Query 015530
Match_columns 405
No_of_seqs 104 out of 118
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 07:10:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015530hhsearch_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 7.1E-35 1.5E-39 259.6 14.3 121 201-322 1-141 (141)
2 PF11460 DUF3007: Protein of u 81.2 9.6 0.00021 33.1 7.9 63 246-308 1-75 (104)
3 COG3355 Predicted transcriptio 68.8 8.3 0.00018 34.5 4.5 46 341-395 31-77 (126)
4 PF01978 TrmB: Sugar-specific 68.0 3.7 8E-05 31.6 1.9 45 341-394 12-56 (68)
5 PF14015 DUF4231: Protein of u 59.4 51 0.0011 27.4 7.4 19 289-307 66-84 (112)
6 smart00550 Zalpha Z-DNA-bindin 54.3 46 0.00099 26.0 5.9 60 333-403 4-66 (68)
7 PHA01814 hypothetical protein 50.6 3.2 7E-05 36.4 -1.2 48 61-115 54-101 (137)
8 PF04369 Lactococcin: Lactococ 46.2 14 0.00031 29.1 1.8 24 49-72 5-28 (60)
9 PRK04214 rbn ribonuclease BN/u 45.5 3.5E+02 0.0076 28.3 12.5 35 351-394 310-344 (412)
10 PRK06743 flagellar motor prote 45.2 1.2E+02 0.0026 30.1 8.5 67 297-367 64-131 (254)
11 PF07120 DUF1376: Protein of u 42.3 50 0.0011 27.1 4.6 63 301-363 22-87 (88)
12 TIGR03433 padR_acidobact trans 40.8 74 0.0016 26.5 5.5 52 341-393 5-58 (100)
13 PF10007 DUF2250: Uncharacteri 37.0 26 0.00056 29.7 2.2 21 376-396 37-57 (92)
14 PF04391 DUF533: Protein of un 34.1 2.4E+02 0.0052 26.8 8.4 23 279-301 34-56 (188)
15 PF11469 Ribonucleas_3_2: Ribo 32.2 45 0.00098 29.3 2.9 48 333-386 58-111 (120)
16 COG1802 GntR Transcriptional r 29.2 74 0.0016 30.0 4.1 54 334-398 23-77 (230)
17 PTZ00095 40S ribosomal protein 27.4 43 0.00093 31.5 2.1 28 377-404 122-149 (169)
18 PRK08990 flagellar motor prote 25.9 4.5E+02 0.0097 26.0 9.0 63 297-365 66-129 (254)
19 KOG3411 40S ribosomal protein 24.9 63 0.0014 29.4 2.6 28 377-405 100-127 (143)
20 PF10785 NADH-u_ox-rdase: NADH 23.5 3.1E+02 0.0066 22.8 6.3 22 245-266 19-40 (86)
21 PLN00134 fumarate hydratase; P 23.3 3.6E+02 0.0079 28.8 8.4 46 30-75 33-85 (458)
22 TIGR02147 Fsuc_second hypothet 23.2 84 0.0018 31.4 3.4 32 364-395 142-174 (271)
23 PHA02888 hypothetical protein; 22.9 84 0.0018 26.3 2.8 27 352-379 36-62 (96)
24 PF11694 DUF3290: Protein of u 22.1 4E+02 0.0087 24.4 7.3 55 247-302 13-73 (149)
25 COG2979 Uncharacterized protei 21.9 2.5E+02 0.0054 27.6 6.2 24 280-303 63-86 (225)
26 PRK13777 transcriptional regul 21.7 6.5E+02 0.014 23.7 8.9 44 345-397 53-96 (185)
27 PF11434 CHIPS: Chemotaxis-inh 21.7 1.6E+02 0.0036 24.1 4.2 44 180-232 8-51 (91)
28 PF10675 DUF2489: Protein of u 21.3 2E+02 0.0043 25.8 5.0 62 285-347 3-66 (131)
29 PF01325 Fe_dep_repress: Iron 21.2 64 0.0014 24.8 1.7 40 349-397 20-59 (60)
30 PF13730 HTH_36: Helix-turn-he 20.6 92 0.002 22.6 2.4 25 365-390 31-55 (55)
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=7.1e-35 Score=259.59 Aligned_cols=121 Identities=40% Similarity=0.647 Sum_probs=108.3
Q ss_pred cceEEEEEeeccccC--------------cCCCCeEEEeeCCCCCCCccccccCCCCCCCChhhHHHHHHHHHHHHHHHH
Q 015530 201 FDRIIVLYRQASTKS--------------KAERGVYLKHFRNIPMADMEIVLPEKKNPGLTPLDWVKFLVSAVVGLVAVI 266 (405)
Q Consensus 201 FkrVVvlyR~k~~k~--------------k~~~~l~LK~FkdIP~aDLE~llPekK~v~~~~~D~~~l~vsavvglvav~ 266 (405)
