RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12719
(116 letters)
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 61.6 bits (150), Expect = 8e-14
Identities = 17/90 (18%), Positives = 42/90 (46%), Gaps = 1/90 (1%)
Query: 6 DRERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLY 65
+++L+ + ++ + +A A ++ A E + +++ +DP+NA Y
Sbjct: 12 KLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAY 71
Query: 66 VHRAMLMLQARGNVDEAIKLIEKAISIDKS 95
+ + G +EA++ EKA+ +D +
Sbjct: 72 YNLGLA-YYKLGKYEEALEAYEKALELDPN 100
Score = 55.8 bits (135), Expect = 1e-11
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 29 EACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEK 88
EA + D+D A EY+ +++ +DP+NA Y + A G +EA++ EK
Sbjct: 1 EALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAA-YYKLGKYEEALEDYEK 59
Query: 89 AISIDKSCMFAYETLG 104
A+ +D AY LG
Sbjct: 60 ALELDPDNAKAYYNLG 75
Score = 31.6 bits (72), Expect = 0.029
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 72 MLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTI 106
+ G+ DEA++ EKA+ +D AY L
Sbjct: 9 LYYKLGDYDEALEYYEKALELDPDNADAYYNLAAA 43
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 57.7 bits (140), Expect = 1e-12
Identities = 18/60 (30%), Positives = 35/60 (58%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISIDK 94
L D+D A E + +++ +DP+NA Y + A+ L+ + +EA++ +EKA+ +D
Sbjct: 10 GNALFKLGDYDEAIEAYEKALELDPDNAEAYYNLALAYLKLGKDYEEALEDLEKALELDP 69
Score = 33.1 bits (76), Expect = 0.005
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 60 ENASLYVHRAMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTI 106
+NA + + + G+ DEAI+ EKA+ +D AY L
Sbjct: 1 DNAEALKNLGNALFK-LGDYDEAIEAYEKALELDPDNAEAYYNLALA 46
>gnl|CDD|233223 TIGR00990, 3a0801s09, mitochondrial precursor proteins import
receptor (72 kDa mitochondrial outermembrane protein)
(mitochondrial import receptor for the ADP/ATP carrier)
(translocase of outermembrane tom70). [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 615
Score = 53.8 bits (129), Expect = 1e-09
Identities = 22/70 (31%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISIDK 94
A + ++ D D AEE F+++++++ E+ +Y HRA L +G +A K +K+I +D
Sbjct: 372 ASMNLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHF-IKGEFAQAGKDYQKSIDLDP 430
Query: 95 SCMFAYETLG 104
+F++ LG
Sbjct: 431 DFIFSHIQLG 440
Score = 50.4 bits (120), Expect = 2e-08
Identities = 29/112 (25%), Positives = 53/112 (47%), Gaps = 6/112 (5%)
Query: 9 RVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLY--- 65
+ S+ FR + + ++L+DQ FD A E F+ +I ++ E +Y
Sbjct: 448 SIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNV 507
Query: 66 ---VHRAMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTIEVQRTFVV 114
+++A+ + Q + + EA L EKA+ ID C A T+ + +Q+ V
Sbjct: 508 LPLINKALALFQWKQDFIEAENLCEKALIIDPECDIAVATMAQLLLQQGDVD 559
Score = 35.7 bits (82), Expect = 0.003
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 42 EDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISIDKS------ 95
+DF AE +++ +DPE A L+LQ +G+VDEA+KL E+A + ++
Sbjct: 522 QDFIEAENLCEKALIIDPECDIAVATMAQLLLQ-QGDVDEALKLFERAAELARTEGELVQ 580
Query: 96 -CMFAYETLGTIEVQRTFVVL 115
+A T I+VQ + VL
Sbjct: 581 AISYAEATRTQIQVQEDYPVL 601
Score = 32.3 bits (73), Expect = 0.035
Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 43 DFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISID 93
A ++SI +DP Y+ RA + L+ G+ D+A + +KA+ ++
Sbjct: 346 KHLEALADLSKSIELDPRVTQSYIKRASMNLE-LGDPDKAEEDFDKALKLN 395
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 45.4 bits (108), Expect = 9e-08
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 24 HSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRV-------DPENASLYVHRAMLMLQAR 76
H ++ A A VL D+D A E +++ + PE A + A L A
Sbjct: 1 HPDLAAALNNLALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARL-YLAL 59
Query: 77 GNVDEAIKLIEKAISIDKS 95
G+ DEA++ +EKA+++ ++
Sbjct: 60 GDYDEALEYLEKALALREA 78
Score = 33.5 bits (77), Expect = 0.004
Identities = 12/54 (22%), Positives = 25/54 (46%)
Query: 7 RERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPE 60
E +E++L+ R + H A A++ + D+D A EY +++ +
Sbjct: 25 LELLEKALELARELGEDHPETARALNNLARLYLALGDYDEALEYLEKALALREA 78
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 44.6 bits (106), Expect = 2e-07
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 1/59 (1%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISID 93
A+ + D+D A ++ P A + +L+ +G + EA L+ A++ D
Sbjct: 4 ARAALRAGDYDEALAALEAALARYPLAAEALLLLGEALLR-QGRLAEAAALLRAALAAD 61
Score = 28.4 bits (64), Expect = 0.20
Identities = 9/57 (15%), Positives = 20/57 (35%)
Query: 6 DRERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENA 62
+++L + + EA L + L+ Q A ++ DP++
Sbjct: 9 RAGDYDEALAALEAALARYPLAAEALLLLGEALLRQGRLAEAAALLRAALAADPDDP 65
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 45.1 bits (107), Expect = 2e-06
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 9 RVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHR 68
RV++++ + + A +L + + DF+ A EY ++ +DPENA+
Sbjct: 344 RVDEAIATLSPALGLDPDDPAALSLLGEAYLALGDFEKAAEYLAKATELDPENAAARTQL 403
Query: 69 AMLMLQARGNVDEAIKLIEKAISID 93
+ L ++G+ EAI +E A +D
