Query 036254
Match_columns 122
No_of_seqs 105 out of 432
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 10:55:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036254.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036254hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04832 SOUL: SOUL heme-bindi 100.0 2.3E-36 4.9E-41 221.5 9.9 112 1-122 44-176 (176)
2 COG3449 DNA gyrase inhibitor [ 93.6 0.44 9.6E-06 34.6 7.0 57 41-108 1-57 (154)
3 PRK10016 DNA gyrase inhibitor; 93.6 0.7 1.5E-05 32.5 8.1 54 42-107 2-55 (156)
4 PF06445 GyrI-like: GyrI-like 92.9 0.33 7.1E-06 32.5 5.3 70 42-120 2-72 (155)
5 PF06445 GyrI-like: GyrI-like 89.9 3.8 8.2E-05 27.2 8.1 69 41-121 83-154 (155)
6 PRK10016 DNA gyrase inhibitor; 86.6 8.4 0.00018 26.9 8.4 69 42-122 83-153 (156)
7 smart00871 AraC_E_bind Bacteri 76.7 17 0.00037 24.0 6.7 61 42-109 1-61 (158)
8 COG4978 Transcriptional regula 65.3 31 0.00067 24.8 6.1 40 42-83 4-43 (153)
9 PRK15121 right oriC-binding tr 53.5 72 0.0016 24.5 6.8 69 42-122 213-288 (289)
10 COG4978 Transcriptional regula 52.7 68 0.0015 23.0 6.1 42 41-85 80-121 (153)
11 smart00871 AraC_E_bind Bacteri 45.3 86 0.0019 20.5 8.1 41 41-83 83-123 (158)
12 KOG4631 NADH:ubiquinone oxidor 44.6 12 0.00026 25.0 1.0 15 71-85 24-38 (100)
13 COG5309 Exo-beta-1,3-glucanase 43.4 44 0.00095 26.8 4.1 42 58-111 247-289 (305)
14 KOG1714 60s ribosomal protein 36.6 54 0.0012 24.5 3.5 25 41-66 88-112 (188)
15 PF14657 Integrase_AP2: AP2-li 35.4 57 0.0012 18.2 2.8 31 51-82 14-44 (46)
16 COG4195 Phage-related replicat 35.1 44 0.00095 25.3 2.8 34 54-87 100-141 (208)
17 PF01187 MIF: Macrophage migra 33.2 92 0.002 20.7 4.0 49 47-107 53-102 (114)
18 PF07157 DNA_circ_N: DNA circu 32.5 44 0.00096 22.2 2.3 41 41-83 37-77 (93)
19 PF09413 DUF2007: Domain of un 28.4 54 0.0012 19.4 2.1 43 69-120 9-51 (67)
20 PF11964 SpoIIAA-like: SpoIIAA 28.1 1.1E+02 0.0023 19.5 3.6 30 54-83 2-31 (109)
21 PF14526 Cass2: Integron-assoc 27.2 95 0.002 20.9 3.4 39 44-83 1-39 (150)
22 KOG3405 RNA polymerase subunit 26.1 21 0.00045 25.2 -0.1 21 15-36 79-99 (136)
23 PHA02763 hypothetical protein; 25.7 47 0.001 22.1 1.5 20 57-76 62-81 (102)
24 PF02120 Flg_hook: Flagellar h 24.8 1.6E+02 0.0034 18.1 3.8 42 42-85 28-70 (85)
25 COG0148 Eno Enolase [Carbohydr 24.7 32 0.0007 28.8 0.7 30 56-85 201-231 (423)
26 TIGR00074 hypC_hupF hydrogenas 22.7 83 0.0018 20.0 2.2 40 41-81 26-67 (76)
27 COG3708 Uncharacterized protei 21.8 3.1E+02 0.0067 19.6 7.7 68 42-121 85-154 (157)
28 PRK10413 hydrogenase 2 accesso 21.2 98 0.0021 20.0 2.3 29 54-82 47-75 (82)
29 PHA02754 hypothetical protein; 20.8 1.1E+02 0.0024 18.8 2.3 21 64-84 12-32 (67)
30 PF01455 HupF_HypC: HupF/HypC 20.3 89 0.0019 19.3 1.9 26 55-80 43-68 (68)
No 1
>PF04832 SOUL: SOUL heme-binding protein; InterPro: IPR006917 This family represents a group of putative haem-binding proteins []. It includes archaeal and bacterial homologues.; PDB: 2HVA_A 2GOV_A 4A1M_A 3R85_E 2YC9_A 3R8K_B 3R8J_B.
