Query 040211
Match_columns 310
No_of_seqs 120 out of 192
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 06:11:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040211.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040211hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3471 RNA polymerase II tran 100.0 2E-107 4E-112 788.6 21.6 295 1-310 112-463 (465)
2 TIGR00625 tfb2 Transcription f 100.0 2E-105 3E-110 791.4 29.3 295 1-310 98-448 (448)
3 COG5144 TFB2 RNA polymerase II 100.0 6.1E-94 1.3E-98 679.1 14.8 290 2-309 103-445 (447)
4 PF03849 Tfb2: Transcription f 100.0 1.3E-80 2.7E-85 604.7 22.7 229 1-242 96-366 (366)
5 PF13625 Helicase_C_3: Helicas 98.8 1.9E-08 4E-13 84.8 9.4 92 183-277 4-98 (129)
6 TIGR00603 rad25 DNA repair hel 81.1 2.4 5.2E-05 46.0 5.2 87 183-271 19-109 (732)
7 PF08356 EF_assoc_2: EF hand a 71.6 4.3 9.4E-05 32.9 3.1 28 79-106 26-58 (89)
8 COG1420 HrcA Transcriptional r 67.3 5 0.00011 39.9 3.1 59 98-179 12-70 (346)
9 PF01978 TrmB: Sugar-specific 63.2 6.9 0.00015 28.9 2.5 51 125-175 12-63 (68)
10 PRK05718 keto-hydroxyglutarate 62.5 51 0.0011 30.4 8.6 157 147-307 1-175 (212)
11 PRK03911 heat-inducible transc 59.9 8.7 0.00019 36.9 3.1 59 98-179 9-67 (260)
12 PF03428 RP-C: Replication pro 54.7 40 0.00086 30.5 6.3 73 96-175 23-113 (177)
13 PF14947 HTH_45: Winged helix- 54.6 4.6 0.0001 31.1 0.3 30 62-91 38-67 (77)
14 PF13591 MerR_2: MerR HTH fami 53.3 28 0.00061 27.3 4.6 42 152-212 14-55 (84)
15 PF10711 DUF2513: Hypothetical 52.2 9.6 0.00021 30.9 1.8 43 64-106 41-93 (102)
16 PF08784 RPA_C: Replication pr 49.5 21 0.00046 28.4 3.4 53 91-167 45-98 (102)
17 PRK06015 keto-hydroxyglutarate 48.4 53 0.0012 30.2 6.2 106 202-307 43-164 (201)
18 PRK13761 hypothetical protein; 45.3 11 0.00024 35.8 1.3 23 219-241 12-35 (248)
19 COG3355 Predicted transcriptio 45.0 24 0.00052 30.4 3.2 56 120-175 12-85 (126)
20 COG3432 Predicted transcriptio 42.9 13 0.00028 30.6 1.2 31 59-89 47-81 (95)
21 PHA00738 putative HTH transcri 42.6 22 0.00047 30.0 2.5 65 124-196 15-82 (108)
22 PF01316 Arg_repressor: Argini 40.9 41 0.00089 26.0 3.6 29 147-175 34-62 (70)
23 COG2238 RPS19A Ribosomal prote 39.1 18 0.0004 31.9 1.6 34 57-90 95-128 (147)
24 PRK09333 30S ribosomal protein 38.5 17 0.00038 32.2 1.4 32 60-91 98-129 (150)
25 PRK13824 replication initiatio 38.4 97 0.0021 31.5 6.9 69 96-174 35-124 (404)
26 PF09639 YjcQ: YjcQ protein; 38.2 14 0.00029 29.4 0.6 45 38-92 25-69 (88)
27 COG4109 Predicted transcriptio 37.7 35 0.00076 34.6 3.5 34 214-260 290-323 (432)
28 PF06969 HemN_C: HemN C-termin 37.7 17 0.00036 26.5 1.0 27 61-87 39-65 (66)
29 TIGR01182 eda Entner-Doudoroff 37.6 1E+02 0.0022 28.4 6.3 119 186-307 33-168 (204)
30 PF08461 HTH_12: Ribonuclease 34.5 30 0.00064 26.1 1.9 27 64-90 39-66 (66)
31 COG1438 ArgR Arginine represso 33.3 64 0.0014 28.6 4.1 42 122-175 22-63 (150)
32 PF03444 HrcA_DNA-bdg: Winged 33.0 37 0.0008 27.0 2.3 20 148-167 37-56 (78)
33 PF01726 LexA_DNA_bind: LexA D 31.4 37 0.00081 25.6 2.0 59 91-170 4-62 (65)
34 PF04023 FeoA: FeoA domain; I 30.1 14 0.00031 27.4 -0.5 33 132-164 2-34 (74)
35 PRK11235 bifunctional antitoxi 29.5 1.4E+02 0.003 23.7 5.0 46 115-160 19-64 (80)
36 COG1701 Uncharacterized protei 29.5 28 0.00061 33.0 1.3 19 219-237 14-32 (256)
37 PF06755 DUF1219: Protein of u 26.9 81 0.0018 26.8 3.4 72 95-166 18-106 (114)
38 PRK05066 arginine repressor; P 26.4 1.3E+02 0.0028 26.6 4.8 42 122-175 25-67 (156)
39 PF03965 Penicillinase_R: Peni 25.1 1E+02 0.0023 25.0 3.8 31 149-179 36-66 (115)
40 KOG2036 Predicted P-loop ATPas 25.1 51 0.0011 36.3 2.4 57 192-259 529-604 (1011)
41 PF01081 Aldolase: KDPG and KH 25.0 80 0.0017 28.9 3.4 105 203-307 48-168 (196)
42 TIGR02010 IscR iron-sulfur clu 24.7 67 0.0015 27.0 2.7 53 126-179 10-69 (135)
43 TIGR00373 conserved hypothetic 24.3 3E+02 0.0065 24.1 6.8 68 120-199 13-82 (158)
44 PRK10265 chaperone-modulator p 23.8 1.5E+02 0.0032 24.1 4.4 42 152-212 21-63 (101)
45 KOG3085 Predicted hydrolase (H 23.3 1.8E+02 0.0039 27.6 5.5 136 84-237 58-211 (237)
46 PF12513 SUV3_C: Mitochondrial 23.3 14 0.0003 26.3 -1.5 19 200-218 9-27 (49)
47 PTZ00095 40S ribosomal protein 22.7 44 0.00095 30.3 1.2 33 58-90 120-154 (169)
48 PRK05256 condesin subunit E; P 22.7 92 0.002 29.6 3.3 45 134-179 138-182 (238)
49 PRK04280 arginine repressor; P 22.3 82 0.0018 27.5 2.8 42 122-175 20-61 (148)
50 PF14338 Mrr_N: Mrr N-terminal 22.1 58 0.0013 25.6 1.7 31 63-93 60-91 (92)
51 PF01090 Ribosomal_S19e: Ribos 21.8 32 0.00069 30.2 0.1 33 58-90 95-128 (139)
52 PRK00082 hrcA heat-inducible t 21.4 89 0.0019 30.8 3.2 36 142-179 35-70 (339)
53 PF05491 RuvB_C: Holliday junc 20.8 28 0.0006 27.6 -0.4 27 65-91 48-74 (76)
54 COG3095 MukE Uncharacterized p 20.2 1.4E+02 0.003 27.7 3.9 52 136-193 138-189 (238)
55 COG1497 Predicted transcriptio 20.1 32 0.0007 33.0 -0.2 58 201-260 177-239 (260)
No 1
>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=2.1e-107 Score=788.64 Aligned_cols=295 Identities=35% Similarity=0.607 Sum_probs=282.0
Q ss_pred ChhhhHHhhCC-----CCCCCCCCCCCCCCCCChHHHHHHHHhhHHHHHHHHhCCcccccccccchhHHHHHHhCCCccc
Q 040211 1 SNLWKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQR 75 (310)
Q Consensus 1 ~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~iL~~mv~~~~~~~~~~~s~~v~~lL~~~~L~~~ 75 (310)
+|+|.||+||| |+++..++++. .++++||+||.+|||||||||||++.+ ..+|+++.++|+++|||++
T Consensus 112 ~s~~~al~gg~~~~s~~s~~l~~~~~~----r~v~~ld~ya~~rwe~ILh~mvgt~~a---~~~se~v~~ll~~a~lm~~ 184 (465)
T KOG3471|consen 112 RSLRDALTGGGKQNSFGSLVLGEDKHN----RDVDFLDKYASERWECILHFMVGTPEA---KAVSEGVLNLLKHAGLMSR 184 (465)
T ss_pred HHHHHHHhcCCCcccCCCcccCCCcCc----ccchhhHHHHHHHHHHHHHHHhCCccc---cccChhHHHHHHhcCccCC
Confidence 48999999999 45667777777 999999999999999999999999765 7899999999999999998
Q ss_pred CCCCCccccccchhcccccchHHHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHHHH
Q 040211 76 DKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMI 155 (310)
Q Consensus 76 ~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~~L 155 (310)
+...++||++||||||+|+++|+|+++++||++.+ ++|||++|||+|||+||++++|++|+++++|++|+.||
T Consensus 185 ~~~~~~IT~~GFQFLL~~~~aQlW~~~LqyLk~~~-------~~~~dlvevL~~LfqL~~~~~G~~Ysvd~~~~~~~~~l 257 (465)
T KOG3471|consen 185 DENQIEITNAGFQFLLLDINAQLWTLVLQYLKLFE-------SSGMDLVEVLEFLFQLSALALGRAYSVDALTETQRILL 257 (465)
T ss_pred CCCCceEeecchhhhhcCcHHHHHHHHHHHHHHHH-------hcCCCHHHHHHHHHHHHHHHhcccceeehhhHHHHHHH
Confidence 87789999999999999999999999999999999 99999999999999999999999999999999999999
Q ss_pred HHHhhcCeeeEeeCCCcceeecCC-----C------------------Cc---ccccceEEEecCChhHHHHHHHHHhhh
Q 040211 156 KDFADLGLVKLQQGRKESWFIPTI-----A------------------DS---LETNFRMYAYSTSKLHCEILRLFSKIE 209 (310)
Q Consensus 156 ~~L~~lGLVy~~~~~~~~fyipT~-----S------------------~g---vETNfRvYAYT~S~LqiaiL~lF~~l~ 209 (310)
+||+|+|||||+|.+..+|| ||+ | -| |||||||||||+||||||||+|||++.
T Consensus 258 q~Lre~GlvfQrk~k~~rfy-ptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~riYAYT~S~lQiAvi~LF~~l~ 336 (465)
T KOG3471|consen 258 QHLRELGLVFQRKIKILRFY-PTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNYRIYAYTNSPLQIAVIALFTELT 336 (465)
T ss_pred HHHHHhhHHHHhhhhhheec-chhhhhccchhhhhhhhhhhcccccccCceEEEEeccEEEEecCCHHHHHHHHHHHHHH
Confidence 99999999999999999999 999 1 14 999999999999999999999999999
Q ss_pred hccCceEEEEeCHHHHHHHHHcCCCccc------cccChhhhhcC--CCCChhHHHHHHHHHHhcCceeecCcEEeccCC
Q 040211 210 YQLPNLIVGAITKESLYNAVENGLTAEQ------QNAHPRVADRI--PSVLENVCDQIRLWESDLNRVEMTPAHYYDEFP 281 (310)
Q Consensus 210 ~rfPNlvvg~iTReSv~~Al~~GITA~Q------~hAHp~m~~~~--p~iP~tV~DQIrLWE~Er~Rl~~~~g~ly~~f~ 281 (310)
|||||||||+|||||||+|+++||||+| +||||||+... |++||||+|||||||.||||+.++|||||++|.
