RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12296
(433 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 = 88.0 bits (219), Expect = 1e-21
Identities = 34/72 (47%), Positives = 50/72 (69%), Gaps = 1/72 (1%)
Query: 3 NGTLGFSIRGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATHSEVLQLI 62
G LGFS+RGG++ G+FVS VEP AER GL +GD+I+ +NG +E TH E ++L+
Sbjct: 11 GGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELL 70
Query: 63 -HSQNIISLKVR 73
+S + ++L VR
Sbjct: 71 KNSGDEVTLTVR 82
Score = 54.9 bits (133), Expect = 7e-10
Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 110 ITLEVPPHGKLGCGICKGPQWKPGIFVQFTKDACVAKDAGLKCGDQILACNGVKFSPDVT 169
+TL P G LG + G GIFV + A+ GL+ GD+IL NGV +T
Sbjct: 4 VTLRKDPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVE-GLT 62
Query: 170 FEHAVSVMKSSCL-LELLV 187
E AV ++K+S + L V
Sbjct: 63 HEEAVELLKNSGDEVTLTV 81
>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 = 78.2 bits (193), Expect = 4e-18
Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 4 GTLGFSIRGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATHSEVLQLIH 63
G LGFS+ GG++ GV VS+V P S A ++GL +GD I+ +NG +E TH E + L+
Sbjct: 12 GGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLK 71
Query: 64 -SQNIISLKVRSVG 76
+ ++L V G
Sbjct: 72 KAGGKVTLTVLRGG 85
Score = 45.1 bits (107), Expect = 2e-06
Identities = 24/75 (32%), Positives = 32/75 (42%), Gaps = 2/75 (2%)
Query: 117 HGKLGCGICKGPQWKPGIFVQFTKDACVAKDAGLKCGDQILACNGVKFSPDVTFEHAVSV 176
G LG + G G+ V A AGL+ GD IL NG +T AV +
Sbjct: 11 GGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVE-GLTHLEAVDL 69
Query: 177 MKSSCL-LELLVHRG 190
+K + + L V RG
Sbjct: 70 LKKAGGKVTLTVLRG 84
>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 = 69.3 bits (170), Expect = 5e-15
Identities = 33/72 (45%), Positives = 45/72 (62%), Gaps = 4/72 (5%)
Query: 4 GTLGFSIRGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATHSEVLQLI- 62
G LGFSIRGG E GV V +VEP S AER+GL GD I+ +NG +++ T +V +L+
Sbjct: 1 GGLGFSIRGGTE--GGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLK 58
Query: 63 -HSQNIISLKVR 73
++L VR
Sbjct: 59 KEVGEKVTLTVR 70
Score = 32.3 bits (74), Expect = 0.049
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 130 WKPGIFVQFTKDACVAKDAGLKCGDQILACNGVKFSPDVTFEHAVSVMK 178
+ G+ V + A+ AGL+ GD ILA NG ++T E ++K
Sbjct: 11 TEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVK-NLTLEDVAELLK 58
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 66.9 bits (164), Expect = 5e-14
Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 3 NGTLGFSIRGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATHSEVLQLI 62
G LGFS+ GG + G+FVS V P AE GL GD+I+ ING +E+ +H E + +
Sbjct: 9 RGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSHDEAVLAL 68
Query: 63 H-SQNIISLKVR 73
S ++L +
Sbjct: 69 KGSGGEVTLTIL 80
Score = 41.5 bits (98), Expect = 4e-05
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 110 ITLEVPPHGKLGCGICKGPQWKPGIFVQFTKDACVAKDAGLKCGDQILACNGVKFSPDVT 169
+TLE G LG + G PGIFV A+ GL+ GD+IL+ NG +++
Sbjct: 2 VTLEKSGRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLE-NLS 60
Query: 170 FEHAVSVMKSSC 181
+ AV +K S
Sbjct: 61 HDEAVLALKGSG 72
>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 = 49.9 bits (120), Expect = 5e-08
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 11 RGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATHSEVLQLIHSQNI--- 67
G + T GV V++V+P S A ++GL GD I+ +NG P++ +++ + +
Sbjct: 17 ELGLKDTKGVLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSV--ADLRRALAELKPGDK 74
Query: 68 ISLKVR 73
++L V
Sbjct: 75 VTLTVL 80
Score = 29.1 bits (66), Expect = 1.0
Identities = 18/46 (39%), Positives = 22/46 (47%)
Query: 145 AKDAGLKCGDQILACNGVKFSPDVTFEHAVSVMKSSCLLELLVHRG 190
A AGLK GD ILA NG A++ +K + L V RG
Sbjct: 37 AAKAGLKPGDVILAVNGKPVKSVADLRRALAELKPGDKVTLTVLRG 82
>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 = 54.1 bits (131), Expect = 7e-08
Identities = 45/181 (24%), Positives = 72/181 (39%), Gaps = 15/181 (8%)
Query: 13 GREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATHSEVLQLIHSQNI---IS 69
G E G V+ V P S AE++GL GD I +NG PI +++ + I + ++
Sbjct: 252 GLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSF--ADLRRAIGTLKPGKKVT 309
Query: 70 LKVRSVGMIPTKERDKSVTWKFVDTNKSNLNQNERFPVVPITLEVPPHGKLGCGICKGPQ 129
L + G KE+ +VT + + + P + +T V +
Sbjct: 310 LGILRKG----KEKTITVT---LGASPEE-QASSSNPFLGLT--VANLSPEIRKELRLKG 359
Query: 130 WKPGIFVQFTKDACVAKDAGLKCGDQILACNGVKFSPDVTFEHAVSVMKSSCLLELLVHR 189
G+ V A AGL+ GD IL+ N S ++ K + LL+ R
Sbjct: 360 DVKGVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKKGGRVALLILR 419
Query: 190 G 190
G
Sbjct: 420 G 420