Probab=100.00 E-value=2.3e-36 Score=221.45 Aligned_cols=112 Identities=35% Similarity=0.567 Sum_probs=84.5
Q ss_pred ChhhhccccCCCCCCCccCcCcceeEEeecCCC----C----Ccccc------------CCceeEEeCCCCcEEEEEEec
Q 036254 1 MRGLYSYFQGNNDQSAKITMTAPVLTNIIPSIN----G----PFCNS------------QLQAHPIKLPKHKYVVVRRFG 60 (122)
Q Consensus 1 F~~L~~YI~G~N~~~~ki~MT~PV~~~~~~~~~----~----~f~~~------------~~~V~i~~~p~~~~v~V~~F~ 60 (122)
|++|++||+|+|+++.||+||+||++++.+... + .|.+| .++|+|+++| ++++||++|+
T Consensus 44 f~~L~~Yi~G~N~~~~ki~mT~PV~~~~~~~~~~~~~~~~t~~f~lP~~~~~~~~P~P~d~~V~i~~~p-~~~~~v~~F~ 122 (176)
T PF04832_consen 44 FRRLFRYIFGKNSAGEKIAMTAPVLTQVIPMTAESCEKEYTMSFFLPSEYQAENPPKPTDPDVFIEEVP-ERTVYVRRFS 122 (176)
T ss_dssp HHHHHHHHCT-CTT------BS-EEEEEEETTTTTCECEEEEEEE--HHHC-TS---BSSTTEEEEEC--SEEEEEEEEC
T ss_pred HHHHHHHHhcCCcccceeeccCCEEEEEEcCCCcccCCcEEEEEEcCcccccccCCCCCCCeEEEEEec-CcEEEEEEEC
Confidence 789999999999999999999999999954311 1 23232 1899999999 9999999999
Q ss_pred cccChhHHHHHHHHHHHHhhcCCCchheeccccccCCceEEEEeCCCCCCC-CCeeeEEEEeC
Q 036254 61 GLMDDTSISTQASALKKSFKNSTWESAIIFNYKISDDHLSVAGYNSPFQNE-NRINKVLLWFD 122 (122)
Q Consensus 61 G~~~~~~~~~~~~~L~~~L~~~g~~~~i~~~~~~~~~~~~~A~Yd~P~~~~-~R~NEVwi~~~ 122 (122)
|++++..+.+++++|+++|+++|+. +.+.+++|+||+||+++ +|||||||.++
T Consensus 123 G~~~~~~~~~~~~~L~~~L~~~g~~---------~~~~~~~a~Yd~P~~~~~~R~NEV~i~v~ 176 (176)
T PF04832_consen 123 GFATDEKIQEEAKKLRAALKKDGLK---------DKGYYYVAGYDPPFTPPFNRRNEVWIPVK 176 (176)
T ss_dssp S--SHHHHHHHHHHHHHHCCCTTHH---------CCCEEEEEESSSS-SSSSSSCEEEEEE--
T ss_pred CcCCHHHHHHHHHHHHHHHHHcCCC---------cCCCeEEEEcCCCCCCccCcceEEEEecC
Confidence 9999999999999999999999854 57899999999996665 99999999985
No 2
>COG3449 DNA gyrase inhibitor [DNA replication, recombination, and repair]
Probab=93.65 E-value=0.44 Score=34.63 Aligned_cols=57 Identities=16% Similarity=0.100 Sum_probs=47.0
Q ss_pred CceeEEeCCCCcEEEEEEeccccChhHHHHHHHHHHHHhhcCCCchheeccccccCCceEEEEeCCCC
Q 036254 41 LQAHPIKLPKHKYVVVRRFGGLMDDTSISTQASALKKSFKNSTWESAIIFNYKISDDHLSVAGYNSPF 108 (122)
Q Consensus 41 ~~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~~L~~~g~~~~i~~~~~~~~~~~~~A~Yd~P~ 108 (122)
.+|.|+++| +..||..+=-| ......+-.++|.+|.+++|+.. ..+..+.-.||+|=
T Consensus 1 mdv~I~e~p-~~~VA~~rh~G--~~~~~~~~~~~l~~W~~~~~l~p--------~~S~~~gI~~ddP~ 57 (154)
T COG3449 1 MDVEIIELP-PIPVAYLRHVG--DPATLKQTFEQLIAWRRENGLLP--------EQSETLGIYQDDPD 57 (154)
T ss_pred CCceEEecC-CceEEEEEeeC--cHHHHHHHHHHHHHHHHHcCCCC--------CCceEEEEecCCCC
Confidence 379999999 99999999999 77788999999999999998642 24666666778885
No 3
>PRK10016 DNA gyrase inhibitor; Provisional
Probab=93.64 E-value=0.7 Score=32.49 Aligned_cols=54 Identities=7% Similarity=0.056 Sum_probs=43.3
Q ss_pred ceeEEeCCCCcEEEEEEeccccChhHHHHHHHHHHHHhhcCCCchheeccccccCCceEEEEeCCC
Q 036254 42 QAHPIKLPKHKYVVVRRFGGLMDDTSISTQASALKKSFKNSTWESAIIFNYKISDDHLSVAGYNSP 107 (122)
Q Consensus 42 ~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~~L~~~g~~~~i~~~~~~~~~~~~~A~Yd~P 107 (122)
+|.|+++| +..|+..+..|...+ ...+.-.+|.+++.++|+. .. .++.-.||.|
T Consensus 2 ~v~i~~~~-~~~va~ir~~g~~~~-~~~~~~~~L~~~~~~~~l~---------~~-~~~~i~~D~p 55 (156)
T PRK10016 2 NYEIKQEQ-KRTIAGFHLVGPWEQ-TVKQGFEQLMMWVDSHNIV---------PK-EWVAVYYDNP 55 (156)
T ss_pred ceEEEEcc-CceEEEEEeecCchh-HHHHHHHHHHHHHHHcCCC---------CC-cEEEEECCCC
Confidence 68999999 999999999996643 3677889999999999853 12 3666788998
No 4
>PF06445 GyrI-like: GyrI-like small molecule binding domain; InterPro: IPR010499 This domain is found in the probable effector binding domain of a number of different bacterial transcription activators [] and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.; PDB: 1JYH_A 1D5Y_B 3B49_A 3E0H_A 2KCU_A 3LUR_B 1EXI_A 3Q3D_A 1EXJ_A 3Q5S_A ....