Sbjct: 404 GISKL-SQGDPSEAIADLETAAQLD 427
Score = 38.9 bits (91), Expect = 2e-04
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 33 LFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISI 92
L + + + D A E F +++ ++P+ + A + +Q GN D+AI+ EK ++I
Sbjct: 470 LLGAIYLGKGDLAKAREAFEKALSIEPDFFPAAANLARIDIQE-GNPDDAIQRFEKVLTI 528
Query: 93 DK 94
D
Sbjct: 529 DP 530
Score = 37.8 bits (88), Expect = 5e-04
Identities = 24/89 (26%), Positives = 45/89 (50%), Gaps = 10/89 (11%)
Query: 7 RERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYV 66
RE E++L +F +N+ A++ + + + D A + F + + +DP+N L
Sbjct: 485 REAFEKALSIEPDFFPAAANL-------ARIDIQEGNPDDAIQRFEKVLTIDPKN--LRA 535
Query: 67 HRAMLMLQAR-GNVDEAIKLIEKAISIDK 94
A+ L R GN +EA+ +EKA ++
Sbjct: 536 ILALAGLYLRTGNEEEAVAWLEKAAELNP 564
Score = 37.4 bits (87), Expect = 7e-04
Identities = 18/104 (17%), Positives = 44/104 (42%), Gaps = 8/104 (7%)
Query: 7 RERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYV 66
R +++ L VD L +L+ + + A + ++I + P N ++ +
Sbjct: 179 RALIDEVLTADPGNVDALL-------LKGDLLLSLGNIELALAAYRKAIALRPNNIAVLL 231
Query: 67 HRAMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTIEVQR 110
A ++++A G +EA K + + + A+ ++ Q+
Sbjct: 232 ALATILIEA-GEFEEAEKHADALLKKAPNSPLAHYLKALVDFQK 274
Score = 36.6 bits (85), Expect = 0.001
Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 1/101 (0%)
Query: 9 RVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHR 68
+++ + + A L + FD A + + P+NASL+
Sbjct: 412 DPSEAIADLETAAQLDPELGRADLLLILSYLRSGQFDKALAAAKKLEKKQPDNASLHNLL 471
Query: 69 AMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTIEVQ 109
+ L +G++ +A + EKA+SI+ A L I++Q
Sbjct: 472 GAIYL-GKGDLAKAREAFEKALSIEPDFFPAAANLARIDIQ 511
Score = 36.6 bits (85), Expect = 0.001
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISIDK 94
AQ+ + + FD A + + DP N + + L L + GN++ A+ KAI++
Sbjct: 166 AQLALAENRFDEARALIDEVLTADPGNVDALLLKGDL-LLSLGNIELALAAYRKAIALRP 224
Query: 95 SCMFAYETLGTI 106
+ + L TI
Sbjct: 225 NNIAVLLALATI 236
Score = 36.2 bits (84), Expect = 0.002
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 34 FAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKA 89
+LV++ + D A +++ + PE A++ H A L L A G EA K ++K
Sbjct: 843 LGWLLVEKGEADRALPLLRKAVNIAPEAAAIRYHLA-LALLATGRKAEARKELDKL 897
Score = 33.1 bits (76), Expect = 0.023
Identities = 13/83 (15%), Positives = 32/83 (38%), Gaps = 1/83 (1%)
Query: 12 QSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAML 71
++L D + EA + + + D + A F + + + P++A +
Sbjct: 585 KALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALL-LLAD 643
Query: 72 MLQARGNVDEAIKLIEKAISIDK 94
N +AI +++A+ +
Sbjct: 644 AYAVMKNYAKAITSLKRALELKP 666
Score = 32.7 bits (75), Expect = 0.031
Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 5/81 (6%)
Query: 16 EFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNR--SIRVDPENASLYVHRAMLML 73
+ +N + N EA L ++ + D+ AE+ + S+ + RA L+
Sbjct: 44 QLKNALQKDPNDAEARFLLGKIYLALGDYAAAEKELRKALSLGYPKNQVLPLLARAYLLQ 103
Query: 74 QARGNVDEAIKLIEKAISIDK 94
G + + + +D
Sbjct: 104 ---GKFQQVLDELPGKTLLDD 121
Score = 30.8 bits (70), Expect = 0.13
Identities = 19/104 (18%), Positives = 47/104 (45%), Gaps = 1/104 (0%)
Query: 7 RERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYV 66
+E +L +R + N + A +L++ +F+ AE++ + ++ P + +
Sbjct: 206 LGNIELALAAYRKAIALRPNNIAVLLALATILIEAGEFEEAEKHADALLKKAPNSPLAHY 265
Query: 67 HRAMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTIEVQR 110
+A++ Q + N ++A + ++ A+ + A G E Q
Sbjct: 266 LKALVDFQ-KKNYEDARETLQDALKSAPEYLPALLLAGASEYQL 308
Score = 30.4 bits (69), Expect = 0.19
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 47 AEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISIDKS 95
A EY R++++ P ++ L+++ +G D A+ L+ KA++I
Sbjct: 822 ALEYAERALKLAPNIPAILDTLGWLLVE-KGEADRALPLLRKAVNIAPE 869
Score = 30.1 bits (68), Expect = 0.21
Identities = 19/104 (18%), Positives = 41/104 (39%), Gaps = 6/104 (5%)
Query: 5 GDRERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPEN-AS 63
G+ E E+ A L A V +++++ A E +++ PE +
Sbjct: 241 GEFEEAEKHADALLKKAPNSP---LAHYLKALVDFQKKNYEDARETLQDALKSAPEYLPA 297
Query: 64 LYVHRAMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTIE 107
L + A GN+++A + + + + + A L +I+
Sbjct: 298 LLL--AGASEYQLGNLEQAYQYLNQILKYAPNSHQARRLLASIQ 339
Score = 28.9 bits (65), Expect = 0.64
Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 1/77 (1%)
Query: 10 VEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRA 69
+ +++ F+ + + A L A +++ A R++ + P+N + A
Sbjct: 617 LNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIGLA 676
Query: 70 MLMLQARGNVDEAIKLI 86
L+L A + A K+
Sbjct: 677 QLLLAA-KRTESAKKIA 692
Score = 26.6 bits (59), Expect = 3.4
Identities = 24/102 (23%), Positives = 50/102 (49%), Gaps = 9/102 (8%)
Query: 9 RVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHR 68
+E LK H N T A++ + Q+D+D A +++ ++ P+NA + +
Sbjct: 758 TLEAWLKT-------HPNDAVLRTALAELYLAQKDYDKAIKHYQTVVKKAPDNAVVLNNL 810
Query: 69 AMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTIEVQR 110
A L L+ + A++ E+A+ + + +TLG + V++
Sbjct: 811 AWLYLELKD--PRALEYAERALKLAPNIPAILDTLGWLLVEK 850
>gnl|CDD|223533 COG0457, NrfG, FOG: TPR repeat [General function prediction only].
