Query psy2601
Match_columns 132
No_of_seqs 112 out of 494
Neff 6.9
Searched_HMMs 46136
Date Fri Aug 16 20:22:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2601.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2601hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4108|consensus 100.0 6.2E-40 1.4E-44 241.7 9.5 122 11-132 51-173 (174)
2 PF03645 Tctex-1: Tctex-1 fami 100.0 2.5E-37 5.4E-42 211.4 13.9 99 34-132 1-101 (101)
3 KOG4081|consensus 100.0 1.5E-30 3.3E-35 178.8 13.0 106 27-132 9-115 (115)
4 TIGR00244 transcriptional regu 62.0 17 0.00037 26.6 4.3 43 30-77 78-120 (147)
5 PF15604 Toxin_43: Putative to 47.3 72 0.0016 23.5 5.5 43 35-77 52-94 (152)
6 PF15603 Imm45: Immunity prote 44.6 36 0.00078 22.4 3.3 27 23-49 48-74 (82)
7 COG1327 Predicted transcriptio 43.0 42 0.00091 24.8 3.7 44 29-77 77-120 (156)
8 PF10752 DUF2533: Protein of u 39.0 81 0.0017 20.9 4.2 43 36-83 28-72 (84)
9 PF13421 Band_7_1: SPFH domain 38.5 85 0.0018 24.0 5.0 48 28-75 125-176 (211)
10 PF10523 BEN: BEN domain; Int 35.4 1.1E+02 0.0023 18.8 4.9 42 27-76 34-75 (79)
11 TIGR00597 rad10 DNA repair pro 33.9 53 0.0012 22.9 3.0 24 66-89 52-75 (112)
12 PF04542 Sigma70_r2: Sigma-70 33.1 75 0.0016 18.5 3.3 43 34-76 21-68 (71)
13 PRK12362 germination protease; 32.7 1.1E+02 0.0024 25.2 5.0 47 29-75 264-310 (318)
14 PF00438 S-AdoMet_synt_N: S-ad 32.2 1.4E+02 0.003 20.4 4.7 32 58-89 15-46 (100)
15 PRK12528 RNA polymerase sigma 31.7 1.1E+02 0.0024 21.3 4.5 45 32-76 27-73 (161)
16 cd07565 aliphatic_amidase alip 30.9 1.5E+02 0.0032 23.3 5.5 84 30-116 20-118 (291)
17 PRK09642 RNA polymerase sigma 30.4 1.2E+02 0.0026 21.0 4.5 45 32-76 18-64 (160)
18 TIGR01441 GPR GPR endopeptidas 29.7 1.4E+02 0.003 25.0 5.2 46 30-75 297-342 (358)
19 PF05903 Peptidase_C97: PPPDE 29.5 91 0.002 22.4 3.7 42 28-70 79-122 (151)
20 TIGR03112 6_pyr_pter_rel 6-pyr 28.5 2E+02 0.0043 19.7 6.6 43 31-74 41-91 (113)
21 KOG0324|consensus 28.4 1E+02 0.0022 23.9 4.0 40 28-68 82-123 (214)
22 PF02971 FTCD: Formiminotransf 28.3 2E+02 0.0044 21.0 5.3 44 64-108 14-63 (145)
23 PRK12523 RNA polymerase sigma 28.2 2.1E+02 0.0045 20.2 5.5 45 32-76 33-79 (172)
24 PF08178 GnsAB: GnsA/GnsB fami 28.0 1E+02 0.0022 18.8 3.1 30 62-91 11-41 (54)
25 KOG4745|consensus 27.7 48 0.001 24.0 1.9 57 71-127 64-122 (141)
26 TIGR01638 Atha_cystat_rel Arab 27.6 2E+02 0.0043 19.4 5.9 47 51-97 3-51 (92)
27 COG5418 Predicted secreted pro 27.1 1.1E+02 0.0025 22.5 3.8 48 51-101 68-118 (164)
28 KOG1404|consensus 26.9 1.5E+02 0.0032 25.4 5.0 43 56-103 332-374 (442)
29 PF04380 BMFP: Membrane fusoge 26.4 1.8E+02 0.004 18.6 4.9 45 32-76 25-69 (79)
30 PF03748 FliL: Flagellar basal 26.3 1.8E+02 0.0039 18.6 4.9 50 38-89 44-94 (99)
31 smart00244 PHB prohibitin homo 25.5 2.2E+02 0.0049 19.4 6.2 41 34-76 89-130 (160)
32 PF13405 EF-hand_6: EF-hand do 25.4 40 0.00087 17.1 0.9 11 103-113 8-18 (31)
33 PRK00464 nrdR transcriptional 25.1 2.7E+02 0.0059 20.3 5.6 21 27-47 57-77 (154)
34 PF06919 Phage_T4_Gp30_7: Phag 24.9 2E+02 0.0042 20.1 4.5 32 85-119 20-51 (121)
35 PF03492 Methyltransf_7: SAM d 24.6 3.1E+02 0.0066 22.3 6.4 56 32-92 278-334 (334)
36 COG1973 HypE Hydrogenase matur 24.2 2.1E+02 0.0045 24.3 5.2 27 51-77 38-64 (449)
37 PRK07037 extracytoplasmic-func 24.2 2.5E+02 0.0054 19.4 5.2 46 32-77 21-68 (163)
38 PF14564 Membrane_bind: Membra 23.0 2.6E+02 0.0057 19.2 4.9 36 80-116 49-86 (110)
39 PRK12527 RNA polymerase sigma 22.2 1.9E+02 0.0041 20.0 4.2 43 32-74 18-62 (159)
40 KOG2917|consensus 22.1 3.3E+02 0.0071 21.6 5.7 94 22-127 119-213 (250)
41 PHA01513 mnt Mnt 22.0 2.3E+02 0.005 18.7 4.2 19 55-73 53-71 (82)
42 TIGR02950 SigM_subfam RNA poly 21.4 1.7E+02 0.0037 19.9 3.8 46 32-77 18-65 (154)
43 PF15054 DUF4535: Domain of un 21.4 71 0.0015 18.7 1.5 12 121-132 5-16 (46)
44 PRK12533 RNA polymerase sigma 21.4 2E+02 0.0042 21.7 4.4 45 32-76 41-87 (216)
45 PF00036 EF-hand_1: EF hand; 21.2 68 0.0015 16.5 1.3 11 104-114 9-19 (29)
46 COG5054 ERV1 Mitochondrial sul 21.0 2.5E+02 0.0054 21.2 4.7 23 53-75 141-163 (181)
47 COG1480 Predicted membrane-ass 21.0 1.5E+02 0.0033 27.0 4.2 48 29-76 637-685 (700)
48 PRK04057 30S ribosomal protein 20.7 3E+02 0.0066 21.1 5.3 60 32-91 126-186 (203)
49 PF07499 RuvA_C: RuvA, C-termi 20.7 1.8E+02 0.0039 16.5 4.2 15 31-45 15-29 (47)
50 PRK07718 fliL flagellar basal 20.7 3.2E+02 0.0069 19.3 5.3 51 39-90 88-138 (142)
51 KOG3355|consensus 20.3 2.4E+02 0.0053 21.2 4.5 57 19-76 86-155 (177)
52 KOG2841|consensus 20.1 1.2E+02 0.0026 24.1 3.0 26 66-91 108-133 (254)
No 1
>KOG4108|consensus
Probab=100.00 E-value=6.2e-40 Score=241.67 Aligned_cols=122 Identities=24% Similarity=0.470 Sum_probs=112.2
Q ss_pred CCCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhccC-CCceEEEEEEEE
Q psy2601 11 STKDVTQSTAAPGGTTEDSKFAVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLD-KPFKYVVNGTVM 89 (132)
Q Consensus 11 ~~~~~~~~nty~~~p~~~~~F~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~-~ryK~vV~v~I~ 89 (132)
|..+.+..|-+-++|.+.++|+++.|+.||+++|.+.|.+..||++.+.+|+++||++|+.+||+++ +||||||+|+|+
T Consensus 51 p~~~~t~r~~~~~rp~~~~~F~~~~v~~iI~~vl~e~L~~~~Y~~~~a~~lt~elae~I~~rvK~l~~~RYK~Vv~V~ig 130 (174)
T KOG4108|consen 51 PGARPTNRMNSLYRPEPGKKFPAERVEKIIEAVLTEKLADAEYDPDEALQLTKELAEEIKDRVKELGYPRYKYVVQVMIG 130 (174)
T ss_pred cccCcccccccccccCcCccCCHHHHHHHHHHHHHHHhhhhccCHHHHHHHHHHHHHHHHHHHHhcCCCceEEEEEEEEh
Confidence 3334444433346677799999999999999999999999999999999999999999999999999 999999999999
Q ss_pred EeCCcceeeeeeeeecCCCCCeEEEEEEcCcEEEEEEEEEEeC
Q psy2601 90 QKLGAGLHTSSSCLWDDNTDGSCTVRWENKTMYCIVSVYALAL 132 (132)
Q Consensus 90 qk~gqgi~~as~~lWD~~~D~~~~~~~~n~~~~~v~tVf~iy~ 132 (132)
|++|||++++|||+||.++|||+++.|+|+++||+|+|||+|.