>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 = 46.5 bits (111), Expect = 7e-07
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 11/87 (12%)
Query: 4 GTLGFSIRGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATHSEVLQLI- 62
LGF G + V P S A ++GL GD+I+ ING I+ +++ +
Sbjct: 1 AILGFVPGG---PPIEPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKSW--EDLVDAVQ 55
Query: 63 -HSQNIISLKVRSVGMIPTKERDKSVT 88
+ ++L V G + ++T
Sbjct: 56 ENPGKPLTLTVERNG----ETITLTLT 78
Score = 28.7 bits (65), Expect = 1.1
Identities = 13/19 (68%), Positives = 14/19 (73%)
Query: 145 AKDAGLKCGDQILACNGVK 163
A AGLK GD+ILA NG K
Sbjct: 25 AAKAGLKAGDRILAINGQK 43
>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 = 42.6 bits (101), Expect = 2e-05
Identities = 14/44 (31%), Positives = 30/44 (68%)
Query: 19 GVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATHSEVLQLI 62
G+ +++V P S A ++G+ GD I+ I+G P++ + +V++L+
Sbjct: 14 GLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLL 57
Score = 31.0 bits (71), Expect = 0.18
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 145 AKDAGLKCGDQILACNGVKFSPDVTFEHAVSVM--KSSCLLELLVHRGVG 192
A AG+K GD I+A +G ++ E V ++ K+ + L + RG G
Sbjct: 26 AAKAGIKAGDIIVAIDGEPVD-GLSLEDVVKLLRGKAGTKVRLTLKRGDG 74
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 46.2 bits (110), Expect = 2e-05
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 19 GVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATHSEVLQLI 62
GV V + S A ++G+ GD II+I+G + + E ++LI
Sbjct: 113 GVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLI 156
Score = 28.8 bits (65), Expect = 5.4
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 148 AGLKCGDQILACNGVKFSPDVTFEHAVSVMK 178
AG+K GD I+ +G V+ + AV +++
Sbjct: 128 AGIKPGDVIIKIDGKSVG-GVSLDEAVKLIR 157
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 40.3 bits (95), Expect = 1e-04
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 4 GTLGFSIRGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATH 55
G +G + TGV V +V+ S A ++GL GD I+ I+G + T
Sbjct: 1 GDIGVRVVQ--NEGTGVTVVSVKEGSPAAKAGLKPGDIILSIDGKKVNSLTE 50
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 39.9 bits (93), Expect = 0.002
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 7/58 (12%)
Query: 4 GTLGFSIR-------GGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDAT 54
G LG G G V V P S A ++G+ GD I +NG P+ +
Sbjct: 249 GYLGVIGEPLTADIALGLPVAAGAVVLGVLPGSPAAKAGIKAGDIITAVNGKPVASLS 306
>gnl|CDD|233696 TIGR02038, protease_degS, periplasmic serine pepetdase DegS. This
family consists of the periplasmic serine protease DegS
(HhoB), a shorter paralog of protease DO (HtrA, DegP)
and DegQ (HhoA). It is found in E. coli and several
other Proteobacteria of the gamma subdivision. It
contains a trypsin domain and a single copy of PDZ
domain (in contrast to DegP with two copies). A critical
role of this DegS is to sense stress in the periplasm
and partially degrade an inhibitor of sigma(E) [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Regulatory functions, Protein
interactions].
Length = 351
Score = 39.0 bits (91), Expect = 0.003
Identities = 11/39 (28%), Positives = 22/39 (56%)
Query: 12 GGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPI 50
G G+ ++ V+P A R+G+L+ D I++ +G +
Sbjct: 272 LGLPDLRGIVITGVDPNGPAARAGILVRDVILKYDGKDV 310
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 38.6 bits (90), Expect = 0.006
Identities = 16/32 (50%), Positives = 20/32 (62%)
Query: 19 GVFVSNVEPKSEAERSGLLIGDQIIRINGFPI 50
G FVS V P S A ++G+ GD I +NG PI
Sbjct: 312 GAFVSQVLPNSSAAKAGIKAGDVITSLNGKPI 343
Score = 34.0 bits (78), Expect = 0.14
Identities = 18/56 (32%), Positives = 36/56 (64%), Gaps = 3/56 (5%)
Query: 19 GVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATHSEVLQLIHSQ-NIISLKVR 73
GV V NV+P + A + GL GD II N P+++ +E+ +++ S+ ++++L ++
Sbjct: 409 GVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNI--AELRKILDSKPSVLALNIQ 462
>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 = 33.6 bits (77), Expect = 0.021
Identities = 12/62 (19%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 22 VSNVEPKSEAERSGLLIGDQIIRINGFP-------IEDATHSEVLQLI--HSQNIISLKV 72
V+ V S A+++GL+ GD+++ +NG+ +++ + ++L +I + +
Sbjct: 16 VTFVRDDSPADKAGLVAGDELVAVNGWRVDALQDRLKEYQAGDPVELTVFRDDRLIEVPL 75
Query: 73 RS 74
Sbjct: 76 TL 77
Score = 27.8 bits (62), Expect = 3.0
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 136 VQFTKDACVAKDAGLKCGDQILACNGVKFS 165
V F +D A AGL GD+++A NG +
Sbjct: 16 VTFVRDDSPADKAGLVAGDELVAVNGWRVD 45
>gnl|CDD|223821 COG0750, COG0750, Predicted membrane-associated Zn-dependent
proteases 1 [Cell envelope biogenesis, outer membrane].
