RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7774
(173 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 = 68.0 bits (167), Expect = 9e-16
Identities = 31/80 (38%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 90 PRFLMIETRKCSNLGISLVGGN--AVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRA 147
R + + LG SL GG GI+V V+ G GLR GDRILE NG +
Sbjct: 1 VRTVTLRKDPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEG 60
Query: 148 ATAEEAAYELAKPADKVTVL 167
T EEA L D+VT+
Sbjct: 61 LTHEEAVELLKNSGDEVTLT 80
Score = 28.3 bits (64), Expect = 0.68
Identities = 6/25 (24%), Positives = 15/25 (60%)
Query: 1 MRSATYQLAASVLRQCGNSITMLVQ 25
+ T++ A +L+ G+ +T+ V+
Sbjct: 58 VEGLTHEEAVELLKNSGDEVTLTVR 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 = 67.8 bits (166), Expect = 1e-15
Identities = 33/73 (45%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 97 TRKCSNLGISLVGG--NAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAA 154
+ LG SLVGG G+ V SV GS AGLR GD ILE NGT + T EA
Sbjct: 8 EKGGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAV 67
Query: 155 YELAKPADKVTVL 167
L K KVT+
Sbjct: 68 DLLKKAGGKVTLT 80
>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 = 3e-13
Identities = 29/77 (37%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 93 LMIETRKCSNLGISLVGGNA--VGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATA 150
+ +E LG SLVGG+ GI+V V G + GL+ GDRIL NG DL +
Sbjct: 2 VTLEKSGRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSH 61
Query: 151 EEAAYELAKPADKVTVL 167
+EA L +VT+
Sbjct: 62 DEAVLALKGSGGEVTLT 78
>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 = 1e-12
Identities = 29/65 (44%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 103 LGISLVGGNAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYEL-AKPA 161
LG S+ GG G+ V SV+ GS AGL+ GD IL NGTD++ T E+ A L +
Sbjct: 3 LGFSIRGGTEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEVG 62
Query: 162 DKVTV 166
+KVT+
Sbjct: 63 EKVTL 67
>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 = 44.6 bits (106), Expect = 1e-06
Identities = 22/53 (41%), Positives = 28/53 (52%)
Query: 114 GIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELAKPADKVTV 166
G+ V SV GS AGL+ GD IL NG +++ A KP DKVT+
Sbjct: 25 GVLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSVADLRRALAELKPGDKVTL 77
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 44.2 bits (105), Expect = 1e-06
Identities = 21/64 (32%), Positives = 31/64 (48%)
Query: 103 LGISLVGGNAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELAKPAD 162
+G+ +V G+ V SV+ GS AGL+ GD IL +G + + T KP D
Sbjct: 3 IGVRVVQNEGTGVTVVSVKEGSPAAKAGLKPGDIILSIDGKKVNSLTELIEVILNGKPGD 62
Query: 163 KVTV 166
V +
Sbjct: 63 TVKL 66
>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 = 41.5 bits (98), Expect = 1e-05
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 103 LGISLVGGNAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELAK-PA 161
LG GG + + V GS AGL+ GDRIL NG + + E+ + + P
Sbjct: 3 LGFV-PGGPPIEPVIGEVVPGSPAAKAGLKAGDRILAINGQ--KIKSWEDLVDAVQENPG 59
Query: 162 DKVTV 166
+T+
Sbjct: 60 KPLTL 64
>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 = 39.5 bits (93), Expect = 6e-05
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 114 GIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELA-KPADKVTV 166
G+ + SV GS AG++ GD I+ +G + + E+ L K KV +
Sbjct: 14 GLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRL 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 = 39.5 bits (93), Expect = 4e-04
Identities = 18/54 (33%), Positives = 24/54 (44%)
Query: 114 GIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELAKPADKVTVL 167
G+ V V SGS AGL+ GD IL N + + AK +V +L
Sbjct: 363 GVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKKGGRVALL 416
Score = 38.4 bits (90), Expect = 0.001
Identities = 19/53 (35%), Positives = 23/53 (43%)
Query: 114 GIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELAKPADKVTV 166
G V V GS AGL+ GD I NG + + A KP KVT+
Sbjct: 258 GALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTL 310
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 38.5 bits (90), Expect = 0.001
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 103 LGISLVGGNAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELA-KPA 161
+GI L + G+ V S GS AG++ GD I++ +G + + +EA + KP
Sbjct: 102 IGIELQMEDIGGVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPG 161
Query: 162 DKVTV 166
KVT+
Sbjct: 162 TKVTL 166
>gnl|CDD|223821 COG0750, COG0750, Predicted membrane-associated Zn-dependent
proteases 1 [Cell envelope biogenesis, outer membrane].
