RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12579
(138 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 = 101 bits (255), Expect = 2e-29
Identities = 44/83 (53%), Positives = 56/83 (67%), Gaps = 2/83 (2%)
Query: 30 PRVVELPK-TDEGLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVE 88
R V L K GLGF++ GGK+ I++SR+ PGG A+R GGL+ GD++L VNGVSVE
Sbjct: 1 VRTVTLRKDPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAER-GGLRVGDRILEVNGVSVE 59
Query: 89 GEDHGKAVELLKQAQRSVKLVVR 111
G H +AVELLK + V L VR
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 = 92.1 bits (229), Expect = 2e-25
Identities = 39/83 (46%), Positives = 55/83 (66%), Gaps = 1/83 (1%)
Query: 30 PRVVELPKTDEGLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEG 89
PR+VEL K GLGF+++GGK++ + +S ++PG A + GL+ GD +L VNG SVEG
Sbjct: 2 PRLVELEKGGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKA-GLRVGDVILEVNGTSVEG 60
Query: 90 EDHGKAVELLKQAQRSVKLVVRY 112
H +AV+LLK+A V L V
Sbjct: 61 LTHLEAVDLLKKAGGKVTLTVLR 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 = 70.7 bits (174), Expect = 3e-17
Identities = 30/80 (37%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 32 VVELPKTDEGLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGED 91
V GLGF+++GG + + I++S ++PGG A+ GGL+ GD++LS+NG +E
Sbjct: 2 VTLEKSGRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEA-GGLQEGDRILSINGQDLENLS 60
Query: 92 HGKAVELLKQAQRSVKLVVR 111
H +AV LK + V L +
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 = 59.2 bits (144), Expect = 8e-13
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 41 GLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEDHGKAVELLK 100
GLGF++ + + + PG A+R GL+ GD +L+VNG V+ ELLK
Sbjct: 2 GLGFSI--RGGTEGGVVVLSVEPGSPAER-AGLQAGDVILAVNGTDVKNLTLEDVAELLK 58
Query: 101 QAQR-SVKLVVR 111
+ V L VR
Sbjct: 59 KEVGEKVTLTVR 70
>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 = 44.9 bits (107), Expect = 3e-07
Identities = 23/86 (26%), Positives = 44/86 (51%), Gaps = 6/86 (6%)
Query: 40 EGLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEDHGKAVELL 99
G+G + K + + I+ ++PG A + G+K GD +++++G V+G V+LL
Sbjct: 2 GGIGLEL---KYDDGGLVITSVLPGSPAAK-AGIKAGDIIVAIDGEPVDGLSLEDVVKLL 57
Query: 100 K-QAQRSVKLVV-RYTPKVLEEMEMR 123
+ +A V+L + R + E R
Sbjct: 58 RGKAGTKVRLTLKRGDGEPREVTLTR 83
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 40.8 bits (96), Expect = 8e-05
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 40 EGLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEDHGKAVELL 99
G+G + E + + I G A + G+K GD ++ ++G SV G +AV+L+
Sbjct: 100 GGIGIEL--QMEDIGGVKVVSPIDGSPAAK-AGIKPGDVIIKIDGKSVGGVSLDEAVKLI 156
Query: 100 KQAQ-RSVKLVVR 111
+ V L +
Sbjct: 157 RGKPGTKVTLTIL 169
>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 = 37.2 bits (87), Expect = 3e-04
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 48 GGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEDHGKAVELLKQAQRSVK 107
G + + ++ + PG A + GLK GD +L+VNG V+ + + V
Sbjct: 18 LGLKDTKGVLVASVDPGSPAAK-AGLKPGDVILAVNGKPVKSVADLRRALAELKPGDKVT 76
Query: 108 LVVR 111
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 = 35.7 bits (83), Expect = 9e-04
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 41 GLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEG-EDHGKAVELL 99
LGF G I ++PG A + G LK GD++L++NG ++ ED AV+
Sbjct: 2 ILGFVPGG---PPIEPVIGEVVPGSPAAKAG-LKAGDRILAINGQKIKSWEDLVDAVQEN 57
Query: 100 KQAQRSVKLVVR 111
+ L V
Sbjct: 58 PGK--PLTLTVE 67
>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 = 36.0 bits (84), Expect = 0.003
Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 57 YISRIIPGGVADRHGGLKRGDQLLSVNGVSVE 88
+++++PG A++ GLK GD + SVNG +
Sbjct: 260 LVAQVLPGSPAEK-AGLKAGDVITSVNGKPIS 290
Score = 28.0 bits (63), Expect = 1.6
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 58 ISRIIPGGVADRHGGLKRGDQLLSVNGVSVE-GEDHGKAVELLKQAQRSVKLVVR 111
+++++ G A R GL+ GD +LSVN V + K + K+ R L++R
Sbjct: 366 VTKVVSGSPAAR-AGLQPGDVILSVNQQPVSSVAELRKVLARAKKGGRVALLILR 419
>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 = 0.014
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 40 EGLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEDHGKAVELL 99
EG+G V + I I G A++ G+K GD+++ +NG SV G AV L+
Sbjct: 51 EGIGIQVGMDDGE---IVIVSPFEGSPAEK-AGIKPGDKIIKINGKSVAGMSLDDAVALI 106
Query: 100 K 100
+
Sbjct: 107 R 107
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 33.3 bits (76), Expect = 0.022
Identities = 21/76 (27%), Positives = 30/76 (39%), Gaps = 9/76 (11%)
Query: 37 KTDEGLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGE-DHGKA 95
D LG V G + ++PG A + G+K GD + +VNG V D A
Sbjct: 259 TADIALGLPVAAG------AVVLGVLPGSPAAK-AGIKAGDIITAVNGKPVASLSDLVAA 311
Query: 96 VELLKQAQRSVKLVVR 111
V + V L +
Sbjct: 312 VASNRPGDE-VALKLL 326
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 31.5 bits (72), Expect = 0.031
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 51 EQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEDHGKAVELLKQAQRSVKLVV 110
+ + + + + G A + GLK GD +LS++G V V L + +VKL V
Sbjct: 10 NEGTGVTVVSVKEGSPAAK-AGLKPGDIILSIDGKKVNSLTELIEVILNGKPGDTVKLTV 68
Query: 111 R 111
Sbjct: 69 Y 69
>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease;
Provisional.
Length = 389
Score = 32.8 bits (75), Expect = 0.036
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 63 PGGVADRHGGLKRGDQLLSVNGVSVEGEDHGKAVELLK-QAQRSVKLVVRYTPKV 116
PGG A R G++ GD +L+++G S EG +A + L+ SV+L +R P+
Sbjct: 111 PGGPAAR-AGIRPGDVILAIDGTSTEGLSLYEAADRLQGPEGSSVELTLRRGPET 164
>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 = 30.0 bits (68), Expect = 0.31
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 69 RHGGLKRGDQLLSVNGVSVEGEDHGKAVELLKQAQ-RSVKLVVRYTPKVLE 118
G++ GD++L +NG ++ D L+ +A + L + K++E
Sbjct: 127 EEAGIQIGDRILKINGEKIKNMDD--LANLINKAGGEKLTLTIERGGKIIE 175
>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 = 28.2 bits (63), Expect = 0.55
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 50 KEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEDHGKAVELLK--QAQRSVK 107
++ ++ + AD GL GD+L++VNG V + LK QA V+
Sbjct: 8 DKEEGLGKVTFVRDDSPAD-KAGLVAGDELVAVNGWRV-----DALQDRLKEYQAGDPVE 61
Query: 108 LVV 110
L V
Sbjct: 62 LTV 64
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 29.3 bits (66), Expect = 0.63
Identities = 22/107 (20%), Positives = 46/107 (42%), Gaps = 7/107 (6%)
Query: 32 VVELPKTDEGLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGED 91
P+ LG V K + I+ + PGG A + GL GD+++++NG+S + +
Sbjct: 443 FTPKPREAYYLGLKV---KSEGGHEKITFVFPGGPAYK-AGLSPGDKIVAINGISDQLDR 498
Query: 92 HGKAVELLKQAQRSVKLVVRYTPKVLEEMEMRFDKQRTARRRQPPSQ 138
+ K + ++ + + K+ + ++ R P+Q
Sbjct: 499 Y-KVNDKIQVHVFREGRLREFLVKLGGDPTAQYIILPIGDR--NPAQ 542
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 29.2 bits (66), Expect = 0.73
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 48 GGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNG 84
GG +Q I ++ + P G A + G++ D ++SVN
Sbjct: 273 GGIDQLQGIVVNEVSPDGPAAK-AGIQVNDLIISVNN 308
>gnl|CDD|220430 pfam09829, DUF2057, Uncharacterized protein conserved in bacteria
(DUF2057). This domain, found in various prokaryotic
proteins, has no known function.
