Query 037682
Match_columns 397
No_of_seqs 75 out of 77
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 03:22:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037682.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037682hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09346 SMI1_KNR4: SMI1 / KNR 96.9 0.00074 1.6E-08 54.4 3.0 28 65-92 1-28 (130)
2 smart00860 SMI1_KNR4 SMI1 / KN 96.8 0.0013 2.8E-08 51.3 3.5 28 65-92 1-28 (129)
3 PF14567 SUKH_5: SMI1-KNR4 cel 96.1 0.0059 1.3E-07 54.6 3.6 44 49-92 2-48 (132)
4 PF14568 SUKH_6: SMI1-KNR4 cel 95.4 0.012 2.6E-07 47.9 2.7 25 68-92 1-25 (120)
5 COG4282 SMI1 Protein involved 92.1 0.2 4.3E-06 47.3 4.4 40 57-96 24-65 (191)
6 PF14433 SUKH-3: SUKH-3 immuni 70.1 50 0.0011 28.8 9.6 130 49-205 2-137 (142)
7 TIGR01926 peroxid_rel uncharac 55.7 30 0.00064 30.7 5.6 67 291-363 80-154 (177)
8 PF13560 HTH_31: Helix-turn-he 55.2 11 0.00024 28.4 2.5 46 344-389 5-52 (64)
9 PF13340 DUF4096: Putative tra 53.8 31 0.00067 27.3 4.9 57 66-128 1-73 (75)
10 PHA02591 hypothetical protein; 49.1 16 0.00034 31.0 2.6 24 345-368 51-74 (83)
11 PRK06130 3-hydroxybutyryl-CoA 47.2 46 0.001 32.2 5.9 47 81-129 257-306 (311)
12 PF00356 LacI: Bacterial regul 46.2 15 0.00032 27.4 1.8 36 349-394 6-41 (46)
13 PF13271 DUF4062: Domain of un 43.8 26 0.00056 28.2 3.0 48 127-174 21-68 (83)
14 TIGR02607 antidote_HigA addict 41.5 32 0.00068 26.4 3.1 47 343-389 7-55 (78)
15 PF14399 Transpep_BrtH: NlpC/p 40.6 59 0.0013 31.2 5.4 121 45-196 1-122 (317)
16 PHA00542 putative Cro-like pro 40.2 44 0.00095 27.1 3.9 50 345-394 23-74 (82)
17 PF01381 HTH_3: Helix-turn-hel 39.9 19 0.00041 25.9 1.5 43 348-390 4-47 (55)
18 cd08779 Death_PIDD Death Domai 38.7 26 0.00055 28.9 2.3 27 64-94 23-49 (86)
19 TIGR02293 TAS_TIGR02293 putati 37.4 33 0.00071 30.2 2.9 52 344-395 27-79 (133)
20 TIGR03070 couple_hipB transcri 36.9 64 0.0014 22.7 3.9 45 344-388 6-51 (58)
21 PF13559 DUF4129: Domain of un 35.0 54 0.0012 24.6 3.4 26 48-73 3-28 (72)
22 PF13551 HTH_29: Winged helix- 34.9 74 0.0016 25.5 4.4 46 348-393 6-72 (112)
23 cd08313 Death_TNFR1 Death doma 33.7 41 0.0009 27.8 2.8 15 65-79 22-36 (80)
24 TIGR00180 parB_part ParB-like 33.2 28 0.00061 31.9 1.9 41 349-389 116-156 (187)
25 PRK13832 plasmid partitioning 32.5 37 0.0008 37.1 2.9 40 349-388 114-153 (520)
26 smart00354 HTH_LACI helix_turn 32.2 85 0.0019 24.4 4.2 36 349-394 7-42 (70)
27 PF11922 DUF3440: Domain of un 31.6 26 0.00057 33.5 1.5 75 64-147 102-178 (181)
28 PF11203 DUF2984: Protein of u 29.8 65 0.0014 27.3 3.4 49 45-106 38-88 (98)
29 smart00530 HTH_XRE Helix-turn- 29.8 61 0.0013 21.1 2.7 45 345-389 2-47 (56)
30 PF02954 HTH_8: Bacterial regu 29.4 72 0.0016 22.7 3.1 27 341-367 6-32 (42)
31 PF01503 PRA-PH: Phosphoribosy 28.6 1.4E+02 0.003 24.1 5.0 47 308-363 33-79 (83)
32 PF00690 Cation_ATPase_N: Cati 28.1 65 0.0014 24.7 2.9 26 55-80 10-35 (69)
33 KOG2264 Exostosin EXT1L [Signa 28.0 55 0.0012 36.7 3.3 31 174-205 190-220 (907)
34 PF02536 mTERF: mTERF; InterP 27.9 82 0.0018 30.7 4.2 72 293-364 175-265 (345)
35 PF04255 DUF433: Protein of un 27.1 55 0.0012 24.8 2.3 23 341-364 20-42 (56)
36 PF14980 TIP39: TIP39 peptide 25.9 19 0.00042 27.9 -0.4 12 285-296 35-46 (51)
37 cd04765 HTH_MlrA-like_sg2 Heli 25.8 1.4E+02 0.0031 25.0 4.8 47 292-345 46-92 (99)
38 PF05687 DUF822: Plant protein 25.3 33 0.00071 32.0 0.9 27 328-368 44-70 (150)
39 PF13011 LZ_Tnp_IS481: leucine 25.2 2E+02 0.0043 24.5 5.4 46 345-390 17-82 (85)
40 PRK11050 manganese transport r 25.2 4.5E+02 0.0097 23.5 8.1 93 289-391 35-146 (152)
41 PF07128 DUF1380: Protein of u 24.7 1.2E+02 0.0026 28.0 4.4 77 305-394 27-104 (139)
42 PF13384 HTH_23: Homeodomain-l 24.7 49 0.0011 23.5 1.6 18 350-367 14-31 (50)
43 TIGR01124 ilvA_2Cterm threonin 23.9 49 0.0011 35.4 2.0 51 40-91 366-438 (499)
44 PRK12449 acyl carrier protein; 23.6 54 0.0012 25.7 1.7 16 71-86 46-61 (80)
45 PRK08269 3-hydroxybutyryl-CoA 23.4 1.7E+02 0.0036 29.3 5.5 32 83-116 259-293 (314)
46 COG4174 ABC-type uncharacteriz 23.2 95 0.0021 32.1 3.7 101 61-203 75-185 (364)
47 PRK05087 D-alanine--poly(phosp 23.2 53 0.0012 26.7 1.7 16 71-86 43-58 (78)
48 PHA01976 helix-turn-helix prot 23.0 1.1E+02 0.0023 22.9 3.2 46 343-388 5-51 (67)
49 PRK13890 conjugal transfer pro 22.8 99 0.0021 26.9 3.4 46 343-389 8-55 (120)
50 PRK07081 acyl carrier protein; 22.4 57 0.0012 26.5 1.7 16 71-86 42-57 (83)
51 COG4451 RbcS Ribulose bisphosp 22.1 2.4E+02 0.0051 25.8 5.6 66 60-160 13-81 (127)
52 cd08503 PBP2_NikA_DppA_OppA_li 21.9 2E+02 0.0043 29.1 5.8 34 145-178 424-458 (460)
53 PF05997 Nop52: Nucleolar prot 21.9 1.3E+02 0.0027 28.8 4.2 62 289-356 110-172 (217)
54 COG3563 KpsC Capsule polysacch 21.7 1.2E+02 0.0026 33.6 4.4 62 137-203 37-100 (671)
55 smart00352 POU Found in Pit-Oc 21.6 3E+02 0.0065 23.0 5.7 42 341-390 12-53 (75)
56 PF02796 HTH_7: Helix-turn-hel 21.4 69 0.0015 23.1 1.8 20 347-366 15-34 (45)
57 PRK13866 plasmid partitioning 21.1 64 0.0014 33.4 2.1 44 345-388 171-215 (336)
58 PF04760 IF2_N: Translation in 20.9 37 0.00081 25.2 0.3 34 48-81 17-54 (54)
59 PF08535 KorB: KorB domain; I 20.9 32 0.00068 28.2 -0.1 37 352-388 2-38 (93)
60 TIGR02297 HpaA 4-hydroxyphenyl 20.7 1.3E+02 0.0029 28.2 4.0 71 290-366 189-264 (287)
61 TIGR00517 acyl_carrier acyl ca 20.6 67 0.0015 25.0 1.7 15 72-86 45-59 (77)
62 PRK07639 acyl carrier protein; 20.5 63 0.0014 26.5 1.6 16 71-86 47-62 (86)
63 COG1813 Predicted transcriptio 20.0 62 0.0014 30.5 1.6 43 347-390 86-130 (165)
No 1
>PF09346 SMI1_KNR4: SMI1 / KNR4 family (SUKH-1); InterPro: IPR018958 Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation [, ]. Yeast members of this family are involved in the regulation of cell wall assembly. Saccharomyces cerevisiae (Baker's yeast) protein KNR4 (SMI1) has a regulatory role in chitin deposition and in cell wall assembly []. It was originally identified as a regulator of chitin synthase expression (acting as a repressor) [] and of 1,3-beta-glucan synthase levels []. It was shown to localise in patches at presumptive bud sites in unbudded cells and at the incipient bud site during bud emergence []. KNR4 is believed to connect the PKC1-SLT2 MAPK pathway with cell proliferation. It has been shown to interact with BCK2, a gene involved in cell cycle progression in S. cerevisiae (forming a complex) to allow PKC1 to coordinate the cell cycle (cell proliferation) with cell wall integrity [, ]. PKC1 plays an essential role in cell wall integrity and cell proliferation through a bifurcated PKC1/mitogen-activated protein (MAP) kinase pathway. KNR4 also interacts with the tyrosine-tRNA synthetase protein encoded by TYS1 and is involved in sporulation process []. Note: previously reported evidence that KNR4 may interact with nuclear matrix-association region [] may be due to an artefact [].; PDB: 3D5P_A 2ICG_A.
Probab=96.90 E-value=0.00074 Score=54.44 Aligned_cols=28 Identities=21% Similarity=0.452 Sum_probs=20.9
Q ss_pred CCCHHHHHHHHHHcCCCCChhHHHHHHc
Q 037682 65 GLSDAEFARAEAEFGFVFPPDLRAILSA 92 (397)
Q Consensus 65 GLSD~Ef~~IEa~fgF~FPpDlRa~L~~ 92 (397)
++|++||+.+|+++|++||+|+|.||+.