Length = 291
Score = 41.0 bits (94), Expect = 4e-05
Identities = 19/102 (18%), Positives = 44/102 (43%)
Query: 5 GDRERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASL 64
GD E + ++ + + EA +L ++ A E ++++++P++ +
Sbjct: 144 GDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAE 203
Query: 65 YVHRAMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTI 106
+ L+ G +EA++ EKA+ +D A L +
Sbjct: 204 ALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALL 245
Score = 40.6 bits (93), Expect = 4e-05
Identities = 21/91 (23%), Positives = 45/91 (49%), Gaps = 2/91 (2%)
Query: 6 DRERVEQSLKEFRNFVDT-HSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASL 64
R E++L+ + + EA + + ++ A EY+ +++ +DP+NA
Sbjct: 179 ALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEA 238
Query: 65 YVHRAMLMLQARGNVDEAIKLIEKAISIDKS 95
+ A+ +L G +EA++ +EKA+ +D
Sbjct: 239 LYNLAL-LLLELGRYEEALEALEKALELDPD 268
Score = 38.7 bits (88), Expect = 2e-04
Identities = 19/75 (25%), Positives = 34/75 (45%)
Query: 29 EACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEK 88
EA +L ++ A E +++ +DP+ A+ L G+ +EA++L EK
Sbjct: 96 EALLNLGLLLEALGKYEEALELLEKALALDPDPDLAEALLALGALYELGDYEEALELYEK 155
Query: 89 AISIDKSCMFAYETL 103
A+ +D E L
Sbjct: 156 ALELDPELNELAEAL 170
>gnl|CDD|215568 PLN03088, PLN03088, SGT1, suppressor of G2 allele of SKP1;
Provisional.
Length = 356
Score = 38.6 bits (90), Expect = 2e-04
Identities = 27/67 (40%), Positives = 35/67 (52%), Gaps = 7/67 (10%)
Query: 42 EDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQAR---GNVDEAIKLIEKAISIDKSCMF 98
+DF A + + ++I +DP NA LY RA QA GN EA+ KAI +D S
Sbjct: 16 DDFALAVDLYTQAIDLDPNNAELYADRA----QANIKLGNFTEAVADANKAIELDPSLAK 71
Query: 99 AYETLGT 105
AY GT
Sbjct: 72 AYLRKGT 78
>gnl|CDD|226687 COG4235, COG4235, Cytochrome c biogenesis factor [Posttranslational
modification, protein turnover, chaperones].
Length = 287
Score = 38.5 bits (90), Expect = 2e-04
Identities = 15/94 (15%), Positives = 37/94 (39%), Gaps = 2/94 (2%)
Query: 4 PGDRERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENAS 63
P + +E + + + E L + + A + ++R+ +N
Sbjct: 132 PPAEQEMEALIARLETHLQQNPGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPE 191
Query: 64 LYVHRA-MLMLQARGNVD-EAIKLIEKAISIDKS 95
+ + A L QA + +A L+ +A+++D +
Sbjct: 192 ILLGLAEALYYQAGQQMTAKARALLRQALALDPA 225
>gnl|CDD|197478 smart00028, TPR, Tetratricopeptide repeats. Repeats present in 4
or more copies in proteins. Contain a minimum of 34
amino acids each and self-associate via a "knobs and
holes" mechanism.
Length = 34
Score = 34.0 bits (79), Expect = 0.001
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 28 VEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPEN 61
EA + D+D A EY+ +++ +DP N
Sbjct: 1 AEALYNLGNAYLKLGDYDEALEYYEKALELDPNN 34
Score = 27.8 bits (63), Expect = 0.22
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 62 ASLYVHRAMLMLQARGNVDEAIKLIEKAISIDKSC 96
A + G+ DEA++ EKA+ +D +
Sbjct: 1 AEALYNLG-NAYLKLGDYDEALEYYEKALELDPNN 34
>gnl|CDD|205609 pfam13431, TPR_17, Tetratricopeptide repeat.
Length = 34
Score = 33.3 bits (77), Expect = 0.002
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 50 YFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIK 84
+ +++ +DP NA Y + A+L L G DEA++
Sbjct: 1 LYEKALELDPNNAEAYYNLALL-LLNLGQYDEALQ 34
>gnl|CDD|236983 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional.
