Query 029356
Match_columns 194
No_of_seqs 132 out of 921
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 11:36:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029356.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029356hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2383 Predicted ATPase [Gene 100.0 4.4E-49 9.6E-54 354.7 12.5 183 2-185 275-464 (467)
2 PF03969 AFG1_ATPase: AFG1-lik 100.0 6.3E-45 1.4E-49 327.4 14.2 146 8-183 216-361 (362)
3 COG1485 Predicted ATPase [Gene 100.0 3.6E-44 7.8E-49 319.0 11.1 148 6-183 217-364 (367)
4 PRK08116 hypothetical protein; 97.3 0.00094 2E-08 58.1 8.1 76 52-128 143-227 (268)
5 PRK06921 hypothetical protein; 96.2 0.017 3.8E-07 50.1 7.0 76 52-128 147-231 (266)
6 PRK07952 DNA replication prote 95.5 0.1 2.3E-06 45.0 9.2 76 52-128 128-211 (244)
7 PRK06835 DNA replication prote 95.5 0.04 8.8E-07 49.5 6.8 76 52-128 212-295 (329)
8 PRK08181 transposase; Validate 95.2 0.1 2.2E-06 45.7 8.2 74 53-128 136-215 (269)
9 PRK12377 putative replication 95.2 0.14 3E-06 44.3 8.8 76 52-128 130-212 (248)
10 PF00308 Bac_DnaA: Bacterial d 94.8 0.089 1.9E-06 44.2 6.4 75 52-127 65-145 (219)
11 PRK05642 DNA replication initi 94.3 0.19 4.2E-06 42.5 7.3 73 52-128 74-146 (234)
12 PF01695 IstB_IS21: IstB-like 93.8 0.19 4.1E-06 41.1 6.2 75 52-128 76-156 (178)
13 PRK08727 hypothetical protein; 93.6 0.21 4.6E-06 42.2 6.2 72 53-128 71-142 (233)
14 PRK06526 transposase; Provisio 93.1 0.21 4.6E-06 43.1 5.7 74 53-128 128-207 (254)
15 PRK09183 transposase/IS protei 92.8 0.45 9.8E-06 41.1 7.2 74 53-128 132-212 (259)
16 PF03969 AFG1_ATPase: AFG1-lik 92.3 0.43 9.3E-06 43.5 6.7 54 74-130 123-176 (362)
17 COG1484 DnaC DNA replication p 91.4 0.29 6.2E-06 42.3 4.3 107 51-188 133-246 (254)
18 PRK08939 primosomal protein Dn 90.5 1.1 2.3E-05 39.9 7.2 102 53-178 186-295 (306)
19 TIGR03420 DnaA_homol_Hda DnaA 89.8 1.4 3.1E-05 36.0 7.0 71 52-126 67-137 (226)
20 PRK14086 dnaA chromosomal repl 89.1 1.1 2.4E-05 43.8 6.6 74 53-127 346-425 (617)
21 PRK08084 DNA replication initi 89.0 1.6 3.6E-05 36.8 6.9 71 53-127 75-146 (235)
22 TIGR00362 DnaA chromosomal rep 86.5 1.8 4E-05 39.3 6.1 75 52-127 167-247 (405)
23 PRK12422 chromosomal replicati 86.2 2.9 6.3E-05 39.1 7.4 76 52-128 170-251 (445)
24 COG1485 Predicted ATPase [Gene 85.8 2.3 5.1E-05 39.0 6.4 56 72-130 124-179 (367)
25 PRK00149 dnaA chromosomal repl 81.9 3 6.5E-05 38.6 5.5 74 53-127 180-259 (450)
26 PRK09087 hypothetical protein; 81.8 3.5 7.6E-05 34.8 5.5 45 80-128 89-133 (226)
27 PRK06893 DNA replication initi 79.6 6.1 0.00013 33.1 6.2 71 53-127 69-140 (229)
28 PRK14087 dnaA chromosomal repl 74.4 9 0.0002 35.8 6.4 74 52-126 172-253 (450)
29 PF14532 Sigma54_activ_2: Sigm 70.5 6.9 0.00015 29.9 3.9 55 70-128 62-116 (138)
30 PRK06620 hypothetical protein; 70.1 10 0.00022 31.7 5.2 44 77-126 84-127 (214)
31 COG0593 DnaA ATPase involved i 65.9 12 0.00026 34.9 5.1 50 78-128 175-224 (408)
32 PRK14088 dnaA chromosomal repl 61.0 16 0.00035 34.0 5.0 73 53-126 162-241 (440)
33 PF10298 WhiA_N: WhiA N-termin 52.9 8.3 0.00018 27.6 1.4 34 91-124 30-63 (86)
34 PRK08903 DnaA regulatory inact 41.6 62 0.0014 26.5 5.2 46 75-123 87-133 (227)
35 TIGR01618 phage_P_loop phage n 41.5 25 0.00055 29.9 2.8 51 77-127 80-148 (220)
36 cd03768 SR_ResInv Serine Recom 32.7 83 0.0018 23.1 4.2 43 72-118 48-90 (126)
37 COG3283 TyrR Transcriptional r 32.2 25 0.00055 33.1 1.4 67 60-129 273-351 (511)
38 PF00158 Sigma54_activat: Sigm 30.5 43 0.00093 26.9 2.4 65 60-128 68-150 (168)
39 cd03770 SR_TndX_transposase Se 29.4 88 0.0019 24.0 3.9 40 76-119 66-106 (140)
40 PF00004 AAA: ATPase family as 27.8 86 0.0019 22.5 3.5 57 71-128 48-117 (132)
41 PRK13413 mpi multiple promoter 27.1 1.1E+02 0.0024 24.8 4.4 44 72-119 55-98 (200)
42 cd01741 GATase1_1 Subgroup of 27.0 1.5E+02 0.0032 23.5 5.0 44 76-119 44-88 (188)
43 KOG2383 Predicted ATPase [Gene 26.9 95 0.0021 29.5 4.2 53 74-129 189-241 (467)
44 PRK05665 amidotransferase; Pro 26.7 1.4E+02 0.0031 25.4 5.1 51 77-127 56-108 (240)
45 KOG3889 Predicted gamma-butyro 25.5 50 0.0011 29.9 2.1 61 51-111 109-169 (371)
46 PF05729 NACHT: NACHT domain 25.5 1.1E+02 0.0023 22.9 3.7 40 81-120 84-128 (166)
47 PF01039 Carboxyl_trans: Carbo 24.8 57 0.0012 30.9 2.4 73 40-116 291-371 (493)
48 cd01120 RecA-like_NTPases RecA 24.7 1.2E+02 0.0026 22.3 3.8 55 71-125 78-140 (165)
49 PF00448 SRP54: SRP54-type pro 23.9 1E+02 0.0022 25.3 3.6 50 77-127 82-131 (196)
50 PF12149 HSV_VP16_C: Herpes si 23.5 21 0.00046 20.9 -0.4 26 47-72 3-28 (30)
51 cd00561 CobA_CobO_BtuR ATP:cor 21.4 1.1E+02 0.0024 24.7 3.2 52 76-128 93-144 (159)
52 PRK15429 formate hydrogenlyase 20.6 1.8E+02 0.0039 28.5 5.1 52 71-126 464-525 (686)
53 cd00338 Ser_Recombinase Serine 20.6 2E+02 0.0043 21.1 4.3 38 78-119 65-102 (137)
54 PRK06490 glutamine amidotransf 20.5 2.2E+02 0.0047 24.2 5.0 40 77-116 51-90 (239)
55 cd00223 TOPRIM_TopoIIB_SPO TOP 20.4 3.3E+02 0.0072 21.3 5.8 54 58-127 11-66 (160)
56 TIGR02410 carnitine_TMLD trime 20.3 59 0.0013 29.3 1.5 50 54-103 101-151 (362)
57 KOG0125 Ataxin 2-binding prote 20.3 87 0.0019 28.8 2.6 37 6-51 136-172 (376)
No 1
>KOG2383 consensus Predicted ATPase [General function prediction only]
Probab=100.00 E-value=4.4e-49 Score=354.72 Aligned_cols=183 Identities=43% Similarity=0.694 Sum_probs=158.4
Q ss_pred CCCCcceeeCCc-chHHHHHHHHHHhhCCCCC-CCceeEEecCeeeEeccccCCEEEeeHHHHhCCCCChhhHHHHhhcc
Q 029356 2 TSAQQGFYFVGK-GSSEVMKQKFRDLIGEHEA-GPQEVEVVMGRKLQVPLGANGCAYFEFEELCDKPLGAADYFGLFKIF 79 (194)
Q Consensus 2 ~~~~~~~y~~~~-~~~~~l~~~f~~l~~~~~~-~~~~i~vv~gR~i~v~~~~~~~a~f~F~eLC~~p~~a~DYl~La~~f 79 (194)
++.++++|+.++ +.+..|+++|+.+.+++.. .+..+.+|+||++.||+++++||||+|++||++|+||+|||.||++|
T Consensus 275 ~~~~~~~yf~~~~d~~~~l~~~fk~~~~dq~d~~~~~~l~v~GR~l~vpk~cg~VA~ftFeeLC~rPlgAaDYL~lak~f 354 (467)
T KOG2383|consen 275 KSAGENYYFISETDVETVLKEWFKLLAADQNDGTRQRTLVVFGRKLIVPKACGGVADFTFEELCGRPLGAADYLGLAKNF 354 (467)
T ss_pred CCCCceeEecChhhHHHHHHHHHHHHhccCCCCCCCcceeeecceEEecccCCCcccccHHHHhCCccchHHHHHHHhhc
Confidence 356678999998 7788999999988887643 34445557999999999999999999999999999999999999999
Q ss_pred CeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhcccccchhhhhhccccccccc--cccccc---
Q 029356 80 HTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFNKIVTISDAQQMAPRTSSRSM--RNDEAD--- 154 (194)
Q Consensus 80 ~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~~~~~~~d~~~~~~~~~~~~~--~~~~~~--- 154 (194)
|||+|+|||+|+.+++|++||||+|||++||++++|+++|++|+++||..... +++...++|+++... .++..+
T Consensus 355 hti~v~dIP~lsl~~r~~~rRFITliD~lYd~~~rlv~sa~~p~~~Lf~~~~~-~e~ls~s~r~~mddl~iks~~~~~~~ 433 (467)
T KOG2383|consen 355 HTIIVRDIPQLSLENRDQARRFITLIDALYDNHVRLVCSAATPLEELFQFTGH-SEALSDSPRTLMDDLGIKSDSAGGSP 433 (467)
T ss_pred ceeEeeccchhhhHHHHHHhhHhHHHHHHhhccceEEecCCCCHHHHhcccCc-ccccccCcccchhhhcccccCccccc
Confidence 99999999999999999999999999999999999999999999999985432 345555666665554 344445
Q ss_pred cccCcchhhhhhhhhhHHhhhCchHHHHHHH
Q 029356 155 LCVDNELGFAKDRTISRLTEMNSKEYLEQHA 185 (194)
Q Consensus 155 ~~~~~~~~Faf~Rt~SRL~EM~s~~Y~~~~~ 185 (194)
+++|+||.|||+||+|||.|||+..||+++.
