Query 020929
Match_columns 319
No_of_seqs 80 out of 82
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 06:16:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020929.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020929hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05687 DUF822: Plant protein 100.0 8.3E-66 1.8E-70 442.0 14.6 145 5-150 1-148 (150)
2 PLN02905 beta-amylase 100.0 1.8E-38 3.8E-43 318.9 12.0 100 2-104 73-172 (702)
3 PLN02705 beta-amylase 100.0 3.6E-35 7.9E-40 294.4 9.7 76 6-81 75-150 (681)
4 PF11914 DUF3432: Domain of un 80.6 3.9 8.5E-05 34.5 5.1 11 158-168 88-98 (99)
5 PF05687 DUF822: Plant protein 65.2 7.5 0.00016 35.0 3.4 25 105-129 84-108 (150)
6 PF11914 DUF3432: Domain of un 63.5 6.3 0.00014 33.3 2.5 32 95-128 21-52 (99)
7 PF00010 HLH: Helix-loop-helix 55.5 47 0.001 23.3 5.5 45 16-60 2-49 (55)
8 PF14111 DUF4283: Domain of un 48.4 10 0.00022 30.6 1.3 33 43-75 110-142 (153)
9 PF14226 DIOX_N: non-haem diox 46.2 20 0.00044 27.6 2.7 39 24-62 11-49 (116)
10 PF00424 REV: REV protein (ant 45.5 27 0.00059 29.1 3.4 26 12-37 32-61 (91)
11 TIGR03674 fen_arch flap struct 45.1 43 0.00093 32.3 5.2 57 9-65 82-145 (338)
12 PRK07309 aromatic amino acid a 44.7 52 0.0011 30.8 5.5 29 44-73 326-356 (391)
13 PF10075 PCI_Csn8: COP9 signal 44.1 22 0.00048 29.3 2.7 26 49-75 109-134 (143)
14 PRK07682 hypothetical protein; 43.6 49 0.0011 30.4 5.2 24 49-73 321-344 (378)
15 PRK08361 aspartate aminotransf 39.7 63 0.0014 30.0 5.3 57 17-74 292-359 (391)
16 PLN02409 serine--glyoxylate am 39.3 93 0.002 29.6 6.4 37 43-79 311-352 (401)
17 PRK05957 aspartate aminotransf 38.6 55 0.0012 30.6 4.7 28 45-73 325-352 (389)
18 KOG0260 RNA polymerase II, lar 37.8 3.8E+02 0.0083 31.8 11.6 13 88-100 1435-1447(1605)
19 PRK05942 aspartate aminotransf 35.9 81 0.0018 29.5 5.4 30 44-74 332-361 (394)
20 KOG0733 Nuclear AAA ATPase (VC 35.4 25 0.00053 38.4 2.1 44 23-66 363-411 (802)
21 PRK09276 LL-diaminopimelate am 34.1 1.2E+02 0.0026 28.0 6.1 28 45-73 329-356 (385)
22 COG0802 Predicted ATPase or ki 33.5 16 0.00036 32.3 0.4 30 283-313 93-124 (149)
23 PRK08363 alanine aminotransfer 33.2 74 0.0016 29.7 4.7 24 50-74 340-363 (398)
24 PRK10646 ADP-binding protein; 33.2 16 0.00035 32.0 0.4 22 291-313 105-127 (153)
25 cd08517 PBP2_NikA_DppA_OppA_li 33.1 66 0.0014 30.3 4.4 20 52-71 313-332 (480)
26 PF02367 UPF0079: Uncharacteri 30.8 18 0.00039 30.6 0.2 28 284-312 84-113 (123)
27 cd08513 PBP2_thermophilic_Hb8_ 30.4 90 0.002 29.6 4.8 49 26-74 272-331 (482)
28 PRK07683 aminotransferase A; V 29.5 1.3E+02 0.0027 28.2 5.5 56 18-74 287-352 (387)
29 TIGR03537 DapC succinyldiamino 28.0 1.2E+02 0.0026 27.7 5.1 29 44-74 294-322 (350)
30 cd00083 HLH Helix-loop-helix d 27.7 93 0.002 21.5 3.4 47 13-59 2-49 (60)
31 cd06451 AGAT_like Alanine-glyo 27.6 1.8E+02 0.0038 26.3 5.9 46 23-68 261-321 (356)
32 cd08497 PBP2_NikA_DppA_OppA_li 27.3 92 0.002 30.1 4.3 25 51-75 319-343 (491)
33 smart00550 Zalpha Z-DNA-bindin 27.3 1.1E+02 0.0023 23.0 3.8 49 28-78 6-67 (68)
34 COG1487 VapC Predicted nucleic 27.2 1.2E+02 0.0025 24.5 4.3 41 26-70 75-115 (133)
35 PRK06108 aspartate aminotransf 26.8 1.6E+02 0.0035 26.8 5.6 55 18-73 286-350 (382)
36 TIGR02864 spore_sspO small, ac 26.8 28 0.0006 26.5 0.6 18 8-25 32-49 (50)
37 TIGR01365 serC_2 phosphoserine 26.2 1.8E+02 0.004 28.4 6.2 61 19-80 261-354 (374)
38 cd08509 PBP2_TmCBP_oligosaccha 26.1 1.3E+02 0.0028 29.2 5.1 24 52-75 324-347 (509)
39 PRK02984 sspO acid-soluble spo 25.6 31 0.00068 26.1 0.7 17 8-24 31-47 (49)
40 PRK07681 aspartate aminotransf 25.4 1.5E+02 0.0033 27.8 5.3 28 45-73 329-356 (399)
41 COG1961 PinR Site-specific rec 25.0 1.5E+02 0.0032 26.0 4.8 46 14-59 122-173 (222)
42 cd06453 SufS_like Cysteine des 24.4 1.6E+02 0.0035 26.8 5.1 45 24-69 278-336 (373)
43 PRK07550 hypothetical protein; 24.0 1.9E+02 0.0041 26.8 5.6 28 45-73 326-354 (386)
44 PTZ00376 aspartate aminotransf 23.9 1.8E+02 0.0038 27.5 5.4 20 51-70 359-378 (404)
45 PRK07908 hypothetical protein; 23.3 1.4E+02 0.003 27.3 4.5 55 17-73 256-316 (349)
46 PRK07392 threonine-phosphate d 23.3 1.1E+02 0.0023 28.2 3.8 34 40-74 295-329 (360)
47 PRK12495 hypothetical protein; 23.2 1E+02 0.0022 29.5 3.7 57 13-80 5-67 (226)
48 TIGR00150 HI0065_YjeE ATPase, 22.7 33 0.00072 29.3 0.4 21 291-312 99-120 (133)
49 KOG3910 Helix loop helix trans 22.2 58 0.0013 34.8 2.1 12 49-60 539-550 (632)
50 PLN02397 aspartate transaminas 22.1 2E+02 0.0044 27.6 5.6 22 48-70 375-396 (423)
51 PRK10534 L-threonine aldolase; 22.0 1.8E+02 0.0038 26.2 4.9 34 40-74 274-308 (333)
52 TIGR03538 DapC_gpp succinyldia 21.6 1.3E+02 0.0029 28.0 4.1 25 49-74 334-358 (393)
53 PRK07590 L,L-diaminopimelate a 21.2 2.7E+02 0.0058 26.3 6.1 29 44-73 351-379 (409)
54 TIGR02294 nickel_nikA nickel A 21.2 1.6E+02 0.0036 28.3 4.8 18 53-70 315-332 (500)
55 cd01560 Thr-synth_2 Threonine 21.2 1.1E+02 0.0024 31.1 3.7 44 29-72 332-391 (460)
56 cd08500 PBP2_NikA_DppA_OppA_li 21.1 1.8E+02 0.0038 28.4 5.0 23 53-75 316-339 (499)
57 smart00345 HTH_GNTR helix_turn 21.1 1.3E+02 0.0029 20.0 3.0 45 27-73 3-58 (60)
58 cd08518 PBP2_NikA_DppA_OppA_li 21.0 1.6E+02 0.0036 28.0 4.7 21 51-71 298-318 (464)
59 PRK08912 hypothetical protein; 20.9 2.2E+02 0.0048 26.4 5.4 25 49-74 329-353 (387)
60 PF02585 PIG-L: GlcNAc-PI de-N 20.4 70 0.0015 25.3 1.8 60 1-62 33-99 (128)
No 1
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=100.00 E-value=8.3e-66 Score=442.01 Aligned_cols=145 Identities=72% Similarity=1.160 Sum_probs=138.0
Q ss_pred CCCCCCCChHHHhhhHHHHHHHHHHHHHHHhhhhhcCCCCCCCccChHHHHHHHHHHhCcEEcCCCceecCCCCCCCCCC
Q 020929 5 GSSGRLPTWKERENNKRRERRRRAIAAKIFSGLRAEGNFKLPKHCDNNEVLKALCAEAGWIVEEDGTTYRKGSRPPRTPS 84 (319)
Q Consensus 5 ~~~~R~ptwrErEnnkrRERrRRAIaakIfaGLR~~Gny~Lpk~~D~NeVlkaLc~eAGw~ve~DGttyr~g~kp~~~~~ 84 (319)
|+++|+||||||||||+|||||||||+|||+|||+||||+|||||||||||||||+||||+||+|||||||+|+|++ .+
T Consensus 1 ~~~~r~pt~kErEnnk~RERrRRAIaakIfaGLR~~Gny~Lp~~aD~NeVLkALc~eAGw~Ve~DGTtyr~~~~~~~-~~ 79 (150)
