RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1156
(671 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 = 87.6 bits (218), Expect = 4e-21
Identities = 35/87 (40%), Positives = 47/87 (54%), Gaps = 6/87 (6%)
Query: 577 HTIVFEKGPGKKGLGFTIVGGKDSPRGAIGIFIKSILDNGQAAEDGRLKEGDEILAINGQ 636
T+ K PG GLGF++ GGKDS G IF+ + G AE G L+ GD IL +NG
Sbjct: 2 RTVTLRKDPGG-GLGFSLRGGKDSGGG---IFVSRVEPGG-PAERGGLRVGDRILEVNGV 56
Query: 637 VCHDLTHLEAISLFKTIKNGSISLHIC 663
LTH EA+ L K + ++L +
Sbjct: 57 SVEGLTHEEAVELLKNSGD-EVTLTVR 82
Score = 64.5 bits (158), Expect = 6e-13
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 395 RRDFNEELGIYIAKIKNSSEGNIGGFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGL 454
R+D LG + K+S GG V+ + GG AE+ G L +GD I+ VNG + GL
Sbjct: 7 RKDPGGGLGFSLRGGKDSG----GGIFVSRVEPGGPAER-GGLRVGDRILEVNGVSVEGL 61
Query: 455 TMTQAKSIISSGPLNMDLLI 474
T +A ++ + + L +
Sbjct: 62 THEEAVELLKNSGDEVTLTV 81
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some PDZs
have been shown to bind C-terminal polypeptides; others
appear to bind internal (non-C-terminal) polypeptides.
Different PDZs possess different binding specificities.
Length = 85
Score = 80.1 bits (198), Expect = 2e-18
Identities = 36/89 (40%), Positives = 50/89 (56%), Gaps = 7/89 (7%)
Query: 577 HTIVFEKGPGKKGLGFTIVGGKDSPRGAIGIFIKSILDNGQAAEDGRLKEGDEILAINGQ 636
+ EKG G GLGF++VGGKD G + + S++ AA+ G L+ GD IL +NG
Sbjct: 3 RLVELEKGGG--GLGFSLVGGKDEGGG---VVVSSVVPGSPAAKAG-LRVGDVILEVNGT 56
Query: 637 VCHDLTHLEAISLFKTIKNGSISLHICRR 665
LTHLEA+ L K G ++L + R
Sbjct: 57 SVEGLTHLEAVDLLKKAG-GKVTLTVLRG 84
Score = 59.3 bits (144), Expect = 4e-11
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 7/86 (8%)
Query: 391 VRVNRRDFNEELGIYIAKIKNSSEGNIGGFVVAHIVSGGLAEKEGCLELGDEIISVNGQR 450
V + + LG + K+ GG VV+ +V G A K G L +GD I+ VNG
Sbjct: 5 VELEKGG--GGLGFSLVGGKD----EGGGVVVSSVVPGSPAAKAG-LRVGDVILEVNGTS 57
Query: 451 LRGLTMTQAKSIISSGPLNMDLLISR 476
+ GLT +A ++ + L + R
Sbjct: 58 VEGLTHLEAVDLLKKAGGKVTLTVLR 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 = 63.4 bits (155), Expect = 1e-12
Identities = 39/85 (45%), Positives = 52/85 (61%), Gaps = 6/85 (7%)
Query: 578 TIVFEKGPGKKGLGFTIVGGKDSPRGAIGIFIKSILDNGQAAEDGRLKEGDEILAINGQV 637
+ EK G+ GLGF++VGG D G GIF+ +L G AAE G L+EGD IL+INGQ
Sbjct: 1 EVTLEK-SGRGGLGFSLVGGSD---GDPGIFVSEVLPGG-AAEAGGLQEGDRILSINGQD 55
Query: 638 CHDLTHLEAISLFKTIKNGSISLHI 662
+L+H EA+ L G ++L I
Sbjct: 56 LENLSHDEAV-LALKGSGGEVTLTI 79
Score = 48.4 bits (116), Expect = 2e-07
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 399 NEELGIYIAKIKNSSEGNIGGFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGLTMTQ 458
LG + S+G+ G FV + ++ GG AE G L+ GD I+S+NGQ L L+ +
Sbjct: 9 RGGLGF---SLVGGSDGDPGIFV-SEVLPGGAAEAGG-LQEGDRILSINGQDLENLSHDE 63
Query: 459 AKSIISSGPLNMDLLI 474
A + + L I
Sbjct: 64 AVLALKGSGGEVTLTI 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 = 60.8 bits (148), Expect = 7e-12
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 588 KGLGFTIVGGKDSPRGAIGIFIKSILDNGQAAEDGRLKEGDEILAINGQVCHDLTHLEAI 647
GLGF+I GG + G+ + S+ A G L+ GD ILA+NG +LT +
Sbjct: 1 GGLGFSIRGGTEG-----GVVVLSVEPGSPAERAG-LQAGDVILAVNGTDVKNLTLEDVA 54
Query: 648 SLFKTIKNGSISLHI 662
L K ++L +
Sbjct: 55 ELLKKEVGEKVTLTV 69
Score = 45.0 bits (107), Expect = 3e-06