T Consensus 434 mf~g~EE~FAf~RtlSRL~eMqt~~y~~~~~ 464 (467)
T KOG2383|consen 434 MFSGEEEGFAFDRTLSRLYEMQTELYWEQPY 464 (467)
T ss_pred cccchHHHHHHHHHHHHHHHhhcchhccccc
Confidence 8999999999999999999999999998653
No 2
>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP. AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding
Probab=100.00 E-value=6.3e-45 Score=327.38 Aligned_cols=146 Identities=40% Similarity=0.791 Sum_probs=135.8
Q ss_pred eeeCCcchHHHHHHHHHHhhCCCCCCCceeEEecCeeeEeccccCCEEEeeHHHHhCCCCChhhHHHHhhccCeEEEcCC
Q 029356 8 FYFVGKGSSEVMKQKFRDLIGEHEAGPQEVEVVMGRKLQVPLGANGCAYFEFEELCDKPLGAADYFGLFKIFHTLALEGI 87 (194)
Q Consensus 8 ~y~~~~~~~~~l~~~f~~l~~~~~~~~~~i~vv~gR~i~v~~~~~~~a~f~F~eLC~~p~~a~DYl~La~~f~ti~I~~V 87 (194)
+||.+.++.+.++++|..++++....+..+. |.||+|.||.++++++||+|+|||++|+|++||++||++|++|+|+||
T Consensus 216 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~-v~gR~i~v~~~~~~va~F~F~eLC~~plg~aDYlaLA~~F~ti~I~~V 294 (362)
T PF03969_consen 216 FYPLDEEADAALERLFQRLTGGEPEEPRTLE-VGGREIPVPRACGGVAWFDFDELCERPLGAADYLALAERFHTIFISDV 294 (362)
T ss_pred cCcchHHHHHHHHHHHHHhccccCCCCceeE-EeeeEEeeecccCCEEEecHHHhhccCCCHHHHHHHHHhCCEEEEcCC
Confidence 5566777788999999999997766777777 589999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhcccccchhhhhhccccccccccccccccccCcchhhhhhh
Q 029356 88 PIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFNKIVTISDAQQMAPRTSSRSMRNDEADLCVDNELGFAKDR 167 (194)
Q Consensus 88 P~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~Faf~R 167 (194)
|.|+..+.|+|||||+|||+|||++|+|+|+|++||++||. ++...|+|+|
T Consensus 295 P~l~~~~~n~arRFI~LID~LYd~~v~L~~sa~~~~~~L~~-----------------------------~~~~~~~f~R 345 (362)
T PF03969_consen 295 PVLSESDRNEARRFITLIDVLYDRKVKLIISAAAPPDELFQ-----------------------------GGRLAFEFQR 345 (362)
T ss_pred CCcccCChhHHHHHHHHHHHHhhCCCcEEEEcCCCHHHHHh-----------------------------CCCchhhhhH
Confidence 99999999999999999999999999999999999999997 3455899999
Q ss_pred hhhHHhhhCchHHHHH
Q 029356 168 TISRLTEMNSKEYLEQ 183 (194)
Q Consensus 168 t~SRL~EM~s~~Y~~~ 183 (194)
|+|||.||||.+|+++
T Consensus 346 T~SRL~Em~~~~y~~~ 361 (362)
T PF03969_consen 346 TASRLSEMQSEEYLAR 361 (362)
T ss_pred HHHHHHHHhhHHHHhc
Confidence 9999999999999974
No 3
>COG1485 Predicted ATPase [General function prediction only]
Probab=100.00 E-value=3.6e-44 Score=319.00 Aligned_cols=148 Identities=32% Similarity=0.561 Sum_probs=139.1
Q ss_pred cceeeCCcchHHHHHHHHHHhhCCCCCCCceeEEecCeeeEeccccCCEEEeeHHHHhCCCCChhhHHHHhhccCeEEEc
Q 029356 6 QGFYFVGKGSSEVMKQKFRDLIGEHEAGPQEVEVVMGRKLQVPLGANGCAYFEFEELCDKPLGAADYFGLFKIFHTLALE 85 (194)
Q Consensus 6 ~~~y~~~~~~~~~l~~~f~~l~~~~~~~~~~i~vv~gR~i~v~~~~~~~a~f~F~eLC~~p~~a~DYl~La~~f~ti~I~ 85 (194)
--+||++.++++.|+++|..+++++...+..|. ++||+|.++..+++++||+|.+||+.|+|+.|||+||++|++|+|+
T Consensus 217 ~y~~Pl~~~~~~~l~~~~~~ls~~~~~~~~~l~-i~gR~i~~~~~~~~~~~f~f~~Lc~~p~s~~DYl~l~~~f~tv~l~ 295 (367)
T COG1485 217 VYLTPLDAEAEAALDKLWAALSDGAPEAAANLE-IKGREIRVPAVAGGLLWFDFAQLCEAPRSASDYLALAERFHTVFLT 295 (367)
T ss_pred eeecCCcHHHHHHHHHHHHHhccCCccCCchhh-ccCceeecccccCcchhccHHHHhhCcCCHHHHHHHHhhccEEEEc
Confidence 346778888899999999999997667777788 5999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhcccccchhhhhhccccccccccccccccccCcchhhhh
Q 029356 86 GIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFNKIVTISDAQQMAPRTSSRSMRNDEADLCVDNELGFAK 165 (194)
Q Consensus 86 ~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~Faf 165 (194)
|||+|+..+.|+|||||+|||+|||+++||++||++||++||. |+...|+|
T Consensus 296 ~vp~m~~~~~~~arRFI~lVD~lYD~~vkL~~Sae~~~~~Ly~-----------------------------~~~~afeF 346 (367)
T COG1485 296 DVPQMDPLDRDEARRFIALVDELYDRGVKLVASAEVPLNELYQ-----------------------------GGRLAFEF 346 (367)
T ss_pred CCCCCChhhhHHHHHHHHHHHHHHhcCCcEEEEccCCHHHhcc-----------------------------CchhhhHH
Confidence 9999999999999999999999999999999999999999998 56779999
Q ss_pred hhhhhHHhhhCchHHHHH
Q 029356 166 DRTISRLTEMNSKEYLEQ 183 (194)
Q Consensus 166 ~Rt~SRL~EM~s~~Y~~~ 183 (194)
+||+|||.||||.+|+..
T Consensus 347 ~Rt~SRL~EMqS~~yl~~ 364 (367)
T COG1485 347 QRTLSRLQEMQSEEYLGI 364 (367)
T ss_pred HHHHHHHHHHHHHHhhcc
Confidence 999999999999999973
No 4
>PRK08116 hypothetical protein; Validated
Probab=97.34 E-value=0.00094 Score=58.07 Aligned_cols=76 Identities=14% Similarity=0.103 Sum_probs=57.6
Q ss_pred CCEEEeeHHHHhCCC---------CChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCC
Q 029356 52 NGCAYFEFEELCDKP---------LGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGS 122 (194)
Q Consensus 52 ~~~a~f~F~eLC~~p---------~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~ 122 (194)
..+++.++.+|...- .+..+++......+.++|+|+-.-.. .......+..+||..|+++.++++++..+
T Consensus 143 ~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~~~dlLviDDlg~e~~-t~~~~~~l~~iin~r~~~~~~~IiTsN~~ 221 (268)
T PRK08116 143 VPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLVNADLLILDDLGAERD-TEWAREKVYNIIDSRYRKGLPTIVTTNLS 221 (268)
T ss_pred CeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhcCCCEEEEecccCCCC-CHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence 456788998887642 23346788788899999999943322 22344567889999999999999999999
Q ss_pred hhhhhc
Q 029356 123 PFQLFN 128 (194)
Q Consensus 123 ~~~Lf~ 128 (194)
|++|-.
T Consensus 222 ~~eL~~ 227 (268)
T PRK08116 222 LEELKN 227 (268)
T ss_pred HHHHHH
Confidence 998764
No 5
>PRK06921 hypothetical protein; Provisional
Probab=96.17 E-value=0.017 Score=50.14 Aligned_cols=76 Identities=17% Similarity=0.203 Sum_probs=53.2
Q ss_pred CCEEEeeHHHHhCCCCCh----hhHHHHhhccCeEEEcCCCCC---CCCCch--HHHHHHHHHHHHHhcCceEEEEccCC
Q 029356 52 NGCAYFEFEELCDKPLGA----ADYFGLFKIFHTLALEGIPIF---GLHNRT--AAYRFVTLVDVMYENRARLLCTAEGS 122 (194)
Q Consensus 52 ~~~a~f~F~eLC~~p~~a----~DYl~La~~f~ti~I~~VP~l---~~~~~d--~arRFI~LID~lYd~~v~L~~~a~~~ 122 (194)
..|+.+++.+|...-..+ .+.+.-....+.++|+|+ .+ +....+ ...-|-.+||.-|+++.++++++..+
T Consensus 147 ~~v~y~~~~~l~~~l~~~~~~~~~~~~~~~~~dlLiIDDl-~~~~~g~e~~t~~~~~~lf~iin~R~~~~k~tIitsn~~ 225 (266)
T PRK06921 147 VPVLYFPFVEGFGDLKDDFDLLEAKLNRMKKVEVLFIDDL-FKPVNGKPRATEWQIEQMYSVLNYRYLNHKPILISSELT 225 (266)
T ss_pred ceEEEEEHHHHHHHHHHHHHHHHHHHHHhcCCCEEEEecc-ccccCCCccCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence 456788877775542111 234555667899999999 33 222222 33458899999999999999999999
Q ss_pred hhhhhc
Q 029356 123 PFQLFN 128 (194)
Q Consensus 123 ~~~Lf~ 128 (194)
|++|..
T Consensus 226 ~~el~~ 231 (266)
T PRK06921 226 IDELLD 231 (266)
T ss_pred HHHHhh
Confidence 999875
No 6
>PRK07952 DNA replication protein DnaC; Validated
Probab=95.55 E-value=0.1 Score=44.97 Aligned_cols=76 Identities=7% Similarity=0.048 Sum_probs=58.1
Q ss_pred CCEEEeeHHHHhCC--------CCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCCh
Q 029356 52 NGCAYFEFEELCDK--------PLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSP 123 (194)
Q Consensus 52 ~~~a~f~F~eLC~~--------p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~ 123 (194)
..++.++..+|... ..+..+.+.-...++.++|+|+.... ....+..-|-.+||.=|+++.+.++++..++
T Consensus 128 ~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l~~~dlLvIDDig~~~-~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl~~ 206 (244)
T PRK07952 128 KSVLIITVADIMSAMKDTFSNSETSEEQLLNDLSNVDLLVIDEIGVQT-ESRYEKVIINQIVDRRSSSKRPTGMLTNSNM 206 (244)
T ss_pred CeEEEEEHHHHHHHHHHHHhhccccHHHHHHHhccCCEEEEeCCCCCC-CCHHHHHHHHHHHHHHHhCCCCEEEeCCCCH
Confidence 45677888888742 22344666667789999999998875 2333445667799999999999999999999
Q ss_pred hhhhc
Q 029356 124 FQLFN 128 (194)
Q Consensus 124 ~~Lf~ 128 (194)
++|-.