T Consensus 131 e~~gqGv~~~sr~lWD~~~D~~~t~~f~~~S~favv~vf~~Y~ 173 (174)
T KOG4108|consen 131 EQLGQGVYIASRCLWDEDRDGFVTYVFENPSLFAVVTVFGLYY 173 (174)
T ss_pred hhhcchHHHHHHhhhccccCCceEEEEecCceeeeehhhhhcc
Confidence 9999999999999999999999999999999999999999983
No 2
>PF03645 Tctex-1: Tctex-1 family; InterPro: IPR005334 Tctex-1 is a dynein light chain. Dynein translocates rhodopsin-bearing vesicles along microtubules and it has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. An efficient vectorial transport system must be required to deliver large numbers of newly synthesized rhodopsin molecules (~107 molecules per day per photoreceptor) to the base of the outer segment of the photoreceptor, Tctex-1 may well play a role in this process. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit the interaction between Tctex-1 and rhodopsin, which may be the molecular basis of retinitis pigmentosa. In the mouse, the chromosomal location and pattern of expression of Tctex-1 make it a candidate for involvement in male sterility [].; PDB: 1YGT_A 3FM7_A 2PG1_E 1XDX_B.
Probab=100.00 E-value=2.5e-37 Score=211.42 Aligned_cols=99 Identities=33% Similarity=0.702 Sum_probs=90.5
Q ss_pred HHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhcc--CCCceEEEEEEEEEeCCcceeeeeeeeecCCCCCe
Q psy2601 34 DEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKL--DKPFKYVVNGTVMQKLGAGLHTSSSCLWDDNTDGS 111 (132)
Q Consensus 34 ~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l--~~ryK~vV~v~I~qk~gqgi~~as~~lWD~~~D~~ 111 (132)
++|++||+++|++.|++..|+++++++|++.|++.|+++|+++ ++||||||+|+|+|++|||++++|+|+||+++|||
T Consensus 1 ~~v~~ii~~~l~~~l~~~~Y~~~~~~~~~~~I~~~i~~~lk~~~~~~ryK~iv~~~I~q~~~qgi~~~s~~lWD~~~D~~ 80 (101)
T PF03645_consen 1 EEVKEIIEEVLEEKLEDQKYDPEKAQQWSKEISDEILERLKKLGYSKRYKFIVQVTIGQKNGQGIHIASRCLWDPETDGY 80 (101)
T ss_dssp HHHHHHHHHHHHHHHCTS---HHHHHHHHHHHHHHHHHHHHCC--T-SCEEEEEEEEEETTTS-EEEEEEEECETTT-EE
T ss_pred CHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHHHHHHHHHHhccCCCceEEEEEEEEecCCCCcchhccceeCCCCCcE
Confidence 5899999999999999999999999999999999999999999 59999999999999999999999999999999999
Q ss_pred EEEEEEcCcEEEEEEEEEEeC
Q psy2601 112 CTVRWENKTMYCIVSVYALAL 132 (132)
Q Consensus 112 ~~~~~~n~~~~~v~tVf~iy~ 132 (132)
++++|+|++++|+|+|||+|+
T Consensus 81 ~~~~~~n~~~~~iv~Vf~iy~ 101 (101)
T PF03645_consen 81 VSYKYENESLFAIVTVFGIYY 101 (101)
T ss_dssp EEEEEESSSEEEEEEEEEEE-
T ss_pred EEEEEEcCCEEEEEEEEEEEC
Confidence 999999999999999999996
No 3
>KOG4081|consensus
Probab=99.97 E-value=1.5e-30 Score=178.84 Aligned_cols=106 Identities=58% Similarity=1.046 Sum_probs=102.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhccCCCceEEEEEEEEEeC-Ccceeeeeeeeec
Q psy2601 27 EDSKFAVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLDKPFKYVVNGTVMQKL-GAGLHTSSSCLWD 105 (132)
Q Consensus 27 ~~~~F~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~~ryK~vV~v~I~qk~-gqgi~~as~~lWD 105 (132)
+...|..+++..|++++|++.+++..|++++..+|...+.++|++.|.+++++|||||+|+|+|+. |.|+|+|+.|+||
T Consensus 9 k~~~f~~~ev~~iik~~le~~ig~~~Y~h~k~~qw~~~vVeqil~~LvKl~k~yKyiVtcti~QK~~~~G~htAs~c~Wd 88 (115)
T KOG4081|consen 9 KEPAFEVEEVHKIIKECLESAIGGNAYQHDKVNQWTQKVVEQILTALVKLGKPYKYIVTCTIVQKSPGAGLHTASSCFWD 88 (115)
T ss_pred hhhhhhHHHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHHHHHHcCCCeEEEEEEEEEeeCCCccceecceeeec
Confidence 356799999999999999999999999999999999999999999999999999999999999999 9999999999999
Q ss_pred CCCCCeEEEEEEcCcEEEEEEEEEEeC
Q psy2601 106 DNTDGSCTVRWENKTMYCIVSVYALAL 132 (132)
Q Consensus 106 ~~~D~~~~~~~~n~~~~~v~tVf~iy~ 132 (132)
..+||..+++|+|++|+|++.||||.+
T Consensus 89 ~~tDgs~tvrwe~kTm~~iV~vf~Iai 115 (115)
T KOG4081|consen 89 TTTDGSYTVRWENKTMYCIVSVFAIAI 115 (115)
T ss_pred cCCCCcEEEEeccceeeeeeEEeEeeC
Confidence 999999999999999999999999975
No 4
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=62.03 E-value=17 Score=26.61 Aligned_cols=43 Identities=16% Similarity=0.173 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhccC
Q psy2601 30 KFAVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLD 77 (132)
Q Consensus 30 ~F~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~ 77 (132)
|.+.+.|+.++.++-.+.... ..-.--+..|.+.++++|++|.
T Consensus 78 pVs~e~ie~~v~~Ie~~l~~~-----~~~EI~S~~IGe~Vm~~L~~lD 120 (147)
T TIGR00244 78 PVSFDDLEHAINHIEAQLRAQ-----GEREVPSELIGQMVMQYLKKLD 120 (147)
T ss_pred CCCHHHHHHHHHHHHHHHHHc-----CCCcccHHHHHHHHHHHHhhcC
Confidence 344444444444444433322 2233446788899999999885
No 5
>PF15604 Toxin_43: Putative toxin 43
Probab=47.31 E-value=72 Score=23.45 Aligned_cols=43 Identities=21% Similarity=0.213 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhccC
Q psy2601 35 EISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLD 77 (132)
Q Consensus 35 ~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~ 77 (132)
+++.-|++.+.+.|....|++..+...+...+..-+..|..|+
T Consensus 52 ~~~~ki~e~~~~~l~s~~~~~~~a~~~A~~~A~~~m~tlAALH 94 (152)
T PF15604_consen 52 ELRDKIEELIEDELLSKGMSPREAEIQAEKQAKEWMKTLAALH 94 (152)
T ss_pred HHHHHHHHHHHHHhhcccCChHHHHHHHHHHHHHHHHHHHhhc
Confidence 3667777778888877889999999999999999999998875
No 6
>PF15603 Imm45: Immunity protein 45
Probab=44.61 E-value=36 Score=22.40 Aligned_cols=27 Identities=15% Similarity=0.083 Sum_probs=22.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhhhC
Q psy2601 23 GGTTEDSKFAVDEISCIIKEAIEDCIG 49 (132)
Q Consensus 23 ~~p~~~~~F~~~~v~~ii~~vl~~~L~ 49 (132)
..|++..++...+++.||+++.+..-+
T Consensus 48 e~P~e~~~it~~e~q~II~aI~~~~~~ 74 (82)
T PF15603_consen 48 EPPHENEPITIAERQKIIEAIEKYFSE 74 (82)
T ss_pred cCCCCCcccCHHHHHHHHHHHHHHHhc
Confidence 457888899999999999999876544
No 7
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=42.96 E-value=42 Score=24.78 Aligned_cols=44 Identities=16% Similarity=0.186 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhccC
Q psy2601 29 SKFAVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLD 77 (132)
Q Consensus 29 ~~F~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~ 77 (132)
.|-..+.|+.++..+..+.... ..-.--++.|.+.+++.|++|.
