Query 042488
Match_columns 78
No_of_seqs 100 out of 148
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 06:41:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042488.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042488hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2351 RNA polymerase II, fou 99.9 2.4E-25 5.1E-30 154.6 6.7 63 13-78 72-134 (134)
2 COG5250 RPB4 RNA polymerase II 99.8 3.9E-20 8.4E-25 128.5 6.5 63 13-78 76-138 (138)
3 smart00657 RPOL4c DNA-directed 99.8 6.6E-20 1.4E-24 122.6 7.1 64 12-78 55-118 (118)
4 PRK14981 DNA-directed RNA poly 99.7 3.7E-17 8.1E-22 109.3 7.0 60 13-75 52-111 (112)
5 PF03874 RNA_pol_Rpb4: RNA pol 99.7 1.4E-16 3E-21 104.3 6.9 60 13-75 58-117 (117)
6 COG1460 Uncharacterized protei 98.2 1E-05 2.3E-10 55.4 7.0 58 16-76 56-113 (114)
7 KOG4168 Predicted RNA polymera 91.4 0.34 7.4E-06 34.7 4.0 54 19-74 77-130 (149)
8 COG4545 Glutaredoxin-related p 81.6 0.57 1.2E-05 30.8 0.5 36 35-77 9-44 (85)
9 PF00619 CARD: Caspase recruit 76.6 13 0.00029 22.1 6.2 55 14-73 18-73 (85)
10 PF06569 DUF1128: Protein of u 73.6 6.3 0.00014 25.0 3.5 39 37-76 33-71 (71)
11 KOG2351 RNA polymerase II, fou 68.4 1.8 3.9E-05 30.6 0.2 16 1-16 1-16 (134)
12 PF09969 DUF2203: Uncharacteri 61.5 9.3 0.0002 25.8 2.6 14 41-54 4-17 (120)
13 PF08667 BetR: BetR domain; I 57.6 54 0.0012 23.2 6.1 57 9-69 2-59 (147)
14 PF08535 KorB: KorB domain; I 54.2 37 0.00081 21.1 4.4 58 16-75 32-90 (93)
15 PF14165 YtzH: YtzH-like prote 51.5 23 0.00051 23.3 3.2 36 38-75 21-59 (87)
16 COG4840 Uncharacterized protei 44.3 36 0.00078 21.7 3.1 59 12-76 11-71 (71)
17 PF02022 Integrase_Zn: Integra 41.5 32 0.00069 19.3 2.3 24 17-40 12-35 (40)
18 PF11459 DUF2893: Protein of u 39.1 47 0.001 20.8 3.1 37 35-75 11-49 (69)
19 cd08788 CARD_NOD2_2_CARD15 Cas 39.0 86 0.0019 20.4 4.3 51 19-73 22-72 (81)
20 cd08325 CARD_CASP1-like Caspas 38.8 97 0.0021 19.3 5.0 49 21-73 26-74 (83)
21 PF11505 DUF3216: Protein of u 38.5 33 0.00071 23.1 2.4 28 46-76 51-78 (97)
22 PF01465 GRIP: GRIP domain; I 37.5 27 0.00058 19.8 1.6 31 37-68 16-46 (46)
23 PF10130 PIN_2: PIN domain; I 37.5 39 0.00084 23.0 2.7 32 42-74 36-67 (133)
24 COG1378 Predicted transcriptio 36.9 60 0.0013 24.2 3.8 33 15-47 3-38 (247)
25 PF01381 HTH_3: Helix-turn-hel 36.4 23 0.00051 19.2 1.3 27 17-43 1-27 (55)
26 PHA00542 putative Cro-like pro 35.8 1.1E+02 0.0023 18.8 4.9 58 15-78 21-78 (82)
27 KOG0042 Glycerol-3-phosphate d 34.3 46 0.001 29.0 3.2 21 57-77 358-378 (680)
28 cd01671 CARD Caspase activatio 34.2 99 0.0022 18.0 6.0 56 13-73 14-70 (80)
29 PF04472 DUF552: Protein of un 32.8 48 0.001 19.9 2.3 36 38-74 5-47 (73)
30 COG3053 CitC Citrate lyase syn 32.1 34 0.00074 27.6 2.0 29 9-42 301-329 (352)
31 PF11116 DUF2624: Protein of u 31.8 1.1E+02 0.0024 19.9 4.0 36 38-74 29-66 (85)
32 PF11198 DUF2857: Protein of u 31.6 1E+02 0.0022 21.9 4.1 52 22-75 23-74 (180)
33 COG4003 Uncharacterized protei 30.8 82 0.0018 21.1 3.3 34 38-72 43-76 (98)
34 COG3753 Uncharacterized protei 30.6 58 0.0012 23.3 2.7 30 14-43 90-120 (143)
35 PF06207 DUF1002: Protein of u 30.1 1.4E+02 0.003 22.3 4.8 45 32-76 164-209 (225)
36 PF10975 DUF2802: Protein of u 28.4 54 0.0012 20.2 2.0 21 17-37 47-67 (70)
37 cd08316 Death_FAS_TNFRSF6 Deat 28.0 1.7E+02 0.0036 19.1 4.4 42 9-50 15-57 (97)
38 cd00542 Ntn_PVA Penicillin V a 27.4 74 0.0016 24.0 3.0 30 24-53 97-126 (303)
39 PF00570 HRDC: HRDC domain Blo 27.4 56 0.0012 18.6 1.9 35 14-48 8-49 (68)
40 PF07299 FBP: Fibronectin-bind 26.7 41 0.00089 24.9 1.5 41 31-74 38-78 (208)
41 PF12162 STAT1_TAZ2bind: STAT1 26.3 46 0.001 17.1 1.2 14 35-48 5-18 (23)
42 PRK09726 antitoxin HipB; Provi 26.2 65 0.0014 19.8 2.1 50 15-71 15-64 (88)
43 PF09868 DUF2095: Uncharacteri 25.8 1.1E+02 0.0024 21.5 3.4 34 38-72 73-106 (128)
44 PF13443 HTH_26: Cro/C1-type H 25.7 44 0.00095 18.7 1.2 49 17-71 2-50 (63)
45 TIGR03070 couple_hipB transcri 25.2 73 0.0016 16.9 2.0 49 16-71 6-54 (58)
46 PF00034 Cytochrom_C: Cytochro 24.4 91 0.002 17.3 2.4 16 60-75 76-91 (91)
47 PF13735 tRNA_NucTran2_2: tRNA 24.2 1.2E+02 0.0026 19.7 3.3 41 31-76 10-50 (149)
48 TIGR03830 CxxCG_CxxCG_HTH puta 24.2 84 0.0018 19.8 2.4 32 11-42 64-95 (127)
49 smart00341 HRDC Helicase and R 23.0 1.7E+02 0.0036 17.0 3.4 59 13-75 10-75 (81)
50 PRK15338 type III secretion sy 22.4 4.3E+02 0.0093 21.5 6.6 62 9-72 89-151 (372)
51 COG3082 Uncharacterized protei 22.4 77 0.0017 20.3 1.9 15 59-73 7-21 (74)
52 cd07922 CarBa CarBa is the A s 21.8 97 0.0021 19.8 2.4 21 16-36 26-46 (81)
53 PF11848 DUF3368: Domain of un 21.7 1E+02 0.0022 17.3 2.2 27 44-70 20-46 (48)
54 cd01902 Ntn_CGH Choloylglycine 21.5 1.1E+02 0.0024 23.0 3.0 31 23-53 94-124 (291)
55 cd04781 HTH_MerR-like_sg6 Heli 21.4 1.4E+02 0.0031 19.3 3.2 49 27-76 2-54 (120)
56 cd01109 HTH_YyaN Helix-Turn-He 21.0 1.9E+02 0.0041 18.4 3.7 47 28-75 3-54 (113)
57 COG3310 Uncharacterized protei 20.9 51 0.0011 24.6 1.0 45 27-75 21-70 (196)
58 cd05029 S-100A6 S-100A6: S-100 20.9 1.9E+02 0.0041 17.9 3.5 32 40-72 48-81 (88)
59 PF05883 Baculo_RING: Baculovi 20.8 1.5E+02 0.0032 20.9 3.3 31 36-69 83-113 (134)
60 PF11829 DUF3349: Protein of u 20.6 1.7E+02 0.0036 19.4 3.4 54 17-73 28-87 (96)
61 cd00045 DED The Death Effector 20.4 76 0.0017 19.4 1.6 51 24-75 10-68 (77)
62 PRK13689 hypothetical protein; 20.4 89 0.0019 20.1 1.9 15 59-73 7-21 (75)
63 PF13720 Acetyltransf_11: Udp 20.4 2.3E+02 0.005 17.6 4.4 49 20-73 22-76 (83)
64 PF04337 DUF480: Protein of un 20.3 2.4E+02 0.0052 20.2 4.3 47 24-73 84-133 (148)
65 cd04761 HTH_MerR-SF Helix-Turn 20.2 90 0.002 16.3 1.7 41 28-68 3-47 (49)
No 1
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=99.92 E-value=2.4e-25 Score=154.62 Aligned_cols=63 Identities=48% Similarity=0.799 Sum_probs=60.4
Q ss_pred cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhcC
Q 042488 13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE 78 (78)
Q Consensus 13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f~ 78 (78)
++.+||++|++.|||+||+||||||||+|+||||+|||||+. ++ +|+.|++||++|+++|+||
T Consensus 72 tv~avr~iLs~~~lhkFE~A~lgnLcpetaEEAkaLvPSL~n--ki-dD~~le~iL~dls~lr~fq 134 (134)
T KOG2351|consen 72 TVRAVRTILSGKGLHKFEVAQLGNLCPETAEEAKALVPSLEN--KI-DDDELEQILKDLSTLRTFQ 134 (134)
T ss_pred HHHHHHHHHhhCCcchhhHHHHhccCcccHHHHHHhcccccc--cc-CHHHHHHHHHHHHHHHhcC
Confidence 588999999999999999999999999999999999999995 46 9999999999999999997
No 2
>COG5250 RPB4 RNA polymerase II, fourth largest subunit [Transcription]
Probab=99.81 E-value=3.9e-20 Score=128.52 Aligned_cols=63 Identities=33% Similarity=0.576 Sum_probs=59.1
Q ss_pred cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhcC
Q 042488 13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE 78 (78)
Q Consensus 13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f~ 78 (78)
...++|++|+..|+|+||+||+++|||+|+||||+|||||+.| . +|+.+|.||++++.+|+||