T Consensus 1 p~t~~~I~~~E~~lg~~LP~~yk~fl~~ 28 (130)
T PF09346_consen 1 PATEEEIQELEEKLGVRLPDDYKEFLKE 28 (130)
T ss_dssp ---HHHHHHHHHHHTS---HHHHHHHH-
T ss_pred CCCHHHHHHHHHHhCCCCcHHHHHHHHh
Confidence 5899999999999999999999999995
No 2
>smart00860 SMI1_KNR4 SMI1 / KNR4 family. Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation.
Probab=96.81 E-value=0.0013 Score=51.27 Aligned_cols=28 Identities=29% Similarity=0.463 Sum_probs=26.7
Q ss_pred CCCHHHHHHHHHHcCCCCChhHHHHHHc
Q 037682 65 GLSDAEFARAEAEFGFVFPPDLRAILSA 92 (397)
Q Consensus 65 GLSD~Ef~~IEa~fgF~FPpDlRa~L~~ 92 (397)
|+|++||..+|+.+|++||+|+|.||+.
T Consensus 1 ~~s~~~i~~~e~~lg~~LP~~y~~f~~~ 28 (129)
T smart00860 1 PASEEEIAELEKKLGIKLPEDYKEFLLL 28 (129)
T ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence 5799999999999999999999999996
No 3
>PF14567 SUKH_5: SMI1-KNR4 cell-wall; PDB: 2PAG_A.
Probab=96.06 E-value=0.0059 Score=54.65 Aligned_cols=44 Identities=23% Similarity=0.450 Sum_probs=29.6
Q ss_pred HHHHHHHhhCC--CccCCC-CCHHHHHHHHHHcCCCCChhHHHHHHc
Q 037682 49 DKVITHLKNSG--IRVQPG-LSDAEFARAEAEFGFVFPPDLRAILSA 92 (397)
Q Consensus 49 ~~vi~~L~~~G--V~i~pG-LSD~Ef~~IEa~fgF~FPpDlRa~L~~ 92 (397)
..+|+.|++.+ ++..-+ =|+++|..+|+..||.||+|+|+||..
T Consensus 2 ~~~i~~L~~~~e~~~~~l~lpd~e~I~~~Ee~L~i~lP~eyk~fL~~ 48 (132)
T PF14567_consen 2 EDIIERLKELNEPVPVPLELPDDEQIVEAEEQLGISLPEEYKEFLLE 48 (132)
T ss_dssp HHHHHHHHHH----SS------HHHHHHHHHHHT----HHHHHHHHH
T ss_pred hHHHHHHHHhcCCccCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence 46899999954 444433 589999999999999999999999986
No 4
>PF14568 SUKH_6: SMI1-KNR4 cell-wall; PDB: 2PRV_A.
Probab=95.40 E-value=0.012 Score=47.86 Aligned_cols=25 Identities=28% Similarity=0.575 Sum_probs=20.2
Q ss_pred HHHHHHHHHHcCCCCChhHHHHHHc
Q 037682 68 DAEFARAEAEFGFVFPPDLRAILSA 92 (397)
Q Consensus 68 D~Ef~~IEa~fgF~FPpDlRa~L~~ 92 (397)
|+||..+|+++|++||.|+|.||.+
T Consensus 1 ee~I~~~E~~Lg~~lP~~Yk~fL~~ 25 (120)
T PF14568_consen 1 EEEIEEAEKKLGVKLPEDYKEFLKE 25 (120)
T ss_dssp -HHHHHHHHHHTS---HHHHHHHHH
T ss_pred ChHHHHHHHHhCCCCCHHHHHHHHH
Confidence 6899999999999999999999996
No 5
>COG4282 SMI1 Protein involved in beta-1,3-glucan synthesis [Carbohydrate transport and metabolism]
Probab=92.15 E-value=0.2 Score=47.30 Aligned_cols=40 Identities=35% Similarity=0.577 Sum_probs=35.3
Q ss_pred hCCCccCCCCCHHHHHHHHHHcCCCCChhHHHHHHc--cCCC
Q 037682 57 NSGIRVQPGLSDAEFARAEAEFGFVFPPDLRAILSA--GLPL 96 (397)
Q Consensus 57 ~~GV~i~pGLSD~Ef~~IEa~fgF~FPpDlRa~L~~--GLPv 96 (397)
..-..+.||-|-..|+++|+.||.+||||.|+.|+. |-|-
T Consensus 24 dl~~~l~pgat~~di~~aE~dlg~tlPpdvResl~iHDGq~d 65 (191)
T COG4282 24 DLLPFLRPGATCGDIQRAEADLGRTLPPDVRESLAIHDGQPD 65 (191)
T ss_pred ccccccCCCccHHHHHHHHHHhcCcCChHHHHHHHhhCCCcC
Confidence 344789999999999999999999999999999986 6663
No 6
>PF14433 SUKH-3: SUKH-3 immunity protein
Probab=70.07 E-value=50 Score=28.81 Aligned_cols=130 Identities=21% Similarity=0.338 Sum_probs=72.7
Q ss_pred HHHHHHHhhCCCccCCCCCHHHHHHHHHHcCCCCChhHHHHHHc--cCCCCCCCCCCCCCcccHHHHHHhhcchhhHHHH
Q 037682 49 DKVITHLKNSGIRVQPGLSDAEFARAEAEFGFVFPPDLRAILSA--GLPLGPGFPDWRATGSARLHLRASLDLPIAAITF 126 (397)
Q Consensus 49 ~~vi~~L~~~GV~i~pGLSD~Ef~~IEa~fgF~FPpDlRa~L~~--GLPvG~gFPdWR~~~~~~~~Lr~~L~~P~~gil~ 126 (397)
++|++.|+++|-.=..-...+.+...=+..|+...|..+.||++ ||-+....|.-+...+..-.+ -|..+...
T Consensus 2 ~~v~~~L~~aGW~~~R~idi~~~~~~~~~~g~~~~paa~~fL~efGgL~i~~~~~~~~~~~~~~~~~-----~P~~~~~~ 76 (142)
T PF14433_consen 2 EKVIELLRAAGWYEGRKIDISLWEKILEEEGYPVFPAAVEFLAEFGGLRINPSGPYGRQDAPSDFDF-----DPLEALGI 76 (142)
T ss_pred HHHHHHHHHcCCCCCcccCHHHHHHHHHhcCCCCCHHHHHHHHHcCCeEEeccCccccccCCceEEe-----Chhhhccc
Confidence 57899999999553333334445544444599999999999997 888876666211110000000 11111100
Q ss_pred HHHhhcccccCCCCCCCCHHHHHHHHHHhhhcCCceeeec----ccccccCCCCCCCCCeEEEeCCceEEEcCchhHHHH
Q 037682 127 QIARNALWSKSWGPRPSDPEKALRVARNALKRAPLLIPIF----NHCYIPCNPTLAGNPIFYVDENRIFCCGLDLSDFFE 202 (397)
Q Consensus 127 ~V~~n~fW~~sWG~RP~~~~eal~~Ar~~l~~aP~LVPIy----gHRYlPs~p~~aGnPVfSV~~tDIi~yG~DLadyf~ 202 (397)
...+.+..-.+.+ -=.|+||= +|-.|-.. .-.=||.++++...++|.|+-+.|.
T Consensus 77 -----------------~~~~~~~~~~~~~--~~~l~PiG~~~~~~~~l~id---e~Grvy~~~~~~~~~lG~~~~~al~ 134 (142)
T PF14433_consen 77 -----------------HDAETLAELEEAL--GTKLFPIGEEHDGHAILAID---ESGRVYGLDDTGLWYLGDDIDEALE 134 (142)
T ss_pred -----------------chHHHHHHHHHHh--CCcEEEEEEecCCCEEEEEe---CCCCEEEecCCeeEEeCCCHHHHHH
Confidence 0011111111112 23588872 33333333 2355888888889999999999887
Q ss_pred Hhh
Q 037682 203 RES 205 (397)
Q Consensus 203 rEf 205 (397)
+-.
T Consensus 135 ~Li 137 (142)
T PF14433_consen 135 NLI 137 (142)
T ss_pred HHH
Confidence 765
No 7
>TIGR01926 peroxid_rel uncharacterized peroxidase-related enzyme. This protein family with length of about 200 amino acids. One member, from Myxococcus xanthus, is a selenoprotein, with an otherwise conserved Cys replaced by Sec. This family is drawn narrowly enough to suggest that These proteins contain a domain described by TIGR00778, with a CxxCxxxHxxxxxxxG motif. Some members of that family are known to act as peroxidases or correlate with resistance to oxidative stress.
Probab=55.71 E-value=30 Score=30.71 Aligned_cols=67 Identities=15% Similarity=0.153 Sum_probs=39.5
Q ss_pred HHHHHHHHHHhhCCCCCchhhhhhhccCCCCcCccccccchHHHH----HHHHHHHHHhhH----HHHhcCCChHHHhHh
Q 037682 291 DYMGQIGSVLREGGWSEPDIVEIVTVSASGFFEGEMVMLDNQSVL----DGLLLKADRLSE----SLRKSGWSSEEVSDA 362 (397)
Q Consensus 291 ~yl~~~~~~LR~GGW~e~di~Em~~~~~~~~~~ge~~~~d~~avl----~~L~~~~d~~s~----sL~raGWs~edV~ea 362 (397)
-|++.=...+++.|-++++|+.+-....+..|+ +.+.++ +++..+-...++ .|+++|||-++|+|.
T Consensus 80 yc~~~H~~~~~~~g~~~~~~~ai~~~~~~~~~~------~~e~a~l~~a~~~~~~~~~v~~~~~~~l~~~g~s~~eivel 153 (177)
T TIGR01926 80 YCAAVHGAALRQLSGDPDLADAVAVNFRDADLS------PRERAMLDFAVKLTATPAKVNEADFAALRAAGFSDLDILDL 153 (177)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHhCcccCCCC------HHHHHHHHHHHHHhhCcccCCHHHHHHHHHcCCCHHHHHHH
Confidence 566666678888888888887766433222222 122221 222222223333 588999999999986
Q ss_pred h
Q 037682 363 F 363 (397)
Q Consensus 363 l 363 (397)
.