T Consensus 337 ~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQIrLWElernR~~~~~g~LYs~Fl 416 (465)
T KOG3471|consen 337 YRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQIRLWELERNRLRMTEGYLYSDFL 416 (465)
T ss_pred hhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHHHHHHHhhcceecccchhHHhhh
Confidence 9999999999999999999999999999 99999999876 899999999999999999999999999999999
Q ss_pred CC------------------ccccccEEEEecccchHHHHHHHhccC
Q 040211 282 SR------------------EDSKKMRLVVNAEIHMHMREFLRGQNK 310 (310)
Q Consensus 282 s~------------------~~~~kr~~~V~~~~h~~vr~f~k~~~~ 310 (310)
|. +|+.||+|||+.+||++|++||||++|
T Consensus 417 s~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k 463 (465)
T KOG3471|consen 417 SLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK 463 (465)
T ss_pred hhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence 98 889999999999999999999999654
No 2
>TIGR00625 tfb2 Transcription factor tfb2. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.6e-105 Score=791.41 Aligned_cols=295 Identities=32% Similarity=0.618 Sum_probs=278.0
Q ss_pred ChhhhHHhhCC-----CCCCCCCCCCCCCCCCChHHHHHHHHhhHHHHHHHHhCCcccccccccchhHHHHHHhCCCccc
Q 040211 1 SNLWKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQR 75 (310)
Q Consensus 1 ~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~iL~~mv~~~~~~~~~~~s~~v~~lL~~~~L~~~ 75 (310)
+|||.||+||| |+|+..++++. +|+++||+||++|||+|||||||++.. ..+|++|+++|+++|||+.
T Consensus 98 ~~lr~aL~g~~~~~s~~v~~~~~d~~~----~~~~~Ld~yA~~~WE~IL~fmVgs~~~---~~~s~~v~~lL~~~~Lm~~ 170 (448)
T TIGR00625 98 QNLRIALTGGGKANSFGVSQLGPDKHA----VDVDSLDKYAEERWETILHFMVGTPSA---KVPSEDVLQLLKQAGLMKS 170 (448)
T ss_pred HHHHHHhcCCCCCCCCCCcccCCCCCC----CCHHHHHHHHHHHHHHHHHHHcCCCCc---CCCchHHHHHHHhCCCCcc
Confidence 48999999999 45565566555 999999999999999999999998753 5789999999999999987
Q ss_pred C--CCCCccccccchhcccccchHHHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHH
Q 040211 76 D--KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRS 153 (310)
Q Consensus 76 ~--~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~ 153 (310)
+ ++.+.||++||||||||+|+|||+||++||++++ ++|||++|+|+|||+||++++|++|++++||++|++
T Consensus 171 ~~~~~~~~IT~~GFqFLLqd~n~QvW~lll~YL~~~e-------~~g~d~vevLsFLf~Ls~l~lG~~Y~~~~Lt~tq~~ 243 (448)
T TIGR00625 171 TEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAE-------SRGMDLVEVLHFLFMLGFLTLGKAYSVDGLSDTQLI 243 (448)
T ss_pred cCCCCCccCchhhHHHHcCChhHHHHHHHHHHHHHHH-------hcCCCHHHHHHHHHHHhccccCCccCCCCCCHHHHH
Confidence 3 3358999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred HHHHHhhcCeeeEeeCCCcceeecCC------C---------------Cc---ccccceEEEecCChhHHHHHHHHHhhh
Q 040211 154 MIKDFADLGLVKLQQGRKESWFIPTI------A---------------DS---LETNFRMYAYSTSKLHCEILRLFSKIE 209 (310)
Q Consensus 154 ~L~~L~~lGLVy~~~~~~~~fyipT~------S---------------~g---vETNfRvYAYT~S~LqiaiL~lF~~l~ 209 (310)
||+||+|+||||++++++++|| ||+ | .| |||||||||||+||||||||+|||+++
T Consensus 244 ~L~dL~dlGLVy~~~~~~~~fY-PTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~~il~lF~~~~ 322 (448)
T TIGR00625 244 MLQDLREYGLVFQRKRKSRRFY-PTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQIALIALFSELL 322 (448)
T ss_pred HHHHHHHcCeEEEecCCCCccc-chHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHHHHHHHHHHHH
Confidence 9999999999999999999999 999 1 13 999999999999999999999999999
Q ss_pred hccCceEEEEeCHHHHHHHHHcCCCccc------cccChhhh-hcCCCCChhHHHHHHHHHHhcCceeecCcEEeccCCC
Q 040211 210 YQLPNLIVGAITKESLYNAVENGLTAEQ------QNAHPRVA-DRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPS 282 (310)
Q Consensus 210 ~rfPNlvvg~iTReSv~~Al~~GITA~Q------~hAHp~m~-~~~p~iP~tV~DQIrLWE~Er~Rl~~~~g~ly~~f~s 282 (310)
|||||||||+|||+||++|+++|||||| +||||+|+ +..|+|||||+|||||||.||||+++++||||++|+|
T Consensus 323 ~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l~~~f~s 402 (448)
T TIGR00625 323 ARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLT 402 (448)
T ss_pred hcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEeecceeeeecCC
Confidence 9999999999999999999999999999 99999998 4789999999999999999999999999999999999
Q ss_pred C------------------ccccccEEEEecccchHHHHHHHhccC
Q 040211 283 R------------------EDSKKMRLVVNAEIHMHMREFLRGQNK 310 (310)
Q Consensus 283 ~------------------~~~~kr~~~V~~~~h~~vr~f~k~~~~ 310 (310)
. +|++||+|||+.+||++||+|||++|+
T Consensus 403 ~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~ 448 (448)
T TIGR00625 403 QVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH 448 (448)
T ss_pred HHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence 6 899999999999999999999999986
No 3
>COG5144 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]
Probab=100.00 E-value=6.1e-94 Score=679.09 Aligned_cols=290 Identities=30% Similarity=0.526 Sum_probs=275.2
Q ss_pred hhhhHHhhCC-----CCCCCCCCCCCCCCCCChHHHHHHHHhhHHHHHHHHhCCcccccccccchhHHHHHHhCCCcccC
Q 040211 2 NLWKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRD 76 (310)
Q Consensus 2 ~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~iL~~mv~~~~~~~~~~~s~~v~~lL~~~~L~~~~ 76 (310)
+|+.|||||+ |+ |..+ +. +|+++||+||.++||+|||||||+..+ .-|+++|.++|+++|||.++
T Consensus 103 sl~~altgg~~~nsfgv-~i~E--~l----vsvd~ld~ys~~kwEtILhfmVgtpea---kip~egVl~lLk~ggLm~~~ 172 (447)
T COG5144 103 SLMDALTGGTMENSFGV-CIGE--KL----VSVDMLDSYSSRKWETILHFMVGTPEA---KIPAEGVLELLKFGGLMGRD 172 (447)
T ss_pred HHHHHhhccccccccce-eecc--ce----eeeehhhhhhhhhHHHHHHHHhCCccc---cCcchhHHHHHHhcccccCC
Confidence 7899999999 55 3322 23 899999999999999999999998876 78999999999999999988
Q ss_pred CCCCccccccchhcccccchHHHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHHHHH
Q 040211 77 KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIK 156 (310)
Q Consensus 77 ~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~~L~ 156 (310)
....+||++|||||||+.|+|+|+++++||++.+ ..-||++++|.||||||.+++|++|++|.||++|+-||+
T Consensus 173 ~ne~kITn~GFqFLLq~in~QlWtLlL~yLK~~e-------~s~md~v~VLhflFmLgal~vG~aY~id~lsdtqqiml~ 245 (447)
T COG5144 173 RNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFE-------GSVMDEVAVLHFLFMLGALAVGTAYKIDALSDTQQIMLM 245 (447)
T ss_pred cccceeehhHHHHHHHHHHHHHHHHHHHHHHHhc-------cccccHHHHHHHHHHhcchhhcceeeecccchHHHHHHH
Confidence 7789999999999999999999999999999999 888999999999999999999999999999999999999
Q ss_pred HHhhcCeeeEeeCCCcceeecCC-------------C--------Cc---ccccceEEEecCChhHHHHHHHHHhhhhcc
Q 040211 157 DFADLGLVKLQQGRKESWFIPTI-------------A--------DS---LETNFRMYAYSTSKLHCEILRLFSKIEYQL 212 (310)
Q Consensus 157 ~L~~lGLVy~~~~~~~~fyipT~-------------S--------~g---vETNfRvYAYT~S~LqiaiL~lF~~l~~rf 212 (310)
|+|++||||+++-.+++|| ||+ | .| ||||||+||||+||||||+++|||++.+||
T Consensus 246 D~R~yglv~q~~i~~~~fY-pt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplqiavi~LF~nl~arf 324 (447)
T COG5144 246 DRRLYGLVEQLGILRKIFY-PTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARF 324 (447)
T ss_pred HHHHhhHHHHhccchhhcc-ccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHHHHHHHHhhhhhccc
Confidence 9999999999988888999 999 1 24 999999999999999999999999999999
Q ss_pred CceEEEEeCHHHHHHHHHcCCCccc------cccChhhhhcCCCCChhHHHHHHHHHHhcCceeecCcEEeccCCCC---
Q 040211 213 PNLIVGAITKESLYNAVENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSR--- 283 (310)
Q Consensus 213 PNlvvg~iTReSv~~Al~~GITA~Q------~hAHp~m~~~~p~iP~tV~DQIrLWE~Er~Rl~~~~g~ly~~f~s~--- 283 (310)
||||+|+|||||||+|+.+||||+| +||||||+++.|.+||||+|||+|||+||||+.+.||+||+||.+.
T Consensus 325 ~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~pG~LysdFlt~s~y 404 (447)
T COG5144 325 PNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDY 404 (447)
T ss_pred chhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEeecchHHhhhhchhhH
Confidence 9999999999999999999999999 9999999999999999999999999999999999999999999987
Q ss_pred ---------------ccccccEEEEecccchHHHHHHHhcc
Q 040211 284 ---------------EDSKKMRLVVNAEIHMHMREFLRGQN 309 (310)
Q Consensus 284 ---------------~~~~kr~~~V~~~~h~~vr~f~k~~~ 309 (310)
+|+.||||||+.+||.+|++|.|++-
T Consensus 405 ~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l 445 (447)
T COG5144 405 QKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL 445 (447)
T ss_pred HHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence 78899999999999999999999864
No 4
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=100.00 E-value=1.3e-80 Score=604.72 Aligned_cols=229 Identities=39% Similarity=0.723 Sum_probs=213.0
Q ss_pred ChhhhHHhhCCC-----CCCCCCCCCCCCCCCChHHHHHHHHhhHHHHHHHHhCCcccccccccchhHHHHHHhCCCccc
Q 040211 1 SNLWKHLINGGA-----LPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQR 75 (310)
Q Consensus 1 ~~lr~aL~ggg~-----~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~iL~~mv~~~~~~~~~~~s~~v~~lL~~~~L~~~ 75 (310)
+|||.||+|||. +|+..++++. +++++||+||++|||+|||||||++.... ..||++|+++|+++|||+.