Length = 389
Score = 35.6 bits (83), Expect = 0.002
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 75 ARGNVDEAIKLIEKAISIDKSCMFAYETLGTIEVQR 110
ARG++D A L++KA++ D C+ A LG + + +
Sbjct: 192 ARGDLDAARALLKKALAADPQCVRASILLGDLALAQ 227
Score = 32.9 bits (76), Expect = 0.021
Identities = 19/84 (22%), Positives = 35/84 (41%)
Query: 7 RERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYV 66
R ++ + + + V A L + + Q D+ A E R DPE S +
Sbjct: 193 RGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVL 252
Query: 67 HRAMLMLQARGNVDEAIKLIEKAI 90
+ M QA G+ E ++ + +A+
Sbjct: 253 PKLMECYQALGDEAEGLEFLRRAL 276
Score = 27.5 bits (62), Expect = 1.7
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 9/58 (15%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLML----QARGNVDEAIKLIEK 88
AQ + + D D A +++ DP+ RA ++L A+G+ AI+ +E+
Sbjct: 187 AQQALARGDLDAARALLKKALAADPQCV-----RASILLGDLALAQGDYAAAIEALER 239
>gnl|CDD|201277 pfam00515, TPR_1, Tetratricopeptide repeat.
Length = 34
Score = 31.6 bits (73), Expect = 0.007
Identities = 6/27 (22%), Positives = 14/27 (51%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPEN 61
+ +D A EY+ +++ ++P N
Sbjct: 8 GNAYLKLGKYDEALEYYEKALELNPNN 34
Score = 28.9 bits (66), Expect = 0.076
Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 62 ASLYVHRAMLMLQARGNVDEAIKLIEKAISIDKSC 96
A + G DEA++ EKA+ ++ +
Sbjct: 1 AKALYNLGNA-YLKLGKYDEALEYYEKALELNPNN 34
>gnl|CDD|191825 pfam07719, TPR_2, Tetratricopeptide repeat. This Pfam entry
includes outlying Tetratricopeptide-like repeats (TPR)
that are not matched by pfam00515.
Length = 34
Score = 31.3 bits (72), Expect = 0.011
Identities = 8/34 (23%), Positives = 15/34 (44%)
Query: 28 VEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPEN 61
EA D++ A E + +++ +DP N
Sbjct: 1 AEALYNLGLAYYKLGDYEEALEAYEKALELDPNN 34
Score = 29.0 bits (66), Expect = 0.070
Identities = 8/32 (25%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 62 ASLYVHRAMLMLQARGNVDEAIKLIEKAISID 93
A + + + G+ +EA++ EKA+ +D
Sbjct: 1 AEALYNLGLAYYK-LGDYEEALEAYEKALELD 31
>gnl|CDD|205362 pfam13181, TPR_8, Tetratricopeptide repeat.
Length = 34
Score = 30.9 bits (71), Expect = 0.014
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 62 ASLYVHRAMLMLQARGNVDEAIKLIEKAISIDKSC 96
A Y + LQ G+ +EA + EKA+ +D +
Sbjct: 1 ARAYYLLGQIYLQL-GDYEEAKEYYEKALELDPNN 34
Score = 30.5 bits (70), Expect = 0.021
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 28 VEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPEN 61
A L Q+ + D++ A+EY+ +++ +DP N
Sbjct: 1 ARAYYLLGQIYLQLGDYEEAKEYYEKALELDPNN 34
>gnl|CDD|227122 COG4783, COG4783, Putative Zn-dependent protease, contains TPR
repeats [General function prediction only].
Length = 484
Score = 32.8 bits (75), Expect = 0.023
Identities = 14/63 (22%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 33 LFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISI 92
L +L++ A E +++ +DP + L ++ A +L+ G EAI+++ + +
Sbjct: 345 LAGDILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKG-GKPQEAIRILNRYLFN 403
Query: 93 DKS 95
D
Sbjct: 404 DPE 406
Score = 27.8 bits (62), Expect = 1.2
Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 11/79 (13%)
Query: 9 RVEQSLKEFRNFV--DTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYV 66
+ +++++ + + D +S +++ AQ L+ A NR + DPE+ + +
Sbjct: 355 KAKEAIERLKKALALDPNSPLLQ--LNLAQALLKGGKPQEAIRILNRYLFNDPEDPNGW- 411
Query: 67 HRAMLMLQAR---GNVDEA 82
L+ QA GN EA
Sbjct: 412 ---DLLAQAYAELGNRAEA 427
>gnl|CDD|222121 pfam13428, TPR_14, Tetratricopeptide repeat.
Length = 44
Score = 30.2 bits (68), Expect = 0.034
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAML 71
A+ L+ D D A R++ +DP++ + A L
Sbjct: 8 ARALLALGDLDEALALLRRALALDPDDPEALLLLARL 44
Score = 24.8 bits (54), Expect = 3.1
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 67 HRAMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTI 106
L A G++DEA+ L+ +A+++D A L +
Sbjct: 5 LALARALLALGDLDEALALLRRALALDPDDPEALLLLARL 44
>gnl|CDD|224643 COG1729, COG1729, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 262
Score = 31.3 bits (71), Expect = 0.085
Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 9/82 (10%)
Query: 17 FRNFVDTHSNVV---EACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLML 73
F+ F+ + N A + L Q D++ A F R ++ P++ A+L L
Sbjct: 164 FQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPK--APDALLKL 221
Query: 74 ----QARGNVDEAIKLIEKAIS 91
GN DEA +++ I
Sbjct: 222 GVSLGRLGNTDEACATLQQVIK 243
>gnl|CDD|131573 TIGR02521, type_IV_pilW, type IV pilus biogenesis/stability protein
PilW. Members of this family are designated PilF in ref
(PMID:8973346) and PilW in ref (PMID:15612916). This
outer membrane protein is required both for pilus
stability and for pilus function such as adherence to
human cells. Members of this family contain copies of
the TPR (tetratricopeptide repeat) domain.