T Consensus 154 ~ 154 (177)
T TIGR01926 154 I 154 (177)
T ss_pred H
Confidence 5
No 8
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=55.15 E-value=11 Score=28.41 Aligned_cols=46 Identities=24% Similarity=0.446 Sum_probs=29.0
Q ss_pred HhhHHHHhcCCChHHHhHhhcCCCCCcc--ccCCcccCCHHHHHHHHH
Q 037682 344 RLSESLRKSGWSSEEVSDAFGFDFRPEK--ERKPAKKLSPELVERIGK 389 (397)
Q Consensus 344 ~~s~sL~raGWs~edV~eal~~d~~~~~--e~~~~~~~~p~~~~~i~~ 389 (397)
++...-+++|||.++|++.+|..-..-. |+....+.+++.+.+|-+
T Consensus 5 ~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~ 52 (64)
T PF13560_consen 5 RLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLAR 52 (64)
T ss_dssp HHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHH
Confidence 3444556789999999999998765544 333333677777766644
No 9
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=53.84 E-value=31 Score=27.27 Aligned_cols=57 Identities=28% Similarity=0.338 Sum_probs=38.7
Q ss_pred CCHHHHHHHHHHcCCCCCh------hHHHHHHccCCC----------CCCCCCCCCCcccHHHHHHhhcchhhHHHHHH
Q 037682 66 LSDAEFARAEAEFGFVFPP------DLRAILSAGLPL----------GPGFPDWRATGSARLHLRASLDLPIAAITFQI 128 (397)
Q Consensus 66 LSD~Ef~~IEa~fgF~FPp------DlRa~L~~GLPv----------G~gFPdWR~~~~~~~~Lr~~L~~P~~gil~~V 128 (397)
|||+|.+.||..|--.-+. |+|.++.+-|=+ ...|++|.+- ....+. |--.|+...|
T Consensus 1 lsD~~W~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg~~~tv---~~~f~r---W~~~G~~~~l 73 (75)
T PF13340_consen 1 LSDEEWALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFGPWSTV---YRRFRR---WSRSGVWERL 73 (75)
T ss_pred CCHHHHHHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhccCcCcH---HHHHHH---HHHcCHHHHH
Confidence 7999999999999866665 899988753322 2568888874 444443 4445555444
No 10
>PHA02591 hypothetical protein; Provisional
Probab=49.14 E-value=16 Score=31.01 Aligned_cols=24 Identities=21% Similarity=0.599 Sum_probs=20.8
Q ss_pred hhHHHHhcCCChHHHhHhhcCCCC
Q 037682 345 LSESLRKSGWSSEEVSDAFGFDFR 368 (397)
Q Consensus 345 ~s~sL~raGWs~edV~eal~~d~~ 368 (397)
+...|++-|+|.++||+.||.+..
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqe 74 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVR 74 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHH
Confidence 456799999999999999998754
No 11
>PRK06130 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=47.21 E-value=46 Score=32.20 Aligned_cols=47 Identities=21% Similarity=0.321 Sum_probs=34.9
Q ss_pred CCChhHHHHHHc---cCCCCCCCCCCCCCcccHHHHHHhhcchhhHHHHHHH
Q 037682 81 VFPPDLRAILSA---GLPLGPGFPDWRATGSARLHLRASLDLPIAAITFQIA 129 (397)
Q Consensus 81 ~FPpDlRa~L~~---GLPvG~gFPdWR~~~~~~~~Lr~~L~~P~~gil~~V~ 129 (397)
..++-++..+.. |.-.|.|||+|.+. .+++++..-+..+..++..+.
T Consensus 257 ~~~~~l~~~~~~g~~G~~~g~gfy~y~~~--~~~~~~~~~~~~~~~~~~~~~ 306 (311)
T PRK06130 257 TPSPLLEEKVEAGELGAKSGQGFYAWPPE--RREEVLADKSAALVEVRAWLE 306 (311)
T ss_pred CCCHHHHHHHHcCCccccCCCcCccCCCC--CHHHHHHHHHHHHHHHHHHhh
Confidence 345556776654 66888999999876 688888888887777776554
No 12
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=46.22 E-value=15 Score=27.35 Aligned_cols=36 Identities=33% Similarity=0.334 Sum_probs=27.1
Q ss_pred HHhcCCChHHHhHhhcCCCCCccccCCcccCCHHHHHHHHHHHhhh
Q 037682 349 LRKSGWSSEEVSDAFGFDFRPEKERKPAKKLSPELVERIGKLAESV 394 (397)
Q Consensus 349 L~raGWs~edV~eal~~d~~~~~e~~~~~~~~p~~~~~i~~la~~v 394 (397)
=+.+|-|.--||-+|+-. ..++++..+||.+.|+.+
T Consensus 6 A~~agvS~~TVSr~ln~~----------~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 6 AREAGVSKSTVSRVLNGP----------PRVSEETRERILEAAEEL 41 (46)
T ss_dssp HHHHTSSHHHHHHHHTTC----------SSSTHHHHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHhCC----------CCCCHHHHHHHHHHHHHH
Confidence 356677777777776532 589999999999999864
No 13
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=43.78 E-value=26 Score=28.19 Aligned_cols=48 Identities=15% Similarity=0.171 Sum_probs=35.3
Q ss_pred HHHhhcccccCCCCCCCCHHHHHHHHHHhhhcCCceeeecccccccCC
Q 037682 127 QIARNALWSKSWGPRPSDPEKALRVARNALKRAPLLIPIFNHCYIPCN 174 (397)
Q Consensus 127 ~V~~n~fW~~sWG~RP~~~~eal~~Ar~~l~~aP~LVPIygHRYlPs~ 174 (397)
.|....+.+..+..-|++....+....+.++++..+|=|+|+||=-..
T Consensus 21 ~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~~ 68 (83)
T PF13271_consen 21 AIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSVP 68 (83)
T ss_pred HHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCCC
Confidence 334444555444445767777788999999999999999999995443
No 14
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=41.52 E-value=32 Score=26.44 Aligned_cols=47 Identities=19% Similarity=0.279 Sum_probs=32.6
Q ss_pred HHhh-HHHHhcCCChHHHhHhhcCCCCCcccc-CCcccCCHHHHHHHHH
Q 037682 343 DRLS-ESLRKSGWSSEEVSDAFGFDFRPEKER-KPAKKLSPELVERIGK 389 (397)
Q Consensus 343 d~~s-~sL~raGWs~edV~eal~~d~~~~~e~-~~~~~~~p~~~~~i~~ 389 (397)
+++. .-+.+.|++.+|+++.+|..-..-..- .-..+++++.+.+|.+
T Consensus 7 ~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~ 55 (78)
T TIGR02607 7 EILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAK 55 (78)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 4566 568899999999999999765443321 2224678887776655
No 15
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=40.61 E-value=59 Score=31.22 Aligned_cols=121 Identities=19% Similarity=0.290 Sum_probs=71.1
Q ss_pred cccHHHHHHHHhhCCCccCCCCCHHHHHHHHHHcCCCCChhHHHHHHccCCCCCCCCCCCCCcccHHHHHHhhcchhhHH
Q 037682 45 SSLADKVITHLKNSGIRVQPGLSDAEFARAEAEFGFVFPPDLRAILSAGLPLGPGFPDWRATGSARLHLRASLDLPIAAI 124 (397)
Q Consensus 45 ~~~~~~vi~~L~~~GV~i~pGLSD~Ef~~IEa~fgF~FPpDlRa~L~~GLPvG~gFPdWR~~~~~~~~Lr~~L~~P~~gi 124 (397)
+|+...+.+.|...|+.+ |+.=+--+-.-+||.+=+ ....+-. .+.+-|..-.-.+.+...+++.+.
T Consensus 1 hC~~~~l~~ll~~~g~~~----~e~l~fglg~g~gf~y~~------~~~~~~~-~~~~~r~~~~~~~~~~~~lG~~~~-- 67 (317)
T PF14399_consen 1 HCESNALRDLLAHYGLPL----SEALIFGLGSGLGFSYLP------FPDSNPP-PLLGGRSPPDFEENLLERLGIKYE-- 67 (317)
T ss_pred CchhHHHHHHHHhcCCCC----CHHHHHHHcCCcceEEEe------ccccCCC-eeecCCCchHHHHHHHHHCCceEE--
Confidence 477888999999999887 565555566777766433 0000000 122222210024445555555443
Q ss_pred HHHHHhhcccccCCCCCCCCHHHHHHHHHHhhhcC-CceeeecccccccCCCCCCCCCeEEEeCCceEEEcCc
Q 037682 125 TFQIARNALWSKSWGPRPSDPEKALRVARNALKRA-PLLIPIFNHCYIPCNPTLAGNPIFYVDENRIFCCGLD 196 (397)
Q Consensus 125 l~~V~~n~fW~~sWG~RP~~~~eal~~Ar~~l~~a-P~LVPIygHRYlPs~p~~aGnPVfSV~~tDIi~yG~D 196 (397)
| ..-.++++++...++.|.+- |++|- ..--|||=.|.-. -.....-.|++||.|
T Consensus 68 ---------~-----~~~~~~~~~~~~l~~~l~~g~pv~~~-~D~~~lpy~~~~~---~~~~~~H~i~v~G~d 122 (317)
T PF14399_consen 68 ---------W-----REFSSPDEAWEELKEALDAGRPVIVW-VDMYYLPYRPNYY---KKHHADHYIVVYGYD 122 (317)
T ss_pred ---------E-----EecCCHHHHHHHHHHHHhCCCceEEE-eccccCCCCcccc---ccccCCcEEEEEEEe
Confidence 0 12357899999999999988 99998 7888888766521 011123466667766
No 16
>PHA00542 putative Cro-like protein
Probab=40.16 E-value=44 Score=27.11 Aligned_cols=50 Identities=24% Similarity=0.331 Sum_probs=35.1
Q ss_pred hhHHHHhcCCChHHHhHhhcCCCCCccc--cCCcccCCHHHHHHHHHHHhhh
Q 037682 345 LSESLRKSGWSSEEVSDAFGFDFRPEKE--RKPAKKLSPELVERIGKLAESV 394 (397)
Q Consensus 345 ~s~sL~raGWs~edV~eal~~d~~~~~e--~~~~~~~~p~~~~~i~~la~~v 394 (397)
+-..|.+.|||..|+++.+|..-..-.+ ....+..+++.+++|-++..-|
T Consensus 23 l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~~~~ 74 (82)
T PHA00542 23 LVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLVLNL 74 (82)
T ss_pred HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHHHh
Confidence 3345678999999999999986554433 2333457888888887776554
No 17
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=39.93 E-value=19 Score=25.91 Aligned_cols=43 Identities=16% Similarity=0.263 Sum_probs=29.4
Q ss_pred HHHhcCCChHHHhHhhcCCCCCcccc-CCcccCCHHHHHHHHHH
Q 037682 348 SLRKSGWSSEEVSDAFGFDFRPEKER-KPAKKLSPELVERIGKL 390 (397)
Q Consensus 348 sL~raGWs~edV~eal~~d~~~~~e~-~~~~~~~p~~~~~i~~l 390 (397)
-+.+.|+|..|+++.+|..-+.-..- +-...++++.+.+|.+.
