RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5188
(109 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 = 73.4 bits (181), Expect = 1e-18
Identities = 30/80 (37%), Positives = 44/80 (55%)
Query: 29 ELKLKKLECEAWGFRLTGGRDFGTPLTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMT 88
+ L+K GF L GG+D G + V RV AE GG+ VGD I+ +NG + +T
Sbjct: 3 TVTLRKDPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLT 62
Query: 89 HVEAQQHIIGSGNTLTLQIL 108
H EA + + SG+ +TL +
Sbjct: 63 HEEAVELLKNSGDEVTLTVR 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 = 67.0 bits (164), Expect = 3e-16
Identities = 27/70 (38%), Positives = 41/70 (58%)
Query: 40 WGFRLTGGRDFGTPLTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGS 99
GF L GG+D G + V V S A + G+ VGD+I+ +NG + +TH+EA + +
Sbjct: 14 LGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKA 73
Query: 100 GNTLTLQILR 109
G +TL +LR
Sbjct: 74 GGKVTLTVLR 83
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 61.5 bits (150), Expect = 4e-14
Identities = 33/80 (41%), Positives = 44/80 (55%)
Query: 29 ELKLKKLECEAWGFRLTGGRDFGTPLTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMT 88
E+ L+K GF L GG D + V V AE GG++ GD I+SINGQ + ++
Sbjct: 1 EVTLEKSGRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLS 60
Query: 89 HVEAQQHIIGSGNTLTLQIL 108
H EA + GSG +TL IL
Sbjct: 61 HDEAVLALKGSGGEVTLTIL 80
>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 = 47.7 bits (114), Expect = 1e-08
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 41 GFRLTGGRDFGTPLTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGS- 99
GF + GG + G + VL V S AE G++ GD+I+++NG + +T + + +
Sbjct: 4 GFSIRGGTEGG--VVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEV 61
Query: 100 GNTLTLQIL 108
G +TL +
Sbjct: 62 GEKVTLTVR 70
>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 = 41.4 bits (98), Expect = 2e-05
Identities = 18/54 (33%), Positives = 29/54 (53%)
Query: 56 VLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGSGNTLTLQILR 109
V +V S AE+ G++ GD+I S+NG+ + + + G +TL ILR
Sbjct: 261 VAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILR 314
Score = 27.6 bits (62), Expect = 1.4
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 56 VLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGSGNTLTLQILR 109
V +V S A G++ GD+I+S+N Q ++ + G + L ILR
Sbjct: 366 VTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKKGGRVALLILR 419
>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 = 38.8 bits (91), Expect = 4e-05
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 43 RLTGGRDFGTPLTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGS--- 99
G + V V S A + G++ GD+I+++NG + + V + +
Sbjct: 15 AEELGLKDTKGVLVASVDPGSPAAKAGLKPGDVILAVNG---KPVKSVADLRRALAELKP 71
Query: 100 GNTLTLQILR 109
G+ +TL +LR
Sbjct: 72 GDKVTLTVLR 81
>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 = 36.8 bits (86), Expect = 2e-04
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 53 PLTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHII-GSGNTLTLQILR 109
+ V S A + G++ GD I++INGQ ++ + + G LTL + R
Sbjct: 13 EPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKSWE--DLVDAVQENPGKPLTLTVER 68
>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 = 38.1 bits (89), Expect = 3e-04
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 5/50 (10%)
Query: 62 TSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHII--GSGNTLTLQILR 109
S EE G+++GD I+ ING+ + M + ++I G LTL I R
Sbjct: 123 HSPGEEAGIQIGDRILKINGEKIKNMDDL---ANLINKAGGEKLTLTIER 169
>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 = 35.7 bits (83), Expect = 5e-04
Identities = 13/48 (27%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 63 SVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGSGNT-LTLQILR 109
S A + G++ GD+IV+I+G+ ++ + + + G T + L + R
Sbjct: 24 SPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRLTLKR 71
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 37.3 bits (87), Expect = 5e-04
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 65 AEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGSGNTL-TLQILR 109
A + G++ GD+I+ I+G+ ++ EA + I G T TL ILR