Probab=92.89 E-value=0.33 Score=32.53 Aligned_cols=70 Identities=14% Similarity=0.090 Sum_probs=52.9
Q ss_pred ceeEEeCCCCcEEEEEEeccccChhH-HHHHHHHHHHHhhcCCCchheeccccccCCceEEEEeCCCCCCCCCeeeEEEE
Q 036254 42 QAHPIKLPKHKYVVVRRFGGLMDDTS-ISTQASALKKSFKNSTWESAIIFNYKISDDHLSVAGYNSPFQNENRINKVLLW 120 (122)
Q Consensus 42 ~V~i~~~p~~~~v~V~~F~G~~~~~~-~~~~~~~L~~~L~~~g~~~~i~~~~~~~~~~~~~A~Yd~P~~~~~R~NEVwi~ 120 (122)
+|.|+++| +++++..+..|-..+.. +.+..++|.+.+...+.. .....++..-||.|.........+++.
T Consensus 2 ~~~i~~~p-~~~v~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~--------~~~~~~~~i~~~~~~~~~~~~~~~~~~ 72 (155)
T PF06445_consen 2 EVEIVTLP-AFRVAGIRRKGPYEEEDSIPELWQRLMSWLKEIGLS--------TDPGPIIGIYYDNPNITDDEEFRYDIG 72 (155)
T ss_dssp CEEEEEEE-EEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHC--------CSSSSEEEEEEECCTSSTGCEEEEEEE
T ss_pred CcEEEEEC-CEEEEEEEEEECCchhhhHHHHHHHHHHHHHHhhcc--------cCCCcceeEEeccccccCCcceEEEEE
Confidence 68999999 99999999999888777 888899999999887632 135566667777776544555555543
No 5
>PF06445 GyrI-like: GyrI-like small molecule binding domain; InterPro: IPR010499 This domain is found in the probable effector binding domain of a number of different bacterial transcription activators [] and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.; PDB: 1JYH_A 1D5Y_B 3B49_A 3E0H_A 2KCU_A 3LUR_B 1EXI_A 3Q3D_A 1EXJ_A 3Q5S_A ....
Probab=89.95 E-value=3.8 Score=27.21 Aligned_cols=69 Identities=16% Similarity=0.176 Sum_probs=50.4
Q ss_pred CceeEEeCCCCcEEEEEEeccccChhHHHHHHHHHHH-HhhcCCCchheeccccccCCceEEEEe-CCCC-CCCCCeeeE
Q 036254 41 LQAHPIKLPKHKYVVVRRFGGLMDDTSISTQASALKK-SFKNSTWESAIIFNYKISDDHLSVAGY-NSPF-QNENRINKV 117 (122)
Q Consensus 41 ~~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~-~L~~~g~~~~i~~~~~~~~~~~~~A~Y-d~P~-~~~~R~NEV 117 (122)
.++....+| +..+++..|.|-. +.+.+-...|.. +|.++|+. ....+.+-.| +.|. ....-.=||
T Consensus 83 ~~~~~~~ip-~g~ya~~~~~G~~--~~l~~~~~~l~~~~l~~~g~~---------~~~~~~~E~y~~~~~~~~~~~~~ei 150 (155)
T PF06445_consen 83 DGMESRTIP-AGKYAVFEHKGPY--DDLQEAYQKLYNEWLPESGYE---------RRDGPDFEIYLNDPDTDEEEYVTEI 150 (155)
T ss_dssp TTSEEEEEE-CEEEEEEEEESCG--HGHHHHHHHHHHCHHHHCTCE---------EESSEEEEEEESSTTTTSCGEEEEE
T ss_pred ceEEEEEEc-CcEEEEEEEEccH--HHHHHHHHHHHhhhHHHCCCc---------cCCCCcEEEECCCCCCCCCceEEEE
Confidence 789999999 9999999999977 667888899999 99999963 1222233333 3444 323566688
Q ss_pred EEEe
Q 036254 118 LLWF 121 (122)
Q Consensus 118 wi~~ 121 (122)
||+|
T Consensus 151 ~iPi 154 (155)
T PF06445_consen 151 YIPI 154 (155)
T ss_dssp EEEE
T ss_pred EEEE
Confidence 9886
No 6
>PRK10016 DNA gyrase inhibitor; Provisional
Probab=86.60 E-value=8.4 Score=26.91 Aligned_cols=69 Identities=7% Similarity=0.009 Sum_probs=45.6
Q ss_pred ceeEEeCCCCcEEEEEEeccccChhHHHHHHHH-HHHHhhcCCCchheeccccccCCceEEEEeC-CCCCCCCCeeeEEE
Q 036254 42 QAHPIKLPKHKYVVVRRFGGLMDDTSISTQASA-LKKSFKNSTWESAIIFNYKISDDHLSVAGYN-SPFQNENRINKVLL 119 (122)
Q Consensus 42 ~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~-L~~~L~~~g~~~~i~~~~~~~~~~~~~A~Yd-~P~~~~~R~NEVwi 119 (122)
.+.+.++| +..+||..+.|. -+.+.+--.. +.++|..+|+.. .+...+-.|. .|.....-.=|||+
T Consensus 83 ~~~~~~ip-~g~yAv~~~~G~--~~~l~~~~~~i~~~Wl~~sgy~~---------~~~p~~E~Y~~~~~~~~~~~tei~i 150 (156)
T PRK10016 83 GVILTEIP-GGQYAVAVARVV--DDDFAKPWYQFFNSLLQDSAYQM---------APKPCFEVYLNDGAEDGYWDIEMYV 150 (156)
T ss_pred CeEEEEEC-CCcEEEEEEECC--HHHHHHHHHHHHHHhchhcCCcc---------CCCCCEEEeCCCCCCCCcEEEEEEE
Confidence 68999999 999999999995 3345555555 778999998652 1123333454 34332232459999
Q ss_pred EeC
Q 036254 120 WFD 122 (122)
Q Consensus 120 ~~~ 122 (122)
++.
T Consensus 151 PI~ 153 (156)
T PRK10016 151 PVQ 153 (156)
T ss_pred EeE
Confidence 873
No 7
>smart00871 AraC_E_bind Bacterial transcription activator, effector binding domain. This domain is found in the probable effector binding domain of a number of different bacterial transcription activators PUBMED:10802742 and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.