Length = 375
Score = 36.3 bits (84), Expect = 0.028
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 6 LGFSIRGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDAT 54
+ F + G + V V V PKS A +GL GD+I+ ++G +
Sbjct: 118 VLFFVIGLVPVASPV-VGEVAPKSAAALAGLRPGDRIVAVDGEKVASWD 165
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 36.2 bits (84), Expect = 0.031
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 5 TLGFSIRGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIE 51
+LG RG + ++ V+P S A ++GL GD+I++++G P+
Sbjct: 211 SLGIRPRGPQIEPV---LAEVQPNSAASKAGLQAGDRIVKVDGQPLT 254
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 35.7 bits (83), Expect = 0.040
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 11 RGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFP 49
GG + G+ V+ V P A ++G+ + D II +N P
Sbjct: 272 GGGIDQLQGIVVNEVSPDGPAAKAGIQVNDLIISVNNKP 310
>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional.
Length = 209
Score = 35.2 bits (81), Expect = 0.042
Identities = 21/79 (26%), Positives = 24/79 (30%), Gaps = 3/79 (3%)
Query: 352 NNNKVDMASFKSFSAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPN 411
N K D+ S S KP V P E PAP P V
Sbjct: 90 NEIKSDLQKATSMSEPATENKPAEVTTPVEPMGLPE---TPPAVPVPAPAPAVAAAAAQA 146
Query: 412 PNEPKVPSKFKFLSNNKPA 430
PK P+K + S A
Sbjct: 147 AAAPKAPAKPRAKSPRPAA 165
>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 = 35.0 bits (81), Expect = 0.072
Identities = 30/105 (28%), Positives = 49/105 (46%), Gaps = 22/105 (20%)
Query: 7 GFSIRGGREHTTGVFV---SNVEPK-----SEAERSGLLIGDQIIRINGFPIEDATHSEV 58
G SI G + +T GV V S++E + S E +G+ IGD+I++ING I++ ++
Sbjct: 95 GQSI-GVKLNTKGVLVVGFSDIETEKGKIHSPGEEAGIQIGDRILKINGEKIKNM--DDL 151
Query: 59 LQLIHSQNIISLKVRSVGMIPTKERDKSVTWKFVDTNKSNLNQNE 103
LI+ L + T ER K ++T + E
Sbjct: 152 ANLINKAGGEKLTL-------TIERGG----KIIETVIKPVKDKE 185
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 34.1 bits (78), Expect = 0.14
Identities = 18/68 (26%), Positives = 22/68 (32%), Gaps = 3/68 (4%)
Query: 362 KSFSAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVPSKF 421
K + PAPA P P P P AP E P ++P+ K
Sbjct: 11 KGEAEQPAPAPPSPAAAPAP---PPPAKTAAPATKAAAPAAAAPRAEKPKKDKPRRERKP 67
Query: 422 KFLSNNKP 429
K S K
Sbjct: 68 KPASLWKL 75
>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta;
Provisional.
Length = 464
Score = 33.7 bits (78), Expect = 0.19
Identities = 14/54 (25%), Positives = 17/54 (31%), Gaps = 7/54 (12%)
Query: 365 SAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVP 418
AAPA A P + K A A AP V +P +P
Sbjct: 88 GAAPAAAAEAAAAAPAAAAAAAAKKAAPAPAAPAAPAAEV-------AADPDIP 134
>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 = 30.8 bits (70), Expect = 0.25
Identities = 15/33 (45%), Positives = 17/33 (51%)
Query: 19 GVFVSNVEPKSEAERSGLLIGDQIIRINGFPIE 51
GV + V S AE + L GD I ING PI
Sbjct: 11 GVVIVGVIVGSPAENAVLHTGDVIYSINGTPIT 43
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 33.3 bits (76), Expect = 0.25
Identities = 18/99 (18%), Positives = 27/99 (27%)
Query: 321 PGSQEEKDKCSDSPPSCPTPDYDTMSVTSHTNNNKVDMASFKSFSAAPAPAKPPPVYFPP 380
P + + D +D P S S + + ++APA PP F P
Sbjct: 433 PATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEP 492
Query: 381 PSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVPS 419
A P + + P P P
Sbjct: 493 APRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPE 531
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 33.2 bits (76), Expect = 0.27
Identities = 20/90 (22%), Positives = 25/90 (27%), Gaps = 7/90 (7%)
Query: 334 PPSCPTPDYDTMSVTSHTNNNKVDMASFKSFSAAPAPAKPPPVYFPPPSGFQDEKNKPEA 393
P P P T + S K+ +AA P K P P P
Sbjct: 362 PVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPV 421
Query: 394 TAVKPAPP-------PVVTLREYPNPNEPK 416
+ P PV +Y P PK
Sbjct: 422 PHTPESAPKLTRAAIPVDEKPKYTPPAPPK 451
Score = 29.0 bits (65), Expect = 6.5
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 365 SAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVP 418
+AAP+P +P P P P+ + A PP V P P P VP
Sbjct: 373 AAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVP----PRPVAPPVP 422
>gnl|CDD|177614 PHA03377, PHA03377, EBNA-3C; Provisional.