T Consensus 207 ~~l~~ 211 (244)
T PRK07952 207 EEMTK 211 (244)
T ss_pred HHHHH
Confidence 99875
No 7
>PRK06835 DNA replication protein DnaC; Validated
Probab=95.54 E-value=0.04 Score=49.51 Aligned_cols=76 Identities=11% Similarity=0.132 Sum_probs=56.7
Q ss_pred CCEEEeeHHHHhCCCCC--------hhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCCh
Q 029356 52 NGCAYFEFEELCDKPLG--------AADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSP 123 (194)
Q Consensus 52 ~~~a~f~F~eLC~~p~~--------a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~ 123 (194)
..|..++..+|...-.. ..+.+.....++.++|+|+-... .+.....-|-.+|+..|+++.++++++..+|
T Consensus 212 ~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~~DLLIIDDlG~e~-~t~~~~~~Lf~iin~R~~~~k~tIiTSNl~~ 290 (329)
T PRK06835 212 KSVIYRTADELIEILREIRFNNDKELEEVYDLLINCDLLIIDDLGTEK-ITEFSKSELFNLINKRLLRQKKMIISTNLSL 290 (329)
T ss_pred CeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhccCCEEEEeccCCCC-CCHHHHHHHHHHHHHHHHCCCCEEEECCCCH
Confidence 46788888888764211 11225667789999999996553 2334456788999999999999999999999
Q ss_pred hhhhc
Q 029356 124 FQLFN 128 (194)
Q Consensus 124 ~~Lf~ 128 (194)
++|-.
T Consensus 291 ~el~~ 295 (329)
T PRK06835 291 EELLK 295 (329)
T ss_pred HHHHH
Confidence 99764
No 8
>PRK08181 transposase; Validated
Probab=95.25 E-value=0.1 Score=45.71 Aligned_cols=74 Identities=16% Similarity=0.194 Sum_probs=58.2
Q ss_pred CEEEeeHHHHhCCC------CChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhh
Q 029356 53 GCAYFEFEELCDKP------LGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQL 126 (194)
Q Consensus 53 ~~a~f~F~eLC~~p------~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~L 126 (194)
.|.+++..+|+..- ......+.-..+++.++|+|+-.... +...+.-+..+|+..|++ .++++++..|+.++
T Consensus 136 ~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l~~~dLLIIDDlg~~~~-~~~~~~~Lf~lin~R~~~-~s~IiTSN~~~~~w 213 (269)
T PRK08181 136 RVLFTRTTDLVQKLQVARRELQLESAIAKLDKFDLLILDDLAYVTK-DQAETSVLFELISARYER-RSILITANQPFGEW 213 (269)
T ss_pred ceeeeeHHHHHHHHHHHHhCCcHHHHHHHHhcCCEEEEeccccccC-CHHHHHHHHHHHHHHHhC-CCEEEEcCCCHHHH
Confidence 47788888888742 23345666677899999999977654 345667899999999997 59999999999998
Q ss_pred hc
Q 029356 127 FN 128 (194)
Q Consensus 127 f~ 128 (194)
..
T Consensus 214 ~~ 215 (269)
T PRK08181 214 NR 215 (269)
T ss_pred HH
Confidence 85
No 9
>PRK12377 putative replication protein; Provisional
Probab=95.20 E-value=0.14 Score=44.30 Aligned_cols=76 Identities=7% Similarity=0.036 Sum_probs=59.5
Q ss_pred CCEEEeeHHHHhCCC-------CChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChh
Q 029356 52 NGCAYFEFEELCDKP-------LGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPF 124 (194)
Q Consensus 52 ~~~a~f~F~eLC~~p-------~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~ 124 (194)
-.|..++..+|...- ....+++.-....+.++|+||-... .+.....-|-.+||.-|+++.++++++..+++
T Consensus 130 ~~v~~i~~~~l~~~l~~~~~~~~~~~~~l~~l~~~dLLiIDDlg~~~-~s~~~~~~l~~ii~~R~~~~~ptiitSNl~~~ 208 (248)
T PRK12377 130 RSVIVVTVPDVMSRLHESYDNGQSGEKFLQELCKVDLLVLDEIGIQR-ETKNEQVVLNQIIDRRTASMRSVGMLTNLNHE 208 (248)
T ss_pred CCeEEEEHHHHHHHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCCC-CCHHHHHHHHHHHHHHHhcCCCEEEEcCCCHH
Confidence 346788888887731 1234678778999999999995443 23457778999999999999999999999998
Q ss_pred hhhc
Q 029356 125 QLFN 128 (194)
Q Consensus 125 ~Lf~ 128 (194)
+|-.
T Consensus 209 ~l~~ 212 (248)
T PRK12377 209 AMST 212 (248)
T ss_pred HHHH
Confidence 8764
No 10
>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.
Probab=94.79 E-value=0.089 Score=44.24 Aligned_cols=75 Identities=15% Similarity=0.248 Sum_probs=59.1
Q ss_pred CCEEEeeHHHHhCC------CCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhh
Q 029356 52 NGCAYFEFEELCDK------PLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQ 125 (194)
Q Consensus 52 ~~~a~f~F~eLC~~------p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~ 125 (194)
..|.+++-.+++.. .-...+|+.--+.++.++|+||-.+.. ......-|..++|.+++++.++++++..+|.+
T Consensus 65 ~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~~l~~-~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~ 143 (219)
T PF00308_consen 65 KRVVYLSAEEFIREFADALRDGEIEEFKDRLRSADLLIIDDIQFLAG-KQRTQEELFHLFNRLIESGKQLILTSDRPPSE 143 (219)
T ss_dssp S-EEEEEHHHHHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGGGGTT-HHHHHHHHHHHHHHHHHTTSEEEEEESS-TTT
T ss_pred ccceeecHHHHHHHHHHHHHcccchhhhhhhhcCCEEEEecchhhcC-chHHHHHHHHHHHHHHhhCCeEEEEeCCCCcc
Confidence 45788876666543 244567888888999999999998873 23456889999999999999999999999998
Q ss_pred hh
Q 029356 126 LF 127 (194)
Q Consensus 126 Lf 127 (194)
|-
T Consensus 144 l~ 145 (219)
T PF00308_consen 144 LS 145 (219)
T ss_dssp TT
T ss_pred cc
Confidence 74
No 11
>PRK05642 DNA replication initiation factor; Validated
Probab=94.25 E-value=0.19 Score=42.51 Aligned_cols=73 Identities=18% Similarity=0.301 Sum_probs=57.9
Q ss_pred CCEEEeeHHHHhCCCCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhc
Q 029356 52 NGCAYFEFEELCDKPLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFN 128 (194)
Q Consensus 52 ~~~a~f~F~eLC~~p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~ 128 (194)
..+++++..++... ..+++.-.+.++.++|+||-.+.... ....-|-++++.+|+++..+++++..+|.++-.
T Consensus 74 ~~v~y~~~~~~~~~---~~~~~~~~~~~d~LiiDDi~~~~~~~-~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~ 146 (234)
T PRK05642 74 EPAVYLPLAELLDR---GPELLDNLEQYELVCLDDLDVIAGKA-DWEEALFHLFNRLRDSGRRLLLAASKSPRELPI 146 (234)
T ss_pred CcEEEeeHHHHHhh---hHHHHHhhhhCCEEEEechhhhcCCh-HHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCc
Confidence 56889999998753 34666667778999999998775432 334569999999999999999999999987653
No 12
>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif. They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.
Probab=93.83 E-value=0.19 Score=41.05 Aligned_cols=75 Identities=19% Similarity=0.208 Sum_probs=56.7
Q ss_pred CCEEEeeHHHHhCC------CCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhh
Q 029356 52 NGCAYFEFEELCDK------PLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQ 125 (194)
Q Consensus 52 ~~~a~f~F~eLC~~------p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~ 125 (194)
..+.++++.+|+.. .-...+++.-..+.+.++|+|+-.... +...+.-|-.+||.-|+++ +.++++..++++
T Consensus 76 ~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~~dlLilDDlG~~~~-~~~~~~~l~~ii~~R~~~~-~tIiTSN~~~~~ 153 (178)
T PF01695_consen 76 YSVLFITASDLLDELKQSRSDGSYEELLKRLKRVDLLILDDLGYEPL-SEWEAELLFEIIDERYERK-PTIITSNLSPSE 153 (178)
T ss_dssp --EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHTSSCEEEETCTSS----HHHHHCTHHHHHHHHHT--EEEEEESS-HHH
T ss_pred cceeEeecCceeccccccccccchhhhcCccccccEecccccceeee-cccccccchhhhhHhhccc-CeEeeCCCchhh
Confidence 45789999999874 233456788888999999999976543 4567778899999999975 899999999999
Q ss_pred hhc
Q 029356 126 LFN 128 (194)
Q Consensus 126 Lf~ 128 (194)
|..
T Consensus 154 l~~ 156 (178)
T PF01695_consen 154 LEE 156 (178)
T ss_dssp HHT
T ss_pred Hhh
Confidence 886
No 13
>PRK08727 hypothetical protein; Validated
Probab=93.57 E-value=0.21 Score=42.20 Aligned_cols=72 Identities=17% Similarity=0.167 Sum_probs=54.2
Q ss_pred CEEEeeHHHHhCCCCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhc
Q 029356 53 GCAYFEFEELCDKPLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFN 128 (194)
Q Consensus 53 ~~a~f~F~eLC~~p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~ 128 (194)
.+.+++..+++... .+.+.-..+.+.++|+|+-.+...... ..-+..+++.+|+++..|++++..+|.++-.
T Consensus 71 ~~~y~~~~~~~~~~---~~~~~~l~~~dlLiIDDi~~l~~~~~~-~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~ 142 (233)
T PRK08727 71 SSAYLPLQAAAGRL---RDALEALEGRSLVALDGLESIAGQRED-EVALFDFHNRARAAGITLLYTARQMPDGLAL 142 (233)
T ss_pred cEEEEeHHHhhhhH---HHHHHHHhcCCEEEEeCcccccCChHH-HHHHHHHHHHHHHcCCeEEEECCCChhhhhh
Confidence 56788888876542 244444567889999999877754433 3455689999999999999999999998853
No 14
>PRK06526 transposase; Provisional
Probab=93.14 E-value=0.21 Score=43.15 Aligned_cols=74 Identities=14% Similarity=0.101 Sum_probs=53.5
Q ss_pred CEEEeeHHHHhCCCC------ChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhh
Q 029356 53 GCAYFEFEELCDKPL------GAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQL 126 (194)
Q Consensus 53 ~~a~f~F~eLC~~p~------~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~L 126 (194)
.|.+++..+|+..-. ...+.+.-..+++.++|+++..+.. +...+.-|-.+||.-|+++ .+++++..|+.++
T Consensus 128 ~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~~~dlLIIDD~g~~~~-~~~~~~~L~~li~~r~~~~-s~IitSn~~~~~w 205 (254)
T PRK06526 128 RVLFATAAQWVARLAAAHHAGRLQAELVKLGRYPLLIVDEVGYIPF-EPEAANLFFQLVSSRYERA-SLIVTSNKPFGRW 205 (254)
T ss_pred chhhhhHHHHHHHHHHHHhcCcHHHHHHHhccCCEEEEcccccCCC-CHHHHHHHHHHHHHHHhcC-CEEEEcCCCHHHH
Confidence 455667777765321 1234444456789999999987753 3455567999999999986 6999999999988
Q ss_pred hc
Q 029356 127 FN 128 (194)
Q Consensus 127 f~ 128 (194)
..