Probab=76.69 E-value=17 Score=23.99 Aligned_cols=61 Identities=16% Similarity=0.061 Sum_probs=42.5
Q ss_pred ceeEEeCCCCcEEEEEEeccccChhHHHHHHHHHHHHhhcCCCchheeccccccCCceEEEEeCCCCC
Q 036254 42 QAHPIKLPKHKYVVVRRFGGLMDDTSISTQASALKKSFKNSTWESAIIFNYKISDDHLSVAGYNSPFQ 109 (122)
Q Consensus 42 ~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~~L~~~g~~~~i~~~~~~~~~~~~~A~Yd~P~~ 109 (122)
.+.|.++| +..++..+..|...+..+.+..++|.+.+...+.... ...+..+..-|+.|..
T Consensus 1 ~~~i~~~~-~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~ 61 (158)
T smart00871 1 EVRIVELP-AFKVAGLRHRGPYEEEKIPELWQRLIAWAKELGLLPI------GPSGPPYGVYYDDPDD 61 (158)
T ss_pred CCEEEEcC-CceEEEEEeecCcccccHHHHHHHHHHHHHHcCCCCC------CCCccEEEEECCCCCC
Confidence 36789999 9999999999987755567777888888877764310 1123456666666653
No 8
>COG4978 Transcriptional regulator, effector-binding domain/component [Transcription / Signal transduction mechanisms]
Probab=65.26 E-value=31 Score=24.84 Aligned_cols=40 Identities=28% Similarity=0.223 Sum_probs=36.4
Q ss_pred ceeEEeCCCCcEEEEEEeccccChhHHHHHHHHHHHHhhcCC
Q 036254 42 QAHPIKLPKHKYVVVRRFGGLMDDTSISTQASALKKSFKNST 83 (122)
Q Consensus 42 ~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~~L~~~g 83 (122)
++.+.+++ ++.|+..++-|- .+..+.+-..+|.+.|...|
T Consensus 4 e~~~~~~~-~~~v~~ir~~~~-~~~~~~~~~~el~~~~~~~~ 43 (153)
T COG4978 4 EVVIKKLE-EIKVVGIRFTGI-PERLIEQVYSELCNFLKSNG 43 (153)
T ss_pred ccEEEeec-ceeEEEEEEecC-cHHHHHHHHHHHHHHHhhcC
Confidence 57889999 999999999998 88889999999999999997
No 9
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=53.53 E-value=72 Score=24.54 Aligned_cols=69 Identities=13% Similarity=0.131 Sum_probs=43.1
Q ss_pred ceeEEeCCCCcEEEEEEeccccChhHHHHHHHHH-HHHhhcCCCchheeccccccCCceEEEEeC----CCC-CCC-CCe
Q 036254 42 QAHPIKLPKHKYVVVRRFGGLMDDTSISTQASAL-KKSFKNSTWESAIIFNYKISDDHLSVAGYN----SPF-QNE-NRI 114 (122)
Q Consensus 42 ~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L-~~~L~~~g~~~~i~~~~~~~~~~~~~A~Yd----~P~-~~~-~R~ 114 (122)
+....++| +.+.||-+|.|-..+ +.+-...+ .+||-..|+.. .+.+-+-.|. +|. ... .-.
T Consensus 213 ~~~~~~Ip-~G~YAvF~~~G~~~~--l~~~~~~Iy~~WLP~sg~~~---------~~~p~~e~y~~~~~~~~~~~~~~~~ 280 (289)
T PRK15121 213 TGHPVMLQ-GGEYVMFTYEGLGTG--LQEFILTVYGTCMPMLNLTR---------RKGQDIERYYPAEDAKAGDRPINLR 280 (289)
T ss_pred CCceEeeC-CCCEEEEEEeCCHHH--HHHHHHHHHHHHCCCCCccc---------cCCCCEEEEecccCccccCCCceEE
Confidence 34678899 999999999997643 55555555 57898888652 2222333442 333 222 333
Q ss_pred eeEEEEeC
Q 036254 115 NKVLLWFD 122 (122)
Q Consensus 115 NEVwi~~~ 122 (122)
=||||+|.
T Consensus 281 ~ei~iPi~ 288 (289)
T PRK15121 281 CEYLIPIR 288 (289)
T ss_pred EEEEEEec
Confidence 49999874
No 10
>COG4978 Transcriptional regulator, effector-binding domain/component [Transcription / Signal transduction mechanisms]
Probab=52.72 E-value=68 Score=23.03 Aligned_cols=42 Identities=12% Similarity=0.145 Sum_probs=36.4
Q ss_pred CceeEEeCCCCcEEEEEEeccccChhHHHHHHHHHHHHhhcCCCc
Q 036254 41 LQAHPIKLPKHKYVVVRRFGGLMDDTSISTQASALKKSFKNSTWE 85 (122)
Q Consensus 41 ~~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~~L~~~g~~ 85 (122)
.++.+.++| ..+++...|.|...+ +.+.-++|..+++++|.+
T Consensus 80 ~~~~~~~~P-~g~~a~~~~~G~~~~--~~~~y~rli~~iee~g~~ 121 (153)
T COG4978 80 IDIKIKTLP-KGKYACIIHKGSYEE--VEQAYKRLIEYIEENGLE 121 (153)
T ss_pred CcceeEEcc-CceEEEEEEEcCccc--HHHHHHHHHHHHHHhCCc
Confidence 789999999 889999999987654 577889999999999865
No 11
>smart00871 AraC_E_bind Bacterial transcription activator, effector binding domain. This domain is found in the probable effector binding domain of a number of different bacterial transcription activators PUBMED:10802742 and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.