T PF05687_consen 1 GSGGRRPTWKERENNKRRERRRRAIAAKIFAGLRAHGNYKLPKHADNNEVLKALCREAGWTVEPDGTTYRKGCKPPE-PM 79 (150)
T ss_pred CCCcccccHhhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcCCHHHHHHHHHHhCCEEEccCCCeeccCCCCCc-cc
Confidence 45699999999999999999999999999999999999999999999999999999999999999999999999995 89
Q ss_pred CCCCCCCccCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCC---CCCccchhhcccCCCCC
Q 020929 85 EITGGSANISTCSSVQPSPQSSAFPSPVPSYQASPTSSSFPSPTRFEGN---PSNYILPFLQNIASVPT 150 (319)
Q Consensus 85 ~~~g~s~~~spcSS~~pSp~ss~fpSP~~SY~~SP~SSSfpSp~~~~~~---~~ssLiPwLk~ls~~~s 150 (319)
+++|.++.++|||++++++.+++|++|++||+++|.+|+||||+++|.. .+++|||||||++++++
T Consensus 80 ~~~g~s~~~sp~ss~~~~~~ss~~~sp~~s~~~s~~ss~~pSp~~~d~~~~~~~~~~~p~~~~~~~~~s 148 (150)
T PF05687_consen 80 EIVGSSASASPCSSYQLSPNSSAFPSPVPSYQPSPSSSSFPSPSSLDSINNSSSSSLIPWLKNLSSGSS 148 (150)
T ss_pred cccccCCCCCCcCCCcCCccccCcCCcccccCCCcCCCCCCCCcccccccccccccccchhhccccCcC
Confidence 9999999999999999999999999999999999999999999998874 34789999999987654
No 2
>PLN02905 beta-amylase
Probab=100.00 E-value=1.8e-38 Score=318.90 Aligned_cols=100 Identities=44% Similarity=0.635 Sum_probs=90.5
Q ss_pred CCCCCCCCCCChHHHhhhHHHHHHHHHHHHHHHhhhhhcCCCCCCCccChHHHHHHHHHHhCcEEcCCCceecCCCCCCC
Q 020929 2 TAGGSSGRLPTWKERENNKRRERRRRAIAAKIFSGLRAEGNFKLPKHCDNNEVLKALCAEAGWIVEEDGTTYRKGSRPPR 81 (319)
Q Consensus 2 t~g~~~~R~ptwrErEnnkrRERrRRAIaakIfaGLR~~Gny~Lpk~~D~NeVlkaLc~eAGw~ve~DGttyr~g~kp~~ 81 (319)
.+||+++|.|+||||||||+|||||||||+|||+|||+||||+||||||+||||||||+||||+||+||||||++|+.+
T Consensus 73 ~~~~~~~~~~~~~ere~~~~rer~rrai~~~i~~glr~~g~~~lp~~~d~n~v~~~l~~eag~~v~~dg~~y~~~~~~~- 151 (702)
T PLN02905 73 PGGGGSRRSRPLEEKERTKLRERHRRAITARILAGLRRHGNYNLRVRADINDVIAALAREAGWVVLPDGTTFPSRSQGT- 151 (702)
T ss_pred CCCCccCCCCchhhhhhhHHHHHHHHHHHHHHHHHHHhhcCCCCCcccchHHHHHHHHHhcCcEEcCCCCcccccCCCC-
Confidence 3577889999999999999999999999999999999999999999999999999999999999999999999776655
Q ss_pred CCCCCCCCCCccCCCCCCCCCCC
Q 020929 82 TPSEITGGSANISTCSSVQPSPQ 104 (319)
Q Consensus 82 ~~~~~~g~s~~~spcSS~~pSp~ 104 (319)
...+|+|+.+.+|++++.-++
T Consensus 152 --~~~~~~~~~~~~~~~~~~~~~ 172 (702)
T PLN02905 152 --RPAGGTSAVAATSSSSHLVSQ 172 (702)
T ss_pred --CCCCCcccccccccccccccc
Confidence 244678888999999985433
No 3
>PLN02705 beta-amylase
Probab=100.00 E-value=3.6e-35 Score=294.44 Aligned_cols=76 Identities=51% Similarity=0.855 Sum_probs=73.6
Q ss_pred CCCCCCChHHHhhhHHHHHHHHHHHHHHHhhhhhcCCCCCCCccChHHHHHHHHHHhCcEEcCCCceecCCCCCCC
Q 020929 6 SSGRLPTWKERENNKRRERRRRAIAAKIFSGLRAEGNFKLPKHCDNNEVLKALCAEAGWIVEEDGTTYRKGSRPPR 81 (319)
Q Consensus 6 ~~~R~ptwrErEnnkrRERrRRAIaakIfaGLR~~Gny~Lpk~~D~NeVlkaLc~eAGw~ve~DGttyr~g~kp~~ 81 (319)
+.+|.|+||||||||+|||||||||+|||+|||+||||+||+|||+||||||||+||||+||+||||||++++|.+
T Consensus 75 ~~~~~~~~~e~e~~~~rer~rrai~~ki~aglr~~g~~~lp~~~d~n~vl~al~~eagw~v~~dg~~yr~~~~~~~ 150 (681)
T PLN02705 75 GKGKREREKEKERTKLRERHRRAITSRMLAGLRQYGNFPLPARADMNDVLAALAREAGWTVEADGTTYRQSPQPSH 150 (681)
T ss_pred CCCCCcchhhhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCcccchHHHHHHHHHhcCcEEcCCCCcccCCCCCcc
Confidence 5578999999999999999999999999999999999999999999999999999999999999999999999884
No 4
>PF11914 DUF3432: Domain of unknown function (DUF3432); InterPro: IPR021839 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with PF00096 from PFAM. This domain has two conserved sequence motifs: YPSPV and PSP.
Probab=80.62 E-value=3.9 Score=34.53 Aligned_cols=11 Identities=55% Similarity=0.594 Sum_probs=8.9
Q ss_pred cccccCCCCCC
Q 020929 158 SNSAPVTPPLS 168 (319)
Q Consensus 158 S~SAPVTPPlS 168 (319)
+.|+||+-+|+
T Consensus 88 ~fsspvst~Ls 98 (99)
T PF11914_consen 88 SFSSPVSTGLS 98 (99)
T ss_pred cccccccccCC
Confidence 66899988875
No 5
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=65.17 E-value=7.5 Score=34.96 Aligned_cols=25 Identities=64% Similarity=0.870 Sum_probs=14.2
Q ss_pred CCCCCCCCCccCCCCCCCCCCCCCC
Q 020929 105 SSAFPSPVPSYQASPTSSSFPSPTR 129 (319)
Q Consensus 105 ss~fpSP~~SY~~SP~SSSfpSp~~ 129 (319)
+|..++|+.+|+.++.+++|+||..
T Consensus 84 ~s~~~sp~ss~~~~~~ss~~~sp~~ 108 (150)
T PF05687_consen 84 SSASASPCSSYQLSPNSSAFPSPVP 108 (150)
T ss_pred cCCCCCCcCCCcCCccccCcCCccc
Confidence 4445556666666666666665544
No 6
>PF11914 DUF3432: Domain of unknown function (DUF3432); InterPro: IPR021839 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with PF00096 from PFAM. This domain has two conserved sequence motifs: YPSPV and PSP.
Probab=63.54 E-value=6.3 Score=33.35 Aligned_cols=32 Identities=50% Similarity=0.942 Sum_probs=14.5
Q ss_pred CCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCC
Q 020929 95 TCSSVQPSPQSSAFPSPVPSYQASPTSSSFPSPT 128 (319)
Q Consensus 95 pcSS~~pSp~ss~fpSP~~SY~~SP~SSSfpSp~ 128 (319)
+-+|| ||+. .++|||+++--.||.+|++|||.
T Consensus 21 ~~tSY-pS~~-tsyPSPV~tsy~sp~~S~ypSPv 52 (99)
T PF11914_consen 21 VATSY-PSPI-TSYPSPVPTSYSSPVSSCYPSPV 52 (99)
T ss_pred ccccC-CCcc-ccCCCccccccCCCCcccccccc
Confidence 33444 3433 44555553333455555554443
No 7
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=55.51 E-value=47 Score=23.30 Aligned_cols=45 Identities=24% Similarity=0.305 Sum_probs=31.9
Q ss_pred HhhhHHHHHHHHHHHHHHHhhhhhcCCCC---CCCccChHHHHHHHHH
Q 020929 16 RENNKRRERRRRAIAAKIFSGLRAEGNFK---LPKHCDNNEVLKALCA 60 (319)
Q Consensus 16 rEnnkrRERrRRAIaakIfaGLR~~Gny~---Lpk~~D~NeVlkaLc~ 60 (319)
|++...+||+||.=-..-|.-|+.+=-.. -..+-|..+||..-++
T Consensus 2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~ 49 (55)
T PF00010_consen 2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAID 49 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHH
Confidence 66778889988887777778888764443 2345777888876554
No 8
>PF14111 DUF4283: Domain of unknown function (DUF4283)
Probab=48.36 E-value=10 Score=30.56 Aligned_cols=33 Identities=33% Similarity=0.506 Sum_probs=30.4
Q ss_pred CCCCCccChHHHHHHHHHHhCcEEcCCCceecC
Q 020929 43 FKLPKHCDNNEVLKALCAEAGWIVEEDGTTYRK 75 (319)
Q Consensus 43 y~Lpk~~D~NeVlkaLc~eAGw~ve~DGttyr~ 75 (319)
|.||.++=+.+++++++...|=+++-|.+|...