T Consensus 76 ~~~a~~~~L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nk--i-dD~~lq~ilkels~l~~~~ 138 (138)
T COG5250 76 VAEALRTTLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNK--I-DDAILQAILKELSLLRKFQ 138 (138)
T ss_pred HHHHHHHHHccCCcchhhHHHhhccccccHHHHHhhccccccc--c-cHHHHHHHHHHHHHHHhhC
Confidence 3578899999999999999999999999999999999999965 5 9999999999999999997
No 3
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=99.81 E-value=6.6e-20 Score=122.57 Aligned_cols=64 Identities=41% Similarity=0.629 Sum_probs=60.1
Q ss_pred ccHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhcC
Q 042488 12 LKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE 78 (78)
Q Consensus 12 ~~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f~ 78 (78)
-+|.++++.|++++||+||+|||+||||+|++||++||||+.. || +++++++||++|++++.|+
T Consensus 55 e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~s~~E~~~lI~sl~~--r~-~ee~l~~iL~~i~~~~~~~ 118 (118)
T smart00657 55 EIVRAVRTLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEE--RI-DEEELEELLDDLSSLLPFY 118 (118)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHhCCCCCCHHHHHHHhhhhhc--cC-CHHHHHHHHHHHHHhcCCC
Confidence 3688999999999999999999999999999999999999984 67 9999999999999999985
No 4
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=99.70 E-value=3.7e-17 Score=109.32 Aligned_cols=60 Identities=17% Similarity=0.199 Sum_probs=53.4
Q ss_pred cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488 13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 75 (78)
Q Consensus 13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r 75 (78)
+...|+++++..+|++|++|+|+||||+|+||||+++||++. ++ ++++|++|||.|++|+
T Consensus 52 a~elve~L~~~~~l~e~~a~~I~nL~P~~~dElrai~~~~~~--~~-~~e~l~~ILd~l~k~~ 111 (112)
T PRK14981 52 AEELVEELLELEKMKEKTAVKIADILPETRDELRAIFAKERY--TL-SPEELDEILDIVKKYR 111 (112)
T ss_pred HHHHHHHHHHccCCCHHHHHHHHhcCCCCHHHHHHHHHHhcc--CC-CHHHHHHHHHHHHHhh
Confidence 345677777777899999999999999999999999999953 56 9999999999999997
No 5
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=99.68 E-value=1.4e-16 Score=104.25 Aligned_cols=60 Identities=30% Similarity=0.467 Sum_probs=53.2
Q ss_pred cHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488 13 KIGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 75 (78)
Q Consensus 13 ~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r 75 (78)
++..+++.|..+||++||++||+|+||+|++|++++||++.. || ++++|++||+.|++||
T Consensus 58 ~~~~l~~~L~~~~L~~~E~~qi~Nl~P~~~~El~~ii~~~~~--r~-~ee~l~~iL~~v~~~~ 117 (117)
T PF03874_consen 58 SIKELREELKKFGLTEFEILQIINLRPTTAVELRAIIESLES--RF-SEEDLEEILDLVSKYR 117 (117)
T ss_dssp HHHHHHHHHTTSTS-HHHHHHHHHH--SSHHHHHHHSTTGTT--TS-THHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHhcccCCHHHHHHHhcCCCCCHHHHHHHHHHhcc--CC-CHHHHHHHHHHHHHhC
Confidence 478888999999999999999999999999999999999984 68 9999999999999986
No 6
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=98.16 E-value=1e-05 Score=55.39 Aligned_cols=58 Identities=19% Similarity=0.283 Sum_probs=48.0
Q ss_pred HHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhh
Q 042488 16 DVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 76 (78)
Q Consensus 16 ~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~ 76 (78)
.|.++++-.++.+-=++-|+.+||.|.+|.|++.-+-.- .. +++++++|||.+.+|+.
T Consensus 56 ~veEL~~i~~~~e~~avkIadI~P~t~~ElRsIla~e~~--~~-s~E~l~~Ildiv~Ky~~ 113 (114)
T COG1460 56 LVEELLSIVKMSEKIAVKIADIMPRTPDELRSILAKERV--ML-SDEELDKILDIVDKYRE 113 (114)
T ss_pred HHHHHHhhccccHHHHHHHHHhCCCCHHHHHHHHHHccC--CC-CHHHHHHHHHHHHHHhc
Confidence 344555555666666999999999999999999999873 45 99999999999999974
No 7
>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]
Probab=91.43 E-value=0.34 Score=34.73 Aligned_cols=54 Identities=24% Similarity=0.410 Sum_probs=45.8
Q ss_pred HHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhh
Q 042488 19 RILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLI 74 (78)
Q Consensus 19 ~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~ 74 (78)
.-+..++|++.|+-||.|+.|-++=|-..+|--..+ ||.+.+++.+++..++++
T Consensus 77 ~k~~~fkLtKAE~LqiiN~rPss~vel~~~iE~~ee--Rf~~ee~i~elv~~i~~~ 130 (149)
T KOG4168|consen 77 TKLKSFKLTKAEILQIINLRPSSSVELYLIIEEVEE--RFQDEEDIEELVETISKT 130 (149)
T ss_pred HHhccccchHHHHHHHhccCcchHHHHHHHHHHHHH--hccchhcHHHHHHhcccc
Confidence 334457999999999999999999999999988874 677889999999888754
No 8
>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=81.60 E-value=0.57 Score=30.78 Aligned_cols=36 Identities=22% Similarity=0.559 Sum_probs=23.2
Q ss_pred hhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhc
Q 042488 35 GNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKF 77 (78)
Q Consensus 35 aNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f 77 (78)
+|+||+++ +|++-+-++.- +-+--+|-..+.++|+|
T Consensus 9 sn~Cpdca-~a~eyl~rl~v------~yd~VeIt~Sm~NlKrF 44 (85)
T COG4545 9 SNLCPDCA-PAVEYLERLNV------DYDFVEITESMANLKRF 44 (85)
T ss_pred cccCcchH-HHHHHHHHcCC------CceeeehhhhhhhHHHH
Confidence 69999998 46777777762 22334455566666655
No 9
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=76.59 E-value=13 Score=22.06 Aligned_cols=55 Identities=20% Similarity=0.242 Sum_probs=44.4
Q ss_pred HHHHHHHHhhC-CCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHh
Q 042488 14 IGDVFRILSRY-QLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73 (78)
Q Consensus 14 i~~Vr~~L~~~-~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~ 73 (78)
+..|...|-.. =++..|...|.+ +|...+-++.|+-.+.+| .+...+..++.|.+
T Consensus 18 ~~~ild~L~~~~vlt~~e~e~I~~-~~t~~~k~~~LLd~l~~k----g~~a~~~F~~~L~~ 73 (85)
T PF00619_consen 18 LDDILDHLLSRGVLTEEEYEEIRS-EPTRQDKARKLLDILKRK----GPEAFDIFCQALRE 73 (85)
T ss_dssp HHHHHHHHHHTTSSSHHHHHHHHT-SSSHHHHHHHHHHHHHHC----CHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHc-cCChHHHHHHHHHHHHHH----CHHHHHHHHHHHHh
Confidence 67777777765 589999999998 999999999999999876 56677777766655
No 10
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=73.59 E-value=6.3 Score=25.04 Aligned_cols=39 Identities=10% Similarity=0.259 Sum_probs=30.5
Q ss_pred cCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhh
Q 042488 37 LCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 76 (78)
Q Consensus 37 LcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~ 76 (78)
.-.+..|+.+-|--...+|+.| +..++|.|.++|.++|+
T Consensus 33 f~~~~yedl~diy~~V~~K~~f-S~sEm~aI~~ELG~LRK 71 (71)
T PF06569_consen 33 FSEEKYEDLKDIYEMVMSKDSF-SPSEMQAIAEELGQLRK 71 (71)
T ss_pred CChhhHHHHHHHHHHHHhccCC-CHHHHHHHHHHHHhhcC
Confidence 3445567777766666666788 99999999999999986
No 11
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=68.37 E-value=1.8 Score=30.56 Aligned_cols=16 Identities=69% Similarity=0.960 Sum_probs=13.8
Q ss_pred CCchhhhhhhhccHHH
Q 042488 1 MSGEEEENAAELKIGD 16 (78)
Q Consensus 1 ~~~~~~~~~~~~~i~~ 16 (78)
|+|++|||||+|++..