Probab=45.25 E-value=86 Score=20.48 Aligned_cols=41 Identities=12% Similarity=0.059 Sum_probs=33.6
Q ss_pred CceeEEeCCCCcEEEEEEeccccChhHHHHHHHHHHHHhhcCC
Q 036254 41 LQAHPIKLPKHKYVVVRRFGGLMDDTSISTQASALKKSFKNST 83 (122)
Q Consensus 41 ~~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~~L~~~g 83 (122)
..+....+| +..+++..|.| .+...+.+-..+|..++..++
T Consensus 83 ~~~~~~~~p-~~~y~~~~~~g-~~~~~~~~~~~~l~~~~~~~~ 123 (158)
T smart00871 83 EGVETKEIP-AGKYAVFTHKG-GSYDEIQETWEAIYGEWLPNS 123 (158)
T ss_pred CCceEEEEC-CCcEEEEEEcC-CCHHHHHHHHHHHHHhhcccC
Confidence 458899999 99999999998 346667888889988887776
No 12
>KOG4631 consensus NADH:ubiquinone oxidoreductase, NDUFB3/B12 subunit [Energy production and conversion]
Probab=44.59 E-value=12 Score=25.04 Aligned_cols=15 Identities=13% Similarity=0.240 Sum_probs=9.2
Q ss_pred HHHHHHHHhhcCCCc
Q 036254 71 QASALKKSFKNSTWE 85 (122)
Q Consensus 71 ~~~~L~~~L~~~g~~ 85 (122)
+..+..+.|.+.|+.
T Consensus 24 qL~~~~k~La~~GLk 38 (100)
T KOG4631|consen 24 QLETIQKKLAAKGLK 38 (100)
T ss_pred cHHHHHHHHHHcccc
Confidence 455566667777654
No 13
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=43.39 E-value=44 Score=26.81 Aligned_cols=42 Identities=5% Similarity=0.251 Sum_probs=30.4
Q ss_pred Eecc-ccChhHHHHHHHHHHHHhhcCCCchheeccccccCCceEEEEeCCCCCCC
Q 036254 58 RFGG-LMDDTSISTQASALKKSFKNSTWESAIIFNYKISDDHLSVAGYNSPFQNE 111 (122)
Q Consensus 58 ~F~G-~~~~~~~~~~~~~L~~~L~~~g~~~~i~~~~~~~~~~~~~A~Yd~P~~~~ 111 (122)
.||+ .++-.+...-.+++..+|++-| .+.|.+-.||.+|+..
T Consensus 247 ~~G~a~pS~anq~~~~~~i~~~~~~~G------------~d~fvfeAFdd~WK~~ 289 (305)
T COG5309 247 TYGSAVPSVANQKIAVQEILNALRSCG------------YDVFVFEAFDDDWKAD 289 (305)
T ss_pred ccCCcCCChhHHHHHHHHHHhhhhccC------------ccEEEeeeccccccCc
Confidence 4444 3555666777778888888876 4568888999999974
No 14
>KOG1714 consensus 60s ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=36.64 E-value=54 Score=24.53 Aligned_cols=25 Identities=16% Similarity=0.064 Sum_probs=21.1
Q ss_pred CceeEEeCCCCcEEEEEEeccccChh
Q 036254 41 LQAHPIKLPKHKYVVVRRFGGLMDDT 66 (122)
Q Consensus 41 ~~V~i~~~p~~~~v~V~~F~G~~~~~ 66 (122)
+|+.+.++| ..+|++.+|+--+-+.
T Consensus 88 dD~rv~~vP-kl~v~al~~t~~ar~r 112 (188)
T KOG1714|consen 88 DDLRVQEVP-KLKVAALRFTKGARAR 112 (188)
T ss_pred ccceeeecc-cceeeeeecccchhhh
Confidence 689999999 9999999998665543
No 15
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=35.44 E-value=57 Score=18.22 Aligned_cols=31 Identities=10% Similarity=0.159 Sum_probs=24.1
Q ss_pred CcEEEEEEeccccChhHHHHHHHHHHHHhhcC
Q 036254 51 HKYVVVRRFGGLMDDTSISTQASALKKSFKNS 82 (122)
Q Consensus 51 ~~~v~V~~F~G~~~~~~~~~~~~~L~~~L~~~ 82 (122)
+......+ +||.+.....+.+.++...|...
T Consensus 14 Gkrk~~~k-~GF~TkkeA~~~~~~~~~~~~~g 44 (46)
T PF14657_consen 14 GKRKQKTK-RGFKTKKEAEKALAKIEAELENG 44 (46)
T ss_pred CCEEEEEc-CCCCcHHHHHHHHHHHHHHHHcC
Confidence 44454444 89999999999999998888764
No 16
>COG4195 Phage-related replication protein [General function prediction only]
Probab=35.07 E-value=44 Score=25.34 Aligned_cols=34 Identities=12% Similarity=0.170 Sum_probs=28.1
Q ss_pred EEEEEeccccC--------hhHHHHHHHHHHHHhhcCCCchh
Q 036254 54 VVVRRFGGLMD--------DTSISTQASALKKSFKNSTWESA 87 (122)
Q Consensus 54 v~V~~F~G~~~--------~~~~~~~~~~L~~~L~~~g~~~~ 87 (122)
=||++|-||+. ...-++.++.|.+.|+..|+...
