Query 014161
Match_columns 429
No_of_seqs 110 out of 125
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 02:26:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014161.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014161hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12576 DUF3754: Protein of u 100.0 1.3E-34 2.9E-39 259.7 14.0 121 202-323 1-141 (141)
2 COG3355 Predicted transcriptio 91.9 0.74 1.6E-05 41.4 7.6 71 342-421 31-110 (126)
3 PF01978 TrmB: Sugar-specific 90.3 0.25 5.5E-06 38.5 2.8 54 343-405 13-68 (68)
4 PF14394 DUF4423: Domain of un 79.1 6.6 0.00014 36.7 6.8 63 353-422 40-111 (171)
5 PF11460 DUF3007: Protein of u 75.5 15 0.00033 32.1 7.5 63 247-309 1-75 (104)
6 COG1378 Predicted transcriptio 75.3 8.3 0.00018 38.2 6.7 71 342-421 20-92 (247)
7 PRK04214 rbn ribonuclease BN/u 67.3 1.2E+02 0.0027 31.9 13.7 39 352-399 310-348 (412)
8 TIGR02147 Fsuc_second hypothet 60.7 26 0.00057 35.3 6.9 38 365-402 142-180 (271)
9 TIGR03433 padR_acidobact trans 56.9 94 0.002 26.1 8.7 82 342-424 5-97 (100)
10 COG1802 GntR Transcriptional r 56.4 18 0.00038 34.5 4.7 61 334-405 22-83 (230)
11 PF14015 DUF4231: Protein of u 54.0 62 0.0013 27.1 7.1 18 291-308 67-84 (112)
12 smart00550 Zalpha Z-DNA-bindin 53.7 59 0.0013 25.6 6.5 56 335-401 5-64 (68)
13 PRK06266 transcription initiat 49.6 1.2E+02 0.0025 28.7 8.9 69 346-423 30-106 (178)
14 PF04369 Lactococcin: Lactococ 47.7 13 0.00027 29.6 1.7 28 46-73 1-29 (60)
15 PRK06743 flagellar motor prote 44.7 1.8E+02 0.004 29.1 9.8 67 298-368 64-131 (254)
16 PRK11534 DNA-binding transcrip 42.5 38 0.00083 31.9 4.5 39 366-405 36-74 (224)
17 PF14338 Mrr_N: Mrr N-terminal 42.4 75 0.0016 26.2 5.8 35 373-407 52-86 (92)
18 PF10007 DUF2250: Uncharacteri 41.9 21 0.00045 30.5 2.4 20 377-396 37-56 (92)
19 PHA01814 hypothetical protein 39.8 5.8 0.00013 35.2 -1.4 58 62-134 55-112 (137)
20 PRK08868 flagellar protein Fla 39.3 27 0.00059 32.2 2.8 63 353-417 68-133 (144)
21 PF07120 DUF1376: Protein of u 39.3 52 0.0011 27.3 4.3 63 302-364 22-87 (88)
22 TIGR00373 conserved hypothetic 38.3 1.7E+02 0.0037 27.0 8.0 72 341-421 17-96 (158)
23 smart00529 HTH_DTXR Helix-turn 35.2 1.2E+02 0.0026 24.5 5.8 32 377-408 15-46 (96)
24 smart00347 HTH_MARR helix_turn 35.1 2.2E+02 0.0048 22.3 8.7 42 346-396 18-59 (101)
25 PF06969 HemN_C: HemN C-termin 34.2 61 0.0013 24.7 3.7 37 366-403 26-62 (66)
26 PF11469 Ribonucleas_3_2: Ribo 33.2 43 0.00093 29.6 2.9 22 334-357 58-79 (120)
27 PF11880 DUF3400: Domain of un 32.1 44 0.00096 25.2 2.4 24 404-427 16-40 (45)
28 cd00092 HTH_CRP helix_turn_hel 31.2 60 0.0013 24.2 3.2 44 351-403 24-67 (67)
29 PF04391 DUF533: Protein of un 30.8 3.2E+02 0.007 26.2 8.7 25 279-303 33-57 (188)
30 PRK10225 DNA-binding transcrip 29.7 78 0.0017 30.6 4.5 41 363-404 36-76 (257)
31 PRK09990 DNA-binding transcrip 29.4 79 0.0017 30.3 4.5 42 363-405 34-75 (251)
32 smart00345 HTH_GNTR helix_turn 28.9 61 0.0013 23.4 2.8 33 366-399 26-58 (60)
33 cd00090 HTH_ARSR Arsenical Res 27.0 1E+02 0.0022 22.6 3.8 54 353-415 21-77 (78)
34 PRK13777 transcriptional regul 26.9 3.4E+02 0.0074 25.8 8.1 71 347-426 54-131 (185)
35 PRK14137 recX recombination re 26.4 65 0.0014 30.9 3.2 66 320-391 21-87 (195)
36 PRK11414 colanic acid/biofilm 26.2 1.1E+02 0.0024 28.8 4.7 39 366-405 40-78 (221)
37 PF03965 Penicillinase_R: Peni 26.1 1.8E+02 0.0039 24.8 5.7 72 346-425 11-86 (115)
38 cd07377 WHTH_GntR Winged helix 26.0 1.2E+02 0.0027 22.2 4.1 57 335-400 4-64 (66)
39 PRK11523 DNA-binding transcrip 25.5 1E+02 0.0022 29.7 4.4 42 363-405 35-76 (253)
40 COG2979 Uncharacterized protei 24.2 2.5E+02 0.0054 27.8 6.7 26 281-306 63-88 (225)
41 PF12597 DUF3767: Protein of u 24.2 3.9E+02 0.0085 23.7 7.5 62 251-315 42-106 (118)
42 PRK10421 DNA-binding transcrip 23.7 1.2E+02 0.0025 29.3 4.5 40 363-403 29-68 (253)
43 TIGR03338 phnR_burk phosphonat 23.5 1.4E+02 0.0031 27.7 4.9 40 365-405 39-78 (212)
44 PF11286 DUF3087: Protein of u 23.0 6.6E+02 0.014 23.9 10.3 41 324-365 95-144 (165)
45 PRK09464 pdhR transcriptional 22.2 1.3E+02 0.0028 28.9 4.5 40 363-403 37-76 (254)
46 PRK07738 flagellar protein Fla 21.8 97 0.0021 27.7 3.2 63 353-417 43-108 (117)
47 PF09840 DUF2067: Uncharacteri 21.8 86 0.0019 30.1 3.1 49 336-410 140-189 (190)
48 PRK14999 histidine utilization 21.7 1.6E+02 0.0035 28.2 5.0 56 363-419 39-96 (241)
49 TIGR01889 Staph_reg_Sar staphy 21.6 2E+02 0.0044 24.3 5.1 60 350-418 41-104 (109)
50 COG5631 Predicted transcriptio 21.6 91 0.002 29.8 3.1 34 371-404 109-145 (199)
51 TIGR01714 phage_rep_org_N phag 21.4 1.6E+02 0.0035 26.3 4.5 37 366-403 57-93 (119)
52 PF10557 Cullin_Nedd8: Cullin 21.1 1.9E+02 0.0041 22.7 4.4 48 349-397 19-66 (68)
53 PF11694 DUF3290: Protein of u 20.8 6.6E+02 0.014 23.2 8.5 23 248-270 13-35 (149)
54 PLN00134 fumarate hydratase; P 20.8 4.2E+02 0.0091 28.6 8.3 40 36-75 39-85 (458)
55 TIGR02325 C_P_lyase_phnF phosp 20.5 1.5E+02 0.0032 28.1 4.4 37 363-400 35-72 (238)
56 COG2165 PulG Type II secretory 20.5 2.9E+02 0.0062 23.3 5.8 30 277-306 15-44 (149)
57 PF10675 DUF2489: Protein of u 20.1 2E+02 0.0044 25.9 4.9 62 286-348 3-66 (131)
58 PRK08990 flagellar motor prote 20.1 8.7E+02 0.019 24.2 9.8 64 297-366 65-129 (254)
No 1
>PF12576 DUF3754: Protein of unknown function (DUF3754); InterPro: IPR022227 This domain family is found in bacteria, archaea and eukaryotes, and is typically between 135 and 166 amino acids in length. There is a single completely conserved residue P that may be functionally important.
