RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10428
(309 letters)
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of
Eumetazoan signaling molecules, often in tandem
arrangements. May be responsible for specific
protein-protein interactions, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of PDZ domains an
N-terminal beta-strand forms the peptide-binding groove
base, a circular permutation with respect to PDZ
domains found in proteases.
Length = 82
Score = 85.3 bits (212), Expect = 3e-21
Identities = 31/83 (37%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 9 VRLCHILKWTDFDGYGFNLHGEKG-KTGQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNIC 67
VR + K G GF+L G K G ++ +V+ G PAE GL+ GD I+EVN V++
Sbjct: 1 VRTVTLRK-DPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVE 59
Query: 68 NENHNQVVQRIKAVPDETKLLVV 90
H + V+ +K DE L V
Sbjct: 60 GLTHEEAVELLKNSGDEVTLTVR 82
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some
PDZs have been shown to bind C-terminal polypeptides;
others appear to bind internal (non-C-terminal)
polypeptides. Different PDZs possess different binding
specificities.
Length = 85
Score = 80.5 bits (199), Expect = 3e-19
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 3/84 (3%)
Query: 8 VVRLCHILKWTDFDGYGFNLHGEKGKT-GQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNI 66
RL + K G GF+L G K + G + V GSPA AGL+ GD I+EVN ++
Sbjct: 1 EPRLVELEK--GGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSV 58
Query: 67 CNENHNQVVQRIKAVPDETKLLVV 90
H + V +K + L V+
Sbjct: 59 EGLTHLEAVDLLKKAGGKVTLTVL 82
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 65.7 bits (161), Expect = 5e-14
Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 22 GYGFNLHGEK-GKTGQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRIKA 80
G GF+L G G G ++ +V G AEA GL+EGD I+ +N ++ N +H++ V +K
Sbjct: 11 GLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSHDEAVLALKG 70
Query: 81 VPDETKLLV 89
E L +
Sbjct: 71 SGGEVTLTI 79
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization
through PDZ-PDZ domain interactions adds to the
domain's versatility, and PDZ domain-mediated
interactions may be modulated dynamically through
target phosphorylation. Some PDZ domains play a role in
scaffolding supramolecular complexes. PDZ domains are
found in diverse signaling proteins in bacteria,
archebacteria, and eurkayotes. This CD contains two
distinct structural subgroups with either a N- or
C-terminal beta-strand forming the peptide-binding
groove base. The circular permutation placing the
strand on the N-terminus appears to be found in
Eumetazoa only, while the C-terminal variant is found
in all three kingdoms of life, and seems to co-occur
with protease domains. PDZ domains have been named
after PSD95(post synaptic density protein), DlgA
(Drosophila disc large tumor suppressor), and ZO1, a
mammalian tight junction protein.
Length = 70
Score = 60.0 bits (146), Expect = 6e-12
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 21 DGYGFNLHGEKGKTGQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRIKA 80
G GF++ G + G + V+ GSPAE AGL+ GD I+ VN ++ N V + +K
Sbjct: 1 GGLGFSIRGG-TEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKK 59
Query: 81 VPDET-KLLVV 90
E L V
Sbjct: 60 EVGEKVTLTVR 70
>gnl|CDD|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 90
Score = 51.5 bits (124), Expect = 8e-09
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 29 GEKGKTGQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRIKA--VPDETK 86
G K G + VD GSPA AGLK GD I+ VN + ++ + + + D+
Sbjct: 19 GLKDTKGVLVASVDPGSPAAKAGLKPGDVILAVNGKPV--KSVADLRRALAELKPGDKVT 76
Query: 87 LLVV 90
L V+
Sbjct: 77 LTVL 80
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be
responsible for substrate recognition and/or binding,
as most PDZ domains bind C-terminal polypeptides, and
binding to internal (non-C-terminal) polypeptides and
even to lipids has been demonstrated. In this subfamily
of protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 79
Score = 47.6 bits (114), Expect = 2e-07
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 37 YIGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRIKAVPDETKLLVV 90
IG+V GSPA AGLK GD I+ +N I ++ +V ++ P + L V
Sbjct: 15 VIGEVVPGSPAAKAGLKAGDRILAINGQKI--KSWEDLVDAVQENPGKPLTLTV 66
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 46.4 bits (111), Expect = 1e-05
Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 35 GQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRIKAVPDETK 86
G + +V GSPAE AGLK GD I VN I + + + I + K
Sbjct: 258 GALVAQVLPGSPAEKAGLKAGDVITSVNGKPI--SSFADLRRAIGTLKPGKK 307