T Consensus 100 ~~vis~HGy~~~~~~~~lvGG~dR~~aa~i~~~L~~aGF~a~ 141 (208)
T COG4195 100 DYVISLHGYADIESKQTLVGGTDRELAAHIARALQLAGFSAE 141 (208)
T ss_pred cEEEEeccccCCCCceeeecCccHHHHHHHHHHHhhCCccHH
Confidence 67999999988 33448899999999999998643
No 17
>PF01187 MIF: Macrophage migration inhibitory factor (MIF); InterPro: IPR001398 Macrophage migration inhibitory factor (MIF) is a key regulatory cytokine within innate and adaptive immune responses, capable of promoting and modulating the magnitude of the response []. MIF is released from T-cells and macrophages, and acts within the neuroendocrine system. MIF is capable of tautomerase activity, although its biological function has not been fully characterised. It is induced by glucocorticoid and is capable of overriding the anti-inflammatory actions of glucocorticoid []. MIF regulates cytokine secretion and the expression of receptors involved in the immune response. It can be taken up into target cells in order to interact with intracellular signalling molecules, inhibiting p53 function, and/or activating components of the mitogen-activated protein kinase and Jun-activation domain-binding protein-1 (Jab-1) []. MIF has been linked to various inflammatory diseases, such as rheumatoid arthritis and atherosclerosis []. The MIF homologue D-dopachrome tautomerase (4.1.1.84 from EC) is involved in detoxification through the conversion of dopaminechrome (and possibly norepinephrinechrome), the toxic quinine product of the neurotransmitter dopamine (and norepinephrine), to an indole derivative that can serve as a precursor to neuromelanin [, ].; PDB: 1UIZ_C 3FWT_A 1HFO_F 2WKB_D 3RF4_B 2OS5_A 3RF5_A 2XCZ_A 3FWU_A 3B64_A ....
Probab=33.19 E-value=92 Score=20.72 Aligned_cols=49 Identities=20% Similarity=0.368 Sum_probs=34.4
Q ss_pred eCCCCcEEEEEEeccccChhHHHHHHHHHHHHhhcC-CCchheeccccccCCceEEEEeCCC
Q 036254 47 KLPKHKYVVVRRFGGLMDDTSISTQASALKKSFKNS-TWESAIIFNYKISDDHLSVAGYNSP 107 (122)
Q Consensus 47 ~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~~L~~~-g~~~~i~~~~~~~~~~~~~A~Yd~P 107 (122)
+-| ...+-+++.|+. +.+.-.+.+++|.+.|++. | .+.+..++..+|.|
T Consensus 53 ~~P-~a~v~l~sig~~-~~~~n~~~s~~i~~~l~~~Lg----------Ip~~Riyi~f~d~~ 102 (114)
T PF01187_consen 53 DDP-AAFVELKSIGGL-DPEQNKKYSAAITEFLEEELG----------IPPDRIYINFHDLP 102 (114)
T ss_dssp -SS--EEEEEEESSSS-SHHHHHHHHHHHHHHHHHHHT------------GGGEEEEEEEET
T ss_pred CCC-EEEEEEEEccCC-CHHHHHHHHHHHHHHHHHHhC----------CCcCceEEEEEECC
Confidence 346 666777777776 7888899999999999886 4 34566777777644
No 18
>PF07157 DNA_circ_N: DNA circularisation protein N-terminus; InterPro: IPR009826 This entry represents the N terminus (approximately 100 residues) of a number of phage DNA circulation proteins.
Probab=32.50 E-value=44 Score=22.15 Aligned_cols=41 Identities=12% Similarity=0.024 Sum_probs=30.7
Q ss_pred CceeEEeCCCCcEEEEEEeccccChhHHHHHHHHHHHHhhcCC
Q 036254 41 LQAHPIKLPKHKYVVVRRFGGLMDDTSISTQASALKKSFKNST 83 (122)
Q Consensus 41 ~~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~~L~~~g 83 (122)
+...++++- +..-..++.++.-.+++..+.++|.++|+..|
T Consensus 37 d~~~vEDlG--~~~r~~~~~a~~~G~dy~~~~~~L~~al~~~G 77 (93)
T PF07157_consen 37 DGPWVEDLG--RKARRIRVTAFFVGDDYEAQRDALIAALEAPG 77 (93)
T ss_pred CCcCeeecC--CCCcEEEEEEEEECCcHHHHHHHHHHHHcCCC
Confidence 334455554 23345677888888899999999999999987
No 19
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=28.44 E-value=54 Score=19.45 Aligned_cols=43 Identities=14% Similarity=0.050 Sum_probs=20.2
Q ss_pred HHHHHHHHHHhhcCCCchheeccccccCCceEEEEeCCCCCCCCCeeeEEEE
Q 036254 69 STQASALKKSFKNSTWESAIIFNYKISDDHLSVAGYNSPFQNENRINKVLLW 120 (122)
Q Consensus 69 ~~~~~~L~~~L~~~g~~~~i~~~~~~~~~~~~~A~Yd~P~~~~~R~NEVwi~ 120 (122)
.-++..++..|+++|+..-+ ++ ...+.+ ++| +|.... =+||+.
T Consensus 9 ~~ea~~i~~~L~~~gI~~~v-~~--~~~~~~--~g~-~g~~~~---~~v~V~ 51 (67)
T PF09413_consen 9 PIEAELIKGLLEENGIPAFV-KN--EHMSGY--AGE-PGTGGQ---VEVYVP 51 (67)
T ss_dssp HHHHHHHHHHHHHTT--EE---S------SS------S--SSS---EEEEEE
T ss_pred HHHHHHHHHHHHhCCCcEEE-EC--Cccchh--hcc-cCccCc---eEEEEC
Confidence 44788999999999986422 11 122222 566 665543 567765
No 20
>PF11964 SpoIIAA-like: SpoIIAA-like; InterPro: IPR021866 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. ; PDB: 2Q3L_B 2OOK_A 3BL4_A.