T Consensus 77 RpVs~e~ie~~v~~ie~~Lr~~-----g~~EV~S~~IG~~VM~~Lk~lD 120 (156)
T COG1327 77 RPVSSEQIEEAVSHIERQLRSS-----GEREVPSKEIGELVMEELKKLD 120 (156)
T ss_pred CCCCHHHHHHHHHHHHHHHHhc-----CCCCCCHHHHHHHHHHHHHhcc
Confidence 3344445555555554444332 2223346788899999999875
No 8
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=39.04 E-value=81 Score=20.89 Aligned_cols=43 Identities=26% Similarity=0.407 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhccC--CCceEE
Q psy2601 36 ISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLD--KPFKYV 83 (132)
Q Consensus 36 v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~--~ryK~v 83 (132)
=+..|++++..+-+|..|+-+.....+++|.+. .+.+ +.-|||
T Consensus 28 RE~aIeeav~~c~~g~pFs~d~IN~vT~~mN~L-----Ak~givP~Rk~V 72 (84)
T PF10752_consen 28 REAAIEEAVSLCKQGEPFSTDKINEVTKEMNEL-----AKQGIVPTRKYV 72 (84)
T ss_pred HHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHH-----HHcCCCCcchhc
Confidence 356789999999999999988887777666433 2223 666665
No 9
>PF13421 Band_7_1: SPFH domain-Band 7 family
Probab=38.52 E-value=85 Score=23.95 Aligned_cols=48 Identities=17% Similarity=0.344 Sum_probs=35.7
Q ss_pred CCCCCHHHHHHHHHHHH----HhhhCCCCcCchhHHHHHHHHHHHHHHHHhc
Q psy2601 28 DSKFAVDEISCIIKEAI----EDCIGGNTYNSAKVSTYVSQVVETIMANLIK 75 (132)
Q Consensus 28 ~~~F~~~~v~~ii~~vl----~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~ 75 (132)
...|..+++++.++..+ .+.|....+...+...-..+|++.++++|..
T Consensus 125 ~~~~~~~~i~~~l~~~i~~~i~~~l~~~~~~~~~i~a~~~eis~~~~~~l~~ 176 (211)
T PF13421_consen 125 QSEFTTEEINEQLRSEIVQAIADALAESKISILDIPAHLDEISEALKEKLNP 176 (211)
T ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45688888777777764 4555556777788888888888888888875
No 10
>PF10523 BEN: BEN domain; InterPro: IPR018379 The BEN domain is found in diverse proteins including: SMAR1 (Scaffold/Matrix attachment region-binding protein 1; also known as BANP), a tumour-suppressor MAR-binding protein that down-regulates Cyclin D1 expression by recruiting HDAC1-mSin3A co-repressor complex at Cyclin D1 promoter locus; SMAR1 is the target of prostaglandin A2 (PGA2) induced growth arrest [, ]. NAC1, a novel member of the POZ/BTB (Pox virus and Zinc finger/Bric-a-bracTramtrack Broad complex), but which varies from other proteins of this class in that it lacks the characteristic DNA-binding motif []. Mod(mdg4) isoform C, the modifier of the mdg4 locus in Drosophila melanogaster (Fruit fly), where mdg4 encodes chromatin proteins which are involved in position effect variegation, establishment of chromatin boundaries, nerve path finding, meiotic chromosome pairing and apoptosis []. Trans-splicing of Mod(mdg4) produces at least 26 transcripts. E5R protein from Chordopoxvirus virosomes, which is found in cytoplasmic sites of viral DNA replication []. Several proteins of polydnaviruses. The BEN domain is predicted to function as an adaptor for the higher-order structuring of chromatin, and recruitment of chromatin modifying factors in transcriptional regulation. It has been suggested to mediate protein-DNA and protein-protein interactions during chromatin organisation and transcription. The presence of BEN domains in a poxviral early virosomal protein and in polydnaviral proteins also suggests a possible role in the organisation of viral DNA during replication or transcription. They are generally linked to other globular domains with functions related to transcriptional regulation and chromatin structure, such as BTB, C4DM, and C2H2 fingers []. This domain is predicted to form an all-alpha fold with four conserved helices. Its conservation pattern revealed several conserved residues, most of which have hydrophobic side-chains and are likely to stabilise the fold through helix-helix packing [].
Probab=35.41 E-value=1.1e+02 Score=18.80 Aligned_cols=42 Identities=10% Similarity=0.076 Sum_probs=27.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhcc
Q psy2601 27 EDSKFAVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKL 76 (132)
Q Consensus 27 ~~~~F~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l 76 (132)
...+.++.++..|..-+....-... ..|. ++...|.+.+...
T Consensus 34 ~k~~Ld~~kl~~I~~~v~~~~~~~~-------~~w~-~~~~~i~~~~~~~ 75 (79)
T PF10523_consen 34 GKPQLDPNKLSAIRNYVEERFPSEK-------RKWR-ECRQSINNKCRDP 75 (79)
T ss_pred CCCCCCHHHHHHHHHHHHHHCCcch-------hhHH-HHHHHHHHHHHHH
Confidence 4678999999888877765433332 5555 6666666665543
No 11
>TIGR00597 rad10 DNA repair protein rad10. All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.91 E-value=53 Score=22.90 Aligned_cols=24 Identities=21% Similarity=0.163 Sum_probs=17.4
Q ss_pred HHHHHHHHhccCCCceEEEEEEEE
Q psy2601 66 VETIMANLIKLDKPFKYVVNGTVM 89 (132)
Q Consensus 66 ~~~I~~~lk~l~~ryK~vV~v~I~ 89 (132)
-+.|.+|+++|++.|+.-|...++
T Consensus 52 peYi~~Ri~~L~~~~~lrvLL~~V 75 (112)
T TIGR00597 52 PDYIHRRLQSLGKNFNLRILLVQV 75 (112)
T ss_pred HHHHHHHHHHhccccceeEEEEEE
Confidence 467899999999889884433333
No 12
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=33.07 E-value=75 Score=18.55 Aligned_cols=43 Identities=14% Similarity=0.314 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhhhCC-CCcC--ch-hHHHHHHHHHH-HHHHHHhcc
Q psy2601 34 DEISCIIKEAIEDCIGG-NTYN--SA-KVSTYVSQVVE-TIMANLIKL 76 (132)
Q Consensus 34 ~~v~~ii~~vl~~~L~~-~~Y~--~~-~~~~~~~~I~~-~I~~~lk~l 76 (132)
+.+++++++++-..++. ..|+ .. ....|...++. .+++.+++.
T Consensus 21 ~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~ 68 (71)
T PF04542_consen 21 EDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKR 68 (71)
T ss_dssp SHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCS
T ss_pred hhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHh
Confidence 68888999998888865 4565 33 56777766654 555555544
No 13
>PRK12362 germination protease; Provisional
Probab=32.72 E-value=1.1e+02 Score=25.22 Aligned_cols=47 Identities=13% Similarity=0.262 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhc
Q psy2601 29 SKFAVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIK 75 (132)
Q Consensus 29 ~~F~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~ 75 (132)
..++.++-+++|+++|.-.+++-.=.|++...+.++++.-|-..|..
T Consensus 264 ~~~~~~ek~~li~evl~p~~~~l~VTPKeID~~i~~~s~iIa~giN~ 310 (318)
T PRK12362 264 KSLNQEEKQQLIKEVLSPYVGNLIVTPKEIDELIENLSKIIAGGINM 310 (318)
T ss_pred hccCHHHHHHHHHHHhCccCCcceECcHhHHHHHHHHHHHHHHHHHH
Confidence 56799999999999999999887777888888888888877777664
No 14
>PF00438 S-AdoMet_synt_N: S-adenosylmethionine synthetase, N-terminal domain; InterPro: IPR022628 The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. This entry represents the N-terminal domain of S-adenosylmethionine synthetase and is found in association with PF02772 from PFAM and PF02773 from PFAM. S-adenosylmethionine synthetase (MAT, 2.5.1.6 from EC) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP []. AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis. In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family. The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex, and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance []; GO: 0004478 methionine adenosyltransferase activity; PDB: 3RV2_A 3TDE_B 3S82_B 3IML_B 2P02_A 2OBV_A 1QM4_B 1O9T_B 1O93_A 1O92_B ....
Probab=32.16 E-value=1.4e+02 Score=20.38 Aligned_cols=32 Identities=16% Similarity=0.199 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHhccCCCceEEEEEEEE
Q psy2601 58 VSTYVSQVVETIMANLIKLDKPFKYVVNGTVM 89 (132)
Q Consensus 58 ~~~~~~~I~~~I~~~lk~l~~ryK~vV~v~I~ 89 (132)
-..+|..|++.|+++.-+..+.-|..|-+.+.