||||||+||.++++. ..+++|+||+||||||+|||+||||+| |+|||+||+++++++++|+++++
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 899999999876432 126999999999999999999999998 89999999999999999999999
Q ss_pred hhcccch----h--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCchh
Q 015530 267 TSAQLHE----I--DLWVGMAILSTVIGYCAKTYFTFQQNMAAYQNMITQSMYDKQLDSGKG 322 (405)
Q Consensus 267 ~~l~~~~----~--~~~~i~a~ls~l~g~~~r~~~~y~~~~~rY~~~lt~~LY~K~l~sn~G 322 (405)
.++.... + .++..+++++++++||+|+|++|+|+|.+||+++|++|||||+|||+|
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 8755443 2 256677888889999999999999999999999999999999999998
No 2
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=81.19 E-value=9.6 Score=33.10 Aligned_cols=63 Identities=14% Similarity=0.239 Sum_probs=36.4
Q ss_pred CChhhHHHHHHHHHHHH-HHHH--hhcccc--hhhHH----HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHH
Q 015530 246 LTPLDWVKFLVSAVVGL-VAVI--TSAQLH--EIDLW----VGMAILSTVIGYCAKTYFT---FQQNMAAYQNMI 308 (405)
Q Consensus 246 ~~~~D~~~l~vsavvgl-vav~--~~l~~~--~~~~~----~i~a~ls~l~g~~~r~~~~---y~~~~~rY~~~l 308 (405)
||..|-+.+++...+.+ ++.. ..+.++ ++..| .++++++=+++|.+|+.++ |.++|.+|...+
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 45556666666555433 3322 122222 23333 2334444467899999976 999999999855
No 3
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=68.76 E-value=8.3 Score=34.52 Aligned_cols=46 Identities=22% Similarity=0.274 Sum_probs=35.6
Q ss_pred HHHHHHh-cCCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCceecccC
Q 015530 341 ISFFILM-EQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARVRL 395 (405)
Q Consensus 341 LAY~~Ll-~~g~lT~~~Ld~~~E~~L~~~fg~~vdFdv~dAL~kL~~LgLv~~~~~ 395 (405)
=+|..|+ .+|++|.++|.+....= +. -|..||++|..-|||.+...
T Consensus 31 ~v~~~LL~~~~~~tvdelae~lnr~---rS------tv~rsl~~L~~~GlV~Rek~ 77 (126)
T COG3355 31 EVYKALLEENGPLTVDELAEILNRS---RS------TVYRSLQNLLEAGLVEREKV 77 (126)
T ss_pred HHHHHHHhhcCCcCHHHHHHHHCcc---HH------HHHHHHHHHHHcCCeeeeee
Confidence 3678888 69999999998766532 11 37899999999999987654
No 4
>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=68.04 E-value=3.7 Score=31.61 Aligned_cols=45 Identities=29% Similarity=0.403 Sum_probs=34.5
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCceeccc
Q 015530 341 ISFFILMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARVR 394 (405)
Q Consensus 341 LAY~~Ll~~g~lT~~~Ld~~~E~~L~~~fg~~vdFdv~dAL~kL~~LgLv~~~~ 394 (405)
=+|..|++.|++|.++|.+.+ |..- =.|.++|++|++.|+|.+..
T Consensus 12 ~vy~~Ll~~~~~t~~eIa~~l--------~i~~-~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEIAEEL--------GISR-STVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHCHEEHHHHHHHH--------TSSH-HHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHcCCCCHHHHHHHH--------CcCH-HHHHHHHHHHHHCCCEEEEc
Confidence 367777788999999887654 3332 24789999999999998876
No 5
>PF14015 DUF4231: Protein of unknown function (DUF4231)
Probab=59.36 E-value=51 Score=27.43 Aligned_cols=19 Identities=16% Similarity=0.440 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 015530 289 YCAKTYFTFQQNMAAYQNM 307 (405)
Q Consensus 289 ~~~r~~~~y~~~~~rY~~~ 307 (405)
-++...+++++++.+|...