Probab=100.00 E-value=1.3e-34 Score=259.73 Aligned_cols=121 Identities=41% Similarity=0.685 Sum_probs=108.9
Q ss_pred cceEEEEEeeccccC--------c------CCCCeEEEeeCCCCCCCccccccCCCCCCCChhhHHHHHHHHHHhHhhhh
Q 014161 202 FDRIIVLYRQASTKS--------K------AERGVYLKHFRNIPMADMEIVLPEKKNPGLTPLDWVKFLVSAVVGLVAVI 267 (429)
Q Consensus 202 FkrVVvlyR~k~~~~--------~------~~~~l~LK~FkdIP~aDLE~llPekK~~~~~~~D~~~l~v~avvg~vav~ 267 (429)
||||||+||.+.++. + .+++|+||+||||||+|||+||||+| |+|+++||+++++++++|+++++
T Consensus 1 f~~vvllyr~~~~~~~~~~~~~~~~~~~~~~~~~i~lK~FkdIP~aDLE~llP~~k-v~~~~~D~~~l~~~~vvg~v~~~ 79 (141)
T PF12576_consen 1 FEEVVLLYRFKDSRKFKAKKESIQEAPKKFKPGPIYLKSFKDIPMADLEMLLPEKK-VRMRPFDRVKLGVSAVVGGVAVF 79 (141)
T ss_pred CcEEEEEEEecccccchhhhhhhhhccccCCCCCeEEEEeCCCCccchhHhCCCCc-CCcCHHHHHHHHHHHHHHHHHHH
Confidence 899999999987543 1 37899999999999999999999998 89999999999999999999999
Q ss_pred hhcccch----hh--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCChh
Q 014161 268 TSAQLHE----ID--LWVGMAILSTVIGYCAKTYFTFQQNMAAYQNMITQSMYDKQLDSGKG 323 (429)
Q Consensus 268 ~~l~~~~----~d--~~v~~a~Ls~l~g~~~R~~~~y~~~r~rY~~~lt~~LY~K~l~nn~G 323 (429)
+++..+. ++ ++..+++++++++||+|+|++|+|+|.+||+++|++|||||+|||+|
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~r~~~~~~~~~~ry~~~l~~~LY~K~l~sn~G 141 (141)
T PF12576_consen 80 VKLVGMSLLLLSDIFLILILSLLSALGGYAFRQYTGYKNNRARYQLLLTKTLYFKNLDSNRG 141 (141)
T ss_pred HHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC
Confidence 8865443 22 56677778899999999999999999999999999999999999998
No 2
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=91.95 E-value=0.74 Score=41.44 Aligned_cols=71 Identities=21% Similarity=0.244 Sum_probs=53.7
Q ss_pred HHHHHHh-hcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCC----Cc----eEEechhhHHHHHh
Q 014161 342 ISFFILM-EQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTI----GR----YYCVGLKRSNEIIG 412 (429)
Q Consensus 342 LAY~~Ll-~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~----g~----~~avpL~~A~~~l~ 412 (429)
=+|..|+ .+|++|.++|.+....= +. -|.+||++|..-|||.+... |+ |.++|.++..+++.
T Consensus 31 ~v~~~LL~~~~~~tvdelae~lnr~---rS------tv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~ 101 (126)
T COG3355 31 EVYKALLEENGPLTVDELAEILNRS---RS------TVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKIL 101 (126)
T ss_pred HHHHHHHhhcCCcCHHHHHHHHCcc---HH------HHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHH
Confidence 3677788 68999999998776532 11 37899999999999988642 43 46999999999988
Q ss_pred hhHHHHHHH
Q 014161 413 TTTEEMVLK 421 (429)
Q Consensus 413 ~~w~~~~~~ 421 (429)
+.-++...+
T Consensus 102 ~~l~~w~~~ 110 (126)
T COG3355 102 KDLDEWYDK 110 (126)
T ss_pred HHHHHHHHH
Confidence 876555444
No 3
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=90.31 E-value=0.25 Score=38.49 Aligned_cols=54 Identities=28% Similarity=0.372 Sum_probs=40.3
Q ss_pred HHHHHhhcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCC--ceEEechh
Q 014161 343 SFFILMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIG--RYYCVGLK 405 (429)
Q Consensus 343 AY~~Ll~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g--~~~avpL~ 405 (429)
+|..|++.|++|.++|...+ |++- =.|.++|++|++.|+|.+...+ .|.|+|++
T Consensus 13 vy~~Ll~~~~~t~~eIa~~l--------~i~~-~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~~pe 68 (68)
T PF01978_consen 13 VYLALLKNGPATAEEIAEEL--------GISR-STVYRALKSLEEKGLVEREEGRPKVYRAVPPE 68 (68)
T ss_dssp HHHHHHHHCHEEHHHHHHHH--------TSSH-HHHHHHHHHHHHTTSEEEEEECCEEEEEE-HH
T ss_pred HHHHHHHcCCCCHHHHHHHH--------CcCH-HHHHHHHHHHHHCCCEEEEcCceEEEEEeCCC
Confidence 57777788999999987654 3332 2578999999999999887643 47888875
No 4
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=79.14 E-value=6.6 Score=36.72 Aligned_cols=63 Identities=22% Similarity=0.275 Sum_probs=44.8
Q ss_pred CCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEec---------hhhHHHHHhhhHHHHHHHH
Q 014161 353 ATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVG---------LKRSNEIIGTTTEEMVLKA 422 (429)
Q Consensus 353 lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avp---------L~~A~~~l~~~w~~~~~~~ 422 (429)
.+++||.++|-- ++..+ +|.+||+.|+++||+.++.+|.|.... ...|+......|-++-..|
T Consensus 40 ~d~~~iak~l~p------~is~~-ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~~~lA~~a 111 (171)
T PF14394_consen 40 PDPEWIAKRLRP------KISAE-EVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTSSEIPSEAVRSYHKQMLELAQEA 111 (171)
T ss_pred CCHHHHHHHhcC------CCCHH-HHHHHHHHHHHCCCeEECCCCcEEEecceeeCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 467766666511 33322 689999999999999999988885544 4667777777777766554
No 5
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=75.53 E-value=15 Score=32.14 Aligned_cols=63 Identities=16% Similarity=0.336 Sum_probs=36.8
Q ss_pred CChhhHHHHHHHHHH-hHhhh--hhhcccc--hhhHH----HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHH
Q 014161 247 LTPLDWVKFLVSAVV-GLVAV--ITSAQLH--EIDLW----VGMAILSTVIGYCAKTYFT---FQQNMAAYQNMI 309 (429)
Q Consensus 247 ~~~~D~~~l~v~avv-g~vav--~~~l~~~--~~d~~----v~~a~Ls~l~g~~~R~~~~---y~~~r~rY~~~l 309 (429)
|+..|-+.+++...+ |+++. +-.++++ ++..| .++++++=+++|.+|+.++ |.++|.+|...+
T Consensus 1 MtR~dvl~Iglgv~~~Gg~~Y~~l~~~G~d~~~AGi~sq~~lv~glvgW~~sYlfRV~t~~MTy~~Q~k~Ye~a~ 75 (104)
T PF11460_consen 1 MTRIDVLLIGLGVFLLGGLLYGGLQAAGLDSLSAGIWSQALLVLGLVGWVSSYLFRVVTGKMTYMQQRKDYEEAV 75 (104)
T ss_pred CcccceeeecHHHHHHHHHHHHHHHHcCCCchhhhHHHHHHHHHHHHHHHhHHHhhhccCCCcHHHHHHHHHHHH
Confidence 344566655555433 33332 3344444 23333 2334445567799999875 999999998865
No 6
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=75.28 E-value=8.3 Score=38.15 Aligned_cols=71 Identities=24% Similarity=0.268 Sum_probs=56.2
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCC--CceEEechhhHHHHHhhhHHHHH
Q 014161 342 ISFFILMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTI--GRYYCVGLKRSNEIIGTTTEEMV 419 (429)
Q Consensus 342 LAY~~Ll~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~--g~~~avpL~~A~~~l~~~w~~~~ 419 (429)
=+|.-|+..|++|+.++-+ ..|+.-. -|=|-|+.|++-|+|...++ ..|.|+|+++.++.+...+++.+
T Consensus 20 ~vY~aLl~~g~~tA~eis~--------~sgvP~~-kvY~vl~sLe~kG~v~~~~g~P~~y~av~p~~~i~~~~~~~~~~~ 90 (247)
T COG1378 20 KVYLALLCLGEATAKEISE--------ASGVPRP-KVYDVLRSLEKKGLVEVIEGRPKKYRAVPPEELIERIKEELQELL 90 (247)
T ss_pred HHHHHHHHhCCccHHHHHH--------HcCCCch-hHHHHHHHHHHCCCEEeeCCCCceEEeCCHHHHHHHHHHHHHHHH
Confidence 3799999999999999864 4455433 25578999999999977532 36999999999999999988876
Q ss_pred HH
Q 014161 420 LK 421 (429)
Q Consensus 420 ~~ 421 (429)
..