T Consensus 15 PDKicDqISDailD~~l~~dp~arVA~E~~~~ 46 (100)
T PF00438_consen 15 PDKICDQISDAILDACLKQDPNARVACETLVS 46 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHH-TT-EEEEEEEEE
T ss_pred chhhhceeeeccchHHHhcCCCCeEEEEEEee
Confidence 45678899999999988887778888877765
No 15
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=31.67 E-value=1.1e+02 Score=21.30 Aligned_cols=45 Identities=2% Similarity=0.126 Sum_probs=32.7
Q ss_pred CHHHHHHHHHHHHHhhhCC-CCcCchhHHHHHHHHHH-HHHHHHhcc
Q psy2601 32 AVDEISCIIKEAIEDCIGG-NTYNSAKVSTYVSQVVE-TIMANLIKL 76 (132)
Q Consensus 32 ~~~~v~~ii~~vl~~~L~~-~~Y~~~~~~~~~~~I~~-~I~~~lk~l 76 (132)
+.+..++++++++-+.+.+ ..++......|.-.|+. .+++.+++.
T Consensus 27 ~~~~AeDivQe~flk~~~~~~~~~~~~~~~wl~~i~~n~~~d~~R~~ 73 (161)
T PRK12528 27 CPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQ 73 (161)
T ss_pred CcccHHHHHHHHHHHHHhccccccccCHHHHHHHHHHHHHHHHHHHH
Confidence 4568899999999998876 35666667889877774 455666654
No 16
>cd07565 aliphatic_amidase aliphatic amidases (class 2 nitrilases). Aliphatic amidases catalyze the hydrolysis of short-chain aliphatic amides to form ammonia and the corresponding organic acid. This group includes Pseudomonas aeruginosa (Pa) AmiE, the amidase from Geobacillus pallidus RAPc8 (RAPc8 amidase), and Helicobacter pylori (Hp) AmiE and AmiF. PaAimE and HpAmiE hydrolyze various very short aliphatic amides, including propionamide, acetamide and acrylamide. HpAmiF is a formamidase which specifically hydrolyzes formamide. These proteins belong to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 2. Members of this superfamily generally form homomeric complexes, the basic
Probab=30.92 E-value=1.5e+02 Score=23.33 Aligned_cols=84 Identities=12% Similarity=0.092 Sum_probs=45.6
Q ss_pred CCCHHHHHHHHHHHHHh--h----------hCCCCcCchhHHHHHHHHHHHHHHHHhccCCCceEEEEEEEEEeCCc--c
Q psy2601 30 KFAVDEISCIIKEAIED--C----------IGGNTYNSAKVSTYVSQVVETIMANLIKLDKPFKYVVNGTVMQKLGA--G 95 (132)
Q Consensus 30 ~F~~~~v~~ii~~vl~~--~----------L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~~ryK~vV~v~I~qk~gq--g 95 (132)
.-+.+++.+.|++.... - +.+..|+......++..+.....++|.++.+.++..+.+-+.++.+. |
T Consensus 20 ~~Nl~~~~~~i~~A~~~~~gadLvvfPE~~ltGy~~~~~~~~~~a~~~~~~~~~~l~~lA~~~~i~i~~g~~e~~~~~~~ 99 (291)
T cd07565 20 LENAERIADMVEGTKRGLPGMDLIVFPEYSTQGLMYDKWTMDETACTVPGPETDIFAEACKEAKVWGVFSIMERNPDHGK 99 (291)
T ss_pred HHHHHHHHHHHHHHHhhCCCCeEEEeCCcccccCCCCcchhhhhccCCCChhHHHHHHHHHHCCeEEEEEeeeecCCCCC
Confidence 34566777777776642 0 11223333444555554445566777777777777666666666533 3
Q ss_pred -eeeeeeeeecCCCCCeEEEEE
Q psy2601 96 -LHTSSSCLWDDNTDGSCTVRW 116 (132)
Q Consensus 96 -i~~as~~lWD~~~D~~~~~~~ 116 (132)
++ =+..+|++ ||-+..+|
T Consensus 100 ~~y-Nsa~~i~~--~G~i~~~Y 118 (291)
T cd07565 100 NPY-NTAIIIDD--QGEIVLKY 118 (291)
T ss_pred ceE-EEEEEECC--CCcEEEEE
Confidence 33 33355665 45443333
No 17
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=30.39 E-value=1.2e+02 Score=21.00 Aligned_cols=45 Identities=9% Similarity=0.146 Sum_probs=35.1
Q ss_pred CHHHHHHHHHHHHHhhhCC-CCcCchhHHHHHHHHHH-HHHHHHhcc
Q psy2601 32 AVDEISCIIKEAIEDCIGG-NTYNSAKVSTYVSQVVE-TIMANLIKL 76 (132)
Q Consensus 32 ~~~~v~~ii~~vl~~~L~~-~~Y~~~~~~~~~~~I~~-~I~~~lk~l 76 (132)
+.+.+++++++++-+.+.. ..|+......|.-.|+. .+.+.+++-
T Consensus 18 ~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~wl~~ia~n~~~d~~Rk~ 64 (160)
T PRK09642 18 HEEDAKDVTQEVFVKIHASLPNYQFRGLKTWMARIATNHAIDYKRKK 64 (160)
T ss_pred CHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHHh
Confidence 5688999999999999987 47887778899988875 455555543
No 18
>TIGR01441 GPR GPR endopeptidase. This model describes a tetrameric protease that makes the rate-limiting first cut in the small, acid-soluble spore proteins (SASP) of Bacillus subtilis and related species. The enzyme lacks clear homology to other known proteases. It processes its own amino end before becoming active to cleave SASPs.
Probab=29.68 E-value=1.4e+02 Score=25.04 Aligned_cols=46 Identities=13% Similarity=0.161 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhc
Q psy2601 30 KFAVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIK 75 (132)
Q Consensus 30 ~F~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~ 75 (132)
.++.++-+++|+++|.-.+++--=.|+++..+.++++.-|-..|..
T Consensus 297 ~~~~~Ek~~li~EvL~P~~~~L~VTPKeID~~i~~~a~iIa~giN~ 342 (358)
T TIGR01441 297 TLDEEEKRQLIYEVLNPLGHNLMVTPKEVDMFIEDMANVIASGLNI 342 (358)
T ss_pred cCCHHHHHHHHHHHhCcccCcceECcHhHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999988887777888888777777766665553
No 19
>PF05903 Peptidase_C97: PPPDE putative peptidase domain; InterPro: IPR008580 This domain consists of the N-terminal portion of several eukaryotic sequences. The function of this domain is unknown.; PDB: 2WP7_A 3EBQ_A.
Probab=29.51 E-value=91 Score=22.38 Aligned_cols=42 Identities=10% Similarity=0.373 Sum_probs=29.7
Q ss_pred CCCCCHHHHHHHHHHHHHhhhCCCCcC--chhHHHHHHHHHHHHH
Q psy2601 28 DSKFAVDEISCIIKEAIEDCIGGNTYN--SAKVSTYVSQVVETIM 70 (132)
Q Consensus 28 ~~~F~~~~v~~ii~~vl~~~L~~~~Y~--~~~~~~~~~~I~~~I~ 70 (132)
...++.++++.++ +.|+..+.+..|+ ...|...++++++.+.
T Consensus 79 ~T~~~~~~~~~~l-~~l~~~~~~~~Y~Ll~~NCNhFs~~l~~~L~ 122 (151)
T PF05903_consen 79 ETTLSEEEFEEIL-RSLSREFTGDSYHLLNRNCNHFSDALCQFLT 122 (151)
T ss_dssp EE---HHHHHHHH-HHHHTT-SGGG-BTTTBSHHHHHHHHHHHHH
T ss_pred CccCCHHHHHHHH-HHHHhhccCCcchhhhhhhhHHHHHHHHHhC
Confidence 3567899999999 6666778888998 5889998888887764
No 20
>TIGR03112 6_pyr_pter_rel 6-pyruvoyl tetrahydropterin synthase-related domain. Members of this family are small proteins, or small domains of larger proteins, that occur in certain Firmicutes in the same regions as members of families TIGR03110 and TIGR03111. Members of TIGR03110 resemble exosortase, a proposed protein sorting transpeptidase (see TIGR02602). TIGR03111 represents a small clade among the group 2 glycosyltransferases. Members of the current protein family resemble eukaryotic known and prokaryotic predicted 6-pyruvoyl tetrahydropterin synthases.
Probab=28.50 E-value=2e+02 Score=19.73 Aligned_cols=43 Identities=5% Similarity=0.149 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHHHhhhCCC-----C-cC--chhHHHHHHHHHHHHHHHHh
Q psy2601 31 FAVDEISCIIKEAIEDCIGGN-----T-YN--SAKVSTYVSQVVETIMANLI 74 (132)
Q Consensus 31 F~~~~v~~ii~~vl~~~L~~~-----~-Y~--~~~~~~~~~~I~~~I~~~lk 74 (132)
.+-.+++++++++++. |+.+ . +. ...+..++.-|.+.+..+|.