T Consensus 1 ~~g~~EEdAa~lk~g~ 16 (134)
T KOG2351|consen 1 PRGEEEEDAAELKLGK 16 (134)
T ss_pred CcchhhccHHhccccH
Confidence 6899999999998754
No 12
>PF09969 DUF2203: Uncharacterized conserved protein (DUF2203); InterPro: IPR018699 This family has no known function.
Probab=61.47 E-value=9.3 Score=25.84 Aligned_cols=14 Identities=43% Similarity=0.695 Sum_probs=12.6
Q ss_pred CHHHHHHhhhcccc
Q 042488 41 TVEEAIAMVPSIKT 54 (78)
Q Consensus 41 t~dEAkaLIPSL~~ 54 (78)
|.+||++++|-+..
T Consensus 4 Tl~EA~~lLP~l~~ 17 (120)
T PF09969_consen 4 TLEEANALLPLLRP 17 (120)
T ss_pred CHHHHHHHHHHHHH
Confidence 78999999999974
No 13
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=57.56 E-value=54 Score=23.20 Aligned_cols=57 Identities=14% Similarity=0.127 Sum_probs=34.1
Q ss_pred hhhccHHHHHHHHhhCCCChHH-HHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHH
Q 042488 9 AAELKIGDVFRILSRYQLAEFE-LCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLN 69 (78)
Q Consensus 9 ~~~~~i~~Vr~~L~~~~L~~fE-~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd 69 (78)
+-...+..||.+|.+.|+.+.. .+.|+++..=+..-|.-= |..+..| +=++|.+|-+
T Consensus 2 ~~~~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RK---L~G~~~f-tl~EI~~Ia~ 59 (147)
T PF08667_consen 2 DDQAIAERVRELLDRKGIPKRKHASELADILGISYSSAYRK---LNGKSPF-TLEEIKKIAK 59 (147)
T ss_pred hhHHHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHH---hcCCCCC-CHHHHHHHHH
Confidence 4456788999999999988877 555666655554444322 2222234 5555555443
No 14
>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=54.16 E-value=37 Score=21.08 Aligned_cols=58 Identities=19% Similarity=0.271 Sum_probs=35.3
Q ss_pred HHHHHHhhCCCChHH-HHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488 16 DVFRILSRYQLAEFE-LCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 75 (78)
Q Consensus 16 ~Vr~~L~~~~L~~fE-~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r 75 (78)
.|+.++....+.... +..|..++-+.++++.++|-.-.. +.. +....+.+.+.|+..+
T Consensus 32 ~i~~~v~~g~~~~~~a~~~L~~~~~~~~~~~~~~v~~~~~-~~~-t~~~~~~~~~~l~~~k 90 (93)
T PF08535_consen 32 EIKELVRSGRISDIRALYELRKLAEKNPEEVEALVAKAKE-EGL-TRAAVKALRRELKEKK 90 (93)
T ss_dssp HHHHHHHTTS---HHHHHHHHHHHHH-HHHHHHHH-HSTT-S---SHHHHHHHHHHHH---
T ss_pred HHHHHHHcCCCchHHHHHHHHHHHHhCHHHHHHHHHHhcc-ccc-cHHHHHHHHHHHHHhh
Confidence 567777776676666 557777888899999999922221 234 7888888888887655
No 15
>PF14165 YtzH: YtzH-like protein
Probab=51.52 E-value=23 Score=23.32 Aligned_cols=36 Identities=25% Similarity=0.327 Sum_probs=26.7
Q ss_pred CCCCHHHH---HHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488 38 CPETVEEA---IAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 75 (78)
Q Consensus 38 cPet~dEA---kaLIPSL~~k~r~~~de~Lq~ILd~L~~~r 75 (78)
|+.|+.|+ ..||-||-.+. - -+.++..+|.+|-+|-
T Consensus 21 ccgTvsEcEQieRLvksLm~n~-~-i~~~ik~~L~~Iy~ys 59 (87)
T PF14165_consen 21 CCGTVSECEQIERLVKSLMANP-N-IDADIKQTLEEIYSYS 59 (87)
T ss_pred ccCcHHHHHHHHHHHHHHHcCC-C-cCHHHHHHHHHHHHHH
Confidence 77888776 46788886543 3 3888999999998773
No 16
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.33 E-value=36 Score=21.73 Aligned_cols=59 Identities=12% Similarity=0.187 Sum_probs=38.6
Q ss_pred ccHHHHHHHHhh--CCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhh
Q 042488 12 LKIGDVFRILSR--YQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 76 (78)
Q Consensus 12 ~~i~~Vr~~L~~--~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~ 76 (78)
..|..|++-|.- .|+-+-|- +--...++..-+--..++|.+| +..+.|.|-++|.++|+
T Consensus 11 fmi~eI~~KLnmvN~gvl~~e~-----~d~~~~edLtdiy~mvkkkenf-SpsEmqaiA~eL~rlRk 71 (71)
T COG4840 11 FMIEEIREKLNMVNVGVLDPEK-----YDNANYEDLTDIYDMVKKKENF-SPSEMQAIADELGRLRK 71 (71)
T ss_pred HHHHHHHHHHhhhhhhccCHHh-----cccccHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHhhC
Confidence 456677776663 23222221 1122455666666777777788 99999999999999985
No 17
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=41.49 E-value=32 Score=19.27 Aligned_cols=24 Identities=13% Similarity=0.328 Sum_probs=17.5
Q ss_pred HHHHHhhCCCChHHHHHHhhcCCC
Q 042488 17 VFRILSRYQLAEFELCVLGNLCPE 40 (78)
Q Consensus 17 Vr~~L~~~~L~~fE~A~LaNLcPe 40 (78)
++.+-.++|+..-+.-+|++-||.
T Consensus 12 ~~~L~~~f~ip~~vAk~IV~~C~~ 35 (40)
T PF02022_consen 12 AKALRHKFGIPRLVAKQIVNQCPK 35 (40)
T ss_dssp HHHHHHHHT--HHHHHHHHHHSCC
T ss_pred HHHHHHHHccCHHHHHHHHHHCHH
Confidence 344444789999999999999996
No 18
>PF11459 DUF2893: Protein of unknwon function (DUF2893); InterPro: IPR021561 This is a bacterial family of uncharacterised proteins.
Probab=39.06 E-value=47 Score=20.82 Aligned_cols=37 Identities=16% Similarity=0.324 Sum_probs=28.6
Q ss_pred hhcCCC--CHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488 35 GNLCPE--TVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 75 (78)
Q Consensus 35 aNLcPe--t~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r 75 (78)
.+..|+ +.+||..|+-+|.. ....-||++|+.-.+.|
T Consensus 11 l~~~p~~~s~e~a~~l~egL~n----Lrp~~lq~LL~~C~svK 49 (69)
T PF11459_consen 11 LSEVPKRQSFEEADELMEGLRN----LRPRVLQELLEHCTSVK 49 (69)
T ss_pred HHhCCccCCHHHHHHHHHHHhh----cCHHHHHHHHHHCccHH
Confidence 456666 57899999999963 47889999998766654
No 19
>cd08788 CARD_NOD2_2_CARD15 Caspase activation and recruitment domain of NOD2, repeat 2. Caspase activation and recruitment domain (CARD) similar to that found in human NOD2 (CARD15), repeat 2. NOD2 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD2, as well as NOD1, the N-terminal effector domain is a CARD. NOD2 contains two N-terminal CARD repeats. Mutations in NOD2 have been associated with Crohns disease and Blau syndrome. Nod2-CARDs have been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are pr
Probab=39.03 E-value=86 Score=20.43 Aligned_cols=51 Identities=12% Similarity=0.135 Sum_probs=37.3
Q ss_pred HHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHh
Q 042488 19 RILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73 (78)
Q Consensus 19 ~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~ 73 (78)
.+|...-+++.|-..|--=.+...|-|+.||-+-+.| .+..-..++..|+.