T Consensus 66 ~~~~~~~~~~~~W~~~r~t 84 (112)
T PF14015_consen 66 ASLAAFFRFHERWIRYRAT 84 (112)
T ss_pred HHHHHHhchhHHHHHHHHH
Confidence 3346778888888888763
No 6
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=54.34 E-value=46 Score=26.02 Aligned_cols=60 Identities=28% Similarity=0.418 Sum_probs=41.7
Q ss_pred hhHhhHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCceecccC-CCCCCCCC
Q 015530 333 QQEVKEVIISFFILMEQGK--ATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARVRL-PGVPHITH 403 (405)
Q Consensus 333 eQe~KEaiLAY~~Ll~~g~--lT~~~Ld~~~E~~L~~~fg~~vdFdv~dAL~kL~~LgLv~~~~~-~~~~~~~~ 403 (405)
+.+++|.||.+ |.++|+ +|..+|. +++|..-. .|...|.+|++.|+|..++. ++.=.+++
T Consensus 4 ~~~~~~~IL~~--L~~~g~~~~ta~eLa--------~~lgl~~~-~v~r~L~~L~~~G~V~~~~~~~~~W~i~~ 66 (68)
T smart00550 4 QDSLEEKILEF--LENSGDETSTALQLA--------KNLGLPKK-EVNRVLYSLEKKGKVCKQGGTPPLWKLTD 66 (68)
T ss_pred chHHHHHHHHH--HHHCCCCCcCHHHHH--------HHHCCCHH-HHHHHHHHHHHCCCEEecCCCCCceEeec
Confidence 34566666654 445555 8988775 45788776 89999999999999988763 24334443
No 7
>PHA01814 hypothetical protein
Probab=50.65 E-value=3.2 Score=36.44 Aligned_cols=48 Identities=25% Similarity=0.351 Sum_probs=38.8
Q ss_pred HhhcCCceeeeecccccccchHHHHHHHhhhccCCCCcCccCceeeecCCCcccc
Q 015530 61 VALSGQYLLHLPITVNESKLDKKLLKRYFEEHHHDHLPDFADKYVIFRRGIGVDQ 115 (405)
Q Consensus 61 ~Al~~~yLl~Lpi~vd~~klD~~ll~~y~~~~~~~~l~~~~d~~liFrRG~g~d~ 115 (405)
.-.++.=||+|.|+||-+|.==..|+-||.+| .+|--+||+||+-...
T Consensus 54 d~~~e~dlftldididikkhvfn~l~~yy~~~-------~~~~~iiykk~v~m~~ 101 (137)
T PHA01814 54 DTKNENDLFTLDIDIDIKKHVFNCLKVYYIEH-------TEDINIIYKKGVYMGC 101 (137)
T ss_pred ccccccceEEEEeeeehhhheeeeEEEeeecc-------cccceeeeecceEEcc
Confidence 45678889999999999988777888888888 5667899999975433
No 8
>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=46.23 E-value=14 Score=29.09 Aligned_cols=24 Identities=29% Similarity=0.331 Sum_probs=18.6
Q ss_pred cCCcccCHHHHHHhhcCCceeeee
Q 015530 49 SNFKITTDEEIDVALSGQYLLHLP 72 (405)
Q Consensus 49 anF~~ls~~e~~~Al~~~yLl~Lp 72 (405)
-||+++|++|++.+-.+.|-+.+.
T Consensus 5 ~nf~~~sdeeL~~i~GG~l~~iqs 28 (60)
T PF04369_consen 5 LNFNILSDEELSKINGGGLPYIQS 28 (60)
T ss_pred ccceecCHHHHhhccCCcceeeee
Confidence 499999999999886665555444
No 9
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=45.51 E-value=3.5e+02 Score=28.28 Aligned_cols=35 Identities=9% Similarity=0.234 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCceeccc
Q 015530 351 KATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARVR 394 (405)
Q Consensus 351 ~lT~~~Ld~~~E~~L~~~fg~~vdFdv~dAL~kL~~LgLv~~~~ 394 (405)
+.|.++|.++.. ...+ .+++-+++|++.|++.+.+
T Consensus 310 ~~t~~~La~~l~--------~~~~-~v~~iL~~L~~agLI~~~~ 344 (412)
T PRK04214 310 ALDVDEIRRLEP--------MGYD-ELGELLCELARIGLLRRGE 344 (412)
T ss_pred CCCHHHHHHHhC--------CCHH-HHHHHHHHHHhCCCeEecC
Confidence 478888765543 3322 5789999999999998654
No 10
>PRK06743 flagellar motor protein MotP; Reviewed
Probab=45.18 E-value=1.2e+02 Score=30.13 Aligned_cols=67 Identities=13% Similarity=0.114 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhhHhhHHHHHHHHHh-cCCCCCHHHHHHHHHHHHHH
Q 015530 297 FQQNMAAYQNMITQSMYDKQLDSGKGTLLHLCDDVIQQEVKEVIISFFILM-EQGKATRQDLDLRCEELIKE 367 (405)
Q Consensus 297 y~~~~~rY~~~lt~~LY~K~l~sn~GvL~~L~d~AeeQe~KEaiLAY~~Ll-~~g~lT~~~Ld~~~E~~L~~ 367 (405)
|+.++..|+..+......-+.+...|.+ +| +.+.++.++.+++.++-+ ..|. +++++.+..|+-+..