Length = 1000
Score = 33.1 bits (75), Expect = 0.37
Identities = 21/79 (26%), Positives = 29/79 (36%), Gaps = 13/79 (16%)
Query: 335 PSCPT-PDYDTMSVTSHTNNNKVDMASFKSFSAAPAPAKPPPVYFPPPSGFQDEKN---- 389
P+ T P T+ TS ++ + +S P P+ P V P E
Sbjct: 422 PTPKTHPVKRTLVKTSGRSD---EAEQAQSTPERPGPSDQPSVPVEPAHLTPVEHTTVIL 478
Query: 390 -----KPEATAVKPAPPPV 403
P A+KPAPPP
Sbjct: 479 HQPPQSPPTVAIKPAPPPS 497
>gnl|CDD|215397 PLN02744, PLN02744, dihydrolipoyllysine-residue acetyltransferase
component of pyruvate dehydrogenase complex.
Length = 539
Score = 32.9 bits (75), Expect = 0.39
Identities = 23/65 (35%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 357 DMASFK----SFSAAPAPAKPPPVYFPPPSGFQDEKNK-PEATAVKPAPPPVVTLREYPN 411
D+ FK S SAAPA K P PP ++ PE A KP+ PP R + +
Sbjct: 193 DIGKFKDYKPSSSAAPAAPKAKPSPPPPKEEEVEKPASSPEPKASKPSAPPSSGDRIFAS 252
Query: 412 PNEPK 416
P K
Sbjct: 253 PLARK 257
>gnl|CDD|147567 pfam05454, DAG1, Dystroglycan (Dystrophin-associated glycoprotein
1). Dystroglycan is one of the dystrophin-associated
glycoproteins, which is encoded by a 5.5 kb transcript
in human. The protein product is cleaved into two
non-covalently associated subunits, [alpha] (N-terminal)
and [beta] (C-terminal). In skeletal muscle the
dystroglycan complex works as a transmembrane linkage
between the extracellular matrix and the cytoskeleton.
[alpha]-dystroglycan is extracellular and binds to
merosin ([alpha]-2 laminin) in the basement membrane,
while [beta]-dystroglycan is a transmembrane protein and
binds to dystrophin, which is a large rod-like
cytoskeletal protein, absent in Duchenne muscular
dystrophy patients. Dystrophin binds to intracellular
actin cables. In this way, the dystroglycan complex,
which links the extracellular matrix to the
intracellular actin cables, is thought to provide
structural integrity in muscle tissues. The dystroglycan
complex is also known to serve as an agrin receptor in
muscle, where it may regulate agrin-induced
acetylcholine receptor clustering at the neuromuscular
junction. There is also evidence which suggests the
function of dystroglycan as a part of the signal
transduction pathway because it is shown that Grb2, a
mediator of the Ras-related signal pathway, can interact
with the cytoplasmic domain of dystroglycan. In general,
aberrant expression of dystrophin-associated protein
complex underlies the pathogenesis of Duchenne muscular
dystrophy, Becker muscular dystrophy and severe
childhood autosomal recessive muscular dystrophy.
Interestingly, no genetic disease has been described for
either [alpha]- or [beta]-dystroglycan. Dystroglycan is
widely distributed in non-muscle tissues as well as in
muscle tissues. During epithelial morphogenesis of
kidney, the dystroglycan complex is shown to act as a
receptor for the basement membrane. Dystroglycan
expression in mouse brain and neural retina has also
been reported. However, the physiological role of
dystroglycan in non-muscle tissues has remained unclear.
Length = 290
Score = 32.3 bits (73), Expect = 0.42
Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 6/76 (7%)
Query: 332 DSPPSCPTPDYDTMSVTSHTNNNKVDMASFKSFSAAPAPAKPPPVYFPPPS---GFQDEK 388
+ P P P+Y +V T N+ + + A P Y PPP + +
Sbjct: 216 EEKPPLPPPEYPNQNVPETTPLNQDLLGEYTPLRDEDPNAPP---YQPPPPFTTPMEGKG 272
Query: 389 NKPEATAVKPAPPPVV 404
++P+ +PPP V
Sbjct: 273 SRPKNMTPYRSPPPYV 288
>gnl|CDD|236940 PRK11633, PRK11633, cell division protein DedD; Provisional.
Length = 226
Score = 31.5 bits (72), Expect = 0.67
Identities = 13/54 (24%), Positives = 17/54 (31%)
Query: 365 SAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVP 418
A AP+ P PP + + E E KP P + P P
Sbjct: 78 GDAAAPSLDPATVAPPNTPVEPEPAPVEPPKPKPVEKPKPKPKPQQKVEAPPAP 131
>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 = 30.7 bits (70), Expect = 0.68
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 4/53 (7%)
Query: 4 GTLGFSIRGGR---EHTTGVFVSNVEPKSEAERSGLL-IGDQIIRINGFPIED 52
G LG S+R + V +V P S A +GL D II + +
Sbjct: 24 GLLGLSLRWCSFSGANENVWHVLDVHPNSPAALAGLQPYSDYIIGTDSGLLRG 76
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 32.0 bits (72), Expect = 0.71
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 359 ASFKSFSAAPAPAKPPPVYFPPPSGFQDEKNKPEATA--VKPAPPPVVTLRE 408
+++++ PA P+Y P Q +PE KPA PP+ E
Sbjct: 460 STYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPEPVVEETKPARPPLYYFEE 511
>gnl|CDD|132322 TIGR03279, cyano_FeS_chp, putative FeS-containing
Cyanobacterial-specific oxidoreductase. Members of
this protein family are predicted FeS-containing
oxidoreductases of unknown function, apparently
restricted to and universal across the Cyanobacteria.