T Consensus 206 ~~ 207 (254)
T PRK06526 206 GE 207 (254)
T ss_pred HH
Confidence 75
No 15
>PRK09183 transposase/IS protein; Provisional
Probab=92.75 E-value=0.45 Score=41.07 Aligned_cols=74 Identities=12% Similarity=0.018 Sum_probs=51.5
Q ss_pred CEEEeeHHHHhCCC------CChhhHH-HHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhh
Q 029356 53 GCAYFEFEELCDKP------LGAADYF-GLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQ 125 (194)
Q Consensus 53 ~~a~f~F~eLC~~p------~~a~DYl-~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~ 125 (194)
.+..++..+|...- .+....+ ......+.++|+++-... .+...+.-|..+||..|+++ .+++++..|+.+
T Consensus 132 ~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~~~~~dlLiiDdlg~~~-~~~~~~~~lf~li~~r~~~~-s~iiTsn~~~~~ 209 (259)
T PRK09183 132 KVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMAPRLLIIDEIGYLP-FSQEEANLFFQVIAKRYEKG-SMILTSNLPFGQ 209 (259)
T ss_pred eEEEEeHHHHHHHHHHHHHCCcHHHHHHHHhcCCCEEEEcccccCC-CChHHHHHHHHHHHHHHhcC-cEEEecCCCHHH
Confidence 45666777776321 1122222 224567899999996544 33466778999999999987 589999999999
Q ss_pred hhc
Q 029356 126 LFN 128 (194)
Q Consensus 126 Lf~ 128 (194)
+..
T Consensus 210 w~~ 212 (259)
T PRK09183 210 WDQ 212 (259)
T ss_pred HHH
Confidence 875
No 16
>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP. AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding
Probab=92.31 E-value=0.43 Score=43.50 Aligned_cols=54 Identities=17% Similarity=0.263 Sum_probs=45.1
Q ss_pred HHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhccc
Q 029356 74 GLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFNKI 130 (194)
Q Consensus 74 ~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~~~ 130 (194)
.|++..+.++++.+-.- +...|.-.-.|...|+++||.|+++|..||++||.+.
T Consensus 123 ~l~~~~~lLcfDEF~V~---DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~Ly~~g 176 (362)
T PF03969_consen 123 ELAKESRLLCFDEFQVT---DIADAMILKRLFEALFKRGVVLVATSNRPPEDLYKNG 176 (362)
T ss_pred HHHhcCCEEEEeeeecc---chhHHHHHHHHHHHHHHCCCEEEecCCCChHHHcCCc
Confidence 67888889999876643 4445777778889999999999999999999999853
No 17
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=91.37 E-value=0.29 Score=42.31 Aligned_cols=107 Identities=15% Similarity=0.135 Sum_probs=74.8
Q ss_pred cCCEEEeeHHHHhCCCCChhh-------HHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCCh
Q 029356 51 ANGCAYFEFEELCDKPLGAAD-------YFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSP 123 (194)
Q Consensus 51 ~~~~a~f~F~eLC~~p~~a~D-------Yl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~ 123 (194)
.-.|..++..||-..-..+-+ .+..-.+++.++|+|+=..... ...+-=|..+|+..|+++.. ++++..|+
T Consensus 133 g~sv~f~~~~el~~~Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~~~~-~~~~~~~~q~I~~r~~~~~~-~~tsN~~~ 210 (254)
T COG1484 133 GISVLFITAPDLLSKLKAAFDEGRLEEKLLRELKKVDLLIIDDIGYEPFS-QEEADLLFQLISRRYESRSL-IITSNLSF 210 (254)
T ss_pred CCeEEEEEHHHHHHHHHHHHhcCchHHHHHHHhhcCCEEEEecccCccCC-HHHHHHHHHHHHHHHhhccc-eeecCCCh
Confidence 456788888888876444333 3556789999999998765532 23445566699999999988 99999998
Q ss_pred hhhhcccccchhhhhhccccccccccccccccccCcchhhhhhhhhhHHhhhCchHHHHHHHHHH
Q 029356 124 FQLFNKIVTISDAQQMAPRTSSRSMRNDEADLCVDNELGFAKDRTISRLTEMNSKEYLEQHAAML 188 (194)
Q Consensus 124 ~~Lf~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~Faf~Rt~SRL~EM~s~~Y~~~~~~~~ 188 (194)
+++-..- +.. . --+|.++||.+|...-++.....++
T Consensus 211 ~~~~~~~---------------------------~~~-~-~~e~~~dRi~~~~~~~~~~g~s~rl 246 (254)
T COG1484 211 GEWDELF---------------------------GDD-A-LTEALLDRILHHSHVIVIKGESYRL 246 (254)
T ss_pred HHHHhhc---------------------------cCc-h-hHHHHHHHHHhcceeeEecchHhhh
Confidence 8866410 100 0 1369999999999877755444433
No 18
>PRK08939 primosomal protein DnaI; Reviewed
Probab=90.50 E-value=1.1 Score=39.91 Aligned_cols=102 Identities=10% Similarity=0.079 Sum_probs=67.6
Q ss_pred CEEEeeHHHHhCCC------CChhhHHHHhhccCeEEEcCCCCCCCCCchHHH-HHH-HHHHHHHhcCceEEEEccCChh
Q 029356 53 GCAYFEFEELCDKP------LGAADYFGLFKIFHTLALEGIPIFGLHNRTAAY-RFV-TLVDVMYENRARLLCTAEGSPF 124 (194)
Q Consensus 53 ~~a~f~F~eLC~~p------~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~ar-RFI-~LID~lYd~~v~L~~~a~~~~~ 124 (194)
.+..+++.+|...- -+..+.+.-..+.+.++|+|+=.-. ..+..+ -++ .+||.-|..+.+.++++..+++
T Consensus 186 ~v~~~~~~~l~~~lk~~~~~~~~~~~l~~l~~~dlLiIDDiG~e~--~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl~~~ 263 (306)
T PRK08939 186 SSTLLHFPEFIRELKNSISDGSVKEKIDAVKEAPVLMLDDIGAEQ--MSSWVRDEVLGVILQYRMQEELPTFFTSNFDFD 263 (306)
T ss_pred CEEEEEHHHHHHHHHHHHhcCcHHHHHHHhcCCCEEEEecCCCcc--ccHHHHHHHHHHHHHHHHHCCCeEEEECCCCHH
Confidence 46677777665431 2345778888999999999995433 333444 243 4568889899999999999999
Q ss_pred hhhcccccchhhhhhccccccccccccccccccCcchhhhhhhhhhHHhhhCch
Q 029356 125 QLFNKIVTISDAQQMAPRTSSRSMRNDEADLCVDNELGFAKDRTISRLTEMNSK 178 (194)
Q Consensus 125 ~Lf~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~Faf~Rt~SRL~EM~s~ 178 (194)
+|..--. .. ..|+.+.-.-+|.++||.++...
