RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8436
(306 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 = 79.9 bits (198), Expect = 3e-19
Identities = 35/75 (46%), Positives = 45/75 (60%), Gaps = 5/75 (6%)
Query: 222 FTVTFQKGPGQKSLGFSIVGGRDSPKGNLGIFVKTIFQSGQAAENEKLREGDEIIAINGV 281
TVT +K PG LGFS+ GG+DS GIFV + + G AE LR GD I+ +NGV
Sbjct: 2 RTVTLRKDPG-GGLGFSLRGGKDS---GGGIFVSRV-EPGGPAERGGLRVGDRILEVNGV 56
Query: 282 PLENKTHAEAIAMFK 296
+E TH EA+ + K
Sbjct: 57 SVEGLTHEEAVELLK 71
Score = 64.1 bits (157), Expect = 2e-13
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 9 RVVKDDSNELGIYIERQDGGAHFSPYLISHIEPGGAIHRDGRFHVGDELIKVNDKRLKGL 68
+ KD LG + + G +S +EPGG R G VGD +++VN ++GL
Sbjct: 5 TLRKDPGGGLGFSL--RGGKDSGGGIFVSRVEPGGPAER-GGLRVGDRILEVNGVSVEGL 61
Query: 69 TIQEAREALNNKDSHVEIVIC 89
T +EA E L N V + +
Sbjct: 62 THEEAVELLKNSGDEVTLTVR 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 = 70.5 bits (173), Expect = 1e-15
Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 221 MFTVTFQKGPGQKSLGFSIVGGRDSPKGNLGIFVKTIFQSGQAAENEKLREGDEIIAING 280
V +KG G LGFS+VGG+D G + V ++ G A LR GD I+ +NG
Sbjct: 2 PRLVELEKGGGG--LGFSLVGGKDEGGG---VVVSSVVP-GSPAAKAGLRVGDVILEVNG 55
Query: 281 VPLENKTHAEAIAMFK 296
+E TH EA+ + K
Sbjct: 56 TSVEGLTHLEAVDLLK 71
Score = 57.0 bits (138), Expect = 1e-10
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 3/79 (3%)
Query: 14 DSNELGIYIERQDGGAHFSPYLISHIEPGGAIHRDGRFHVGDELIKVNDKRLKGLTIQEA 73
LG + G ++S + PG + G VGD +++VN ++GLT EA
Sbjct: 10 GGGGLGFSL--VGGKDEGGGVVVSSVVPGSPAAKAG-LRVGDVILEVNGTSVEGLTHLEA 66
Query: 74 REALNNKDSHVEIVICRNP 92
+ L V + + R
Sbjct: 67 VDLLKKAGGKVTLTVLRGG 85
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 58.4 bits (142), Expect = 2e-11
Identities = 36/76 (47%), Positives = 46/76 (60%), Gaps = 5/76 (6%)
Query: 223 TVTFQKGPGQKSLGFSIVGGRDSPKGNLGIFVKTIFQSGQAAENEKLREGDEIIAINGVP 282
VT +K G+ LGFS+VGG D G+ GIFV + G AAE L+EGD I++ING
Sbjct: 1 EVTLEK-SGRGGLGFSLVGGSD---GDPGIFVSEV-LPGGAAEAGGLQEGDRILSINGQD 55
Query: 283 LENKTHAEAIAMFKDI 298
LEN +H EA+ K
Sbjct: 56 LENLSHDEAVLALKGS 71
Score = 39.9 bits (94), Expect = 1e-04
Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 3/80 (3%)
Query: 9 RVVKDDSNELGIYIERQDGGAHFSPYLISHIEPGGAIHRDGRFHVGDELIKVNDKRLKGL 68
+ K LG + G +S + PGGA G GD ++ +N + L+ L
Sbjct: 3 TLEKSGRGGLGFSLVGGSDGDP--GIFVSEVLPGGAAEAGG-LQEGDRILSINGQDLENL 59
Query: 69 TIQEAREALNNKDSHVEIVI 88
+ EA AL V + I
Sbjct: 60 SHDEAVLALKGSGGEVTLTI 79
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization through
PDZ-PDZ domain interactions adds to the domain's
versatility, and PDZ domain-mediated interactions may be
modulated dynamically through target phosphorylation.