Length = 234
Score = 30.8 bits (70), Expect = 0.11
Identities = 26/98 (26%), Positives = 44/98 (44%), Gaps = 16/98 (16%)
Query: 5 GDRERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASL 64
G+ E+ E S FR + + N + + L Q ++ A + F ++I DP L
Sbjct: 79 GELEKAEDS---FRRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIE-DP----L 130
Query: 65 YVHRA-------MLMLQARGNVDEAIKLIEKAISIDKS 95
Y A + L+A G+ D+A K + +A+ ID
Sbjct: 131 YPQPARSLENAGLCALKA-GDFDKAEKYLTRALQIDPQ 167
Score = 29.6 bits (67), Expect = 0.24
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 40 DQEDFDGAEEYFNRSIRVDPENA-SLY--VHRAMLMLQARGNVDEAIKLIEK 88
DFD AE+Y R++++DP+ SL L RG +A +E+
Sbjct: 147 KAGDFDKAEKYLTRALQIDPQRPESLLELAELYYL----RGQYKDARAYLER 194
Score = 28.5 bits (64), Expect = 0.70
Identities = 13/57 (22%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAIS 91
A + + AE+ F R++ ++P N + + L +G ++A++ E+AI
Sbjct: 72 ALYYQQLGELEKAEDSFRRALTLNPNNGDVLNNYGTF-LCQQGKYEQAMQQFEQAIE 127
>gnl|CDD|188247 TIGR02795, tol_pal_ybgF, tol-pal system protein YbgF. Members of
this protein family are the product of one of seven
genes regularly clustered in operons to encode the
proteins of the tol-pal system, which is critical for
maintaining the integrity of the bacterial outer
membrane. The gene for this periplasmic protein has been
designated orf2 and ybgF. All members of the seed
alignment were from unique tol-pal gene regions from
completed bacterial genomes. The architecture of this
protein is a signal sequence, a low-complexity region
usually rich in Asn and Gln, a well-conserved region
with tandem repeats that resemble the tetratricopeptide
(TPR) repeat, involved in protein-protein interaction.
Length = 117
Score = 29.2 bits (66), Expect = 0.21
Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 9/83 (10%)
Query: 16 EFRNFVDTHSNVV---EACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLM 72
F+ F+ + A + Q D+ A + F ++ P++ A+L
Sbjct: 22 AFQAFLKKYPKSTYAPNAHYWLGEAYYAQGDYADAAKAFLAVVKKYPKSPK--APDALLK 79
Query: 73 L----QARGNVDEAIKLIEKAIS 91
L Q G+ ++A +++ I
Sbjct: 80 LGMSLQELGDKEKAKATLQQVIK 102
>gnl|CDD|234406 TIGR03939, PGA_TPR_OMP, poly-beta-1,6 N-acetyl-D-glucosamine export
porin PgaA. Members of this protein family are the
poly-beta-1,6 N-acetyl-D-glucosamine (PGA) export porin
PgaA of Gram-negative bacteria. There is no counterpart
in the poly-beta-1,6 N-acetyl-D-glucosamine biosynthesis
systems of Gram-positive bacteria such as Staphylococcus
epidermidis. The PGA polysaccharide adhesin is a
critical determinant of biofilm formation. The conserved
C-terminal domain of this outer membrane protein is
preceded by a variable number of TPR repeats.
Length = 800
Score = 30.0 bits (68), Expect = 0.26
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 19 NFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGN 78
+ V + V+EA A+ +++ +D A E + + ++ DP N + A+ + A G
Sbjct: 80 SPVGLPARVLEA---LAKAYRNEKQWDKALELYRKLLQRDPNNPDGLLGLALTLADA-GK 135
Query: 79 VDEAIKLI 86
EA+K +
Sbjct: 136 DAEALKYL 143
Score = 26.2 bits (58), Expect = 4.8
Identities = 11/53 (20%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIE 87
A V + AE+ + ++ +DP++ S +A L +A +L +
Sbjct: 436 ADVYRARGWPRRAEQEYKQAESLDPDSLSAERGQAETAL-DLQEWRQAEQLTD 487
>gnl|CDD|227343 COG5010, TadD, Flp pilus assembly protein TadD, contains TPR
repeats [Intracellular trafficking and secretion].
Length = 257
Score = 29.7 bits (67), Expect = 0.26
Identities = 10/53 (18%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 41 QEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISID 93
+F A ++ R+ P + + + Q G DEA + +A+ +
Sbjct: 113 NGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQ-LGRFDEARRAYRQALELA 164
Score = 29.3 bits (66), Expect = 0.32
Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 1/85 (1%)
Query: 7 RERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYV 66
+++ R EA L L FD A + +++ + P S+
Sbjct: 113 NGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPSIAN 172
Query: 67 HRAMLMLQARGNVDEAIKLIEKAIS 91
+ M +L RG++++A L+ A
Sbjct: 173 NLGMSLL-LRGDLEDAETLLLPAYL 196
>gnl|CDD|225605 COG3063, PilF, Tfp pilus assembly protein PilF [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 250
Score = 29.3 bits (66), Expect = 0.34
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 41 QEDFDGAEEYFNRSIRVDPENAS 63
FD AEEY R++ +DP+
Sbjct: 152 AGQFDQAEEYLKRALELDPQFPP 174
Score = 27.0 bits (60), Expect = 2.3
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 60 ENASLYVHRAMLMLQARGNVDEAIKLIEKAISIDKSCM-------FAYETLGTIE 107
E A + A+ LQ G+ +A K +EKA+ D S Y+ LG +
Sbjct: 33 EAAKARLQLALGYLQQ-GDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGEND 86
>gnl|CDD|205550 pfam13371, TPR_9, Tetratricopeptide repeat.