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 4455566788887777777778888843 33 333445567788877654 2344 677776666655543
No 11
>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=42.29 E-value=50 Score=27.11 Aligned_cols=63 Identities=13% Similarity=0.220 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHH-HHhccCchhHHHHHHHHH--HhhHhhHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 015530 301 MAAYQNMITQSMY-DKQLDSGKGTLLHLCDDV--IQQEVKEVIISFFILMEQGKATRQDLDLRCEE 363 (405)
Q Consensus 301 ~~rY~~~lt~~LY-~K~l~sn~GvL~~L~d~A--eeQe~KEaiLAY~~Ll~~g~lT~~~Ld~~~E~ 363 (405)
+-.|..++-.+.. .+.+-++..+|..++... +.+...+.+|..+|....|......+++++++
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 4456666655444 567889999999999876 66788899999999666777887777777664
No 12
>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=40.84 E-value=74 Score=26.50 Aligned_cols=52 Identities=19% Similarity=0.310 Sum_probs=36.5
Q ss_pred HHHHHH--hcCCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCceecc
Q 015530 341 ISFFIL--MEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARV 393 (405)
Q Consensus 341 LAY~~L--l~~g~lT~~~Ld~~~E~~L~~~fg~~vdFdv~dAL~kL~~LgLv~~~ 393 (405)
+.|++| +..++.+.-+|-+.+++.....+..+- =.+-.+|.+|++.|+|+..
T Consensus 5 l~~~iL~~L~~~~~~GYei~~~l~~~~~~~~~i~~-gtlY~~L~rLe~~GlI~~~ 58 (100)
T TIGR03433 5 LDLLILKTLSLGPLHGYGIAQRIQQISEDVLQVEE-GSLYPALHRLERRGWIAAE 58 (100)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHcCCccccCC-CcHHHHHHHHHHCCCeEEE
Confidence 455555 457889999999999887532222221 1366799999999999873
No 13
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=36.97 E-value=26 Score=29.69 Aligned_cols=21 Identities=38% Similarity=0.676 Sum_probs=18.1
Q ss_pred cHHHHHHHHHHcCceecccCC
Q 015530 376 DVDDAVHKLEKLGIVARVRLP 396 (405)
Q Consensus 376 dv~dAL~kL~~LgLv~~~~~~ 396 (405)
+|.+++++|+++||+++.+..
T Consensus 37 ~v~~~l~~Le~~GLler~~g~ 57 (92)
T PF10007_consen 37 EVREALEKLEEMGLLERVEGK 57 (92)
T ss_pred HHHHHHHHHHHCCCeEEecCc
Confidence 688999999999999887743
No 14
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=34.12 E-value=2.4e+02 Score=26.84 Aligned_cols=23 Identities=30% Similarity=0.348 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 015530 279 GMAILSTVIGYCAKTYFTFQQNM 301 (405)
Q Consensus 279 i~a~ls~l~g~~~r~~~~y~~~~ 301 (405)
..+.++++++.++|.|.+|++++
T Consensus 34 ~~Gg~AalG~lA~~ayq~~q~~~ 56 (188)
T PF04391_consen 34 KYGGLAALGGLAYKAYQNWQQNQ 56 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHhccC
Confidence 35666778899999999997764
No 15
>PF11469 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR021568 This archaeal family of proteins has no known function. ; PDB: 1ZTD_A.