T Consensus 41 vDf~~lk~~l~~v~~~-~DH~~LNdv~~f~~~~PTaEniA~~i~~~l~~~l~ 91 (113)
T TIGR03112 41 ILFNDVEKKVEKYLKP-YQNKYLNDLEPFDKINPTLENIGDYFFDEIKKLLK 91 (113)
T ss_pred EEHHHHHHHHHHHHHc-CCCceeccCCccCCCCCCHHHHHHHHHHHHHHhhc
Confidence 6788999999998763 5432 2 32 24677777778777777775
No 21
>KOG0324|consensus
Probab=28.36 E-value=1e+02 Score=23.94 Aligned_cols=40 Identities=18% Similarity=0.401 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHHHHHHHhhhCCCCcC--chhHHHHHHHHHHH
Q psy2601 28 DSKFAVDEISCIIKEAIEDCIGGNTYN--SAKVSTYVSQVVET 68 (132)
Q Consensus 28 ~~~F~~~~v~~ii~~vl~~~L~~~~Y~--~~~~~~~~~~I~~~ 68 (132)
...|+.++|+++|++.=+ .+.|..|+ ...|...++.+|..
T Consensus 82 ~Td~~~~~v~~~le~L~~-ey~G~~YhL~~kNCNHFsn~la~~ 123 (214)
T KOG0324|consen 82 STDLTEDDVRRILEELSE-EYRGNSYHLLTKNCNHFSNELALQ 123 (214)
T ss_pred CCCCCHHHHHHHHHHHHh-hcCCceehhhhhccchhHHHHHHH
Confidence 356889999999988654 77788887 45555555555543
No 22
>PF02971 FTCD: Formiminotransferase domain; InterPro: IPR013802 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. In humans, deficiency of this enzyme results in a disease phenotype []. This entry represents the C-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 1QD1_B 2PFD_C.
Probab=28.32 E-value=2e+02 Score=20.99 Aligned_cols=44 Identities=18% Similarity=0.157 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhccC------CCceEEEEEEEEEeCCcceeeeeeeeecCCC
Q psy2601 64 QVVETIMANLIKLD------KPFKYVVNGTVMQKLGAGLHTSSSCLWDDNT 108 (132)
Q Consensus 64 ~I~~~I~~~lk~l~------~ryK~vV~v~I~qk~gqgi~~as~~lWD~~~ 108 (132)
+|++.|-..++.-+ .++|+| ...=..-.+.|+...|..+||.+.
T Consensus 14 ~iA~~IA~~iR~sgrg~~~PGgl~~V-kAiG~~l~~~~~aQVSmNltd~~~ 63 (145)
T PF02971_consen 14 EIAKKIAKAIRESGRGKDQPGGLKYV-KAIGWYLEERGIAQVSMNLTDYEK 63 (145)
T ss_dssp HHHHHHHHHHCTTTTCTTC--SCTTE-EEEEEEETTTTEEEEEEEES-TTT
T ss_pred HHHHHHHHHHHhcCCCCCCCCCccee-eEeEEeeccCCeeEEEEeeecCCC
Confidence 44455555555554 678887 555556678899999999999764
No 23
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=28.15 E-value=2.1e+02 Score=20.16 Aligned_cols=45 Identities=4% Similarity=0.170 Sum_probs=33.5
Q ss_pred CHHHHHHHHHHHHHhhhCCCCcC-chhHHHHHHHHHHH-HHHHHhcc
Q psy2601 32 AVDEISCIIKEAIEDCIGGNTYN-SAKVSTYVSQVVET-IMANLIKL 76 (132)
Q Consensus 32 ~~~~v~~ii~~vl~~~L~~~~Y~-~~~~~~~~~~I~~~-I~~~lk~l 76 (132)
+.+..++++++++-+.+....|. ......|.-.|+.. +.+.+++-
T Consensus 33 ~~~~AeDlvQevflk~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~ 79 (172)
T PRK12523 33 CRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRRA 79 (172)
T ss_pred CHhhHHHHHHHHHHHHHcccccCcchhHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999765444 45678898888764 55566543
No 24
>PF08178 GnsAB: GnsA/GnsB family; InterPro: IPR012563 This family consists of the GnsA/GnsB family. GnsA and GnsB are multicopy suppressors of the secG null mutation. These proteins participate in the synthesis of phospholipids, suggesting the functional relationship between SecG and membrane phospholipids. Over expression of gnsA and gnsB causes a remarkable increase in the unsaturated fatty acid content. However, the gnsA-gnsB double null mutant exhibits no effect. Both proteins are predicted to possess a helix-turn-helix structure [].
Probab=28.05 E-value=1e+02 Score=18.79 Aligned_cols=30 Identities=17% Similarity=0.156 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHhccC-CCceEEEEEEEEEe
Q psy2601 62 VSQVVETIMANLIKLD-KPFKYVVNGTVMQK 91 (132)
Q Consensus 62 ~~~I~~~I~~~lk~l~-~ryK~vV~v~I~qk 91 (132)
=.+|++-|.+++.+|+ +.=|.++.+--+-+
T Consensus 11 EeeI~~lI~kKi~ELrk~~Gke~sei~~~~~ 41 (54)
T PF08178_consen 11 EEEISALITKKIAELRKKTGKEVSEIEFIAR 41 (54)
T ss_pred HHHHHHHHHHHHHHhccccCceeeeeeehHH
Confidence 3589999999999999 77788887655543
No 25
>KOG4745|consensus
Probab=27.69 E-value=48 Score=24.03 Aligned_cols=57 Identities=23% Similarity=0.283 Sum_probs=40.0
Q ss_pred HHHhccCCCceEEEEEEEEEeCC--cceeeeeeeeecCCCCCeEEEEEEcCcEEEEEEE
Q psy2601 71 ANLIKLDKPFKYVVNGTVMQKLG--AGLHTSSSCLWDDNTDGSCTVRWENKTMYCIVSV 127 (132)
Q Consensus 71 ~~lk~l~~ryK~vV~v~I~qk~g--qgi~~as~~lWD~~~D~~~~~~~~n~~~~~v~tV 127 (132)
.+.+.++.+|++.++|+|.+--+ .=+....-|+|-+--=..-.+-|+.+++.|+.-|
T Consensus 64 ~qre~~~~~y~~~c~C~vt~C~~ipC~lss~~~ClWtd~l~~~~~~g~q~~h~ac~~~~ 122 (141)
T KOG4745|consen 64 TQREGLNHWYHVGCNCTVTPCPSIPCFLSSPDECLWTDWLLEETNYGYQAKHYACIKRV 122 (141)
T ss_pred HHhccccceeeecccceeeecCCCccccCCCCceEechhhhccccccccccceEEeecc
Confidence 34556679999999999998654 3456688899976444444455677777777654
No 26
>TIGR01638 Atha_cystat_rel Arabidopsis thaliana cystatin-related protein. This model represents a family similar in sequence and probably homologous to a large family of cysteine proteinase inhibitors, or cystatins, as described by pfam model pfam00031. Cystatins may help plants resist attack by insects.
Probab=27.63 E-value=2e+02 Score=19.40 Aligned_cols=47 Identities=6% Similarity=-0.048 Sum_probs=37.4
Q ss_pred CCcCc-hhHHHHHHHHHHHHHHHHhccC-CCceEEEEEEEEEeCCccee
Q psy2601 51 NTYNS-AKVSTYVSQVVETIMANLIKLD-KPFKYVVNGTVMQKLGAGLH 97 (132)
Q Consensus 51 ~~Y~~-~~~~~~~~~I~~~I~~~lk~l~-~ryK~vV~v~I~qk~gqgi~ 97 (132)
..+++ .....+.++++....++..+.. .++.||=.|-...+-|+|+.