Length = 375
Score = 35.9 bits (83), Expect = 0.006
Identities = 17/74 (22%), Positives = 23/74 (31%), Gaps = 6/74 (8%)
Query: 105 ISLVGGNAVGI--YVHSVQSGSLGYSAGLRTGDRILEYNGTDLR----AATAEEAAYELA 158
+ V G V V S AGLR GDRI+ +G + AA
Sbjct: 119 LFFVIGLVPVASPVVGEVAPKSAAALAGLRPGDRIVAVDGEKVASWDDVRRLLVAAAGDV 178
Query: 159 KPADKVTVLAHSDT 172
+ V+
Sbjct: 179 FNLLTILVIRLDGE 192
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 34.5 bits (79), Expect = 0.021
Identities = 17/53 (32%), Positives = 25/53 (47%)
Query: 114 GIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELAKPADKVTV 166
G V V GS AG++ GD I NG + + + AA +P D+V +
Sbjct: 271 GAVVLGVLPGSPAAKAGIKAGDIITAVNGKPVASLSDLVAAVASNRPGDEVAL 323
>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 = 31.6 bits (72), Expect = 0.042
Identities = 19/59 (32%), Positives = 26/59 (44%)
Query: 114 GIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELAKPADKVTVLAHSDT 172
G+ + V GS +A L TGD I NGT + A + KP + +TV T
Sbjct: 11 GVVIVGVIVGSPAENAVLHTGDVIYSINGTPITTLEDFMEALKPTKPGEVITVTVLPST 69
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 33.2 bits (76), Expect = 0.049
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 96 ETRKCSNLGISLVGGNAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLR 146
+ R+ LG+ V + V G Y AGL GD+I+ NG +
Sbjct: 446 KPREAYYLGLK-VKSEGGHEKITFVFPGGPAYKAGLSPGDKIVAINGISDQ 495
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 32.0 bits (73), Expect = 0.14
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 120 VQSGSLGYSAGLRTGDRILEYNGTDLRA 147
VQ S AGL+ GDRI++ +G L
Sbjct: 228 VQPNSAASKAGLQAGDRIVKVDGQPLTQ 255
>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 = 31.5 bits (72), Expect = 0.18
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 16/54 (29%)
Query: 105 ISLV-GGNAVGIYVHSVQSGSLGYS---------------AGLRTGDRILEYNG 142
I ++ GG ++G+ +++ +G+S AG++ GDRIL+ NG
Sbjct: 89 IKVIPGGQSIGVKLNTKGVLVVGFSDIETEKGKIHSPGEEAGIQIGDRILKING 142
>gnl|CDD|225575 COG3031, PulC, Type II secretory pathway, component PulC
[Intracellular trafficking and secretion].
Length = 275
Score = 31.0 bits (70), Expect = 0.25
Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 109 GGNAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYEL--AKPADKVTV 166
G + GSL Y +GL+ GD + N DL ++ P+ ++TV
Sbjct: 203 NEKIEGYRFEPGKDGSLFYKSGLQRGDIAVAINNLDLTDPEDMFRLLQMLRNMPSLQLTV 262
Query: 167 L 167
+
Sbjct: 263 I 263
>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease;
Provisional.
Length = 389
Score = 30.5 bits (69), Expect = 0.39
Identities = 18/53 (33%), Positives = 23/53 (43%)
Query: 109 GGNAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELAKPA 161
G G+ V + G AG+R GD IL +GT + EAA L P
Sbjct: 98 DGPPAGLVVVAPAPGGPAARAGIRPGDVILAIDGTSTEGLSLYEAADRLQGPE 150
>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 = 29.8 bits (67), Expect = 0.58
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 108 VGGNAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLR 146
G ++ + SL Y +GL+ GD + NG DLR
Sbjct: 186 KNDKLEGYRLNPGKDPSLFYKSGLQDGDIAVALNGLDLR 224
>gnl|CDD|184986 PRK15026, PRK15026, aminoacyl-histidine dipeptidase; Provisional.
Length = 485
Score = 29.7 bits (66), Expect = 0.87
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 136 RILEYNGTDLRAATAEEAAYELAKPADKVTVL 167
R++++NG LR A EA +A ADKV L
Sbjct: 245 RLIDFNGGTLRNAIPREAFATIAVAADKVDAL 276
>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 = 28.5 bits (64), Expect = 1.7
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 115 IYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYEL-AKPADKVTV 166
I + S GS AG++ GD+I++ NG + + ++A + K KV++
Sbjct: 64 IVIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIRGKKGTKVSL 116
>gnl|CDD|216130 pfam00809, Pterin_bind, Pterin binding enzyme. This family
includes a variety of pterin binding enzymes that all
adopt a TIM barrel fold. The family includes
dihydropteroate synthase EC:2.5.1.15 as well as a group
methyltransferase enzymes including
methyltetrahydrofolate, corrinoid iron-sulfur protein
methyltransferase (MeTr) that catalyzes a key step in
the Wood-Ljungdahl pathway of carbon dioxide fixation.