T Consensus 91 ~~ 92 (247)
T COG1378 91 RE 92 (247)
T ss_pred HH
Confidence 55
No 7
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=67.27 E-value=1.2e+02 Score=31.86 Aligned_cols=39 Identities=10% Similarity=0.309 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCce
Q 014161 352 KATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRY 399 (429)
Q Consensus 352 ~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~ 399 (429)
+.|.++|.++. +.+.+ .+++-+++|++.|++.++.+|.|
T Consensus 310 ~~t~~~La~~l--------~~~~~-~v~~iL~~L~~agLI~~~~~g~~ 348 (412)
T PRK04214 310 ALDVDEIRRLE--------PMGYD-ELGELLCELARIGLLRRGERGQW 348 (412)
T ss_pred CCCHHHHHHHh--------CCCHH-HHHHHHHHHHhCCCeEecCCCce
Confidence 37888876554 33332 57899999999999998776654
No 8
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=60.74 E-value=26 Score=35.26 Aligned_cols=38 Identities=18% Similarity=0.325 Sum_probs=28.8
Q ss_pred HHHHHhCCcceec-HHHHHHHHHHcCeeeecCCCceEEe
Q 014161 365 LIKEEFGESCNFD-VDDAVHKLEKLGIVARDTIGRYYCV 402 (429)
Q Consensus 365 wL~~~fg~~vdFd-v~dAL~kL~rLgLv~~d~~g~~~av 402 (429)
||....+-.|.=+ |.+||+.|+++||+.++.+|.|..+
T Consensus 142 ~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y~~t 180 (271)
T TIGR02147 142 ELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFYKQT 180 (271)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcEEee
Confidence 4445556555554 8999999999999999988987443
No 9
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=56.91 E-value=94 Score=26.12 Aligned_cols=82 Identities=12% Similarity=0.160 Sum_probs=53.8
Q ss_pred HHHHH--HhhcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeec--C--CC----ceEEechh-hHHHH
Q 014161 342 ISFFI--LMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARD--T--IG----RYYCVGLK-RSNEI 410 (429)
Q Consensus 342 LAY~~--Ll~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d--~--~g----~~~avpL~-~A~~~ 410 (429)
+.|++ ++..++.+.-+|-+.+++.....+..+- =.+-.+|.+|++.|+|+.. . .| .|..+|-- ++++.
T Consensus 5 l~~~iL~~L~~~~~~GYei~~~l~~~~~~~~~i~~-gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~ 83 (100)
T TIGR03433 5 LDLLILKTLSLGPLHGYGIAQRIQQISEDVLQVEE-GSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAA 83 (100)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHcCCccccCC-CcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHH
Confidence 34444 3357889999999999887532222221 1366799999999999872 1 12 25555543 44566
Q ss_pred HhhhHHHHHHHHhc
Q 014161 411 IGTTTEEMVLKAQQ 424 (429)
Q Consensus 411 l~~~w~~~~~~~~~ 424 (429)
..+.|+++.....+
T Consensus 84 ~~~~~~~~~~~i~~ 97 (100)
T TIGR03433 84 ETESWARLSAAIAR 97 (100)
T ss_pred HHHHHHHHHHHHHH
Confidence 88889998876554
No 10
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=56.39 E-value=18 Score=34.48 Aligned_cols=61 Identities=30% Similarity=0.387 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHHhhcCC-CCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEechh
Q 014161 334 QQEVKEVIISFFILMEQGK-ATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVGLK 405 (429)
Q Consensus 334 eQe~KEaiLAY~~Ll~~g~-lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avpL~ 405 (429)
-++++|+|+.--+- +|. ++ |+.|.++||++- -.|-+||..|+..|||...++..+.+.|++
T Consensus 22 y~~Lr~~Il~g~l~--pG~~l~--------e~~La~~~gvSr-tPVReAL~rL~~eGlv~~~p~rG~~V~~~~ 83 (230)
T COG1802 22 YEELREAILSGELA--PGERLS--------EEELAEELGVSR-TPVREALRRLEAEGLVEIEPNRGAFVAPLS 83 (230)
T ss_pred HHHHHHHHHhCCCC--CCCCcc--------HHHHHHHhCCCC-ccHHHHHHHHHHCCCeEecCCCCCeeCCCC
Confidence 35666666643321 332 44 566778899885 489999999999999999987665555544
No 11
>PF14015 DUF4231: Protein of unknown function (DUF4231)
Probab=54.00 E-value=62 Score=27.14 Aligned_cols=18 Identities=17% Similarity=0.504 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 014161 291 CAKTYFTFQQNMAAYQNM 308 (429)
Q Consensus 291 ~~R~~~~y~~~r~rY~~~ 308 (429)
++...++|++++.+|...
T Consensus 67 ~~~~~~~~~~~W~~~r~t 84 (112)
T PF14015_consen 67 SLAAFFRFHERWIRYRAT 84 (112)
T ss_pred HHHHHhchhHHHHHHHHH
Confidence 457778899998888763
No 12
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=53.73 E-value=59 Score=25.61 Aligned_cols=56 Identities=25% Similarity=0.394 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHhhcCC--CCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecC-C-CceEE
Q 014161 335 QEVKEVIISFFILMEQGK--ATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDT-I-GRYYC 401 (429)
Q Consensus 335 Qe~KEaiLAY~~Ll~~g~--lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~-~-g~~~a 401 (429)
.+.+|.||.+ |.++|+ +|..+|. .++|..-. .|...|.+|++.|+|.+++ . +.|..
T Consensus 5 ~~~~~~IL~~--L~~~g~~~~ta~eLa--------~~lgl~~~-~v~r~L~~L~~~G~V~~~~~~~~~W~i 64 (68)
T smart00550 5 DSLEEKILEF--LENSGDETSTALQLA--------KNLGLPKK-EVNRVLYSLEKKGKVCKQGGTPPLWKL 64 (68)
T ss_pred hHHHHHHHHH--HHHCCCCCcCHHHHH--------HHHCCCHH-HHHHHHHHHHHCCCEEecCCCCCceEe
Confidence 4556666654 445666 8888765 45788877 8999999999999998865 3 45543
No 13
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=49.56 E-value=1.2e+02 Score=28.69 Aligned_cols=69 Identities=23% Similarity=0.284 Sum_probs=52.6
Q ss_pred HHhhcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeee----c-CCCceEE---echhhHHHHHhhhHHH
Q 014161 346 ILMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVAR----D-TIGRYYC---VGLKRSNEIIGTTTEE 417 (429)
Q Consensus 346 ~Ll~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~----d-~~g~~~a---vpL~~A~~~l~~~w~~ 417 (429)
.|..+|.+|.++|.. ..|.+.. +|...|.+|.+.|||+. + ..|+++. +..+++..+|..+=..
T Consensus 30 ~L~~~g~~tdeeLA~--------~Lgi~~~-~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~~~ 100 (178)
T PRK06266 30 ALIKKGEVTDEEIAE--------QTGIKLN-TVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKKKME 100 (178)
T ss_pred HHHHcCCcCHHHHHH--------HHCCCHH-HHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHHHHH
Confidence 466788899988764 4576554 78999999999999983 3 2366544 8889999999988877
Q ss_pred HHHHHh
Q 014161 418 MVLKAQ 423 (429)
Q Consensus 418 ~~~~~~ 423 (429)
++.+-+
T Consensus 101 ~~~klk 106 (178)
T PRK06266 101 ELKKLK 106 (178)
T ss_pred HHHHHH
Confidence 776643
No 14
>PF04369 Lactococcin: Lactococcin-like family; InterPro: IPR007464 Bacteriocins are produced by bacteria to inhibit the growth of similar or closely related bacterial strains. The class II bacteriocins are small heat-stable proteins for which disulphide bonds are the only modification to the peptide. Lactococcin A and B are class-IId bacteriocins (one-peptide non-pediocin-like bacteriocin) [, ].; GO: 0042742 defense response to bacterium, 0005576 extracellular region
Probab=47.65 E-value=13 Score=29.60 Aligned_cols=28 Identities=29% Similarity=0.370 Sum_probs=20.7
Q ss_pred hhhc-CCcccCHHHHHHHhcCCceeeecc
Q 014161 46 MDKS-NFKITTDEEIDVALSGQYLLHLPI 73 (429)
Q Consensus 46 m~~a-nF~~Ls~~e~~~Al~~~yll~Lpi 73 (429)
|++- ||+++|++|++..-.+.|-+.+..
T Consensus 1 m~~~~nf~~~sdeeL~~i~GG~l~~iqs~ 29 (60)
T PF04369_consen 1 MENQLNFNILSDEELSKINGGGLPYIQSN 29 (60)
T ss_pred CcccccceecCHHHHhhccCCcceeeeec
Confidence 3444 999999999999877755555543
No 15
>PRK06743 flagellar motor protein MotP; Reviewed
Probab=44.65 E-value=1.8e+02 Score=29.08 Aligned_cols=67 Identities=15% Similarity=0.121 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCChhHHHHHHhHHHHHHHHHHHHHHHHH-hhcCCCCHHHHHHHHHHHHHH
Q 014161 298 FQQNMAAYQNMITQSMYDKQLDSGKGTLLHLCDDVIQQEVKEVIISFFIL-MEQGKATRQDLDLRCEELIKE 368 (429)
Q Consensus 298 y~~~r~rY~~~lt~~LY~K~l~nn~GvL~~L~D~AeeQe~KEaiLAY~~L-l~~g~lT~~~Ld~~~E~wL~~ 368 (429)
|+.++..|+..+......-+.+...|++ +| +.+.++.++..+..++- ...|. +++++.+..|+-+..