Probab=28.14 E-value=1.1e+02 Score=19.49 Aligned_cols=30 Identities=13% Similarity=0.265 Sum_probs=22.9
Q ss_pred EEEEEeccccChhHHHHHHHHHHHHhhcCC
Q 036254 54 VVVRRFGGLMDDTSISTQASALKKSFKNST 83 (122)
Q Consensus 54 v~V~~F~G~~~~~~~~~~~~~L~~~L~~~g 83 (122)
+.+.+++|..+.+++++-...+.+.++..|
T Consensus 2 il~v~~~g~~t~ed~~~~~~~~~~~~~~~~ 31 (109)
T PF11964_consen 2 ILAVRVSGKLTEEDYKELLPALEELIADHG 31 (109)
T ss_dssp -EEEEEEEEE-HHHHHHHHHHHHHHHTTSS
T ss_pred EEEEEEeeeeCHHHHHHHHHHHHHHHhcCC
Confidence 346788899999999998888888877554
No 21
>PF14526 Cass2: Integron-associated effector binding protein; PDB: 3GK6_A.
Probab=27.20 E-value=95 Score=20.92 Aligned_cols=39 Identities=18% Similarity=0.136 Sum_probs=26.1
Q ss_pred eEEeCCCCcEEEEEEeccccChhHHHHHHHHHHHHhhcCC
Q 036254 44 HPIKLPKHKYVVVRRFGGLMDDTSISTQASALKKSFKNST 83 (122)
Q Consensus 44 ~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~~L~~~g 83 (122)
+|.++| +.+|.-++......+.....+...|.+.+.+++
T Consensus 1 ~iv~~~-~~~vig~~~r~~~~~~~~~~~i~~lw~~~~~~~ 39 (150)
T PF14526_consen 1 EIVELP-SFTVIGIRVRTPNYDEDSNKKIGELWQEFFKEG 39 (150)
T ss_dssp EEEEE---EEEEEEEEEE-HHHHHTT--HHHHHHHHHHHT
T ss_pred CcEEeC-CEEEEEEEEEecChhhhhhhHHHHHHHHHHHhc
Confidence 478999 999988888766555445577888888888776
No 22
>KOG3405 consensus RNA polymerase subunit K [Transcription]
Probab=26.15 E-value=21 Score=25.22 Aligned_cols=21 Identities=29% Similarity=0.599 Sum_probs=14.6
Q ss_pred CCccCcCcceeEEeecCCCCCc
Q 036254 15 SAKITMTAPVLTNIIPSINGPF 36 (122)
Q Consensus 15 ~~ki~MT~PV~~~~~~~~~~~f 36 (122)
...|+|.|||++...-. ..|+
T Consensus 79 AlQIsm~APvmVeLegE-TdPL 99 (136)
T KOG3405|consen 79 ALQISMNAPVMVELEGE-TDPL 99 (136)
T ss_pred HHHHhcCCCeEEecCCC-CCHH
Confidence 34799999999988433 4443
No 23
>PHA02763 hypothetical protein; Provisional
Probab=25.70 E-value=47 Score=22.09 Aligned_cols=20 Identities=20% Similarity=0.312 Sum_probs=16.8
Q ss_pred EEeccccChhHHHHHHHHHH
Q 036254 57 RRFGGLMDDTSISTQASALK 76 (122)
Q Consensus 57 ~~F~G~~~~~~~~~~~~~L~ 76 (122)
.+||||-+-+.+..++++|.
T Consensus 62 v~~SGFe~VEeWl~eArrLh 81 (102)
T PHA02763 62 VKFSGFENVEEWLNEARRLH 81 (102)
T ss_pred hhhcchhhHHHHHHHHHHHh
Confidence 37999999999988888765
No 24
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=24.80 E-value=1.6e+02 Score=18.06 Aligned_cols=42 Identities=10% Similarity=-0.007 Sum_probs=27.7
Q ss_pred ceeEEeCCCCcEEEEEEeccc-cChhHHHHHHHHHHHHhhcCCCc
Q 036254 42 QAHPIKLPKHKYVVVRRFGGL-MDDTSISTQASALKKSFKNSTWE 85 (122)
Q Consensus 42 ~V~i~~~p~~~~v~V~~F~G~-~~~~~~~~~~~~L~~~L~~~g~~ 85 (122)
.|+|.... . .+-+.-...- .+-...+++...|++.|...|+.