T Consensus 4 ~r~~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~ 47 (55)
T PF01381_consen 4 LRKEKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKA 47 (55)
T ss_dssp HHHHTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHH
Confidence 35688999999999999665544332 33566888888877654
No 18
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=38.72 E-value=26 Score=28.94 Aligned_cols=27 Identities=30% Similarity=0.228 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHHHHcCCCCChhHHHHHHccC
Q 037682 64 PGLSDAEFARAEAEFGFVFPPDLRAILSAGL 94 (397)
Q Consensus 64 pGLSD~Ef~~IEa~fgF~FPpDlRa~L~~GL 94 (397)
=|||+.+|+.||..| |.|++.--..+|
T Consensus 23 LGlse~~Id~Ie~~~----~~dl~eq~~~mL 49 (86)
T cd08779 23 LGLSYRELQRIKYNN----RDDLDEQIFDML 49 (86)
T ss_pred cCCCHHHHHHHHHHC----ccCHHHHHHHHH
Confidence 389999999999998 566665544444
No 19
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=37.42 E-value=33 Score=30.23 Aligned_cols=52 Identities=21% Similarity=0.215 Sum_probs=38.7
Q ss_pred HhhHHHHhcCCChHHHhHhhcCCCCCccccCC-cccCCHHHHHHHHHHHhhhh
Q 037682 344 RLSESLRKSGWSSEEVSDAFGFDFRPEKERKP-AKKLSPELVERIGKLAESVS 395 (397)
Q Consensus 344 ~~s~sL~raGWs~edV~eal~~d~~~~~e~~~-~~~~~p~~~~~i~~la~~v~ 395 (397)
.+..-...-|.|.+|++..||..-+.-++++. ..+|+++.-+|+-+|+.-.+
T Consensus 27 ~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l~ri~~ 79 (133)
T TIGR02293 27 ALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARVARVWK 79 (133)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHHHHHHH
Confidence 33344456689999999999988666555433 35999999999999987554
No 20
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=36.91 E-value=64 Score=22.74 Aligned_cols=45 Identities=13% Similarity=0.181 Sum_probs=26.9
Q ss_pred HhhHHHHhcCCChHHHhHhhcCCCCCcccc-CCcccCCHHHHHHHH
Q 037682 344 RLSESLRKSGWSSEEVSDAFGFDFRPEKER-KPAKKLSPELVERIG 388 (397)
Q Consensus 344 ~~s~sL~raGWs~edV~eal~~d~~~~~e~-~~~~~~~p~~~~~i~ 388 (397)
++-.-..+.|||.+|+++.+|..-..-.+= +.....+.+.+.+|.
T Consensus 6 ~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~g~~~~~~~~~~~i~ 51 (58)
T TIGR03070 6 LVRARRKALGLTQADLADLAGVGLRFIRDVENGKPTVRLDKVLRVL 51 (58)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHH
Confidence 344455678999999999999764443321 112244555544443
No 21
>PF13559 DUF4129: Domain of unknown function (DUF4129)
Probab=34.97 E-value=54 Score=24.59 Aligned_cols=26 Identities=27% Similarity=0.433 Sum_probs=22.2
Q ss_pred HHHHHHHHhhCCCccCCCCCHHHHHH
Q 037682 48 ADKVITHLKNSGIRVQPGLSDAEFAR 73 (397)
Q Consensus 48 ~~~vi~~L~~~GV~i~pGLSD~Ef~~ 73 (397)
-..++.+|+..|++..||.|..|+.+
T Consensus 3 y~~l~~~~~~~g~~~~~~~T~~E~~~ 28 (72)
T PF13559_consen 3 YRALLRLLARRGIPRRPSETPREYAR 28 (72)
T ss_pred HHHHHHHHHHcCCCCCCCcCHHHHHH
Confidence 34677799999999999999999764
No 22
>PF13551 HTH_29: Winged helix-turn helix
Probab=34.88 E-value=74 Score=25.48 Aligned_cols=46 Identities=30% Similarity=0.449 Sum_probs=31.3
Q ss_pred HHHhcCCC-hHHHhHhhcCC------------------CCCcccc--CCcccCCHHHHHHHHHHHhh
Q 037682 348 SLRKSGWS-SEEVSDAFGFD------------------FRPEKER--KPAKKLSPELVERIGKLAES 393 (397)
Q Consensus 348 sL~raGWs-~edV~eal~~d------------------~~~~~e~--~~~~~~~p~~~~~i~~la~~ 393 (397)
.|...|++ ..+|++.||.. +-+.+.+ ++.++|+|+..+.|..+...
T Consensus 6 ~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~ 72 (112)
T PF13551_consen 6 LLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRE 72 (112)
T ss_pred HHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHH
Confidence 46677886 88888888764 2232332 44555999999988877653
No 23
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=33.73 E-value=41 Score=27.84 Aligned_cols=15 Identities=47% Similarity=0.680 Sum_probs=13.5
Q ss_pred CCCHHHHHHHHHHcC
Q 037682 65 GLSDAEFARAEAEFG 79 (397)
Q Consensus 65 GLSD~Ef~~IEa~fg 79 (397)
||||.+|+.||..+.
T Consensus 22 Glse~~Id~ie~~~~ 36 (80)
T cd08313 22 GLSDNEIERVELDHR 36 (80)
T ss_pred CCCHHHHHHHHHhCC
Confidence 899999999999773
No 24
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=33.23 E-value=28 Score=31.91 Aligned_cols=41 Identities=20% Similarity=0.173 Sum_probs=31.4
Q ss_pred HHhcCCChHHHhHhhcCCCCCccccCCcccCCHHHHHHHHH
Q 037682 349 LRKSGWSSEEVSDAFGFDFRPEKERKPAKKLSPELVERIGK 389 (397)
Q Consensus 349 L~raGWs~edV~eal~~d~~~~~e~~~~~~~~p~~~~~i~~ 389 (397)
+.+.|||.++|+++||..-+--+..-...+|||++.+.+..
T Consensus 116 ~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~lp~~v~~~~~~ 156 (187)
T TIGR00180 116 LEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPE 156 (187)
T ss_pred HHHhCCCHHHHHHHHCcCHHHHHHHHHHHcCCHHHHHHHHh
Confidence 34579999999999998655444444566799999988764
No 25
>PRK13832 plasmid partitioning protein; Provisional
Probab=32.55 E-value=37 Score=37.09 Aligned_cols=40 Identities=18% Similarity=0.455 Sum_probs=33.5
Q ss_pred HHhcCCChHHHhHhhcCCCCCccccCCcccCCHHHHHHHH
Q 037682 349 LRKSGWSSEEVSDAFGFDFRPEKERKPAKKLSPELVERIG 388 (397)
Q Consensus 349 L~raGWs~edV~eal~~d~~~~~e~~~~~~~~p~~~~~i~ 388 (397)
|.+.|||.|+|+..||..-.--+.++.-.+|+|+|.+.+.
T Consensus 114 Lie~G~T~EeIA~~lG~S~~~V~rlllLA~L~P~lLdal~ 153 (520)
T PRK13832 114 LVALGWTEEAIAVALALPVRQIRKLRLLANVLPAMLDHMA 153 (520)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 4579999999999999987777655667799999988775
No 26
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=32.23 E-value=85 Score=24.38 Aligned_cols=36 Identities=25% Similarity=0.231 Sum_probs=27.7
Q ss_pred HHhcCCChHHHhHhhcCCCCCccccCCcccCCHHHHHHHHHHHhhh
Q 037682 349 LRKSGWSSEEVSDAFGFDFRPEKERKPAKKLSPELVERIGKLAESV 394 (397)
Q Consensus 349 L~raGWs~edV~eal~~d~~~~~e~~~~~~~~p~~~~~i~~la~~v 394 (397)
=+++|.|..-|+..|.- ...++|+...||.+.|+..
T Consensus 7 A~~~gvS~~TVSr~ln~----------~~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 7 ARLAGVSKATVSRVLNG----------NGRVSEETREKVLAAMEEL 42 (70)
T ss_pred HHHHCCCHHHHHHHHCC----------CCCCCHHHHHHHHHHHHHh
Confidence 35679999999998831 1346899999999988764
No 27
>PF11922 DUF3440: Domain of unknown function (DUF3440); InterPro: IPR021845 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 53 to 190 amino acids in length. This domain is found associated with PF01507 from PFAM. This domain has a conserved KND sequence motif.
Probab=31.60 E-value=26 Score=33.46 Aligned_cols=75 Identities=19% Similarity=0.238 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHcCCCCChhHHHHHHccCCCC-CCCCCCCCCcccHHHHHHhhcch-hhHHHHHHHhhcccccCCCCC
Q 037682 64 PGLSDAEFARAEAEFGFVFPPDLRAILSAGLPLG-PGFPDWRATGSARLHLRASLDLP-IAAITFQIARNALWSKSWGPR 141 (397)
Q Consensus 64 pGLSD~Ef~~IEa~fgF~FPpDlRa~L~~GLPvG-~gFPdWR~~~~~~~~Lr~~L~~P-~~gil~~V~~n~fW~~sWG~R 141 (397)
-+|.|+.|+.+|+. |+.|---...-....-|+- +..-|| .|+..=++| ...|+..|.+|+||++.-|--
T Consensus 102 ~~lpde~i~~L~~~-~~~~~~~~~~~~t~~~~~r~~~~~D~--------~i~~~k~iPswkRic~~ilKND~~cr~lsFs 172 (181)
T PF11922_consen 102 GCLPDETIQELEEA-GIPIEVNGKNYRTDKKPVRMEYPDDI--------DIENFKDIPSWKRICKCILKNDYWCRYLSFS 172 (181)
T ss_pred CCCCHHHHHHHHhc-CCceeecccccccccCCccccCCCcc--------CccccccCchHHHHHHHHHccchhhhhccCC
Confidence 67888888888875 4443322222222222221 111222 111111122 356899999999999998887
Q ss_pred CCCHHH
Q 037682 142 PSDPEK 147 (397)
Q Consensus 142 P~~~~e 147 (397)
|.-.+.