T Consensus 96 ~~Lr~aL~ggg~~~~~~~~~~~~~~~~----~~~~~Ld~yA~~rWE~IL~~mVgs~~~~~-~~~s~~v~~lL~~sgLm~~ 170 (366)
T PF03849_consen 96 KNLRNALTGGGKPWSFGVPSEEPDKKA----PDVEFLDEYARERWESILHYMVGSSSSSN-SSPSQDVKQLLKRSGLMKR 170 (366)
T ss_pred HHHHHHHhCCCCCcccCcccccccCCC----CCHHHHHHHHHHHHHHHHHHHhcCccccc-CCCCHHHHHHHHHcCCCcC
Confidence 489999999994 4455544455 99999999999999999999999987522 2299999999999999998
Q ss_pred --CCCCCccccccchhcccccchHHHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHH
Q 040211 76 --DKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRS 153 (310)
Q Consensus 76 --~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~ 153 (310)
++++..||++||||||+|+|+|||++|++||++++ ++|+|++|+|+|||+||++++|++|++++||++|++
T Consensus 171 ~~~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e-------~~~~~~~~~l~flf~L~~~~~g~~Y~~~~ls~~q~~ 243 (366)
T PF03849_consen 171 SESGGSLKITSKGFQFLLQDTNAQLWTLLLQYLKMAE-------ARGMDLVEVLSFLFQLSFLELGKAYSTEGLSETQKN 243 (366)
T ss_pred cCCCCCCcEehhheeeecCChHHHHHHHHHHHHHHHH-------hcCCCHHHHHHHHHHhcccccCCcCcCCCCCHHHHH
Confidence 45688999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred HHHHHhhcCeeeEeeCCCcceeecCC------C--------------------Cc---ccccceEEEecCChhHHHHHHH
Q 040211 154 MIKDFADLGLVKLQQGRKESWFIPTI------A--------------------DS---LETNFRMYAYSTSKLHCEILRL 204 (310)
Q Consensus 154 ~L~~L~~lGLVy~~~~~~~~fyipT~------S--------------------~g---vETNfRvYAYT~S~LqiaiL~l 204 (310)
||+||+|+||||++++++++|| ||| | .| |||||||||||+||||||||+|
T Consensus 244 ~L~~l~~~GLvy~~~~~~~~fy-pT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~s~l~iaiL~l 322 (366)
T PF03849_consen 244 MLQDLRELGLVYQRKRKSRRFY-PTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTNSPLQIAILSL 322 (366)
T ss_pred HHHHHHHCCeEEEecCCCCeEe-chHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecCCHHHHHHHHH
Confidence 9999999999999999999999 999 1 12 9999999999999999999999
Q ss_pred HHhhhhccCceEEEEeCHHHHHHHHHcCCCccc------cccCh
Q 040211 205 FSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ------QNAHP 242 (310)
Q Consensus 205 F~~l~~rfPNlvvg~iTReSv~~Al~~GITA~Q------~hAHp 242 (310)
||+++|||||||||+||||||++|+++|||||| +||||
T Consensus 323 F~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp 366 (366)
T PF03849_consen 323 FCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP 366 (366)
T ss_pred HHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence 999999999999999999999999999999999 99998
No 5
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=98.84 E-value=1.9e-08 Score=84.76 Aligned_cols=92 Identities=22% Similarity=0.307 Sum_probs=75.6
Q ss_pred ccccceEEEecCCh--hHHHHHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccccccChhhhhc-CCCCChhHHHHH
Q 040211 183 LETNFRMYAYSTSK--LHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQQNAHPRVADR-IPSVLENVCDQI 259 (310)
Q Consensus 183 vETNfRvYAYT~S~--LqiaiL~lF~~l~~rfPNlvvg~iTReSv~~Al~~GITA~Q~hAHp~m~~~-~p~iP~tV~DQI 259 (310)
|+.||.|.+++.+| -....|..|+++ .+..+|.+..||+.|+.+|++.|+|+++..+- +.+. ..-||+||..+|
T Consensus 4 Vqpd~~I~v~~~~~~~~~~~~L~~fae~-~s~~~~~~yrlT~~Sl~~A~~~G~~~e~i~~~--L~~~S~~~lP~~v~~~i 80 (129)
T PF13625_consen 4 VQPDFEILVEPGHPSPADAWFLARFAEL-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEF--LERYSKNPLPQNVEQSI 80 (129)
T ss_pred ECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHH--HHHHcCCCCCHHHHHHH
Confidence 78899999987775 456899999999 67799999999999999999999999992111 1111 234899999999
Q ss_pred HHHHHhcCceeecCcEEe
Q 040211 260 RLWESDLNRVEMTPAHYY 277 (310)
Q Consensus 260 rLWE~Er~Rl~~~~g~ly 277 (310)
+-|...-.|+++.++.+|
T Consensus 81 ~~w~~~~g~v~l~~~~~~ 98 (129)
T PF13625_consen 81 EDWARRYGRVRLYKGAYL 98 (129)
T ss_pred HHHHHhcCCEEEecCeEE
Confidence 999999999999885433
No 6
>TIGR00603 rad25 DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=81.12 E-value=2.4 Score=46.02 Aligned_cols=87 Identities=21% Similarity=0.262 Sum_probs=67.4
Q ss_pred ccccceEEEecCChhH---HHHHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccc-cccChhhhhcCCCCChhHHHH
Q 040211 183 LETNFRMYAYSTSKLH---CEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ-QNAHPRVADRIPSVLENVCDQ 258 (310)
Q Consensus 183 vETNfRvYAYT~S~Lq---iaiL~lF~~l~~rfPNlvvg~iTReSv~~Al~~GITA~Q-~hAHp~m~~~~p~iP~tV~DQ 258 (310)
|..+=+|.-=|.||+- -.-|.-|+|+..|--+|...+||-=|+-+|...|+++++ ...--...| ..||++|++.
T Consensus 19 v~~d~~i~lE~~~p~~~~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~sk--~~~p~~i~~~ 96 (732)
T TIGR00603 19 VAPDGHIFLESFSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSK--TPIPKGIIEF 96 (732)
T ss_pred EcCCCeEEEEeCCccHHHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHhC--CCCCHHHHHH
Confidence 3444444444556554 267899999999999999999999999999999999999 222222222 3699999999
Q ss_pred HHHHHHhcCceee
Q 040211 259 IRLWESDLNRVEM 271 (310)
Q Consensus 259 IrLWE~Er~Rl~~ 271 (310)
|+.+-.--.++++
T Consensus 97 i~~~~~~ygk~kl 109 (732)
T TIGR00603 97 IRLCTQSYGKVKL 109 (732)
T ss_pred HHHHHHhcCcEEE
Confidence 9999998888776
No 7
>PF08356 EF_assoc_2: EF hand associated; InterPro: IPR013567 This region predominantly appears near EF-hands (IPR002048 from INTERPRO) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Probab=71.65 E-value=4.3 Score=32.90 Aligned_cols=28 Identities=25% Similarity=0.510 Sum_probs=23.5
Q ss_pred CCccccccchhc-----ccccchHHHHHHHHHH
Q 040211 79 APRLTESGFQFL-----LMDTNAQLWYIVREYI 106 (310)
Q Consensus 79 ~~~IT~~GFqFL-----L~d~~~QlW~lll~yL 106 (310)
.-.||.+||-|| -+.+++-.|++|+.+=
T Consensus 26 ~~GiT~~GFl~L~~lfierGR~ETtW~vLR~Fg 58 (89)
T PF08356_consen 26 DNGITLDGFLFLNKLFIERGRHETTWTVLRKFG 58 (89)
T ss_pred CCccchhhHHHHHHHHHHhCcchHHHHHHHHcC
Confidence 346999999888 7889999999998763
No 8
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=67.27 E-value=5 Score=39.85 Aligned_cols=59 Identities=27% Similarity=0.439 Sum_probs=44.0
Q ss_pred HHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCeeeEeeCCCcceeec
Q 040211 98 LWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIP 177 (310)
Q Consensus 98 lW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~~L~~L~~lGLVy~~~~~~~~fyip 177 (310)
+|.++-.||.+.+ + .|+-.+-+-|..+--+-|-++.+.+|.++|++++.--.+.| +|
T Consensus 12 L~aIV~~Yi~t~e------------P---------VGSk~L~e~~~l~~SsATIRN~Ma~LE~~GlI~k~HtSsGR--vP 68 (346)
T COG1420 12 LRAIVEDYLATGE------------P---------VGSKTLSEKYNLDLSSATIRNEMADLEKLGLIEKPHTSSGR--VP 68 (346)
T ss_pred HHHHHHHHHhcCC------------c---------cchHHHHHHhCCCCCchhHHHHHHHHHHCCCccCccccCCc--CC
Confidence 5788889999887 2 34444555666555578999999999999999998544555 37
Q ss_pred CC
Q 040211 178 TI 179 (310)
Q Consensus 178 T~ 179 (310)
|.
T Consensus 69 T~ 70 (346)
T COG1420 69 TD 70 (346)
T ss_pred cH
Confidence 66
No 9
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=63.18 E-value=6.9 Score=28.86 Aligned_cols=51 Identities=22% Similarity=0.227 Sum_probs=30.7
Q ss_pred HHHHHHHHhcccccCccccCCCCCHHH-HHHHHHHhhcCeeeEeeCCCccee
Q 040211 125 DLISFLLELSFHVAGEAYNLKTLSEIQ-RSMIKDFADLGLVKLQQGRKESWF 175 (310)
Q Consensus 125 e~L~FLf~Ls~~~~g~~Y~~~~lt~~q-~~~L~~L~~lGLVy~~~~~~~~fy 175 (310)
.++..|+.-+-.+.-+--..-+++.+. ...|..|.+.|||.....+...|+
T Consensus 12 ~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~ 63 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYR 63 (68)
T ss_dssp HHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEE
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEE
Confidence 344444433333332222233455444 789999999999998876665555
No 10
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=62.48 E-value=51 Score=30.42 Aligned_cols=157 Identities=15% Similarity=0.135 Sum_probs=93.7
Q ss_pred CCHHHHHHHHHHhhcCeeeEeeCCC-cceeecCCCCcccccceEEEec-CChhHHHHHHHHHhhhhccCceEEE---EeC
Q 040211 147 LSEIQRSMIKDFADLGLVKLQQGRK-ESWFIPTIADSLETNFRMYAYS-TSKLHCEILRLFSKIEYQLPNLIVG---AIT 221 (310)
Q Consensus 147 lt~~q~~~L~~L~~lGLVy~~~~~~-~~fyipT~S~gvETNfRvYAYT-~S~LqiaiL~lF~~l~~rfPNlvvg---~iT 221 (310)
+++++..+++.|.+.|+|-.-...+ .... +.-..=++--+++--.| ++|- =+..+.++..+||++.|| ++|
T Consensus 1 ~~~~~~~~~~~l~~~~~iaV~r~~~~~~a~-~i~~al~~~Gi~~iEitl~~~~---~~~~I~~l~~~~p~~~IGAGTVl~ 76 (212)
T PRK05718 1 MKNWKTSIEEILRAGPVVPVIVINKLEDAV-PLAKALVAGGLPVLEVTLRTPA---ALEAIRLIAKEVPEALIGAGTVLN 76 (212)
T ss_pred CchhHHHHHHHHHHCCEEEEEEcCCHHHHH-HHHHHHHHcCCCEEEEecCCcc---HHHHHHHHHHHCCCCEEEEeeccC
Confidence 3678888999999999986543221 1111 00000022223333333 2343 345556666789999996 789
Q ss_pred HHHHHHHHHcCCCccc-cccChhhhh-----cCCCCCh--hHHHHHHHHHHhcCceeecCcEEe--ccCCCC---ccccc
Q 040211 222 KESLYNAVENGLTAEQ-QNAHPRVAD-----RIPSVLE--NVCDQIRLWESDLNRVEMTPAHYY--DEFPSR---EDSKK 288 (310)
Q Consensus 222 ReSv~~Al~~GITA~Q-~hAHp~m~~-----~~p~iP~--tV~DQIrLWE~Er~Rl~~~~g~ly--~~f~s~---~~~~k 288 (310)
.+.++.|++.|-.-== -+..|.+.+ ..+.+|- |..+=...|+.--+-+++.|+-.+ -+|.+. --+.-
T Consensus 77 ~~~a~~a~~aGA~FivsP~~~~~vi~~a~~~~i~~iPG~~TptEi~~a~~~Ga~~vKlFPa~~~gg~~~lk~l~~p~p~~ 156 (212)
T PRK05718 77 PEQLAQAIEAGAQFIVSPGLTPPLLKAAQEGPIPLIPGVSTPSELMLGMELGLRTFKFFPAEASGGVKMLKALAGPFPDV 156 (212)
T ss_pred HHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCCEeCCCCCHHHHHHHHHCCCCEEEEccchhccCHHHHHHHhccCCCC
Confidence 9999999999843222 334444332 3577876 446633499999999999886433 122222 23456
Q ss_pred cEEEEecccchHHHHHHHh
Q 040211 289 MRLVVNAEIHMHMREFLRG 307 (310)
Q Consensus 289 r~~~V~~~~h~~vr~f~k~ 307 (310)
+++.+..=.-+.+++|++.