Score = 40.7 bits (96), Expect = 8e-04
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 38 IGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENH-NQVVQRIKAVPDETKLLVV 90
+ KV GSPA AGL+ GD I+ VN + + +V+ R K LL++
Sbjct: 366 VTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKK-GGRVALLIL 418
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function
in posttranslational protein processing, maturation,
and disassembly or degradation, in Bacteria, Archaea,
and plant chloroplasts. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 85
Score = 40.7 bits (96), Expect = 6e-05
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 38 IGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRIK 79
I V GSPA AG+K GD I+ ++ + + VV+ ++
Sbjct: 17 ITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLR 58
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 38.4 bits (90), Expect = 4e-04
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 34 TGQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNI 66
TG + V EGSPA AGLK GD I+ ++ +
Sbjct: 13 TGVTVVSVKEGSPAAKAGLKPGDIILSIDGKKV 45
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 41.0 bits (96), Expect = 5e-04
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 28 HGEKGKTGQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRI 78
G G + V GSPA AG+K GD I VN + + + +V +
Sbjct: 264 LGLPVAAGAVVLGVLPGSPAAKAGIKAGDIITAVNGKPV--ASLSDLVAAV 312
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 39.2 bits (92), Expect = 0.002
Identities = 13/39 (33%), Positives = 25/39 (64%)
Query: 41 VDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRIK 79
+GSPA AG+K GD II+++ ++ + ++ V+ I+
Sbjct: 119 PIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIR 157
>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc). A C-terminal peptidase
with different substrates in different species including
processing of D1 protein of the photosystem II reaction
center in higher plants and cleavage of a peptide of 11
residues from the precursor form of penicillin-binding
protein in E.coli E.coli and H influenza have the most
distal branch of the tree and their proteins have an
N-terminal 200 amino acids that show no homology to
other proteins in the database [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Protein fate, Protein modification and repair].
Length = 334
Score = 38.5 bits (90), Expect = 0.003
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 19 DFDGYGFNLHGEKGKTGQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRI 78
+G G + + G+ I EGSPAE AG+K GD II++N ++ + + V I
Sbjct: 49 SLEGIGIQVGMDDGEI--VIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALI 106
Query: 79 K 79
+
Sbjct: 107 R 107
>gnl|CDD|232801 TIGR00054, TIGR00054, RIP metalloprotease RseP. Members of this
nearly universal bacterial protein family are regulated
intramembrane proteolysis (RIP) proteases. Older and
synonymous gene symbols include yaeL in E. coli, mmpA in
Caulobacter crescentus, etc. This family includes a
region that hits the PDZ domain, found in a number of
proteins targeted to the membrane by binding to a
peptide ligand. The N-terminal region of this family
contains a perfectly conserved motif HEXGH as found in a
number of metalloproteinases, where the Glu is the
active site and the His residues coordinate the metal
cation [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 419
Score = 36.7 bits (85), Expect = 0.013
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 10/72 (13%)
Query: 38 IGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRIKAVPDETKLLVVDVASEEY 97
+ V SPAE AGLKEGD+I +N + + V +K P + +D+
Sbjct: 206 LSDVTPNSPAEKAGLKEGDYIQSINGEKL--RSWTDFVSAVKENPGK----SMDIK---- 255
Query: 98 FKSNNITISSSL 109
+ N T+S SL
Sbjct: 256 VERNGETLSISL 267
>gnl|CDD|234035 TIGR02860, spore_IV_B, stage IV sporulation protein B. SpoIVB, the
stage IV sporulation protein B of endospore-forming
bacteria such as Bacillus subtilis, is a serine
proteinase, expressed in the spore (rather than mother
cell) compartment, that participates in a proteolytic
activation cascade for Sigma-K. It appears to be
universal among endospore-forming bacteria and occurs
nowhere else [Cellular processes, Sporulation and
germination].
Length = 402
Score = 36.2 bits (84), Expect = 0.020
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 39 GKVDEGSPAEAAGLKEGDHIIEVNSVNICNENH 71
GK+ SP E AG++ GD I+++N I N +
Sbjct: 120 GKIH--SPGEEAGIQIGDRILKINGEKIKNMDD 150
>gnl|CDD|223821 COG0750, COG0750, Predicted membrane-associated Zn-dependent
proteases 1 [Cell envelope biogenesis, outer membrane].