T Consensus 22 ~ll~~G~is~~Ecd~Ir~p~~T~sqqARrLLD~V~~K----G~~A~~~ll~~vq~ 72 (81)
T cd08788 22 LLLTRGFFSSYDCDEIRLPIFTPSQQARRLLDLVKAK----GEGAAKFLLEYVQQ 72 (81)
T ss_pred HHHHcCCccHhhcchhhcCCCChHHHHHHHHHHHHHH----hHHHHHHHHHHHHh
Confidence 3444567999998888866788899999999999877 34444555555543
No 20
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=38.83 E-value=97 Score=19.29 Aligned_cols=49 Identities=20% Similarity=0.214 Sum_probs=36.0
Q ss_pred HhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHh
Q 042488 21 LSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73 (78)
Q Consensus 21 L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~ 73 (78)
+.+.=|++.|+..|..=-+...|-|+.||-|+.+| .+...+-.++.|.+
T Consensus 26 l~~~Vl~~~E~e~i~~~~~t~~dkar~Lid~v~~K----G~~A~~iF~~~L~~ 74 (83)
T cd08325 26 LEKNVLNEEEMEKIKEENNTIMDKARVLVDSVTEK----GQEAGQIFIKHLLN 74 (83)
T ss_pred HHcCCCCHHHHHHHHhccCCHHHHHHHHHHHHHHH----hHHHHHHHHHHHHh
Confidence 34456888898888766667899999999999976 45555555555544
No 21
>PF11505 DUF3216: Protein of unknown function (DUF3216); InterPro: IPR023108 This domain is found in a family of proteins with unknown function and appears to be restricted to the Thermococcaceae. ; PDB: 2HJM_A.
Probab=38.50 E-value=33 Score=23.10 Aligned_cols=28 Identities=18% Similarity=0.404 Sum_probs=20.7
Q ss_pred HHhhhcccccCCCCCHHHHHHHHHHHHhhhh
Q 042488 46 IAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 76 (78)
Q Consensus 46 kaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~ 76 (78)
--++-+|+.| |+|+.++.+|+.++..|.
T Consensus 51 EGiLttLk~K---~~deri~~Lle~Vr~~R~ 78 (97)
T PF11505_consen 51 EGILTTLKLK---YEDERIGELLEKVRARRE 78 (97)
T ss_dssp HHHHHHHTTT------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHH---hccHHHHHHHHHHHHHHH
Confidence 4578899865 599999999999998763
No 22
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=37.54 E-value=27 Score=19.82 Aligned_cols=31 Identities=26% Similarity=0.260 Sum_probs=18.4
Q ss_pred cCCCCHHHHHHhhhcccccCCCCCHHHHHHHH
Q 042488 37 LCPETVEEAIAMVPSIKTRGRAHDDEAIEKML 68 (78)
Q Consensus 37 LcPet~dEAkaLIPSL~~k~r~~~de~Lq~IL 68 (78)
|+..++.+...|+|-+.+==+| ++++.++|+
T Consensus 16 l~~~~~~~~~~llpvi~tlL~f-s~~e~~~i~ 46 (46)
T PF01465_consen 16 LESREPSEREQLLPVIATLLKF-SPEEKQKIL 46 (46)
T ss_dssp HTTSS---HHHHHHHHHHHTT---HHHHHHHH
T ss_pred hcCCchhhHHHHHHHHHHHHCC-CHHHHHhhC
Confidence 5556677888888888643367 888887764
No 23
>PF10130 PIN_2: PIN domain; InterPro: IPR019298 This entry represents a set of bacterial and archaeal proteins that are predicted to be RNases (from similarities to 5'-exonucleases).
Probab=37.47 E-value=39 Score=23.03 Aligned_cols=32 Identities=28% Similarity=0.400 Sum_probs=27.2
Q ss_pred HHHHHHhhhcccccCCCCCHHHHHHHHHHHHhh
Q 042488 42 VEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLI 74 (78)
Q Consensus 42 ~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~ 74 (78)
.+|++..+|-|.+|++. +++++.++|+.+.+.
T Consensus 36 ~~Ei~kh~~~I~~k~~l-~~~~~~~~l~~l~~~ 67 (133)
T PF10130_consen 36 LEEIEKHLPKIAKKSKL-SEEELEEVLNILFSR 67 (133)
T ss_pred HHHHHHHHHHHHHHhCC-CHHHHHHHHHHHHhh
Confidence 67999999999887777 999999999988765
No 24
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=36.87 E-value=60 Score=24.17 Aligned_cols=33 Identities=24% Similarity=0.221 Sum_probs=26.0
Q ss_pred HHHHHHHhhCCCChHHH---HHHhhcCCCCHHHHHH
Q 042488 15 GDVFRILSRYQLAEFEL---CVLGNLCPETVEEAIA 47 (78)
Q Consensus 15 ~~Vr~~L~~~~L~~fE~---A~LaNLcPet~dEAka 47 (78)
..+.+.|+..||++.|. ..|.+++|-|+-|.-.
T Consensus 3 ~~~~~~L~~lGlt~yEa~vY~aLl~~g~~tA~eis~ 38 (247)
T COG1378 3 EELEENLQKLGLTEYEAKVYLALLCLGEATAKEISE 38 (247)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHHHHhCCccHHHHHH
Confidence 35788999999999994 4566778899888643
No 25
>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=36.40 E-value=23 Score=19.23 Aligned_cols=27 Identities=15% Similarity=0.123 Sum_probs=18.9
Q ss_pred HHHHHhhCCCChHHHHHHhhcCCCCHH
Q 042488 17 VFRILSRYQLAEFELCVLGNLCPETVE 43 (78)
Q Consensus 17 Vr~~L~~~~L~~fE~A~LaNLcPet~d 43 (78)
+++.+...|++..|.|...++-|.|+-
T Consensus 1 ik~~r~~~gls~~~la~~~gis~~~i~ 27 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLGISRSTIS 27 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHTS-HHHHH
T ss_pred CHHHHHHcCCCHHHHHHHhCCCcchhH
Confidence 456667789999998888887776654
No 26
>PHA00542 putative Cro-like protein
Probab=35.77 E-value=1.1e+02 Score=18.83 Aligned_cols=58 Identities=10% Similarity=0.105 Sum_probs=40.8
Q ss_pred HHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhhcC
Q 042488 15 GDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE 78 (78)
Q Consensus 15 ~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~f~ 78 (78)
..+...+...|++.-+.|....+.+.|+-....-- .+..+.+.+++|++.+..+..|+
T Consensus 21 ~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~------~~~p~~~~l~ki~~~~~~~~~~~ 78 (82)
T PHA00542 21 DELVCALIRAGWSQEQIADATDVSQPTICRIYSGR------HKDPRYSVVEKLRHLVLNLDDFQ 78 (82)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCC------CCCCCHHHHHHHHHHHHHhchhh
Confidence 35667777889999999999999877765543211 01236778888888888776654
No 27
>KOG0042 consensus Glycerol-3-phosphate dehydrogenase [Energy production and conversion]
Probab=34.34 E-value=46 Score=28.99 Aligned_cols=21 Identities=14% Similarity=0.327 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHHHHHhhhhc
Q 042488 57 RAHDDEAIEKMLNDLSLIKKF 77 (78)
Q Consensus 57 r~~~de~Lq~ILd~L~~~r~f 77 (78)
...++++||-||++++.|-.|
T Consensus 358 P~PtE~dIqfIL~ev~~yl~~ 378 (680)
T KOG0042|consen 358 PTPTEDDIQFILKEVQHYLSF 378 (680)
T ss_pred CCCCHHHHHHHHHHHHHhhCC
Confidence 346899999999999999665
No 28
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. 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 of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=34.16 E-value=99 Score=18.02 Aligned_cols=56 Identities=18% Similarity=0.200 Sum_probs=41.4
Q ss_pred cHHHHHHHHhhCC-CChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHh
Q 042488 13 KIGDVFRILSRYQ-LAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73 (78)
Q Consensus 13 ~i~~Vr~~L~~~~-L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~ 73 (78)
.+..|...|...| ++..|...|.. +|...+-++.||=.|..| .+......++.|.+
T Consensus 14 ~~~~il~~L~~~~vlt~~e~~~i~~-~~~~~~k~~~Lld~l~~k----g~~af~~F~~~L~~ 70 (80)
T cd01671 14 DVEDVLDHLLSDGVLTEEEYEKIRS-ESTRQDKARKLLDILPRK----GPKAFQSFLQALQE 70 (80)
T ss_pred cHHHHHHHHHHcCCCCHHHHHHHHc-CCChHHHHHHHHHHHHhc----ChHHHHHHHHHHHh
Confidence 5666666666654 66666666665 677999999999999875 67777777777764
No 29
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=32.84 E-value=48 Score=19.93 Aligned_cols=36 Identities=28% Similarity=0.413 Sum_probs=24.5
Q ss_pred CCCCHHHHHHhhhccccc-------CCCCCHHHHHHHHHHHHhh
Q 042488 38 CPETVEEAIAMVPSIKTR-------GRAHDDEAIEKMLNDLSLI 74 (78)
Q Consensus 38 cPet~dEAkaLIPSL~~k-------~r~~~de~Lq~ILd~L~~~ 74 (78)
-|.+.++|..++-.|..+ ... +++..++++|-|+..