Some PDZ domains play a role in scaffolding
supramolecular complexes. PDZ domains are found in
diverse signaling proteins in bacteria, archebacteria,
and eurkayotes. This CD contains two distinct structural
subgroups with either a N- or C-terminal beta-strand
forming the peptide-binding groove base. The circular
permutation placing the strand on the N-terminus appears
to be found in Eumetazoa only, while the C-terminal
variant is found in all three kingdoms of life, and
seems to co-occur with protease domains. PDZ domains
have been named after PSD95(post synaptic density
protein), DlgA (Drosophila disc large tumor suppressor),
and ZO1, a mammalian tight junction protein.
Length = 70
Score = 53.8 bits (130), Expect = 9e-10
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 233 KSLGFSIVGGRDSPKGNLGIFVKTIFQSGQAAENEKLREGDEIIAINGVPLENKTHAEAI 292
LGFSI GG G+ V ++ AE L+ GD I+A+NG ++N T +
Sbjct: 1 GGLGFSIRGG-----TEGGVVVLSVEPGS-PAERAGLQAGDVILAVNGTDVKNLTLEDVA 54
Query: 293 AMFKDIFPQSSKL 305
+ K + L
Sbjct: 55 ELLKKEVGEKVTL 67
Score = 40.4 bits (95), Expect = 6e-05
Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 16 NELGIYIERQDGGAHFSPYLISHIEPGGAIHRDGRFHVGDELIKVNDKRLKGLTIQEARE 75
LG I G ++ +EPG R G GD ++ VN +K LT+++ E
Sbjct: 1 GGLGFSI----RGGTEGGVVVLSVEPGSPAERAG-LQAGDVILAVNGTDVKNLTLEDVAE 55
Query: 76 ALNNKDSH-VEIVI 88
L + V + +
Sbjct: 56 LLKKEVGEKVTLTV 69
>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 = 2e-04
Identities = 17/83 (20%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 18 LGIYIERQDGGAHFSPYLISHIEPGGAIHRDGRFHVGDELIKVNDKRLKGLTIQEAREAL 77
+G+ ++ DGG +I+ + PG + G GD ++ ++ + + GL++++ + L
Sbjct: 4 IGLELKYDDGG-----LVITSVLPGSPAAKAG-IKAGDIIVAIDGEPVDGLSLEDVVKLL 57
Query: 78 NNK-DSHVEIVICRNPDDAKSAT 99
K + V + + R + + T
Sbjct: 58 RGKAGTKVRLTLKRGDGEPREVT 80
Score = 38.4 bits (90), Expect = 4e-04
Identities = 10/46 (21%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 251 GIFVKTIFQSGQAAENEKLREGDEIIAINGVPLENKTHAEAIAMFK 296
G+ + ++ G A ++ GD I+AI+G P++ + + + + +
Sbjct: 14 GLVITSVL-PGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLR 58
>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 = 33.0 bits (76), Expect = 0.027
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 259 QSGQAAENEKLREGDEIIAINGVPLEN 285
G A L+ GD I+AING +++
Sbjct: 20 VPGSPAAKAGLKAGDRILAINGQKIKS 46
Score = 30.3 bits (69), Expect = 0.23
Identities = 13/66 (19%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 27 GGAHFSPYLISHIEPGGAIHRDGRFHVGDELIKVNDKRLKGLTIQEAREAL-NNKDSHVE 85
G +I + PG + G GD ++ +N +++K + ++ +A+ N +
Sbjct: 7 PGGPPIEPVIGEVVPGSPAAKAG-LKAGDRILAINGQKIK--SWEDLVDAVQENPGKPLT 63
Query: 86 IVICRN 91
+ + RN
Sbjct: 64 LTVERN 69
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 33.1 bits (76), Expect = 0.15