T Consensus 110 ~glP~~~~~~~~~~~i~~~iG~~i~vD~~t~~~ 142 (153)
T PF14111_consen 110 YGLPLHLWSEEILKAIGSKIGEPIEVDENTLKR 142 (153)
T ss_pred ccCCHHHhhhHHHHHHHHhcCCeEEEEcCCCCc
Confidence 469999999999999999999999999998865
No 9
>PF14226 DIOX_N: non-haem dioxygenase in morphine synthesis N-terminal; PDB: 3OOX_A 1BK0_A 1IPS_B 1QIQ_A 1OC1_A 2Y86_A 2Y60_A 1W03_A 2VE1_A 1QJF_A ....
Probab=46.20 E-value=20 Score=27.64 Aligned_cols=39 Identities=23% Similarity=0.273 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhhhhcCCCCCCCccChHHHHHHHHHHh
Q 020929 24 RRRRAIAAKIFSGLRAEGNFKLPKHCDNNEVLKALCAEA 62 (319)
Q Consensus 24 RrRRAIaakIfaGLR~~Gny~Lpk~~D~NeVlkaLc~eA 62 (319)
-.|.+++++|...++.+|-|.|=-|.-..+++..+.+.+
T Consensus 11 ~~~~~~~~~l~~A~~~~GFf~l~nhGi~~~l~~~~~~~~ 49 (116)
T PF14226_consen 11 ADREEVAEQLRDACEEWGFFYLVNHGIPQELIDRVFAAA 49 (116)
T ss_dssp HHHHHHHHHHHHHHHHTSEEEEESSSSSHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHhCCEEEEecccccchhhHHHHHHH
Confidence 457889999999999999999999988887777665543
No 10
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=45.53 E-value=27 Score=29.11 Aligned_cols=26 Identities=42% Similarity=0.610 Sum_probs=17.3
Q ss_pred ChHHHhhhHHHHHHH----HHHHHHHHhhh
Q 020929 12 TWKERENNKRRERRR----RAIAAKIFSGL 37 (319)
Q Consensus 12 twrErEnnkrRERrR----RAIaakIfaGL 37 (319)
|.+-|.|.+||-|+| ++|+.+||+-.
T Consensus 32 Tr~aRRnRRRRWR~rq~QI~~lseRIl~t~ 61 (91)
T PF00424_consen 32 TRQARRNRRRRWRARQRQIRALSERILSTC 61 (91)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred ccccccchhhhHHHHHHHHHHHHHHHHHhc
Confidence 455666666655544 68999999854
No 11
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=45.07 E-value=43 Score=32.26 Aligned_cols=57 Identities=21% Similarity=0.093 Sum_probs=33.4
Q ss_pred CCCChHHHhhhHHHHHHHHHHHHHH-------HhhhhhcCCCCCCCccChHHHHHHHHHHhCcE
Q 020929 9 RLPTWKERENNKRRERRRRAIAAKI-------FSGLRAEGNFKLPKHCDNNEVLKALCAEAGWI 65 (319)
Q Consensus 9 R~ptwrErEnnkrRERrRRAIaakI-------faGLR~~Gny~Lpk~~D~NeVlkaLc~eAGw~ 65 (319)
..|+.|..+..+|+++|-.|...-. ...++++.+-..+-.-++.+.++.|++..|+-
T Consensus 82 ~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip 145 (338)
T TIGR03674 82 KPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIP 145 (338)
T ss_pred CChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCe
Confidence 3578999999999999877543311 11223333222222244667777777777753
No 12
>PRK07309 aromatic amino acid aminotransferase; Validated
Probab=44.68 E-value=52 Score=30.78 Aligned_cols=29 Identities=17% Similarity=0.343 Sum_probs=21.0
Q ss_pred CCCCcc--ChHHHHHHHHHHhCcEEcCCCcee
Q 020929 44 KLPKHC--DNNEVLKALCAEAGWIVEEDGTTY 73 (319)
Q Consensus 44 ~Lpk~~--D~NeVlkaLc~eAGw~ve~DGtty 73 (319)
+||++. |..++.+.||.++|+.|- .|..|
T Consensus 326 ~l~~~~~~~~~~~~~~l~~~~gv~v~-pg~~f 356 (391)
T PRK07309 326 KIPAGYNQDSFKFLQDFARKKAVAFI-PGAAF 356 (391)
T ss_pred ECCCCCCCCHHHHHHHHHHhCCEEEe-Cchhh
Confidence 466654 456788899999999996 45555
No 13
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=44.06 E-value=22 Score=29.34 Aligned_cols=26 Identities=27% Similarity=0.585 Sum_probs=13.2
Q ss_pred cChHHHHHHHHHHhCcEEcCCCceecC
Q 020929 49 CDNNEVLKALCAEAGWIVEEDGTTYRK 75 (319)
Q Consensus 49 ~D~NeVlkaLc~eAGw~ve~DGttyr~ 75 (319)
.+ .+-|..+|.+.||.++.||..+..
T Consensus 109 ~~-~~el~~~~~~~gW~~d~~~~~~~~ 134 (143)
T PF10075_consen 109 LS-EEELEKFIKSRGWTVDGDGVLFPP 134 (143)
T ss_dssp S--HHHHHHHHHHHT-EE-----EE--
T ss_pred CC-HHHHHHHHHHcCCEECCCccEEec
Confidence 45 556677888889999999988873
No 14
>PRK07682 hypothetical protein; Validated
Probab=43.60 E-value=49 Score=30.42 Aligned_cols=24 Identities=21% Similarity=0.264 Sum_probs=19.4
Q ss_pred cChHHHHHHHHHHhCcEEcCCCcee
Q 020929 49 CDNNEVLKALCAEAGWIVEEDGTTY 73 (319)
Q Consensus 49 ~D~NeVlkaLc~eAGw~ve~DGtty 73 (319)
.|..++.+.|++++|..|-+ |..|
T Consensus 321 ~~~~~~~~~ll~~~gv~v~p-g~~f 344 (378)
T PRK07682 321 LSSEEFAEQLLLEEKVAVVP-GSVF 344 (378)
T ss_pred CCHHHHHHHHHHhCCEEEcC-chhh
Confidence 46678888888899999876 7777
No 15
>PRK08361 aspartate aminotransferase; Provisional
Probab=39.67 E-value=63 Score=30.05 Aligned_cols=57 Identities=19% Similarity=0.360 Sum_probs=34.0
Q ss_pred hhhHHHHHHHHHHHHHHHh---hhh---hcCCC----CCCC-ccChHHHHHHHHHHhCcEEcCCCceec
Q 020929 17 ENNKRRERRRRAIAAKIFS---GLR---AEGNF----KLPK-HCDNNEVLKALCAEAGWIVEEDGTTYR 74 (319)
Q Consensus 17 EnnkrRERrRRAIaakIfa---GLR---~~Gny----~Lpk-~~D~NeVlkaLc~eAGw~ve~DGttyr 74 (319)
++.+++-++||.+..+-+. |+. ..|+| +||. ..|..++.+.|.++.|..|. +|+.|.
T Consensus 292 ~~~~~~~~~~~~~~~~~L~~~~~~~~~~p~g~~~~~~~l~~~~~~~~~l~~~l~~~~gv~v~-pg~~f~ 359 (391)
T PRK08361 292 EEMRKEYNERRKLVLKRLKEMPHIKVFEPKGAFYVFANIDETGMSSEDFAEWLLEKARVVVI-PGTAFG 359 (391)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCeecCCCEEEEEEEECCCCCCCHHHHHHHHHHhCCEEEc-CchhhC
Confidence 3444444444554444443 332 24443 4553 45778888888888999998 466663
No 16
>PLN02409 serine--glyoxylate aminotransaminase
Probab=39.31 E-value=93 Score=29.55 Aligned_cols=37 Identities=19% Similarity=0.293 Sum_probs=27.7
Q ss_pred CCCCCccChHHHHHHHHHHhCcEEcC-----CCceecCCCCC
Q 020929 43 FKLPKHCDNNEVLKALCAEAGWIVEE-----DGTTYRKGSRP 79 (319)
Q Consensus 43 y~Lpk~~D~NeVlkaLc~eAGw~ve~-----DGttyr~g~kp 79 (319)
+++|+..|..+|.+.|.++.|.++.. .|..+|-|+-.
T Consensus 311 ~~~p~~~~~~~l~~~l~~~~~i~i~~G~~~~~~~~~Rig~~g 352 (401)
T PLN02409 311 VVVPEGIDSAEIVKNAWKKYNLSLGLGLNKVAGKVFRIGHLG 352 (401)
T ss_pred EeCCCCCCHHHHHHHHHHhCCEEEEcCCCcccCCEEEEcCCC
Confidence 45566677788999999998888873 57778876654
No 17
>PRK05957 aspartate aminotransferase; Provisional
Probab=38.60 E-value=55 Score=30.60 Aligned_cols=28 Identities=29% Similarity=0.330 Sum_probs=21.7
Q ss_pred CCCccChHHHHHHHHHHhCcEEcCCCcee
Q 020929 45 LPKHCDNNEVLKALCAEAGWIVEEDGTTY 73 (319)
Q Consensus 45 Lpk~~D~NeVlkaLc~eAGw~ve~DGtty 73 (319)
++...|..|+.+.|+++.|+.|-+ |+.|
T Consensus 325 ~~~~~~~~~~~~~l~~~~gv~v~p-g~~f 352 (389)
T PRK05957 325 VNTDLNDFELVKQLIREYRVAVIP-GTTF 352 (389)
T ss_pred CCCCCChHHHHHHHHHHCCEEEcc-chhh
Confidence 455567778999999999999886 5555
No 18
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=37.76 E-value=3.8e+02 Score=31.80 Aligned_cols=13 Identities=31% Similarity=0.061 Sum_probs=7.4
Q ss_pred CCCCccCCCCCCC
Q 020929 88 GGSANISTCSSVQ 100 (319)
Q Consensus 88 g~s~~~spcSS~~ 100 (319)
+.+...+|-+||.