Length = 73
Score = 27.9 bits (63), Expect = 0.40
Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 36 QVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISID 93
+ + +EDF+ A R + + P++ R +L G A+ +E + +
Sbjct: 3 AIYLREEDFERALAVVERLLLLAPDDPYERRDRGLL-YAQLGCFQAALADLEYFLELC 59
>gnl|CDD|225504 COG2956, COG2956, Predicted N-acetylglucosaminyl transferase
[Carbohydrate transport and metabolism].
Length = 389
Score = 29.3 bits (66), Expect = 0.46
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 60 ENASLYVHRAMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTIEVQR 110
E A Y A L A +VD A +L++KA+ DK C+ A LG +E+ +
Sbjct: 178 EIAQFYCELAQQAL-ASSDVDRARELLKKALQADKKCVRASIILGRVELAK 227
Score = 28.9 bits (65), Expect = 0.61
Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 18/94 (19%)
Query: 31 CTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLML----QARGNVDEAIKLI 86
C L AQ + D D A E ++++ D + RA ++L A+G+ +A++ +
Sbjct: 184 CEL-AQQALASSDVDRARELLKKALQADKKCV-----RASIILGRVELAKGDYQKAVEAL 237
Query: 87 EKAISIDKS--------CMFAYETLGTIEVQRTF 112
E+ + + Y LG F
Sbjct: 238 ERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNF 271
>gnl|CDD|198111 smart01043, BTAD, Bacterial transcriptional activator domain.
Found in the DNRI/REDD/AFSR family of regulators. This
region of AFSR along with the C terminal region is
capable of independently directing actinorhodin
production. This family contains TPR repeats.
Length = 145
Score = 28.4 bits (64), Expect = 0.49
Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 1/56 (1%)
Query: 28 VEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAI 83
+EA A+ L+ + A R + +DP L+ M L G EA+
Sbjct: 61 LEALEALAEALLALGRHEEALALLERLLALDPLRERLH-RLLMRALYRAGRRAEAL 115
>gnl|CDD|193336 pfam12862, Apc5, Anaphase-promoting complex subunit 5. Apc5 is a
subunit of the anaphase-promoting complex/cyclosome
(APC/C) which is a multisubunit ubiquitin ligase that
mediates the proteolysis of cell cycle proteins in
mitosis and G1. Apc5, although it does not harbour a
classical RNA binding domain, Apc5 binds the poly(A)
binding protein (PABP), which directly binds the
internal ribosome entry site (IRES) of growth factor 2
mRNA. PABP was found to enhance IRES-mediated
translation, whereas Apc5 over-expression counteracted
this effect. In addition to its association with the
APC/C complex, Apc5 binds much heavier complexes and
co-sediments with the ribosomal fraction. The
N-terminus of Afi1 serves to stabilise the union
between Apc4 and Apc5, both of which lie towards the
bottom-front of the APC. This region of the Apc5 member
proteins carries a TPR-like motif.
Length = 91
Score = 27.9 bits (63), Expect = 0.58
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 16/67 (23%)
Query: 43 DFDGAEE----YFNRSIRVDPENASLYVHRAML---MLQAR-GNVDEAIKLIEKAISI-- 92
D+ GA + YF+ S+ N A+L L A G+ +EAI IE+AI +
Sbjct: 13 DYQGALDSLHRYFDYSLT---SNEKSSYQYALLNLASLHADFGHNEEAIAAIEEAIRLAR 69
Query: 93 ---DKSC 96
D +C
Sbjct: 70 ENKDTAC 76
>gnl|CDD|147106 pfam04781, DUF627, Protein of unknown function (DUF627). This
family represents the N-terminal region of several plant
proteins of unknown function.
Length = 112
Score = 28.0 bits (63), Expect = 0.66
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 75 ARGNVDEAIKLIEKAISI---DKSCMFAYETLGTI 106
A+G+ +A+++IE +IS D+S + GTI
Sbjct: 8 AKGDYIKALEIIEDSISDHGKDESAWLLHILQGTI 42
>gnl|CDD|233013 TIGR00540, TPR_hemY_coli, heme biosynthesis-associated TPR protein.
Members of this protein family are uncharacterized
tetratricopeptide repeat (TPR) proteins invariably found
in heme biosynthesis gene clusters. The absence of any
invariant residues other than Ala argues against this
protein serving as an enzyme per se. The gene symbol
hemY assigned in E. coli is unfortunate in that an
unrelated protein, protoporphyrinogen oxidase (HemG in
E. coli) is designated HemY in Bacillus subtilis
[Unknown function, General].
Length = 367
Score = 28.4 bits (64), Expect = 0.87
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 40 DQEDFDGAEEYFN---RSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKA 89
+ED D + ++ R+ R +PE A L G+ DEA KLIE+A
Sbjct: 221 REEDADALKTWWKQLPRAERQEPELAVAAAEA----LIQLGDHDEAEKLIEEA 269
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 28.0 bits (63), Expect = 1.0
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 43 DFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISID 93
D A EY +++I P LY+ +A ++ A G++ +A + +E+A S+D
Sbjct: 208 SRDKALEYIDKAIEHTPTLVELYMTKARILKHA-GDLQKAAEAMEEARSLD 257
>gnl|CDD|183140 PRK11447, PRK11447, cellulose synthase subunit BcsC; Provisional.