Sbjct: 125 AAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILR 170
>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 = 36.7 bits (85), Expect = 9e-04
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 54 LTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGSGNT-LTLQILR 109
LTV+RV + A G++ D+IV I+ + T MT +A + G +T +T+ + R
Sbjct: 153 LTVVRVIPGTPAARAGLQRNDVIVKIDDESTVNMTLNDAVGRLRGPPDTKVTIWVRR 209
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 36.7 bits (85), Expect = 0.001
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 6/57 (10%)
Query: 56 VLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGS---GNTLTLQILR 109
V +V S A + G++ GD+I S+NG+ + + AQ +G+ G+ LTL +LR
Sbjct: 315 VSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQ---VGTMPVGSKLTLGLLR 368
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 32.6 bits (75), Expect = 0.007
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 41 GFRLTGGRDFGTPLTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGSG 100
G R+ G TV+ V S A + G++ GD+I+SI+G+ ++T + G
Sbjct: 4 GVRVVQNEGTGV--TVVSVKEGSPAAKAGLKPGDIILSIDGKKVNSLTELIEVILNGKPG 61
Query: 101 NTLTLQILR 109
+T+ L + R
Sbjct: 62 DTVKLTVYR 70
>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 = 33.9 bits (78), Expect = 0.009
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 65 AEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGSGNT-LTLQILR 109
AE+ G++ GD I+ ING+ M+ +A I G T ++L+ILR
Sbjct: 75 AEKAGIKPGDKIIKINGKSVAGMSLDDAVALIRGKKGTKVSLEILR 120
>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 = 32.8 bits (75), Expect = 0.021
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 56 VLRVTGTSVAEEGGMEVGDMIVSINGQ 82
+ V S+AEE G E GD +VSING
Sbjct: 2 ISAVLPGSIAEELGFEPGDALVSINGV 28
>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 = 32.5 bits (74), Expect = 0.025
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 35 LECEAWGFRLTGGRDFGTP---LTVLRVTGTSVAEEGGMEVGDMIVSINGQ 82
E E W F + P + VT S AE+ G++ GD I SING+
Sbjct: 182 AERENWTFEVMKELIPRGPKIEPVLSDVTPNSPAEKAGLKEGDYIQSINGE 232
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 31.8 bits (72), Expect = 0.044
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 46 GGRDFGTPLTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGS---GNT 102
G VL V S A + G++ GD+I ++NG + + + + S G+
Sbjct: 264 LGLPVAAGAVVLGVLPGSPAAKAGIKAGDIITAVNG---KPVASLSDLVAAVASNRPGDE 320
Query: 103 LTLQILR 109
+ L++LR
Sbjct: 321 VALKLLR 327
>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease;
Provisional.
Length = 389
Score = 31.6 bits (72), Expect = 0.056
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 46 GGRDFGTPLTVLRVTGT--SVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIG-SGNT 102
G P ++ V A G+ GD+I++I+G T+ ++ EA + G G++
Sbjct: 94 PTGSDGPPAGLVVVAPAPGGPAARAGIRPGDVILAIDGTSTEGLSLYEAADRLQGPEGSS 153
Query: 103 LTLQILR 109
+ L + R
Sbjct: 154 VELTLRR 160
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 30.4 bits (69), Expect = 0.13
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 59 VTGTSVAEEGGMEVGDMIVSINGQ-CTQAMTHVEAQQHIIGSGNTLTLQILR 109
V S A + G++ GD IV ++GQ TQ T V + G L L+I R
Sbjct: 228 VQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRD--NPGKPLALEIER 277
>gnl|CDD|239153 cd02752, MopB_Formate-Dh-Na-like, Formate dehydrogenase N, alpha
subunit (Formate-Dh-Na) is a major component of nitrate
respiration in bacteria such as in the E. coli formate
dehydrogenase N (Fdh-N). Fdh-N is a membrane protein
that is a complex of three different subunits and is the
major electron donor to the nitrate respiratory chain.
Also included in this CD is the Desulfovibrio gigas
tungsten formate dehydrogenase, DgW-FDH. In contrast to
Fdh-N, which is a functional heterotrimer, DgW-FDH is a
heterodimer. The DgW-FDH complex is composed of a large
subunit carrying the W active site and one [4Fe-4S]
center, and a small subunit that harbors a series of
three [4Fe-4S] clusters as well as a putative vacant
binding site for a fourth cluster. The smaller subunit
is not included in this alignment. Members of the
MopB_Formate-Dh-Na-like CD belong to the
molybdopterin_binding (MopB) superfamily of proteins.