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 401 ELGIYIAKIKNSSEGNIGGFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGLTMTQAK 460
LG I G GG VV + G AE+ G L+ GD I++VNG ++ LT+
Sbjct: 2 GLGFSIRG------GTEGGVVVLSVEPGSPAERAG-LQAGDVILAVNGTDVKNLTLEDVA 54
Query: 461 SII 463
++
Sbjct: 55 ELL 57
>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 = 41.8 bits (99), Expect = 5e-05
Identities = 14/58 (24%), Positives = 30/58 (51%), Gaps = 8/58 (13%)
Query: 402 LGIYIAKIKNSSEGNIGGFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGLTMTQA 459
+G+ + GG V+ ++ G A K G ++ GD I++++G+ + GL++
Sbjct: 4 IGLELKYDD-------GGLVITSVLPGSPAAKAG-IKAGDIIVAIDGEPVDGLSLEDV 53
Score = 41.4 bits (98), Expect = 8e-05
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 606 GIFIKSILDNGQAAEDGRLKEGDEILAINGQVCHDLTHLEAISLFK 651
G+ I S+L AA+ G +K GD I+AI+G+ L+ + + L +
Sbjct: 14 GLVITSVLPGSPAAKAG-IKAGDIIVAIDGEPVDGLSLEDVVKLLR 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 = 41.5 bits (98), Expect = 7e-05
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 421 VVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGLTMTQAKSIISSGP-LNMDLLISR 476
V+ +V G A K G L+ GD I+++NGQ+++ + + P + L + R
Sbjct: 15 VIGEVVPGSPAAKAG-LKAGDRILAINGQKIK--SWEDLVDAVQENPGKPLTLTVER 68
Score = 38.8 bits (91), Expect = 6e-04
Identities = 20/48 (41%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 589 GLGFTIVGGKDSPRGAIGIFIKSILDNGQAAEDGRLKEGDEILAINGQ 636
LGF G P I ++ AA+ G LK GD ILAINGQ
Sbjct: 2 ILGFVPGGPPIEPV------IGEVVPGSPAAKAG-LKAGDRILAINGQ 42
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 38.8 bits (91), Expect = 6e-04
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 589 GLGFTIVGGKDSPRGAIGIFIKSILDNGQAAEDGRLKEGDEILAINGQVCHDLTHLEAIS 648
+G +V G+ + S+ + AA+ G LK GD IL+I+G+ + LT L +
Sbjct: 2 DIGVRVV-----QNEGTGVTVVSVKEGSPAAKAG-LKPGDIILSIDGKKVNSLTELIEVI 55
Query: 649 LFKTI 653
L
Sbjct: 56 LNGKP 60
Score = 30.7 bits (70), Expect = 0.39
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 419 GFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGLTMTQAKSIISSGP 467
G V + G A K G L+ GD I+S++G+++ ++T+ +I +G
Sbjct: 14 GVTVVSVKEGSPAAKAG-LKPGDIILSIDGKKVN--SLTELIEVILNGK 59
>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 = 38.0 bits (89), Expect = 0.001
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 606 GIFIKSILDNGQAAEDGRLKEGDEILAINGQVCHDLTHLEAISLFKTIKNGSISLHICR 664
G+ + S+ AA+ G LK GD ILA+NG+ + L L + ++L + R
Sbjct: 25 GVLVASVDPGSPAAKAG-LKPGDVILAVNGKPVKSVADLRRA-LAELKPGDKVTLTVLR 81
Score = 35.3 bits (82), Expect = 0.013
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 416 NIGGFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGLTMTQAKSIISSGPLN--MDLL 473
+ G +VA + G A K G L+ GD I++VNG+ ++ ++ + ++ + L
Sbjct: 22 DTKGVLVASVDPGSPAAKAG-LKPGDVILAVNGKPVK--SVADLRRALAELKPGDKVTLT 78
Query: 474 ISR 476
+ R
Sbjct: 79 VLR 81
>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 = 0.005
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 597 GKDSPRGAIGIFIKSILDNGQAAEDGRLKEGDEILAINGQVCHDLTHL-EAISLFKTIKN 655
G + RGA + +L A + G LK GD I ++NG+ L AI T+K
Sbjct: 252 GLEKQRGA---LVAQVLPGSPAEKAG-LKAGDVITSVNGKPISSFADLRRAIG---TLKP 304
Query: 656 GS-ISLHICRRLKSKK 670
G ++L I R+ K K
Sbjct: 305 GKKVTLGILRKGKEKT 320
Score = 35.7 bits (83), Expect = 0.081