It transfers the N5-methyl group from
methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide
centre in another protein, the corrinoid iron-sulfur
protein. MeTr is a member of a family of proteins that
includes methionine synthase and methanogenic enzymes
that activate the methyl group of
methyltetra-hydromethano(or -sarcino)pterin.
Length = 210
Score = 28.0 bits (63), Expect = 1.9
Identities = 11/43 (25%), Positives = 14/43 (32%), Gaps = 4/43 (9%)
Query: 129 AGLRTGDRILEYNGTDLRAATAEEAAYELAKPADKVTVLAHSD 171
A L+ G I+ D + LA VL H D
Sbjct: 87 AALKAGADII----NDSSGGKDDPEMAPLAAEYGAPVVLMHMD 125
>gnl|CDD|238348 cd00641, GTP_cyclohydro2, GTP cyclohydrolase II (RibA). GTP
cyclohydrolase II catalyzes the conversion of GTP to
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'
phosphate, formate, pyrophosphate (APy), and GMP in the
biosynthetic pathway of riboflavin. Riboflavin is the
precursor molecule for the synthesis of the coenzymes
flavin mononucleotide (FMN) and flavin adenine
dinucleotide (FAD) which are essential to cell
metabolism. The enzyme is present in plants and numerous
pathogenic bacteria, especially gram negative organisms,
who are dependent on endogenous synthesis of the vitamin
because they lack an appropriate uptake system. For
animals and humans, which lack this biosynthetic
pathway, riboflavin is the essential vitamin B2. GTP
cyclohydrolase II requires magnesium ions for activity
and has a bound catalytic zinc. The functionally active
form is thought to be a homodimer. A paralogous protein
is encoded in the genome of Streptomyces coelicolor,
which converts GTP to
2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone
5'-phosphate (FAPy), an activity that has otherwise been
reported for unrelated GTP cyclohydrolases III.
Length = 193
Score = 27.8 bits (63), Expect = 2.4
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 1 MRSATYQLAASVLRQCGNSITMLVQYSPDKYHELEGSG 38
R Y LAA +LR G L+ +PDK LEG G
Sbjct: 126 ARD--YGLAAQILRDLGIKSVRLLTNNPDKIDALEGYG 161
>gnl|CDD|235964 PRK07204, PRK07204, 3-oxoacyl-(acyl carrier protein) synthase III;
Reviewed.
Length = 329
Score = 27.9 bits (62), Expect = 3.2
Identities = 22/76 (28%), Positives = 30/76 (39%), Gaps = 4/76 (5%)
Query: 69 IQHNTSTLTRTHVCKDERSGEPRFLMIETRKCSNLGISLVGGNAVGIYVHSVQSGS---- 124
+ H S + K E RF+ I + + S+ I VQ G+
Sbjct: 254 VPHQASGPAMRLIRKKLGVDEERFVTIFEDHGNMIAASIPVALFEAIKQKKVQRGNKILL 313
Query: 125 LGYSAGLRTGDRILEY 140
LG SAGL G +LEY
Sbjct: 314 LGTSAGLSIGGILLEY 329
>gnl|CDD|181359 PRK08293, PRK08293, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 287
Score = 27.2 bits (61), Expect = 4.8
Identities = 10/34 (29%), Positives = 13/34 (38%)
Query: 130 GLRTGDRILEYNGTDLRAATAEEAAYELAKPADK 163
GL T I A++AA L + DK
Sbjct: 239 GLDTAYNITSNWAEATDDENAKKAAALLKEYIDK 272
>gnl|CDD|185708 cd07897, Adenylation_DNA_ligase_Bac1, Adenylation domain of
putative bacterial ATP-dependent DNA ligases. Bacterial
DNA ligases are divided into two broad classes:
NAD-dependent and ATP-dependent. All bacterial species
have a NAD-dependent DNA ligase (LigA). Some bacterial
genomes contain multiple genes for DNA ligases that are
predicted to use ATP as their cofactor, including
Mycobacterium tuberculosis LigB, LigC, and LigD. This
group is composed of predicted bacterial ATP-dependent
DNA ligases. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three-step reaction mechanism.
The adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
most members of the ATP-dependent DNA ligase family,
including this group. The adenylation domain binds ATP
and contains many of the active site residues.