Length = 375
Score = 35.9 bits (83), Expect = 0.021
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 7/41 (17%)
Query: 22 GYGFNLHGEKGKTGQYIGKVDEGSPAEAAGLKEGDHIIEVN 62
G +G+V S A AGL+ GD I+ V+
Sbjct: 124 GLVPVASP-------VVGEVAPKSAAALAGLRPGDRIVAVD 157
>gnl|CDD|234386 TIGR03900, prc_long_Delta, putative carboxyl-terminal-processing
protease, deltaproteobacterial. This model describes a
multidomain protein of about 1070 residues, restricted
to the order Myxococcales in the Deltaproteobacteria.
Members contain a PDZ domain (pfam00595), an S41 family
peptidase domain (pfam03572), and an SH3 domain
(pfam06347). A core region of this family, including PDZ
and S41 regions, is described by TIGR00225, C-terminal
processing peptidase, which recognizes the Prc protease.
The species distribution of this family approximates
that of largely Deltaproteobacterial C-terminal putative
protein-sorting domain, TIGR03901, analogous to LPXTG
and PEP-CTERM, but the co-occurrence may reflect shared
restriction to the Myxococcales rather than a
substrate/target relationship.
Length = 973
Score = 34.8 bits (80), Expect = 0.070
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 40 KVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRIKAVPD 83
+V G+PA AGL+ D I++++ + N N V R++ PD
Sbjct: 157 RVIPGTPAARAGLQRNDVIVKIDDESTVNMTLNDAVGRLRGPPD 200
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 34.3 bits (79), Expect = 0.084
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 40 KVDEGSPAEAAGLKEGDHIIEVNSVNI 66
+V S A AGL+ GD I++V+ +
Sbjct: 227 EVQPNSAASKAGLQAGDRIVKVDGQPL 253
>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase;
Provisional.
Length = 481
Score = 32.9 bits (74), Expect = 0.20
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 160 PATSGNSNHVEKPSSEESNNSTNQSLTNNTPTPTTNTNNTTNHENQNNLNLNMSA 214
PA S N+N + + N+ + +TP+ TNTN +N +N N N +
Sbjct: 306 PAPSTNTN---ANKTNTNTNTNTNNTNTSTPSKNTNTNTNSNTNTNSNTNANQGS 357
Score = 31.3 bits (70), Expect = 0.71
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 160 PATSGNSNHVEKPSSEESNNSTNQSLTNNTPTPTTNTNNTTNHENQN----NLNLNMSAK 215
P+T+ N+N ++ +NN+ + + NT T T + NT ++ N N N N N SA
Sbjct: 308 PSTNTNANKTNTNTNTNTNNTNTSTPSKNTNTNTNSNTNTNSNTNANQGSSNNNSNSSAS 367
Query: 216 ELRAK 220
+ A+
Sbjct: 368 AIIAE 372
Score = 29.8 bits (66), Expect = 2.2
Identities = 12/56 (21%), Positives = 26/56 (46%)
Query: 159 TPATSGNSNHVEKPSSEESNNSTNQSLTNNTPTPTTNTNNTTNHENQNNLNLNMSA 214
+ T+ N + ++ + N++ S NT T + N+ + NQ + N N ++
Sbjct: 309 STNTNANKTNTNTNTNTNNTNTSTPSKNTNTNTNSNTNTNSNTNANQGSSNNNSNS 364
Score = 29.4 bits (65), Expect = 2.7
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 243 STNQSLTNNTPTPTTNTNNTTNHENQNNLNLN 274
+ + NT TP+ NTN TN N N N
Sbjct: 321 TNTNTNNTNTSTPSKNTNTNTNSNTNTNSNTN 352
Score = 28.6 bits (63), Expect = 4.8
Identities = 24/119 (20%), Positives = 39/119 (32%), Gaps = 31/119 (26%)
Query: 159 TPATSGNSNHVEKPSSEESNNSTNQSLTNNTPT--------PTTNTNNTTNHENQNNLNL 210
P N+N ++E+ +T Q PT P+TNTN + N N