T Consensus 1435 ~~~~~~sp~~s~~ 1447 (1605)
T KOG0260|consen 1435 NMSSPASPGSSYS 1447 (1605)
T ss_pred ccCCCCCCCCCCC
Confidence 3445556666665
No 19
>PRK05942 aspartate aminotransferase; Provisional
Probab=35.86 E-value=81 Score=29.47 Aligned_cols=30 Identities=13% Similarity=0.288 Sum_probs=23.5
Q ss_pred CCCCccChHHHHHHHHHHhCcEEcCCCceec
Q 020929 44 KLPKHCDNNEVLKALCAEAGWIVEEDGTTYR 74 (319)
Q Consensus 44 ~Lpk~~D~NeVlkaLc~eAGw~ve~DGttyr 74 (319)
++|...|..+++..|+++.|..|-+ |+.|.
T Consensus 332 ~~~~~~~~~~~~~~~l~~~gV~v~~-g~~f~ 361 (394)
T PRK05942 332 PCPVGMGSTDFALNVLQKTGVVVTP-GNAFG 361 (394)
T ss_pred ECCCCCCHHHHHHHHHHHCCEEEeC-ChhhC
Confidence 4676677888898899999998864 66664
No 20
>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=35.40 E-value=25 Score=38.43 Aligned_cols=44 Identities=34% Similarity=0.496 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHhhhhhcCCCCCCC-----ccChHHHHHHHHHHhCcEE
Q 020929 23 ERRRRAIAAKIFSGLRAEGNFKLPK-----HCDNNEVLKALCAEAGWIV 66 (319)
Q Consensus 23 ERrRRAIaakIfaGLR~~Gny~Lpk-----~~D~NeVlkaLc~eAGw~v 66 (319)
|-.|+.|-.+|..|||--|+|.+-+ +.=.+.=|+|||.|||.+-
T Consensus 363 e~aR~~IL~~~~~~lrl~g~~d~~qlA~lTPGfVGADL~AL~~~Aa~vA 411 (802)
T KOG0733|consen 363 ETAREEILRIICRGLRLSGDFDFKQLAKLTPGFVGADLMALCREAAFVA 411 (802)
T ss_pred hHHHHHHHHHHHhhCCCCCCcCHHHHHhcCCCccchhHHHHHHHHHHHH
Confidence 3456779999999999999998653 3445666999999999763
No 21
>PRK09276 LL-diaminopimelate aminotransferase; Provisional
Probab=34.05 E-value=1.2e+02 Score=28.00 Aligned_cols=28 Identities=29% Similarity=0.471 Sum_probs=21.6
Q ss_pred CCCccChHHHHHHHHHHhCcEEcCCCcee
Q 020929 45 LPKHCDNNEVLKALCAEAGWIVEEDGTTY 73 (319)
Q Consensus 45 Lpk~~D~NeVlkaLc~eAGw~ve~DGtty 73 (319)
||...|..++.++|+++.|..|-+ |+-|
T Consensus 329 ~~~~~~~~~l~~~ll~~~gi~v~~-g~~f 356 (385)
T PRK09276 329 VPKGYTSAEFATLLLDKAGVVVTP-GNGF 356 (385)
T ss_pred CCCCCCHHHHHHHHHHhCCEEECC-chhh
Confidence 556667889999999999998864 5555
No 22
>COG0802 Predicted ATPase or kinase [General function prediction only]
Probab=33.51 E-value=16 Score=32.34 Aligned_cols=30 Identities=30% Similarity=0.460 Sum_probs=20.5
Q ss_pred CcccccCCc-ccCCcCccccc-cccccceeccC
Q 020929 283 SEFEFESER-VKPWEGERIHE-VSVDDLELTLG 313 (319)
Q Consensus 283 ~eF~F~~g~-VKpWEGERIHE-~g~DdLELTLG 313 (319)
+||=+++|. |--| ||++.+ .-..+||+++-
T Consensus 93 ~e~~~~~gv~lIEW-~e~~~~~lp~~~l~I~i~ 124 (149)
T COG0802 93 DEYFDGDGICLIEW-PERLAELLPDADLEITIT 124 (149)
T ss_pred HHHhCCCcEEEEEC-cchhccCCCCceEEEEEE
Confidence 455555553 6678 677877 47888888863
No 23
>PRK08363 alanine aminotransferase; Validated
Probab=33.23 E-value=74 Score=29.67 Aligned_cols=24 Identities=21% Similarity=0.346 Sum_probs=18.1
Q ss_pred ChHHHHHHHHHHhCcEEcCCCceec
Q 020929 50 DNNEVLKALCAEAGWIVEEDGTTYR 74 (319)
Q Consensus 50 D~NeVlkaLc~eAGw~ve~DGttyr 74 (319)
|..++++.++.++|..|- +|+.|.
T Consensus 340 ~~~~~~~~~l~~~gV~v~-~g~~f~ 363 (398)
T PRK08363 340 DDKEFVLDVLHEAHVLFV-HGSGFG 363 (398)
T ss_pred CHHHHHHHHHHhCCEEEe-CchhhC
Confidence 456777888899998876 477773
No 24
>PRK10646 ADP-binding protein; Provisional
Probab=33.15 E-value=16 Score=32.02 Aligned_cols=22 Identities=23% Similarity=0.365 Sum_probs=14.1
Q ss_pred cccCCcCcccccc-ccccceeccC
Q 020929 291 RVKPWEGERIHEV-SVDDLELTLG 313 (319)
Q Consensus 291 ~VKpWEGERIHE~-g~DdLELTLG 313 (319)
.|=-| .|||-+. -.++|++++-
T Consensus 105 ~~IEW-~e~~~~~lp~~~l~i~i~ 127 (153)
T PRK10646 105 CLVEW-PQQGAGVLPDPDVEIHLD 127 (153)
T ss_pred EEEEC-CcchhhcCCcCcEEEEEE
Confidence 36678 8888553 5566766653
No 25
>cd08517 PBP2_NikA_DppA_OppA_like_13 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=33.14 E-value=66 Score=30.27 Aligned_cols=20 Identities=35% Similarity=0.380 Sum_probs=15.5
Q ss_pred HHHHHHHHHHhCcEEcCCCc
Q 020929 52 NEVLKALCAEAGWIVEEDGT 71 (319)
Q Consensus 52 NeVlkaLc~eAGw~ve~DGt 71 (319)
-|--|+|.+||||..+.||+
T Consensus 313 ~~~A~~lL~~aG~~~~~~G~ 332 (480)
T cd08517 313 VAKAEALLDEAGYPRGADGI 332 (480)
T ss_pred HHHHHHHHHHcCCCcCCCCc
Confidence 35677899999998776664
No 26
>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.
Probab=30.75 E-value=18 Score=30.59 Aligned_cols=28 Identities=39% Similarity=0.733 Sum_probs=15.7
Q ss_pred cccccCC-cccCCcCccccc-cccccceecc
Q 020929 284 EFEFESE-RVKPWEGERIHE-VSVDDLELTL 312 (319)
Q Consensus 284 eF~F~~g-~VKpWEGERIHE-~g~DdLELTL 312 (319)
|+.++++ .|=-|- |+|-+ .-.+.|+++|
T Consensus 84 e~~~~~~i~~IEW~-e~~~~~l~~~~l~i~i 113 (123)
T PF02367_consen 84 EYLFEDGICVIEWP-ERLKELLPEDRLEIEI 113 (123)
T ss_dssp TCSSSSEEEEEESG-GGGTTTS---SEEEEE
T ss_pred hhhCCCCEEEEECc-ccccccCCCCcEEEEE
Confidence 4444444 367785 88877 4667777765
No 27
>cd08513 PBP2_thermophilic_Hb8_like The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold. This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium, and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporter
Probab=30.41 E-value=90 Score=29.59 Aligned_cols=49 Identities=29% Similarity=0.443 Sum_probs=28.0
Q ss_pred HHHHHHHHHhhhhhcCCCCCCCcc-----------ChHHHHHHHHHHhCcEEcCCCceec
Q 020929 26 RRAIAAKIFSGLRAEGNFKLPKHC-----------DNNEVLKALCAEAGWIVEEDGTTYR 74 (319)
Q Consensus 26 RRAIaakIfaGLR~~Gny~Lpk~~-----------D~NeVlkaLc~eAGw~ve~DGttyr 74 (319)
|.+|+..+|.|.-.-.+.-+|.-. -+=|--|+|.+||||..+.||..+-
T Consensus 272 r~~i~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~d~~kAk~lL~eaG~~~~~~g~~~~ 331 (482)
T cd08513 272 RDAIVKTLYGGKATPAPTPVPPGSWADDPLVPAYEYDPEKAKQLLDEAGWKLGPDGGIRE 331 (482)
T ss_pred HHHHHHHHhcCccceeccCCCCCccccCCCcccCCCCHHHHHHHHHHcCCccCCCCcEEc
Confidence 344556667665443333333221 1234567899999998777774433
No 28
>PRK07683 aminotransferase A; Validated
Probab=29.52 E-value=1.3e+02 Score=28.21 Aligned_cols=56 Identities=18% Similarity=0.294 Sum_probs=33.7
Q ss_pred hhHHHHHHHHHHHHHHHhh--hhh---cCC-CC---CCC-ccChHHHHHHHHHHhCcEEcCCCceec
Q 020929 18 NNKRRERRRRAIAAKIFSG--LRA---EGN-FK---LPK-HCDNNEVLKALCAEAGWIVEEDGTTYR 74 (319)
Q Consensus 18 nnkrRERrRRAIaakIfaG--LR~---~Gn-y~---Lpk-~~D~NeVlkaLc~eAGw~ve~DGttyr 74 (319)
+.+++-++||+++.+++.. +.. .|+ |- +|+ ..+..++.+.|++++|..|-+ |..|.