T Consensus 157 ~~~ptGGV~~~ni~~~l~a 175 (212)
T PRK05718 157 RFCPTGGISPANYRDYLAL 175 (212)
T ss_pred eEEEeCCCCHHHHHHHHhC
Confidence 6666555555789999874
No 11
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=59.88 E-value=8.7 Score=36.85 Aligned_cols=59 Identities=25% Similarity=0.345 Sum_probs=44.5
Q ss_pred HHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCeeeEeeCCCcceeec
Q 040211 98 LWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIP 177 (310)
Q Consensus 98 lW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~~L~~L~~lGLVy~~~~~~~~fyip 177 (310)
+..+|-.|+++.+ + .|+.++.+.|..+--+.|-++.+.+|.+.|++.++-..++| ||
T Consensus 9 L~~iV~~Yi~t~~------------P---------VGSk~L~~~~~l~~SsATIRn~m~~LE~~G~L~qpHtSsGR--IP 65 (260)
T PRK03911 9 LDSIIQTYLQDNE------------P---------IGSNELKSLMNLKISAATIRNYFKKLSDEGLLTQLHISGGR--IP 65 (260)
T ss_pred HHHHHHHHhccCC------------c---------cCHHHHHHHcCCCCCcHHHHHHHHHHHHCcCccCCcCCCCc--CC
Confidence 3457778888876 2 35555666777777788999999999999999998655555 47
Q ss_pred CC
Q 040211 178 TI 179 (310)
Q Consensus 178 T~ 179 (310)
|.
T Consensus 66 T~ 67 (260)
T PRK03911 66 TI 67 (260)
T ss_pred CH
Confidence 77
No 12
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=54.72 E-value=40 Score=30.49 Aligned_cols=73 Identities=16% Similarity=0.346 Sum_probs=43.7
Q ss_pred hHHHHHHHHHHHhcccchhhHHhhCCCHH--HHHHHHHHhcccc---cCc---cc--------cCCCCCHHH-HHHHHHH
Q 040211 96 AQLWYIVREYISNSQHDSMLAYERGINQA--DLISFLLELSFHV---AGE---AY--------NLKTLSEIQ-RSMIKDF 158 (310)
Q Consensus 96 ~QlW~lll~yL~~~e~~~~~~~~~g~~~~--e~L~FLf~Ls~~~---~g~---~Y--------~~~~lt~~q-~~~L~~L 158 (310)
..=|.++..--+... ..|++.. .+|..|+...--+ .|. .| .+.+++++. +..|..|
T Consensus 23 ~~k~~ll~~l~~a~~-------~lgl~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~s~~tlrR~l~~L 95 (177)
T PF03428_consen 23 VTKWQLLRALKEARP-------ALGLSDRALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGMSERTLRRHLARL 95 (177)
T ss_pred CCHHHHHHHHHHHHH-------hcCCChhHHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCCCHHHHHHHHHHH
Confidence 345776666555554 5576543 5555555443321 111 12 225787776 7799999
Q ss_pred hhcCeeeEe-eCCCccee
Q 040211 159 ADLGLVKLQ-QGRKESWF 175 (310)
Q Consensus 159 ~~lGLVy~~-~~~~~~fy 175 (310)
.|.|||..+ ..+++||-
T Consensus 96 veaGLI~rrDS~NgkRy~ 113 (177)
T PF03428_consen 96 VEAGLIVRRDSPNGKRYA 113 (177)
T ss_pred HHCCCeeeccCCCCCccC
Confidence 999999876 45556655
No 13
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=54.56 E-value=4.6 Score=31.08 Aligned_cols=30 Identities=33% Similarity=0.422 Sum_probs=24.2
Q ss_pred hHHHHHHhCCCcccCCCCCccccccchhcc
Q 040211 62 STMKVFQRGLLIQRDKEAPRLTESGFQFLL 91 (310)
Q Consensus 62 ~v~~lL~~~~L~~~~~~~~~IT~~GFqFLL 91 (310)
..++-|...||++.+++...||++|-+||-
T Consensus 38 ~yL~~L~~~gLI~~~~~~Y~lTekG~~~l~ 67 (77)
T PF14947_consen 38 KYLKELEEKGLIKKKDGKYRLTEKGKEFLE 67 (77)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHH
T ss_pred HHHHHHHHCcCeeCCCCEEEECccHHHHHH
Confidence 346778999999887778899999999873
No 14
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=53.32 E-value=28 Score=27.28 Aligned_cols=42 Identities=19% Similarity=0.398 Sum_probs=36.3
Q ss_pred HHHHHHHhhcCeeeEeeCCCcceeecCCCCcccccceEEEecCChhHHHHHHHHHhhhhcc
Q 040211 152 RSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQL 212 (310)
Q Consensus 152 ~~~L~~L~~lGLVy~~~~~~~~fyipT~S~gvETNfRvYAYT~S~LqiaiL~lF~~l~~rf 212 (310)
..++..|.+.|+|-+.......|| ++-+++-+...+++++-|
T Consensus 14 ~~~l~~lve~Gli~p~~~~~~~~f-------------------~~~~l~rl~~~~rL~~Dl 55 (84)
T PF13591_consen 14 PEFLRELVEEGLIEPEGEEEEWYF-------------------SEEDLARLRRIRRLHRDL 55 (84)
T ss_pred HHHHHHHHHCCCeeecCCCCeeeE-------------------CHHHHHHHHHHHHHHHHc
Confidence 578999999999999876666677 899999999999999877
No 15
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=52.19 E-value=9.6 Score=30.91 Aligned_cols=43 Identities=28% Similarity=0.420 Sum_probs=33.2
Q ss_pred HHHHHhCCCcccCCC----------CCccccccchhcccccchHHHHHHHHHH
Q 040211 64 MKVFQRGLLIQRDKE----------APRLTESGFQFLLMDTNAQLWYIVREYI 106 (310)
Q Consensus 64 ~~lL~~~~L~~~~~~----------~~~IT~~GFqFLL~d~~~QlW~lll~yL 106 (310)
+.+|..+||+..... ...||.+|.+||=.=++.-+|.=...-+
T Consensus 41 l~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~IRd~~vW~k~K~~i 93 (102)
T PF10711_consen 41 LKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDAIRDDTVWNKTKDKI 93 (102)
T ss_pred HHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHHhcCchHHHHHHHHH
Confidence 567778888874321 2489999999999999999998776544
No 16
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=49.50 E-value=21 Score=28.43 Aligned_cols=53 Identities=15% Similarity=0.290 Sum_probs=34.1
Q ss_pred ccccchHHHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHH-HHHHHHHhhcCeeeEe
Q 040211 91 LMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQ-RSMIKDFADLGLVKLQ 167 (310)
Q Consensus 91 L~d~~~QlW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q-~~~L~~L~~lGLVy~~ 167 (310)
+.+...+|+.+|.. .... +.|+...++..-| ++++.+ +..|++|.+-|.||.-
T Consensus 45 ~~~~~~~Vl~~i~~--~~~~-------~~Gv~v~~I~~~l---------------~~~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQ--QPNS-------EEGVHVDEIAQQL---------------GMSENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp S-HHHHHHHHHHHC-------------TTTEEHHHHHHHS---------------TS-HHHHHHHHHHHHHTTSEEES
T ss_pred CCHHHHHHHHHHHh--cCCC-------CCcccHHHHHHHh---------------CcCHHHHHHHHHHHHhCCeEecc
Confidence 45556666666665 1111 5688888888743 334444 8899999999999963
No 17
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=48.36 E-value=53 Score=30.19 Aligned_cols=106 Identities=13% Similarity=0.160 Sum_probs=74.6
Q ss_pred HHHHHhhhhccCceEEE---EeCHHHHHHHHHcCCCccc-cccChhhhh-----cCCCCCh--hHHHHHHHHHHhcCcee
Q 040211 202 LRLFSKIEYQLPNLIVG---AITKESLYNAVENGLTAEQ-QNAHPRVAD-----RIPSVLE--NVCDQIRLWESDLNRVE 270 (310)
Q Consensus 202 L~lF~~l~~rfPNlvvg---~iTReSv~~Al~~GITA~Q-~hAHp~m~~-----~~p~iP~--tV~DQIrLWE~Er~Rl~ 270 (310)
+..+.++..++|++.|| ++|.|.+++|.+.|-.-== -+..|.+.+ ..|.+|= |..+=..-|+.=-+-+|
T Consensus 43 ~~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aGA~FivSP~~~~~vi~~a~~~~i~~iPG~~TptEi~~A~~~Ga~~vK 122 (201)
T PRK06015 43 LDAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAGSRFIVSPGTTQELLAAANDSDVPLLPGAATPSEVMALREEGYTVLK 122 (201)
T ss_pred HHHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCCEeCCCCCHHHHHHHHHCCCCEEE
Confidence 34555677788999996 6899999999999953222 455555543 3577875 77888889999999999
Q ss_pred ecCcEEe--ccCCCC---ccccccEEEEecccchHHHHHHHh
Q 040211 271 MTPAHYY--DEFPSR---EDSKKMRLVVNAEIHMHMREFLRG 307 (310)
Q Consensus 271 ~~~g~ly--~~f~s~---~~~~kr~~~V~~~~h~~vr~f~k~ 307 (310)
+.|+-.+ -+|-+. --+.-++|.+..=.-+++.+|++.