Sbjct: 268 APVVKENTN-TNTATTEKKETTTQQQTAPKAPTEAAKPAPAPSTNTNANKTNTNTNTNTN 326
Query: 211 NMSAKELRAKLASRKKYDPKKDYLDIKKKYDISTNQSLTNNTPTPTTNTNNTTNHENQN 269
N + P K+ + + +N TN N +++ N N
Sbjct: 327 NTNTST------------PSKN----------TNTNTNSNTNTNSNTNANQGSSNNNSN 363
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 32.8 bits (75), Expect = 0.22
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 24 GFNLHGEKGKTGQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNICN 68
G L + G G + V G+PA GLK+GD II N + N
Sbjct: 398 GAELSNKGGDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKN 442
>gnl|CDD|238491 cd00991, PDZ_archaeal_metalloprotease, PDZ domain of archaeal
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be
responsible for substrate recognition and/or binding,
as most PDZ domains bind C-terminal polypeptides, and
binding to internal (non-C-terminal) polypeptides and
even to lipids has been demonstrated. In this subfamily
of protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 79
Score = 30.4 bits (69), Expect = 0.23
Identities = 13/25 (52%), Positives = 14/25 (56%)
Query: 38 IGKVDEGSPAEAAGLKEGDHIIEVN 62
I V GSPAE A L GD I +N
Sbjct: 14 IVGVIVGSPAENAVLHTGDVIYSIN 38
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 32.3 bits (74), Expect = 0.29
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 40 KVDEGSPAEAAGLKEGDHIIEVN 62
+V PA AG++ D II VN
Sbjct: 285 EVSPDGPAAKAGIQVNDLIISVN 307
>gnl|CDD|238490 cd00990, PDZ_glycyl_aminopeptidase, PDZ domain associated with
archaeal and bacterial M61 glycyl-aminopeptidases. May
be responsible for substrate recognition and/or
binding, as most PDZ domains bind C-terminal
polypeptides, and binding to internal (non-C-terminal)
polypeptides and even to lipids has been demonstrated.
In this subfamily of protease-associated PDZ domains a
C-terminal beta-strand is presumed to form the
peptide-binding groove base, a circular permutation
with respect to PDZ domains found in Eumetazoan
signaling proteins.
Length = 80
Score = 30.1 bits (68), Expect = 0.32
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 8/69 (11%)
Query: 23 YGFNLHGEKGKTGQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENHNQVVQRIK-AV 81
G L E+G + V + SPA+ AGL GD ++ VN + + + R+K
Sbjct: 3 LGLTLDKEEGLG--KVTFVRDDSPADKAGLVAGDELVAVNGWRV-----DALQDRLKEYQ 55
Query: 82 PDETKLLVV 90
+ L V
Sbjct: 56 AGDPVELTV 64
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 31.9 bits (72), Expect = 0.42
Identities = 34/123 (27%), Positives = 44/123 (35%), Gaps = 17/123 (13%)
Query: 166 SNHVEKPSSEESNNSTNQSLTNNTPTPTTNTNNTTNHENQN-------NLNLNMSAKELR 218
S P+ + +T +NTPT TT TN NQ N N ++
Sbjct: 350 SPTPASPNVRNTQIATQVPNPDNTPT-TTAVPGITNSSNQGDPQASTFNGVPNANSSGFA 408
Query: 219 AKLASRKKYDPKKDYLDIKKKYDISTNQSLTNNTPTPTTN--TNNT-------TNHENQN 269
A P L I IS + S TN + TPTT +N+T N N
Sbjct: 409 AHTQDLSSVIPGWTMLPIPGTRRISQSTSTTNPSATPTTGDPSNSTYGGPQTFPNSGNNP 468
Query: 270 NLN 272
N N
Sbjct: 469 NFN 471
>gnl|CDD|223118 COG0040, HisG, ATP phosphoribosyltransferase [Amino acid transport
and metabolism].