Probab=32.16 E-value=45 Score=29.28 Aligned_cols=48 Identities=27% Similarity=0.486 Sum_probs=26.2
Q ss_pred hhHhhHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhCCcc-ee-----cHHHHHHHHHH
Q 015530 333 QQEVKEVIISFFILMEQGKATRQDLDLRCEELIKEEFGESC-NF-----DVDDAVHKLEK 386 (405)
Q Consensus 333 eQe~KEaiLAY~~Ll~~g~lT~~~Ld~~~E~~L~~~fg~~v-dF-----dv~dAL~kL~~ 386 (405)
--++.||++||+||- |.+|.+|- =+-+++.|..+| +| .|-.|+..|.+
T Consensus 58 kGd~aEA~iAyAWLe--g~it~eEa----veil~~nl~~dv~~fsrkke~ig~Ala~Ll~ 111 (120)
T PF11469_consen 58 KGDIAEALIAYAWLE--GKITIEEA----VEILKANLTEDVLHFSRKKEAIGKALAELLK 111 (120)
T ss_dssp HHHHHHHHHHHHHHT--TSS-HHHH----HHHHHCT--GGGG-TTTHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHh--ccccHHHH----HHHHHhcCchhhcchhHHHHHHHHHHHHHHH
Confidence 356789999999994 77776542 233444444332 22 34555555543
No 16
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=29.16 E-value=74 Score=29.96 Aligned_cols=54 Identities=33% Similarity=0.425 Sum_probs=38.1
Q ss_pred hHhhHHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCceecccCCCC
Q 015530 334 QEVKEVIISFFILMEQGK-ATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARVRLPGV 398 (405)
Q Consensus 334 Qe~KEaiLAY~~Ll~~g~-lT~~~Ld~~~E~~L~~~fg~~vdFdv~dAL~kL~~LgLv~~~~~~~~ 398 (405)
++.+|+|+.--+ .+|. + .|+.|.++||++- -+|-+||..|++.|||...+..|.
T Consensus 23 ~~Lr~~Il~g~l--~pG~~l--------~e~~La~~~gvSr-tPVReAL~rL~~eGlv~~~p~rG~ 77 (230)
T COG1802 23 EELREAILSGEL--APGERL--------SEEELAEELGVSR-TPVREALRRLEAEGLVEIEPNRGA 77 (230)
T ss_pred HHHHHHHHhCCC--CCCCCc--------cHHHHHHHhCCCC-ccHHHHHHHHHHCCCeEecCCCCC
Confidence 556666654322 2343 4 3566778899875 489999999999999988876553
No 17
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=27.39 E-value=43 Score=31.50 Aligned_cols=28 Identities=25% Similarity=0.266 Sum_probs=21.6
Q ss_pred HHHHHHHHHHcCceecccCCCCCCCCCC
Q 015530 377 VDDAVHKLEKLGIVARVRLPGVPHITHH 404 (405)
Q Consensus 377 v~dAL~kL~~LgLv~~~~~~~~~~~~~~ 404 (405)
+..+|+.||++|+|+++...+...+|-.
T Consensus 122 iR~~LQqLE~~glVek~~~~~GR~lT~~ 149 (169)
T PTZ00095 122 LRWICQQLEKLGLVEQGPKKKGRRLTRK 149 (169)
T ss_pred HHHHHHHHHHCCCEEecCCCCCCEECHh
Confidence 5678999999999998865466666643
No 18
>PRK08990 flagellar motor protein PomA; Reviewed
Probab=25.88 E-value=4.5e+02 Score=26.04 Aligned_cols=63 Identities=14% Similarity=0.144 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhhHhhHHHHHHHHHhc-CCCCCHHHHHHHHHHHH
Q 015530 297 FQQNMAAYQNMITQSMYDKQLDSGKGTLLHLCDDVIQQEVKEVIISFFILME-QGKATRQDLDLRCEELI 365 (405)
Q Consensus 297 y~~~~~rY~~~lt~~LY~K~l~sn~GvL~~L~d~AeeQe~KEaiLAY~~Ll~-~g~lT~~~Ld~~~E~~L 365 (405)
|+.++..|...+......-..+...|.+. +++ +++...++.-...+- .|. .++++.+..|+-+
T Consensus 66 ~~~~~~~~~~~i~~l~~la~~aR~~Glla--LE~---~~i~d~f~~~~l~l~vdg~-~~~~i~~~l~~~~ 129 (254)
T PRK08990 66 FMFKIDKPEDLIEQIVEMADAARKGGFLA--LEE---AEISNSFMQKGVDLLVDGH-DGDVVRAALEKDI 129 (254)
T ss_pred hcCCCCCHHHHHHHHHHHHHHHhhccHhh--hhc---cccchHHHHHHHHHHhcCC-CHHHHHHHHHHHH
Confidence 55566678788877777777788888765 332 245556666655532 333 5555554444443
No 19
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=24.94 E-value=63 Score=29.44 Aligned_cols=28 Identities=32% Similarity=0.534 Sum_probs=21.5
Q ss_pred HHHHHHHHHHcCceecccCCCCCCCCCCC
Q 015530 377 VDDAVHKLEKLGIVARVRLPGVPHITHHG 405 (405)
Q Consensus 377 v~dAL~kL~~LgLv~~~~~~~~~~~~~~~ 405 (405)
...+|+.|+.+|+|++++. |.+.||-.|
T Consensus 100 ~rkvlQ~Le~~~~ve~hp~-gGR~lt~~G 127 (143)
T KOG3411|consen 100 ARKVLQALEKMGIVEKHPK-GGRRLTEQG 127 (143)
T ss_pred HHHHHHHHHhCCceeeCCC-CcceeCccc
Confidence 5789999999999998885 455555433
No 20
>PF10785 NADH-u_ox-rdase: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit; InterPro: IPR019721 This domain is found in the N-terminal region of NADH-ubiquinone oxidoreductase 21kDa subunits from plants and fungi [].