T Consensus 3 ~a~~p~~T~rd~~~~la~~al~k~N~~~~t~lEfV~vVrAn~~~~~g~~ 51 (92)
T TIGR01638 3 EAIRPIETNRDLLERLSYVASKKYNDTKFLNLELVEVVRANYRGGAKSK 51 (92)
T ss_pred cccccccCHHHHHHHHHHHHHHHhhhhcCceEEEEEEEEEEeeccceEE
Confidence 44565 6778889999999999999876 89999988877777777743
No 27
>COG5418 Predicted secreted protein [Function unknown]
Probab=27.11 E-value=1.1e+02 Score=22.51 Aligned_cols=48 Identities=15% Similarity=0.164 Sum_probs=38.3
Q ss_pred CCcCchhHHHHHHHHHHHHHHHHhccC-CCceEEEEEEEEEeC--Ccceeeeee
Q psy2601 51 NTYNSAKVSTYVSQVVETIMANLIKLD-KPFKYVVNGTVMQKL--GAGLHTSSS 101 (132)
Q Consensus 51 ~~Y~~~~~~~~~~~I~~~I~~~lk~l~-~ryK~vV~v~I~qk~--gqgi~~as~ 101 (132)
..||+..-.+.++.|++-|-+-|.+.. +.||++ .||=++ ..|+...++
T Consensus 68 e~~d~~~yRr~c~ki~~pi~~~l~e~k~d~~kii---~IGV~~SpTCgVy~tt~ 118 (164)
T COG5418 68 EVFDHPGYRRVCRKIADPIGRVLEEEKPDGIKII---FIGVKGSPTCGVYTTTS 118 (164)
T ss_pred HHhcchhHHHHHHHHHHHHHHHHHHhCcCCceEE---EEecCCCCccceEeccC
Confidence 368889999999999999999999999 899998 345443 357666655
No 28
>KOG1404|consensus
Probab=26.90 E-value=1.5e+02 Score=25.44 Aligned_cols=43 Identities=14% Similarity=0.198 Sum_probs=32.9
Q ss_pred hhHHHHHHHHHHHHHHHHhccCCCceEEEEEEEEEeCCcceeeeeeee
Q psy2601 56 AKVSTYVSQVVETIMANLIKLDKPFKYVVNGTVMQKLGAGLHTSSSCL 103 (132)
Q Consensus 56 ~~~~~~~~~I~~~I~~~lk~l~~ryK~vV~v~I~qk~gqgi~~as~~l 103 (132)
++-++-+.+.....+++|+++.+++-+| +.-+|.|+-...--.
T Consensus 332 e~LqE~aa~vG~yl~~~l~~l~d~h~iI-----GdVRG~GLm~GvE~V 374 (442)
T KOG1404|consen 332 ENLQENAAEVGSYLLEKLAALKDKHPII-----GDVRGRGLMLGVELV 374 (442)
T ss_pred HhHHHHHHHHHHHHHHHHHHHhhcCCce-----eecccceeEEEEEEe
Confidence 6677888899999999999999887765 566777765554433
No 29
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=26.35 E-value=1.8e+02 Score=18.59 Aligned_cols=45 Identities=13% Similarity=0.104 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhcc
Q psy2601 32 AVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKL 76 (132)
Q Consensus 32 ~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l 76 (132)
..++++..++..+.+.|.+-.+-..+-=..-..+....+.+|..|
T Consensus 25 ~~~e~e~~~r~~l~~~l~kldlVtREEFd~q~~~L~~~r~kl~~L 69 (79)
T PF04380_consen 25 PREEIEKNIRARLQSALSKLDLVTREEFDAQKAVLARTREKLEAL 69 (79)
T ss_pred hHHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHHHHHHH
Confidence 456788888888888888876665444444455566666666654
No 30
>PF03748 FliL: Flagellar basal body-associated protein FliL; InterPro: IPR005503 This FliL protein controls the rotational direction of the flagella during chemotaxis []. FliL is a cytoplasmic membrane protein associated with the basal body [].; GO: 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009425 bacterial-type flagellum basal body
Probab=26.30 E-value=1.8e+02 Score=18.56 Aligned_cols=50 Identities=16% Similarity=0.092 Sum_probs=34.4
Q ss_pred HHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhc-cCCCceEEEEEEEE
Q psy2601 38 CIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIK-LDKPFKYVVNGTVM 89 (132)
Q Consensus 38 ~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~-l~~ryK~vV~v~I~ 89 (132)
..|++.+-..|.+..++.-....=-..|-+++++++.+ +++.. |..|.+.
T Consensus 44 ~~ird~ii~~l~~~~~~~l~~~~g~~~Lk~~l~~~in~~l~~~~--V~~V~ft 94 (99)
T PF03748_consen 44 PRIRDAIISYLSSKTAEDLSGPEGKERLKDELKDRINKILGKGK--VKDVYFT 94 (99)
T ss_pred HHHHHHHHHHHHcCCHHHhcChhhHHHHHHHHHHHHHHhhccCc--EEEEEEE
Confidence 47888889999998888666666666777778888874 34221 4455443
No 31
>smart00244 PHB prohibitin homologues. prohibitin homologues
Probab=25.54 E-value=2.2e+02 Score=19.36 Aligned_cols=41 Identities=17% Similarity=0.212 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhhhCCCCcCchhHHH-HHHHHHHHHHHHHhcc
Q psy2601 34 DEISCIIKEAIEDCIGGNTYNSAKVST-YVSQVVETIMANLIKL 76 (132)
Q Consensus 34 ~~v~~ii~~vl~~~L~~~~Y~~~~~~~-~~~~I~~~I~~~lk~l 76 (132)
+.++.+++..+++.+. .|+..++.. --..|++.+++.|++.
T Consensus 89 ~~l~~~i~~~ir~~i~--~~~~~~i~~~~r~~i~~~v~~~l~~~ 130 (160)
T smart00244 89 AVIEQLAQTTLRSVIG--KMTLDELLTDEREKISENIREELNER 130 (160)
T ss_pred HHHHHHHHHHHHHHHc--cccHHHHHHhhHHHHHHHHHHHHHHH
Confidence 4788889888888888 455555544 3455666666666643
No 32
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=25.44 E-value=40 Score=17.14 Aligned_cols=11 Identities=27% Similarity=0.610 Sum_probs=8.1
Q ss_pred eecCCCCCeEE
Q psy2601 103 LWDDNTDGSCT 113 (132)
Q Consensus 103 lWD~~~D~~~~ 113 (132)
.||.+.||+++
T Consensus 8 ~~D~d~dG~I~ 18 (31)
T PF13405_consen 8 MFDKDGDGFID 18 (31)
T ss_dssp HH-TTSSSEEE
T ss_pred HHCCCCCCcCc
Confidence 47899999876
No 33
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=25.12 E-value=2.7e+02 Score=20.32 Aligned_cols=21 Identities=14% Similarity=0.213 Sum_probs=17.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhh
Q psy2601 27 EDSKFAVDEISCIIKEAIEDC 47 (132)
Q Consensus 27 ~~~~F~~~~v~~ii~~vl~~~ 47 (132)
...+|+..+|...|.......
T Consensus 57 ~~v~Fd~~KI~~AI~kA~~a~ 77 (154)
T PRK00464 57 RREPFDREKLRRGLRRACEKR 77 (154)
T ss_pred cCCCcCHHHHHHHHHHHHHhC
Confidence 468899999999998888765
No 34
>PF06919 Phage_T4_Gp30_7: Phage Gp30.7 protein; InterPro: IPR009690 This family consists of several phage Gp30.7 proteins of 121 residues in length. Family members seem to be exclusively from the T4-like viruses. The function of this family is unknown.
Probab=24.91 E-value=2e+02 Score=20.09 Aligned_cols=32 Identities=19% Similarity=0.121 Sum_probs=24.0
Q ss_pred EEEEEEeCCcceeeeeeeeecCCCCCeEEEEEEcC
Q psy2601 85 NGTVMQKLGAGLHTSSSCLWDDNTDGSCTVRWENK 119 (132)
Q Consensus 85 ~v~I~qk~gqgi~~as~~lWD~~~D~~~~~~~~n~ 119 (132)
..+..++...|-.+.-..+| +|+|+-..|||+
T Consensus 20 ~~~~lw~H~NGtv~qI~~Y~---~pNYvf~~FEnG 51 (121)
T PF06919_consen 20 ATICLWKHKNGTVAQIEQYM---TPNYVFMRFENG 51 (121)
T ss_pred eeEEEEecCCCcEEEEeeec---CCCEEEEEecCC
Confidence 34556666677777777788 588999999985
No 35
>PF03492 Methyltransf_7: SAM dependent carboxyl methyltransferase; InterPro: IPR005299 This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine [].; GO: 0008168 methyltransferase activity; PDB: 2EFJ_A 1M6E_X 2EG5_C 3B5I_B.