Length = 290
Score = 31.4 bits (72), Expect = 0.55
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 11/66 (16%)
Query: 41 VDEGSPAEAAGLKEGDHIIEVNSVNICNENH---------NQVVQRIKAV--PDETKLLV 89
V G+ +A GLKE + I + ++ I N +Q+V R+K V +K ++
Sbjct: 163 VSTGTTLKANGLKEIEVIYDSSARLIVNAKASLKDKQELIDQLVTRLKGVIEARGSKYIM 222
Query: 90 VDVASE 95
++ E
Sbjct: 223 LNAPRE 228
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 31.3 bits (71), Expect = 0.68
Identities = 27/161 (16%), Positives = 56/161 (34%), Gaps = 11/161 (6%)
Query: 105 ISSSLPDIVHLRTPATSGNSNHVEKPSSEAASEEYFKSNNITISSSLPDIVHLRTPATSG 164
+ + DI P S S + +S+++ + + +
Sbjct: 126 LFNLNSDISDYEQPRNSEKSTNDSNKNSDSSIKNDTDTQSSKQDK---------ADNQKA 176
Query: 165 NSNHVEKPSSEESNNSTNQSLTNNTPTPTTNTNNTTNHENQNNLNLNMSAKELRAKLA-- 222
S++ KPS+ ++ + N +++T N ++ + N +MS L + L
Sbjct: 177 PSSNNTKPSTSNKQPNSPKPTQPNQSNSQPASDDTANQKSSSKDNQSMSDSALDSILDQY 236
Query: 223 SRKKYDPKKDYLDIKKKYDISTNQSLTNNTPTPTTNTNNTT 263
S +KDY KK T+ + PT + +
Sbjct: 237 SEDAKKTQKDYASQSKKDKTETSNTKNPQLPTQDELKHKSK 277
Score = 27.8 bits (62), Expect = 8.7
Identities = 21/142 (14%), Positives = 44/142 (30%), Gaps = 2/142 (1%)
Query: 157 LRTPATSGNSNHVEKPSSEESNNSTNQSLTNNTPTPTTNTNNTTNHENQNNLNLNMSAKE 216
L P + + + + P + + +T+ + T+ ++ + + + N N S ++
Sbjct: 15 LVLPTLTSPTAYADDPQKDSTAKTTSHDSKKSNDDETSKDTSSKDTDKAD--NNNTSNQD 72
Query: 217 LRAKLASRKKYDPKKDYLDIKKKYDISTNQSLTNNTPTPTTNTNNTTNHENQNNLNLNMS 276
K S I Y ++ + N + QN NLN
Sbjct: 73 NNDKKFSTIDSSTSDSNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSD 132
Query: 277 AKELRAKLASRKKYDPKKDYLD 298
+ S K + D
Sbjct: 133 ISDYEQPRNSEKSTNDSNKNSD 154
>gnl|CDD|115579 pfam06933, SSP160, Special lobe-specific silk protein SSP160. This
family consists of several special lobe-specific silk
protein SSP160 sequences which appear to be specific to
Chironomus (Midge) species.
Length = 758
Score = 31.3 bits (70), Expect = 0.71
Identities = 15/42 (35%), Positives = 25/42 (59%)
Query: 166 SNHVEKPSSEESNNSTNQSLTNNTPTPTTNTNNTTNHENQNN 207
+N +S ++NST+ S TN+ T TTN+ +TN + +N
Sbjct: 277 ANGSASANSTSNSNSTSNSTTNSNSTTTTNSTTSTNSTSSSN 318
Score = 28.2 bits (62), Expect = 7.2
Identities = 15/62 (24%), Positives = 31/62 (50%)
Query: 153 DIVHLRTPATSGNSNHVEKPSSEESNNSTNQSLTNNTPTPTTNTNNTTNHENQNNLNLNM 212
+I +++ + S + N +S ++NST + + + TT T+N+T+ N + L
Sbjct: 94 NIQAIQSGSGSASGNSSSSANSTSNSNSTTSNNSTTSSNSTTTTSNSTSSSNSTSSGLTS 153
Query: 213 SA 214
A
Sbjct: 154 GA 155
>gnl|CDD|152310 pfam11874, DUF3394, Domain of unknown function (DUF3394). This
domain is functionally uncharacterized. This domain is
found in bacteria. This presumed domain is about 190
amino acids in length. This domain is found associated
with pfam06808.
Length = 183
Score = 30.6 bits (70), Expect = 0.73
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 1 MSEDKTPVVRLCHILKWTDFDGYGFNLHGEKGKTGQYIGKVDEGSPAEAAGLKEGDHIIE 60
+ E RL + G L E GK + +V+ GSPAE AG+ I+E
Sbjct: 100 LGEGADGEERL---------EDAGLTLREEGGKV--IVDEVEFGSPAEKAGIDFDWEIVE 148
Query: 61 V 61
V
Sbjct: 149 V 149
>gnl|CDD|215411 PLN02768, PLN02768, AMP deaminase.
Length = 835
Score = 31.4 bits (71), Expect = 0.73
Identities = 21/105 (20%), Positives = 41/105 (39%), Gaps = 6/105 (5%)
Query: 158 RTPATSGNS-NHVEKPSSEESNNSTNQSLTNNTPTPTTNTNNTTNHENQNNLNLNMSAKE 216
++P S ++ VE S++ +N T+ + T T +H + N + + A
Sbjct: 135 KSPVASASAFESVE--GSDDEDNLTDNEKLDTTYLHTNGNVELPDHADANGEQIPIPASS 192
Query: 217 L-RAKLASRKKYDPKKDYL--DIKKKYDISTNQSLTNNTPTPTTN 258
+ R+ S + + D + DI +K N TP +
Sbjct: 193 MIRSHSVSGDLHGVQPDPIAADILRKEPEQETFVRLNITPLEVPS 237
>gnl|CDD|203029 pfam04495, GRASP55_65, GRASP55/65 PDZ-like domain. GRASP55
(Golgi re-assembly stacking protein of 55 kDa) and
GRASP65 (a 65 kDa) protein are highly homologous.