Length = 1157
Score = 28.1 bits (63), Expect = 1.1
Identities = 9/29 (31%), Positives = 19/29 (65%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPENAS 63
V + ++D+ AE Y+ +++R+DP N +
Sbjct: 392 GDVAMARKDYAAAERYYQQALRMDPGNTN 420
Score = 25.8 bits (57), Expect = 6.1
Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 38 LVDQEDFDGAEEYFNRSIRVDPENASLYVHRAM-LMLQARGNVDEAIKLIEKAISIDK 94
VD A +++R +P+++ A+ +G+ A+ EKA+++D
Sbjct: 279 AVDSGQGGKAIPELQQAVRANPKDSEA--LGALGQAYSQQGDRARAVAQFEKALALDP 334
>gnl|CDD|236716 PRK10564, PRK10564, maltose regulon periplasmic protein;
Provisional.
Length = 303
Score = 28.1 bits (63), Expect = 1.1
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 26/66 (39%)
Query: 48 EEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISIDKSCMFAYETLGTIE 107
E YFN++I+ +A+ +G+VD+A+KL+++A E LG+
Sbjct: 257 ESYFNQAIK-----------QAV----KKGDVDKALKLLDEA-----------ERLGSTS 290
Query: 108 VQRTFV 113
+ TF+
Sbjct: 291 ARSTFI 296
>gnl|CDD|189027 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Exonuclease-1 (EXO1) is involved
in multiple, eukaryotic DNA metabolic pathways,
including DNA replication processes (5' flap DNA
endonuclease activity and double stranded DNA
5'-exonuclease activity), DNA repair processes (DNA
mismatch repair (MMR) and post-replication repair
(PRR)), recombination, and telomere integrity. EXO1
functions in the MMS2 error-free branch of the PRR
pathway in the maintenance and repair of stalled
replication forks. Studies also suggest that EXO1 plays
both structural and catalytic roles during MMR-mediated
mutation avoidance. EXO1 belongs to the FEN1-EXO1-like
family of structure-specific, 5' nucleases. These
nucleases contain a PIN (PilT N terminus) domain with a
helical arch/clamp region (I domain) of variable length
(approximately 43 residues in EXO1 PIN domains) and a
H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). EXO1 nucleases also have
C-terminal Mlh1- and Msh2-binding domains which allow
interaction with MMR and PRR proteins, respectively.
Length = 210
Score = 27.5 bits (62), Expect = 1.4
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 35 AQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARG 77
A L+ + + A E F R++ + PE A H + L+ G
Sbjct: 103 ALELLREGNRSEARECFQRAVDITPEMA----HELIKALRKEG 141
>gnl|CDD|226156 COG3629, DnrI, DNA-binding transcriptional activator of the SARP
family [Signal transduction mechanisms].
Length = 280
Score = 27.4 bits (61), Expect = 1.5
Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 1/60 (1%)
Query: 30 ACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKA 89
A T A+ L+ D E+ R I +DP + Y R M G AI+ +
Sbjct: 155 ALTKLAEALIACGRADAVIEHLERLIELDPYDEPAY-LRLMEAYLVNGRQSAAIRAYRQL 213
>gnl|CDD|225950 COG3416, COG3416, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 233
Score = 27.2 bits (60), Expect = 2.1
Identities = 13/48 (27%), Positives = 20/48 (41%)
Query: 45 DGAEEYFNRSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEKAISI 92
AE ++ P+ A R ++ QA IK +EK I+I
Sbjct: 26 PQAEALIAEAVAKQPDAAYYLAQRVLIQEQALKKASTQIKELEKRIAI 73
>gnl|CDD|225461 COG2909, MalT, ATP-dependent transcriptional regulator
[Transcription].
Length = 894
Score = 27.0 bits (60), Expect = 2.4
Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 9/88 (10%)
Query: 8 ERVEQSLKEFRNFVDTHSNVVEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVH 67
R+E LK + + E L AQV +++ D + AE+ ++ PE A Y
Sbjct: 439 ARLEHFLKAPMHSRQG-DLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAA--YRS 495
Query: 68 RA------MLMLQARGNVDEAIKLIEKA 89
R RG + +A+ L+++A
Sbjct: 496 RIVALSVLGEAAHIRGELTQALALMQQA 523
>gnl|CDD|177516 PHA03070, PHA03070, DNA-binding virion core protein; Provisional.
Length = 249
Score = 26.9 bits (60), Expect = 2.6
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 8/49 (16%)
Query: 25 SNVVEACTLFAQVLVDQEDFD----GAEEYFNRSI----RVDPENASLY 65
N+ + LFA + +D + GA+ F RS + P N + Y
Sbjct: 6 ENLFDEDALFAAGITRYDDLELVIAGAKVKFPRSFLSIFNIVPRNMTKY 54
>gnl|CDD|227124 COG4785, NlpI, Lipoprotein NlpI, contains TPR repeats [General
function prediction only].
Length = 297
Score = 26.7 bits (59), Expect = 3.3
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 38 LVDQEDFDGAEEYFNRSIRVDPENASLYVHRAM 70
L +FD A E F+ + +DP +++R +
Sbjct: 109 LTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGI 141
>gnl|CDD|236875 PRK11189, PRK11189, lipoprotein NlpI; Provisional.
Length = 296
Score = 26.4 bits (59), Expect = 4.1
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 41 QEDFDGAEEYFNRSIRVDPENASLYVHRA 69
+FD A E F+ + +DP Y++R
Sbjct: 111 AGNFDAAYEAFDSVLELDPTYNYAYLNRG 139
>gnl|CDD|234474 TIGR04113, cas_csx17, CRISPR-associated protein Csx17, subtype
Dpsyc. Members of this protein family are found
exclusively in CRISPR-associated (cas) type I system
gene clusters of the Dpsyc subtype. Markers for that
type include a variant form of cas3 (model TIGR02621)
and the GSU0054-like protein family (model TIGR02165).
This family occurs in less than half of known Dpsyc
clusters.