Probab=24.64 E-value=3.1e+02 Score=22.34 Aligned_cols=56 Identities=11% Similarity=0.203 Sum_probs=36.2
Q ss_pred CHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhccC-CCceEEEEEEEEEeC
Q psy2601 32 AVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLD-KPFKYVVNGTVMQKL 92 (132)
Q Consensus 32 ~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~-~ryK~vV~v~I~qk~ 92 (132)
-..-++.+++-.|..+|+. +-+..+=.+..+.+.+.+.... ...+++..++.+.|+
T Consensus 278 ~~~~iRA~~e~~l~~hfG~-----ei~D~LF~r~~~~v~~~~~~~~~~~~~~~~i~~~L~Rk 334 (334)
T PF03492_consen 278 VANYIRAVFEPLLKAHFGE-----EIMDELFERYAKKVAEHLEKEKSRNMKFVNIVVSLTRK 334 (334)
T ss_dssp HHHHHHHHHHHHHHHHH-H-----HHHHHHHHHHHHHHHHHHHHTHTT-BEEEEEEEEEEE-
T ss_pred HHHhHHHHHHHHHHHHhCh-----HHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEeeC
Confidence 3455677777777777753 4566666677777777775544 567888888877663
No 36
>COG1973 HypE Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=24.25 E-value=2.1e+02 Score=24.26 Aligned_cols=27 Identities=15% Similarity=0.310 Sum_probs=24.2
Q ss_pred CCcCchhHHHHHHHHHHHHHHHHhccC
Q psy2601 51 NTYNSAKVSTYVSQVVETIMANLIKLD 77 (132)
Q Consensus 51 ~~Y~~~~~~~~~~~I~~~I~~~lk~l~ 77 (132)
+.++.+.+.+|++.+..+++.-+|.++
T Consensus 38 kd~d~e~a~e~a~avl~Evk~t~K~~~ 64 (449)
T COG1973 38 KDWDRERAEEIADAVLEEVKNTLKGLG 64 (449)
T ss_pred hccCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 468999999999999999999998765
No 37
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=24.24 E-value=2.5e+02 Score=19.40 Aligned_cols=46 Identities=9% Similarity=0.171 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHHhhhCC-CCcCchhHHHHHHHHH-HHHHHHHhccC
Q psy2601 32 AVDEISCIIKEAIEDCIGG-NTYNSAKVSTYVSQVV-ETIMANLIKLD 77 (132)
Q Consensus 32 ~~~~v~~ii~~vl~~~L~~-~~Y~~~~~~~~~~~I~-~~I~~~lk~l~ 77 (132)
+.+.+++++++++-+.... ..++......|.-.|+ +.+.+.+++..
T Consensus 21 ~~~~aeDivQe~~l~l~~~~~~~~~~~~~~wl~~iarn~~~d~~R~~~ 68 (163)
T PRK07037 21 CRSRAEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYRRQA 68 (163)
T ss_pred CHhHHHHHHHHHHHHHHhccccCCcccHHHHHHHHHHHHHHHHHHhhc
Confidence 4568899999998887754 3455555668887777 45666666543
No 38
>PF14564 Membrane_bind: Membrane binding; PDB: 1YHP_A 2B1O_A.
Probab=22.97 E-value=2.6e+02 Score=19.22 Aligned_cols=36 Identities=17% Similarity=0.220 Sum_probs=24.4
Q ss_pred ceEEEEEEEEEeC-Ccceeeeeeee-ecCCCCCeEEEEE
Q psy2601 80 FKYVVNGTVMQKL-GAGLHTSSSCL-WDDNTDGSCTVRW 116 (132)
Q Consensus 80 yK~vV~v~I~qk~-gqgi~~as~~l-WD~~~D~~~~~~~ 116 (132)
=-+++++.|-+.. |+=+..+|-.+ ||+. +|-+++.-
T Consensus 49 ~~iv~~I~Vr~~~~g~~v~nGsvYFkY~~s-~g~V~~~~ 86 (110)
T PF14564_consen 49 SEIVCQISVRDTDWGQYVANGSVYFKYNPS-TGEVSIRK 86 (110)
T ss_dssp SEEEEEEEEEESST-SEEEEEEEEEEEETT-TTEEEEE-
T ss_pred CcEEEEEEEEeccCCceEecceEEEEECCC-CCeEEEee
Confidence 4689999999987 55455555555 8976 67777665
No 39
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.22 E-value=1.9e+02 Score=20.03 Aligned_cols=43 Identities=2% Similarity=0.023 Sum_probs=31.1
Q ss_pred CHHHHHHHHHHHHHhhhCCC-CcCchhHHHHHHHHHHHH-HHHHh
Q psy2601 32 AVDEISCIIKEAIEDCIGGN-TYNSAKVSTYVSQVVETI-MANLI 74 (132)
Q Consensus 32 ~~~~v~~ii~~vl~~~L~~~-~Y~~~~~~~~~~~I~~~I-~~~lk 74 (132)
+.+..++++++++-+.+++. .+.......|.-.|+... .+.++
T Consensus 18 ~~~~aeDi~Qevf~~l~~~~~~~~~~~~~~wL~~ia~n~~~d~~R 62 (159)
T PRK12527 18 NRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHR 62 (159)
T ss_pred CHhhHHHHHHHHHHHHHhccccccccchHHHHHHHHHHHHHHHHH
Confidence 45678999999999988763 466667788988887643 33444
No 40
>KOG2917|consensus
Probab=22.07 E-value=3.3e+02 Score=21.57 Aligned_cols=94 Identities=11% Similarity=0.141 Sum_probs=51.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhccC-CCceEEEEEEEEEeCCcceeeee
Q psy2601 22 PGGTTEDSKFAVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLD-KPFKYVVNGTVMQKLGAGLHTSS 100 (132)
Q Consensus 22 ~~~p~~~~~F~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~-~ryK~vV~v~I~qk~gqgi~~as 100 (132)
-++|-...|+++.-|++.++++--.+-.+ ..+.+.+.++...+.+. +- .|-|.=+-+.|-.+.|..++---
T Consensus 119 ~vnpetkRpyp~s~iekal~e~hfsv~~n-----k~sK~QaleaIkkL~~~---~pI~rarMrlRv~v~~~~~~~l~ekl 190 (250)
T KOG2917|consen 119 CVNPETKRPYPPSMIEKALQEIHFSVKTN-----KSSKQQALEAIKKLKEK---MPIERARMRLRVSVPVKEGKELKEKL 190 (250)
T ss_pred hcCCccCCcCCHHHHHHHHHhcceeecCC-----chHHHHHHHHHHHHHHh---CchhhhceeEEEEEeccchHHHHHHH
Confidence 45677788888887777766654332222 23444444444444433 44 56666666667666666666555
Q ss_pred eeeecCCCCCeEEEEEEcCcEEEEEEE
Q psy2601 101 SCLWDDNTDGSCTVRWENKTMYCIVSV 127 (132)
Q Consensus 101 ~~lWD~~~D~~~~~~~~n~~~~~v~tV 127 (132)
+-+-| ..-+..|..+.+.|++.+
T Consensus 191 ~~l~~----~ve~e~~~~~~~~~~~lI 213 (250)
T KOG2917|consen 191 KELID----SVESEDWDPDQLECVCLI 213 (250)
T ss_pred HHHhh----ccccccCCCCceEEEEEE
Confidence 44433 122223444566666654
No 41
>PHA01513 mnt Mnt
Probab=22.04 E-value=2.3e+02 Score=18.68 Aligned_cols=19 Identities=5% Similarity=0.057 Sum_probs=13.1
Q ss_pred chhHHHHHHHHHHHHHHHH
Q psy2601 55 SAKVSTYVSQVVETIMANL 73 (132)
Q Consensus 55 ~~~~~~~~~~I~~~I~~~l 73 (132)
.+++.++++..++.+++-+
T Consensus 53 ~~~~~~~a~~~~~~~~~~~ 71 (82)
T PHA01513 53 RDDAERLADEQSELVKKMV 71 (82)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5777777777777666544
No 42
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=21.42 E-value=1.7e+02 Score=19.93 Aligned_cols=46 Identities=4% Similarity=0.110 Sum_probs=34.6
Q ss_pred CHHHHHHHHHHHHHhhhCC-CCcCchhHHHHHHHHHHH-HHHHHhccC
Q psy2601 32 AVDEISCIIKEAIEDCIGG-NTYNSAKVSTYVSQVVET-IMANLIKLD 77 (132)
Q Consensus 32 ~~~~v~~ii~~vl~~~L~~-~~Y~~~~~~~~~~~I~~~-I~~~lk~l~ 77 (132)
+.+..++++++++-..++. ..|+......|...|+.. +.+.+++..
T Consensus 18 ~~~~aeD~~Qe~~~~l~~~~~~~~~~~f~~wl~~i~~~~~~d~~r~~~ 65 (154)
T TIGR02950 18 DKHLAEDLLQETFLKAYIHLHSFKDSSIKPWLFRIARNAFIDWYRKDK 65 (154)
T ss_pred CHHHHHHHHHHHHHHHHHhHHHhcCCchHHHHHHHHHHHHHHHHHHhh
Confidence 5788999999999988876 467766777888888664 555665443
No 43
>PF15054 DUF4535: Domain of unknown function (DUF4535)
Probab=21.39 E-value=71 Score=18.74 Aligned_cols=12 Identities=0% Similarity=-0.025 Sum_probs=9.6
Q ss_pred EEEEEEEEEEeC
Q psy2601 121 MYCIVSVYALAL 132 (132)
Q Consensus 121 ~~~v~tVf~iy~ 132 (132)
-|+++++.|||+
T Consensus 5 sF~~G~~~GiY~ 16 (46)
T PF15054_consen 5 SFGAGTYTGIYV 16 (46)
T ss_pred EEeeccEEEEEe
Confidence 367888999985
No 44
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.37 E-value=2e+02 Score=21.72 Aligned_cols=45 Identities=7% Similarity=0.183 Sum_probs=34.9
Q ss_pred CHHHHHHHHHHHHHhhhCC-CCcCchhHHHHHHHHHHH-HHHHHhcc
Q psy2601 32 AVDEISCIIKEAIEDCIGG-NTYNSAKVSTYVSQVVET-IMANLIKL 76 (132)
Q Consensus 32 ~~~~v~~ii~~vl~~~L~~-~~Y~~~~~~~~~~~I~~~-I~~~lk~l 76 (132)
+.+..++++++++-+.+.. ..|+......|.-.|+.. +++.+++.