T Consensus 173 ~tK~~~ 178 (181)
T PF11922_consen 173 PTKREQ 178 (181)
T ss_pred CCchhh
Confidence 765443
No 28
>PF11203 DUF2984: Protein of unknown function (DUF2984); InterPro: IPR021368 This entry represents the transmembrane protein EccE found in the Actinobacteria, which are part of type VII secretion system (T7SS) [].
Probab=29.76 E-value=65 Score=27.31 Aligned_cols=49 Identities=29% Similarity=0.545 Sum_probs=36.9
Q ss_pred cccHHHHHHHHhhCCCccCCCCCHHHHHHHHHHcCCCCChhHHHHHHccCCC--CCCCCCCCCC
Q 037682 45 SSLADKVITHLKNSGIRVQPGLSDAEFARAEAEFGFVFPPDLRAILSAGLPL--GPGFPDWRAT 106 (397)
Q Consensus 45 ~~~~~~vi~~L~~~GV~i~pGLSD~Ef~~IEa~fgF~FPpDlRa~L~~GLPv--G~gFPdWR~~ 106 (397)
..-+..|.++|++.|+.-.+ |+..|+...-.... .|++. .+.|-.|+++
T Consensus 38 ~~a~~Rla~~L~~~G~~a~~-l~a~el~~~~~~~~------------~~~~~~~~E~W~~~~~~ 88 (98)
T PF11203_consen 38 AAAARRLADRLREAGIRARV-LTADELPAALAALA------------DGLPPAPRETWRGWRGG 88 (98)
T ss_pred HHHHHHHHHHHHHCCCCcee-cChhhhHHHHHHhh------------ccCCCCCCCCcceEeeC
Confidence 34578899999999999888 88888876654433 44444 6788888876
No 29
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=29.75 E-value=61 Score=21.13 Aligned_cols=45 Identities=22% Similarity=0.321 Sum_probs=27.8
Q ss_pred hhHHHHhcCCChHHHhHhhcCCCCCcccc-CCcccCCHHHHHHHHH
Q 037682 345 LSESLRKSGWSSEEVSDAFGFDFRPEKER-KPAKKLSPELVERIGK 389 (397)
Q Consensus 345 ~s~sL~raGWs~edV~eal~~d~~~~~e~-~~~~~~~p~~~~~i~~ 389 (397)
+...+.+.|+|..|+++.+|..-..-..- .....++.+.+.+|..
T Consensus 2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~ 47 (56)
T smart00530 2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAK 47 (56)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHH
Confidence 34557788999999999998764433221 1122346666665544
No 30
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=29.35 E-value=72 Score=22.72 Aligned_cols=27 Identities=11% Similarity=0.281 Sum_probs=21.6
Q ss_pred HHHHhhHHHHhcCCChHHHhHhhcCCC
Q 037682 341 KADRLSESLRKSGWSSEEVSDAFGFDF 367 (397)
Q Consensus 341 ~~d~~s~sL~raGWs~edV~eal~~d~ 367 (397)
.-+.+...|.+.||+...+++.||..-
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lgisr 32 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLGISR 32 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHTS-H
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCCCH
Confidence 456678899999999999999999863
No 31
>PF01503 PRA-PH: Phosphoribosyl-ATP pyrophosphohydrolase; InterPro: IPR021130 Phosphoribosyl-ATP pyrophosphatase, 3.6.1.31 from EC catalyses the second step in the histidine biosynthetic pathway: 5-phosphoribosyl-ATP + H2O = 5-phosphoribosyl-AMP + PPi The Neurospora crassa enzyme also catalyzes the reactions of histidinol dehydrogenase (1.1.1.23 from EC) and phosphoribosyl-AMP cyclohydrolase (3.5.4.19 from EC). This entry also includes the Bacillus subtilis Cof proteins, which catalyze the hydrolysis of 4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate to 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate []. ; PDB: 2A7W_K 3NL9_A 1YXB_D 1YVW_A 2YFD_C 2YFC_B 2YF3_C 2YF4_A 2YEU_E 2YF9_A ....
Probab=28.60 E-value=1.4e+02 Score=24.07 Aligned_cols=47 Identities=26% Similarity=0.275 Sum_probs=38.2
Q ss_pred chhhhhhhccCCCCcCccccccchHHHHHHHHHHHHHhhHHHHhcCCChHHHhHhh
Q 037682 308 PDIVEIVTVSASGFFEGEMVMLDNQSVLDGLLLKADRLSESLRKSGWSSEEVSDAF 363 (397)
Q Consensus 308 ~di~Em~~~~~~~~~~ge~~~~d~~avl~~L~~~~d~~s~sL~raGWs~edV~eal 363 (397)
+|..|++.....+ |.+.++++++--.=.+...|...|.+.++|-+.+
T Consensus 33 EE~~E~~~A~~~~---------d~~~~~~e~aDlly~~~~~~~~~gi~~~~v~~ev 79 (83)
T PF01503_consen 33 EEAGELIEAAKNG---------DKEEVADELADLLYHLLGLLASMGIDLDEVFDEV 79 (83)
T ss_dssp HHHHHHHHHHHCS---------HHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHHHHcC---------CHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 6888888765544 8999999999989999999999999999987765
No 32
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=28.06 E-value=65 Score=24.70 Aligned_cols=26 Identities=27% Similarity=0.385 Sum_probs=21.6
Q ss_pred HhhCCCccCCCCCHHHHHHHHHHcCC
Q 037682 55 LKNSGIRVQPGLSDAEFARAEAEFGF 80 (397)
Q Consensus 55 L~~~GV~i~pGLSD~Ef~~IEa~fgF 80 (397)
++..++...-|||++|.+.--++||-
T Consensus 10 ~~~l~t~~~~GLs~~ev~~r~~~~G~ 35 (69)
T PF00690_consen 10 LKRLNTSSSQGLSSEEVEERRKKYGP 35 (69)
T ss_dssp HHHHTTBTSSBBTHHHHHHHHHHHSS
T ss_pred HHHHCcCCCCCCCHHHHHHHHHhccc
Confidence 34445778999999999999999994
No 33
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=27.97 E-value=55 Score=36.72 Aligned_cols=31 Identities=16% Similarity=0.371 Sum_probs=26.3
Q ss_pred CCCCCCCCeEEEeCCceEEEcCchhHHHHHhh
Q 037682 174 NPTLAGNPIFYVDENRIFCCGLDLSDFFERES 205 (397)
Q Consensus 174 ~p~~aGnPVfSV~~tDIi~yG~DLadyf~rEf 205 (397)
++-+.|-||+ ||+.|+|..|.++-.|+.+-|
T Consensus 190 CsltSgfPVY-vyd~D~~~~G~~~d~~lk~~f 220 (907)
T KOG2264|consen 190 CSLTSGFPVY-VYDSDIITSGQSEDEWLKQVF 220 (907)
T ss_pred ccccCCceeE-EeccceeecccchHHHHHHHH
Confidence 3446789984 999999999999999998766
No 34
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=27.95 E-value=82 Score=30.69 Aligned_cols=72 Identities=21% Similarity=0.169 Sum_probs=38.4
Q ss_pred HHHHHHHHhhCCCCCchhhhhhhccCCCCcCc-cccccchH-----------HHHH-------HHHHHHHHhhHHHHhcC
Q 037682 293 MGQIGSVLREGGWSEPDIVEIVTVSASGFFEG-EMVMLDNQ-----------SVLD-------GLLLKADRLSESLRKSG 353 (397)
Q Consensus 293 l~~~~~~LR~GGW~e~di~Em~~~~~~~~~~g-e~~~~d~~-----------avl~-------~L~~~~d~~s~sL~raG 353 (397)
++.....|++=||+++||..|+.-.+.-+.-. +....-.. .|+. -=.-+++.--+.|.+.|
T Consensus 175 ~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG 254 (345)
T PF02536_consen 175 LKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLG 254 (345)
T ss_dssp CHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhc
Confidence 34555678899999999999998766442211 11000000 1110 00113444455677799
Q ss_pred CChHHHhHhhc
Q 037682 354 WSSEEVSDAFG 364 (397)
Q Consensus 354 Ws~edV~eal~ 364 (397)
||.+||..++-
T Consensus 255 ~s~~ei~~mv~ 265 (345)
T PF02536_consen 255 FSEEEIAKMVR 265 (345)
T ss_dssp --HHHHHHHHH
T ss_pred CcHHHHHHHHH
Confidence 99999998874
No 35
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=27.13 E-value=55 Score=24.83 Aligned_cols=23 Identities=22% Similarity=0.394 Sum_probs=16.3
Q ss_pred HHHHhhHHHHhcCCChHHHhHhhc
Q 037682 341 KADRLSESLRKSGWSSEEVSDAFG 364 (397)
Q Consensus 341 ~~d~~s~sL~raGWs~edV~eal~ 364 (397)
.|+.+-+.+ ++|||.|||.+...