T Consensus 264 el~~~~~--------------~~--------~~g~~e~~~a~ri~dRI~~~~~~ 295 (306)
T PRK08939 264 ELEHHLA--------------YT--------QRGEDETWKAARIMERIRYLAKE 295 (306)
T ss_pred HHHHHHh--------------hh--------ccCcchhhHHHHHHHHHHHhcEE
Confidence 9875210 00 00221233457999999988643
No 19
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=89.82 E-value=1.4 Score=35.98 Aligned_cols=71 Identities=17% Similarity=0.247 Sum_probs=53.3
Q ss_pred CCEEEeeHHHHhCCCCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhh
Q 029356 52 NGCAYFEFEELCDKPLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQL 126 (194)
Q Consensus 52 ~~~a~f~F~eLC~~p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~L 126 (194)
..+.+++..+++..+ .+.+...+...+++|++|..++.. .+....+..++|.+++.+..+++++..++.++
T Consensus 67 ~~~~~i~~~~~~~~~---~~~~~~~~~~~lLvIDdi~~l~~~-~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~ 137 (226)
T TIGR03420 67 KSAIYLPLAELAQAD---PEVLEGLEQADLVCLDDVEAIAGQ-PEWQEALFHLYNRVREAGGRLLIAGRAAPAQL 137 (226)
T ss_pred CcEEEEeHHHHHHhH---HHHHhhcccCCEEEEeChhhhcCC-hHHHHHHHHHHHHHHHcCCeEEEECCCChHHC
Confidence 356788888887654 355555567789999999988643 23356777889999999889999998777554
No 20
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=89.11 E-value=1.1 Score=43.81 Aligned_cols=74 Identities=12% Similarity=0.237 Sum_probs=56.0
Q ss_pred CEEEeeHHHHhCCC------CChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhh
Q 029356 53 GCAYFEFEELCDKP------LGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQL 126 (194)
Q Consensus 53 ~~a~f~F~eLC~~p------~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~L 126 (194)
.+.+++..+++..- -....|.+--+.++.++|+||-.+.... ....-|.++|+.+|+++..+++++..+|.+|
T Consensus 346 ~V~Yitaeef~~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l~gke-~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL 424 (617)
T PRK14086 346 RVRYVSSEEFTNEFINSIRDGKGDSFRRRYREMDILLVDDIQFLEDKE-STQEEFFHTFNTLHNANKQIVLSSDRPPKQL 424 (617)
T ss_pred eEEEeeHHHHHHHHHHHHHhccHHHHHHHhhcCCEEEEehhccccCCH-HHHHHHHHHHHHHHhcCCCEEEecCCChHhh
Confidence 56788888877431 1223455556678999999999886433 2346688999999999999999999999887
Q ss_pred h
Q 029356 127 F 127 (194)
Q Consensus 127 f 127 (194)
=
T Consensus 425 ~ 425 (617)
T PRK14086 425 V 425 (617)
T ss_pred h
Confidence 3
No 21
>PRK08084 DNA replication initiation factor; Provisional
Probab=89.00 E-value=1.6 Score=36.81 Aligned_cols=71 Identities=15% Similarity=0.193 Sum_probs=52.7
Q ss_pred CEEEeeHHHHhCCCCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcC-ceEEEEccCChhhhh
Q 029356 53 GCAYFEFEELCDKPLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENR-ARLLCTAEGSPFQLF 127 (194)
Q Consensus 53 ~~a~f~F~eLC~~p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~-v~L~~~a~~~~~~Lf 127 (194)
.+...++++... ...+.+.--++++.++|+||-.+... .....-|-++++.+|+.+ +++++++..||.++-
T Consensus 75 ~v~y~~~~~~~~---~~~~~~~~~~~~dlliiDdi~~~~~~-~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~ 146 (235)
T PRK08084 75 AVGYVPLDKRAW---FVPEVLEGMEQLSLVCIDNIECIAGD-ELWEMAIFDLYNRILESGRTRLLITGDRPPRQLN 146 (235)
T ss_pred eEEEEEHHHHhh---hhHHHHHHhhhCCEEEEeChhhhcCC-HHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcC
Confidence 366778877543 23455555567789999999888643 334456889999999987 589999999998864
No 22
>TIGR00362 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
Probab=86.49 E-value=1.8 Score=39.29 Aligned_cols=75 Identities=13% Similarity=0.250 Sum_probs=56.0
Q ss_pred CCEEEeeHHHHhCC------CCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhh
Q 029356 52 NGCAYFEFEELCDK------PLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQ 125 (194)
Q Consensus 52 ~~~a~f~F~eLC~~------p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~ 125 (194)
..+.+++..++... .-...+|....+..+.++|+||-.+.... ....-|..+++.+|+.+..+++++..+|.+
T Consensus 167 ~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~~-~~~~~l~~~~n~~~~~~~~iiits~~~p~~ 245 (405)
T TIGR00362 167 AKVVYVSSEKFTNDFVNALRNNKMEEFKEKYRSVDLLLIDDIQFLAGKE-RTQEEFFHTFNALHENGKQIVLTSDRPPKE 245 (405)
T ss_pred CcEEEEEHHHHHHHHHHHHHcCCHHHHHHHHHhCCEEEEehhhhhcCCH-HHHHHHHHHHHHHHHCCCCEEEecCCCHHH
Confidence 34677887776542 12344566666778999999999886322 234569999999999999999999999988
Q ss_pred hh
Q 029356 126 LF 127 (194)
Q Consensus 126 Lf 127 (194)
|-
T Consensus 246 l~ 247 (405)
T TIGR00362 246 LP 247 (405)
T ss_pred Hh
Confidence 74
No 23
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=86.20 E-value=2.9 Score=39.09 Aligned_cols=76 Identities=12% Similarity=0.186 Sum_probs=56.1
Q ss_pred CCEEEeeHHHHhCCC------CChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhh
Q 029356 52 NGCAYFEFEELCDKP------LGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQ 125 (194)
Q Consensus 52 ~~~a~f~F~eLC~~p------~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~ 125 (194)
..+..++..++...- -....+...-+..+.++|+||-.+.... ....-|..+++.+|+.+..+++++..+|.+
T Consensus 170 ~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~l~~k~-~~qeelf~l~N~l~~~~k~IIlts~~~p~~ 248 (445)
T PRK12422 170 GKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALFIEDIEVFSGKG-ATQEEFFHTFNSLHTEGKLIVISSTCAPQD 248 (445)
T ss_pred CCEEEeeHHHHHHHHHHHHhcchHHHHHHHcccCCEEEEcchhhhcCCh-hhHHHHHHHHHHHHHCCCcEEEecCCCHHH
Confidence 456777777665321 1223566666788999999998876322 245678899999999999999999999998
Q ss_pred hhc
Q 029356 126 LFN 128 (194)
Q Consensus 126 Lf~ 128 (194)
|..
T Consensus 249 l~~ 251 (445)
T PRK12422 249 LKA 251 (445)
T ss_pred Hhh
Confidence 864
No 24
>COG1485 Predicted ATPase [General function prediction only]
Probab=85.85 E-value=2.3 Score=39.00 Aligned_cols=56 Identities=14% Similarity=0.196 Sum_probs=45.6
Q ss_pred HHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhccc
Q 029356 72 YFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFNKI 130 (194)
Q Consensus 72 Yl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~~~ 130 (194)
=.+|++++++++++..- ..+-..|.-.-.|..+|..+||.|++++..+|++||.+.
T Consensus 124 A~~~~~~~~vLCfDEF~---VtDI~DAMiL~rL~~~Lf~~GV~lvaTSN~~P~~LY~dG 179 (367)
T COG1485 124 ADELAAETRVLCFDEFE---VTDIADAMILGRLLEALFARGVVLVATSNTAPDNLYKDG 179 (367)
T ss_pred HHHHHhcCCEEEeeeee---ecChHHHHHHHHHHHHHHHCCcEEEEeCCCChHHhcccc
Confidence 45688888888887544 334556777778999999999999999999999999864
No 25
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=81.93 E-value=3 Score=38.59 Aligned_cols=74 Identities=12% Similarity=0.238 Sum_probs=55.3
Q ss_pred CEEEeeHHHHhCC------CCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhh
Q 029356 53 GCAYFEFEELCDK------PLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQL 126 (194)
Q Consensus 53 ~~a~f~F~eLC~~------p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~L 126 (194)
.+.+++..++... .....++..--+.++.++|+||-.+... .....-|..++|.+|+.+..+++++..+|.+|
T Consensus 180 ~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~-~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l 258 (450)
T PRK00149 180 KVVYVTSEKFTNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAGK-ERTQEEFFHTFNALHEAGKQIVLTSDRPPKEL 258 (450)
T ss_pred eEEEEEHHHHHHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhhhcCC-HHHHHHHHHHHHHHHHCCCcEEEECCCCHHHH
Confidence 3667777766542 1233456666667899999999988632 22456899999999999999999999999886
Q ss_pred h
Q 029356 127 F 127 (194)
Q Consensus 127 f 127 (194)
-
T Consensus 259 ~ 259 (450)
T PRK00149 259 P 259 (450)
T ss_pred H
Confidence 4
No 26
>PRK09087 hypothetical protein; Validated
Probab=81.81 E-value=3.5 Score=34.83 Aligned_cols=45 Identities=18% Similarity=0.166 Sum_probs=36.6
Q ss_pred CeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhc
Q 029356 80 HTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFN 128 (194)
Q Consensus 80 ~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~ 128 (194)
..++|+||..+... . .-|-++++.+|+++..+++++..+|.++-.
T Consensus 89 ~~l~iDDi~~~~~~--~--~~lf~l~n~~~~~g~~ilits~~~p~~~~~ 133 (226)
T PRK09087 89 GPVLIEDIDAGGFD--E--TGLFHLINSVRQAGTSLLMTSRLWPSSWNV 133 (226)
T ss_pred CeEEEECCCCCCCC--H--HHHHHHHHHHHhCCCeEEEECCCChHHhcc
Confidence 68999999877422 1 339999999999999999999998887643
No 27
>PRK06893 DNA replication initiation factor; Validated
Probab=79.64 E-value=6.1 Score=33.13 Aligned_cols=71 Identities=14% Similarity=0.126 Sum_probs=50.3
Q ss_pred CEEEeeHHHHhCCCCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceE-EEEccCChhhhh
Q 029356 53 GCAYFEFEELCDKPLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARL-LCTAEGSPFQLF 127 (194)
Q Consensus 53 ~~a~f~F~eLC~~p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L-~~~a~~~~~~Lf 127 (194)
++.+++..+.+.. ..+.+.-.++++.++|+||-.+.... ....-+.++++.+|+.+..+ ++++..+|.++-
T Consensus 69 ~~~y~~~~~~~~~---~~~~~~~~~~~dlLilDDi~~~~~~~-~~~~~l~~l~n~~~~~~~~illits~~~p~~l~ 140 (229)
T PRK06893 69 TAIYIPLSKSQYF---SPAVLENLEQQDLVCLDDLQAVIGNE-EWELAIFDLFNRIKEQGKTLLLISADCSPHALS 140 (229)
T ss_pred CeEEeeHHHhhhh---hHHHHhhcccCCEEEEeChhhhcCCh-HHHHHHHHHHHHHHHcCCcEEEEeCCCChHHcc
Confidence 5667777655432 12445555678999999998876432 34456999999999988664 678888888764
No 28
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=74.43 E-value=9 Score=35.81 Aligned_cols=74 Identities=16% Similarity=0.269 Sum_probs=53.3
Q ss_pred CCEEEeeHHHHhCCCCC--------hhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCCh
Q 029356 52 NGCAYFEFEELCDKPLG--------AADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSP 123 (194)
Q Consensus 52 ~~~a~f~F~eLC~~p~~--------a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~ 123 (194)
..++.++..++...... ..++..-....+.++|+||-.+.. ......-|-++++.+|+++..+++++..+|
T Consensus 172 ~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDDiq~l~~-k~~~~e~lf~l~N~~~~~~k~iIltsd~~P 250 (450)
T PRK14087 172 LKVSYMSGDEFARKAVDILQKTHKEIEQFKNEICQNDVLIIDDVQFLSY-KEKTNEIFFTIFNNFIENDKQLFFSSDKSP 250 (450)
T ss_pred CeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHhccCCEEEEeccccccC-CHHHHHHHHHHHHHHHHcCCcEEEECCCCH
Confidence 35677777776654211 123444456788999999987753 223445799999999999999999999999
Q ss_pred hhh
Q 029356 124 FQL 126 (194)
Q Consensus 124 ~~L 126 (194)
.++
T Consensus 251 ~~l 253 (450)
T PRK14087 251 ELL 253 (450)
T ss_pred HHH
Confidence 776
No 29
>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H.
Probab=70.54 E-value=6.9 Score=29.88 Aligned_cols=55 Identities=20% Similarity=0.195 Sum_probs=40.4
Q ss_pred hhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhc
Q 029356 70 ADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFN 128 (194)
Q Consensus 70 ~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~ 128 (194)
.|.+.-+ .=.|++|.+|..|+ .+...++..+++..=..+++|++++..+++++..
T Consensus 62 ~~~l~~a-~~gtL~l~~i~~L~---~~~Q~~L~~~l~~~~~~~~RlI~ss~~~l~~l~~ 116 (138)
T PF14532_consen 62 AELLEQA-KGGTLYLKNIDRLS---PEAQRRLLDLLKRQERSNVRLIASSSQDLEELVE 116 (138)
T ss_dssp HHHHHHC-TTSEEEEECGCCS----HHHHHHHHHHHHHCTTTTSEEEEEECC-CCCHHH
T ss_pred HHHHHHc-CCCEEEECChHHCC---HHHHHHHHHHHHhcCCCCeEEEEEeCCCHHHHhh
Confidence 4544444 55699999999986 5566677777776336789999999999999875
No 30
>PRK06620 hypothetical protein; Validated
Probab=70.05 E-value=10 Score=31.69 Aligned_cols=44 Identities=14% Similarity=0.306 Sum_probs=36.4
Q ss_pred hccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhh
Q 029356 77 KIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQL 126 (194)
Q Consensus 77 ~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~L 126 (194)
+..+.++|+||-.+. -.-|-++++.++|.|..+++++..+|..+
T Consensus 84 ~~~d~lliDdi~~~~------~~~lf~l~N~~~e~g~~ilits~~~p~~l 127 (214)
T PRK06620 84 EKYNAFIIEDIENWQ------EPALLHIFNIINEKQKYLLLTSSDKSRNF 127 (214)
T ss_pred hcCCEEEEeccccch------HHHHHHHHHHHHhcCCEEEEEcCCCcccc
Confidence 467899999998552 13577999999999999999999999864
No 31
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=65.85 E-value=12 Score=34.93 Aligned_cols=50 Identities=20% Similarity=0.342 Sum_probs=43.5
Q ss_pred ccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhc
Q 029356 78 IFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFN 128 (194)
Q Consensus 78 ~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~ 128 (194)
..+.++|+||-.+.....- ..-|-+++..+++.+-.|++++..+|.+|=.