T Consensus 5 ~p~~~~D~~~i~~~l~~g~~Vivnl~~l-~~~~~~Ri~Dfl~G~ 47 (73)
T PF04472_consen 5 EPKSFEDAREIVDALREGKIVIVNLENL-DDEEAQRILDFLSGA 47 (73)
T ss_dssp E-SSGGGHHHHHHHHHTT--EEEE-TTS--HHHHHHHHHHHHHH
T ss_pred eeCCHHHHHHHHHHHHcCCEEEEECCCC-CHHHHHHHHHHHhch
Confidence 477777777777777653 145 788899999988753
No 30
>COG3053 CitC Citrate lyase synthetase [Energy production and conversion]
Probab=32.13 E-value=34 Score=27.57 Aligned_cols=29 Identities=24% Similarity=0.405 Sum_probs=23.2
Q ss_pred hhhccHHHHHHHHhhCCCChHHHHHHhhcCCCCH
Q 042488 9 AAELKIGDVFRILSRYQLAEFELCVLGNLCPETV 42 (78)
Q Consensus 9 ~~~~~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~ 42 (78)
..-.+...||.+|++.+ .+.|+||.|+|.
T Consensus 301 ~~~ISAS~VR~~l~~~~-----~~~ia~lVP~tT 329 (352)
T COG3053 301 EMPISASRVRQLLAKND-----LEAIANLVPATT 329 (352)
T ss_pred CCcccHHHHHHHHHhCC-----HHHHHhhCcHHH
Confidence 34567889999998766 468999999985
No 31
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=31.79 E-value=1.1e+02 Score=19.90 Aligned_cols=36 Identities=14% Similarity=0.254 Sum_probs=28.7
Q ss_pred CCCCHHHHHHhhhccccc--CCCCCHHHHHHHHHHHHhh
Q 042488 38 CPETVEEAIAMVPSIKTR--GRAHDDEAIEKMLNDLSLI 74 (78)
Q Consensus 38 cPet~dEAkaLIPSL~~k--~r~~~de~Lq~ILd~L~~~ 74 (78)
.|=|...|+.++.-++.+ +.| ++++-.++|.+|++.
T Consensus 29 i~it~~QA~~I~~~lr~k~inIf-n~~~r~~llkeia~i 66 (85)
T PF11116_consen 29 ISITKKQAEQIANILRGKNINIF-NEQERKKLLKEIAKI 66 (85)
T ss_pred CCCCHHHHHHHHHHHhcCCCCCC-CHHHHHHHHHHHHHh
Confidence 366888888888888766 356 899999999998875
No 32
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=31.62 E-value=1e+02 Score=21.91 Aligned_cols=52 Identities=12% Similarity=0.085 Sum_probs=36.2
Q ss_pred hhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488 22 SRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 75 (78)
Q Consensus 22 ~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r 75 (78)
...|+++.|+.+|-++.+.+....-.--++.-+ ..++.+.|+.+|......+
T Consensus 23 ~~lG~~~eel~~L~~ls~~~l~~L~~~~v~~~~--i~in~~~l~~~L~~~~~~~ 74 (180)
T PF11198_consen 23 EALGFSPEELDALQQLSLDDLHYLANSSVSFVS--ISINHDVLWRLLEQARREQ 74 (180)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHhcCCcceee--eeeCHHHHHHHHHHHHHHH
Confidence 347999999999999977666544433333322 2248899999999877654
No 33
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.80 E-value=82 Score=21.13 Aligned_cols=34 Identities=24% Similarity=0.313 Sum_probs=25.3
Q ss_pred CCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHH
Q 042488 38 CPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 72 (78)
Q Consensus 38 cPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~ 72 (78)
.|+|.+||..+|--+...|.. +.+.-..+=-.+.
T Consensus 43 rCdT~EEAlEii~yleKrGEi-~~E~A~~L~~~~~ 76 (98)
T COG4003 43 RCDTEEEALEIINYLEKRGEI-TPEMAKALRVTLV 76 (98)
T ss_pred HhCcHHHHHHHHHHHHHhCCC-CHHHHHHHHhhHH
Confidence 478999999999999877777 7776555544443
No 34
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.56 E-value=58 Score=23.31 Aligned_cols=30 Identities=23% Similarity=0.269 Sum_probs=24.1
Q ss_pred HHHHHHHHhhCCCChHH-HHHHhhcCCCCHH
Q 042488 14 IGDVFRILSRYQLAEFE-LCVLGNLCPETVE 43 (78)
Q Consensus 14 i~~Vr~~L~~~~L~~fE-~A~LaNLcPet~d 43 (78)
-..++++-.+.|+.+-| .++|+...|+-+|
T Consensus 90 ~~~l~~la~~~Gld~~El~~~Ls~~LP~~Vd 120 (143)
T COG3753 90 TDTLSQLAQKTGLDEQELLKQLSEQLPGIVD 120 (143)
T ss_pred hhHHHHHHHHhCCCHHHHHHHHHHHhHHHHH
Confidence 34566666678999999 9999999998665
No 35
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=30.13 E-value=1.4e+02 Score=22.33 Aligned_cols=45 Identities=22% Similarity=0.256 Sum_probs=35.3
Q ss_pred HHHhhcCCCCHHHHHHhhhcccc-cCCCCCHHHHHHHHHHHHhhhh
Q 042488 32 CVLGNLCPETVEEAIAMVPSIKT-RGRAHDDEAIEKMLNDLSLIKK 76 (78)
Q Consensus 32 A~LaNLcPet~dEAkaLIPSL~~-k~r~~~de~Lq~ILd~L~~~r~ 76 (78)
.+++.--|+|.++.+.+|--... .+...++++++.|.+.+.+++.
T Consensus 164 ~~va~~~~~t~~eI~~IV~~~~~~~~i~ls~~q~~~i~~l~~~~~~ 209 (225)
T PF06207_consen 164 EEVAKQKPKTDEEIRNIVNNVLNNYNINLSDEQIQQIVNLMKKIQN 209 (225)
T ss_pred HHHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHc
Confidence 35677889999999999865532 2444599999999999999865
No 36
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=28.42 E-value=54 Score=20.17 Aligned_cols=21 Identities=24% Similarity=0.216 Sum_probs=15.8
Q ss_pred HHHHHhhCCCChHHHHHHhhc
Q 042488 17 VFRILSRYQLAEFELCVLGNL 37 (78)
Q Consensus 17 Vr~~L~~~~L~~fE~A~LaNL 37 (78)
+.++..++||++-|.-.|.+|
T Consensus 47 ~~el~~~CgL~~aEAeLl~~L 67 (70)
T PF10975_consen 47 VEELMEECGLSRAEAELLLSL 67 (70)
T ss_pred HHHHHHHcCCCHHHHHHHHHH
Confidence 456677788888888777765
No 37
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. 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 and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=27.99 E-value=1.7e+02 Score=19.06 Aligned_cols=42 Identities=17% Similarity=0.204 Sum_probs=33.7
Q ss_pred hhhccHHHHHHHHhhCCCChHHHHHHhhcCCCCHHHHH-Hhhh
Q 042488 9 AAELKIGDVFRILSRYQLAEFELCVLGNLCPETVEEAI-AMVP 50 (78)
Q Consensus 9 ~~~~~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAk-aLIP 50 (78)
|.++.+.++++.-.+.||++-++-.|.+=.|.+..|.+ .++-
T Consensus 15 a~~~~~~~wK~faR~lglse~~Id~I~~~~~~d~~Eq~~qmL~ 57 (97)
T cd08316 15 ADVMTLKDVKKFVRKSGLSEPKIDEIKLDNPQDTAEQKVQLLR 57 (97)
T ss_pred HHHcCHHHHHHHHHHcCCCHHHHHHHHHcCCCChHHHHHHHHH
Confidence 55678889999888899999999999999998765543 3443
No 38
>cd00542 Ntn_PVA Penicillin V acylase (PVA), also known as conjugated bile salt acid hydrolase (CBAH), catalyzes the hydrolysis of penicillin V to yield 6-amino penicillanic acid (6-APA), an important key intermediate of semisynthetic penicillins. PVA has an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which PVA belongs. This nucleophilic cysteine is exposed by post-translational prossessing of the PVA precursor. PVA forms a homotetramer.