T Consensus 64 f~~~~~~~~~~i~~l~~la~~aRr~GlL-aL--E~~~~~~~d~fl~~gl~l~vdg~-~~e~i~~~le~~~~~ 131 (254)
T PRK06743 64 LHRREEDLEQLTDLFVDFSKKSKKHGLL-SL--EVDGEQVDNPFIQKGIRLMLSGY-DEDELKEVLMKDVET 131 (254)
T ss_pred HcCCCCCHHHHHHHHHHHHHHHHhcCHH-HH--HhhccCCccHHHHHHHHHHHCCC-CHHHHHHHHHHHHHH
Confidence 4455667888888877778888888843 33 33345556788888873 33454 666666655555443
No 16
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=42.48 E-value=38 Score=31.92 Aligned_cols=39 Identities=10% Similarity=0.188 Sum_probs=30.9
Q ss_pred HHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEechh
Q 014161 366 IKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVGLK 405 (429)
Q Consensus 366 L~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avpL~ 405 (429)
|.++||+.-. .|-+||..|+..|||...++..+.+.++.
T Consensus 36 Lae~lgVSRt-pVREAL~~L~~eGlv~~~~~~G~~V~~~~ 74 (224)
T PRK11534 36 LTSRYALGVG-PLREALSQLVAERLVTVVNQKGYRVASMS 74 (224)
T ss_pred HHHHHCCChH-HHHHHHHHHHHCCCEEEeCCCceEeCCCC
Confidence 5677888875 99999999999999988776555555544
No 17
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=42.39 E-value=75 Score=26.24 Aligned_cols=35 Identities=20% Similarity=0.190 Sum_probs=29.8
Q ss_pred cceecHHHHHHHHHHcCeeeecCCCceEEechhhH
Q 014161 373 SCNFDVDDAVHKLEKLGIVARDTIGRYYCVGLKRS 407 (429)
Q Consensus 373 ~vdFdv~dAL~kL~rLgLv~~d~~g~~~avpL~~A 407 (429)
...+.+.=|+..|.+-|+|.+...|.|...+.-.+
T Consensus 52 ~~~~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G~~ 86 (92)
T PF14338_consen 52 RFKNRIRWARSYLKKAGLIERPKRGIWRITEKGRK 86 (92)
T ss_pred hHHHhHHHHHHHHHHCCCccCCCCCceEECHhHHH
Confidence 68889999999999999998877798988876443
No 18
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=41.91 E-value=21 Score=30.50 Aligned_cols=20 Identities=35% Similarity=0.606 Sum_probs=17.7
Q ss_pred cHHHHHHHHHHcCeeeecCC
Q 014161 377 DVDDAVHKLEKLGIVARDTI 396 (429)
Q Consensus 377 dv~dAL~kL~rLgLv~~d~~ 396 (429)
+|.+++++|+++|||.+..+
T Consensus 37 ~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 37 EVREALEKLEEMGLLERVEG 56 (92)
T ss_pred HHHHHHHHHHHCCCeEEecC
Confidence 68899999999999988764
No 19
>PHA01814 hypothetical protein
Probab=39.80 E-value=5.8 Score=35.17 Aligned_cols=58 Identities=24% Similarity=0.371 Sum_probs=43.1
Q ss_pred HhcCCceeeeccccccccchHHHHHHHhhhccCCCCcCccCceeeecCCCccccCcchhhHHhHHHHHHHHHH
Q 014161 62 ALSGQYLLHLPITVNESKLDKKLLKRYFEEHHHDHLPDFADKYVIFRRGIGVDQTTDYFFMEKVDMLIGRFWS 134 (429)
Q Consensus 62 Al~~~yll~Lpi~vd~~klD~~ll~~y~~~~~~~~Lp~~~d~~liFrRG~g~d~~~g~~~~eKld~L~~~~~~ 134 (429)
-.++.=||||.|++|-+|.==..|+-||.+|.++ --+||+||+-. .-.+|-.+|.+=.
T Consensus 55 ~~~e~dlftldididikkhvfn~l~~yy~~~~~~-------~~iiykk~v~m--------~~tiddvls~fek 112 (137)
T PHA01814 55 TKNENDLFTLDIDIDIKKHVFNCLKVYYIEHTED-------INIIYKKGVYM--------GCTIDDVLSNFEK 112 (137)
T ss_pred cccccceEEEEeeeehhhheeeeEEEeeeccccc-------ceeeeecceEE--------ccCHHHHHhhccC
Confidence 4577789999999999998777788888877665 46899998743 3446666665543
No 20
>PRK08868 flagellar protein FlaG; Provisional
Probab=39.34 E-value=27 Score=32.24 Aligned_cols=63 Identities=19% Similarity=0.230 Sum_probs=49.5
Q ss_pred CCHHHHHHHHH---HHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEechhhHHHHHhhhHHH
Q 014161 353 ATRQDLDLRCE---ELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVGLKRSNEIIGTTTEE 417 (429)
Q Consensus 353 lT~~~Ld~~~E---~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avpL~~A~~~l~~~w~~ 417 (429)
++.++|...+| .+|. .++.++.|.+++-..+.. -.++..+++..+.=+|.+++++++...|+.
T Consensus 68 ~~~eel~~aVeklNe~~~-~~n~~L~F~vdeetgr~V-VkViD~~T~EVIRQIP~Ee~L~la~~l~e~ 133 (144)
T PRK08868 68 LNREELEKMVEQMNEFVK-SINKGLSFRVDEESGRDV-VTIYEASTGDIIRQIPDEEMLEVLRRLAEQ 133 (144)
T ss_pred cCHHHHHHHHHHHHHHHH-hhcCceEEEEecCCCCEE-EEEEECCCCceeeeCCCHHHHHHHHHHHHh
Confidence 67888876655 5664 679999999998765554 446666777889999999999999998853
No 21
>PF07120 DUF1376: Protein of unknown function (DUF1376); InterPro: IPR010781 This entry is represented by Bacteriophage PBC5 (Sinorhizobium phage PBC5), Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown.
Probab=39.26 E-value=52 Score=27.25 Aligned_cols=63 Identities=13% Similarity=0.220 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHHH-HHhhcCChhHHHHHHhHH--HHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Q 014161 302 MAAYQNMITQSMY-DKQLDSGKGTLLHLCDDV--IQQEVKEVIISFFILMEQGKATRQDLDLRCEE 364 (429)
Q Consensus 302 r~rY~~~lt~~LY-~K~l~nn~GvL~~L~D~A--eeQe~KEaiLAY~~Ll~~g~lT~~~Ld~~~E~ 364 (429)
+-.|..++-.+.. .+.+-++..+|..++... +.+...+.+|..+|....|......+++++++
T Consensus 22 ~gaY~~Ll~~~~~~~~plp~d~~~Lar~~~~s~~~~~~a~~~ll~~f~~~~dg~~~~~r~e~Ei~~ 87 (88)
T PF07120_consen 22 HGAYMRLLDLYYDTEGPLPDDDKRLARICGCSTKEWRKALDFLLREFFRLEDGRWWNKRCEEEIAK 87 (88)
T ss_pred HHHHHHHHHHHHHhCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHhCCCCCCCCEehHHHHHHHHh
Confidence 4566666655444 567889999999999876 66788899999999666677887777777664
No 22
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=38.34 E-value=1.7e+02 Score=26.98 Aligned_cols=72 Identities=22% Similarity=0.340 Sum_probs=52.8
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeec----CC-Cc---eEEechhhHHHHHh
Q 014161 341 IISFFILMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARD----TI-GR---YYCVGLKRSNEIIG 412 (429)
Q Consensus 341 iLAY~~Ll~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d----~~-g~---~~avpL~~A~~~l~ 412 (429)
+..--.|..+|.+|.++|.. ..|.+.+ +|.+.|.+|.+.|||+.. .+ |. +..+..+++...|.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~--------~Lgi~~~-~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik 87 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISL--------ELGIKLN-EVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLK 87 (158)
T ss_pred HHHHHHHhccCCCCHHHHHH--------HHCCCHH-HHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHH
Confidence 44444577788899988764 4577766 699999999999999432 22 32 23579999999999
Q ss_pred hhHHHHHHH
Q 014161 413 TTTEEMVLK 421 (429)
Q Consensus 413 ~~w~~~~~~ 421 (429)
.+=..++.+
T Consensus 88 ~~~~~~~~~ 96 (158)
T TIGR00373 88 RKLEETAKK 96 (158)
T ss_pred HHHHHHHHH
Confidence 887777665
No 23
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=35.17 E-value=1.2e+02 Score=24.54 Aligned_cols=32 Identities=25% Similarity=0.215 Sum_probs=25.4
Q ss_pred cHHHHHHHHHHcCeeeecCCCceEEechhhHH
Q 014161 377 DVDDAVHKLEKLGIVARDTIGRYYCVGLKRSN 408 (429)
Q Consensus 377 dv~dAL~kL~rLgLv~~d~~g~~~avpL~~A~ 408 (429)
.+.+++..|++.|+|.+.+++.+...|.-.+.