T Consensus 287 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~gI~v~p-g~~f~ 352 (387)
T PRK07683 287 MMRHQYKKRRDYVYNRLISMGLDVEKPTGAFYLFPSIGHFTMSSFDFALDLVEEAGLAVVP-GSAFS 352 (387)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCcccCCCeeEEEEEecccCCCCHHHHHHHHHHhCCEEEcC-chhhC
Confidence 3344445666777777764 321 122 22 233 345667888899999999875 66664
No 29
>TIGR03537 DapC succinyldiaminopimelate transaminase. Note: the detailed information included in the EC:2.6.1.17 record includes the assertions that the enzyme uses the pyridoxal pyrophosphate cofactor, which is consistent with the pfam00155 family, and the assertion that the amino group donor is L-glutamate, which is undetermined for the sequences in this clade.
Probab=27.97 E-value=1.2e+02 Score=27.75 Aligned_cols=29 Identities=24% Similarity=0.429 Sum_probs=20.4
Q ss_pred CCCCccChHHHHHHHHHHhCcEEcCCCceec
Q 020929 44 KLPKHCDNNEVLKALCAEAGWIVEEDGTTYR 74 (319)
Q Consensus 44 ~Lpk~~D~NeVlkaLc~eAGw~ve~DGttyr 74 (319)
++|...+..++.++|++ +|..|-+ |+.|.
T Consensus 294 ~~~~~~~~~~l~~~L~~-~gv~v~~-g~~f~ 322 (350)
T TIGR03537 294 KVPSGIDAKDYALRLLE-NGIVVAP-GENFG 322 (350)
T ss_pred ECCCCCCHHHHHHHHHH-CCEEEcC-chhhC
Confidence 45665567778888865 7988775 77774
No 30
>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and
Probab=27.68 E-value=93 Score=21.46 Aligned_cols=47 Identities=30% Similarity=0.323 Sum_probs=30.0
Q ss_pred hHHHhhhHHHHHHHHHHHHHHHhhhhhcCCCC-CCCccChHHHHHHHH
Q 020929 13 WKERENNKRRERRRRAIAAKIFSGLRAEGNFK-LPKHCDNNEVLKALC 59 (319)
Q Consensus 13 wrErEnnkrRERrRRAIaakIfaGLR~~Gny~-Lpk~~D~NeVlkaLc 59 (319)
...|.+...+||+||.=-...|..|+..=-.. .-++.|--+||..-+
T Consensus 2 ~~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~ 49 (60)
T cd00083 2 KSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAV 49 (60)
T ss_pred cHHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
Confidence 34577788899999987788888887652111 124456666665433
No 31
>cd06451 AGAT_like Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT), serine-glyoxylate aminotransferase (SGAT), and 3-hydroxykynurenine transaminase (HKT). AGAT is a homodimeric protein, which catalyses the transamination of glyoxylate to glycine, and SGAT converts serine and glyoxylate to hydroxypyruvate and glycine. HKT catalyzes the PLP-dependent transamination of 3-hydroxykynurenine, a potentially toxic metabolite of the kynurenine pathway.
Probab=27.60 E-value=1.8e+02 Score=26.32 Aligned_cols=46 Identities=26% Similarity=0.345 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhhhhhcCC---------------CCCCCccChHHHHHHHHHHhCcEEcC
Q 020929 23 ERRRRAIAAKIFSGLRAEGN---------------FKLPKHCDNNEVLKALCAEAGWIVEE 68 (319)
Q Consensus 23 ERrRRAIaakIfaGLR~~Gn---------------y~Lpk~~D~NeVlkaLc~eAGw~ve~ 68 (319)
.++.+..+.++..+|+..|- +.+|...+-.++.++|.++.|+.|-+
T Consensus 261 ~~~~~~~~~~l~~~L~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~gI~~~~ 321 (356)
T cd06451 261 WARHRRLAKALREGLEALGLKLLAKPELRSPTVTAVLVPEGVDGDEVVRRLMKRYNIEIAG 321 (356)
T ss_pred HHHHHHHHHHHHHHHHHcCCeeccCcccCCCceEEEECCCCCCHHHHHHHHHHhCCEEEec
Confidence 34445555666666655431 12233345567888887776988743
No 32
>cd08497 PBP2_NikA_DppA_OppA_like_14 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=27.34 E-value=92 Score=30.11 Aligned_cols=25 Identities=32% Similarity=0.367 Sum_probs=18.0
Q ss_pred hHHHHHHHHHHhCcEEcCCCceecC
Q 020929 51 NNEVLKALCAEAGWIVEEDGTTYRK 75 (319)
Q Consensus 51 ~NeVlkaLc~eAGw~ve~DGttyr~ 75 (319)
+-|--|+|.+||||..+.||-.+.+
T Consensus 319 d~~kAk~lL~~aG~~~~~g~~~~~~ 343 (491)
T cd08497 319 NLRKALELLAEAGWTVRGGDILVNA 343 (491)
T ss_pred CHHHHHHHHHHcCCccCCCCEEECC
Confidence 5577788999999998765434444
No 33
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=27.26 E-value=1.1e+02 Score=22.97 Aligned_cols=49 Identities=27% Similarity=0.477 Sum_probs=31.5
Q ss_pred HHHHHHHhhhhhcCC--C---------CCCCccChHHHHHHHHHHhCcEEcCCC--ceecCCCC
Q 020929 28 AIAAKIFSGLRAEGN--F---------KLPKHCDNNEVLKALCAEAGWIVEEDG--TTYRKGSR 78 (319)
Q Consensus 28 AIaakIfaGLR~~Gn--y---------~Lpk~~D~NeVlkaLc~eAGw~ve~DG--ttyr~g~k 78 (319)
....+|+.-|+..|. + .|++. ..|-+|..| .+.|+|+-..+ .+|+-+++
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~-~v~r~L~~L-~~~G~V~~~~~~~~~W~i~~~ 67 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKK-EVNRVLYSL-EKKGKVCKQGGTPPLWKLTDK 67 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHH-HHHHHHHHH-HHCCCEEecCCCCCceEeecC
Confidence 455688888888887 3 34444 456666655 56699876442 46776654
No 34
>COG1487 VapC Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=27.22 E-value=1.2e+02 Score=24.48 Aligned_cols=41 Identities=27% Similarity=0.269 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhhhhcCCCCCCCccChHHHHHHHHHHhCcEEcCCC
Q 020929 26 RRAIAAKIFSGLRAEGNFKLPKHCDNNEVLKALCAEAGWIVEEDG 70 (319)
Q Consensus 26 RRAIaakIfaGLR~~Gny~Lpk~~D~NeVlkaLc~eAGw~ve~DG 70 (319)
-..++++|++.|++.|. ...++.-++.|-|...|..+--..
T Consensus 75 ~a~~~~~i~~~l~~~G~----~~~~~D~lIAa~A~~~~~~LvT~d 115 (133)
T COG1487 75 AAEIAAEIQARLRKEGI----PIGLNDLLIAATAIAHGLLLVTRD 115 (133)
T ss_pred HHHHHHHHHHHHHhcCC----CCChHHHHHHHHHHHcCCEEEEcC
Confidence 34568999999999999 234444456888888887654433
No 35
>PRK06108 aspartate aminotransferase; Provisional
Probab=26.85 E-value=1.6e+02 Score=26.81 Aligned_cols=55 Identities=25% Similarity=0.384 Sum_probs=33.4
Q ss_pred hhHHHHHHHHHHHHHHHh---hhhh----cCCC---CCCCccChHHHHHHHHHHhCcEEcCCCcee
Q 020929 18 NNKRRERRRRAIAAKIFS---GLRA----EGNF---KLPKHCDNNEVLKALCAEAGWIVEEDGTTY 73 (319)
Q Consensus 18 nnkrRERrRRAIaakIfa---GLR~----~Gny---~Lpk~~D~NeVlkaLc~eAGw~ve~DGtty 73 (319)
+.+++-+.+|.+..+.+. |++- .|.| +||...|..++.++|.++.|..|- .|+.|
T Consensus 286 ~~~~~~~~~~~~l~~~L~~~~~~~~~~p~~g~~~~~~l~~~~~~~~~~~~ll~~~gV~v~-pg~~f 350 (382)
T PRK06108 286 ELVARLRRSRDHLVDALRALPGVEVAKPDGAMYAFFRIPGVTDSLALAKRLVDEAGLGLA-PGTAF 350 (382)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCcccCCCeeEEEEEeCCCCCCHHHHHHHHHHhCCEEEe-Cchhh
Confidence 344444445555555443 3332 2334 566656778899999999999885 46666
No 36
>TIGR02864 spore_sspO small, acid-soluble spore protein O. This model represents a minor (low-abundance) spore protein, designated SspO. It is found in a very limited subset of the already small group of endospore-forming bacteria, but these species include Oceanobacillus iheyensis, Geobacillus kaustophilus, Bacillus subtilis, B. halodurans, and B. cereus. This protein was previously called CotK.