Probab=27.45 E-value=74 Score=24.03 Aligned_cols=30 Identities=23% Similarity=0.161 Sum_probs=25.4
Q ss_pred CCCChHHHHHHhhcCCCCHHHHHHhhhccc
Q 042488 24 YQLAEFELCVLGNLCPETVEEAIAMVPSIK 53 (78)
Q Consensus 24 ~~L~~fE~A~LaNLcPet~dEAkaLIPSL~ 53 (78)
.++..++..+.+==.++|++||+..+..+.
T Consensus 97 ~~l~~~~~i~~iL~n~~TV~Ev~~~l~~i~ 126 (303)
T cd00542 97 TNIAPFEFITWVLGNFASVEEVKEALKNIN 126 (303)
T ss_pred CccCHHHHHHHHHHcCCCHHHHHHHhcCce
Confidence 478899987777777899999999998774
No 39
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=27.38 E-value=56 Score=18.55 Aligned_cols=35 Identities=20% Similarity=0.310 Sum_probs=23.0
Q ss_pred HHHHHHHHhh-CC------CChHHHHHHhhcCCCCHHHHHHh
Q 042488 14 IGDVFRILSR-YQ------LAEFELCVLGNLCPETVEEAIAM 48 (78)
Q Consensus 14 i~~Vr~~L~~-~~------L~~fE~A~LaNLcPet~dEAkaL 48 (78)
+.+.|.-+.+ .+ +++.-+..||...|.|.+|...+
T Consensus 8 L~~~R~~~A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i 49 (68)
T PF00570_consen 8 LKEWREELAREEDVPPYRILSDEALLEIAKRLPTSIEELLQI 49 (68)
T ss_dssp HHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTS
T ss_pred HHHHHHHHHHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHc
Confidence 3445555554 23 55566889999999999999987
No 40
>PF07299 FBP: Fibronectin-binding protein (FBP); InterPro: IPR010841 This entry consists of several bacterial fibronectin-binding proteins which are thought to be involved in virulence in Listeria species [,].; PDB: 4ADO_B 4ADN_B 2YB5_F.
Probab=26.73 E-value=41 Score=24.94 Aligned_cols=41 Identities=27% Similarity=0.305 Sum_probs=30.6
Q ss_pred HHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhh
Q 042488 31 LCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLI 74 (78)
Q Consensus 31 ~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~ 74 (78)
..-|.+++|+-.+|-+.|+..+.. .. +.++.++.|+.|..|
T Consensus 38 ~~ki~~~f~~~~~eq~~ll~~i~~--i~-~~~~~~~~L~~L~~y 78 (208)
T PF07299_consen 38 IEKILELFPELTEEQKELLEQIMD--IK-TREEAEKYLEELKPY 78 (208)
T ss_dssp HHHHHHHHCTTTHHHCCHHHHHTS--TT--HHHHHHHHHHHHCC
T ss_pred HHHHHHHcccCCHHHHHHHHHHhc--cC-CHHHHHHHHHHHHHH
Confidence 345677888888888888887764 23 788888888888776
No 41
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=26.29 E-value=46 Score=17.05 Aligned_cols=14 Identities=14% Similarity=0.318 Sum_probs=7.8
Q ss_pred hhcCCCCHHHHHHh
Q 042488 35 GNLCPETVEEAIAM 48 (78)
Q Consensus 35 aNLcPet~dEAkaL 48 (78)
-|++|-++|+-++|
T Consensus 5 dnmmPMSPddy~~l 18 (23)
T PF12162_consen 5 DNMMPMSPDDYDEL 18 (23)
T ss_dssp TS---S-HHHHHHH
T ss_pred hcccCCCHHHHHHH
Confidence 58999999987765
No 42
>PRK09726 antitoxin HipB; Provisional
Probab=26.22 E-value=65 Score=19.77 Aligned_cols=50 Identities=12% Similarity=0.023 Sum_probs=32.4
Q ss_pred HHHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHH
Q 042488 15 GDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 71 (78)
Q Consensus 15 ~~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L 71 (78)
..++.+..+.|++..|.|...++-+.|+---.. . .+..+-+.|.+|.+.+
T Consensus 15 ~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~------g-~~~ps~~~l~~ia~~l 64 (88)
T PRK09726 15 NAMKLVRQQNGWTQSELAKKIGIKQATISNFEN------N-PDNTTLTTFFKILQSL 64 (88)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC------C-CCCCCHHHHHHHHHHc
Confidence 456666677899999999999988776543221 1 1222556666666544
No 43
>PF09868 DUF2095: Uncharacterized protein conserved in archaea (DUF2095); InterPro: IPR018662 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=25.84 E-value=1.1e+02 Score=21.49 Aligned_cols=34 Identities=24% Similarity=0.296 Sum_probs=26.1
Q ss_pred CCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHH
Q 042488 38 CPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 72 (78)
Q Consensus 38 cPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~ 72 (78)
.|+|.+||.-+|--|.+.|.. +.+.-..+--.|.
T Consensus 73 RC~T~EEALEVInylek~GEI-t~e~A~eLr~~L~ 106 (128)
T PF09868_consen 73 RCKTDEEALEVINYLEKRGEI-TPEEAKELRSILV 106 (128)
T ss_pred HhCcHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHH
Confidence 478999999999999887777 7776665555443
No 44
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=25.70 E-value=44 Score=18.67 Aligned_cols=49 Identities=10% Similarity=0.209 Sum_probs=26.8
Q ss_pred HHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHH
Q 042488 17 VFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 71 (78)
Q Consensus 17 Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L 71 (78)
++.+|.+.|++..+.|.-+.+-+.|.-.-.. ++.... +-+.|.+|-+.+
T Consensus 2 L~~~m~~~~it~~~La~~~gis~~tl~~~~~-----~~~~~~-~~~~l~~ia~~l 50 (63)
T PF13443_consen 2 LKELMAERGITQKDLARKTGISRSTLSRILN-----GKPSNP-SLDTLEKIAKAL 50 (63)
T ss_dssp HHHHHHHTT--HHHHHHHHT--HHHHHHHHT-----TT------HHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh-----cccccc-cHHHHHHHHHHc
Confidence 6778888899999999888888776655443 110123 555666555443
No 45
>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=25.19 E-value=73 Score=16.87 Aligned_cols=49 Identities=12% Similarity=0.076 Sum_probs=30.5
Q ss_pred HHHHHHhhCCCChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHH
Q 042488 16 DVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 71 (78)
Q Consensus 16 ~Vr~~L~~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L 71 (78)
.++....+.|++.-+.|....+.|.++-... +. .+.++.+.+.++.+.+
T Consensus 6 ~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e------~g-~~~~~~~~~~~i~~~l 54 (58)
T TIGR03070 6 LVRARRKALGLTQADLADLAGVGLRFIRDVE------NG-KPTVRLDKVLRVLDAL 54 (58)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH------CC-CCCCCHHHHHHHHHHc
Confidence 4556666789999999999888776554332 11 1122566666666543
No 46
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=24.43 E-value=91 Score=17.30 Aligned_cols=16 Identities=31% Similarity=0.407 Sum_probs=13.2
Q ss_pred CHHHHHHHHHHHHhhh
Q 042488 60 DDEAIEKMLNDLSLIK 75 (78)
Q Consensus 60 ~de~Lq~ILd~L~~~r 75 (78)
++++++.|+.=|.++|
T Consensus 76 s~~e~~~l~ayl~slk 91 (91)
T PF00034_consen 76 SDEEIADLAAYLRSLK 91 (91)
T ss_dssp SHHHHHHHHHHHHHTS
T ss_pred CHHHHHHHHHHHHHhC
Confidence 8899999988887764
No 47
>PF13735 tRNA_NucTran2_2: tRNA nucleotidyltransferase domain 2 putative; PDB: 1MIY_A 1MIV_B 1MIW_B.
Probab=24.20 E-value=1.2e+02 Score=19.69 Aligned_cols=41 Identities=22% Similarity=0.232 Sum_probs=20.8
Q ss_pred HHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhhh
Q 042488 31 LCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKK 76 (78)
Q Consensus 31 ~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r~ 76 (78)
.|.+.-++.-+.++|+.++-.|+ | +...++.+...+..+..