GRASP55 is a component of the Golgi stacking machinery.
GRASP65, an N-ethylmaleimide- sensitive membrane
protein required for the stacking of Golgi cisternae in
a cell-free system. This region appears to be related
to the PDZ domain.
Length = 136
Score = 29.9 bits (68), Expect = 0.78
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 41 VDEGSPAEAAGLKE-GDHII 59
V SPA AGL+ D+II
Sbjct: 48 VHPNSPAALAGLQPYSDYII 67
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 30.9 bits (70), Expect = 0.87
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 29 GEKGKTGQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNICNENH 71
+G + I V G PA AGL GD I+ +N ++ + +
Sbjct: 458 KSEGG-HEKITFVFPGGPAYKAGLSPGDKIVAINGISDQLDRY 499
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 30.7 bits (69), Expect = 1.0
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 32 GKTGQYIGKVDEGSPAEAAGLKEGDHIIEVN 62
G G I +V +GSPA AGL++ D II VN
Sbjct: 388 GTKGIKIDEVVKGSPAAQAGLQKDDVIIGVN 418
>gnl|CDD|215637 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
Length = 1634
Score = 30.7 bits (69), Expect = 1.2
Identities = 18/109 (16%), Positives = 34/109 (31%), Gaps = 22/109 (20%)
Query: 181 TNQSLTNNTPTPTTNTNNTTNHENQNNLNLNMSAKELRAKL----------------ASR 224
+++ N T ++N T + NL ++SA E A+
Sbjct: 312 WCKTVQNEG-TAFNSSNATLYALMEGNLAQSVSATEAAMPFNDTLVDWAYRANGYCCANS 370
Query: 225 KKYDPKKDYLDIKKKYDISTNQSLTNNTPTPTTNTNNTTNHENQNNLNL 273
P Y+ + + + T N + N N N+N+
Sbjct: 371 PDLMPS-----TWYGYNFNHSSAWTANFSNTGIASGNVYWTRNLFNVNM 414
>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope
glycoprotein (BLLF1). This family consists of the BLLF1
viral late glycoprotein, also termed gp350/220. It is
the most abundantly expressed glycoprotein in the viral
envelope of the Herpesviruses and is the major antigen
responsible for stimulating the production of
neutralising antibodies in vivo.
Length = 830
Score = 30.1 bits (67), Expect = 1.9
Identities = 23/111 (20%), Positives = 41/111 (36%), Gaps = 12/111 (10%)
Query: 104 TISSSLPDIVH----LRTPATSGNSNHVEKPSSEAASEEYFKSNNITISSSLPDIVHLRT 159
T SS+LP+ + + S + A S K+++ ++S IV T
Sbjct: 477 TTSSTLPEDTSPTSRTTSATPNATSPTPAVTTPNATSPTTQKTSDTPNATSPTPIVIGVT 536
Query: 160 P--------ATSGNSNHVEKPSSEESNNSTNQSLTNNTPTPTTNTNNTTNH 202
TS + + + E N+TN + + P+ T+ T H
Sbjct: 537 TTATSPPTGTTSVPNATSPQVTEESPVNNTNTPVVTSAPSVLTSAVTTGQH 587
>gnl|CDD|238486 cd00986, PDZ_LON_protease, PDZ domain of ATP-dependent LON serine
proteases. Most PDZ domains bind C-terminal
polypeptides, though binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this bacterial subfamily of
protease-associated PDZ domains a C-terminal
beta-strand is thought to form the peptide-binding
groove base, a circular permutation with respect to PDZ
domains found in Eumetazoan signaling proteins.
Length = 79
Score = 27.4 bits (61), Expect = 2.6
Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 35 GQYIGKVDEGSPAEAAGLKEGDHIIEVNSVNI 66
G Y+ V EG PA LK GDHII V+
Sbjct: 9 GVYVTSVVEGMPAAGK-LKAGDHIIAVDGKPF 39
>gnl|CDD|223110 COG0031, CysK, Cysteine synthase [Amino acid transport and
metabolism].