Length = 207
Score = 26.7 bits (60), Expect = 5.3
Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 127 YSAGLRTGDRILEYNGTDLRAATAEE 152
A R D +LE NG DLRA E
Sbjct: 111 APAAFRAYD-LLELNGEDLRALPLRE 135
>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 = 25.9 bits (57), Expect = 5.3
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 4/62 (6%)
Query: 103 LGISLVGGNAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEEAAYELAKPAD 162
LG++L +G V V+ S AGL GD ++ NG + A + + D
Sbjct: 3 LGLTLDKEEGLG-KVTFVRDDSPADKAGLVAGDELVAVNGWRVDALQDR---LKEYQAGD 58
Query: 163 KV 164
V
Sbjct: 59 PV 60
>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 = 27.0 bits (60), Expect = 5.6
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 117 VHSVQSGSLGYSAGLRTGDRILEYNGTDLR 146
+ +V GS+ G GD ++ NG R
Sbjct: 2 ISAVLPGSIAEELGFEPGDALVSINGVAPR 31
>gnl|CDD|234428 TIGR03979, His_Ser_Rich, His-Xaa-Ser repeat protein HxsA. Members
of this protein share two defining regions. One is a
histidine/serine-rich cluster, typically
H-R-S-H-S-S-H-R-S-H-S-S-H. Members are found always in
the context of a pair of radical SAM proteins, HxsB and
HxsC, and a fourth protein HxsD. The system is predicted
to perform peptide modifications, likely in the
His-Xaa-Ser region, to produce some uncharacterized
natural product.
Length = 186
Score = 26.8 bits (59), Expect = 5.6
Identities = 18/77 (23%), Positives = 25/77 (32%), Gaps = 4/77 (5%)
Query: 26 YSPDKYHELEGSGSSSAENESVSGRGSGS----PTPCNSPGTNRKSSIQHNTSTLTRTHV 81
+S + H S S A G S P P S + SSIQ ST
Sbjct: 56 HSSHRSHSSHSSHYSGAGGSYSVPSGDTSTYSYPVPSPSYSPSPGSSIQSLPSTTGVRPQ 115
Query: 82 CKDERSGEPRFLMIETR 98
E + + ++ R
Sbjct: 116 SSAENANSEKRKLLVIR 132
>gnl|CDD|227408 COG5076, COG5076, Transcription factor involved in chromatin
remodeling, contains bromodomain [Chromatin structure
and dynamics / Transcription].
Length = 371
Score = 26.7 bits (59), Expect = 6.4
Identities = 9/44 (20%), Positives = 16/44 (36%)
Query: 27 SPDKYHELEGSGSSSAENESVSGRGSGSPTPCNSPGTNRKSSIQ 70
+ GS ++ ++ G + SP N P + R I
Sbjct: 62 TSIVDDREPGSMANVNDDLENVGGITYSPFEKNRPESLRFDEIV 105
>gnl|CDD|216257 pfam01034, Syndecan, Syndecan domain. Syndecans are
transmembrane heparin sulfate proteoglycans which are
implicated in the binding of extracellular matrix
components and growth factors.
Length = 207
Score = 26.2 bits (58), Expect = 7.7
Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 21/77 (27%)
Query: 24 VQYSPDKYHELEGSGSSSA-------ENESVSGRGS------------GSPTPCNSPGTN 64
+Y ++Y + EGSG + S SG G+ S TP T
Sbjct: 25 AEYPDERYLDEEGSGDDDEFIDDEMDDEYSGSGSGATPSDDEDSEPVTTSATPPKLTTT- 83
Query: 65 RKSSIQHNTSTLTRTHV 81
SS ++T+T + +
Sbjct: 84 -SSSPSNDTTTASTSTK 99
>gnl|CDD|183506 PRK12406, PRK12406, long-chain-fatty-acid--CoA ligase; Provisional.
Length = 509
Score = 26.6 bits (59), Expect = 8.7
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 129 AGLRTGDRILEYNGTDLRAATAEEAAYELA-KPADKVTVLAHSD 171
A + +GDR ++ RAA A L +P D V +L +D
Sbjct: 3 ATIISGDRRRSFDELAQRAARAAGGLAALGVRPGDCVALLMRND 46
>gnl|CDD|226143 COG3616, COG3616, Predicted amino acid aldolase or racemase [Amino
acid transport and metabolism].
Length = 368
Score = 26.2 bits (58), Expect = 9.4
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 5/78 (6%)
Query: 93 LMIETRKCSNLGISLVGGNAVGIYVHSVQSGSLGYSAGLRTGDRILEYNGTDLRAATAEE 152
++T KC L + A GI ++ + AG+ D +L Y A
Sbjct: 48 PHVKTHKCPELARIQLDAGAWGITCATLGEAEVFADAGID--DILLAYPLPGRAAL---A 102
Query: 153 AAYELAKPADKVTVLAHS 170
A EL +++VL S
Sbjct: 103 ALAELLADPPRISVLIDS 120
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
0.310 0.125 0.352
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: 8,060,885
Number of extensions: 692082
Number of successful extensions: 514
Number of sequences better than 10.0: 1
Number of HSP's gapped: 511
Number of HSP's successfully gapped: 44
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.0 bits)