T Consensus 20 ~v~~i~~~~-~~G~s~eeI~~~yp 42 (56)
T PF04255_consen 20 PVRDILDLL-AAGESPEEIAEDYP 42 (56)
T ss_dssp BHHHHHHHH-HTT--HHHHHHHST
T ss_pred cHHHHHHHH-HcCCCHHHHHHHCC
Confidence 456666667 99999999999864
No 36
>PF14980 TIP39: TIP39 peptide
Probab=25.93 E-value=19 Score=27.89 Aligned_cols=12 Identities=33% Similarity=0.963 Sum_probs=10.2
Q ss_pred CchhHHHHHHHH
Q 037682 285 IPKWVDDYMGQI 296 (397)
Q Consensus 285 ~~~Wv~~yl~~~ 296 (397)
-.+||+.|+.++
T Consensus 35 R~~WLnSYMqkL 46 (51)
T PF14980_consen 35 RQKWLNSYMQKL 46 (51)
T ss_pred HHHHHHHHHHHH
Confidence 369999999876
No 37
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=25.83 E-value=1.4e+02 Score=25.03 Aligned_cols=47 Identities=13% Similarity=0.149 Sum_probs=33.1
Q ss_pred HHHHHHHHHhhCCCCCchhhhhhhccCCCCcCccccccchHHHHHHHHHHHHHh
Q 037682 292 YMGQIGSVLREGGWSEPDIVEIVTVSASGFFEGEMVMLDNQSVLDGLLLKADRL 345 (397)
Q Consensus 292 yl~~~~~~LR~GGW~e~di~Em~~~~~~~~~~ge~~~~d~~avl~~L~~~~d~~ 345 (397)
-|..|-..||+.|.+-++|.+|+.....+ ..+.+++++.|=-..+.+
T Consensus 46 ~l~~I~~llr~~G~~l~~i~~~l~~~~~~-------~~~~~~~~~~~~~~~~~~ 92 (99)
T cd04765 46 LLLLIKHLLYEKGYTIEGAKQALKEDGAA-------AIREEEAEERLPSIRAEL 92 (99)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHhcccc-------ccchhhHHHHHHHHHHHH
Confidence 34455556799999999999999877665 456677766665444443
No 38
>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=25.31 E-value=33 Score=31.96 Aligned_cols=27 Identities=41% Similarity=0.727 Sum_probs=20.0
Q ss_pred ccchHHHHHHHHHHHHHhhHHHHhcCCChHHHhHhhcCCCC
Q 037682 328 MLDNQSVLDGLLLKADRLSESLRKSGWSSEEVSDAFGFDFR 368 (397)
Q Consensus 328 ~~d~~avl~~L~~~~d~~s~sL~raGWs~edV~eal~~d~~ 368 (397)
..|+..||.||. +.|||.+|+ =|..++
T Consensus 44 ~aD~NeVLkALc----------~eAGw~Ve~----DGTtyr 70 (150)
T PF05687_consen 44 HADNNEVLKALC----------REAGWTVEP----DGTTYR 70 (150)
T ss_pred cCCHHHHHHHHH----------HhCCEEEcc----CCCeec
Confidence 579999999986 468997765 355554
No 39
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=25.20 E-value=2e+02 Score=24.47 Aligned_cols=46 Identities=22% Similarity=0.525 Sum_probs=33.3
Q ss_pred hhHHHHhcCCChHHHhHhhcCC------------------CCCcc--ccCCcccCCHHHHHHHHHH
Q 037682 345 LSESLRKSGWSSEEVSDAFGFD------------------FRPEK--ERKPAKKLSPELVERIGKL 390 (397)
Q Consensus 345 ~s~sL~raGWs~edV~eal~~d------------------~~~~~--e~~~~~~~~p~~~~~i~~l 390 (397)
|.......||+.-+|++.+|.- |.-++ .++...+++|+++.+|-.|
T Consensus 17 lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~~~~I~~l 82 (85)
T PF13011_consen 17 LVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEVERRIIEL 82 (85)
T ss_pred HHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHHHHHHHHH
Confidence 4445567899999999998853 22222 3466788999999999776
No 40
>PRK11050 manganese transport regulator MntR; Provisional
Probab=25.16 E-value=4.5e+02 Score=23.49 Aligned_cols=93 Identities=19% Similarity=0.215 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHh-hCCCCCchhhhhhhccCCC------------CcC---cccc--ccchHHHHHHHHHHHHHhhHHHH
Q 037682 289 VDDYMGQIGSVLR-EGGWSEPDIVEIVTVSASG------------FFE---GEMV--MLDNQSVLDGLLLKADRLSESLR 350 (397)
Q Consensus 289 v~~yl~~~~~~LR-~GGW~e~di~Em~~~~~~~------------~~~---ge~~--~~d~~avl~~L~~~~d~~s~sL~ 350 (397)
..+|++.|-..+- .|+++-.||.+.+.++.+- ++. +..+ .-..+.++..+....+.+..-|.
T Consensus 35 ~e~~l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~~~~~~~le~~l~ 114 (152)
T PRK11050 35 IEDYVELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQESRERHQIVENFLL 114 (152)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHHHHHHHHHHHHHH
Confidence 5688888776664 5889999999988877654 221 1111 12344455555555556666677
Q ss_pred hcCCChHHHhH-hhcCCCCCccccCCcccCCHHHHHHHHHHH
Q 037682 351 KSGWSSEEVSD-AFGFDFRPEKERKPAKKLSPELVERIGKLA 391 (397)
Q Consensus 351 raGWs~edV~e-al~~d~~~~~e~~~~~~~~p~~~~~i~~la 391 (397)
+.|++.+++-. +-. -...|+|+...+|.++-
T Consensus 115 ~lg~~~~~~~~~a~~----------le~~is~~~i~r~~~~l 146 (152)
T PRK11050 115 ALGVSPETARRDAEG----------IEHHVSEETLAAFRRFL 146 (152)
T ss_pred HcCCCHHHHHHHHHH----------hhhcCCHHHHHHHHHHH
Confidence 78988887655 222 23478999888887653
No 41
>PF07128 DUF1380: Protein of unknown function (DUF1380); InterPro: IPR009811 This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be specific to Enterobacteria. The function of this family is unknown.
Probab=24.74 E-value=1.2e+02 Score=28.00 Aligned_cols=77 Identities=19% Similarity=0.323 Sum_probs=51.3
Q ss_pred CCCchhhhhhhccCCCCcCccccccchHHHHHHHHHHHHHh-hHHHHhcCCChHHHhHhhcCCCCCccccCCcccCCHHH
Q 037682 305 WSEPDIVEIVTVSASGFFEGEMVMLDNQSVLDGLLLKADRL-SESLRKSGWSSEEVSDAFGFDFRPEKERKPAKKLSPEL 383 (397)
Q Consensus 305 W~e~di~Em~~~~~~~~~~ge~~~~d~~avl~~L~~~~d~~-s~sL~raGWs~edV~eal~~d~~~~~e~~~~~~~~p~~ 383 (397)
|+++||.+|...-.-- ..+ -+.++| +...+-+ .+.-.+.|=|.+-|.|.+.- .+ +..+.+.+|-++
T Consensus 27 WT~eDV~~~a~gme~~-lTd----~E~~aV----L~~I~~~~~~~~~~~GVs~~~V~el~~~-~r---~~~R~VtVPA~l 93 (139)
T PF07128_consen 27 WTREDVRALADGMEYN-LTD----DEARAV----LARIGDIPEDQRHEEGVSSGTVMELIRE-VR---RAARQVTVPADL 93 (139)
T ss_pred ecHHHHHHHHhcCCCC-CCH----HHHHHH----HHHHhcCccccchhccccHHHHHHHHHH-HH---hcCCcccccHHH
Confidence 9999999986311100 011 123344 5555665 44568899999999887753 22 234789999999
Q ss_pred HHHHHHHHhhh
Q 037682 384 VERIGKLAESV 394 (397)
Q Consensus 384 ~~~i~~la~~v 394 (397)
.+++=++|++.
T Consensus 94 Le~vl~~A~~~ 104 (139)
T PF07128_consen 94 LERVLRLAEQA 104 (139)
T ss_pred HHHHHHHHHHH
Confidence 99999999863
No 42
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.71 E-value=49 Score=23.53 Aligned_cols=18 Identities=28% Similarity=0.667 Sum_probs=12.1
Q ss_pred HhcCCChHHHhHhhcCCC
Q 037682 350 RKSGWSSEEVSDAFGFDF 367 (397)
Q Consensus 350 ~raGWs~edV~eal~~d~ 367 (397)
...|||..+|++.||..-
T Consensus 14 ~~~G~s~~~ia~~lgvs~ 31 (50)
T PF13384_consen 14 LREGWSIREIAKRLGVSR 31 (50)
T ss_dssp HHHT--HHHHHHHHTS-H
T ss_pred HHCCCCHHHHHHHHCcCH
Confidence 334999999999999753
No 43
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic, long form. Forms scoring between the trusted and noise cutoff tend to branch with this subgroup of threonine ammonia-lyase phylogenetically but have only a single copy of the C-terminal domain.
Probab=23.87 E-value=49 Score=35.40 Aligned_cols=51 Identities=27% Similarity=0.463 Sum_probs=40.5
Q ss_pred ccccccc----cHHHHHHHHhhCCCccCCCCCHHHHHHH---------------HHHcCCCCChh---HHHHHH
Q 037682 40 GLVSFSS----LADKVITHLKNSGIRVQPGLSDAEFARA---------------EAEFGFVFPPD---LRAILS 91 (397)
Q Consensus 40 ~~~sf~~----~~~~vi~~L~~~GV~i~pGLSD~Ef~~I---------------Ea~fgF~FPpD---lRa~L~ 91 (397)
+.+.+.. --.+|++.|++.|.++.- |||.|+.+. |..|-|+||.- ||.||.
T Consensus 366 v~vgie~~~~~~~~~l~~~L~~~Gy~~~d-ls~ne~~k~h~r~~~g~~~~~~~~e~~~~~~fperpgaL~~Fl~ 438 (499)
T TIGR01124 366 IFVGVQLSNPQERQEILARLNDGGYSVVD-LTDDELAKLHVRYMVGGRPPHVENERLYSFEFPERPGALLRFLN 438 (499)
T ss_pred EEEEEEeCCHHHHHHHHHHHHHcCCCeEE-CCCCHHHHHHHHhccCCCCCCCCCceEEEEeCCCCccHHHHHHH
Confidence 4445443 447899999999966654 499999977 77899999977 999999
No 44
>PRK12449 acyl carrier protein; Provisional
Probab=23.59 E-value=54 Score=25.69 Aligned_cols=16 Identities=25% Similarity=0.434 Sum_probs=13.2
Q ss_pred HHHHHHHcCCCCChhH
Q 037682 71 FARAEAEFGFVFPPDL 86 (397)
Q Consensus 71 f~~IEa~fgF~FPpDl 86 (397)
+..+|.+||+.+|++-
T Consensus 46 i~~lE~~f~i~i~~~~ 61 (80)
T PRK12449 46 IINVEDEFHIAIPDED 61 (80)
T ss_pred HHHHHHHhCCCCCHHH
Confidence 3569999999999863
No 45
>PRK08269 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=23.42 E-value=1.7e+02 Score=29.33 Aligned_cols=32 Identities=25% Similarity=0.386 Sum_probs=19.5
Q ss_pred ChhHHHHHHc---cCCCCCCCCCCCCCcccHHHHHHh
Q 037682 83 PPDLRAILSA---GLPLGPGFPDWRATGSARLHLRAS 116 (397)
Q Consensus 83 PpDlRa~L~~---GLPvG~gFPdWR~~~~~~~~Lr~~ 116 (397)
++-++..... |.-.|.|||+|... +...++.+
T Consensus 259 ~~~l~~~v~~g~~G~ksG~GfY~y~~~--~~~~~~~~ 293 (314)
T PRK08269 259 PAIVVRNMEEGRDGLRTGAGFYDYAGV--DVPAYRRQ 293 (314)
T ss_pred CHHHHHHHHCCCCcccCCCcceeCCCC--chHHHHHH
Confidence 3345555554 67788999999553 34444443
No 46
>COG4174 ABC-type uncharacterized transport system, permease component [General function prediction only]
Probab=23.25 E-value=95 Score=32.12 Aligned_cols=101 Identities=26% Similarity=0.358 Sum_probs=64.5
Q ss_pred ccCCCCCHHHHHHHHHHcCCCCChhHHHHHHc----cCCCCCCCCCCCCCcccHHHHHHhhcchhh------HHHHHHHh
Q 037682 61 RVQPGLSDAEFARAEAEFGFVFPPDLRAILSA----GLPLGPGFPDWRATGSARLHLRASLDLPIA------AITFQIAR 130 (397)
Q Consensus 61 ~i~pGLSD~Ef~~IEa~fgF~FPpDlRa~L~~----GLPvG~gFPdWR~~~~~~~~Lr~~L~~P~~------gil~~V~~ 130 (397)
.=..||..+-++.||+.|||.=||--|-+++. -+.-|+.|. |+.+ -.+-|++.|-..+. -|.+-|.