Probab=26.84 E-value=28 Score=26.54 Aligned_cols=18 Identities=39% Similarity=0.503 Sum_probs=14.2
Q ss_pred CCCCChHHHhhhHHHHHH
Q 020929 8 GRLPTWKERENNKRRERR 25 (319)
Q Consensus 8 ~R~ptwrErEnnkrRERr 25 (319)
.-.-|..||.|||.|..+
T Consensus 32 nepLt~aerqnNKKrKKn 49 (50)
T TIGR02864 32 NEPLTAAERQNNKKRKKN 49 (50)
T ss_pred cccCCHHHHHhchhhhcc
Confidence 455689999999998643
No 37
>TIGR01365 serC_2 phosphoserine aminotransferase, Methanosarcina type. This model represents a variant form of the serine biosynthesis enzyme phosphoserine aminotransferase, as found in a small number of distantly related species, including Caulobacter crescentus, Mesorhizobium loti, and the archaeon Methanosarcina barkeri.
Probab=26.23 E-value=1.8e+02 Score=28.42 Aligned_cols=61 Identities=13% Similarity=0.029 Sum_probs=40.9
Q ss_pred hHHHHHHHHHHHHHHHhhhhhcC-CCCCCCc-----------------c-----C-----hHHHHHHHHHHhCcEEc---
Q 020929 19 NKRRERRRRAIAAKIFSGLRAEG-NFKLPKH-----------------C-----D-----NNEVLKALCAEAGWIVE--- 67 (319)
Q Consensus 19 nkrRERrRRAIaakIfaGLR~~G-ny~Lpk~-----------------~-----D-----~NeVlkaLc~eAGw~ve--- 67 (319)
-..|.+|-++.|..++++|.++| -+-++++ - | .+++.+ ++++.|.++.
T Consensus 261 le~~~~Rh~~~a~~l~~~l~~lg~l~~~~~~~~~rS~tvt~v~~~~~~~~~~~~~~~~~~~~~~~~-~l~~~gi~i~~G~ 339 (374)
T TIGR01365 261 LKPLIARADDNLAVLEAFVAKNNWIHFLAETPEIRSNTSVCLKVVDPAIDALDEDAQADFAKELIS-TLEKEGVAYDIGS 339 (374)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCcccCCCChhhcCCCeEEEEeCCccccccccchhhHHHHHHHH-HHHHCCEEEeccc
Confidence 56677888899999999999999 4444310 1 1 244444 4456698776
Q ss_pred --CCCceecCCCCCC
Q 020929 68 --EDGTTYRKGSRPP 80 (319)
Q Consensus 68 --~DGttyr~g~kp~ 80 (319)
.-|++||-||-+-
T Consensus 340 ~~~~~~~fRIg~~G~ 354 (374)
T TIGR01365 340 YRDAPSGLRIWCGAT 354 (374)
T ss_pred cccCCCceEEecCCc
Confidence 2367888877553
No 38
>cd08509 PBP2_TmCBP_oligosaccharides_like The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of a cellulose-binding protein from the hyperthermophilic bacterium Thermotoga maritima (TmCBP) and its closest related proteins. TmCBP binds a variety of lengths of beta-1,4-linked glucose oligomers, ranging from two sugar rings (cellobiose) to five (cellopentose). TmCBP is structurally homologous to domains I and III of the ATP-binding cassette (ABC)-type oligopeptide-binding proteins and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. L
Probab=26.14 E-value=1.3e+02 Score=29.17 Aligned_cols=24 Identities=29% Similarity=0.446 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhCcEEcCCCceecC
Q 020929 52 NEVLKALCAEAGWIVEEDGTTYRK 75 (319)
Q Consensus 52 NeVlkaLc~eAGw~ve~DGttyr~ 75 (319)
-|--|+|.+||||.++.||.-|.+
T Consensus 324 ~~~A~~lL~~aG~~~~~~G~~~~~ 347 (509)
T cd08509 324 PDKAKKLLESAGFKKDKDGKWYTP 347 (509)
T ss_pred HHHHHHHHHHcCCeECCCCeEECC
Confidence 345568889999999889966543
No 39
>PRK02984 sspO acid-soluble spore protein O; Provisional
Probab=25.60 E-value=31 Score=26.14 Aligned_cols=17 Identities=41% Similarity=0.513 Sum_probs=13.5
Q ss_pred CCCCChHHHhhhHHHHH
Q 020929 8 GRLPTWKERENNKRRER 24 (319)
Q Consensus 8 ~R~ptwrErEnnkrRER 24 (319)
.-.-|..||+|||.|..
T Consensus 31 nepLt~aqrQnNKKrKk 47 (49)
T PRK02984 31 NEPLTEAERQNNKKRKK 47 (49)
T ss_pred cccCCHHHHHhhhhhhc
Confidence 34568999999999864
No 40
>PRK07681 aspartate aminotransferase; Provisional
Probab=25.40 E-value=1.5e+02 Score=27.77 Aligned_cols=28 Identities=25% Similarity=0.356 Sum_probs=21.4
Q ss_pred CCCccChHHHHHHHHHHhCcEEcCCCcee
Q 020929 45 LPKHCDNNEVLKALCAEAGWIVEEDGTTY 73 (319)
Q Consensus 45 Lpk~~D~NeVlkaLc~eAGw~ve~DGtty 73 (319)
||+..|..++.+.|++++|..|-+ |+.|
T Consensus 329 l~~~~~~~~~~~~l~~~~gv~v~p-g~~f 356 (399)
T PRK07681 329 IPKGWTSLSFAYALMDRANVVVTP-GHAF 356 (399)
T ss_pred CCCCCCHHHHHHHHHHhCCEEEeC-Chhh
Confidence 445567788999999989988865 6666
No 41
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=24.97 E-value=1.5e+02 Score=26.01 Aligned_cols=46 Identities=22% Similarity=0.138 Sum_probs=31.5
Q ss_pred HHHhhhHHHHHHHHHHHHHHHhhhhhcCC------CCCCCccChHHHHHHHH
Q 020929 14 KERENNKRRERRRRAIAAKIFSGLRAEGN------FKLPKHCDNNEVLKALC 59 (319)
Q Consensus 14 rErEnnkrRERrRRAIaakIfaGLR~~Gn------y~Lpk~~D~NeVlkaLc 59 (319)
-|-|.+..+||.|+.|+++--.|....+. +.+++-.+..+.++.|.
T Consensus 122 Ae~Er~~i~er~~~g~~~a~~~G~~~g~~~~~~~~~~~~~~~~~~~~v~~l~ 173 (222)
T COG1961 122 AEFERELISERTRAGIEAARKAGKEGGRPPGYKIKKGRKKAEEQAAAVRRLL 173 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCcCCCCCccccccccccccchhHHHHHHHH
Confidence 47788899999999999988888776643 23454455544444443
No 42
>cd06453 SufS_like Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L-selenocystine to produce L-alanine; and selenocysteine lyase catalyzes the decomposition of L-selenocysteine.
Probab=24.36 E-value=1.6e+02 Score=26.75 Aligned_cols=45 Identities=13% Similarity=0.138 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhhhhhcCCCCCC--------------CccChHHHHHHHHHHhCcEEcCC
Q 020929 24 RRRRAIAAKIFSGLRAEGNFKLP--------------KHCDNNEVLKALCAEAGWIVEED 69 (319)
Q Consensus 24 RrRRAIaakIfaGLR~~Gny~Lp--------------k~~D~NeVlkaLc~eAGw~ve~D 69 (319)
.+.++++..+.++|..++++.+. +..+.+++.+.|. +.|++|...