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 401 ELGIYIAKIKNSSEGNIGGFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLR 452
L I K G++ G VV +VSG A + G L+ GD I+SVN Q +
Sbjct: 346 NLSPEIRKELRLK-GDVKGVVVTKVVSGSPAARAG-LQPGDVILSVNQQPVS 395
Score = 33.7 bits (78), Expect = 0.27
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 418 GGFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLR 452
G +VA ++ G AEK G L+ GD I SVNG+ +
Sbjct: 257 RGALVAQVLPGSPAEKAG-LKAGDVITSVNGKPIS 290
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 38.1 bits (89), Expect = 0.013
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 400 EELGIYIAKIKNSSEGNIGGFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGLTMTQA 459
+GI + +IGG V + G A K G ++ GD II ++G+ + G+++ +A
Sbjct: 100 GGIGIELQME------DIGGVKVVSPIDGSPAAKAG-IKPGDVIIKIDGKSVGGVSLDEA 152
Score = 37.7 bits (88), Expect = 0.019
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 606 GIFIKSILDNGQAAEDGRLKEGDEILAINGQVCHDLTHLEAISLFKTIKNGSISLHICRR 665
G+ + S +D AA+ G +K GD I+ I+G+ ++ EA+ L + ++L I R
Sbjct: 113 GVKVVSPIDGSPAAKAG-IKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILRA 171
Query: 666 LKSKK 670
K
Sbjct: 172 GGGKP 176
>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 = 0.16
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 606 GIFIKSILDNGQAAEDGRLKEGDEILAINGQ 636
G + +L AA+ G +K GD I A+NG+
Sbjct: 271 GAVVLGVLPGSPAAKAG-IKAGDIITAVNGK 300
Score = 31.0 bits (70), Expect = 1.8
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 419 GFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGLTMTQA 459
G VV ++ G A K G ++ GD I +VNG+ + L+ A
Sbjct: 271 GAVVLGVLPGSPAAKAG-IKAGDIITAVNGKPVASLSDLVA 310
>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 = 0.22
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 417 IGGFVVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGLT 455
+ G V+ ++ G AE L GD I S+NG + L
Sbjct: 9 VAGVVIVGVIVGSPAENAV-LHTGDVIYSINGTPITTLE 46
Score = 26.9 bits (60), Expect = 9.1
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 606 GIFIKSILDNGQAAEDGRLKEGDEILAINGQ 636
G+ I ++ G AE+ L GD I +ING
Sbjct: 11 GVVIVGVI-VGSPAENAVLHTGDVIYSINGT 40
>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 = 0.29
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 607 IFIKSILDNGQAAEDGRLKEGDEILAINGQVCHDLTHLEAISLFKTIKNGSISLHICRRL 666
I I S + A + G +K GD+I+ ING+ ++ +A++L + K +SL I R
Sbjct: 64 IVIVSPFEGSPAEKAG-IKPGDKIIKINGKSVAGMSLDDAVALIRGKKGTKVSLEILRAG 122
Query: 667 KSK 669
KSK
Sbjct: 123 KSK 125
>gnl|CDD|222884 PHA02573, 30.3, hypothetical protein; Provisional.
Length = 148
Score = 31.3 bits (71), Expect = 0.75
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 7/47 (14%)
Query: 532 SINNKLLRKAIISTG------SISG-DEEETILTSTNFCTLPRRPRS 571
+I NK RKA+++T SI + ETILT FC+ R R
Sbjct: 100 AIQNKGFRKALLATKNKVLTHSIGKLKKNETILTEQEFCSNLNRLRD 146
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 32.0 bits (73), Expect = 1.2
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 421 VVAHIVSGGLAEKEGCLELGDEIISVNGQRLRG 453
V+A + A K G L+ GD I+ V+GQ L
Sbjct: 224 VLAEVQPNSAASKAG-LQAGDRIVKVDGQPLTQ 255
>gnl|CDD|223430 COG0353, RecR, Recombinational DNA repair protein (RecF pathway)
[DNA replication, recombination, and repair].