T Consensus 10 wa~l~~~~~~~~~~a~~~L~~lk----~-Sn~~i~~v~~l~~~~~~ 50 (149)
T PF13735_consen 10 WALLLLLLGLDPEEAREILKRLK----F-SNKEIKRVLSLVELHMR 50 (149)
T ss_dssp HHHHHHHTT---S-HHHHHHHTT-------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhccHHHHHHHHHHHhC----C-CHHHHHHHHHHHHHHHH
Confidence 34444455556666777776664 3 66666666666655543
No 48
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=24.19 E-value=84 Score=19.83 Aligned_cols=32 Identities=19% Similarity=0.065 Sum_probs=26.2
Q ss_pred hccHHHHHHHHhhCCCChHHHHHHhhcCCCCH
Q 042488 11 ELKIGDVFRILSRYQLAEFELCVLGNLCPETV 42 (78)
Q Consensus 11 ~~~i~~Vr~~L~~~~L~~fE~A~LaNLcPet~ 42 (78)
.+....++.+..+.|+++-+.|.+..+-|.|+
T Consensus 64 ~~~~~~i~~~r~~~gltq~~lA~~lg~~~~ti 95 (127)
T TIGR03830 64 LLTPPEIRRIRKKLGLSQREAAELLGGGVNAF 95 (127)
T ss_pred CcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHH
Confidence 45566788888889999999999999887664
No 49
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=22.99 E-value=1.7e+02 Score=16.95 Aligned_cols=59 Identities=14% Similarity=0.154 Sum_probs=34.9
Q ss_pred cHHHHHHHHhh-CC------CChHHHHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488 13 KIGDVFRILSR-YQ------LAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 75 (78)
Q Consensus 13 ~i~~Vr~~L~~-~~------L~~fE~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r 75 (78)
.+...|.-+.+ .+ +++..+..|+...|.|.++...+- -+.. +. -...-..+++.|+.+.
T Consensus 10 ~L~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~-g~~~--~~-~~~~g~~~~~~i~~~~ 75 (81)
T smart00341 10 RLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAID-GVGE--EK-ARRYGKDLLAVIQEAS 75 (81)
T ss_pred HHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCC-CCCH--HH-HHHHHHHHHHHHHHHH
Confidence 34455665553 23 556668999999999999887753 2221 11 2333455666666554
No 50
>PRK15338 type III secretion system regulator InvE; Provisional
Probab=22.43 E-value=4.3e+02 Score=21.51 Aligned_cols=62 Identities=16% Similarity=0.171 Sum_probs=44.9
Q ss_pred hhhccHHHHHHHHhhCCCChHH-HHHHhhcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHH
Q 042488 9 AAELKIGDVFRILSRYQLAEFE-LCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 72 (78)
Q Consensus 9 ~~~~~i~~Vr~~L~~~~L~~fE-~A~LaNLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~ 72 (78)
-|.-++..+...|+..+.+.-+ ...+-.+.|+..|=..+|---+.++ +. ++..+..|=+.+.
T Consensus 89 ~aDeKl~~l~~~Lk~~~~~~~~ll~~arq~FpD~SDl~~aLreLl~r~-kL-~~~~~~~le~al~ 151 (372)
T PRK15338 89 EALPKAKQILKLISVHGGALEEFLRQARKLFPDPSDLVLVLRELLRRK-QL-EEIVRKKLESLLK 151 (372)
T ss_pred chHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHHHHhCc-cC-CHHHHHHHHHHHH
Confidence 4556788888999877777778 8999999998888888888777753 55 7744444433333
No 51
>COG3082 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.42 E-value=77 Score=20.35 Aligned_cols=15 Identities=40% Similarity=0.636 Sum_probs=12.8
Q ss_pred CCHHHHHHHHHHHHh
Q 042488 59 HDDEAIEKMLNDLSL 73 (78)
Q Consensus 59 ~~de~Lq~ILd~L~~ 73 (78)
|+|+.++.||.+|-.
T Consensus 7 YsDe~ve~il~e~ia 21 (74)
T COG3082 7 YSDEQVEQILNELIA 21 (74)
T ss_pred ccHHHHHHHHHHHHH
Confidence 499999999998754
No 52
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=21.83 E-value=97 Score=19.80 Aligned_cols=21 Identities=24% Similarity=0.314 Sum_probs=16.2
Q ss_pred HHHHHHhhCCCChHHHHHHhh
Q 042488 16 DVFRILSRYQLAEFELCVLGN 36 (78)
Q Consensus 16 ~Vr~~L~~~~L~~fE~A~LaN 36 (78)
+=..+++++||++.|++.|-+
T Consensus 26 DPea~~~~~gLt~eE~~aL~~ 46 (81)
T cd07922 26 DPSAVFEEYGLTPAERAALRE 46 (81)
T ss_pred CHHHHHHHcCCCHHHHHHHHc
Confidence 334567789999999988764
No 53
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=21.75 E-value=1e+02 Score=17.30 Aligned_cols=27 Identities=19% Similarity=0.310 Sum_probs=20.9
Q ss_pred HHHHhhhcccccCCCCCHHHHHHHHHH
Q 042488 44 EAIAMVPSIKTRGRAHDDEAIEKMLND 70 (78)
Q Consensus 44 EAkaLIPSL~~k~r~~~de~Lq~ILd~ 70 (78)
+++.+|-.|...|..+++.-++.+|..
T Consensus 20 ~~~~~l~~l~~~g~~is~~l~~~~L~~ 46 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPKLIEEILRR 46 (48)
T ss_pred hHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence 777778888776766688888888864
No 54
>cd01902 Ntn_CGH Choloylglycine hydrolase (CGH) is a bile salt-modifying enzyme that hydrolyzes non-peptide carbon-nitrogen bonds in choloylglycine and choloyltaurine, both of which are present in bile. CGH is present in a number of probiotic microbial organisms that inhabit the gut. CGH has an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which CGH belongs.
Probab=21.51 E-value=1.1e+02 Score=22.95 Aligned_cols=31 Identities=19% Similarity=-0.047 Sum_probs=25.5
Q ss_pred hCCCChHHHHHHhhcCCCCHHHHHHhhhccc
Q 042488 23 RYQLAEFELCVLGNLCPETVEEAIAMVPSIK 53 (78)
Q Consensus 23 ~~~L~~fE~A~LaNLcPet~dEAkaLIPSL~ 53 (78)
+.+|..++..+.+==.++|++||+..+....
T Consensus 94 ~~~l~~~~~~~~vL~~~~tV~Ea~~~l~~~~ 124 (291)
T cd01902 94 KPTLSAGAWGQYLLDNYATVEEAVKALAKEP 124 (291)
T ss_pred CCccCHHHHHHHHHhcCCCHHHHHHHHhcCc
Confidence 4578889987777778999999999998763
No 55
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=21.45 E-value=1.4e+02 Score=19.27 Aligned_cols=49 Identities=20% Similarity=0.276 Sum_probs=32.4
Q ss_pred ChHHHHHHhhcCCCCHH--HHHHhhhccccc--CCCCCHHHHHHHHHHHHhhhh
Q 042488 27 AEFELCVLGNLCPETVE--EAIAMVPSIKTR--GRAHDDEAIEKMLNDLSLIKK 76 (78)
Q Consensus 27 ~~fE~A~LaNLcPet~d--EAkaLIPSL~~k--~r~~~de~Lq~ILd~L~~~r~ 76 (78)
+=.|.|.+.++-+.|.- |-+=|+|+-.+. .|.|+++++..+- .+..+|.
T Consensus 2 ~IgevA~~~gvs~~tlRyYe~~GLl~p~~~~~gyR~Y~~~~l~~l~-~I~~lr~ 54 (120)
T cd04781 2 DIAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRLA-LIALGRA 54 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCceecCHHHHHHHH-HHHHHHH
Confidence 34578888888888743 445777765332 3677999988874 5555553
No 56
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.95 E-value=1.9e+02 Score=18.36 Aligned_cols=47 Identities=19% Similarity=0.294 Sum_probs=29.6
Q ss_pred hHHHHHHhhcCCCCHH--HHHHhhhccccc---CCCCCHHHHHHHHHHHHhhh
Q 042488 28 EFELCVLGNLCPETVE--EAIAMVPSIKTR---GRAHDDEAIEKMLNDLSLIK 75 (78)
Q Consensus 28 ~fE~A~LaNLcPet~d--EAkaLIPSL~~k---~r~~~de~Lq~ILd~L~~~r 75 (78)
-.|.|.+.++.|.|.- |-+-|||+-.+. .|.|+++++..+ ..|..+|
T Consensus 3 i~e~a~~~gvs~~tlr~ye~~gll~~~~r~~~gyR~Y~~~~l~~l-~~I~~lr 54 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWL-EFIKCLR 54 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHH-HHHHHHH
Confidence 4577888888888743 556778543221 266799988865 3444444
No 57
>COG3310 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.91 E-value=51 Score=24.55 Aligned_cols=45 Identities=22% Similarity=0.330 Sum_probs=26.9
Q ss_pred ChHHHHHHh-hcCCCC-HHHHH---HhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488 27 AEFELCVLG-NLCPET-VEEAI---AMVPSIKTRGRAHDDEAIEKMLNDLSLIK 75 (78)
Q Consensus 27 ~~fE~A~La-NLcPet-~dEAk---aLIPSL~~k~r~~~de~Lq~ILd~L~~~r 75 (78)
+=-|.|+|| ||||=- +=-.| .+.-|-. +. .+.-|+.+-+++..+|
T Consensus 21 ~Wle~aVIGLNLCPFAka~~vkqqvri~vSeA---~~-~e~lLehl~~ell~L~ 70 (196)
T COG3310 21 QWLEKAVIGLNLCPFAKAPHVKQQVRIAVSEA---TH-LEALLEHLDEELLRLR 70 (196)
T ss_pred HHHHHHHHhhccCccccchhhhhhhheeeecc---cC-hHHHHHHHHHHHHHhc
Confidence 445778887 999953 11122 2334444 33 5666777777776665
No 58
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=20.86 E-value=1.9e+02 Score=17.91 Aligned_cols=32 Identities=9% Similarity=0.116 Sum_probs=18.7
Q ss_pred CCHHHHHHhhhccccc--CCCCCHHHHHHHHHHHH
Q 042488 40 ETVEEAIAMVPSIKTR--GRAHDDEAIEKMLNDLS 72 (78)
Q Consensus 40 et~dEAkaLIPSL~~k--~r~~~de~Lq~ILd~L~ 72 (78)
-|.+|+..++-.+... |++ +=+++-.++..|.