Length = 649
Score = 30.4 bits (69), Expect = 0.14
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 52 TPLTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEA---QQHIIGSGNTLTLQIL 108
TP V + G +E ++V +M + G+ + T + A QH +GS N + IL
Sbjct: 242 TPEEVEDICGVP--KEDFLKVAEMFAA-TGRPDKPGTILYAMGWTQHTVGSQNIRAMCIL 298
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 29.6 bits (67), Expect = 0.29
Identities = 13/56 (23%), Positives = 28/56 (50%)
Query: 54 LTVLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGSGNTLTLQILR 109
+ V V+ A + G++V D+I+S+N + + Q I G+ + + ++R
Sbjct: 281 IVVNEVSPDGPAAKAGIQVNDLIISVNNKPAISALETMDQVAEIRPGSVIPVVVMR 336
>gnl|CDD|227558 COG5233, GRH1, Peripheral Golgi membrane protein [Intracellular
trafficking and secretion].
Length = 417
Score = 29.3 bits (65), Expect = 0.35
Identities = 16/28 (57%), Positives = 18/28 (64%)
Query: 54 LTVLRVTGTSVAEEGGMEVGDMIVSING 81
L VLRV S AE+ GM VGD I+ IN
Sbjct: 65 LEVLRVNPESPAEKAGMVVGDYILGINE 92
>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 = 0.67
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 14/57 (24%)
Query: 62 TSVAE----EGGMEVGDMIVSINGQCTQAMTHVEAQQHI--IGS---GNTLTLQILR 109
TSV E G ++ GD I++++G+ EA++ I I S G+T+ L++ R
Sbjct: 13 TSVVEGMPAAGKLKAGDHIIAVDGK-----PFKEAEELIDYIQSKKEGDTVKLKVKR 64
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 26.7 bits (60), Expect = 2.4
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 20/61 (32%)
Query: 16 LIQLILTKEVMCEELK-LKKLECEAWGFRLTGGRDFGTPLTVLRVTGTSVAEE---GGME 71
+IQ+++ K+V E + +KKL+ E +V+ VTGT A GG+E
Sbjct: 45 IIQVVVKKKVDEELFETIKKLKRE----------------SVVSVTGTVKANPKAPGGVE 88
Query: 72 V 72
V
Sbjct: 89 V 89
>gnl|CDD|222904 PHA02601, int, integrase; Provisional.
Length = 333
Score = 26.6 bits (59), Expect = 2.7
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 81 GQCTQAMTHVEAQQHIIGSGNTLTLQ-IL 108
GQ T + H A ++ GN L LQ IL
Sbjct: 275 GQATHVLRHTFASHFMMNGGNILVLQRIL 303
>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 = 25.4 bits (56), Expect = 3.8
Identities = 13/47 (27%), Positives = 19/47 (40%)
Query: 63 SVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGSGNTLTLQILR 109
S AE + GD+I SING + G +T+ +L
Sbjct: 21 SPAENAVLHTGDVIYSINGTPITTLEDFMEALKPTKPGEVITVTVLP 67
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 25.9 bits (57), Expect = 5.8
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 30 LKLKKLECEAWGFRLTGGRDFGTPLTVLRVTGTSVAEEGGMEVGDMIVSING 81
L EA+ L + G + V A + G+ GD IV+ING
Sbjct: 441 LTFTPKPREAYYLGLKVKSEGGHEK-ITFVFPGGPAYKAGLSPGDKIVAING 491
>gnl|CDD|238739 cd01462, VWA_YIEM_type, VWA YIEM type: Von Willebrand factor type A
(vWA) domain was originally found in the blood
coagulation protein von Willebrand factor (vWF).
Typically, the vWA domain is made up of approximately
200 amino acid residues folded into a classic a/b
para-rossmann type of fold. The vWA domain, since its
discovery, has drawn great interest because of its
widespread occurrence and its involvement in a wide
variety of important cellular functions. These include
basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains. Members of this subgroup have a conserved MIDAS
motif, however, their biochemical function is not well
characterised.