Length = 198
Score = 31.0 bits (71), Expect = 1.2
Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 561 NFCTLPRRPRSAICTFHT----IVFEKGPGKKGLGFTIVGGKDSPRGAIG---IFIKSIL 613
+ C+ R +S +C + EK +GL ++GG SP IG + I +L
Sbjct: 70 DICSDESRDKSQLCVVEEPKDVLALEKTGEFRGLYH-VLGGLLSPLDGIGPEDLNIDELL 128
Query: 614 DNGQAAEDGRLKEGDEILAIN 634
Q +G +KE ILA N
Sbjct: 129 ---QRLAEGSIKE--VILATN 144
>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 = 29.3 bits (66), Expect = 1.3
Identities = 10/27 (37%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 609 IKSILDNGQAAEDGRLKEGDEILAING 635
+ + D+ A + G L GDE++A+NG
Sbjct: 16 VTFVRDDSPADKAG-LVAGDELVAVNG 41
>gnl|CDD|218317 pfam04894, DUF650, Archaeal protein of unknown function (DUF650).
This family represents the amino terminal region of an
archaeal protein of unknown function.
Length = 271
Score = 31.4 bits (72), Expect = 1.4
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 141 KAISDKYFKSNKIIVKLYSNNKKSTTRRQRSFSFGAL 177
K I D K+ + I++LY QR S G L
Sbjct: 161 KVIYDTDLKAEEAIIELY-RRGFDVYYIQRLLSVGLL 196
>gnl|CDD|132322 TIGR03279, cyano_FeS_chp, putative FeS-containing
Cyanobacterial-specific oxidoreductase. Members of this
protein family are predicted FeS-containing
oxidoreductases of unknown function, apparently
restricted to and universal across the Cyanobacteria.
The high trusted cutoff score for this model, 700 bits,
excludes homologs from other lineages. This exclusion
seems justified because a significant number of sequence
positions are simultaneously unique to and invariant
across the Cyanobacteria, suggesting a specialized,
conserved function, perhaps related to photosynthesis. A
distantly related protein family, TIGR03278, in
universal in and restricted to archaeal methanogens, and
may be linked to methanogenesis.
Length = 433
Score = 31.6 bits (72), Expect = 1.4
Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 421 VVAHIVSGGLAEKEGCLELGDEIISVNGQRLRGL 454
+++ ++ G +AE+ G E GD ++S+NG R L
Sbjct: 1 LISAVLPGSIAEELG-FEPGDALVSINGVAPRDL 33
>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 = 1.5
Identities = 12/45 (26%), Positives = 27/45 (60%), Gaps = 3/45 (6%)
Query: 433 KEGCLELGDEIISVNGQRLRGLTMTQAKSIIS-SGPLNMDLLISR 476
+E +++GD I+ +NG++++ M ++I+ +G + L I R
Sbjct: 127 EEAGIQIGDRILKINGEKIK--NMDDLANLINKAGGEKLTLTIER 169
>gnl|CDD|197339 cd10312, Deadenylase_CCR4b, C-terminal deadenylase domain of CCR4b,
also known as CCR4-NOT transcription complex subunit
6-like. This subfamily contains the C-terminal
catalytic domain of the deadenylase, CCR4b, also known
as CCR4-NOT transcription complex subunit 6-like
(CNOT6L). CCR4 belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. CCR4 is the major deadenylase subunit of the
CCR4-NOT transcription complex, which contains two
deadenylase subunits and several noncatalytic subunits.
The other deadenylase subunit, Caf1, is a DEDD-type
protein and does not belong in this superfamily. There
are two vertebrate CCR4 proteins, CCR4a (also called
CCR4-NOT transcription complex subunit 6 or CNOT6) and
CCR4b. CCR4b associates with other components, such as
CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit
complex, which regulates transcription and mRNA
degradation. The nuclease domain of CCR4b exhibits
Mg2+-dependent deadenylase activity with strict
specificity for poly (A) RNA as substrate. CCR4b is
mainly localized in the cytoplasm. It regulates cell
growth and influences cell cycle progression by
regulating p27/Kip1 mRNA levels. It contributes to the
prevention of cell death by regulating insulin-like
growth factor-binding protein 5.