T Consensus 175 ~~dlllIDDiq~l~gk~~~-qeefFh~FN~l~~~~kqIvltsdr~P~~l~~ 224 (408)
T COG0593 175 SLDLLLIDDIQFLAGKERT-QEEFFHTFNALLENGKQIVLTSDRPPKELNG 224 (408)
T ss_pred ccCeeeechHhHhcCChhH-HHHHHHHHHHHHhcCCEEEEEcCCCchhhcc
Confidence 7899999999999854433 6778999999999999999999999998764
No 32
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=61.00 E-value=16 Score=34.01 Aligned_cols=73 Identities=8% Similarity=0.167 Sum_probs=49.8
Q ss_pred CEEEeeHHHHhCCC------CChhhHHHHh-hccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhh
Q 029356 53 GCAYFEFEELCDKP------LGAADYFGLF-KIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQ 125 (194)
Q Consensus 53 ~~a~f~F~eLC~~p------~~a~DYl~La-~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~ 125 (194)
.+.+++..++.... -...++..-- ...+.++|+++-.+... ......|..+++.+|+.+..+++++..+|.+
T Consensus 162 ~v~yi~~~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~~-~~~q~elf~~~n~l~~~~k~iIitsd~~p~~ 240 (440)
T PRK14088 162 RVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQFLIGK-TGVQTELFHTFNELHDSGKQIVICSDREPQK 240 (440)
T ss_pred eEEEEEHHHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechhhhcCc-HHHHHHHHHHHHHHHHcCCeEEEECCCCHHH
Confidence 56777777655431 1222343322 25789999999877422 1233568899999999999999999888887
Q ss_pred h
Q 029356 126 L 126 (194)
Q Consensus 126 L 126 (194)
|
T Consensus 241 l 241 (440)
T PRK14088 241 L 241 (440)
T ss_pred H
Confidence 5
No 33
>PF10298 WhiA_N: WhiA N-terminal LAGLIDADG-like domain; InterPro: IPR018478 This entry represents the N-terminal domain of sporulation factor WhiA []. This domain is related to the LAGLIDADG homing endonuclease domain while the C-terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain [].; PDB: 3HYI_A 3HYJ_D.
Probab=52.86 E-value=8.3 Score=27.60 Aligned_cols=34 Identities=12% Similarity=0.172 Sum_probs=24.9
Q ss_pred CCCCchHHHHHHHHHHHHHhcCceEEEEccCChh
Q 029356 91 GLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPF 124 (194)
Q Consensus 91 ~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~ 124 (194)
..++...|||+.+||-.+|+-++.+.+.-...+.
T Consensus 30 ~ten~~vARri~~llk~~f~i~~ei~v~~~~~l~ 63 (86)
T PF10298_consen 30 STENAAVARRIYSLLKKLFDIDPEISVRRSRNLK 63 (86)
T ss_dssp EES-HHHHHHHHHHHHHTT--EEEEEEEE-SSSB
T ss_pred EeCCHHHHHHHHHHHHHHhCCCeEEEEecCCCCC
Confidence 3568889999999999999999999887654444
No 34
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=41.56 E-value=62 Score=26.50 Aligned_cols=46 Identities=11% Similarity=0.137 Sum_probs=33.9
Q ss_pred HhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCce-EEEEccCCh
Q 029356 75 LFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRAR-LLCTAEGSP 123 (194)
Q Consensus 75 La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~-L~~~a~~~~ 123 (194)
......+++|+||..++. .....+..+++.+++++.. +++++..++
T Consensus 87 ~~~~~~~liiDdi~~l~~---~~~~~L~~~~~~~~~~~~~~vl~~~~~~~ 133 (227)
T PRK08903 87 FDPEAELYAVDDVERLDD---AQQIALFNLFNRVRAHGQGALLVAGPAAP 133 (227)
T ss_pred hcccCCEEEEeChhhcCc---hHHHHHHHHHHHHHHcCCcEEEEeCCCCH
Confidence 345678999999988763 4456678889999998874 666665554
No 35
>TIGR01618 phage_P_loop phage nucleotide-binding protein. This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.
Probab=41.52 E-value=25 Score=29.90 Aligned_cols=51 Identities=16% Similarity=0.193 Sum_probs=38.0
Q ss_pred hccCeEEEcCCCCCCC---------------C---CchHHHHHHHHHHHHHhcCceEEEEccCChhhhh
Q 029356 77 KIFHTLALEGIPIFGL---------------H---NRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLF 127 (194)
Q Consensus 77 ~~f~ti~I~~VP~l~~---------------~---~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf 127 (194)
..|++|+|++|-.|.. . -.....+|+.++..|++.+..++++|....++..
T Consensus 80 ~~ydtVVIDsI~~l~~~~~~~~~r~~k~~~~~~~~yg~~~~~fl~~l~~L~~~g~nII~tAhe~~~~~~ 148 (220)
T TIGR01618 80 VKYDNIVIDNISALQNLWLENIGRAAKNGQPELQHYQKLDLWFLDLLTVLKESNKNIYATAWELTNQSS 148 (220)
T ss_pred ccCCEEEEecHHHHHHHHHHHHhhhcCCCCcccccHHHHHHHHHHHHHHHHhCCCcEEEEEeecccccc
Confidence 4599999998876543 0 0124568999999999999999999976554433
No 36
>cd03768 SR_ResInv Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some
Probab=32.73 E-value=83 Score=23.12 Aligned_cols=43 Identities=14% Similarity=0.166 Sum_probs=33.1
Q ss_pred HHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEE
Q 029356 72 YFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCT 118 (194)
Q Consensus 72 Yl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~ 118 (194)
.++.++.+++|+|.++-.|+... .-++.+++.|=++||+|++.
T Consensus 48 ll~~~~~~d~lvv~~~dRl~R~~----~e~~~~~~~l~~~gi~l~~~ 90 (126)
T cd03768 48 LLEDLREGDTLVVTKLDRLGRST----KDLLEIVEELREKGVSLRSL 90 (126)
T ss_pred HHHhCcCCCEEEEEEcchhcCcH----HHHHHHHHHHHHCCCEEEEe
Confidence 34455589999999999987433 33667777888899999986
No 37
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=32.18 E-value=25 Score=33.05 Aligned_cols=67 Identities=21% Similarity=0.350 Sum_probs=50.7
Q ss_pred HHHhCCCCChh---hHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhc---------CceEEEEccCChhhhh
Q 029356 60 EELCDKPLGAA---DYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYEN---------RARLLCTAEGSPFQLF 127 (194)
Q Consensus 60 ~eLC~~p~~a~---DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~---------~v~L~~~a~~~~~~Lf 127 (194)
.||+|..-|.. -+++.|.. .||+++.|-.|+..-+....||.+ |-.+-+ +|+++|+..+++.++.
T Consensus 273 sElFG~apg~~gk~GffE~Ang-GTVlLDeIgEmSp~lQaKLLRFL~--DGtFRRVGee~Ev~vdVRVIcatq~nL~~lv 349 (511)
T COG3283 273 SELFGHAPGDEGKKGFFEQANG-GTVLLDEIGEMSPRLQAKLLRFLN--DGTFRRVGEDHEVHVDVRVICATQVNLVELV 349 (511)
T ss_pred HHHhcCCCCCCCccchhhhccC-CeEEeehhhhcCHHHHHHHHHHhc--CCceeecCCcceEEEEEEEEecccccHHHHH
Confidence 67888755444 35555543 599999999999888888899965 555433 6899999999998876
Q ss_pred cc
Q 029356 128 NK 129 (194)
Q Consensus 128 ~~ 129 (194)
..
T Consensus 350 ~~ 351 (511)
T COG3283 350 QK 351 (511)
T ss_pred hc
Confidence 53
No 38
>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....
Probab=30.45 E-value=43 Score=26.91 Aligned_cols=65 Identities=15% Similarity=0.141 Sum_probs=43.9
Q ss_pred HHHhCCCCCh--------hhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHH----------HhcCceEEEEccC
Q 029356 60 EELCDKPLGA--------ADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVM----------YENRARLLCTAEG 121 (194)
Q Consensus 60 ~eLC~~p~~a--------~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~l----------Yd~~v~L~~~a~~ 121 (194)
.+|+|...++ .-.++.|+ --|+||++|..|+ .+...+...+|+.= ...+++|++++..
T Consensus 68 ~~LFG~~~~~~~~~~~~~~G~l~~A~-~GtL~Ld~I~~L~---~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~ 143 (168)
T PF00158_consen 68 SELFGHEKGAFTGARSDKKGLLEQAN-GGTLFLDEIEDLP---PELQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSK 143 (168)
T ss_dssp HHHHEBCSSSSTTTSSEBEHHHHHTT-TSEEEEETGGGS----HHHHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS
T ss_pred hhhhccccccccccccccCCceeecc-ceEEeecchhhhH---HHHHHHHHHHHhhchhccccccccccccceEEeecCc
Confidence 5788765432 23666664 4799999999996 45566667777742 2338999999999
Q ss_pred Chhhhhc
Q 029356 122 SPFQLFN 128 (194)
Q Consensus 122 ~~~~Lf~ 128 (194)
+++++..
T Consensus 144 ~l~~~v~ 150 (168)
T PF00158_consen 144 DLEELVE 150 (168)
T ss_dssp -HHHHHH
T ss_pred CHHHHHH
Confidence 9999775
No 39
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=29.38 E-value=88 Score=24.04 Aligned_cols=40 Identities=5% Similarity=0.229 Sum_probs=32.0
Q ss_pred hhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhc-CceEEEEc
Q 029356 76 FKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYEN-RARLLCTA 119 (194)
Q Consensus 76 a~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~-~v~L~~~a 119 (194)
...+++|++..+-+|+.. ..-++.+++.|-++ ||+|++..