T Consensus 123 ~FPa~~~GG~~yikal~~plp~~~l~ptGGV~~~n~~~~l~a 164 (201)
T PRK06015 123 FFPAEQAGGAAFLKALSSPLAGTFFCPTGGISLKNARDYLSL 164 (201)
T ss_pred ECCchhhCCHHHHHHHHhhCCCCcEEecCCCCHHHHHHHHhC
Confidence 9998655 255544 224555665544445789999874
No 18
>PRK13761 hypothetical protein; Provisional
Probab=45.33 E-value=11 Score=35.76 Aligned_cols=23 Identities=43% Similarity=0.632 Sum_probs=19.7
Q ss_pred EeCHHHHHHHHHcCCCccc-cccC
Q 040211 219 AITKESLYNAVENGLTAEQ-QNAH 241 (310)
Q Consensus 219 ~iTReSv~~Al~~GITA~Q-~hAH 241 (310)
.+|||.+-.++++||||.| ..||
T Consensus 12 L~~Rekiveg~~~Gi~a~qGLIAh 35 (248)
T PRK13761 12 LLTREKIVEGVEKGITAKQGLIAH 35 (248)
T ss_pred HHHHHHHHHHHHcCcccccchhhc
Confidence 4789999999999999999 4444
No 19
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=45.04 E-value=24 Score=30.41 Aligned_cols=56 Identities=13% Similarity=0.239 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHhccccc---------CccccCCCCC-------HHHHHHHHHHhhcCeeeEeeC--CCccee
Q 040211 120 GINQADLISFLLELSFHVA---------GEAYNLKTLS-------EIQRSMIKDFADLGLVKLQQG--RKESWF 175 (310)
Q Consensus 120 g~~~~e~L~FLf~Ls~~~~---------g~~Y~~~~lt-------~~q~~~L~~L~~lGLVy~~~~--~~~~fy 175 (310)
..+..++|.|.+-|+-.++ ..+-.++.+. .+....|+.|.+.|||+..+. ++.+||
T Consensus 12 ~~~~~dvl~c~~GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~ 85 (126)
T COG3355 12 EFRCEDVLKCVYGLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYY 85 (126)
T ss_pred cCcHHHHHHHHhCCcHHHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCcee
Confidence 3567788888777776532 3444554443 456779999999999998863 344544
No 20
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=42.92 E-value=13 Score=30.55 Aligned_cols=31 Identities=23% Similarity=0.273 Sum_probs=24.0
Q ss_pred cchhHHHHHHhCCCcccCC-C---CCccccccchh
Q 040211 59 FCSSTMKVFQRGLLIQRDK-E---APRLTESGFQF 89 (310)
Q Consensus 59 ~s~~v~~lL~~~~L~~~~~-~---~~~IT~~GFqF 89 (310)
..+.+++-|...|++.... + ...||++|..|
T Consensus 47 ~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~f 81 (95)
T COG3432 47 RAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRF 81 (95)
T ss_pred HHHHHHHHHHhCCCEEeccCCccceEEEChhHHHH
Confidence 4467788999999776533 2 57999999999
No 21
>PHA00738 putative HTH transcription regulator
Probab=42.58 E-value=22 Score=29.97 Aligned_cols=65 Identities=14% Similarity=0.195 Sum_probs=41.5
Q ss_pred HHHHHHHHH---hcccccCccccCCCCCHHHHHHHHHHhhcCeeeEeeCCCcceeecCCCCcccccceEEEecCCh
Q 040211 124 ADLISFLLE---LSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYSTSK 196 (310)
Q Consensus 124 ~e~L~FLf~---Ls~~~~g~~Y~~~~lt~~q~~~L~~L~~lGLVy~~~~~~~~fyipT~S~gvETNfRvYAYT~S~ 196 (310)
-.+|.+|.. ++.+++...+.++. ++--.=|.-|++-|||-.++....+|| .+..|...|.--+|.
T Consensus 15 r~IL~lL~~~e~~~V~eLae~l~lSQ--ptVS~HLKvLreAGLV~srK~Gr~vyY------~Ln~~~~~~~l~~~~ 82 (108)
T PHA00738 15 RKILELIAENYILSASLISHTLLLSY--TTVLRHLKILNEQGYIELYKEGRTLYA------KIRENSKEIQILNSE 82 (108)
T ss_pred HHHHHHHHHcCCccHHHHHHhhCCCH--HHHHHHHHHHHHCCceEEEEECCEEEE------EECCCccHHHHHhhH
Confidence 366666665 34445555554432 555667888999999999987777777 355555555444443
No 22
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=40.90 E-value=41 Score=25.97 Aligned_cols=29 Identities=24% Similarity=0.502 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHHhhcCeeeEeeCCCccee
Q 040211 147 LSEIQRSMIKDFADLGLVKLQQGRKESWF 175 (310)
Q Consensus 147 lt~~q~~~L~~L~~lGLVy~~~~~~~~fy 175 (310)
.+-+|-++=+||+++|+|..+..++...|
T Consensus 34 i~vTQaTiSRDLkeL~~vKv~~~~g~~~Y 62 (70)
T PF01316_consen 34 IEVTQATISRDLKELGAVKVPDGNGKYRY 62 (70)
T ss_dssp -T--HHHHHHHHHHHT-EEEECTTSSEEE
T ss_pred CCcchhHHHHHHHHcCcEEeeCCCCCEEE
Confidence 34789999999999999999976766666
No 23
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=39.10 E-value=18 Score=31.86 Aligned_cols=34 Identities=15% Similarity=0.265 Sum_probs=28.2
Q ss_pred cccchhHHHHHHhCCCcccCCCCCccccccchhc
Q 040211 57 INFCSSTMKVFQRGLLIQRDKEAPRLTESGFQFL 90 (310)
Q Consensus 57 ~~~s~~v~~lL~~~~L~~~~~~~~~IT~~GFqFL 90 (310)
..+...+++=|..+|+++...++..||++|-.||
T Consensus 95 gsI~RkilqqLE~~G~V~k~~~GR~ltp~Grsll 128 (147)
T COG2238 95 GSIIRKVLQQLEKAGLVEKTPKGRVLTPKGRSLL 128 (147)
T ss_pred chHHHHHHHHHHHCCceeecCCCceeCccchhHH
Confidence 4566678888999999997666778999999876
No 24
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=38.50 E-value=17 Score=32.17 Aligned_cols=32 Identities=16% Similarity=0.288 Sum_probs=26.5
Q ss_pred chhHHHHHHhCCCcccCCCCCccccccchhcc
Q 040211 60 CSSTMKVFQRGLLIQRDKEAPRLTESGFQFLL 91 (310)
Q Consensus 60 s~~v~~lL~~~~L~~~~~~~~~IT~~GFqFLL 91 (310)
-..+++-|...||++.+.++..||++|=+||=
T Consensus 98 iR~~LqqLE~~glVek~~~GR~lT~~G~~~LD 129 (150)
T PRK09333 98 IRKILQQLEKAGLVEKTKKGRVITPKGRSLLD 129 (150)
T ss_pred HHHHHHHHHHCCCeeeCCCCCEeCHHHHHHHH
Confidence 44568889999999977678889999998863
No 25
>PRK13824 replication initiation protein RepC; Provisional
Probab=38.44 E-value=97 Score=31.45 Aligned_cols=69 Identities=14% Similarity=0.322 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHHhcccchhhHHhhCCCHH--HHHHHHHHhcccccCccc---------c--------CCCCCHHH-HHHH
Q 040211 96 AQLWYIVREYISNSQHDSMLAYERGINQA--DLISFLLELSFHVAGEAY---------N--------LKTLSEIQ-RSMI 155 (310)
Q Consensus 96 ~QlW~lll~yL~~~e~~~~~~~~~g~~~~--e~L~FLf~Ls~~~~g~~Y---------~--------~~~lt~~q-~~~L 155 (310)
..=|.++..-.+... ..|++.. .+|.-|+ +| .+..++ + +.+++++. +..|
T Consensus 35 v~Kw~l~r~l~~a~~-------~lGl~~~~l~vL~aLl--sf-~p~~~~~~~~~~IVfpSN~~La~r~~Gms~~tlrRhl 104 (404)
T PRK13824 35 VDKWKLFRDLCEARA-------LLGVSDRALAVLNALL--SF-YPETELSEEAGLVVFPSNAQLSLRAHGMAGATLRRHL 104 (404)
T ss_pred CCHHHHHHHHHHHHH-------hcCCChhHHHHHHHHH--hh-CCcccccCCCCceechhHHHHHHHHcCCCHHHHHHHH
Confidence 356888888777776 6687664 3444443 33 333332 2 24677776 7799
Q ss_pred HHHhhcCeeeEe-eCCCcce
Q 040211 156 KDFADLGLVKLQ-QGRKESW 174 (310)
Q Consensus 156 ~~L~~lGLVy~~-~~~~~~f 174 (310)
..|.|.|||..+ ..+++||
T Consensus 105 a~LveaGLI~rrDSpNGKRy 124 (404)
T PRK13824 105 AALVEAGLIIRRDSPNGKRY 124 (404)
T ss_pred HHHHHCCCeEeecCCCCccc
Confidence 999999999776 4566675
No 26
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=38.19 E-value=14 Score=29.43 Aligned_cols=45 Identities=18% Similarity=0.276 Sum_probs=22.4
Q ss_pred hhHHHHHHHHhCCcccccccccchhHHHHHHhCCCcccCCCCCccccccchhccc
Q 040211 38 GQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTESGFQFLLM 92 (310)
Q Consensus 38 ~~WE~iL~~mv~~~~~~~~~~~s~~v~~lL~~~~L~~~~~~~~~IT~~GFqFLL~ 92 (310)
..|..|+..|+..+--.+ -..... ..+. ....+.||.+|.+||-.
T Consensus 25 ~~~~~il~~L~d~GyI~G-~~~~~~--------~~~~-~~~~~~IT~~Gi~YL~E 69 (88)
T PF09639_consen 25 SYWSDILRMLQDEGYIKG-VSVVRY--------SPYV-ALSDPRITLKGIEYLEE 69 (88)
T ss_dssp HHHHHHHHHHHHHTSEE---EESSS--------SEE---SS--EE-HHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCccc-eEEEec--------ccee-ecCCceEcHHHHHHHHH
Confidence 678888888875433211 111111 1111 12466899999999863
No 27
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=37.73 E-value=35 Score=34.63 Aligned_cols=34 Identities=32% Similarity=0.596 Sum_probs=28.1
Q ss_pred ceEEEEeCHHHHHHHHHcCCCccccccChhhhhcCCCCChhHHHHHH
Q 040211 214 NLIVGAITKESLYNAVENGLTAEQQNAHPRVADRIPSVLENVCDQIR 260 (310)
Q Consensus 214 Nlvvg~iTReSv~~Al~~GITA~Q~hAHp~m~~~~p~iP~tV~DQIr 260 (310)
|=.+|+|||..|-+|+ ||....|-+++|+-|||-
T Consensus 290 ~~llGiitR~dvlk~l-------------q~~q~qpqvget~~d~I~ 323 (432)
T COG4109 290 NTLLGIITRQDVLKSL-------------QMIQRQPQVGETISDQIA 323 (432)
T ss_pred ceEEEEEEHHHHHHHH-------------HHhccCCcccccHHHHHH
Confidence 3457999999999999 466677889999999985
No 28
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=37.66 E-value=17 Score=26.48 Aligned_cols=27 Identities=30% Similarity=0.340 Sum_probs=21.0
Q ss_pred hhHHHHHHhCCCcccCCCCCccccccc
Q 040211 61 SSTMKVFQRGLLIQRDKEAPRLTESGF 87 (310)
Q Consensus 61 ~~v~~lL~~~~L~~~~~~~~~IT~~GF 87 (310)
...++-|...||+..+++.+.+|++|+
T Consensus 39 ~~~l~~l~~~Gll~~~~~~l~lT~~G~ 65 (66)
T PF06969_consen 39 QKELEELQEDGLLEIDGGRLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHHTTSEEE-SSEEEE-TTTG
T ss_pred HHHHHHHHHCCCEEEeCCEEEECcccC
Confidence 455777888899998888999999996
No 29
>TIGR01182 eda Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida
Probab=37.63 E-value=1e+02 Score=28.39 Aligned_cols=119 Identities=14% Similarity=0.239 Sum_probs=78.6
Q ss_pred cceEEEec-CChhHHHHHHHHHhhhhccCceEEE---EeCHHHHHHHHHcCCCccc-cccChhhhh-----cCCCCCh--
Q 040211 186 NFRMYAYS-TSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAVENGLTAEQ-QNAHPRVAD-----RIPSVLE-- 253 (310)
Q Consensus 186 NfRvYAYT-~S~LqiaiL~lF~~l~~rfPNlvvg---~iTReSv~~Al~~GITA~Q-~hAHp~m~~-----~~p~iP~-- 253 (310)
-+|+...| ++|--... +.++..++|++.|| ++|.+.++.|.+.|-.-=- -+..|.+.+ ..|.+|=
T Consensus 33 Gi~~iEit~~t~~a~~~---i~~l~~~~~~~~vGAGTVl~~~~a~~a~~aGA~FivsP~~~~~v~~~~~~~~i~~iPG~~ 109 (204)
T TIGR01182 33 GLRVLEVTLRTPVALDA---IRLLRKEVPDALIGAGTVLNPEQLRQAVDAGAQFIVSPGLTPELAKHAQDHGIPIIPGVA 109 (204)
T ss_pred CCCEEEEeCCCccHHHH---HHHHHHHCCCCEEEEEeCCCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCcEECCCC
Confidence 34444444 34544444 44555688999996 6899999999999854333 344444432 2577874
Q ss_pred hHHHHHHHHHHhcCceeecCcEEec--cCCCC---ccccccEEEEecccchHHHHHHHh
Q 040211 254 NVCDQIRLWESDLNRVEMTPAHYYD--EFPSR---EDSKKMRLVVNAEIHMHMREFLRG 307 (310)
Q Consensus 254 tV~DQIrLWE~Er~Rl~~~~g~ly~--~f~s~---~~~~kr~~~V~~~~h~~vr~f~k~ 307 (310)
|-.+=..-|+.=-+-+|+.|+-.+- +|-+. --+.-++|.+..=.-+++.+|++.