Probab=23.49 E-value=3.1e+02 Score=22.81 Aligned_cols=22 Identities=9% Similarity=0.036 Sum_probs=17.2
Q ss_pred CCChhhHHHHHHHHHHHHHHHH
Q 015530 245 GLTPLDWVKFLVSAVVGLVAVI 266 (405)
Q Consensus 245 ~~~~~D~~~l~vsavvglvav~ 266 (405)
.+|+.|.......+.++.....
T Consensus 19 ~~R~sDy~~~a~~ta~~p~~~~ 40 (86)
T PF10785_consen 19 YFRPSDYAIWAGATAASPPLGY 40 (86)
T ss_pred hCCHHHHHHHHHHHHHHHHHHH
Confidence 6799999988888777765554
No 21
>PLN00134 fumarate hydratase; Provisional
Probab=23.25 E-value=3.6e+02 Score=28.84 Aligned_cols=46 Identities=15% Similarity=0.158 Sum_probs=25.9
Q ss_pred CCccchhhhhchHHHHhhhcCCcccCHHHHH---Hhhc----CCceeeeeccc
Q 015530 30 PISHFVMFSYFPFMQVMDKSNFKITTDEEID---VALS----GQYLLHLPITV 75 (405)
Q Consensus 30 ~~~~~~~~~~~~~~q~m~~anF~~ls~~e~~---~Al~----~~yLl~Lpi~v 75 (405)
|....++++.....-++..+.-.+|++++-+ .|+. +.+--++|+.+
T Consensus 33 ~~~~i~a~~~v~~A~a~~l~~~G~l~~~~a~~I~~al~ei~~~~~~~~f~~~~ 85 (458)
T PLN00134 33 PEPIVRAFGIVKKAAAKVNMEYGLLDPDIGKAIMQAADEVAEGKLDDHFPLVV 85 (458)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHcCcccCCccccc
Confidence 3334457777655555555555679988876 2332 33444556555
No 22
>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=23.16 E-value=84 Score=31.43 Aligned_cols=32 Identities=16% Similarity=0.273 Sum_probs=23.4
Q ss_pred HHHHHhCCcceec-HHHHHHHHHHcCceecccC
Q 015530 364 LIKEEFGESCNFD-VDDAVHKLEKLGIVARVRL 395 (405)
Q Consensus 364 ~L~~~fg~~vdFd-v~dAL~kL~~LgLv~~~~~ 395 (405)
||..+.+-.|.=+ |.+||+.|+++||+.+++.