T Consensus 41 d~~dAEDlvQEvflkl~~~~~~~~~~~~~aWL~~IarN~~~d~~Rk~ 87 (216)
T PRK12533 41 NASDADDVVQEACMRALRFFDSFRGDNARPWLLAIVRHTWYSEWRRR 87 (216)
T ss_pred CHhhHHHHHHHHHHHHHHhHHhcCccchHhHHHHHHHHHHHHHHHhh
Confidence 5678899999999998887 468877789999888764 55556544
No 45
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=21.22 E-value=68 Score=16.48 Aligned_cols=11 Identities=27% Similarity=0.616 Sum_probs=8.4
Q ss_pred ecCCCCCeEEE
Q psy2601 104 WDDNTDGSCTV 114 (132)
Q Consensus 104 WD~~~D~~~~~ 114 (132)
.|.+.||+++.
T Consensus 9 ~D~d~dG~I~~ 19 (29)
T PF00036_consen 9 FDKDGDGKIDF 19 (29)
T ss_dssp HSTTSSSEEEH
T ss_pred HCCCCCCcCCH
Confidence 47888998763
No 46
>COG5054 ERV1 Mitochondrial sulfhydryl oxidase involved in the biogenesis of cytosolic Fe/S proteins [Posttranslational modification, protein turnover, chaperones]
Probab=21.04 E-value=2.5e+02 Score=21.21 Aligned_cols=23 Identities=17% Similarity=0.224 Sum_probs=18.8
Q ss_pred cCchhHHHHHHHHHHHHHHHHhc
Q psy2601 53 YNSAKVSTYVSQVVETIMANLIK 75 (132)
Q Consensus 53 Y~~~~~~~~~~~I~~~I~~~lk~ 75 (132)
=+.+.+..|.-++=+.+.++|++
T Consensus 141 ~SRea~~~W~CevHN~VNekL~K 163 (181)
T COG5054 141 SSREAATTWACEVHNKVNEKLGK 163 (181)
T ss_pred ccHHHHHHHHHHHHHHHHHHhCC
Confidence 34577889999999999999986
No 47
>COG1480 Predicted membrane-associated HD superfamily hydrolase [General function prediction only]
Probab=21.00 E-value=1.5e+02 Score=26.98 Aligned_cols=48 Identities=6% Similarity=0.162 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHHHHHHHhhhCCCCcCchh-HHHHHHHHHHHHHHHHhcc
Q psy2601 29 SKFAVDEISCIIKEAIEDCIGGNTYNSAK-VSTYVSQVVETIMANLIKL 76 (132)
Q Consensus 29 ~~F~~~~v~~ii~~vl~~~L~~~~Y~~~~-~~~~~~~I~~~I~~~lk~l 76 (132)
+.-++++++++|+.+++..|++.+.+... .-+=...|++...+-|+.+
T Consensus 637 ~~p~~~ki~~~v~~II~~rl~DgQl~~s~lT~~El~~I~~~fv~tl~g~ 685 (700)
T COG1480 637 KEPNPEKIEEMVDKIIQARLQDGQLSESGLTLKELEIIADSFVQTLQGI 685 (700)
T ss_pred cCCCHHHHHHHHHHHHHHHHhcCCccccCCcHHHHHHHHHHHHHHHHHH
Confidence 34689999999999999999998877522 2222334555555555544
No 48
>PRK04057 30S ribosomal protein S3Ae; Validated
Probab=20.73 E-value=3e+02 Score=21.05 Aligned_cols=60 Identities=15% Similarity=0.134 Sum_probs=44.8
Q ss_pred CHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhccC-CCceEEEEEEEEEe
Q psy2601 32 AVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLD-KPFKYVVNGTVMQK 91 (132)
Q Consensus 32 ~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~-~ryK~vV~v~I~qk 91 (132)
....|+++|.++|.+...+..++.---.-....|+.+|..+.+++- -|.=+|--+-+...
T Consensus 126 q~~~IRk~m~~~i~~~~~~~~~~e~V~~~i~g~i~~eI~~~~k~IyPlr~veIrKvkvl~~ 186 (203)
T PRK04057 126 QKHAIRKIMEEIIEEKASELTFEEFVQEIVFGKLASEIYKEAKKIYPLRRVEIRKSKVLAR 186 (203)
T ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHccchHHHHHHHhhhhccCcceEEEEEEEEEec
Confidence 4568999999999999998777655444556678889999999887 45555666666654
No 49
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=20.71 E-value=1.8e+02 Score=16.50 Aligned_cols=15 Identities=13% Similarity=0.295 Sum_probs=10.1
Q ss_pred CCHHHHHHHHHHHHH
Q psy2601 31 FAVDEISCIIKEAIE 45 (132)
Q Consensus 31 F~~~~v~~ii~~vl~ 45 (132)
|...+++++++++..
T Consensus 15 y~~~e~~~av~~~~~ 29 (47)
T PF07499_consen 15 YSKAEAQKAVSKLLE 29 (47)
T ss_dssp S-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhhc
Confidence 667777777777765
No 50
>PRK07718 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=20.68 E-value=3.2e+02 Score=19.33 Aligned_cols=51 Identities=14% Similarity=0.058 Sum_probs=34.6
Q ss_pred HHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhccCCCceEEEEEEEEE
Q psy2601 39 IIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLDKPFKYVVNGTVMQ 90 (132)
Q Consensus 39 ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l~~ryK~vV~v~I~q 90 (132)
.|++.+-..|.+.+++.-..++=-..+-++|+++++..-.+-+ |..|.+.+
T Consensus 88 ~Ird~ii~~L~~~~~~~l~~~~G~~~Lr~el~~~in~~l~~g~-V~~Vyft~ 138 (142)
T PRK07718 88 QVKNIIIEELADMNAEDFKGKKGLEALKEQLKEKINNLMQEGK-VEKVYITS 138 (142)
T ss_pred hhHHHHHHHHHcCCHHHhcChhHHHHHHHHHHHHHHHhhccCc-eEEEEEEe
Confidence 7888999999999887766555566777788888865432112 55555443
No 51
>KOG3355|consensus
Probab=20.31 E-value=2.4e+02 Score=21.25 Aligned_cols=57 Identities=14% Similarity=0.201 Sum_probs=35.7
Q ss_pred cCCCCCCCCCCC-------------CCHHHHHHHHHHHHHhhhCCCCcCchhHHHHHHHHHHHHHHHHhcc
Q psy2601 19 TAAPGGTTEDSK-------------FAVDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKL 76 (132)
Q Consensus 19 nty~~~p~~~~~-------------F~~~~v~~ii~~vl~~~L~~~~Y~~~~~~~~~~~I~~~I~~~lk~l 76 (132)
-.||.+|+++++ ++-.+-..=.++.|++.- -+.=+.+...+|.-.+=+.+.++|.+.
T Consensus 86 A~yP~~PT~eqk~~~~sFi~~~s~~yPC~eCa~dl~K~l~~np-pq~~SRe~~~~W~C~vHN~VNekLgKp 155 (177)
T KOG3355|consen 86 ANYPDRPTPEQKDDMRSFIHLFSKFYPCGECAKDLRKILRKNP-PQTSSREAFTQWLCHVHNKVNEKLGKP 155 (177)
T ss_pred HhCCCCCChHHHHHHHHHHHHhhhhcchHHHHHHHHHHHHhCC-CCcchHHHHHHHHHHHHHHHHHHcCCC
Confidence 368888886543 344444444444444411 123345678899999999999998874
No 52
>KOG2841|consensus
Probab=20.12 E-value=1.2e+02 Score=24.15 Aligned_cols=26 Identities=23% Similarity=0.180 Sum_probs=22.2
Q ss_pred HHHHHHHHhccCCCceEEEEEEEEEe
Q psy2601 66 VETIMANLIKLDKPFKYVVNGTVMQK 91 (132)
Q Consensus 66 ~~~I~~~lk~l~~ryK~vV~v~I~qk 91 (132)
-+.|..||+.+++|||..|.+..+.-
T Consensus 108 pdYi~~Ri~~l~k~yk~~VLl~~vd~ 133 (254)
T KOG2841|consen 108 PDYIYRRIRKLGKNYKLRVLLVHVDM 133 (254)
T ss_pred cHHHHHHHHHhcccccceEEEEEecC
Confidence 47899999999999999988877753
Done!