Length = 152
Score = 25.4 bits (56), Expect = 6.1
Identities = 16/66 (24%), Positives = 24/66 (36%), Gaps = 10/66 (15%)
Query: 13 FDILIQL-ILTKEVMCEELKLKKLECEAWGFRLTGGRDFGTPLTVLRVTGTSVAEEGGME 71
FD Q I+ K EE ++ L G +L GG D L + E
Sbjct: 44 FDSEFQTKIVDKTDDLEEP-VEFLS----GVQLGGGTDINKALR----YALELIERRDPR 94
Query: 72 VGDMIV 77
D+++
Sbjct: 95 KADIVL 100
>gnl|CDD|131487 TIGR02434, CobF, precorrin-6A synthase (deacetylating). In the
aerobic cobalamin biosythesis pathway, four enzymes are
involved in the conversion of precorrin-3A to
precorrin-6A. The first of the four steps is carried out
by EC 1.14.13.83, precorrin-3B synthase (CobG), yielding
precorrin-3B as the product. This is followed by three
methylation reactions, which introduce a methyl group at
C-17 (CobJ; EC 2.1.1.131), C-11 (CobM; EC 2.1.1.133) and
C-1 (CobF; EC 2.1.1.152) of the macrocycle, giving rise
to precorrin-4, precorrin-5 and precorrin-6A,
respectively. This model identifies CobF in High GC gram
positive, alphaproteobacteria and pseudomonas-related
species.
Length = 249
Score = 25.4 bits (56), Expect = 6.2
Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 51 GTPLTVLRVTGTSVAEEGGMEVGDMIVSINGQCT 84
G P+ + TG +AE G E ++V ++G+
Sbjct: 160 GEPVQIT--TGRRLAEGGFPEGDTVVVMLDGEQA 191
>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 = 24.7 bits (54), Expect = 6.6
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 56 VLRVTGTSVAEEGGMEVGDMIVSING 81
V V S A++ G+ GD +V++NG
Sbjct: 16 VTFVRDDSPADKAGLVAGDELVAVNG 41
>gnl|CDD|163409 TIGR03697, NtcA_cyano, global nitrogen regulator NtcA,
cyanobacterial. Members of this protein family, found
in the cyanobacteria, are the global nitrogen regulator
NtcA. This DNA-binding transcriptional regulator is
required for expressing many different
ammonia-repressible genes. The consensus NtcA-binding
site is G T A N(8)T A C [Regulatory functions, DNA
interactions].
Length = 193
Score = 25.2 bits (55), Expect = 7.8
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 20 ILTKEVMCEELKLKKLECEAWGFRLTGGRDFGTP----LTV-LRVTGTSVAEEGG 69
IL E+M E L + + F L RDFG P +T+ LR++ ++AE G
Sbjct: 100 ILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIG 154
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 25.3 bits (55), Expect = 8.7
Identities = 14/54 (25%), Positives = 27/54 (50%)
Query: 56 VLRVTGTSVAEEGGMEVGDMIVSINGQCTQAMTHVEAQQHIIGSGNTLTLQILR 109
V V S + + G++ GD+I S+NG+ + + ++ G + L +LR
Sbjct: 294 VSEVLPNSGSAKAGVKAGDIITSLNGKPLNSFAELRSRIATTEPGTKVKLGLLR 347
>gnl|CDD|223821 COG0750, COG0750, Predicted membrane-associated Zn-dependent
proteases 1 [Cell envelope biogenesis, outer membrane].
Length = 375
Score = 25.2 bits (55), Expect = 10.0
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 46 GGRDFGTPLTVLRVTGTSVAEEGGMEVGDMIVSINGQ 82
G +P+ V S A G+ GD IV+++G+
Sbjct: 124 GLVPVASPVVG-EVAPKSAAALAGLRPGDRIVAVDGE 159
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
0.323 0.139 0.413
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: 5,456,798
Number of extensions: 455790
Number of successful extensions: 335
Number of sequences better than 10.0: 1
Number of HSP's gapped: 335
Number of HSP's successfully gapped: 42
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.3 bits)