T Consensus 142 ~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~ 174 (271)
T TIGR02147 142 ELAKRCFPKISAEQVKESLDLLERLGLIKKNED 174 (271)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCC
Confidence 3444445444444 8999999999999998873
No 23
>PHA02888 hypothetical protein; Provisional
Probab=22.85 E-value=84 Score=26.26 Aligned_cols=27 Identities=26% Similarity=0.267 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHHHHHHHhCCcceecHHH
Q 015530 352 ATRQDLDLRCEELIKEEFGESCNFDVDD 379 (405)
Q Consensus 352 lT~~~Ld~~~E~~L~~~fg~~vdFdv~d 379 (405)
+|++||. -+.+||.++-+.=++|++|=
T Consensus 36 mt~~el~-yiq~wllekhdlfiefpidl 62 (96)
T PHA02888 36 MTPQELA-YIQEWLLEKHDLFIEFPIDL 62 (96)
T ss_pred CCHHHHH-HHHHHHHhhcceeEEccHHH
Confidence 8999996 47889999999999999874
No 24
>PF11694 DUF3290: Protein of unknown function (DUF3290); InterPro: IPR021707 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=22.14 E-value=4e+02 Score=24.40 Aligned_cols=55 Identities=16% Similarity=0.237 Sum_probs=31.2
Q ss_pred ChhhHHHHHHHHHHHHHHHHhhcccc----hhhHHH--HHHHHHHHHHHHHHHHHHHHHHHH
Q 015530 247 TPLDWVKFLVSAVVGLVAVITSAQLH----EIDLWV--GMAILSTVIGYCAKTYFTFQQNMA 302 (405)
Q Consensus 247 ~~~D~~~l~vsavvglvav~~~l~~~----~~~~~~--i~a~ls~l~g~~~r~~~~y~~~~~ 302 (405)
...||++..+.+++.++.++..+..- ....++ +++++.+ +..+.=+|..|++++.
T Consensus 13 ~~~~~~~~~~i~~ll~~l~~~~~~Y~r~r~~tKyRDL~II~~L~l-l~l~giq~~~y~~~~~ 73 (149)
T PF11694_consen 13 SQNDYLRYILIIILLLVLIFFFIKYLRNRLDTKYRDLSIIALLLL-LLLIGIQYSDYQQNQN 73 (149)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhHHHHHHHHH-HHHHHHHHHHHHHHhh
Confidence 56889998888887776666544211 122233 3333332 3444567777776544
No 25
>COG2979 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.92 E-value=2.5e+02 Score=27.56 Aligned_cols=24 Identities=17% Similarity=0.256 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 015530 280 MAILSTVIGYCAKTYFTFQQNMAA 303 (405)
Q Consensus 280 ~a~ls~l~g~~~r~~~~y~~~~~r 303 (405)
++.+.++++.+.++|.+|++++.+
T Consensus 63 ~GglAAlG~laY~aY~N~q~~q~~ 86 (225)
T COG2979 63 LGGLAALGALAYKAYQNYQKGQIP 86 (225)
T ss_pred hhhHHHHHHHHHHHHHHHhccCcc
Confidence 455666777888999999987743
No 26
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=21.74 E-value=6.5e+02 Score=23.67 Aligned_cols=44 Identities=14% Similarity=0.025 Sum_probs=28.7
Q ss_pred HHhcCCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCceecccCCC
Q 015530 345 ILMEQGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARVRLPG 397 (405)
Q Consensus 345 ~Ll~~g~lT~~~Ld~~~E~~L~~~fg~~vdFdv~dAL~kL~~LgLv~~~~~~~ 397 (405)
.|...+++|..+|.+. +..++. .+...+++|++.|+|.+...++
T Consensus 53 ~L~~~~~itq~eLa~~---l~l~~s------Tvtr~l~rLE~kGlI~R~~~~~ 96 (185)
T PRK13777 53 IAYHLKGASISEIAKF---GVMHVS------TAFNFSKKLEERGYLTFSKKED 96 (185)
T ss_pred HHHhCCCcCHHHHHHH---HCCCHh------hHHHHHHHHHHCCCEEecCCCC
Confidence 3345667888877543 222211 2788999999999998765443
No 27
>PF11434 CHIPS: Chemotaxis-inhibiting protein CHIPS; InterPro: IPR020986 Chemotaxis inhibitory protein (also knows as CHIPS) is a Staphylococcus aureus-secreted virulence factor that impairs the response of neutrophils and monocytes to FPR and C5a []. CHIPS has been shown to reduce neutrophil recruitment toward C5a in mouse models (its activity is more potent on human than on mouse cells). As such, its properties may make it a candidate new anti-inflammatory therapeutic compound []. CHIPS also plays an key role in bacterial invasion, by inhibiting FMLP- and C5a-induced calcium moblisation []. By influencing 2 related receptors with very different ligand specificities (C5aR and FPR), the protein has a unique role; nevertheless, neither the manner in which it binds such structurally different molecules nor how its expression is regulated are currently unknown []. The structure of a CHIPS fragment (residues 31-121) has been solved by NMR spectroscopy []. This fragment has the same activity in blocking the C5aR relative to full-length CHIPS, but lacks FPR antagonism []. The protein has a compact fold comprising 2 short alpha-helices packed onto a 4-stranded anti-parallel beta-sheet: strands-2 and -3 are joined by a loop with a well-defined conformation []. The protein shares a high degree of structural similarity with a number of proteins, including the C-terminal domain of staphylococcal superantigen-like proteins (SSLs) 5 and 7, staphyloccocal and streptococcal superantigens TSST-1 and SPE-C, and various domains of the staphylococcal extracellullar adherence protein (EAP) [].; PDB: 2K3U_A 1XEE_A.