Length = 300
Score = 28.7 bits (65), Expect = 3.5
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 11/66 (16%)
Query: 6 TPVVRLCHILKWTDFDGY----GFNLHGE-KGKTGQYIGKVDEGSPAEAAG-LKEGDHII 59
TP+VRL + T + Y FN G K + Y+ +++ AE G LK G I+
Sbjct: 12 TPLVRLNRLSPGTGVEIYAKLESFNPGGSVKDRIALYM--IED---AEKRGLLKPGGTIV 66
Query: 60 EVNSVN 65
E S N
Sbjct: 67 EATSGN 72
>gnl|CDD|204902 pfam12396, DUF3659, Protein of unknown function (DUF3659). This
domain family is found in bacteria and eukaryotes, and
is approximately 70 amino acids in length.
Length = 64
Score = 26.3 bits (59), Expect = 4.2
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 13/56 (23%)
Query: 32 GKTGQYIGKVDEGSPAEAAGLK---EGDHIIEVNSVNICNENHNQVVQRIKAVPDE 84
K G +G+V EG P + AG K +GD I +++ N V+ R + +P+E
Sbjct: 17 DKDGNVVGRVVEGDPKKLAGRKVDEDGD---------ILDKDGN-VIGRAELIPEE 62
>gnl|CDD|167650 PRK03967, PRK03967, histidinol-phosphate aminotransferase;
Provisional.
Length = 337
Score = 28.5 bits (64), Expect = 4.6
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 54 EGDHIIEVNS----VNICNENH----NQVVQRIKAVPDETKLLVVDVASEEYFKSNNITI 105
+G+ I E V IC+ N+ Q + I V + K +V+D A E+ + I +
Sbjct: 130 DGERIAEKAKNASAVFICSPNNPTGNLQPEEEILKVLETGKPVVLDEAYAEFSGKSLIGL 189
Query: 106 SSSLPDIVHLRT 117
P+++ LRT
Sbjct: 190 IDEYPNLILLRT 201
>gnl|CDD|114270 pfam05539, Pneumo_att_G, Pneumovirinae attachment membrane
glycoprotein G.
Length = 408
Score = 28.5 bits (63), Expect = 4.8
Identities = 16/144 (11%), Positives = 40/144 (27%), Gaps = 3/144 (2%)
Query: 132 SEAASEEYFKSNNITISSSLPDIVHLRTPATSGNSNHVEKPSSEESNNSTNQSLTNNTPT 191
S+ + + +++ + T G + E S +
Sbjct: 191 SQVTPQSQPATQGHQTATANQRLSSTEPVGTQGTTTSSNPEPQTEPPPSQRGPSGSPQHP 250
Query: 192 PTTNTNNTTNHENQNNLNLNMS---AKELRAKLASRKKYDPKKDYLDIKKKYDISTNQSL 248
P+T + + + + A R S P + + T +
Sbjct: 251 PSTTSQDQSTTGDGQEHTQRRKTPPATSNRRSPHSTATPPPTTKRQETGRPTPRPTATTQ 310
Query: 249 TNNTPTPTTNTNNTTNHENQNNLN 272
+ ++P ++ N QN ++
Sbjct: 311 SGSSPPHSSPPGVQANPTTQNLVD 334
>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional.
Length = 331
Score = 28.1 bits (63), Expect = 6.2
Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 6/62 (9%)
Query: 159 TPATSGNSNHVEKPSSEESNNSTNQS------LTNNTPTPTTNTNNTTNHENQNNLNLNM 212
PA N V PS + + + P PT +T + N L +N
Sbjct: 199 APAVDPQQNAVVAPSQANVDTAATPAPAAPATPDGAAPLPTDQAGVSTPAADPNALVMNF 258
Query: 213 SA 214
+A
Sbjct: 259 TA 260
>gnl|CDD|188493 TIGR03978, rSAM_paired_1, His-Xaa-Ser system radical SAM maturase
HxsB. This model describes the upstream member, HxsB,
of a pair of uncharacterized radical SAM proteins,
regularly found in the context of a small protein with
four or more repeats of the tripeptide His-Xaa-Ser
(HXS). This enzyme appears to be part of a peptide
modification system.