T Consensus 110 TptEi~~A~~~Ga~~vKlFPA~~~GG~~yikal~~plp~i~~~ptGGV~~~N~~~~l~a 168 (204)
T TIGR01182 110 TPSEIMLALELGITALKLFPAEVSGGVKMLKALAGPFPQVRFCPTGGINLANVRDYLAA 168 (204)
T ss_pred CHHHHHHHHHCCCCEEEECCchhcCCHHHHHHHhccCCCCcEEecCCCCHHHHHHHHhC
Confidence 7777788999999999999986552 44443 224555665544445789999874
No 30
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=34.52 E-value=30 Score=26.11 Aligned_cols=27 Identities=22% Similarity=0.377 Sum_probs=19.6
Q ss_pred HHHHHhCCCcccCC-CCCccccccchhc
Q 040211 64 MKVFQRGLLIQRDK-EAPRLTESGFQFL 90 (310)
Q Consensus 64 ~~lL~~~~L~~~~~-~~~~IT~~GFqFL 90 (310)
++.|...|++.+.+ .+..||++|..+|
T Consensus 39 Lr~me~~Glt~~~g~~G~~iT~~G~~~L 66 (66)
T PF08461_consen 39 LRAMERDGLTRKVGRQGRIITEKGLDEL 66 (66)
T ss_pred HHHHHHCCCccccCCcccccCHHHHhhC
Confidence 45677888888643 4668999998765
No 31
>COG1438 ArgR Arginine repressor [Transcription]
Probab=33.25 E-value=64 Score=28.61 Aligned_cols=42 Identities=26% Similarity=0.470 Sum_probs=30.9
Q ss_pred CHHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCeeeEeeCCCccee
Q 040211 122 NQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWF 175 (310)
Q Consensus 122 ~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~~L~~L~~lGLVy~~~~~~~~fy 175 (310)
+..|+...|-+-|+ .=+|-++=+||.++|+|..+..++..+|
T Consensus 22 TQ~Elv~~L~~~Gi------------~vTQaTvSRDlkelglvKv~~~~g~~~Y 63 (150)
T COG1438 22 TQEELVELLQEEGI------------EVTQATVSRDLKELGLVKVRNEKGTYVY 63 (150)
T ss_pred CHHHHHHHHHHcCC------------eEehHHHHHHHHHcCCEEecCCCCcEEE
Confidence 45566666654433 3578888999999999999976666656
No 32
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=32.98 E-value=37 Score=27.01 Aligned_cols=20 Identities=35% Similarity=0.547 Sum_probs=17.6
Q ss_pred CHHHHHHHHHHhhcCeeeEe
Q 040211 148 SEIQRSMIKDFADLGLVKLQ 167 (310)
Q Consensus 148 t~~q~~~L~~L~~lGLVy~~ 167 (310)
+.+-++.+++|.++|||...
T Consensus 37 ~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 37 PATIRNEMADLEELGLVESQ 56 (78)
T ss_pred hHHHHHHHHHHHHCCCccCC
Confidence 57899999999999999743
No 33
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=31.39 E-value=37 Score=25.57 Aligned_cols=59 Identities=22% Similarity=0.410 Sum_probs=35.3
Q ss_pred ccccchHHHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCeeeEeeCC
Q 040211 91 LMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGR 170 (310)
Q Consensus 91 L~d~~~QlW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~~L~~L~~lGLVy~~~~~ 170 (310)
|-+++.+|..+|..|++. .|..+. .-|+++.+.+. -+.+-...|..|.+-|+|-....+
T Consensus 4 LT~rQ~~vL~~I~~~~~~----------~G~~Pt----------~rEIa~~~g~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEE----------NGYPPT----------VREIAEALGLK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp --HHHHHHHHHHHHHHHH----------HSS-------------HHHHHHHHTSS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred CCHHHHHHHHHHHHHHHH----------cCCCCC----------HHHHHHHhCCC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 446677888888888764 344331 11222223332 147788999999999999766543
No 34
>PF04023 FeoA: FeoA domain; InterPro: IPR007167 This entry represents the core domain of the ferrous iron (Fe2+) transport protein FeoA found in bacteria. This domain also occurs at the C terminus in related proteins. The transporter Feo is composed of three proteins: FeoA a small, soluble SH3-domain protein probably located in the cytosol; FeoB, a large protein with a cytosolic N-terminal G-protein domain and a C-terminal integral inner-membrane domain containing two 'Gate' motifs which likely functions as the Fe2+ permease; and FeoC, a small protein apparently functioning as an [Fe-S]-dependent transcriptional repressor [, ]. Feo allows the bacterial cell to acquire iron from its environment. ; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 1G3T_A 1C0W_B 1BI3_A 1QVP_A 1BI1_A 1BYM_A 2QQB_A ....
Probab=30.06 E-value=14 Score=27.38 Aligned_cols=33 Identities=30% Similarity=0.444 Sum_probs=27.7
Q ss_pred HhcccccCccccCCCCCHHHHHHHHHHhhcCee
Q 040211 132 ELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLV 164 (310)
Q Consensus 132 ~Ls~~~~g~~Y~~~~lt~~q~~~L~~L~~lGLV 164 (310)
.|+.+..|+.|-+..+.+....+++.|.++||.
T Consensus 2 ~L~~~~~g~~~~I~~i~~~d~~~~~~L~~lGl~ 34 (74)
T PF04023_consen 2 PLSELPPGERARIVRISDEDPELLRRLADLGLT 34 (74)
T ss_dssp BGGGSSTTEEEEEEEESTSSHHHHHHHHHCT-S
T ss_pred ChhHCCCCCEEEEEEEECCCHHHHHHHHHCCCC
Confidence 378889999999988887668999999999994
No 35
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=29.46 E-value=1.4e+02 Score=23.73 Aligned_cols=46 Identities=11% Similarity=0.247 Sum_probs=40.2
Q ss_pred hHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhh
Q 040211 115 LAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFAD 160 (310)
Q Consensus 115 ~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~~L~~L~~ 160 (310)
+.++.|+++.++++.++.=...+=|-+|+...+|+.+...|.--++
T Consensus 19 vl~~lGls~S~Ai~~fl~qi~~~~~iPF~~~~~s~ed~~~l~~~re 64 (80)
T PRK11235 19 VLEKLGVTPSEALRLLLQYVAENGRLPFKTVLLSDEDAALLETVRE 64 (80)
T ss_pred HHHHhCCCHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHH
Confidence 3557899999999999999999999999999999999999887443
No 36
>COG1701 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.46 E-value=28 Score=32.96 Aligned_cols=19 Identities=26% Similarity=0.520 Sum_probs=17.6
Q ss_pred EeCHHHHHHHHHcCCCccc
Q 040211 219 AITKESLYNAVENGLTAEQ 237 (310)
Q Consensus 219 ~iTReSv~~Al~~GITA~Q 237 (310)
.+.||.+-.++..|||+.|
T Consensus 14 Ll~Reki~eg~~~Gi~~~q 32 (256)
T COG1701 14 LLIREKIIEGFEKGITVPQ 32 (256)
T ss_pred HHHHHHHHHHHHcCccccc
Confidence 3679999999999999999
No 37
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=26.93 E-value=81 Score=26.82 Aligned_cols=72 Identities=21% Similarity=0.406 Sum_probs=41.3
Q ss_pred chHHHHHHHHHHHhcc-----cc------hhh--HHhhCCCHHHHHHHHHHhcccc-cC-ccccCCCCCH--HHHHHHHH
Q 040211 95 NAQLWYIVREYISNSQ-----HD------SML--AYERGINQADLISFLLELSFHV-AG-EAYNLKTLSE--IQRSMIKD 157 (310)
Q Consensus 95 ~~QlW~lll~yL~~~e-----~~------~~~--~~~~g~~~~e~L~FLf~Ls~~~-~g-~~Y~~~~lt~--~q~~~L~~ 157 (310)
.-++|+.++.||=..- ++ .++ .-+.|+++.|+++||.+---+. +. .+|+...-|+ +.-++|+-
T Consensus 18 pV~vWQ~llt~LL~~HYGLtLNDT~f~de~vI~~hidaGIs~~~AVN~LVeKY~LvRiD~~gFs~~~qsP~l~~~DilrA 97 (114)
T PF06755_consen 18 PVEVWQQLLTYLLEQHYGLTLNDTPFSDETVIQEHIDAGISPADAVNFLVEKYELVRIDRNGFSWQEQSPYLTAIDILRA 97 (114)
T ss_pred HHHHHHHHHHHHHHHhcCCccCCCccchHHHHHHHHHhCCCHHHHHHHHHHHHhhhhcCCcccCccCCCchhhHHHHHHH
Confidence 4578888888871100 00 000 1256999999999998754332 11 2455433333 33567777
Q ss_pred HhhcCeeeE
Q 040211 158 FADLGLVKL 166 (310)
Q Consensus 158 L~~lGLVy~ 166 (310)
=+.-||...