T Consensus 28 ~v~l~~~~-~-~l~v~~~~~~~~~~~~L~~~~~~L~~~L~~~G~~ 70 (85)
T PF02120_consen 28 EVKLRLQG-G-NLSVQFTAENPETKELLRQNLPELKERLQAQGLE 70 (85)
T ss_dssp EEEEEEET-T-EEEEEEE--SSHHHHHHHHTHHHHHHHHHTTT-E
T ss_pred EEEEEEeC-C-EEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCC
Confidence 56666666 5 3333333333 46677899999999999999975
No 25
>COG0148 Eno Enolase [Carbohydrate transport and metabolism]
Probab=24.74 E-value=32 Score=28.84 Aligned_cols=30 Identities=20% Similarity=0.238 Sum_probs=19.5
Q ss_pred EEEeccccC-hhHHHHHHHHHHHHhhcCCCc
Q 036254 56 VRRFGGLMD-DTSISTQASALKKSFKNSTWE 85 (122)
Q Consensus 56 V~~F~G~~~-~~~~~~~~~~L~~~L~~~g~~ 85 (122)
|--=|||+. -.+-.+-...|.++.++.|.+
T Consensus 201 vGDEGgfAP~l~~~eeald~i~~Aie~agy~ 231 (423)
T COG0148 201 VGDEGGFAPNLKSNEEALDILVEAIEEAGYE 231 (423)
T ss_pred ccCCcccCCCCCccHHHHHHHHHHHHHhCCC
Confidence 555568854 333566677777788887765
No 26
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=22.70 E-value=83 Score=20.00 Aligned_cols=40 Identities=8% Similarity=-0.128 Sum_probs=25.6
Q ss_pred CceeEEeCCCCcE--EEEEEeccccChhHHHHHHHHHHHHhhc
Q 036254 41 LQAHPIKLPKHKY--VVVRRFGGLMDDTSISTQASALKKSFKN 81 (122)
Q Consensus 41 ~~V~i~~~p~~~~--v~V~~F~G~~~~~~~~~~~~~L~~~L~~ 81 (122)
..|.+.-+| +.. =||..+-||+-+..-.+++++..+.|++
T Consensus 26 ~~v~l~lv~-~~~vGD~VLVH~G~Ai~~ide~eA~e~l~~l~e 67 (76)
T TIGR00074 26 RDVSLDLVG-EVKVGDYVLVHVGFAISVLDEEEARETLDALQE 67 (76)
T ss_pred EEEEEEeeC-CCCCCCEEEEecChhhhhCCHHHHHHHHHHHHH
Confidence 345544444 322 3789999998777666677666666654
No 27
>COG3708 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.81 E-value=3.1e+02 Score=19.64 Aligned_cols=68 Identities=15% Similarity=0.213 Sum_probs=46.1
Q ss_pred ceeEEeCCCCcEEEEEEeccccChhHHHHHHHHHHHH-hhcCCCchheeccccccCCceEEEEeCCC-CCCCCCeeeEEE
Q 036254 42 QAHPIKLPKHKYVVVRRFGGLMDDTSISTQASALKKS-FKNSTWESAIIFNYKISDDHLSVAGYNSP-FQNENRINKVLL 119 (122)
Q Consensus 42 ~V~i~~~p~~~~v~V~~F~G~~~~~~~~~~~~~L~~~-L~~~g~~~~i~~~~~~~~~~~~~A~Yd~P-~~~~~R~NEVwi 119 (122)
.....++| +.+.+|-..-|-..+ +++--+.+... +...+..+ ..+. .+=.||+= -...+=.=||||
T Consensus 85 ~~~~i~iP-a~~YavFt~~G~~~~--i~etw~~I~~~~~~~~~~~~--------~~~~-~fE~Yd~~~~~~~~~~veIyI 152 (157)
T COG3708 85 GMEVIEIP-ASTYAVFTHKGPIEE--IQETWQEIWKEWFPSSGYRH--------AEGP-EFEVYDERDPDSGNGKVEIYI 152 (157)
T ss_pred CceEEEec-cceEEEEEecCCHHH--HHHHHHHHHHhhcccccccc--------cCCC-ceEEecCCCCCCCCceEEEEE
Confidence 56778999 999999999998877 66666666555 56665432 2222 45578763 111366789999
Q ss_pred Ee
Q 036254 120 WF 121 (122)
Q Consensus 120 ~~ 121 (122)
+|
T Consensus 153 pV 154 (157)
T COG3708 153 PV 154 (157)
T ss_pred EE
Confidence 87
No 28
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=21.24 E-value=98 Score=19.99 Aligned_cols=29 Identities=14% Similarity=0.001 Sum_probs=21.7
Q ss_pred EEEEEeccccChhHHHHHHHHHHHHhhcC
Q 036254 54 VVVRRFGGLMDDTSISTQASALKKSFKNS 82 (122)
Q Consensus 54 v~V~~F~G~~~~~~~~~~~~~L~~~L~~~ 82 (122)
=||..+-||+-+..-.+++++-.+.|++-
T Consensus 47 DyVLVHaGfAi~~ideeeA~etl~~l~el 75 (82)
T PRK10413 47 QWVLVHVGFAMSIIDEDEAKATLDALRQM 75 (82)
T ss_pred CEEEEecchhhhhCCHHHHHHHHHHHHHH
Confidence 37889999987777777777777766653
No 29
>PHA02754 hypothetical protein; Provisional
Probab=20.79 E-value=1.1e+02 Score=18.79 Aligned_cols=21 Identities=10% Similarity=0.118 Sum_probs=18.5
Q ss_pred ChhHHHHHHHHHHHHhhcCCC
Q 036254 64 DDTSISTQASALKKSFKNSTW 84 (122)
Q Consensus 64 ~~~~~~~~~~~L~~~L~~~g~ 84 (122)
.+.++.+-.++|++-|.+.|+
T Consensus 12 ~eK~Fke~MRelkD~LSe~Gi 32 (67)
T PHA02754 12 MEKDFKEAMRELKDILSEAGI 32 (67)
T ss_pred HHhHHHHHHHHHHHHHhhCce
Confidence 467889999999999999985
No 30
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=20.26 E-value=89 Score=19.31 Aligned_cols=26 Identities=12% Similarity=0.033 Sum_probs=20.0
Q ss_pred EEEEeccccChhHHHHHHHHHHHHhh
Q 036254 55 VVRRFGGLMDDTSISTQASALKKSFK 80 (122)
Q Consensus 55 ~V~~F~G~~~~~~~~~~~~~L~~~L~ 80 (122)
||..+.||+-+..-.+++++..+.|+
T Consensus 43 ~VLVHaG~Ai~~ideeeA~e~l~~l~ 68 (68)
T PF01455_consen 43 YVLVHAGFAIEKIDEEEAEETLDLLE 68 (68)
T ss_dssp EEEEETTEEEEEE-HHHHHHHHHHHH
T ss_pred EEEEecChhheeCCHHHHHHHHHHhC
Confidence 78999999988777778877777663
Done!