Length = 704
Score = 26.2 bits (58), Expect = 4.4
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 53 RSIRVDPENASLYVHRAMLMLQARGNVDEAIKLIEK 88
R + SL V RA+L L G+ D A++L +
Sbjct: 621 RRALAETGGRSLPVPRAVLRLLRAGDADRAVELALR 656
>gnl|CDD|236644 PRK10049, pgaA, outer membrane protein PgaA; Provisional.
Length = 765
Score = 26.2 bits (58), Expect = 4.5
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 28 VEACTLFAQVLVDQEDFDGAEEYFNRSIRVDPENASLYVHRAMLMLQARG 77
++ +L +QV D AE P N L + A + LQARG
Sbjct: 359 LQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDYASV-LQARG 407
>gnl|CDD|217162 pfam02645, DegV, Uncharacterized protein, DegV family COG1307. The
structure of this protein revealed a bound fatty-acid
molecule in a pocket between the two protein domains.
The structure indicates that this family has the
molecular function of fatty-acid binding and may play a
role in the cellular functions of fatty acid transport
or metabolism.
Length = 211
Score = 26.0 bits (58), Expect = 5.2
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 47 AEEYFNRSIRV-DPENAS----LYVHRAMLMLQARGNVDEAIKLIEKAISIDKSCM-FAY 100
EE +RV D ++ S L V A + +A + +E +K +E+ +++ F
Sbjct: 33 KEELPGVKVRVIDSKSVSMGLGLLVLEAARLAKAGKSFEEILKKLEEI--RERTKAYFTV 90
Query: 101 ETL 103
+ L
Sbjct: 91 DDL 93
>gnl|CDD|205553 pfam13374, TPR_10, Tetratricopeptide repeat.
Length = 42
Score = 24.1 bits (53), Expect = 6.4
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 71 LMLQARGNVDEAIKLIEKAISI 92
L+A+G +EA +L+E+A++I
Sbjct: 10 RALRAQGRYEEAEELLEEALAI 31
>gnl|CDD|226498 COG4010, COG4010, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 170
Score = 25.6 bits (56), Expect = 6.7
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 1 MIVPGDRERVEQSLKEFRNF 20
+ + GD +RV+++LKE +F
Sbjct: 147 VAIYGDSDRVKKALKEIGSF 166
>gnl|CDD|182415 PRK10370, PRK10370, formate-dependent nitrite reductase complex
subunit NrfG; Provisional.
Length = 198
Score = 25.2 bits (55), Expect = 8.2
Identities = 16/57 (28%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 41 QEDFDGAEEYFNRSIRVDPENASLYVHRA-MLMLQARGNVDEAIK-LIEKAISIDKS 95
+ D+D A + +++++ ENA LY A +L QA ++ + +I+KA+++D +
Sbjct: 86 RNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDAN 142
>gnl|CDD|223056 PHA03362, PHA03362, single-stranded binding protein UL29;
Provisional.
Length = 1189
Score = 25.4 bits (56), Expect = 8.5
Identities = 8/46 (17%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 5 GDRERVEQSLKEFRNFVDTHSNVVE-ACTLFAQVLVDQEDFDGAEE 49
G+ + + F + + V+ F + LV+ D+ E
Sbjct: 598 GEDTSIIRDRASFMTALSNLNRTVDEEAEQFMRNLVEARDYKIREG 643
>gnl|CDD|180363 PRK06038, PRK06038, N-ethylammeline chlorohydrolase; Provisional.
Length = 430
Score = 25.5 bits (56), Expect = 8.7
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 1 MIVPGDRERVEQSLKEFRNFV 21
MI GD E+ E LKE + FV
Sbjct: 144 MIDLGDDEKGEAELKEGKRFV 164
>gnl|CDD|221837 pfam12895, Apc3, Anaphase-promoting complex, cyclosome, subunit 3.
Apc3, otherwise known as Cdc27, is one of the subunits
of the anaphase-promoting complex or cyclosome. The
anaphase-promoting complex is a multiprotein subunit E3
ubiquitin ligase complex that controls segregation of
chromosomes and exit from mitosis in eukaryotes. The
protein members of this family contain TPR repeats just
as those of Apc7 do, and it appears that these TPR units
bind the C-termini of the APC co-activators CDH1 and
CDC20.
Length = 80
Score = 24.1 bits (53), Expect = 9.6
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 76 RGNVDEAIKLIEKAISIDKSCMFAY 100
+GN + AI L EK +++ S AY
Sbjct: 2 QGNYENAIFLAEKLLALTPSNEDAY 26
>gnl|CDD|221958 pfam13176, TPR_7, Tetratricopeptide repeat.
Length = 36
Score = 23.3 bits (51), Expect = 9.6
Identities = 7/24 (29%), Positives = 16/24 (66%)
Query: 72 MLQARGNVDEAIKLIEKAISIDKS 95
+ + G+ ++AI L E+A+++ K
Sbjct: 8 LYRKLGDYEKAISLYERALALAKD 31
>gnl|CDD|182115 PRK09855, PRK09855, PTS system N-acetylgalactosamine-specific
transporter subunit IID; Provisional.
Length = 263
Score = 25.1 bits (55), Expect = 9.7
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 2 IVPGDRERVEQSLKEFRNFVDTHSNVV 28
I D+ + ++K+ F++TH N+V
Sbjct: 45 IYKDDKPGLSAAMKDNLEFINTHPNLV 71
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.136 0.388
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,941,996
Number of extensions: 520512
Number of successful extensions: 803
Number of sequences better than 10.0: 1
Number of HSP's gapped: 783
Number of HSP's successfully gapped: 120
Length of query: 116
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 37
Effective length of database: 7,433,636
Effective search space: 275044532
Effective search space used: 275044532
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)