T Consensus 98 r~a~gl~~~ 106 (114)
T PF06755_consen 98 RRATGLMKR 106 (114)
T ss_pred HHHhchhhh
Confidence 777888643
No 38
>PRK05066 arginine repressor; Provisional
Probab=26.39 E-value=1.3e+02 Score=26.64 Aligned_cols=42 Identities=19% Similarity=0.357 Sum_probs=31.0
Q ss_pred CHHHHHHHHHHhcccccCccccCCCCC-HHHHHHHHHHhhcCeeeEeeCCCccee
Q 040211 122 NQADLISFLLELSFHVAGEAYNLKTLS-EIQRSMIKDFADLGLVKLQQGRKESWF 175 (310)
Q Consensus 122 ~~~e~L~FLf~Ls~~~~g~~Y~~~~lt-~~q~~~L~~L~~lGLVy~~~~~~~~fy 175 (310)
+..|++..|-+-|+ + -+|-++=+|++|+|+|..+..++...|
T Consensus 25 tQeeL~~~L~~~Gi------------~~vTQATiSRDikeL~lvKv~~~~G~~~Y 67 (156)
T PRK05066 25 SQGEIVTALQEQGF------------DNINQSKVSRMLTKFGAVRTRNAKMEMVY 67 (156)
T ss_pred CHHHHHHHHHHCCC------------CeecHHHHHHHHHHcCCEEeeCCCCCEEE
Confidence 45667776665443 4 388999999999999998876665555
No 39
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=25.14 E-value=1e+02 Score=24.99 Aligned_cols=31 Identities=10% Similarity=0.299 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhhcCeeeEeeCCCcceeecCC
Q 040211 149 EIQRSMIKDFADLGLVKLQQGRKESWFIPTI 179 (310)
Q Consensus 149 ~~q~~~L~~L~~lGLVy~~~~~~~~fyipT~ 179 (310)
.|-+++|..|.+-|+|-..+.....+|.|+.
T Consensus 36 sTv~t~L~rL~~Kg~l~~~~~gr~~~Y~p~i 66 (115)
T PF03965_consen 36 STVQTLLNRLVEKGFLTREKIGRAYVYSPLI 66 (115)
T ss_dssp HHHHHHHHHHHHTTSEEEEEETTCEEEEESS
T ss_pred hHHHHHHHHHHhCCceeEeecCCceEEEeCC
Confidence 6779999999999999888644444453555
No 40
>KOG2036 consensus Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=25.07 E-value=51 Score=36.35 Aligned_cols=57 Identities=25% Similarity=0.434 Sum_probs=41.0
Q ss_pred ecCChhHHHHHH------HHHhh------hhccCceEE-------EEeCHHHHHHHHHcCCCccccccChhhhhcCCCCC
Q 040211 192 YSTSKLHCEILR------LFSKI------EYQLPNLIV-------GAITKESLYNAVENGLTAEQQNAHPRVADRIPSVL 252 (310)
Q Consensus 192 YT~S~LqiaiL~------lF~~l------~~rfPNlvv-------g~iTReSv~~Al~~GITA~Q~hAHp~m~~~~p~iP 252 (310)
|.+||-.+.+|+ |||=+ .-.+|..++ |.|+|+|+.+.+..|=.|. ...||
T Consensus 529 YKNSPNDLQllsDAPaH~LFvLl~PVd~~~~~iPdvlcviQv~lEG~isr~si~~sL~~G~~a~-----------GdlIp 597 (1011)
T KOG2036|consen 529 YKNSPNDLQLLSDAPAHHLFVLLGPVDPSQNAIPDVLCVIQVCLEGRISRQSIENSLRRGKRAA-----------GDLIP 597 (1011)
T ss_pred ccCCchhhhhhccCcccceEEEecCcCcccCCCCcceEEEEEeecceecHHHHHHHHhcccccc-----------CCccc
Confidence 678888888875 77644 346676432 9999999999999995542 45666
Q ss_pred hhHHHHH
Q 040211 253 ENVCDQI 259 (310)
Q Consensus 253 ~tV~DQI 259 (310)
=+|+.|.
T Consensus 598 W~vseQf 604 (1011)
T KOG2036|consen 598 WTVSEQF 604 (1011)
T ss_pred eehhhhh
Confidence 6777665
No 41
>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....
Probab=24.99 E-value=80 Score=28.92 Aligned_cols=105 Identities=17% Similarity=0.257 Sum_probs=66.3
Q ss_pred HHHHhhhhccCceEEE---EeCHHHHHHHHHcCCCccc-cccChhhhh-----cCCCCCh--hHHHHHHHHHHhcCceee
Q 040211 203 RLFSKIEYQLPNLIVG---AITKESLYNAVENGLTAEQ-QNAHPRVAD-----RIPSVLE--NVCDQIRLWESDLNRVEM 271 (310)
Q Consensus 203 ~lF~~l~~rfPNlvvg---~iTReSv~~Al~~GITA~Q-~hAHp~m~~-----~~p~iP~--tV~DQIrLWE~Er~Rl~~ 271 (310)
.....+..++|+|.|| ++|.|.+++|.+.|-.-== -+..|.+.+ ..|.+|= |..+=...|+.=.+-+|+
T Consensus 48 ~~I~~l~~~~p~~~vGAGTV~~~e~a~~a~~aGA~FivSP~~~~~v~~~~~~~~i~~iPG~~TptEi~~A~~~G~~~vK~ 127 (196)
T PF01081_consen 48 EAIEALRKEFPDLLVGAGTVLTAEQAEAAIAAGAQFIVSPGFDPEVIEYAREYGIPYIPGVMTPTEIMQALEAGADIVKL 127 (196)
T ss_dssp HHHHHHHHHHTTSEEEEES--SHHHHHHHHHHT-SEEEESS--HHHHHHHHHHTSEEEEEESSHHHHHHHHHTT-SEEEE
T ss_pred HHHHHHHHHCCCCeeEEEeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCcccCCcCCHHHHHHHHHCCCCEEEE
Confidence 3445566788999997 6899999999999843222 455555543 3577773 667777899999999999
Q ss_pred cCcEEec--cCCCC-c--cccccEEEEecccchHHHHHHHh
Q 040211 272 TPAHYYD--EFPSR-E--DSKKMRLVVNAEIHMHMREFLRG 307 (310)
Q Consensus 272 ~~g~ly~--~f~s~-~--~~~kr~~~V~~~~h~~vr~f~k~ 307 (310)
.|+-.+- +|.+. . -+.-++|.+..=.-+++++|++.
T Consensus 128 FPA~~~GG~~~ik~l~~p~p~~~~~ptGGV~~~N~~~~l~a 168 (196)
T PF01081_consen 128 FPAGALGGPSYIKALRGPFPDLPFMPTGGVNPDNLAEYLKA 168 (196)
T ss_dssp TTTTTTTHHHHHHHHHTTTTT-EEEEBSS--TTTHHHHHTS
T ss_pred ecchhcCcHHHHHHHhccCCCCeEEEcCCCCHHHHHHHHhC
Confidence 9986553 44443 2 23455555544445679999874
No 42
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=24.66 E-value=67 Score=26.96 Aligned_cols=53 Identities=17% Similarity=0.275 Sum_probs=32.9
Q ss_pred HHHHHHHhcccccCccccCCCC------C-HHHHHHHHHHhhcCeeeEeeCCCcceeecCC
Q 040211 126 LISFLLELSFHVAGEAYNLKTL------S-EIQRSMIKDFADLGLVKLQQGRKESWFIPTI 179 (310)
Q Consensus 126 ~L~FLf~Ls~~~~g~~Y~~~~l------t-~~q~~~L~~L~~lGLVy~~~~~~~~fyipT~ 179 (310)
.|..+..|+...-+...+.+.+ + ..-..+|+.|++-|||--.+....-|. |++
T Consensus 10 Al~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~-l~~ 69 (135)
T TIGR02010 10 AVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQ-LGR 69 (135)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEe-ccC
Confidence 4555555555443444554433 2 233679999999999987665555666 555
No 43
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=24.26 E-value=3e+02 Score=24.10 Aligned_cols=68 Identities=15% Similarity=0.124 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHhcccccCc-cccCCCCC-HHHHHHHHHHhhcCeeeEeeCCCcceeecCCCCcccccceEEEecCChh
Q 040211 120 GINQADLISFLLELSFHVAGE-AYNLKTLS-EIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYSTSKL 197 (310)
Q Consensus 120 g~~~~e~L~FLf~Ls~~~~g~-~Y~~~~lt-~~q~~~L~~L~~lGLVy~~~~~~~~fyipT~S~gvETNfRvYAYT~S~L 197 (310)
|-+-+.++..|+.=+-++--. +.-+ +++ ..-+.+|..|.+.|||-.++.+. .+|+...|-|.-++-
T Consensus 13 g~~~v~Vl~aL~~~~~~tdEeLa~~L-gi~~~~VRk~L~~L~e~~Lv~~~r~r~-----------~~~gw~~Y~w~i~~~ 80 (158)
T TIGR00373 13 EEEVGLVLFSLGIKGEFTDEEISLEL-GIKLNEVRKALYALYDAGLADYKRRKD-----------DETGWYEYTWRINYE 80 (158)
T ss_pred ChhHHHHHHHHhccCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCCceeeeeee-----------cCCCcEEEEEEeCHH
Confidence 444566666665333322111 1111 333 45588999999999996443221 355556788776665
Q ss_pred HH
Q 040211 198 HC 199 (310)
Q Consensus 198 qi 199 (310)
++
T Consensus 81 ~i 82 (158)
T TIGR00373 81 KA 82 (158)
T ss_pred HH
Confidence 54
No 44
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=23.82 E-value=1.5e+02 Score=24.08 Aligned_cols=42 Identities=10% Similarity=0.226 Sum_probs=32.8
Q ss_pred HHHHHHHhhcCeeeEeeCC-CcceeecCCCCcccccceEEEecCChhHHHHHHHHHhhhhcc
Q 040211 152 RSMIKDFADLGLVKLQQGR-KESWFIPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQL 212 (310)
Q Consensus 152 ~~~L~~L~~lGLVy~~~~~-~~~fyipT~S~gvETNfRvYAYT~S~LqiaiL~lF~~l~~rf 212 (310)
.+++..|.++|||-+.... ...+| +..+++.+...+++.+-|
T Consensus 21 ~~~l~eLve~GlIep~~~~~~~~~F-------------------~~~~l~r~~~a~rL~~dl 63 (101)
T PRK10265 21 EEELNEIVGLGVIEPREIQETTWVF-------------------DDHAAIVVQRAVRLRHEL 63 (101)
T ss_pred HHHHHHHHHCCCeecCCCCcccceE-------------------CHHHHHHHHHHHHHHHHc
Confidence 5789999999999886554 34456 677888888888888776
No 45
>KOG3085 consensus Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=23.34 E-value=1.8e+02 Score=27.56 Aligned_cols=136 Identities=18% Similarity=0.171 Sum_probs=69.5
Q ss_pred cccchhcccc---cchHHHH-HHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccC-ccccCCCCCHHHHHHHHHH
Q 040211 84 ESGFQFLLMD---TNAQLWY-IVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAG-EAYNLKTLSEIQRSMIKDF 158 (310)
Q Consensus 84 ~~GFqFLL~d---~~~QlW~-lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g-~~Y~~~~lt~~q~~~L~~L 158 (310)
.+|.+|.+.. +..|+|. ++.++...... -...+...++..--+.+.+ .+|++ +.+.| .+|+-|
T Consensus 58 ~~~p~~~~~~g~l~~~~ww~~lv~~~f~~~~~---------~~~~~~~~~~~~~~~s~~~~~~~~~--~~~~~-~~lq~l 125 (237)
T KOG3085|consen 58 EKGPFFGLYSGELTLSQWWPKLVESTFGKAGI---------DYEEELLENFSFRLFSTFAPSAWKY--LDGMQ-ELLQKL 125 (237)
T ss_pred ccCCcccccCCcccHHHHHHHHHHHHhccccc---------hhHHHHHhhhhhheeccccccCcee--ccHHH-HHHHHH
Confidence 4555555554 5889999 88888876651 1234444344333333332 34444 34777 999999
Q ss_pred hhcCeeeEeeCC-CcceeecCCCCcccccceEEEecCChh----------HHHHHHHHHhhhhccCc--eEEEEeCHHHH
Q 040211 159 ADLGLVKLQQGR-KESWFIPTIADSLETNFRMYAYSTSKL----------HCEILRLFSKIEYQLPN--LIVGAITKESL 225 (310)
Q Consensus 159 ~~lGLVy~~~~~-~~~fyipT~S~gvETNfRvYAYT~S~L----------qiaiL~lF~~l~~rfPN--lvvg~iTReSv 225 (310)
|+-|.+----.+ .+|+. . +.-++.+-+|-+--+ .-.|..+=++..---|- +.+|-.=+.-+
T Consensus 126 R~~g~~l~iisN~d~r~~-~-----~l~~~~l~~~fD~vv~S~e~g~~KPDp~If~~al~~l~v~Pee~vhIgD~l~nD~ 199 (237)
T KOG3085|consen 126 RKKGTILGIISNFDDRLR-L-----LLLPLGLSAYFDFVVESCEVGLEKPDPRIFQLALERLGVKPEECVHIGDLLENDY 199 (237)
T ss_pred HhCCeEEEEecCCcHHHH-H-----HhhccCHHHhhhhhhhhhhhccCCCChHHHHHHHHHhCCChHHeEEecCcccccc
Confidence 999933222111 12222 1 112222111111000 00111111111111154 66688888889
Q ss_pred HHHHHcCCCccc
Q 040211 226 YNAVENGLTAEQ 237 (310)
Q Consensus 226 ~~Al~~GITA~Q 237 (310)
..|-+-|++|-+
T Consensus 200 ~gA~~~G~~ail 211 (237)
T KOG3085|consen 200 EGARNLGWHAIL 211 (237)
T ss_pred HhHHHcCCEEEE
Confidence 999999999988
No 46
>PF12513 SUV3_C: Mitochondrial degradasome RNA helicase subunit C terminal; InterPro: IPR022192 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00271 from PFAM. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 3RC8_A 3RC3_A.