Length = 466
Score = 28.0 bits (63), Expect = 7.0
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 96 EYFKSNNITISSSL--PDIVHLRT-PATSGNSNH 126
++FK + + IS+SL P+ +H + P GNS
Sbjct: 185 DFFKDHKVLISTSLDGPEALHNKNRPLPGGNSYE 218
Score = 28.0 bits (63), Expect = 7.0
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 138 EYFKSNNITISSSL--PDIVHLRT-PATSGNSNH 168
++FK + + IS+SL P+ +H + P GNS
Sbjct: 185 DFFKDHKVLISTSLDGPEALHNKNRPLPGGNSYE 218
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 28.0 bits (62), Expect = 7.1
Identities = 14/86 (16%), Positives = 27/86 (31%)
Query: 131 SSEAASEEYFKSNNITISSSLPDIVHLRTPATSGNSNHVEKPSSEESNNSTNQSLTNNTP 190
SS A + + S + R + E S E + + +T
Sbjct: 135 SSAARRSSGEHRSAASSQGSRHTKLKKRKNIHNLKRRSPELSSKREVSFTLESPSVPDTA 194
Query: 191 TPTTNTNNTTNHENQNNLNLNMSAKE 216
T NN + +++ + + S E
Sbjct: 195 TRVKEGNNGGSTKSRGVSSEDNSEGE 220
>gnl|CDD|233574 TIGR01782, TonB-Xanth-Caul, TonB-dependent receptor. This model
represents a family of TonB-dependent outer-membrane
receptors which are found mainly in Xanthomonas and
Caulobacter. These appear to represent the expansion of
a paralogous family in that the 22 X. axonopodis (21 in
X. campestris) and 18 C. crescentus sequences are more
closely related to each other than any of the many
TonB-dependent receptors found in other species. In
fact, the Crescentus and Xanthomonas sequences are
inseparable on a phylogenetic tree using a PAM-weighted
neighbor-joining method, indicating that one of the two
genuses may have acquired this set of receptors from the
other. The mechanism by which this family is shared
between Xanthomonas, a gamma proteobacterial plant
pathogen and Caulobacter, an alpha proteobacterial
aquatic organism is unclear [Transport and binding
proteins, Porins].
Length = 845
Score = 28.1 bits (63), Expect = 7.5
Identities = 20/135 (14%), Positives = 35/135 (25%), Gaps = 16/135 (11%)
Query: 177 SNNSTNQSLTNNTPTPTTNTNNTTNHENQNN--------LNLNMSAKELRAKLA-----S 223
+ ++NQ+ T+ T N E + N L L R L S
Sbjct: 273 TVITSNQTATSGALVQGTVANLQILVEARYNEEKETTTSLTLGGEWTGDRWTLDGDLGYS 332
Query: 224 RKKYDPKKDYLDIKKKYD--ISTNQSLTNNTPTPTTNTNNTTNHENQNNLNLNMSAKELR 281
+ D + T T T + N N + ++
Sbjct: 333 KATRDRPDRVTRFFTAPTPGYDFDYR-GGPTLTLGTPADGDDASNYTNPANGELRRTQIS 391
Query: 282 AKLASRKKYDPKKDY 296
+ A + + D
Sbjct: 392 YQKAEDSEDAAQLDA 406
>gnl|CDD|240427 PTZ00470, PTZ00470, glycoside hydrolase family 47 protein;
Provisional.
Length = 522
Score = 28.2 bits (63), Expect = 7.6
Identities = 11/45 (24%), Positives = 18/45 (40%)
Query: 176 ESNNSTNQSLTNNTPTPTTNTNNTTNHENQNNLNLNMSAKELRAK 220
+ + + ++ N NN N N NN N ++K R K
Sbjct: 4 LREHLSVHNNADDNYNNNNNNNNQINSNNPNNNGNNQASKLPRGK 48
>gnl|CDD|235682 PRK06041, PRK06041, flagellar assembly protein J; Reviewed.
Length = 553
Score = 28.0 bits (63), Expect = 7.7
Identities = 7/35 (20%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 274 NMSAKELRAKLASRKKYDPKKDYLDIKKKYDIVQK 308
++ E+ L+ +++Y +K Y +V K
Sbjct: 90 DIDRDEIFRILSEKEEYGALAKE--FRKIYVLVDK 122
>gnl|CDD|234999 PRK02101, PRK02101, hypothetical protein; Validated.
Length = 255
Score = 27.1 bits (61), Expect = 10.0
Identities = 7/13 (53%), Positives = 12/13 (92%)
Query: 88 LVVDVASEEYFKS 100
++V++AS EYFK+
Sbjct: 164 VLVNLASSEYFKA 176
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
0.305 0.123 0.338
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,783,267
Number of extensions: 1326451
Number of successful extensions: 1244
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1160
Number of HSP's successfully gapped: 133
Length of query: 309
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 212
Effective length of database: 6,635,264
Effective search space: 1406675968
Effective search space used: 1406675968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 59 (26.6 bits)