T Consensus 48 ~t~~ev~~m~~~~D~d~dG~I-df~EFv~lm~~l~ 81 (88)
T cd05029 48 LQDAEIAKLMEDLDRNKDQEV-NFQEYVTFLGALA 81 (88)
T ss_pred CCHHHHHHHHHHhcCCCCCCC-cHHHHHHHHHHHH
Confidence 3777888887766532 344 5555555555444
No 59
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=20.76 E-value=1.5e+02 Score=20.86 Aligned_cols=31 Identities=19% Similarity=0.245 Sum_probs=22.8
Q ss_pred hcCCCCHHHHHHhhhcccccCCCCCHHHHHHHHH
Q 042488 36 NLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLN 69 (78)
Q Consensus 36 NLcPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd 69 (78)
|.=|.|.+||++||---+ .|+.|++.++.+.
T Consensus 83 ~fPf~~~~ec~~~L~~~~---~FIGde~~d~~f~ 113 (134)
T PF05883_consen 83 NFPFKNLEECKSFLEKSK---GFIGDEEKDEVFK 113 (134)
T ss_pred eCCCCCHHHHHHHHHhcc---CcCCChHHHHHHH
Confidence 345889999999998775 3567777666554
No 60
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=20.58 E-value=1.7e+02 Score=19.37 Aligned_cols=54 Identities=17% Similarity=0.217 Sum_probs=32.1
Q ss_pred HHHHHhhCCCChHHHHHHhhcC------CCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHh
Q 042488 17 VFRILSRYQLAEFELCVLGNLC------PETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73 (78)
Q Consensus 17 Vr~~L~~~~L~~fE~A~LaNLc------Pet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~ 73 (78)
+..+|.+. |++.|+.+++.-. |.|.++....|-..-. ...+++++.++..-|..
T Consensus 28 LlALL~r~-Ltd~ev~~Va~~L~~~~~~~~~~~dI~~~I~~vt~--~~P~~~di~RV~~~Laa 87 (96)
T PF11829_consen 28 LLALLRRR-LTDDEVAEVAAELAARGDPPVDRIDIGVAITRVTD--ELPTPEDIERVRARLAA 87 (96)
T ss_dssp HHHHHTTT-S-HHHHHHHHHHHHHHTSS-BSCCHHHHHHHHHCS--S-S-HHHHHHHHHHHHT
T ss_pred HHHHhccc-CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHc--CCcCHHHHHHHHHHHHh
Confidence 33455554 8888877766332 3466677777766653 34578888888777654
No 61
>cd00045 DED The Death Effector Domain: a protein-protein interaction domain. Death Effector Domains comprise a subfamily of the Death Domain (DD) superfamily. DED-containing proteins include Fas-Associated via Death Domain (FADD), Astrocyte phosphoprotein PEA-15, the initiator caspases (caspase-8 and -10), and FLICE-inhibitory protein (FLIP), among others. These proteins are prominent components of the programmed cell death (apoptosis) pathway. Some members also have non-apoptotic functions such as regulation of insulin signaling (DEDD and PEA15) and cell cycle progression (DEDD). 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 PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes.
Probab=20.43 E-value=76 Score=19.40 Aligned_cols=51 Identities=18% Similarity=0.318 Sum_probs=31.2
Q ss_pred CCCChHHHHHHhhcCCCC--------HHHHHHhhhcccccCCCCCHHHHHHHHHHHHhhh
Q 042488 24 YQLAEFELCVLGNLCPET--------VEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSLIK 75 (78)
Q Consensus 24 ~~L~~fE~A~LaNLcPet--------~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~~r 75 (78)
.+|+..|...|--||.+. +.-+..+.--|.+.+.. +++.+.-+-+.+..+.
T Consensus 10 ~~Lt~~el~~lkFLc~d~i~~~~le~~~s~l~lf~~Le~~~~l-~~~nl~~L~~lL~~i~ 68 (77)
T cd00045 10 KELTSEELEALKFLCKDDIPDGELEKIKTPFDLFLVLERQGKL-GEDNLSYLEELLRSIG 68 (77)
T ss_pred HHcCHHHHHHHHHHhHhhcCHHHHHccCCHHHHHHHHHHcCCC-CCchHHHHHHHHHHcC
Confidence 478888888888888753 23334466666655555 6655555555554443
No 62
>PRK13689 hypothetical protein; Provisional
Probab=20.40 E-value=89 Score=20.13 Aligned_cols=15 Identities=33% Similarity=0.545 Sum_probs=12.8
Q ss_pred CCHHHHHHHHHHHHh
Q 042488 59 HDDEAIEKMLNDLSL 73 (78)
Q Consensus 59 ~~de~Lq~ILd~L~~ 73 (78)
|+|+++++||.+|-.
T Consensus 7 Ysd~qvE~il~el~~ 21 (75)
T PRK13689 7 YSDEQVEQLLAELLA 21 (75)
T ss_pred ccHHHHHHHHHHHHH
Confidence 499999999998754
No 63
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=20.40 E-value=2.3e+02 Score=17.60 Aligned_cols=49 Identities=18% Similarity=0.196 Sum_probs=30.5
Q ss_pred HHhhCCCChHHHHHHhhc------CCCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHh
Q 042488 20 ILSRYQLAEFELCVLGNL------CPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73 (78)
Q Consensus 20 ~L~~~~L~~fE~A~LaNL------cPet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~ 73 (78)
-|++.|+++.++..|-.. .+.+.+||..-|-.... ++.+++.|++=+.+
T Consensus 22 GLrR~Gfs~~~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~-----~~~~v~~~~~Fi~~ 76 (83)
T PF13720_consen 22 GLRRRGFSKEEISALRRAYRILFRSGLTLEEALEELEEEYP-----DSPEVREIVDFIRN 76 (83)
T ss_dssp HHHHTTS-HHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTT-----SCHHHHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhcc-----CCHHHHHHHHHHHh
Confidence 356777777777766532 45677888777766431 46777777776653
No 64
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3BZ6_A.
Probab=20.35 E-value=2.4e+02 Score=20.20 Aligned_cols=47 Identities=28% Similarity=0.284 Sum_probs=33.5
Q ss_pred CCCChHHHHHHhhcC---CCCHHHHHHhhhcccccCCCCCHHHHHHHHHHHHh
Q 042488 24 YQLAEFELCVLGNLC---PETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73 (78)
Q Consensus 24 ~~L~~fE~A~LaNLc---Pet~dEAkaLIPSL~~k~r~~~de~Lq~ILd~L~~ 73 (78)
.++++.|.|.|+-|+ |+|+.|.++=---+- .|-+-++++..|+.|..
T Consensus 84 l~l~~~e~All~~LlLRGpQT~GELR~Rs~Rl~---~F~d~~~Ve~~L~~L~~ 133 (148)
T PF04337_consen 84 LQLSPQELALLCLLLLRGPQTPGELRTRSERLH---EFADVAEVEAVLERLAE 133 (148)
T ss_dssp HT--HHHHHHHHHHHHH-SB-HHHHHHHHTTTS-----SSHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHcCCCchhHHHhhhcccc---CCCCHHHHHHHHHHHHh
Confidence 467788888888774 999999998777665 46566889999988865
No 65
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.16 E-value=90 Score=16.30 Aligned_cols=41 Identities=27% Similarity=0.374 Sum_probs=24.0
Q ss_pred hHHHHHHhhcCCCCHH--HHHHhhhccccc--CCCCCHHHHHHHH
Q 042488 28 EFELCVLGNLCPETVE--EAIAMVPSIKTR--GRAHDDEAIEKML 68 (78)
Q Consensus 28 ~fE~A~LaNLcPet~d--EAkaLIPSL~~k--~r~~~de~Lq~IL 68 (78)
-.|.|.+.++.|.|+. +.+-+||+-... .+.|+.+++..+-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~l~~~~~~~~~~~y~~~~v~~l~ 47 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLR 47 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCEEeCHHHHHHhh
Confidence 4566777777776654 445566643211 2444888887763
Done!