The high trusted cutoff score for this model, 700 bits,
excludes homologs from other lineages. This exclusion
seems justified because a significant number of
sequence positions are simultaneously unique to and
invariant across the Cyanobacteria, suggesting a
specialized, conserved function, perhaps related to
photosynthesis. A distantly related protein family,
TIGR03278, in universal in and restricted to archaeal
methanogens, and may be linked to methanogenesis.
Length = 433
Score = 31.6 bits (72), Expect = 0.75
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 22 VSNVEPKSEAERSGLLIGDQIIRING 47
+S V P S AE G GD ++ ING
Sbjct: 2 ISAVLPGSIAEELGFEPGDALVSING 27
>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 = 31.6 bits (72), Expect = 0.77
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 27 PKSEAERSGLLIGDQIIRING 47
S AE++G+ GD+II+ING
Sbjct: 71 EGSPAEKAGIKPGDKIIKING 91
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 31.8 bits (72), Expect = 0.81
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 19 GVFVSNVEPKSEAERSGLLIGDQIIRINGFPI 50
G FVS V P S + ++G+ GD I +NG P+
Sbjct: 291 GAFVSEVLPNSGSAKAGVKAGDIITSLNGKPL 322
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 31.6 bits (72), Expect = 0.84
Identities = 18/109 (16%), Positives = 29/109 (26%), Gaps = 14/109 (12%)
Query: 325 EEKDKCSDSPPSCPTPDYDTMSVTSHTNNNKVDMASFKSFSAA-------------PAPA 371
+E + + P D ++ ++ SF + PAP+
Sbjct: 158 DEDADVATTNSDNSFPGEDADPASASPSDPPSSSPGVPSFPSPPEDPSSPSDSSLPPAPS 217
Query: 372 KPPPVYFPPPSGFQDEKNKPEATAVKPAPPP-VVTLREYPNPNEPKVPS 419
PP + P A P PP V P P +
Sbjct: 218 SFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPTPPSASA 266
>gnl|CDD|225939 COG3404, COG3404, Methenyl tetrahydrofolate cyclohydrolase [Amino
acid transport and metabolism].
Length = 208
Score = 30.8 bits (70), Expect = 0.99
Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 10/96 (10%)
Query: 241 SLEDVTQARAEPRTLHNGGGGASLSSAISEEIKRRSERLNSGK---EFVKVETTKNNIEE 297
SL++ A A + GG ++L A+ + L GK E E + +EE
Sbjct: 7 SLKEFLDALASEKPTPGGGSASALVGAMGCALASMVANLTRGKKGYEDYDDEMKE-ILEE 65
Query: 298 DSSYHLKLQTLMKEVKEAHN------KMFPGSQEEK 327
+L L+ + +EA N K+ ++EEK
Sbjct: 66 LQKIKAELLALIDKDEEAFNLIMAAYKLPKSTEEEK 101
>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 = 31.7 bits (72), Expect = 1.0
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 4 GTLGF--SIRGGREHTTGVFVSNVEPKSEAERSGLLIGDQIIRIN 46
G LG +R + V V P + A R+GL D I++I+
Sbjct: 140 GGLGIVIGMRDRN-----LTVVRVIPGTPAARAGLQRNDVIVKID 179
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 31.4 bits (71), Expect = 1.2
Identities = 24/73 (32%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 331 SDSPPSCPTPDYDTMSVTSHTNNNKVDMASFKSFSAAPAPAKPPPVYFPPPS-GFQDEKN 389
+D PP PTP+ ++ S T A+ ++ A PA PP V P + G
Sbjct: 2699 ADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPA 2758
Query: 390 KPEATAVKPAPPP 402
+P TA PAP P
Sbjct: 2759 RPPTTAGPPAPAP 2771
Score = 31.4 bits (71), Expect = 1.3
Identities = 18/66 (27%), Positives = 22/66 (33%), Gaps = 9/66 (13%)
Query: 365 SAAPAPAKPPPVYFPP---------PSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEP 415
SA P PPP PP P G + + A KPA P +R P
Sbjct: 2833 SAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVS 2892
Query: 416 KVPSKF 421
+ F
Sbjct: 2893 RSTESF 2898
Score = 30.3 bits (68), Expect = 2.5
Identities = 12/53 (22%), Positives = 18/53 (33%)
Query: 366 AAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVP 418
A PA ++ + PP + +P P P + P P P P
Sbjct: 2887 ARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRP 2939
Score = 29.1 bits (65), Expect = 6.6
Identities = 22/105 (20%), Positives = 33/105 (31%), Gaps = 8/105 (7%)
Query: 321 PGSQEEKDKCSDSPPSCPTPDYDTMSVTSHTNNNKVD--MASFKSFSAAPAPAKPPPVYF 378
PG D + PS P + ++ + + ++ A PPP+
Sbjct: 2498 PGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWIRGLEELASDDAGDPPPPLPP 2557
Query: 379 PPPSGFQDEKNKPEATAVKPAPPPVVTLREY-----PNPNEPKVP 418
P D P A +P P VT R P P+ P
Sbjct: 2558 AAPPAAPDRSVPPPRPAPRP-SEPAVTSRARRPDAPPQSARPRAP 2601
Score = 28.8 bits (64), Expect = 7.9
Identities = 15/60 (25%), Positives = 22/60 (36%), Gaps = 7/60 (11%)
Query: 360 SFKSFSAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVPS 419