T Consensus 66 ~g~vd~vvv~~ldRl~R~----~~d~~~~~~~l~~~~gv~l~~~~ 106 (140)
T cd03770 66 AGKIDIVIVKDMSRLGRN----YLKVGLYMEILFPKKGVRFIAIN 106 (140)
T ss_pred cCCCCEEEEeccchhccC----HHHHHHHHHHHHhhcCcEEEEec
Confidence 357899999999988744 34477889999887 99998865
No 40
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=27.82 E-value=86 Score=22.52 Aligned_cols=57 Identities=18% Similarity=0.207 Sum_probs=40.9
Q ss_pred hHHHHhhcc---CeEEEcCCCCCCCCC--------chHHHHHHHHHHHHHhc--CceEEEEccCChhhhhc
Q 029356 71 DYFGLFKIF---HTLALEGIPIFGLHN--------RTAAYRFVTLVDVMYEN--RARLLCTAEGSPFQLFN 128 (194)
Q Consensus 71 DYl~La~~f---~ti~I~~VP~l~~~~--------~d~arRFI~LID~lYd~--~v~L~~~a~~~~~~Lf~ 128 (194)
+++.-++.. ..++|+++-.+.... ......+..++|..... ++.+++++.. ++.+..
T Consensus 48 ~~~~~~~~~~~~~vl~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~-~~~i~~ 117 (132)
T PF00004_consen 48 DFFKKAKKSAKPCVLFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNS-PDKIDP 117 (132)
T ss_dssp HHHHHHHHTSTSEEEEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESS-GGGSCH
T ss_pred cccccccccccceeeeeccchhcccccccccccccccccceeeecccccccccccceeEEeeCC-hhhCCH
Confidence 455555433 699999999988655 55678899999999884 6777777765 555543
No 41
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=27.14 E-value=1.1e+02 Score=24.81 Aligned_cols=44 Identities=7% Similarity=0.177 Sum_probs=34.7
Q ss_pred HHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEc
Q 029356 72 YFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTA 119 (194)
Q Consensus 72 Yl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a 119 (194)
.|+-++..++|+|..+-+|+.. ..=++.+++.|.++||.|++..
T Consensus 55 ll~~~~~gd~lvv~~ldRl~R~----~~d~~~~~~~l~~~gv~l~~~~ 98 (200)
T PRK13413 55 LLKKMRKGDILIVSELSRLGRN----LMEIMSILNICMEKEVIVYTIK 98 (200)
T ss_pred HHHHHhCCCEEEEEeCchhcCC----HHHHHHHHHHHHHCCCEEEEEe
Confidence 3445666799999999999854 3447788999999999998764
No 42
>cd01741 GATase1_1 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. This group contains a subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the glutaminase active site. In this subgroup this triad is conserved. GATase activity can be found in a range of biosynthetic enzymes, including: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase , anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. Glutamine amidotransferase (GATase) domains can occur either as single polypeptides, as in glutamine
Probab=27.01 E-value=1.5e+02 Score=23.52 Aligned_cols=44 Identities=11% Similarity=0.101 Sum_probs=34.7
Q ss_pred hhccCeEEEcCCCCCC-CCCchHHHHHHHHHHHHHhcCceEEEEc
Q 029356 76 FKIFHTLALEGIPIFG-LHNRTAAYRFVTLVDVMYENRARLLCTA 119 (194)
Q Consensus 76 a~~f~ti~I~~VP~l~-~~~~d~arRFI~LID~lYd~~v~L~~~a 119 (194)
.+.|+.|+|.+=|.-. ....+..+....+|+.+++++++++-..
T Consensus 44 ~~~~dgvil~Gg~~~~~~~~~~~~~~~~~~i~~~~~~~~pilgiC 88 (188)
T cd01741 44 LDDYDGLVILGGPMSVDEDDYPWLKKLKELIRQALAAGKPVLGIC 88 (188)
T ss_pred cccCCEEEECCCCccCCccCChHHHHHHHHHHHHHHCCCCEEEEC
Confidence 4689999999988654 3455667889999999999999887443
No 43
>KOG2383 consensus Predicted ATPase [General function prediction only]
Probab=26.86 E-value=95 Score=29.48 Aligned_cols=53 Identities=15% Similarity=0.265 Sum_probs=34.7
Q ss_pred HHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhcc
Q 029356 74 GLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFNK 129 (194)
Q Consensus 74 ~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~~ 129 (194)
+||+.=..++.+..-+-+ -..|.-.=-|.-.|..+||-|++++..+|++||..
T Consensus 189 eIa~ea~lLCFDEfQVTD---VADAmiL~rLf~~Lf~~GvVlvATSNR~P~dLYkn 241 (467)
T KOG2383|consen 189 EIAEEAILLCFDEFQVTD---VADAMILKRLFEHLFKNGVVLVATSNRAPEDLYKN 241 (467)
T ss_pred HHhhhceeeeechhhhhh---HHHHHHHHHHHHHHHhCCeEEEEeCCCChHHHhhc
Confidence 355554555554443322 22333333455678889999999999999999975
No 44
>PRK05665 amidotransferase; Provisional
Probab=26.69 E-value=1.4e+02 Score=25.42 Aligned_cols=51 Identities=18% Similarity=0.206 Sum_probs=39.6
Q ss_pred hccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEE--EEccCChhhhh
Q 029356 77 KIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLL--CTAEGSPFQLF 127 (194)
Q Consensus 77 ~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~--~~a~~~~~~Lf 127 (194)
+.|+-|+|+|=|.-.........+...+|-.+|+++++++ |.+..-+..-+
T Consensus 56 ~~~dgiiitGs~~~v~~~~pwi~~l~~~i~~~~~~~~PilGIC~GhQlla~Al 108 (240)
T PRK05665 56 EKFDAYLVTGSKADSFGTDPWIQTLKTYLLKLYERGDKLLGVCFGHQLLALLL 108 (240)
T ss_pred ccCCEEEECCCCCCccccchHHHHHHHHHHHHHhcCCCEEEEeHHHHHHHHHh
Confidence 3699999999998776677788999999999999999886 44443333333
No 45
>KOG3889 consensus Predicted gamma-butyrobetaine,2-oxoglutarate dioxygenase [Lipid transport and metabolism]
Probab=25.52 E-value=50 Score=29.87 Aligned_cols=61 Identities=10% Similarity=0.207 Sum_probs=52.5
Q ss_pred cCCEEEeeHHHHhCCCCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhc
Q 029356 51 ANGCAYFEFEELCDKPLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYEN 111 (194)
Q Consensus 51 ~~~~a~f~F~eLC~~p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~ 111 (194)
..++.+|+--.+-....+..-++.=.-+|..+||+|||.-.+...-.++|..-+-|-+|-+
T Consensus 109 ~erhlrfd~p~~~~s~~~l~sf~~nlv~YGi~fvd~V~pT~e~TEkl~~r~~pv~~TffG~ 169 (371)
T KOG3889|consen 109 KERHLRFDVPRISKSTLSLQSFSKNLVKYGIIFVDGVEPTSEATEKLCQRLVPVHDTFFGQ 169 (371)
T ss_pred hccccCCCchhhhhccHHHHHHHHHHHheeEEEEcCCCchhHHHHHHHHHhhHHHHhhhhe
Confidence 3566788888888888888889998999999999999998877778899999999999854
No 46
>PF05729 NACHT: NACHT domain
Probab=25.45 E-value=1.1e+02 Score=22.86 Aligned_cols=40 Identities=18% Similarity=0.375 Sum_probs=28.0
Q ss_pred eEEEcCCCCCCCCCch-HHHHHHHHHHHHHhc----CceEEEEcc
Q 029356 81 TLALEGIPIFGLHNRT-AAYRFVTLVDVMYEN----RARLLCTAE 120 (194)
Q Consensus 81 ti~I~~VP~l~~~~~d-~arRFI~LID~lYd~----~v~L~~~a~ 120 (194)
.++|+|+..+...... ...++..++..+... ++++++++.
T Consensus 84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r 128 (166)
T PF05729_consen 84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSR 128 (166)
T ss_pred EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEc
Confidence 6889999999875443 455666555555444 899998875
No 47
>PF01039 Carboxyl_trans: Carboxyl transferase domain; InterPro: IPR000022 Members in this domain include biotin dependent carboxylases [, ]. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxo acid as the acceptor molecule of carbon dioxide. All of the members in this family utilise acyl-CoA as the acceptor molecule.; GO: 0016874 ligase activity; PDB: 2F9Y_B 1XO6_B 1XNV_B 3MFM_C 3IBB_A 1XNW_F 3IAV_B 1XNY_A 3IB9_A 3U9S_F ....
Probab=24.77 E-value=57 Score=30.88 Aligned_cols=73 Identities=15% Similarity=0.126 Sum_probs=47.4
Q ss_pred ecCeeeEeccccCCE--EEeeHHHHhCCCCChhhHHHHhhccC--eEEEcCCCCCCCCC----chHHHHHHHHHHHHHhc
Q 029356 40 VMGRKLQVPLGANGC--AYFEFEELCDKPLGAADYFGLFKIFH--TLALEGIPIFGLHN----RTAAYRFVTLVDVMYEN 111 (194)
Q Consensus 40 v~gR~i~v~~~~~~~--a~f~F~eLC~~p~~a~DYl~La~~f~--ti~I~~VP~l~~~~----~d~arRFI~LID~lYd~ 111 (194)
++|+++=|.....+. -.++ .+ ...-++.++.+|++|+ .|+|.|+|-+.... ...++.-..+++.+.+.
T Consensus 291 l~G~pVGiian~~~~~~G~~~-~~---~a~K~arfi~lcd~~~iPlv~l~dtpGf~~g~~~E~~g~~~~ga~~~~a~~~~ 366 (493)
T PF01039_consen 291 LGGRPVGIIANNPRQRAGALD-PD---GARKAARFIRLCDAFNIPLVTLVDTPGFMPGPEAERAGIIRAGARLLYALAEA 366 (493)
T ss_dssp ETTEEEEEEEE-TTCGGGEB--HH---HHHHHHHHHHHHHHTT--EEEEEEECEB--SHHHHHTTHHHHHHHHHHHHHHH
T ss_pred eCCcceEEEEeccccccccCC-hH---HHHHHHHHHHHHHhhCCceEEEeecccccccchhhhcchHHHHHHHHHHHHcC
Confidence 467887776665320 0111 11 1244678999999998 79999999998643 33567788999999999
Q ss_pred CceEE
Q 029356 112 RARLL 116 (194)
Q Consensus 112 ~v~L~ 116 (194)
.|+.+
T Consensus 367 ~vP~i 371 (493)
T PF01039_consen 367 TVPKI 371 (493)
T ss_dssp -S-EE
T ss_pred CCCEE
Confidence 98876
No 48
>cd01120 RecA-like_NTPases RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Probab=24.72 E-value=1.2e+02 Score=22.30 Aligned_cols=55 Identities=5% Similarity=-0.072 Sum_probs=39.1
Q ss_pred hHHHHhhccCeEEEcCCCCCCCC--------CchHHHHHHHHHHHHHhcCceEEEEccCChhh
Q 029356 71 DYFGLFKIFHTLALEGIPIFGLH--------NRTAAYRFVTLVDVMYENRARLLCTAEGSPFQ 125 (194)
Q Consensus 71 DYl~La~~f~ti~I~~VP~l~~~--------~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~ 125 (194)
.|++....++.++|+.+..+... .....+.+..|.+.+-+.++.+++....+-..