T Consensus 278 ~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~-~~gi~i~~g 336 (373)
T cd06453 278 AHEHELTAYALERLSEIPGVRVYGDAEDRAGVVSFNLEGIHPHDVATILD-QYGIAVRAG 336 (373)
T ss_pred HHHHHHHHHHHHHHhcCCCeEEeCCccccCCeEEEEECCcCHHHHHHHHH-HCCEEeccC
Confidence 33446677777788777654442 1125577888775 479988643
No 43
>PRK07550 hypothetical protein; Provisional
Probab=23.95 E-value=1.9e+02 Score=26.82 Aligned_cols=28 Identities=32% Similarity=0.441 Sum_probs=20.2
Q ss_pred CCC-ccChHHHHHHHHHHhCcEEcCCCcee
Q 020929 45 LPK-HCDNNEVLKALCAEAGWIVEEDGTTY 73 (319)
Q Consensus 45 Lpk-~~D~NeVlkaLc~eAGw~ve~DGtty 73 (319)
+|. .-|..++.+.|+++.|..|-+ |..|
T Consensus 326 ~~~~~~~~~~l~~~l~~~~gv~v~p-g~~f 354 (386)
T PRK07550 326 HPFPDRPSREVARRLAKEAGILCLP-GTMF 354 (386)
T ss_pred CCCCCCCHHHHHHHHHHhcCEEEeC-chhh
Confidence 444 345678888888999998875 5555
No 44
>PTZ00376 aspartate aminotransferase; Provisional
Probab=23.87 E-value=1.8e+02 Score=27.52 Aligned_cols=20 Identities=15% Similarity=0.240 Sum_probs=16.6
Q ss_pred hHHHHHHHHHHhCcEEcCCC
Q 020929 51 NNEVLKALCAEAGWIVEEDG 70 (319)
Q Consensus 51 ~NeVlkaLc~eAGw~ve~DG 70 (319)
.+|+.+.|.+|+|-.|-+.|
T Consensus 359 ~~~~~~~L~~~~~v~v~p~~ 378 (404)
T PTZ00376 359 TKEQVERLIEKYHIYLLDNG 378 (404)
T ss_pred CHHHHHHHHHhCCEeecCCC
Confidence 46888999999998887765
No 45
>PRK07908 hypothetical protein; Provisional
Probab=23.31 E-value=1.4e+02 Score=27.28 Aligned_cols=55 Identities=27% Similarity=0.302 Sum_probs=28.8
Q ss_pred hhhHHHHHHHHHHHHHHHhh--hh----hcCCCCCCCccChHHHHHHHHHHhCcEEcCCCcee
Q 020929 17 ENNKRRERRRRAIAAKIFSG--LR----AEGNFKLPKHCDNNEVLKALCAEAGWIVEEDGTTY 73 (319)
Q Consensus 17 EnnkrRERrRRAIaakIfaG--LR----~~Gny~Lpk~~D~NeVlkaLc~eAGw~ve~DGtty 73 (319)
++.+++-++||....+.+.. ++ ..|+|-+-+.-+ .+.+..++++.|..|. +|+.|
T Consensus 256 ~~~~~~~~~~r~~l~~~L~~~~~~~~~p~~g~~~~~~~~~-~~~~~~~l~~~gI~v~-~g~~f 316 (349)
T PRK07908 256 AADAARLAADRAEMVAGLRAVGARVVDPAAAPFVLVRVPD-AELLRKRLRERGIAVR-RGDTF 316 (349)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCcEeccCCCceEEEEECCc-HHHHHHHHHhCCEEEE-ECCCC
Confidence 34445555555555555543 22 223442221112 4566667789998886 45555
No 46
>PRK07392 threonine-phosphate decarboxylase; Validated
Probab=23.30 E-value=1.1e+02 Score=28.22 Aligned_cols=34 Identities=15% Similarity=0.241 Sum_probs=23.0
Q ss_pred cCCCCCCCc-cChHHHHHHHHHHhCcEEcCCCceec
Q 020929 40 EGNFKLPKH-CDNNEVLKALCAEAGWIVEEDGTTYR 74 (319)
Q Consensus 40 ~Gny~Lpk~-~D~NeVlkaLc~eAGw~ve~DGttyr 74 (319)
.|+|-+.+- .|..++.++|.+++|+.|- +|+.|.
T Consensus 295 ~~~fl~~~~~~~~~~l~~~ll~~~gv~v~-pg~~f~ 329 (360)
T PRK07392 295 AANFLLVQSQGSALQLQEKLLQQHRILIR-DCLSFP 329 (360)
T ss_pred CCCEEEEEcCCCHHHHHHHHHhhCCEEEE-eCCCCC
Confidence 355644322 1567788888889999987 677773
No 47
>PRK12495 hypothetical protein; Provisional
Probab=23.16 E-value=1e+02 Score=29.48 Aligned_cols=57 Identities=30% Similarity=0.453 Sum_probs=36.7
Q ss_pred hHHHhhhHHHHH-----HHHHHHHHHHhhhhhcCCCCCCCccC-hHHHHHHHHHHhCcEEcCCCceecCCCCCC
Q 020929 13 WKERENNKRRER-----RRRAIAAKIFSGLRAEGNFKLPKHCD-NNEVLKALCAEAGWIVEEDGTTYRKGSRPP 80 (319)
Q Consensus 13 wrErEnnkrRER-----rRRAIaakIfaGLR~~Gny~Lpk~~D-~NeVlkaLc~eAGw~ve~DGttyr~g~kp~ 80 (319)
.||.|+.|+||. .+|. +.|+.+-|-..|.--|.+||. =+.-|= ..+|.+|=..|+-.
T Consensus 5 DkEaEREkLREKye~d~~~R~-~~~~ma~lL~~gatmsa~hC~~CG~PIp----------a~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 5 DKEAEREKLREKYEQDEQKRE-ATERMSELLLQGATMTNAHCDECGDPIF----------RHDGQEFCPTCQQP 67 (226)
T ss_pred hHHHHHHHHHHHHhhhHHHHH-HHHHHHHHHHhhcccchhhcccccCccc----------CCCCeeECCCCCCc
Confidence 478888888885 3333 456666777777788888883 232222 34777776667643
No 48
>TIGR00150 HI0065_YjeE ATPase, YjeE family. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.
Probab=22.65 E-value=33 Score=29.31 Aligned_cols=21 Identities=24% Similarity=0.400 Sum_probs=15.6
Q ss_pred cccCCcCcccccc-ccccceecc
Q 020929 291 RVKPWEGERIHEV-SVDDLELTL 312 (319)
Q Consensus 291 ~VKpWEGERIHE~-g~DdLELTL 312 (319)
.|.-| +|+|-++ -.++|++++
T Consensus 99 ~~IEW-~e~~~~~lp~~~l~i~i 120 (133)
T TIGR00150 99 CLVEW-PEEGLEILPDYDLQIKI 120 (133)
T ss_pred EEEEC-CccccccCCcccEEEEE
Confidence 47889 8998664 667787775
No 49
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=22.22 E-value=58 Score=34.75 Aligned_cols=12 Identities=42% Similarity=0.385 Sum_probs=8.8
Q ss_pred cChHHHHHHHHH
Q 020929 49 CDNNEVLKALCA 60 (319)
Q Consensus 49 ~D~NeVlkaLc~ 60 (319)
-||||-+|.|-+
T Consensus 539 RDINeAfKELGR 550 (632)
T KOG3910|consen 539 RDINEAFKELGR 550 (632)
T ss_pred hhHHHHHHHHHH
Confidence 488888887743
No 50
>PLN02397 aspartate transaminase
Probab=22.14 E-value=2e+02 Score=27.64 Aligned_cols=22 Identities=18% Similarity=0.252 Sum_probs=17.8
Q ss_pred ccChHHHHHHHHHHhCcEEcCCC
Q 020929 48 HCDNNEVLKALCAEAGWIVEEDG 70 (319)
Q Consensus 48 ~~D~NeVlkaLc~eAGw~ve~DG 70 (319)
.++ .++.+.|.+|+|..|-.+|
T Consensus 375 ~l~-~~~~~~Ll~~~~V~v~~~~ 396 (423)
T PLN02397 375 GLN-KEQVDRMTKEYHIYMTRDG 396 (423)
T ss_pred CCC-HHHHHHHHHhCCEEECCCC
Confidence 345 5688899999999998777
No 51
>PRK10534 L-threonine aldolase; Provisional
Probab=22.03 E-value=1.8e+02 Score=26.19 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=18.8
Q ss_pred cCCCCCCCccC-hHHHHHHHHHHhCcEEcCCCceec
Q 020929 40 EGNFKLPKHCD-NNEVLKALCAEAGWIVEEDGTTYR 74 (319)
Q Consensus 40 ~Gny~Lpk~~D-~NeVlkaLc~eAGw~ve~DGttyr 74 (319)
.+||-+-+.-+ ..+-+..+..+.|+.|-+ |..+|
T Consensus 274 ~~nfv~~~~~~~~~~~~~~~l~~~gi~v~~-~~~~r 308 (333)
T PRK10534 274 DTNMLFVRVGEEQAAALGEYMRERNVLINA-SPIVR 308 (333)
T ss_pred CceEEEEECCchhHHHHHHHHHHcCeeecC-CceEE
Confidence 35555444321 233345677888999954 54334
No 52
>TIGR03538 DapC_gpp succinyldiaminopimelate transaminase. This family of succinyldiaminopimelate transaminases (DapC) includes the experimentally characterized enzyme from Bordatella pertussis. The majority of genes in this family are proximal to genes encoding components of the lysine biosynthesis via diaminopimelate pathway (GenProp0125).