S +SF+ P + PP P + + +P PPP P P P P+
Sbjct: 2894 STESFALPPDQPERPP---QPQAPPPPQPQPQPPPPPQPQPPP----PPPPRPQPPLAPT 2946
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 31.3 bits (71), Expect = 1.3
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 19 GVFVSNVEPKSEAERSGLLIGDQIIRINGF 48
++ V P A ++GL GD+I+ ING
Sbjct: 463 HEKITFVFPGGPAYKAGLSPGDKIVAINGI 492
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 30.9 bits (70), Expect = 1.5
Identities = 18/67 (26%), Positives = 23/67 (34%), Gaps = 1/67 (1%)
Query: 365 SAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVPSKF-KF 423
AAP PA PPV P+ + P A PP + + F F
Sbjct: 397 PAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPPARSADPAAAASAGDRWRAFVAF 456
Query: 424 LSNNKPA 430
+ KPA
Sbjct: 457 VKGKKPA 463
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 31.0 bits (70), Expect = 1.5
Identities = 25/157 (15%), Positives = 44/157 (28%), Gaps = 4/157 (2%)
Query: 270 EEIKRRSERLNSGKEFVKVETTKNNIEEDSSYHLKLQTLMKEVK-EAHNKMFPGSQEEKD 328
EE KR R S + + N +E + Q + VK + +E+++
Sbjct: 162 EEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEE 221
Query: 329 ---KCSDSPPSCPTPDYDTMSVTSHTNNNKVDMASFKSFSAAPAPAKPPPVYFPPPSGFQ 385
K ++ S D S ++ S S A +
Sbjct: 222 DDGKDRETTTSPMEEDESRQSSEISRRSSSSLKKPDPSPSMASPETRESSKRTETRPRTS 281
Query: 386 DEKNKPEATAVKPAPPPVVTLREYPNPNEPKVPSKFK 422
+ +PAPP V + + K
Sbjct: 282 LRPPSARPASARPAPPRVKRKEIVTVLQDAQGVGKIV 318
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 31.0 bits (70), Expect = 1.6
Identities = 16/56 (28%), Positives = 19/56 (33%), Gaps = 1/56 (1%)
Query: 365 SAAPAPAKPPPVYFP-PPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVPS 419
+AAPA A P P P + A A PAP P E P+
Sbjct: 455 AAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPA 510
Score = 29.1 bits (65), Expect = 5.9
Identities = 14/55 (25%), Positives = 17/55 (30%), Gaps = 1/55 (1%)
Query: 366 AAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVPSK 420
A PA A PV P P+ A A PA P P++
Sbjct: 372 AGPATAAAAPVAQPAPAA-AAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPAR 425
>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 = 30.6 bits (69), Expect = 1.7
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 22 VSNVEPKSEAERSGLLIGDQIIRINGFP 49
+S+V P S AE++GL GD I ING
Sbjct: 206 LSDVTPNSPAEKAGLKEGDYIQSINGEK 233
Score = 29.0 bits (65), Expect = 4.7
Identities = 14/30 (46%), Positives = 16/30 (53%)
Query: 145 AKDAGLKCGDQILACNGVKFSPDVTFEHAV 174
A+ AGLK GD I + NG K F AV
Sbjct: 215 AEKAGLKEGDYIQSINGEKLRSWTDFVSAV 244
>gnl|CDD|236768 PRK10819, PRK10819, transport protein TonB; Provisional.
Length = 246
Score = 29.7 bits (67), Expect = 2.3
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 367 APAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVPSKFK 422
APA +PP PPP + + +PE P PVV + P P +PK K K
Sbjct: 54 APADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIPKPEPKP-KPKPKPKPK 108
Score = 29.3 bits (66), Expect = 3.5
Identities = 22/67 (32%), Positives = 29/67 (43%), Gaps = 11/67 (16%)
Query: 368 PAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPN----PNEPKVPSKFKF 423
P P K PV P P + KP+ KP P PV + E P P EP+ S F+
Sbjct: 82 PEPPKEAPVVIPKP------EPKPKPK-PKPKPKPVKKVEEQPKREVKPVEPRPASPFEN 134
Query: 424 LSNNKPA 430
+ +P
Sbjct: 135 TAPARPT 141
>gnl|CDD|225575 COG3031, PulC, Type II secretory pathway, component PulC
[Intracellular trafficking and secretion].
Length = 275
Score = 29.9 bits (67), Expect = 2.6
Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 1/63 (1%)
Query: 15 EHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATH-SEVLQLIHSQNIISLKVR 73
E G + S +SGL GD + IN + D +LQ++ + + L V
Sbjct: 204 EKIEGYRFEPGKDGSLFYKSGLQRGDIAVAINNLDLTDPEDMFRLLQMLRNMPSLQLTVI 263
Query: 74 SVG 76
G
Sbjct: 264 RRG 266
>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed.
Length = 1228
Score = 30.2 bits (69), Expect = 2.9
Identities = 9/43 (20%), Positives = 10/43 (23%), Gaps = 2/43 (4%)
Query: 365 SAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLR 407
+A P PA A A V LR
Sbjct: 81 AAPPKPAAAAAA--AAAPAAPPAAAAAAAPAAAAVEDEVTPLR 121
>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional.