T Consensus 75 rg~~GlDpe~i~~i~~~~GFDKp~~eR~~~Ml~~y~rfDfGeS~f--r~~~-VidLI~eklPVSiSlGlw~tli~YliS- 150 (364)
T COG4174 75 RGAQGLDPELIAEIEKQYGFDKPPLERYFLMLWDYARFDFGESFF--RDAS-VIDLIKEKLPVSISLGLWSTLIIYLIS- 150 (364)
T ss_pred ccccCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhccccHHhh--cCCh-HHHHHHHhCCcEEEhHHHHHHHHHHHh-
Confidence 34579999999999999999999999999884 566666664 5542 23344443322111 1112221
Q ss_pred hcccccCCCCCCCCHHHHHHHHHHhhhcCCceeeecccccccCCCCCCCCCeEEEeCCceEEEcCchhHHHHH
Q 037682 131 NALWSKSWGPRPSDPEKALRVARNALKRAPLLIPIFNHCYIPCNPTLAGNPIFYVDENRIFCCGLDLSDFFER 203 (397)
Q Consensus 131 n~fW~~sWG~RP~~~~eal~~Ar~~l~~aP~LVPIygHRYlPs~p~~aGnPVfSV~~tDIi~yG~DLadyf~r 203 (397)
-|-...+|++ . +-.|-||.+-||..|+-+-.|+--
T Consensus 151 ----------IPLGI~KAv~---------------------------~-gs~fDvwsS~viiigyAiP~Flfa 185 (364)
T COG4174 151 ----------IPLGIRKAVR---------------------------N-GSRFDVWSSAVIIIGYAIPAFLFA 185 (364)
T ss_pred ----------cchhHHHHHh---------------------------C-CCcceeeeeeeEEEecccHHHHHH
Confidence 2322222221 1 345889999999999999998743
No 47
>PRK05087 D-alanine--poly(phosphoribitol) ligase subunit 2; Validated
Probab=23.19 E-value=53 Score=26.70 Aligned_cols=16 Identities=19% Similarity=0.310 Sum_probs=13.7
Q ss_pred HHHHHHHcCCCCChhH
Q 037682 71 FARAEAEFGFVFPPDL 86 (397)
Q Consensus 71 f~~IEa~fgF~FPpDl 86 (397)
+..+|..||+++|++-
T Consensus 43 i~~lE~~fgi~i~~~e 58 (78)
T PRK05087 43 LVELENRFDIEVPVSE 58 (78)
T ss_pred HHHHHHHhCCccChHh
Confidence 4678999999999874
No 48
>PHA01976 helix-turn-helix protein
Probab=23.00 E-value=1.1e+02 Score=22.87 Aligned_cols=46 Identities=15% Similarity=0.164 Sum_probs=27.5
Q ss_pred HHhhHHHHhcCCChHHHhHhhcCCCCCcccc-CCcccCCHHHHHHHH
Q 037682 343 DRLSESLRKSGWSSEEVSDAFGFDFRPEKER-KPAKKLSPELVERIG 388 (397)
Q Consensus 343 d~~s~sL~raGWs~edV~eal~~d~~~~~e~-~~~~~~~p~~~~~i~ 388 (397)
+++-.-..+.|+|.+|+++.+|..-..-..= +.....+.+.+.+|-
T Consensus 5 ~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia 51 (67)
T PHA01976 5 IQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLA 51 (67)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Confidence 3444556789999999999999764333221 222334555554443
No 49
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=22.77 E-value=99 Score=26.91 Aligned_cols=46 Identities=15% Similarity=0.150 Sum_probs=32.0
Q ss_pred HHhhHHHHhcCCChHHHhHhhcCCCCCcc--ccCCcccCCHHHHHHHHH
Q 037682 343 DRLSESLRKSGWSSEEVSDAFGFDFRPEK--ERKPAKKLSPELVERIGK 389 (397)
Q Consensus 343 d~~s~sL~raGWs~edV~eal~~d~~~~~--e~~~~~~~~p~~~~~i~~ 389 (397)
.++-.-+.+.|+|.+||++.+|..-.--. |+.. ...+.+++.+|-+
T Consensus 8 ~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~-~~ps~~~l~kIa~ 55 (120)
T PRK13890 8 TNVLRLLDERHMTKKELSERSGVSISFLSDLTTGK-ANPSLKVMEAIAD 55 (120)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCC-CCCCHHHHHHHHH
Confidence 45667788999999999999997644322 3322 3578887776654
No 50
>PRK07081 acyl carrier protein; Provisional
Probab=22.38 E-value=57 Score=26.50 Aligned_cols=16 Identities=19% Similarity=0.457 Sum_probs=13.7
Q ss_pred HHHHHHHcCCCCChhH
Q 037682 71 FARAEAEFGFVFPPDL 86 (397)
Q Consensus 71 f~~IEa~fgF~FPpDl 86 (397)
+..||.+||+.+|++.
T Consensus 42 i~~lE~~f~I~i~~~~ 57 (83)
T PRK07081 42 MLAIEDAFDIEIPDEM 57 (83)
T ss_pred HHHHHHHhCCcCCHHH
Confidence 4579999999999984
No 51
>COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]
Probab=22.12 E-value=2.4e+02 Score=25.81 Aligned_cols=66 Identities=26% Similarity=0.502 Sum_probs=48.9
Q ss_pred CccCCCCCHHHHHHHHHHcCCCCChhHHHHHHccCCCCCCCCCCCCCcccHHHHHHhhcchhhHHHHHHHhhcccccCCC
Q 037682 60 IRVQPGLSDAEFARAEAEFGFVFPPDLRAILSAGLPLGPGFPDWRATGSARLHLRASLDLPIAAITFQIARNALWSKSWG 139 (397)
Q Consensus 60 V~i~pGLSD~Ef~~IEa~fgF~FPpDlRa~L~~GLPvG~gFPdWR~~~~~~~~Lr~~L~~P~~gil~~V~~n~fW~~sWG 139 (397)
....|-|||+|++. ..|.+|.+|.-+|--|-|=|.+ ++.+|- .||
T Consensus 13 ~s~lp~Ltd~qi~~-----------QVrylL~QGykigvE~~d~rrp-----------------------rtgsWt-~wg 57 (127)
T COG4451 13 LSSLPPLTDEQIAE-----------QVRYLLSQGYKIGVEYVDDRRP-----------------------RTGSWT-MWG 57 (127)
T ss_pred eecCCcCcHHHHHH-----------HHHHHHhCCcccceeecccCCc-----------------------ccceee-ecC
Confidence 45678899987763 6899999999999888888876 455664 677
Q ss_pred C---CCCCHHHHHHHHHHhhhcCC
Q 037682 140 P---RPSDPEKALRVARNALKRAP 160 (397)
Q Consensus 140 ~---RP~~~~eal~~Ar~~l~~aP 160 (397)
. --.+-.+|+......++.-|
T Consensus 58 ~p~f~~~~~~evlaele~Cr~dhp 81 (127)
T COG4451 58 TPMFGAKTAGEVLAELEACRADHP 81 (127)
T ss_pred CccccccchHHHHHHHHHHHHhCC
Confidence 6 33566777877777776643
No 52
>cd08503 PBP2_NikA_DppA_OppA_like_17 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=21.88 E-value=2e+02 Score=29.12 Aligned_cols=34 Identities=12% Similarity=0.215 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhhhc-CCceeeecccccccCCCCCC
Q 037682 145 PEKALRVARNALKR-APLLIPIFNHCYIPCNPTLA 178 (397)
Q Consensus 145 ~~eal~~Ar~~l~~-aP~LVPIygHRYlPs~p~~a 178 (397)
..++.+.+.+.|.. .|.++|+|.+.++...+...
T Consensus 424 r~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~v~ 458 (460)
T cd08503 424 RKELYAEMQQILHDEGGIIIPYFRSYLDAHSDKVK 458 (460)
T ss_pred HHHHHHHHHHHHHhcCCeEeEeecchhhhcccccc
Confidence 34445555666554 89999999997666665543
No 53
>PF05997 Nop52: Nucleolar protein,Nop52; InterPro: IPR010301 Nop52 is believed to be involved in the generation of 28S rRNA [].; GO: 0006364 rRNA processing, 0030688 preribosome, small subunit precursor
Probab=21.87 E-value=1.3e+02 Score=28.82 Aligned_cols=62 Identities=24% Similarity=0.330 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHHhhCCCCCchhhhhhhccCCCCcCccccccchHHHHHHHHHHH-HHhhHHHHhcCCCh
Q 037682 289 VDDYMGQIGSVLREGGWSEPDIVEIVTVSASGFFEGEMVMLDNQSVLDGLLLKA-DRLSESLRKSGWSS 356 (397)
Q Consensus 289 v~~yl~~~~~~LR~GGW~e~di~Em~~~~~~~~~~ge~~~~d~~avl~~L~~~~-d~~s~sL~raGWs~ 356 (397)
|+.++.+....|++.||..+-|++.+.+=..+++..+. + +-.||..|+ |-+-++|.+.+=+.