Probab=21.64 E-value=1.3e+02 Score=28.00 Aligned_cols=25 Identities=24% Similarity=0.239 Sum_probs=19.1
Q ss_pred cChHHHHHHHHHHhCcEEcCCCceec
Q 020929 49 CDNNEVLKALCAEAGWIVEEDGTTYR 74 (319)
Q Consensus 49 ~D~NeVlkaLc~eAGw~ve~DGttyr 74 (319)
.|..++.++|++++|..|-+ |+.|-
T Consensus 334 ~~~~~~~~~l~~~~gV~v~p-g~~f~ 358 (393)
T TIGR03538 334 GDDEAFARALYEEENVTVLP-GRFLA 358 (393)
T ss_pred CCHHHHHHHHHHHCCEEEeC-Ccccc
Confidence 36788999999999998874 55553
No 53
>PRK07590 L,L-diaminopimelate aminotransferase; Validated
Probab=21.24 E-value=2.7e+02 Score=26.30 Aligned_cols=29 Identities=21% Similarity=0.321 Sum_probs=21.1
Q ss_pred CCCCccChHHHHHHHHHHhCcEEcCCCcee
Q 020929 44 KLPKHCDNNEVLKALCAEAGWIVEEDGTTY 73 (319)
Q Consensus 44 ~Lpk~~D~NeVlkaLc~eAGw~ve~DGtty 73 (319)
+||+..+..++.+.|++++|.+|-+ |+.|
T Consensus 351 ~~~~~~~~~~~~~~l~~~~gv~v~p-g~~f 379 (409)
T PRK07590 351 KTPDGMSSWDFFDKLLQEANVVGTP-GSGF 379 (409)
T ss_pred ECCCCCCHHHHHHHHHHHCCEEEeC-hhHh
Confidence 4555556677888888999998864 6666
No 54
>TIGR02294 nickel_nikA nickel ABC transporter, periplasmic nickel-binding protein. Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Nickel is bound specifically, albeit weakly, through water molecules positioned in the binding site. The amino acids whose side chains line the binding site include Tyr-44, Met-49, Trp-122, Arg-159, Trp-420, and Tyr-424 (numbering based on the precursor sequence of E. coli NikA) with the Arg contributing a hydrogen bond indirectly through a water molecule. Sequences that exactly (or mostly) have the same binding site residues score above the trusted (or noise) cutoffs to this model. Most appear to be lipoproteins.
Probab=21.24 E-value=1.6e+02 Score=28.34 Aligned_cols=18 Identities=33% Similarity=0.549 Sum_probs=13.5
Q ss_pred HHHHHHHHHhCcEEcCCC
Q 020929 53 EVLKALCAEAGWIVEEDG 70 (319)
Q Consensus 53 eVlkaLc~eAGw~ve~DG 70 (319)
|--|+|.+||||....+|
T Consensus 315 ~kAk~lL~~aG~~~~~g~ 332 (500)
T TIGR02294 315 KKANALLDEAGWKLGKGK 332 (500)
T ss_pred HHHHHHHHHcCCcccCCC
Confidence 447889999999875443
No 55
>cd01560 Thr-synth_2 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria, archaebacteria and eubacterial groups. This CD, Thr-synth_2, includes enzymes from fungi and eubacterial groups, as well as, metazoan threonine synthase-like proteins.
Probab=21.21 E-value=1.1e+02 Score=31.07 Aligned_cols=44 Identities=20% Similarity=0.479 Sum_probs=34.7
Q ss_pred HHHHHHhhhhhcCCCCCCC-------------ccChHHHHHHH---HHHhCcEEcCCCce
Q 020929 29 IAAKIFSGLRAEGNFKLPK-------------HCDNNEVLKAL---CAEAGWIVEEDGTT 72 (319)
Q Consensus 29 IaakIfaGLR~~Gny~Lpk-------------~~D~NeVlkaL---c~eAGw~ve~DGtt 72 (319)
..+..+..|.+.|.|.|++ .++..|+++++ .++.|++|||-+-+
T Consensus 332 ~~~~~m~~~~~~g~~~~~~~~l~~~~~~f~a~~vsD~ei~~~i~~~~~~~G~~vdPhtAv 391 (460)
T cd01560 332 KVKMLMEEFEATGFLSLPKEELKKLREDFSSGSVSDEETLETIREVYEETGYLIDPHTAV 391 (460)
T ss_pred HHHHHHHHHHhcCCEecCHHHHHhhhccceEEEECHHHHHHHHHHHHHhcCEEECchHHH
Confidence 3467888899999999886 67888877655 56789999998743
No 56
>cd08500 PBP2_NikA_DppA_OppA_like_4 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=21.14 E-value=1.8e+02 Score=28.35 Aligned_cols=23 Identities=26% Similarity=0.309 Sum_probs=17.8
Q ss_pred HHHHHHHHHhCcE-EcCCCceecC
Q 020929 53 EVLKALCAEAGWI-VEEDGTTYRK 75 (319)
Q Consensus 53 eVlkaLc~eAGw~-ve~DGttyr~ 75 (319)
|--|+|.+||||. +..||..|.+
T Consensus 316 e~Ak~lL~~aG~~~~~~dG~~~~~ 339 (499)
T cd08500 316 DKANKLLDEAGLKKKDADGFRLDP 339 (499)
T ss_pred HHHHHHHHHcCCcccCCCCcEECC
Confidence 5567899999997 7788876643
No 57
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=21.09 E-value=1.3e+02 Score=19.96 Aligned_cols=45 Identities=29% Similarity=0.405 Sum_probs=24.6
Q ss_pred HHHHHHHHhhhhhcCCCCCC-----------CccChHHHHHHHHHHhCcEEcCCCcee
Q 020929 27 RAIAAKIFSGLRAEGNFKLP-----------KHCDNNEVLKALCAEAGWIVEEDGTTY 73 (319)
Q Consensus 27 RAIaakIfaGLR~~Gny~Lp-----------k~~D~NeVlkaLc~eAGw~ve~DGtty 73 (319)
++|..+|..+.-..|. .|| .+......|+.|.+ .||+....|.-|
T Consensus 3 ~~l~~~i~~~~~~~~~-~l~s~~~la~~~~vs~~tv~~~l~~L~~-~g~i~~~~~~g~ 58 (60)
T smart00345 3 ERLREDIVSGELRPGD-KLPSERELAAQLGVSRTTVREALSRLEA-EGLVQRRPGSGT 58 (60)
T ss_pred HHHHHHHHcCCCCCCC-cCcCHHHHHHHHCCCHHHHHHHHHHHHH-CCCEEEecCCee
Confidence 3555666666433343 343 12334556666664 599876666544
No 58
>cd08518 PBP2_NikA_DppA_OppA_like_19 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=20.97 E-value=1.6e+02 Score=27.96 Aligned_cols=21 Identities=38% Similarity=0.635 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHhCcEEcCCCc
Q 020929 51 NNEVLKALCAEAGWIVEEDGT 71 (319)
Q Consensus 51 ~NeVlkaLc~eAGw~ve~DGt 71 (319)
+-|--|+|.+||||....||.
T Consensus 298 d~~~Ak~lL~eaG~~~~~~g~ 318 (464)
T cd08518 298 DPEKAKKILEEAGWKDGDDGG 318 (464)
T ss_pred CHHHHHHHHHHcCCCcCCCCe
Confidence 345677899999998877775
No 59
>PRK08912 hypothetical protein; Provisional
Probab=20.92 E-value=2.2e+02 Score=26.40 Aligned_cols=25 Identities=20% Similarity=0.194 Sum_probs=18.2
Q ss_pred cChHHHHHHHHHHhCcEEcCCCceec
Q 020929 49 CDNNEVLKALCAEAGWIVEEDGTTYR 74 (319)
Q Consensus 49 ~D~NeVlkaLc~eAGw~ve~DGttyr 74 (319)
-|..++.+.|+++.|+.|. +|..|.
T Consensus 329 ~~~~~~~~~l~~~~gV~v~-pg~~f~ 353 (387)
T PRK08912 329 EDDVAFCRRLVEEAGVAAI-PVSAFY 353 (387)
T ss_pred CCHHHHHHHHHhcCCEEEe-cchhhC
Confidence 3556688888889999887 556664
No 60
>PF02585 PIG-L: GlcNAc-PI de-N-acetylase; InterPro: IPR003737 A number of the members of this family have been characterised as a probable N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase, (3.5.1.89 from EC) that catalyses the second step in glycosylphosphatidylinositol (GPI) biosynthesis [, ]. The family also includes a number of thiol biosynthesis proteins. ; PDB: 2XAD_C 2X9L_A 3DFK_A 3DFM_A 3DFF_A 2IXD_A 1UAN_A 1Q74_B 1Q7T_B 3DFI_A.
Probab=20.39 E-value=70 Score=25.26 Aligned_cols=60 Identities=27% Similarity=0.235 Sum_probs=29.6
Q ss_pred CCCCCCCCCCCChHHHhhhHHHHHHHHHHHHHHHhhhhhcCCCCCC-----C--ccChHHHHHHHHHHh
Q 020929 1 MTAGGSSGRLPTWKERENNKRRERRRRAIAAKIFSGLRAEGNFKLP-----K--HCDNNEVLKALCAEA 62 (319)
Q Consensus 1 mt~g~~~~R~ptwrErEnnkrRERrRRAIaakIfaGLR~~Gny~Lp-----k--~~D~NeVlkaLc~eA 62 (319)
||.|..+.....+..++..+.|++--++. ++++ |+..+=.+.+| . .-+..+.|+.++++.
T Consensus 33 ~t~G~~~~~~~~~~~~~~~~~R~~E~~~a-~~~l-Gv~~~~~l~~~D~~~~~~~~~~~~~~l~~~i~~~ 99 (128)
T PF02585_consen 33 LTDGEAGHPDPTPWARELGEIRRAEARAA-AEIL-GVENVIFLDFPDGQLPGWSWEELVRDLEDLIREF 99 (128)
T ss_dssp CE--TTTSSSSHHHHHSCHHHHHHHHHHH-HHHC-T-EEEEEEEECTTSCTCHHHHHHHHHHHHHHHHH
T ss_pred ecccccCCcccchhhHhHHHHHHHHHHHH-HHHc-CCceEEEeecCCCCcccccHHHHHHHHHHHHHHc
Confidence 56777777777776655554443333332 4565 77443333333 3 344445556666655
Done!