Length = 348
Score = 31.1 bits (70), Expect = 1.8
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 199 DSGIVNSSTNSSVVDDHYDFRATRKENC 226
DSG+V +N V D+H DF+ R C
Sbjct: 226 DSGVVEYLSNGGVADNHKDFKELRYNEC 253
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 31.3 bits (71), Expect = 2.2
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 418 GGFVVAHIVSGGLAEKEGCLELGDEIISVNG 448
G + + GG A K G L GD+I+++NG
Sbjct: 462 GHEKITFVFPGGPAYKAG-LSPGDKIVAING 491
>gnl|CDD|236312 PRK08617, PRK08617, acetolactate synthase; Reviewed.
Length = 552
Score = 31.0 bits (71), Expect = 2.6
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 6/34 (17%)
Query: 626 EGDEILAINGQVCHD----LTH--LEAISLFKTI 653
EGD ++AI GQV TH ++ ++LF+ I
Sbjct: 92 EGDPVVAIGGQVKRADRLKRTHQSMDNVALFRPI 125
>gnl|CDD|182958 PRK11096, ansB, L-asparaginase II; Provisional.
Length = 347
Score = 29.7 bits (67), Expect = 5.5
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 387 GQTMVRVNRRDFNEELGIYIAKIKNSSEGNIGGFVVAH 424
G+ +V + +D N+E+ + +AK N+ GFV+ H
Sbjct: 71 GEQVVNIGSQDMNDEVWLTLAKKINTDCDKTDGFVITH 108
>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 = 29.4 bits (66), Expect = 6.4
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 421 VVAHIVSGGLAEKEGCLELGDEIISVNGQRLR 452
V++ + AEK G L+ GD I S+NG++LR
Sbjct: 205 VLSDVTPNSPAEKAG-LKEGDYIQSINGEKLR 235
Score = 29.0 bits (65), Expect = 9.9
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 609 IKSILDNGQAAEDGRLKEGDEILAINGQVCHDLTHLEAISLFKTIKNGSISLHICR 664
+ + N A + G LKEGD I +ING+ T +S K S+ + + R
Sbjct: 206 LSDVTPNSPAEKAG-LKEGDYIQSINGEKLRSWTDF--VSAVKENPGKSMDIKVER 258
>gnl|CDD|131471 TIGR02418, acolac_catab, acetolactate synthase, catabolic.
Acetolactate synthase (EC 2.2.1.6) combines two
molecules of pyruvate to yield 2-acetolactate with the
release of CO2. This reaction may be involved in either
valine biosynthesis (biosynthetic) or conversion of
pyruvate to acetoin and possibly to 2,3-butanediol
(catabolic). The biosynthetic type, described by
TIGR00118, is also capable of forming
acetohydroxybutyrate from pyruvate and 2-oxobutyrate for
isoleucine biosynthesis. The family described here, part
of the same larger family of thiamine
pyrophosphate-dependent enzymes (pfam00205, pfam02776)
is the catabolic form, generally found associated with
in species with acetolactate decarboxylase and usually
found in the same operon. The model may not encompass
all catabolic acetolactate synthases, but rather one
particular clade in the larger TPP-dependent enzyme
family [Energy metabolism, Fermentation].
Length = 539
Score = 29.3 bits (66), Expect = 7.7
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 626 EGDEILAINGQVCHD----LTH--LEAISLFKTIKNGSISLH 661
EGD ++AI GQV LTH ++ ++LF+ I S +
Sbjct: 86 EGDPVVAIGGQVKRADLLKLTHQSMDNVALFRPITKYSAEVQ 127
>gnl|CDD|237173 PRK12684, PRK12684, transcriptional regulator CysB-like protein;
Reviewed.
Length = 313
Score = 28.8 bits (65), Expect = 9.4
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 438 ELGDEIISVNGQRLRGLT 455
ELG EI + +G+RLRGLT
Sbjct: 43 ELGVEIFTRHGKRLRGLT 60
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 0.127 0.353
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: 31,500,443
Number of extensions: 2959950
Number of successful extensions: 1819
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1808
Number of HSP's successfully gapped: 65
Length of query: 671
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 568
Effective length of database: 6,369,140
Effective search space: 3617671520
Effective search space used: 3617671520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 62 (27.7 bits)