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 251 GIFVKTIFQSGQAAENEKLREGDEIIAINGVPLENKTHAEAIAMFK 296
G+ V + A ++ GD II I+G + + EA+ + +
Sbjct: 113 GVKVVSPIDGS-PAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIR 157
Score = 28.1 bits (63), Expect = 6.2
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 18 LGIYIERQDGGAHFSPYLISHIEPGGAIHRDGRFHVGDELIKVNDKRLKGLTIQEAREAL 77
+GI ++ +D G + G + G GD +IK++ K + G+++ EA + +
Sbjct: 102 IGIELQMEDIGGVK----VVSPIDGSPAAKAG-IKPGDVIIKIDGKSVGGVSLDEAVKLI 156
Query: 78 NNKD-SHVEIVICRNPDD 94
K + V + I R
Sbjct: 157 RGKPGTKVTLTILRAGGG 174
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 30.7 bits (70), Expect = 0.16
Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 235 LGFSIVGGRDSPKGNLGIFVKTIFQSGQAAENEKLREGDEIIAINGVPLENKTHAEAIAM 294
+G +V + G+ V ++ + AA+ L+ GD I++I+G + + T + +
Sbjct: 3 IGVRVVQNEGT-----GVTVVSVKEGSPAAKA-GLKPGDIILSIDGKKVNSLTELIEVIL 56
Query: 295 FKDI 298
Sbjct: 57 NGKP 60
>gnl|CDD|99787 cd06190, T4MO_e_transfer_like, Toluene-4-monoxygenase electron
transfer component of Pseudomonas mendocina
hydroxylates toluene and forms p-cresol as part of a
three component toluene-4-monoxygenase system. Electron
transfer is from NADH to an NADH:ferredoxin
oxidoreductase (TmoF in P. mendocina) to ferredoxin to
an iron-containing oxygenase. TmoF is homologous to
other mono- and dioxygenase systems within the
ferredoxin reductase family.
Length = 232
Score = 31.1 bits (71), Expect = 0.60
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 13 DDSNELGIYIERQDGGAHFSPYLISHIEPGGAIHRDG 49
+ S E I+R+ GGA S L ++EPG + DG
Sbjct: 50 NASGEWEFIIKRKPGGA-ASNALFDNLEPGDELELDG 85
>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 = 31.0 bits (71), Expect = 0.73
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 259 QSGQAAENEKLREGDEIIAINGVPLEN 285
SG A L+ GD I+++N P+ +
Sbjct: 370 VSGSPAARAGLQPGDVILSVNQQPVSS 396
Score = 28.0 bits (63), Expect = 7.7
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 251 GIFVKTIFQSGQAAENEKLREGDEIIAINGVPLENKTH-AEAIAMFK 296
G V + G AE L+ GD I ++NG P+ + AI K
Sbjct: 258 GALVAQVLP-GSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLK 303
>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 = 28.8 bits (65), Expect = 1.1
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 246 PKGNLGIFVKTIFQSGQAAENEKLREGDEIIAINGVPLEN 285
K G+ V ++ G A L+ GD I+A+NG P+++
Sbjct: 20 LKDTKGVLVASV-DPGSPAAKAGLKPGDVILAVNGKPVKS 58
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 30.2 bits (68), Expect = 1.4
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 35 LISHIEPGGAIHRDGRFHVGDELIKVNDKRLKGLTIQEAREALNNKDSHVEIVICRN 91
++ + PG + G GD + VN K + L+ A A N V + + R
Sbjct: 273 VVLGVLPGSPAAKAG-IKAGDIITAVNGKPVASLSDLVAAVASNRPGDEVALKLLRG 328
>gnl|CDD|227376 COG5043, MRS6, Vacuolar protein sorting-associated protein
[Intracellular trafficking and secretion].