T Consensus 15 tvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~ 46 (96)
T smart00529 15 TVTQMLKKLEKDGLVEYEPYRGITLTEKGRRL 46 (96)
T ss_pred HHHHHHHHHHHCCCEEEcCCCceEechhHHHH
Confidence 46789999999999999887777776655543
No 24
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=35.07 E-value=2.2e+02 Score=22.35 Aligned_cols=42 Identities=33% Similarity=0.473 Sum_probs=30.0
Q ss_pred HHhhcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCC
Q 014161 346 ILMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTI 396 (429)
Q Consensus 346 ~Ll~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~ 396 (429)
.|...|++|..+|... ++.+ .-.+..++.+|++.|+|++...
T Consensus 18 ~l~~~~~~~~~~la~~--------~~~s-~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 18 ILYEEGPLSVSELAKR--------LGVS-PSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred HHHHcCCcCHHHHHHH--------HCCC-chhHHHHHHHHHHCCCeEecCC
Confidence 3445677888888544 2333 3458899999999999987643
No 25
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=34.23 E-value=61 Score=24.71 Aligned_cols=37 Identities=19% Similarity=0.338 Sum_probs=23.7
Q ss_pred HHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEec
Q 014161 366 IKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVG 403 (429)
Q Consensus 366 L~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avp 403 (429)
+.++||.+..=...++++++++.|+|..+ ++++.+.|
T Consensus 26 ~~~~~g~~~~~~~~~~l~~l~~~Gll~~~-~~~l~lT~ 62 (66)
T PF06969_consen 26 FEQRFGIDFAEEFQKELEELQEDGLLEID-GGRLRLTE 62 (66)
T ss_dssp HHHHTT--THHH-HHHHHHHHHTTSEEE--SSEEEE-T
T ss_pred HHHHHCcCHHHHHHHHHHHHHHCCCEEEe-CCEEEECc
Confidence 44567776333337789999999999775 57777765
No 26
>PF11469 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR021568 This archaeal family of proteins has no known function. ; PDB: 1ZTD_A.
Probab=33.15 E-value=43 Score=29.64 Aligned_cols=22 Identities=27% Similarity=0.572 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHhhcCCCCHHH
Q 014161 334 QQEVKEVIISFFILMEQGKATRQD 357 (429)
Q Consensus 334 eQe~KEaiLAY~~Ll~~g~lT~~~ 357 (429)
--++.||++||+|| .|.+|.+|
T Consensus 58 kGd~aEA~iAyAWL--eg~it~eE 79 (120)
T PF11469_consen 58 KGDIAEALIAYAWL--EGKITIEE 79 (120)
T ss_dssp HHHHHHHHHHHHHH--TTSS-HHH
T ss_pred ccHHHHHHHHHHHH--hccccHHH
Confidence 45788999999999 47777654
No 27
>PF11880 DUF3400: Domain of unknown function (DUF3400); InterPro: IPR021817 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 50 amino acids in length. This domain is found associated with PF02754 from PFAM, PF02913 from PFAM, PF01565 from PFAM.
Probab=32.09 E-value=44 Score=25.16 Aligned_cols=24 Identities=17% Similarity=0.332 Sum_probs=19.9
Q ss_pred hhhHHHHHhhhH-HHHHHHHhcCCC
Q 014161 404 LKRSNEIIGTTT-EEMVLKAQQGIS 427 (429)
Q Consensus 404 L~~A~~~l~~~w-~~~~~~~~~~~~ 427 (429)
.+=|.++|++.| .+.|.+|++|+-
T Consensus 16 VEmA~~lLGe~W~~~~v~~a~~GGI 40 (45)
T PF11880_consen 16 VEMARHLLGENWQQDYVERANNGGI 40 (45)
T ss_pred HHHHHHHhhhhHHHHHHHHHHcCCe
Confidence 356899999999 578999999963
No 28
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=31.17 E-value=60 Score=24.23 Aligned_cols=44 Identities=25% Similarity=0.354 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEec
Q 014161 351 GKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVG 403 (429)
Q Consensus 351 g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avp 403 (429)
+++|.++|.+. +|.. .-.+.+++.+|++.|+|..+..|.|...|
T Consensus 24 ~~~s~~ela~~--------~g~s-~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 24 LPLTRQEIADY--------LGLT-RETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred CCcCHHHHHHH--------HCCC-HHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 34666666543 4443 34578999999999999887657776544
No 29
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=30.81 E-value=3.2e+02 Score=26.18 Aligned_cols=25 Identities=28% Similarity=0.351 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 014161 279 VGMAILSTVIGYCAKTYFTFQQNMA 303 (429)
Q Consensus 279 v~~a~Ls~l~g~~~R~~~~y~~~r~ 303 (429)
...+.++++++.++|.|.+|++++.
T Consensus 33 ~~~Gg~AalG~lA~~ayq~~q~~~~ 57 (188)
T PF04391_consen 33 LKYGGLAALGGLAYKAYQNWQQNQG 57 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCC
Confidence 3455567788899999999977643
No 30
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=29.65 E-value=78 Score=30.55 Aligned_cols=41 Identities=24% Similarity=0.209 Sum_probs=30.5
Q ss_pred HHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEech
Q 014161 363 EELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVGL 404 (429)
Q Consensus 363 E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avpL 404 (429)
|+-|.++||+.-. .|-+||..|+..|||...++....+.+.
T Consensus 36 E~eLa~~~gVSRt-pVREAL~~L~~eGlV~~~~~~G~~V~~~ 76 (257)
T PRK10225 36 EREIAEMLDVTRT-VVREALIMLEIKGLVEVRRGAGIYVLDS 76 (257)
T ss_pred HHHHHHHhCCCHH-HHHHHHHHHHHCCCEEEecCCEEEEeCC
Confidence 4445667888754 7999999999999998777655555444
No 31
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=29.43 E-value=79 Score=30.33 Aligned_cols=42 Identities=19% Similarity=0.221 Sum_probs=31.7
Q ss_pred HHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEechh
Q 014161 363 EELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVGLK 405 (429)
Q Consensus 363 E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avpL~ 405 (429)
|+-|.++||+.= =.|-+||..|+..|||...++....+.++.
T Consensus 34 E~eLa~~~gVSR-tpVREAL~~L~~eGlV~~~~~~G~~V~~~~ 75 (251)
T PRK09990 34 ERRLCEKLGFSR-SALREGLTVLRGRGIIETAQGRGSFVARLN 75 (251)
T ss_pred HHHHHHHHCCCH-HHHHHHHHHHHHCCCEEEeCCCeeEEecCC
Confidence 455667888874 489999999999999988776555555543
No 32
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=28.87 E-value=61 Score=23.37 Aligned_cols=33 Identities=27% Similarity=0.361 Sum_probs=25.2
Q ss_pred HHHHhCCcceecHHHHHHHHHHcCeeeecCCCce
Q 014161 366 IKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRY 399 (429)
Q Consensus 366 L~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~ 399 (429)
|.+.+|+.. =.|.+++.+|++.|++....++.+
T Consensus 26 la~~~~vs~-~tv~~~l~~L~~~g~i~~~~~~g~ 58 (60)
T smart00345 26 LAAQLGVSR-TTVREALSRLEAEGLVQRRPGSGT 58 (60)
T ss_pred HHHHHCCCH-HHHHHHHHHHHHCCCEEEecCCee
Confidence 445667764 579999999999999987665444
No 33
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=27.05 E-value=1e+02 Score=22.59 Aligned_cols=54 Identities=28% Similarity=0.390 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCc--eEEech-hhHHHHHhhhH
Q 014161 353 ATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGR--YYCVGL-KRSNEIIGTTT 415 (429)
Q Consensus 353 lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~--~~avpL-~~A~~~l~~~w 415 (429)
.+.+++.. .+|+. .=.+..++..|++.|++.....+. +..+.. +++.+.+.+.|
T Consensus 21 ~~~~ei~~--------~~~i~-~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~g~~~~~~~~~~~ 77 (78)
T cd00090 21 LTVSELAE--------RLGLS-QSTVSRHLKKLEEAGLVESRREGRRVYYSLTDAERLLALLESLL 77 (78)
T ss_pred cCHHHHHH--------HHCcC-HhHHHHHHHHHHHCCCeEEEEeccEEEEEeCCchHHHHHHHHhh
Confidence 66666533 34543 234789999999999998765542 233322 56666666655
No 34
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=26.89 E-value=3.4e+02 Score=25.78 Aligned_cols=71 Identities=13% Similarity=0.048 Sum_probs=40.0
Q ss_pred HhhcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecC---CCceEEech-hhHHHHHhh---hHHHHH
Q 014161 347 LMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDT---IGRYYCVGL-KRSNEIIGT---TTEEMV 419 (429)
Q Consensus 347 Ll~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~---~g~~~avpL-~~A~~~l~~---~w~~~~ 419 (429)
|...+.+|..+|.+. +..++. .+...+++|++-|+|.+.. +.+...+-| +++.+.+++ .+++.-
T Consensus 54 L~~~~~itq~eLa~~---l~l~~s------Tvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~~~~~~~e 124 (185)
T PRK13777 54 AYHLKGASISEIAKF---GVMHVS------TAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETMEEYDPEN 124 (185)
T ss_pred HHhCCCcCHHHHHHH---HCCCHh------hHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHHHHH
Confidence 344566887776543 222211 2788999999999999864 345444444 444444443 344444
Q ss_pred HHHhcCC
Q 014161 420 LKAQQGI 426 (429)
Q Consensus 420 ~~~~~~~ 426 (429)
.++-+|-
T Consensus 125 ~~~~~~~ 131 (185)
T PRK13777 125 NSVFNGA 131 (185)
T ss_pred HHHHhcc
Confidence 4444443
No 35
>PRK14137 recX recombination regulator RecX; Provisional
Probab=26.40 E-value=65 Score=30.90 Aligned_cols=66 Identities=14% Similarity=0.205 Sum_probs=44.8
Q ss_pred CChhHHHHHHhHHHHHHHHHHHHHHHH-HhhcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCee
Q 014161 320 SGKGTLLHLCDDVIQQEVKEVIISFFI-LMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIV 391 (429)
Q Consensus 320 nn~GvL~~L~D~AeeQe~KEaiLAY~~-Ll~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv 391 (429)
+..++...-+.....+|..+.+..|++ +++...-|..||...-..+ |.+ +-.|+.+|.+|.+.|++
T Consensus 21 ~~~~~~~~~~~~~~~~e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~k-----g~~-~e~Ie~vI~rL~e~gyL 87 (195)
T PRK14137 21 TEGPVRPERRTPPTPDEAREALLAYAFRALAARAMTAAELRAKLERR-----SED-EALVTEVLERVQELGYQ 87 (195)
T ss_pred CCCCccccccCCCCHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHhc-----CCC-HHHHHHHHHHHHHcCCC
Confidence 334444444555678899999999997 7766666777765433222 222 35688999999999988
No 36
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=26.22 E-value=1.1e+02 Score=28.79 Aligned_cols=39 Identities=15% Similarity=0.262 Sum_probs=30.5
Q ss_pred HHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEechh
Q 014161 366 IKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVGLK 405 (429)
Q Consensus 366 L~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avpL~ 405 (429)
|.++||++-. .|-+||..|+..|||+..++..+.+.++.