Probab=21.70 E-value=1.6e+02 Score=24.07 Aligned_cols=44 Identities=27% Similarity=0.507 Sum_probs=29.8
Q ss_pred cchhhHHHhhhcccccccccccceEEEEEeeccccCcCCCCeEEEeeCCCCCC
Q 015530 180 LENMELSFRNLLGKVTIQEPTFDRIIVLYRQASTKSKAERGVYLKHFRNIPMA 232 (405)
Q Consensus 180 l~~~~~~~~~lf~k~~lqep~FkrVVvlyR~k~~k~k~~~~l~LK~FkdIP~a 232 (405)
+-++...++|+++|-+-.-..|+.+|++-..+ =+--.|-|.|+|
T Consensus 8 lgklderlrnylkkgtknsaqfekmviltenk---------gyytvylntpla 51 (91)
T PF11434_consen 8 LGKLDERLRNYLKKGTKNSAQFEKMVILTENK---------GYYTVYLNTPLA 51 (91)
T ss_dssp HHHHHHHHHHHHHCC-S-GCCEEEEEEEESTT----------EEEEETTS---
T ss_pred hHHHHHHHHHHHHhcccchhhheeEEEEEcCC---------ceEEEEEcCcch
Confidence 34566789999999999999999999998443 455666677766
No 28
>PF10675 DUF2489: Protein of unknown function (DUF2489); InterPro: IPR019617 This entry represents bacterial uncharacterised proteins.
Probab=21.26 E-value=2e+02 Score=25.79 Aligned_cols=62 Identities=11% Similarity=0.207 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhhHhh--HHHHHHHHHh
Q 015530 285 TVIGYCAKTYFTFQQNMAAYQNMITQSMYDKQLDSGKGTLLHLCDDVIQQEVK--EVIISFFILM 347 (405)
Q Consensus 285 ~l~g~~~r~~~~y~~~~~rY~~~lt~~LY~K~l~sn~GvL~~L~d~AeeQe~K--EaiLAY~~Ll 347 (405)
++++|+++.+...++++...+.. ...-..+..++=...+..++.++.+++|- |..+=-..|+
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 45688888888877776443322 22233344444556677777777777663 5555555554
No 29
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=21.19 E-value=64 Score=24.78 Aligned_cols=40 Identities=23% Similarity=0.341 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHhCCcceecHHHHHHHHHHcCceecccCCC
Q 015530 349 QGKATRQDLDLRCEELIKEEFGESCNFDVDDAVHKLEKLGIVARVRLPG 397 (405)
Q Consensus 349 ~g~lT~~~Ld~~~E~~L~~~fg~~vdFdv~dAL~kL~~LgLv~~~~~~~ 397 (405)
.++++..+|.+ .+|++- =-|.+++.+|++.|+|..++-.|
T Consensus 20 ~~~v~~~~iA~--------~L~vs~-~tvt~ml~~L~~~GlV~~~~y~g 59 (60)
T PF01325_consen 20 GGPVRTKDIAE--------RLGVSP-PTVTEMLKRLAEKGLVEYEPYKG 59 (60)
T ss_dssp TSSBBHHHHHH--------HHTS-H-HHHHHHHHHHHHTTSEEEETTTE
T ss_pred CCCccHHHHHH--------HHCCCh-HHHHHHHHHHHHCCCEEecCCCC
Confidence 44577776643 334321 14789999999999998776544
No 30
>PF13730 HTH_36: Helix-turn-helix domain
Probab=20.60 E-value=92 Score=22.55 Aligned_cols=25 Identities=28% Similarity=0.571 Sum_probs=20.2
Q ss_pred HHHHhCCcceecHHHHHHHHHHcCce
Q 015530 365 IKEEFGESCNFDVDDAVHKLEKLGIV 390 (405)
Q Consensus 365 L~~~fg~~vdFdv~dAL~kL~~LgLv 390 (405)
|.+..|+. .=.|.+|++.|++.|++
T Consensus 31 la~~~g~s-~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 31 LAKDLGVS-RRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHCcC-HHHHHHHHHHHHHCcCC
Confidence 33445888 77899999999999975
Done!