Length = 2552
Score = 30.2 bits (68), Expect = 1.9
Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 2/88 (2%)
Query: 166 KIRNKVTGMRKFSCQFDGISPRRRQSVVDHNRSNVAATPNNSNATVKRPKSLSLSMFTVT 225
+ + VT + F R+ + +RS +S TV + +
Sbjct: 1251 DLIDVVTTFFRIDSSFSTSENLPRELDSEFDRSGTPVKLKHSKKTVVETLDILFTFKLPK 1310
Query: 226 FQKGPGQKSLGFSIVGGRDSPKGNLGIF 253
+ + F I GG + N+ F
Sbjct: 1311 IRLNLYTGT--FGIHGGDLTGLHNILFF 1336
>gnl|CDD|237306 PRK13208, valS, valyl-tRNA synthetase; Reviewed.
Length = 800
Score = 29.8 bits (68), Expect = 2.4
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 7/33 (21%)
Query: 44 AIHRDGRFHVGDELIKVNDKRLKGLTIQEAREA 76
I DGR + +L GLTI+EAR+
Sbjct: 294 IIDEDGR-------MTEAAGKLAGLTIEEARKK 319
>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 = 29.3 bits (66), Expect = 2.4
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 261 GQAAENEKLREGDEIIAINGVPLENKTHAEAIAMFK 296
G AE ++ GD+II ING + + +A+A+ +
Sbjct: 72 GSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIR 107
>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 = 2.8
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 8/64 (12%)
Query: 246 PKGNLGIFVK--------TIFQSGQAAENEKLREGDEIIAINGVPLENKTHAEAIAMFKD 297
LG+ VK T G A L GD+I+AING+ + + +
Sbjct: 449 EAYYLGLKVKSEGGHEKITFVFPGGPAYKAGLSPGDKIVAINGISDQLDRYKVNDKIQVH 508
Query: 298 IFPQ 301
+F +
Sbjct: 509 VFRE 512
>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 = 29.0 bits (65), Expect = 3.7
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 259 QSGQAAENEKLREGDEIIAINGVPLENKT 287
AE L+EGD I +ING L + T
Sbjct: 210 TPNSPAEKAGLKEGDYIQSINGEKLRSWT 238
>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 = 28.8 bits (65), Expect = 3.8
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 264 AENEKLREGDEIIAINGVPLENKTHA 289
E ++ GD I+ ING ++N
Sbjct: 126 GEEAGIQIGDRILKINGEKIKNMDDL 151
>gnl|CDD|187831 cd09700, Csx10, CRISPR/Cas system-associated RAMP superfamily
protein Csx10. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Duplicated RAMP domains.
Length = 386
Score = 28.7 bits (64), Expect = 4.1
Identities = 27/132 (20%), Positives = 46/132 (34%), Gaps = 23/132 (17%)
Query: 20 IYIERQDGGAHFSPYLISHIEPGGAIHRD-GRFHVGDELIKVNDKRLKGLTIQEAREALN 78
IY+++ D S L GG++ R GR + V +G R
Sbjct: 194 IYVDKDDLAELLSSLLRHIYRLGGSVSRGYGR-------VTVAADEPQGFPDIVERVIPF 246
Query: 79 NKDSHVEIVICRNPDDAKSATNCDNLQPNPKNLPKKNIIINQRQKNIVEKSLMPER-QVS 137
N +++I R D D L P P + + ++PE QV+
Sbjct: 247 N-----QVLIDRWQDWVVLLG--DTLVPLPAKRTYFST-------GLYSWDILPELWQVA 292
Query: 138 MPEIERNKTEVI 149
+P + + + E
Sbjct: 293 LPPMLQVEAEHE 304
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 28.9 bits (65), Expect = 4.2
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 7/51 (13%)
Query: 234 SLGFSIVGGRDSPKGNLGIFVKTIFQSGQAAENEKLREGDEIIAINGVPLE 284
SLG G + P V Q AA L+ GD I+ ++G PL
Sbjct: 211 SLGIRPRGPQIEP-------VLAEVQPNSAASKAGLQAGDRIVKVDGQPLT 254
>gnl|CDD|205321 pfam13140, DUF3980, Domain of unknown function (DUF3980). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is approximately
90 amino acids in length.