Length = 991
Score = 30.0 bits (67), Expect = 3.0
Identities = 19/92 (20%), Positives = 26/92 (28%), Gaps = 6/92 (6%)
Query: 334 PPSCPTPDYDTMSVTSHTNNN--KVDMASFKSFSAAPAPAKPP---PVYFPPPSGFQDEK 388
P TP T + H + AP +PP P PP+
Sbjct: 655 PQVEITPYKPTWTQIGHIPYQPSPTGANTMLPIQWAPGTMQPPPRAPTPMRPPAAPPGRA 714
Query: 389 NKPEATAVKPAPPPVVTLREYPNPNEPKVPSK 420
+P A A A PP P ++
Sbjct: 715 QRPAA-ATGRARPPAAAPGRARPPAAAPGRAR 745
>gnl|CDD|235826 PRK06549, PRK06549, acetyl-CoA carboxylase biotin carboxyl carrier
protein subunit; Validated.
Length = 130
Score = 28.6 bits (64), Expect = 3.4
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 5/46 (10%)
Query: 356 VDMASFKSFSAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPP 401
V+M + + A APA+P P P + P+ A P P
Sbjct: 16 VEMEEIGAPAQAAAPAQPASTPVPVP-----TEASPQVEAQAPQPA 56
>gnl|CDD|220260 pfam09483, HpaP, Type III secretion protein (HpaP). This entry
represents proteins encoded by genes which are always
found in type III secretion operons, although their
function in the processes of secretion and virulence is
unclear. Hpa stands for Hrp-associated gene, where Hrp
stands for hypersensitivity response and virulence. see
also PMID:18584024.
Length = 185
Score = 29.0 bits (65), Expect = 3.4
Identities = 12/50 (24%), Positives = 15/50 (30%), Gaps = 2/50 (4%)
Query: 363 SFSAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNP 412
+ A P PP P + +P PAPP P P
Sbjct: 23 AARAGPPGTPAPPG--PAEDAHPEFPERPRDAPAPPAPPRATDGDRDPQP 70
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 29.4 bits (66), Expect = 3.8
Identities = 17/73 (23%), Positives = 25/73 (34%), Gaps = 2/73 (2%)
Query: 331 SDSPPSCPTPDYDTMSVTSHTNNNKVDMASFKSFSAAPAPAKPPPVYFPPPSGFQDEKNK 390
S+ + P +T N + ++ S +S A A A P+ P
Sbjct: 347 SEGVAAVAPPAPAPADLTQRLNRLEKEVRSLRSAPTAAATAAGAPLPDFDPRP--RGPPA 404
Query: 391 PEATAVKPAPPPV 403
PE APP V
Sbjct: 405 PEPARSAEAPPLV 417
>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 = 28.7 bits (65), Expect = 4.1
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 14 REHTTGVFVSNVEPKSEAERSGLLIGDQIIRI 45
RE V V VE S AE++G+ +I+ +
Sbjct: 118 REEGGKVIVDEVEFGSPAEKAGIDFDWEIVEV 149
>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 29.2 bits (66), Expect = 4.8
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 357 DMASFKS-FSAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEP 415
D+A+ +AAPA A+PPP P ++P A A +PAP V + E
Sbjct: 47 DLAALAPPAAAAPAAAQPPPAAAPAAV------SRPAAPAAEPAPWLVEHAKRLTAQREQ 100
>gnl|CDD|219321 pfam07174, FAP, Fibronectin-attachment protein (FAP). This family
contains bacterial fibronectin-attachment proteins
(FAP). Family members are rich in alanine and proline,
are approximately 300 long, and seem to be restricted to
mycobacteria. These proteins contain a
fibronectin-binding motif that allows mycobacteria to
bind to fibronectin in the extracellular matrix.
Length = 297
Score = 29.1 bits (65), Expect = 5.1
Identities = 18/54 (33%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 365 SAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVP 418
+AA APA P PPP+ + A P PPP P P +P P
Sbjct: 50 TAAAAPAPAAPPPPPPPAAPPAPQPDDPNAA--PPPPPADPNAPPPPPVDPNAP 101
Score = 28.7 bits (64), Expect = 5.8
Identities = 20/54 (37%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 366 AAPAPAKPPPVYFPPPSGFQDEKNK----PEATAVKPAPPPVVTLREYPNPNEP 415
APA PPP PP+ D+ N P A P PPPV P EP
Sbjct: 55 PAPAAPPPPPPPAAPPAPQPDDPNAAPPPPPADPNAPPPPPVDPNAPPPPAPEP 108
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 29.3 bits (66), Expect = 5.1
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 268 ISEEIKRRSERLNSGKEFVKVETTKNNIEEDSSYHLKLQTLMKEVKEA 315
+ EE+++ E L + K+ + IEE S +L+ L KE+++
Sbjct: 693 LEEELEQLREELEELLK--KLGEIEQLIEELESRKAELEELKKELEKL 738
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 29.1 bits (66), Expect = 5.8
Identities = 15/62 (24%), Positives = 18/62 (29%), Gaps = 2/62 (3%)
Query: 358 MASFKSFSAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKV 417
M +F + P P PP P+ P A P P V P V
Sbjct: 356 MLAFHPAAPLPEPEVPPQS--AAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAV 413
Query: 418 PS 419
P
Sbjct: 414 PL 415
>gnl|CDD|202531 pfam03091, CutA1, CutA1 divalent ion tolerance protein. Several
gene loci with a possible involvement in cellular
tolerance to copper have been identified. One such locus
in eubacteria and archaebacteria, cutA, is thought to be
involved in cellular tolerance to a wide variety of
divalent cations other than copper. The cutA locus
consists of two operons, of one and two genes. The CutA1
protein is a cytoplasmic protein, encoded by the
single-gene operon and has been linked to divalent
cation tolerance. It has no recognised structural
motifs. This family also contains putative proteins from
eukaryotes (human and Drosophila).
