
to membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 216
Score = 29.1 bits (66), Expect = 5.7
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 367 RKAQFTIRVRNNKNLDYERTR 387
+K + TI+ R++K LDY++ +
Sbjct: 110 KKIRKTIKKRDHKKLDYDKLQ 130
>gnl|CDD|216106 pfam00762, Ferrochelatase, Ferrochelatase.
Length = 311
Score = 29.0 bits (66), Expect = 8.3
Identities = 14/70 (20%), Positives = 19/70 (27%), Gaps = 24/70 (34%)
Query: 285 SPQSSTATIALVFDQAINT-------------PPYFDTVQYIT--------HLDENSPQG 323
PQ S +T D+ Y+D YI L +
Sbjct: 121 YPQYSASTTGSYLDELARALKKGRPAPEVRVIRRYYDHPGYIEALADSIREALAKL-GDP 179
Query: 324 TALIFAESFH 333
L+F S H
Sbjct: 180 DRLLF--SAH 187
>gnl|CDD|212684 cd11734, Ssq1_like_NBD, Nucleotide-binding domain of Saccharomyces
cerevisiae Ssq1 and similar proteins. Ssq1p (also
called Stress-seventy subfamily Q protein 1, Ssc2p,
Ssh1p, mtHSP70 homolog) belongs to the heat shock
protein 70 (HSP70) family of chaperones that assist in
protein folding and assembly, and can direct incompetent
"client" proteins towards degradation. Typically, HSP70s
have a nucleotide-binding domain (NBD) and a
substrate-binding domain (SBD). The nucleotide sits in a
deep cleft formed between the two lobes of the NBD. The
two subdomains of each lobe change conformation between
ATP-bound, ADP-bound, and nucleotide-free states. ATP
binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). S. cerevisiae Ssq1p is a mitochondrial
chaperone that is involved in iron-sulfur (Fe/S) center
biogenesis. Ssq1p plays a role in the maturation of
Yfh1p, a nucleus-encoded mitochondrial protein involved
in iron homeostasis (and a homolog of human frataxin,
implicated in the neurodegenerative disease,
Friedreich's ataxia).
Length = 373
Score = 29.0 bits (65), Expect = 9.6
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 446 VVQVKATDVDTNLGGEILYTAILGY 470
V +VKAT+ DT LGGE AI+ Y
Sbjct: 210 VFEVKATNGDTMLGGEDFDNAIVQY 234
>gnl|CDD|176960 CHL00017, ndhH, NADH dehydrogenase subunit 7.
Length = 393
Score = 28.9 bits (65), Expect = 9.9
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 22 PPIFINIQPVIQLAPNLTMNDVLTKITAID 51
PP FIN+Q + QL + + D++T + +ID
Sbjct: 356 PPGFINLQILPQLVKRMKLADIMTILGSID 385
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
0.318 0.134 0.385
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,999,538
Number of extensions: 3245215
Number of successful extensions: 2447
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2440
Number of HSP's successfully gapped: 30
Length of query: 653
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 550
Effective length of database: 6,369,140
Effective search space: 3503027000
Effective search space used: 3503027000
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 (21.7 bits)
S2: 62 (27.8 bits)