Length = 87
Score = 26.7 bits (59), Expect = 4.6
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 216 SLSLSMFTVTFQKGPGQKSLGFSIVGGRDSPKGNLGIFVKTIFQS 260
S+ ++ T +F G G +S+ S G I + +IFQS
Sbjct: 25 SILAAVSTGSFINGSGFQSISVSGAGAATGF-----IALGSIFQS 64
>gnl|CDD|129405 TIGR00305, TIGR00305, putative toxin-antitoxin system toxin
component, PIN family. This uncharacterized protein
family, part of the PIN domain superfamily, is
restricted to bacteria and archaea. A comprehensive in
silico study of toxin-antitoxin systems by Makarova, et
al. (2009) finds evidence this family represents the
toxin-like component of one class of type 2
toxin-antitoxin systems [Cellular processes, Other,
Transcription, Degradation of RNA].
Length = 114
Score = 27.0 bits (60), Expect = 5.1
Identities = 11/38 (28%), Positives = 14/38 (36%), Gaps = 4/38 (10%)
Query: 63 KRLKGLTIQEAREALNNK----DSHVEIVICRNPDDAK 96
K TI E L K + + E CR+ D K
Sbjct: 54 KYFALETILEILLLLGEKSTIINPNPEFDDCRDKKDNK 91
>gnl|CDD|165121 PHA02754, PHA02754, hypothetical protein; Provisional.
Length = 67
Score = 26.1 bits (57), Expect = 6.2
Identities = 14/25 (56%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 1 MEKQFKVF-RVVKDDSNELGIYIER 24
MEK FK R +KD +E GIYI+R
Sbjct: 12 MEKDFKEAMRELKDILSEAGIYIDR 36
>gnl|CDD|239919 cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of the
archaea-specific RecJ-like exonuclease. The function of
this family is not fully understood. In Escherichia
coli, RecJ degrades single-stranded DNA in the 5'-3'
direction and participates in homologous recombination
and mismatch repair.
Length = 77
Score = 26.4 bits (59), Expect = 6.2
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 43 GAIHR---DGRFHVGDELI-KVNDKRLKG 67
G IHR + VGDE+I +V D G
Sbjct: 42 GLIHRSNLLRDYEVGDEVIVQVTDIPENG 70
>gnl|CDD|133420 cd00704, MDH, Malate dehydrogenase. Malate dehydrogenase (MDH) is
one of the key enzymes in the citric acid cycle,
facilitating both the conversion of malate to
oxaloacetate and replenishing levels of oxalacetate by
reductive carboxylation of pyruvate. MDHs belong to the
NAD-dependent, lactate dehydrogenase (LDH)-like,
2-hydroxycarboxylate dehydrogenase family, which also
includes the GH4 family of glycoside hydrolases. They
are part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 323
Score = 27.6 bits (62), Expect = 8.8
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 10/63 (15%)
Query: 56 ELIKVNDKRLKGLTIQEAREALNNKDS-HVEIVICRNPDDAKSATNCDNLQPNPKNLPKK 114
+L++ N K K E EALN V++++ NP + TN N NLP K
Sbjct: 96 DLLRKNAKIFK-----EQGEALNKVAKPTVKVLVVGNP----ANTNALIALKNAPNLPPK 146
Query: 115 NII 117
N
Sbjct: 147 NFT 149
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
0.314 0.131 0.368
Gapped
Lambda K H
0.267 0.0487 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,117,141
Number of extensions: 1419217
Number of successful extensions: 963
Number of sequences better than 10.0: 1
Number of HSP's gapped: 957
Number of HSP's successfully gapped: 44
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
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 (22.0 bits)
S2: 59 (27.1 bits)