T Consensus 40 La~~lgVSRt-pVREAL~~L~~eGLV~~~~~~g~~v~~~~ 78 (221)
T PRK11414 40 LAEQLGMSIT-PVREALLRLVSVNALSVAPAQAFTVPEVS 78 (221)
T ss_pred HHHHHCCCch-hHHHHHHHHHHCCCEEecCCCceeecCCC
Confidence 6778898754 89999999999999988776555554443
No 37
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=26.14 E-value=1.8e+02 Score=24.84 Aligned_cols=72 Identities=25% Similarity=0.396 Sum_probs=52.1
Q ss_pred HHhhcCCCCHHHHHHHHHH---HHHHHhCCcceecHHHHHHHHHHcCeeeecCCCc-eEEechhhHHHHHhhhHHHHHHH
Q 014161 346 ILMEQGKATRQDLDLRCEE---LIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGR-YYCVGLKRSNEIIGTTTEEMVLK 421 (429)
Q Consensus 346 ~Ll~~g~lT~~~Ld~~~E~---wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~-~~avpL~~A~~~l~~~w~~~~~~ 421 (429)
+||.+|++|..++-+.+.+ |=++ .|---|.+|.+-|+|++...|+ +...|+-.--+.......+++.+
T Consensus 11 ~lW~~~~~t~~eI~~~l~~~~~~~~s--------Tv~t~L~rL~~Kg~l~~~~~gr~~~Y~p~is~~e~~~~~~~~~l~~ 82 (115)
T PF03965_consen 11 ILWESGEATVREIHEALPEERSWAYS--------TVQTLLNRLVEKGFLTREKIGRAYVYSPLISREEYLAQELRQFLDR 82 (115)
T ss_dssp HHHHHSSEEHHHHHHHHCTTSS--HH--------HHHHHHHHHHHTTSEEEEEETTCEEEEESSSHHHHHHHHHHHHHHH
T ss_pred HHHhCCCCCHHHHHHHHHhccccchh--------HHHHHHHHHHhCCceeEeecCCceEEEeCCcHHHHHHHHHHHHHHH
Confidence 5788889999998777653 3222 3667899999999999987664 56667766677777777777776
Q ss_pred HhcC
Q 014161 422 AQQG 425 (429)
Q Consensus 422 ~~~~ 425 (429)
.-.|
T Consensus 83 ~~~g 86 (115)
T PF03965_consen 83 LFDG 86 (115)
T ss_dssp HSTT
T ss_pred HhCC
Confidence 5544
No 38
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=25.96 E-value=1.2e+02 Score=22.16 Aligned_cols=57 Identities=21% Similarity=0.365 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHh--hcCC-CC-HHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceE
Q 014161 335 QEVKEVIISFFILM--EQGK-AT-RQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYY 400 (429)
Q Consensus 335 Qe~KEaiLAY~~Ll--~~g~-lT-~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~ 400 (429)
+++.|.|....... ..|. ++ .++ |.+.+|+. .=.+.+++.+|++.|+|+..+...+.
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~--------la~~~~is-~~~v~~~l~~L~~~G~i~~~~~~~~~ 64 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERE--------LAEELGVS-RTTVREALRELEAEGLVERRPGRGTF 64 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHH--------HHHHHCCC-HHHHHHHHHHHHHCCCEEecCCCeEE
Confidence 45555555554432 2333 22 443 55566776 36788999999999999876544443
No 39
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=25.46 E-value=1e+02 Score=29.75 Aligned_cols=42 Identities=26% Similarity=0.146 Sum_probs=31.4
Q ss_pred HHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEechh
Q 014161 363 EELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVGLK 405 (429)
Q Consensus 363 E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avpL~ 405 (429)
|+-|.++||+.- -.|-+||..|+..|||+..++....+.++.
T Consensus 35 E~eLae~~gVSR-tpVREAL~~L~~eGlV~~~~~~G~~V~~~~ 76 (253)
T PRK11523 35 ERFIADEKNVSR-TVVREAIIMLEVEGYVEVRKGSGIHVVSNQ 76 (253)
T ss_pred HHHHHHHHCCCH-HHHHHHHHHHHHCCCEEEecCCeeEEecCC
Confidence 445667888874 489999999999999987776555555543
No 40
>COG2979 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.23 E-value=2.5e+02 Score=27.82 Aligned_cols=26 Identities=15% Similarity=0.206 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 014161 281 MAILSTVIGYCAKTYFTFQQNMAAYQ 306 (429)
Q Consensus 281 ~a~Ls~l~g~~~R~~~~y~~~r~rY~ 306 (429)
++.++++++.+.++|.+|++++.+-+
T Consensus 63 ~GglAAlG~laY~aY~N~q~~q~~~~ 88 (225)
T COG2979 63 LGGLAALGALAYKAYQNYQKGQIPAA 88 (225)
T ss_pred hhhHHHHHHHHHHHHHHHhccCcccc
Confidence 45567778888899999998875433
No 41
>PF12597 DUF3767: Protein of unknown function (DUF3767); InterPro: IPR022533 This group of proteins includes mitochodrial cytochrome c oxidase proteins [], and some transmembrane domain-containing proteins of unknown function known as FAM36A. Proteins in this family are typically between 112 and 199 amino acids in length.
Probab=24.20 E-value=3.9e+02 Score=23.73 Aligned_cols=62 Identities=13% Similarity=0.169 Sum_probs=31.6
Q ss_pred hHHHHHHHH--HHhHhhhhhhcccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 014161 251 DWVKFLVSA--VVGLVAVITSAQLH-EIDLWVGMAILSTVIGYCAKTYFTFQQNMAAYQNMITQSMYD 315 (429)
Q Consensus 251 D~~~l~v~a--vvg~vav~~~l~~~-~~d~~v~~a~Ls~l~g~~~R~~~~y~~~r~rY~~~lt~~LY~ 315 (429)
|-++.++++ ++|++.++..-... +.+|-+..-+++.+++| .|=.|+.++.+.+...+...|.