T Consensus 78 ~~~~~~~~~~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~~~~~~~~ 140 (165)
T cd01120 78 ERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSGD 140 (165)
T ss_pred HHHHhCCCCEEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEEEecCCcc
Confidence 57778888899999999976422 22234455567777777799999988866544
No 49
>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....
Probab=23.92 E-value=1e+02 Score=25.35 Aligned_cols=50 Identities=10% Similarity=0.086 Sum_probs=40.0
Q ss_pred hccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhh
Q 029356 77 KIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLF 127 (194)
Q Consensus 77 ~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf 127 (194)
+.++.|+|+ -|-.+..+.+....+-.+++.+....+-|+++|....+.+-
T Consensus 82 ~~~D~vlID-T~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~ 131 (196)
T PF00448_consen 82 KGYDLVLID-TAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLE 131 (196)
T ss_dssp TTSSEEEEE-E-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHH
T ss_pred cCCCEEEEe-cCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHH
Confidence 348888887 67777777778888999999998888999999987776654
No 50
>PF12149 HSV_VP16_C: Herpes simplex virus virion protein 16 C terminal; InterPro: IPR021051 This domain is about 30 amino acids in length. It is found in association with PF02232 from PFAM. This domain is found in the C-terminal region of the HSV virion protein 16 (alpha-TIF). This protein is a transcription promoter. The C-terminal domain is the carboxyl subdomain of the acidic transcriptional activation domain. The protein binds to DNA binding proteins to carry out its function. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc. Alpha-TIF (VP16) from Herpes Simplex virus is an essential tegument protein involved in the transcriptional activation of viral immediate early (IE) promoters (alpha genes) during the lytic phase of viral infection. VP16 associates with cellular transcription factors to enhance transcription rates, including the general transcription factor TFIIB and the transcriptional coactivator PC4. The N-terminal residues of VP16 confer specificity for the IE genes, while the C-terminal residues are responsible for transcriptional activation. Within the C-terminal region are two activation regions that can independently and cooperatively activate transcription []. VP16 forms a transcriptional regulatory complex with two cellular proteins, the POU-domain transcription factor Oct-1 and the cell-proliferation factor HCF-1 []. VP16 is an alpha/beta protein with an unusual fold. Other transcription factors may have a similar topology.; PDB: 2K2U_B 2PHG_B 2PHE_C.
Probab=23.55 E-value=21 Score=20.95 Aligned_cols=26 Identities=38% Similarity=0.712 Sum_probs=20.4
Q ss_pred eccccCCEEEeeHHHHhCCCCChhhH
Q 029356 47 VPLGANGCAYFEFEELCDKPLGAADY 72 (194)
Q Consensus 47 v~~~~~~~a~f~F~eLC~~p~~a~DY 72 (194)
++..+-.++-|.|++.....+|..||
T Consensus 3 ~~ygald~adfefeqmftdalgid~f 28 (30)
T PF12149_consen 3 APYGALDMADFEFEQMFTDALGIDEF 28 (30)
T ss_dssp -TTCCCTCCCCCHHCCCCCCCCTCCC
T ss_pred cccccchhhhHHHHHHHhhhhCcccc
Confidence 34455677889999999999998876
No 51
>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.
Probab=21.40 E-value=1.1e+02 Score=24.72 Aligned_cols=52 Identities=17% Similarity=0.111 Sum_probs=39.8
Q ss_pred hhccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhhc
Q 029356 76 FKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLFN 128 (194)
Q Consensus 76 a~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf~ 128 (194)
...|+.++++.|-..-....=...-++.+|+.-++ ++.|++++..+|++|..
T Consensus 93 ~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~-~~evIlTGr~~p~~l~e 144 (159)
T cd00561 93 SGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPE-DLELVLTGRNAPKELIE 144 (159)
T ss_pred cCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCC-CCEEEEECCCCCHHHHH
Confidence 35799999998876533333344557778888887 68999999999999986
No 52
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=20.64 E-value=1.8e+02 Score=28.49 Aligned_cols=52 Identities=13% Similarity=0.248 Sum_probs=36.3
Q ss_pred hHHHHhhccCeEEEcCCCCCCCCCchHHHHHHHHHHHH-H---------hcCceEEEEccCChhhh
Q 029356 71 DYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVTLVDVM-Y---------ENRARLLCTAEGSPFQL 126 (194)
Q Consensus 71 DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~LID~l-Y---------d~~v~L~~~a~~~~~~L 126 (194)
..++.|+. .|+||++|..|+.. ...++..+|+.- | ..++++++++..++.++
T Consensus 464 g~le~a~~-GtL~Ldei~~L~~~---~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~l~~~ 525 (686)
T PRK15429 464 GRFELADK-SSLFLDEVGDMPLE---LQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKM 525 (686)
T ss_pred hHHHhcCC-CeEEEechhhCCHH---HHHHHHHHHHhCCEEeCCCCCcccceEEEEEeCCCCHHHH
Confidence 45666665 79999999998744 444555555542 1 24789999999888654
No 53
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=20.59 E-value=2e+02 Score=21.15 Aligned_cols=38 Identities=8% Similarity=0.171 Sum_probs=29.2
Q ss_pred ccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEc
Q 029356 78 IFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTA 119 (194)
Q Consensus 78 ~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a 119 (194)
.+++|+|.++-.|+.... ++ +.++..|-.+|++|++..
T Consensus 65 ~~d~ivv~~~~Rl~R~~~-~~---~~~~~~l~~~gi~l~~~~ 102 (137)
T cd00338 65 KIDVVLVEKLDRLSRNLV-DL---LELLELLEAHGVRVVTAD 102 (137)
T ss_pred CCCEEEEEecchhhCCHH-HH---HHHHHHHHHCCCEEEEec
Confidence 899999999999986443 33 345566777899999876
No 54
>PRK06490 glutamine amidotransferase; Provisional
Probab=20.54 E-value=2.2e+02 Score=24.22 Aligned_cols=40 Identities=13% Similarity=0.080 Sum_probs=30.5
Q ss_pred hccCeEEEcCCCCCCCCCchHHHHHHHHHHHHHhcCceEE
Q 029356 77 KIFHTLALEGIPIFGLHNRTAAYRFVTLVDVMYENRARLL 116 (194)
Q Consensus 77 ~~f~ti~I~~VP~l~~~~~d~arRFI~LID~lYd~~v~L~ 116 (194)
+.|+.|+|++=|.-..+..+...+.+.+|..+++.+++++
T Consensus 51 ~~~dgvii~Ggp~~~~d~~~wi~~~~~~i~~~~~~~~PvL 90 (239)
T PRK06490 51 EDHAGAVIFGGPMSANDPDDFIRREIDWISVPLKENKPFL 90 (239)
T ss_pred cccCEEEEECCCCCCCCCchHHHHHHHHHHHHHHCCCCEE
Confidence 4588899988775444455566778889999999998876
No 55
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=20.42 E-value=3.3e+02 Score=21.34 Aligned_cols=54 Identities=17% Similarity=0.339 Sum_probs=36.3
Q ss_pred eHHHHhCCCCChhhHHHHhhccCeEEEc--CCCCCCCCCchHHHHHHHHHHHHHhcCceEEEEccCChhhhh
Q 029356 58 EFEELCDKPLGAADYFGLFKIFHTLALE--GIPIFGLHNRTAAYRFVTLVDVMYENRARLLCTAEGSPFQLF 127 (194)
Q Consensus 58 ~F~eLC~~p~~a~DYl~La~~f~ti~I~--~VP~l~~~~~d~arRFI~LID~lYd~~v~L~~~a~~~~~~Lf 127 (194)
.|..||...... ..++++|+ |.| ....|+|+..+.... +++++......|.-+-
T Consensus 11 vf~~L~~~~~~~--------~~~~ilit~kG~P------~~~tr~~l~~L~~~~--~~~~~~l~D~DP~Gi~ 66 (160)
T cd00223 11 VFQRLIEEGFHE--------RNNCILITGKGYP------DRATRRFLRRLHEEL--DLPVYILVDGDPYGIS 66 (160)
T ss_pred HHHHHHHcCccc--------cCCEEEEEcCCcC------CHHHHHHHHHHHHhh--CCCEEEEECCCcchhh
Confidence 377787753221 44556655 444 356799999887665 8999998888886543
No 56
>TIGR02410 carnitine_TMLD trimethyllysine dioxygenase. Members of this family with known function act as trimethyllysine dioxygenase, an enzyme in the pathway for carnitine biosynthesis from lysine. This enzyme is homologous to gamma-butyrobetaine,2-oxoglutarate dioxygenase, which catalyzes the last step in carnitine biosynthesis. Members of this family appear to be eukaryotic only.
Probab=20.31 E-value=59 Score=29.32 Aligned_cols=50 Identities=8% Similarity=0.057 Sum_probs=36.9
Q ss_pred EEEeeHHHHhCC-CCChhhHHHHhhccCeEEEcCCCCCCCCCchHHHHHHH
Q 029356 54 CAYFEFEELCDK-PLGAADYFGLFKIFHTLALEGIPIFGLHNRTAAYRFVT 103 (194)
Q Consensus 54 ~a~f~F~eLC~~-p~~a~DYl~La~~f~ti~I~~VP~l~~~~~d~arRFI~ 103 (194)
..+|+|+++... .-...+.+....++..++|.|+|.=......-++||--
T Consensus 101 ~~~~~~~~~~~~~d~~l~~~l~~l~~~G~v~~~g~~~~~~~~~~~a~riG~ 151 (362)
T TIGR02410 101 DPSVHFKTTYDHTDSTLKSFSKNIYKYGFTFVDNVPVTPEATEKLCERISI 151 (362)
T ss_pred CCceeHHHHhccCHHHHHHHHHHHHhhCEEEEcCCCCCHHHHHHHHHHhcc
Confidence 467899999985 66788899999999999999999622223344445443
No 57
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=20.31 E-value=87 Score=28.82 Aligned_cols=37 Identities=32% Similarity=0.443 Sum_probs=21.1
Q ss_pred cceeeCCcchHHHHHHHHHHhhCCCCCCCceeEEecCeeeEecccc
Q 029356 6 QGFYFVGKGSSEVMKQKFRDLIGEHEAGPQEVEVVMGRKLQVPLGA 51 (194)
Q Consensus 6 ~~~y~~~~~~~~~l~~~f~~l~~~~~~~~~~i~vv~gR~i~v~~~~ 51 (194)
+++=|+..++.+--++.=.++-| .+|.||+|+|..+.
T Consensus 136 KGFGFVTmen~~dadRARa~LHg---------t~VEGRkIEVn~AT 172 (376)
T KOG0125|consen 136 KGFGFVTMENPADADRARAELHG---------TVVEGRKIEVNNAT 172 (376)
T ss_pred CccceEEecChhhHHHHHHHhhc---------ceeeceEEEEeccc
Confidence 34555555554444444444444 23579999987765
Done!