Length = 189
Score = 28.8 bits (65), Expect = 0.74
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 78 QLLSVNGVSVEGE--DHGKAVELLKQAQRSVKLVVRYTPKVLEEMEMRF 124
+LL+VNG V G ++EL ++VVRY +
Sbjct: 10 ELLAVNGKKVSGSLFSGTSSLELPDGEN---QIVVRYEKLFDSGGDREL 55
>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 = 28.5 bits (64), Expect = 0.96
Identities = 13/28 (46%), Positives = 20/28 (71%), Gaps = 1/28 (3%)
Query: 58 ISRIIPGGVADRHGGLKRGDQLLSVNGV 85
IS ++PG +A+ G + GD L+S+NGV
Sbjct: 2 ISAVLPGSIAEELG-FEPGDALVSINGV 28
>gnl|CDD|178504 PLN02916, PLN02916, pectinesterase family protein.
Length = 502
Score = 28.4 bits (63), Expect = 1.5
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 43 GFNVMGGKEQNSPIYISRIIPG 64
GF+V+ G E+ SP +SR I G
Sbjct: 466 GFHVLRGTEEASPFTVSRFIQG 487
>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 = 28.2 bits (63), Expect = 1.5
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 41 GLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEDHGKAVELLK 100
GLG V+G +++N + + R+IPG A R GL+R D ++ ++ S AV L+
Sbjct: 141 GLGI-VIGMRDRN--LTVVRVIPGTPAAR-AGLQRNDVIVKIDDESTVNMTLNDAVGRLR 196
Query: 101 -QAQRSVKLVVR 111
V + VR
Sbjct: 197 GPPDTKVTIWVR 208
>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 = 27.9 bits (62), Expect = 1.9
Identities = 11/50 (22%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 63 PGGVADRHGGLKRGDQLLSVNGVSV-EGEDHGKAVELLKQAQRSVKLVVR 111
GL+ GD +++NG+ + + E +A+++L++ + ++ L V
Sbjct: 199 KDPSLFYKSGLQDGDIAVALNGLDLRDPEQAFQALQMLRE-ETNLTLTVE 247
>gnl|CDD|226287 COG3764, SrtA, Sortase (surface protein transpeptidase) [Cell
envelope biogenesis, outer membrane].
Length = 210
Score = 27.4 bits (61), Expect = 2.7
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 19/80 (23%)
Query: 19 AAFAASEGHAHPRVVELPK----------TDE-----GLGF---NVMGGKEQNSPIYISR 60
+F + + +E+P TDE G+G + + G+ N + R
Sbjct: 62 VSFYSPDKGEVIGYLEIPSIEVKLPIYEGTDEEDLLYGVGHYKESQVPGENGNYVLAGHR 121
Query: 61 IIPGGVADRH-GGLKRGDQL 79
G R G LK GD++
Sbjct: 122 GTRYGSLFRPLGKLKVGDKI 141
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 27.0 bits (60), Expect = 3.8
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 63 PGGVADRH-----GGLKRGDQLLSVNGVSVEGEDHGKAVELLKQAQRS 105
PGG+A H L R +QL+ V+ +AV+L+ R+
Sbjct: 230 PGGIATIHANNAKAALDRLEQLIQEVSVTPMQTLIAEAVDLVIFIART 277
>gnl|CDD|218622 pfam05521, Phage_H_T_join, Phage head-tail joining protein.
Length = 96
Score = 25.7 bits (57), Expect = 4.1
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 101 QAQRSVKLVVRYTPKVLEEMEMRFDKQR 128
QA+ +V++ +RY P + +M +RF +
Sbjct: 49 QAEVTVRITIRYRPDITADMRIRFGGRI 76
>gnl|CDD|235885 PRK06918, PRK06918, 4-aminobutyrate aminotransferase; Reviewed.
Length = 451
Score = 26.7 bits (59), Expect = 4.6
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 26 GHAHPRVVE-LPKTDEGL---GFNVM 47
GH+HP+V E L K + GFNVM
Sbjct: 69 GHSHPKVKEALHKQVDQYIHTGFNVM 94
>gnl|CDD|181546 PRK08751, PRK08751, putative long-chain fatty acyl CoA ligase;
Provisional.