T Consensus 42 ~slL~Gi~~G~~vG~~~fl~~~~~~~A~nwavgsF~l~s~~~w---e~Cr~~r~~~~~~~~~~~e~~~ 106 (118)
T PF12597_consen 42 DSLLYGIAGGFGVGGLRFLFTSNPRKAANWAVGSFFLGSLGSW---EYCRYNRRKERQQMKRAVEAMQ 106 (118)
T ss_pred HHHHHHHHHHHHHHhhhhcccCCCccchhhhhHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
Confidence 555555554 55555555443332 33455544444444454 4455556666666555554443
No 42
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=23.75 E-value=1.2e+02 Score=29.30 Aligned_cols=40 Identities=23% Similarity=0.272 Sum_probs=30.4
Q ss_pred HHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEec
Q 014161 363 EELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVG 403 (429)
Q Consensus 363 E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avp 403 (429)
|+-|.++||+.-. .|-+||..|+..|||+..+++...+.+
T Consensus 29 E~eLae~~gVSRt-pVREAL~~Le~~GlV~~~~~~G~~V~~ 68 (253)
T PRK10421 29 ERQLAMQLGVSRN-SLREALAKLVSEGVLLSRRGGGTFIRW 68 (253)
T ss_pred HHHHHHHhCCCHH-HHHHHHHHHHHCCCEEEeCCCeEEEec
Confidence 4556677888754 899999999999999877664455544
No 43
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=23.47 E-value=1.4e+02 Score=27.70 Aligned_cols=40 Identities=23% Similarity=0.311 Sum_probs=29.9
Q ss_pred HHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEechh
Q 014161 365 LIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVGLK 405 (429)
Q Consensus 365 wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avpL~ 405 (429)
=|.++||++-. .|-+||..|+..|||...++..+.+.++.
T Consensus 39 ~La~~lgVSRt-pVReAL~~L~~eGlv~~~~~~G~~V~~~~ 78 (212)
T TIGR03338 39 DIAARLGVSRG-PVREAFRALEEAGLVRNEKNRGVFVREIS 78 (212)
T ss_pred HHHHHhCCChH-HHHHHHHHHHHCCCEEEecCCCeEEecCC
Confidence 34567787743 79999999999999988776556555543
No 44
>PF11286 DUF3087: Protein of unknown function (DUF3087); InterPro: IPR021438 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=23.00 E-value=6.6e+02 Score=23.86 Aligned_cols=41 Identities=22% Similarity=0.277 Sum_probs=21.7
Q ss_pred HHHHHHhHHHHHHHHHH--HHHHHHHhhc------C-CCCHHHHHHHHHHH
Q 014161 324 TLLHLCDDVIQQEVKEV--IISFFILMEQ------G-KATRQDLDLRCEEL 365 (429)
Q Consensus 324 vL~~L~D~AeeQe~KEa--iLAY~~Ll~~------g-~lT~~~Ld~~~E~w 365 (429)
.++.+-.+|++-+ -.| +|.||+.... + ..|-.++..+.|+.
T Consensus 95 kl~~ik~aa~~~d-~~Al~iL~FYy~g~~Q~~~LD~NTltl~~l~~e~~~l 144 (165)
T PF11286_consen 95 KLHKIKAAAEQGD-PDALKILRFYYQGLRQVYQLDDNTLTLSDLEKEQEQL 144 (165)
T ss_pred HHHHHHHHHHcCC-HHHHHHHHHHHHhHHHHHHhcCCcccHHHHHHHHHHH
Confidence 3455555555444 344 4566665532 2 27777776665543
No 45
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=22.17 E-value=1.3e+02 Score=28.90 Aligned_cols=40 Identities=23% Similarity=0.374 Sum_probs=29.7
Q ss_pred HHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEec
Q 014161 363 EELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVG 403 (429)
Q Consensus 363 E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avp 403 (429)
|.-|.++||+.- -.|-+||..|+..|||+..+++...+.+
T Consensus 37 E~eLa~~lgVSR-tpVREAL~~L~~eGlv~~~~~~G~~V~~ 76 (254)
T PRK09464 37 ERELAKQFDVSR-PSLREAIQRLEAKGLLLRRQGGGTFVQS 76 (254)
T ss_pred HHHHHHHhCCCH-HHHHHHHHHHHHCCCEEEecCceeEEec
Confidence 344556788774 4799999999999999887765444544
No 46
>PRK07738 flagellar protein FlaG; Provisional
Probab=21.85 E-value=97 Score=27.66 Aligned_cols=63 Identities=16% Similarity=0.216 Sum_probs=46.8
Q ss_pred CCHHHHHHHH---HHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEechhhHHHHHhhhHHH
Q 014161 353 ATRQDLDLRC---EELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVGLKRSNEIIGTTTEE 417 (429)
Q Consensus 353 lT~~~Ld~~~---E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avpL~~A~~~l~~~w~~ 417 (429)
.+.++++..+ +++|. ..+..+.|.+++-..... -.++..+++..+.=+|.+++++++...|+.
T Consensus 43 ~s~eel~~aveklN~~l~-~~~~~L~F~vdeet~~~v-VkVvD~~T~EVIRQIPpEe~L~l~~~m~e~ 108 (117)
T PRK07738 43 VSKEDLEEVVDGMNELLE-PSQTSLKFELHEKLNEYY-VQVVDERTNEVIREIPPKKLLDMYAAMMEF 108 (117)
T ss_pred CCHHHHHHHHHHHHHHHH-hcCCceEEEEecCCCcEE-EEEEECCCCeeeeeCCCHHHHHHHHHHHHH
Confidence 5667777655 56665 589999999998653221 225555666789999999999999999874
No 47
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=21.83 E-value=86 Score=30.07 Aligned_cols=49 Identities=14% Similarity=0.232 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCCce-EEechhhHHHH
Q 014161 336 EVKEVIISFFILMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRY-YCVGLKRSNEI 410 (429)
Q Consensus 336 e~KEaiLAY~~Ll~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~-~avpL~~A~~~ 410 (429)
+.|+++.+|+.+. +-+++|+++.+.+.|+..++.+|+| -..+.++|+..
T Consensus 140 ~aK~vi~~~s~~~--------------------------g~~p~evie~~~e~Gll~~~E~~k~~L~~~~~~a~~~ 189 (190)
T PF09840_consen 140 KAKRVIAAVSYAT--------------------------GLDPEEVIEELLEKGLLEEGEDGKIELRKDWEQALRR 189 (190)
T ss_pred HHHHHHHHHHHHh--------------------------CCCHHHHHHHHHhCcccccCCCceEEEecCHHHHHhc
Confidence 4788888888875 3468899999999999999887855 56677777654
No 48
>PRK14999 histidine utilization repressor; Provisional
Probab=21.71 E-value=1.6e+02 Score=28.21 Aligned_cols=56 Identities=18% Similarity=0.241 Sum_probs=36.6
Q ss_pred HHHHHHHhCCcceecHHHHHHHHHHcCeeeecCC-CceEEec-hhhHHHHHhhhHHHHH
Q 014161 363 EELIKEEFGESCNFDVDDAVHKLEKLGIVARDTI-GRYYCVG-LKRSNEIIGTTTEEMV 419 (429)
Q Consensus 363 E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~-g~~~avp-L~~A~~~l~~~w~~~~ 419 (429)
|+-|.++||+. .-.|-+||..|++.|+|.+..+ |.+.+-+ .......+...++++.