T Consensus 110 vR~~~~~~~~~l~~~~w~~~~v~~~~~~l~~~~l~~~~-----~-~p~Gl~~H~~Di~ldEL~k~~~~~ 172 (217)
T PF05997_consen 110 VRRFLRQSFRFLKKNGWDKELVEEFNEILSETPLNPND-----Q-VPNGLRYHFADIFLDELEKVGGSE 172 (217)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHccCCCcC-----C-CchhHHHHHHHHHHHHHHHHhccc
Confidence 88899999999999999999999998776655433322 2 556888885 77778888887644
No 54
>COG3563 KpsC Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]
Probab=21.73 E-value=1.2e+02 Score=33.61 Aligned_cols=62 Identities=23% Similarity=0.424 Sum_probs=40.7
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCceeeecccccccC-CCCCCCCCeEEEeCCce-EEEcCchhHHHHH
Q 037682 137 SWGPRPSDPEKALRVARNALKRAPLLIPIFNHCYIPC-NPTLAGNPIFYVDENRI-FCCGLDLSDFFER 203 (397)
Q Consensus 137 sWG~RP~~~~eal~~Ar~~l~~aP~LVPIygHRYlPs-~p~~aGnPVfSV~~tDI-i~yG~DLadyf~r 203 (397)
.||-+|++. .|...|++. +.| .|- ...-||-+ +=+..|.|-||++.+|| |||-...-.=+++
T Consensus 37 gwg~k~s~~-ka~~fa~~~--~~~-fi~-ledgflrsl~lgv~~~p~fs~v~ddigiyyd~t~psrlen 100 (671)
T COG3563 37 GWGLKPSTH-KARAFAKEH--QLP-FIA-LEDGFLRSLGLGVEGYPPFSIVYDDIGIYYDTTRPSRLEN 100 (671)
T ss_pred ecccCcccH-HHHHHHHHh--CCC-eEE-echhhhhhhcCCcCCCCCceeEeecceeeecCCCchHHHH
Confidence 499999765 444555543 333 232 23344544 66788999999999888 8888876555544
No 55
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=21.62 E-value=3e+02 Score=22.98 Aligned_cols=42 Identities=24% Similarity=0.335 Sum_probs=32.7
Q ss_pred HHHHhhHHHHhcCCChHHHhHhhcCCCCCccccCCcccCCHHHHHHHHHH
Q 037682 341 KADRLSESLRKSGWSSEEVSDAFGFDFRPEKERKPAKKLSPELVERIGKL 390 (397)
Q Consensus 341 ~~d~~s~sL~raGWs~edV~eal~~d~~~~~e~~~~~~~~p~~~~~i~~l 390 (397)
-++++=.--++.|.|-.||++++|..++| -+|+..++|++++
T Consensus 12 ~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~--------i~SQstISR~Es~ 53 (75)
T smart00352 12 FAKTFKQRRIKLGFTQADVGLALGALYGP--------DFSQTTICRFEAL 53 (75)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcccccC--------cCCHHHHHHHHhc
Confidence 34556666788999999999999998887 3667777777764
No 56
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=21.36 E-value=69 Score=23.07 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=14.8
Q ss_pred HHHHhcCCChHHHhHhhcCC
Q 037682 347 ESLRKSGWSSEEVSDAFGFD 366 (397)
Q Consensus 347 ~sL~raGWs~edV~eal~~d 366 (397)
..|...|.|..||++.||.-
T Consensus 15 ~~l~~~G~si~~IA~~~gvs 34 (45)
T PF02796_consen 15 KELYAEGMSIAEIAKQFGVS 34 (45)
T ss_dssp HHHHHTT--HHHHHHHTTS-
T ss_pred HHHHHCCCCHHHHHHHHCcC
Confidence 35889999999999999864
No 57
>PRK13866 plasmid partitioning protein RepB; Provisional
Probab=21.06 E-value=64 Score=33.41 Aligned_cols=44 Identities=18% Similarity=0.274 Sum_probs=33.8
Q ss_pred hhHHHHhcCCChHHHhHhhcCCCCCccccCC-cccCCHHHHHHHH
Q 037682 345 LSESLRKSGWSSEEVSDAFGFDFRPEKERKP-AKKLSPELVERIG 388 (397)
Q Consensus 345 ~s~sL~raGWs~edV~eal~~d~~~~~e~~~-~~~~~p~~~~~i~ 388 (397)
+...|...|.+.++|+++||.+-.--.+--. +..||.+|+..||
T Consensus 171 ~a~~L~~~g~~~~~i~~aL~~~~s~vS~~l~v~~~lP~~li~~iG 215 (336)
T PRK13866 171 FALRLEDAGFDRATIIAALSTDKADLSRYITVARGIPLNLATQIG 215 (336)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHhCCHHHHHhhc
Confidence 5678899999999999999986544433334 4469999999775
No 58
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=20.92 E-value=37 Score=25.16 Aligned_cols=34 Identities=29% Similarity=0.503 Sum_probs=24.7
Q ss_pred HHHHHHHH-hhCCCc---cCCCCCHHHHHHHHHHcCCC
Q 037682 48 ADKVITHL-KNSGIR---VQPGLSDAEFARAEAEFGFV 81 (397)
Q Consensus 48 ~~~vi~~L-~~~GV~---i~pGLSD~Ef~~IEa~fgF~ 81 (397)
.++||+.| ++.|+. ..--|++++...|-+.||+.
T Consensus 17 ~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~~k 54 (54)
T PF04760_consen 17 SKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFGVK 54 (54)
T ss_dssp HHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH---
T ss_pred HHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhCcC
Confidence 57899999 558966 66789999999999999874
No 59
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=20.92 E-value=32 Score=28.20 Aligned_cols=37 Identities=22% Similarity=0.322 Sum_probs=22.3
Q ss_pred cCCChHHHhHhhcCCCCCccccCCcccCCHHHHHHHH
Q 037682 352 SGWSSEEVSDAFGFDFRPEKERKPAKKLSPELVERIG 388 (397)
Q Consensus 352 aGWs~edV~eal~~d~~~~~e~~~~~~~~p~~~~~i~ 388 (397)
.||+-+||+..||.+-.--..+-....+|++|-+.|.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~Ll~lP~~i~~~v~ 38 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLALLDLPEEIKELVR 38 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHGGGS--HHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHcCCHHHHHHHH
Confidence 5999999999999874444444456678888877665
No 60
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=20.66 E-value=1.3e+02 Score=28.24 Aligned_cols=71 Identities=10% Similarity=0.164 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHhhCCCCCchhhhhhhccCCCC---cCc--cccccchHHHHHHHHHHHHHhhHHHHhcCCChHHHhHhhc
Q 037682 290 DDYMGQIGSVLREGGWSEPDIVEIVTVSASGF---FEG--EMVMLDNQSVLDGLLLKADRLSESLRKSGWSSEEVSDAFG 364 (397)
Q Consensus 290 ~~yl~~~~~~LR~GGW~e~di~Em~~~~~~~~---~~g--e~~~~d~~avl~~L~~~~d~~s~sL~raGWs~edV~eal~ 364 (397)
...++-|-.-+.+ .|+-+++.+.+.++.+-+ |-- .+.+ .|=+.+ ..+.+...-|+..++|+.||++.+|
T Consensus 189 ~~~~~~I~~~~~~-~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t~--~~yi~~---~Rl~~A~~lL~~t~~sI~eIA~~~G 262 (287)
T TIGR02297 189 NRFNFLIEENYKQ-HLRLPEYADRLGISESRLNDICRRFSALSP--KRLIIE---RVMQEARRLLLFTQHSINQIAYDLG 262 (287)
T ss_pred HHHHHHHHHhhcc-CCCHHHHHHHHCCCHHHHHHHHHHHhCCCH--HHHHHH---HHHHHHHHHHHcCCCCHHHHHHHhC
Confidence 3444445555666 699999999999888663 322 1222 122221 1344445558899999999999999
Q ss_pred CC
Q 037682 365 FD 366 (397)
Q Consensus 365 ~d 366 (397)
|.
T Consensus 263 F~ 264 (287)
T TIGR02297 263 YK 264 (287)
T ss_pred CC
Confidence 97
No 61
>TIGR00517 acyl_carrier acyl carrier protein. S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site.
Probab=20.58 E-value=67 Score=24.96 Aligned_cols=15 Identities=27% Similarity=0.417 Sum_probs=13.2
Q ss_pred HHHHHHcCCCCChhH
Q 037682 72 ARAEAEFGFVFPPDL 86 (397)
Q Consensus 72 ~~IEa~fgF~FPpDl 86 (397)
..||.+||+++|++.
T Consensus 45 ~~lE~~f~i~i~~~~ 59 (77)
T TIGR00517 45 MALEEEFDIEIPDEE 59 (77)
T ss_pred HHHHHHHCCCCCHHH
Confidence 469999999999885
No 62
>PRK07639 acyl carrier protein; Provisional
Probab=20.53 E-value=63 Score=26.54 Aligned_cols=16 Identities=19% Similarity=0.297 Sum_probs=13.5
Q ss_pred HHHHHHHcCCCCChhH
Q 037682 71 FARAEAEFGFVFPPDL 86 (397)
Q Consensus 71 f~~IEa~fgF~FPpDl 86 (397)
+..+|.+||+++|++-
T Consensus 47 v~~lE~~fgi~i~d~~ 62 (86)
T PRK07639 47 IVYIEMDVKLCVPEDE 62 (86)
T ss_pred HHHHHHHHCCccCHHH
Confidence 4569999999999873
No 63
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=20.04 E-value=62 Score=30.53 Aligned_cols=43 Identities=21% Similarity=0.288 Sum_probs=26.8
Q ss_pred HHHHhcCCChHHHhHhhcCCCCCcc--ccCCcccCCHHHHHHHHHH
Q 037682 347 ESLRKSGWSSEEVSDAFGFDFRPEK--ERKPAKKLSPELVERIGKL 390 (397)
Q Consensus 347 ~sL~raGWs~edV~eal~~d~~~~~--e~~~~~~~~p~~~~~i~~l 390 (397)
.-=.+.|||.||.|..|+..-.--+ |+ --..=..++|.+++++
T Consensus 86 ~ARE~~G~SqedLA~ki~ek~svI~~iE~-g~~~P~~~~akkLEk~ 130 (165)
T COG1813 86 EAREKRGLSQEDLAAKLKEKVSVIRRIER-GEATPNIKVAKKLEKL 130 (165)
T ss_pred HHHHHcCCCHHHHHHHhcccHHHHHHHHh-cccCccHHHHHHHHHH
Confidence 3345789999999999986543322 22 1112245677777765
Done!