Length = 560
Score = 26.8 bits (59), Expect = 4.7
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 12/43 (27%)
Query: 3 LGSPDVRASATAKATVAAFAASEGHAHPRVVE----LPKTDEG 41
L + DV+A A A T G+ PR++E LPKT+ G
Sbjct: 513 LTAEDVKAHARANLT--------GYKQPRIIEFRKELPKTNVG 547
>gnl|CDD|181493 PRK08593, PRK08593, 4-aminobutyrate aminotransferase;
Provisional.
Length = 445
Score = 26.2 bits (58), Expect = 6.5
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 8/28 (28%)
Query: 7 DVRASATAKATVAAFAASEGHAHPRVVE 34
D+ ASA+++ GHA PRVVE
Sbjct: 46 DLLASASSQNV--------GHAPPRVVE 65
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 24.4 bits (54), Expect = 7.0
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 111 RYTPKVLEEMEMRFDKQR--TARRRQ 134
+TP+ LEE+E F+K R +A R+
Sbjct: 6 TFTPEQLEELEKEFEKNRYPSAEERE 31
>gnl|CDD|153365 cd07681, F-BAR_PACSIN3, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons 3 (PACSIN3). F-BAR
domains are dimerization modules that bind and bend
membranes and are found in proteins involved in membrane
dynamics and actin reorganization. Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins,
also called Synaptic dynamin-associated proteins
(Syndapins), act as regulators of cytoskeletal and
membrane dynamics. Vetebrates harbor three isoforms with
distinct expression patterns and specific functions.
PACSIN 3 or Syndapin III is expressed ubiquitously and
regulates glucose uptake in adipocytes through its role
in GLUT1 trafficking. It also modulates the subcellular
localization and stimulus-specific function of the
cation channel TRPV4. PACSIN 3 contains an N-terminal
F-BAR domain and a C-terminal SH3 domain. F-BAR domains
form banana-shaped dimers with a positively-charged
concave surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 258
Score = 26.1 bits (57), Expect = 7.1
Identities = 10/34 (29%), Positives = 23/34 (67%)
Query: 101 QAQRSVKLVVRYTPKVLEEMEMRFDKQRTARRRQ 134
Q +++++ + RY P+ +E+ME F+ + A R++
Sbjct: 190 QYEKALEELNRYNPRYMEDMEQAFEICQEAERKR 223
>gnl|CDD|233917 TIGR02544, III_secr_YscJ, type III secretion apparatus lipoprotein,
YscJ/HrcJ family. All members of this protein family
are predicted lipoproteins with a conserved Cys near the
N-terminus for cleavage and modification, and are part
of known or predicted type III secretion systems.
Members are found in both plant and animal pathogens,
including the obligately intracellular chlamydial
species and (non-pathogenic) root nodule bacteria. The
most closely related proteins outside this family are
examples of the flagellar M-ring protein FliF [Protein
fate, Protein and peptide secretion and trafficking,
Cellular processes, Pathogenesis].
Length = 193
Score = 25.7 bits (57), Expect = 7.2
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 67 ADRHGGLKRGDQLLSVNGVSVEGEDHGKAVELLKQAQ 103
A++ G K G +SVE D +AVELL+Q
Sbjct: 45 AEKEGSGKGG------YTISVEESDFARAVELLRQYG 75
>gnl|CDD|180426 PRK06148, PRK06148, hypothetical protein; Provisional.
Length = 1013
Score = 26.1 bits (58), Expect = 7.9
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 26 GHAHPRVVE 34
GHAHPRVV
Sbjct: 637 GHAHPRVVA 645
>gnl|CDD|224639 COG1725, COG1725, Predicted transcriptional regulators
[Transcription].
Length = 125
Score = 25.3 bits (56), Expect = 8.1
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 14/58 (24%)
Query: 54 SPIY--ISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEDHG-------KAVELLKQA 102
PIY I+ I +A LK GD+L SV +D G +A + L++
Sbjct: 10 KPIYEQIANQIKEQIASGE--LKPGDKLPSVR---ELAKDLGVNPNTVQRAYQELERE 62
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
0.315 0.132 0.371
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: 7,023,188
Number of extensions: 629627
Number of successful extensions: 532
Number of sequences better than 10.0: 1
Number of HSP's gapped: 524
Number of HSP's successfully gapped: 50
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (24.6 bits)