T Consensus 39 E~eLa~~~gVS-R~TVR~Al~~L~~eGli~r~~GkGTfV~~~~~~~~~~~~~~~~~~~~ 96 (241)
T PRK14999 39 EAELVAQYGFS-RMTINRALRELTDEGWLVRLQGVGTFVAEPKGQSALFEVRSIAEEIA 96 (241)
T ss_pred HHHHHHHHCCC-HHHHHHHHHHHHHCCCEEEecCcEEEECCCCccccHHHHHHHHHHHH
Confidence 45566788876 3579999999999999988654 4554322 2333344555555543
No 49
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=21.63 E-value=2e+02 Score=24.26 Aligned_cols=60 Identities=18% Similarity=0.171 Sum_probs=41.6
Q ss_pred cCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCC---Cc-eEEechhhHHHHHhhhHHHH
Q 014161 350 QGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTI---GR-YYCVGLKRSNEIIGTTTEEM 418 (429)
Q Consensus 350 ~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~---g~-~~avpL~~A~~~l~~~w~~~ 418 (429)
.|+.|..+|... .+.+ .=.|..++.+|++.|+|.+..+ .| ..+.+-+++.+.+++.++++
T Consensus 41 ~~~~t~~eL~~~--------l~~~-~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~ 104 (109)
T TIGR01889 41 EGKLTLKEIIKE--------ILIK-QSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLISEI 104 (109)
T ss_pred CCcCcHHHHHHH--------HCCC-HHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHHHHH
Confidence 356888877543 2333 3357899999999999997553 33 56666677777788777664
No 50
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=21.61 E-value=91 Score=29.76 Aligned_cols=34 Identities=24% Similarity=0.405 Sum_probs=26.4
Q ss_pred CCcceecHHHHHHHHHHcCeeeecCCCc---eEEech
Q 014161 371 GESCNFDVDDAVHKLEKLGIVARDTIGR---YYCVGL 404 (429)
Q Consensus 371 g~~vdFdv~dAL~kL~rLgLv~~d~~g~---~~avpL 404 (429)
+.+=.-++.-+|.||++.||++++.+|+ |.++|+
T Consensus 109 n~eDth~itYslrKL~k~gLit~t~~gkevTy~vTa~ 145 (199)
T COG5631 109 NREDTHNITYSLRKLLKGGLITRTGSGKEVTYEVTAL 145 (199)
T ss_pred ccccchhHHHHHHHHHhccceecCCCCceEEEEEecc
Confidence 4444567899999999999999988775 555555
No 51
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=21.39 E-value=1.6e+02 Score=26.30 Aligned_cols=37 Identities=19% Similarity=0.448 Sum_probs=27.9
Q ss_pred HHHHhCCcceecHHHHHHHHHHcCeeeecCCCceEEec
Q 014161 366 IKEEFGESCNFDVDDAVHKLEKLGIVARDTIGRYYCVG 403 (429)
Q Consensus 366 L~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g~~~avp 403 (429)
|...|+.+++ +|.-||.-++++||+..+.+|.+...-
T Consensus 57 LA~~~~~~~~-~V~~Al~~f~k~glIe~~d~g~i~i~~ 93 (119)
T TIGR01714 57 LATMFNRNVG-DIRITLQTLESLGLIEKKNNGDIFLEN 93 (119)
T ss_pred HHHHHCCCHH-HHHHHHHHHHHCCCEEEecCCcEEehh
Confidence 3455666666 688999999999999988777655443
No 52
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=21.08 E-value=1.9e+02 Score=22.74 Aligned_cols=48 Identities=21% Similarity=0.259 Sum_probs=38.4
Q ss_pred hcCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCeeeecCCC
Q 014161 349 EQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARDTIG 397 (429)
Q Consensus 349 ~~g~lT~~~Ld~~~E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~g 397 (429)
+.+.++.++|-.+|.+.+...|..+. -++..+++.|-+-|.+.+|+++
T Consensus 19 ~~k~~~~~~L~~~v~~~l~~~f~~~~-~~ik~~Ie~LIekeyi~Rd~~d 66 (68)
T PF10557_consen 19 QEKKLSHDELINEVIEELKKRFPPSV-SDIKKRIESLIEKEYIERDEDD 66 (68)
T ss_dssp HSSEEEHHHHHHHHHHHTTTTS---H-HHHHHHHHHHHHTTSEEEESSE
T ss_pred hcCceeHHHHHHHHHHHhcCCcCCCH-HHHHHHHHHHHHhhhhhcCCCC
Confidence 44559999999999999988787664 4799999999999999998753
No 53
>PF11694 DUF3290: Protein of unknown function (DUF3290); InterPro: IPR021707 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=20.84 E-value=6.6e+02 Score=23.18 Aligned_cols=23 Identities=13% Similarity=0.345 Sum_probs=15.5
Q ss_pred ChhhHHHHHHHHHHhHhhhhhhc
Q 014161 248 TPLDWVKFLVSAVVGLVAVITSA 270 (429)
Q Consensus 248 ~~~D~~~l~v~avvg~vav~~~l 270 (429)
...||++..+.+++.++.++..+
T Consensus 13 ~~~~~~~~~~i~~ll~~l~~~~~ 35 (149)
T PF11694_consen 13 SQNDYLRYILIIILLLVLIFFFI 35 (149)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 56688888888776665555443
No 54
>PLN00134 fumarate hydratase; Provisional
Probab=20.81 E-value=4.2e+02 Score=28.64 Aligned_cols=40 Identities=15% Similarity=0.182 Sum_probs=22.7
Q ss_pred hhhhchHHHHhhhcCCcccCHHHHHH---Hh----cCCceeeecccc
Q 014161 36 MFSYFPFMQVMDKSNFKITTDEEIDV---AL----SGQYLLHLPITV 75 (429)
Q Consensus 36 ~~~~~~~~q~m~~anF~~Ls~~e~~~---Al----~~~yll~Lpi~v 75 (429)
+++....--++..+.-.+|++++-+. |+ .+.+--++|+++
T Consensus 39 a~~~v~~A~a~~l~~~G~l~~~~a~~I~~al~ei~~~~~~~~f~~~~ 85 (458)
T PLN00134 39 AFGIVKKAAAKVNMEYGLLDPDIGKAIMQAADEVAEGKLDDHFPLVV 85 (458)
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHcCcccCCccccc
Confidence 55555444444444456799888774 33 234445666665
No 55
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=20.45 E-value=1.5e+02 Score=28.07 Aligned_cols=37 Identities=24% Similarity=0.405 Sum_probs=28.6
Q ss_pred HHHHHHHhCCcceecHHHHHHHHHHcCeeeecCC-CceE
Q 014161 363 EELIKEEFGESCNFDVDDAVHKLEKLGIVARDTI-GRYY 400 (429)
Q Consensus 363 E~wL~~~fg~~vdFdv~dAL~kL~rLgLv~~d~~-g~~~ 400 (429)
|+-|.++||+.-. -|-+||+.|+..|+|.+..+ |.+.
T Consensus 35 E~eLa~~~~VSR~-TvR~Al~~L~~eGli~r~~G~GtfV 72 (238)
T TIGR02325 35 EMQLAERFGVNRH-TVRRAIAALVERGLLRAEQGRGTFV 72 (238)
T ss_pred HHHHHHHHCCCHH-HHHHHHHHHHHCCCEEEecCCEEEE
Confidence 4456678898755 89999999999999988654 4443
No 56
>COG2165 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.45 E-value=2.9e+02 Score=23.25 Aligned_cols=30 Identities=13% Similarity=0.116 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 014161 277 LWVGMAILSTVIGYCAKTYFTFQQNMAAYQ 306 (429)
Q Consensus 277 ~~v~~a~Ls~l~g~~~R~~~~y~~~r~rY~ 306 (429)
+++++++++++++.+.-.+.++.++..+.+
T Consensus 15 lLVvl~Iigil~~~~~p~~~~~~~~~~~~~ 44 (149)
T COG2165 15 LLVVLAIIGILAALALPSLQGSIDKAKRLE 44 (149)
T ss_pred HHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence 456667777777777777777766654433
No 57
>PF10675 DUF2489: Protein of unknown function (DUF2489); InterPro: IPR019617 This entry represents bacterial uncharacterised proteins.
Probab=20.11 E-value=2e+02 Score=25.92 Aligned_cols=62 Identities=11% Similarity=0.207 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCChhHHHHHHhHHHHHHHH--HHHHHHHHHh
Q 014161 286 TVIGYCAKTYFTFQQNMAAYQNMITQSMYDKQLDSGKGTLLHLCDDVIQQEVK--EVIISFFILM 348 (429)
Q Consensus 286 ~l~g~~~R~~~~y~~~r~rY~~~lt~~LY~K~l~nn~GvL~~L~D~AeeQe~K--EaiLAY~~Ll 348 (429)
++++|+++.+...++++...+.. ...-..+..++=...+..++.++.+++|- |.-+=-..|+
T Consensus 3 ~La~YA~~Ll~~l~~q~~~~~~~-~~~~~~~r~~~i~eSI~iIA~Am~~~qc~lsEg~iRi~~Ll 66 (131)
T PF10675_consen 3 ALAGYAGYLLLKLKKQKEEQQQQ-QAQAIQERRARILESIRIIAKAMLQEQCDLSEGAIRIKVLL 66 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHHHHH
Confidence 45778888888877766443322 22223334444455666667777666653 4444444444
No 58
>PRK08990 flagellar motor protein PomA; Reviewed
Probab=20.08 E-value=8.7e+02 Score=24.21 Aligned_cols=64 Identities=14% Similarity=0.150 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCChhHHHHHHhHHHHHHHHHHHHHHHHHh-hcCCCCHHHHHHHHHHHH
Q 014161 297 TFQQNMAAYQNMITQSMYDKQLDSGKGTLLHLCDDVIQQEVKEVIISFFILM-EQGKATRQDLDLRCEELI 366 (429)
Q Consensus 297 ~y~~~r~rY~~~lt~~LY~K~l~nn~GvL~~L~D~AeeQe~KEaiLAY~~Ll-~~g~lT~~~Ld~~~E~wL 366 (429)
.|+.++..|...+......-..+...|.+. +++ +++...++.-...+ ..|. .++++.+..|+-+
T Consensus 65 ~~~~~~~~~~~~i~~l~~la~~aR~~Glla--LE~---~~i~d~f~~~~l~l~vdg~-~~~~i~~~l~~~~ 129 (254)
T PRK08990 65 AFMFKIDKPEDLIEQIVEMADAARKGGFLA--LEE---AEISNSFMQKGVDLLVDGH-DGDVVRAALEKDI 129 (254)
T ss_pred hhcCCCCCHHHHHHHHHHHHHHHhhccHhh--hhc---cccchHHHHHHHHHHhcCC-CHHHHHHHHHHHH
Confidence 355666778888888777778888888766 332 24555666666533 3343 5555544444333
Done!