Probab=23.34 E-value=14 Score=26.26 Aligned_cols=19 Identities=21% Similarity=0.644 Sum_probs=15.6
Q ss_pred HHHHHHHhhhhccCceEEE
Q 040211 200 EILRLFSKIEYQLPNLIVG 218 (310)
Q Consensus 200 aiL~lF~~l~~rfPNlvvg 218 (310)
.++.+++=+.+|||++.+.
T Consensus 9 k~l~lYlWLs~Rfp~~F~d 27 (49)
T PF12513_consen 9 KVLDLYLWLSYRFPDVFPD 27 (49)
T ss_dssp HHHHHHHHHHCC-TTTSTT
T ss_pred HHHHHHHHHHHHcccccCC
Confidence 6899999999999998653
No 47
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=22.67 E-value=44 Score=30.26 Aligned_cols=33 Identities=18% Similarity=0.279 Sum_probs=25.7
Q ss_pred ccchhHHHHHHhCCCcccCC--CCCccccccchhc
Q 040211 58 NFCSSTMKVFQRGLLIQRDK--EAPRLTESGFQFL 90 (310)
Q Consensus 58 ~~s~~v~~lL~~~~L~~~~~--~~~~IT~~GFqFL 90 (310)
.+-..+++-|...||++.+. ++..||++|=+||
T Consensus 120 ~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~L 154 (169)
T PTZ00095 120 KILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFA 154 (169)
T ss_pred HHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHH
Confidence 34455678889999999652 5779999998886
No 48
>PRK05256 condesin subunit E; Provisional
Probab=22.65 E-value=92 Score=29.59 Aligned_cols=45 Identities=18% Similarity=0.218 Sum_probs=36.3
Q ss_pred cccccCccccCCCCCHHHHHHHHHHhhcCeeeEeeCCCcceeecCC
Q 040211 134 SFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTI 179 (310)
Q Consensus 134 s~~~~g~~Y~~~~lt~~q~~~L~~L~~lGLVy~~~~~~~~fyipT~ 179 (310)
+.-..|.+++...+-+--+.-|..|+.+|.|+.-..++.+|- +|.
T Consensus 138 n~R~~GsDlD~~Kl~ekvr~sLrrLrRlgmI~~l~~d~~kF~-ite 182 (238)
T PRK05256 138 NNRSTGSDLDKQKLQEKVRTSLNRLRRLGMVWFMGHDSSKFR-ITE 182 (238)
T ss_pred cCCCCcchhhHHHHHHHHHHHHHHHHhccceeeecCCCceEE-ecH
Confidence 355678888888888888999999999999996655777888 555
No 49
>PRK04280 arginine repressor; Provisional
Probab=22.32 E-value=82 Score=27.55 Aligned_cols=42 Identities=24% Similarity=0.302 Sum_probs=30.5
Q ss_pred CHHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCeeeEeeCCCccee
Q 040211 122 NQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWF 175 (310)
Q Consensus 122 ~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~~L~~L~~lGLVy~~~~~~~~fy 175 (310)
+..|++.-|-.-| .+-+|-++=+|++|+|+|..+..++..+|
T Consensus 20 tQeeL~~~L~~~G------------i~vTQATiSRDikeL~lvKv~~~~G~~~Y 61 (148)
T PRK04280 20 TQDELVDRLREEG------------FNVTQATVSRDIKELHLVKVPLPDGRYKY 61 (148)
T ss_pred CHHHHHHHHHHcC------------CCeehHHHHHHHHHcCCEEeecCCCcEEE
Confidence 4456666555443 34678889999999999998876766666
No 50
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=22.09 E-value=58 Score=25.58 Aligned_cols=31 Identities=29% Similarity=0.303 Sum_probs=24.5
Q ss_pred HHHHHHhCCCcccCC-CCCccccccchhcccc
Q 040211 63 TMKVFQRGLLIQRDK-EAPRLTESGFQFLLMD 93 (310)
Q Consensus 63 v~~lL~~~~L~~~~~-~~~~IT~~GFqFLL~d 93 (310)
.+.-|..+|++++.+ +-..||++|-++|-..
T Consensus 60 a~~~L~~aGli~~~~rG~~~iT~~G~~~l~~~ 91 (92)
T PF14338_consen 60 ARSYLKKAGLIERPKRGIWRITEKGRKALAEH 91 (92)
T ss_pred HHHHHHHCCCccCCCCCceEECHhHHHHHhhC
Confidence 367789999999753 5679999999988643
No 51
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=21.79 E-value=32 Score=30.15 Aligned_cols=33 Identities=24% Similarity=0.399 Sum_probs=25.1
Q ss_pred ccchhHHHHHHhCCCcccC-CCCCccccccchhc
Q 040211 58 NFCSSTMKVFQRGLLIQRD-KEAPRLTESGFQFL 90 (310)
Q Consensus 58 ~~s~~v~~lL~~~~L~~~~-~~~~~IT~~GFqFL 90 (310)
.+-..+++-|...||++.+ +++..||++|-+||
T Consensus 95 ~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~l 128 (139)
T PF01090_consen 95 SIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDL 128 (139)
T ss_dssp HHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHH
T ss_pred HHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHH
Confidence 3445567888999999976 55778999998875
No 52
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=21.45 E-value=89 Score=30.77 Aligned_cols=36 Identities=31% Similarity=0.440 Sum_probs=25.4
Q ss_pred ccCCCCCHHHHHHHHHHhhcCeeeEeeCCCcceeecCC
Q 040211 142 YNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTI 179 (310)
Q Consensus 142 Y~~~~lt~~q~~~L~~L~~lGLVy~~~~~~~~fyipT~ 179 (310)
|..+--+.|-++-+.+|.+.|++.+.-..+.| |||.
T Consensus 35 ~~l~~S~aTIR~dm~~Le~~G~l~~~h~sagr--IPT~ 70 (339)
T PRK00082 35 YGLGVSSATIRNDMADLEELGLLEKPHTSSGR--IPTD 70 (339)
T ss_pred hCCCCChHHHHHHHHHHHhCCCcCCCcCCCCC--CcCH
Confidence 33333368899999999999999876433333 4776
No 53
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=20.77 E-value=28 Score=27.60 Aligned_cols=27 Identities=19% Similarity=0.119 Sum_probs=21.5
Q ss_pred HHHHhCCCcccCCCCCccccccchhcc
Q 040211 65 KVFQRGLLIQRDKEAPRLTESGFQFLL 91 (310)
Q Consensus 65 ~lL~~~~L~~~~~~~~~IT~~GFqFLL 91 (310)
-.|.+.|++.+...+..+|++|+++|-
T Consensus 48 PyLiq~G~I~RT~rGR~~T~~a~~~l~ 74 (76)
T PF05491_consen 48 PYLIQIGFIQRTPRGRVATPKAYEHLG 74 (76)
T ss_dssp HHHHHTTSEEEETTEEEE-HHHHHHTT
T ss_pred HHHHHhhhHhhCccHHHhHHHHHHHhC
Confidence 357889999987777899999999874
No 54
>COG3095 MukE Uncharacterized protein involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=20.17 E-value=1.4e+02 Score=27.65 Aligned_cols=52 Identities=25% Similarity=0.305 Sum_probs=39.7
Q ss_pred cccCccccCCCCCHHHHHHHHHHhhcCeeeEeeCCCcceeecCCCCcccccceEEEec
Q 040211 136 HVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYS 193 (310)
Q Consensus 136 ~~~g~~Y~~~~lt~~q~~~L~~L~~lGLVy~~~~~~~~fyipT~S~gvETNfRvYAYT 193 (310)
-.-|.+-+-..|.+--+.-|..|+.+|+|+.-..++.+|-| .|.=||.-|=-
T Consensus 138 rssgsdldkqkl~ekvr~sl~rlrrlgmi~~~g~~sgkf~i------teavfrfgadv 189 (238)
T COG3095 138 RSTGSDLDRQKLQEKVRSSLNRLRRLGMVWFMGHDSGKFRI------TESVFRFGADV 189 (238)
T ss_pred cCccccccHHHHHHHHHHHHHHHHHhceeEEeccCCCceee------eHHHhhccccc
Confidence 34566666666778888999999999999998778888886 66666655543
No 55
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=20.09 E-value=32 Score=32.98 Aligned_cols=58 Identities=17% Similarity=0.179 Sum_probs=36.4
Q ss_pred HHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccc----cccChhhhhc-CCCCChhHHHHHH
Q 040211 201 ILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ----QNAHPRVADR-IPSVLENVCDQIR 260 (310)
Q Consensus 201 iL~lF~~l~~rfPNlvvg~iTReSv~~Al~~GITA~Q----~hAHp~m~~~-~p~iP~tV~DQIr 260 (310)
.|..+.++..-.| ++|.+--++.-.|=+-||..|= .+|-+....+ .++|=-.+.++++
T Consensus 177 dld~~~el~~s~d--~iaAmG~~a~va~rklgiePdi~Fg~~~a~ieAa~rGl~vlvv~t~~ml~ 239 (260)
T COG1497 177 DLDRLKELSASED--IIAAMGTEALVALRKLGIEPDIEFGTLEAAIEAAVRGLSVLVVITRRMLR 239 (260)
T ss_pred chHHHHHhhcccc--hhhhhhHHHHHHHHHcCCCCCeeecccHHHHHHHhcCCcEEEEEeHHHHH
Confidence 3556667777777 7888888888888888998877 3332222222 3444445555554
Done!