Length = 102
Score = 27.3 bits (61), Expect = 5.9
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 7/33 (21%)
Query: 292 KNNIEEDSSYHLKLQT-------LMKEVKEAHN 317
+ IEEDS L ++T L + VKE H
Sbjct: 43 EGKIEEDSEVLLIIKTSSEKFPALEERVKELHP 75
>gnl|CDD|166942 PRK00404, tatB, sec-independent translocase; Provisional.
Length = 141
Score = 27.9 bits (62), Expect = 6.1
Identities = 16/55 (29%), Positives = 19/55 (34%), Gaps = 3/55 (5%)
Query: 365 SAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAP-PPVVTLREYPNPNEPKVP 418
A P P PP P+ AV PAP V P P++P P
Sbjct: 85 PAPPEPVTPPTA--QSPAPAVPTPPPTSTPAVPPAPAAAVPAPAAAPPPSDPPQP 137
>gnl|CDD|233542 TIGR01713, typeII_sec_gspC, type II secretion system protein C.
This model represents GspC, protein C of the main
terminal branch of the general secretion pathway, also
called type II secretion. This system transports folded
proteins across the bacterial outer membrane and is
widely distributed in Gram-negative pathogens [Protein
fate, Protein and peptide secretion and trafficking].
Length = 259
Score = 28.3 bits (63), Expect = 6.9
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 15 EHTTGVFVSNVEPKSEAERSGLLIGDQIIRINGFPIEDATH-SEVLQLIHSQNIISLKVR 73
+ G ++ + S +SGL GD + +NG + D + LQ++ + ++L V
Sbjct: 188 DKLEGYRLNPGKDPSLFYKSGLQDGDIAVALNGLDLRDPEQAFQALQMLREETNLTLTVE 247
Query: 74 SVG 76
G
Sbjct: 248 RDG 250
>gnl|CDD|223066 PHA03379, PHA03379, EBNA-3A; Provisional.
Length = 935
Score = 28.9 bits (64), Expect = 7.0
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 374 PPVYFPPPSGFQDEKNKPEATAVK-PAPPPVVTLREYP 410
PPV P P Q + + + P PPPV L P
Sbjct: 418 PPVEKPRPEVPQSLETATSHGSAQVPEPPPVHDLEPGP 455
>gnl|CDD|225629 COG3087, FtsN, Cell division protein [Cell division and chromosome
partitioning].
Length = 264
Score = 28.3 bits (63), Expect = 8.4
Identities = 9/40 (22%), Positives = 11/40 (27%)
Query: 365 SAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVV 404
+ P KP P P +P A K P
Sbjct: 140 TVQTQPVKPKPRPEKPQPVAPAPAPEPVEKAPKAEAAPPP 179
>gnl|CDD|240415 PTZ00429, PTZ00429, beta-adaptin; Provisional.
Length = 746
Score = 28.4 bits (63), Expect = 8.4
Identities = 23/88 (26%), Positives = 33/88 (37%), Gaps = 7/88 (7%)
Query: 350 HTNNNKVDMASF-KSFSAAPAPAKPPPVYFPPPSGFQDEKNKPEAT-----AVKPAPPPV 403
T ++ + MA KS + A P F PP G D + E T P+ P +
Sbjct: 568 STFSDAMTMADLKKSLNTAAIVFARPYQSFLPPYGLADVELDEEDTEDDDAVELPSTPSM 627
Query: 404 VTLREYPNPNE-PKVPSKFKFLSNNKPA 430
T P P+ P F+F + A
Sbjct: 628 GTQDGSPAPSAAPAGYDIFEFAGDGTGA 655
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 28.5 bits (64), Expect = 8.7
Identities = 16/56 (28%), Positives = 18/56 (32%), Gaps = 7/56 (12%)
Query: 365 SAAPAPAKPPPVYFPPPSGFQDEKNKPEATAVKPAPPPVVTLREYPNPNEPKVPSK 420
+AA APA PP P P P A A AP P P +
Sbjct: 409 AAASAPAAPPAAAPPAPVA------APAAAAPAAAPAAAPAAVA-LAPAPPAQAAP 457
>gnl|CDD|140280 PTZ00253, PTZ00253, tryparedoxin peroxidase; Provisional.
Length = 199
Score = 27.9 bits (62), Expect = 9.2
Identities = 7/33 (21%), Positives = 20/33 (60%)
Query: 330 CSDSPPSCPTPDYDTMSVTSHTNNNKVDMASFK 362
C D+ + P P ++ +++ + + K+ ++S+K
Sbjct: 3 CGDAKINHPAPSFEEVALMPNGSFKKISLSSYK 35
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
0.313 0.131 0.387
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: 21,240,358
Number of extensions: 1984255
Number of successful extensions: 2189
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2023
Number of HSP's successfully gapped: 129
Length of query: 433
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 333
Effective length of database: 6,502,202
Effective search space: 2165233266
Effective search space used: 2165233266
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 60 (27.0 bits)