Query gi|254780800|ref|YP_003065213.1| hypothetical protein CLIBASIA_03455 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 192
No_of_seqs 115 out of 360
Neff 3.3
Searched_HMMs 39220
Date Sun May 29 19:03:20 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780800.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3820 Uncharacterized protei 100.0 0 0 627.3 7.8 189 1-191 1-190 (230)
2 pfam06242 DUF1013 Protein of u 100.0 0 0 505.1 11.2 140 35-174 1-140 (141)
3 TIGR00938 thrB_alt homoserine 71.0 2.3 6E-05 24.1 1.6 108 19-135 5-130 (312)
4 smart00347 HTH_MARR helix_turn 60.5 9.8 0.00025 20.4 3.1 47 107-153 14-63 (101)
5 pfam01047 MarR MarR family. Th 56.2 13 0.00032 19.7 3.1 34 107-140 7-40 (59)
6 PRK09954 hypothetical protein; 44.8 28 0.00072 17.6 3.4 12 57-68 170-181 (362)
7 pfam02787 CPSase_L_D3 Carbamoy 44.2 15 0.00038 19.3 1.9 24 117-140 71-94 (122)
8 smart00760 Bac_DnaA_C Bacteria 43.4 15 0.00038 19.3 1.8 22 107-128 35-56 (60)
9 COG4977 Transcriptional regula 42.5 18 0.00046 18.7 2.1 18 118-135 237-254 (328)
10 TIGR01369 CPSaseII_lrg carbamo 41.6 18 0.00046 18.7 2.0 38 103-141 489-532 (1089)
11 cd05131 RasGAP_IQGAP2 IQGAP2 i 40.3 22 0.00056 18.2 2.3 48 102-159 142-197 (339)
12 PRK12520 RNA polymerase sigma 37.6 31 0.0008 17.3 2.7 33 108-140 138-170 (191)
13 pfam11762 Arabinose_Iso_C L-ar 37.3 16 0.0004 19.1 1.1 23 16-38 91-113 (115)
14 KOG0237 consensus 37.0 15 0.00038 19.2 1.0 44 15-58 46-102 (788)
15 pfam03376 Adeno_E3B Adenovirus 36.2 16 0.0004 19.1 1.0 18 111-128 72-89 (90)
16 cd00015 ALBUMIN Albumin domain 35.5 29 0.00073 17.5 2.2 28 107-134 138-165 (185)
17 pfam08299 Bac_DnaA_C domain. 35.0 24 0.00061 18.0 1.8 29 107-135 35-64 (70)
18 PRK03573 transcriptional regul 34.8 43 0.0011 16.4 3.1 33 108-140 37-69 (144)
19 cd05133 RasGAP_IQGAP1 IQGAP1 i 33.4 34 0.00086 17.1 2.3 47 103-159 143-197 (360)
20 PRK10681 DNA-binding transcrip 31.1 37 0.00095 16.8 2.2 20 14-33 15-34 (252)
21 TIGR02739 TraF type-F conjugat 30.7 31 0.00078 17.3 1.7 23 150-172 240-262 (270)
22 pfam05917 DUF874 Helicobacter 30.6 25 0.00063 17.9 1.2 14 98-111 89-102 (417)
23 PRK03975 tfx putative transcri 30.2 38 0.00096 16.8 2.1 55 117-171 19-81 (139)
24 cd06171 Sigma70_r4 Sigma70, re 29.7 52 0.0013 15.9 2.8 34 107-140 16-49 (55)
25 cd01388 SOX-TCF_HMG-box SOX-TC 29.1 31 0.00079 17.3 1.5 20 111-130 20-39 (72)
26 pfam08281 Sigma70_r4_2 Sigma-7 29.0 54 0.0014 15.8 2.8 32 107-138 16-47 (54)
27 pfam11199 DUF2891 Protein of u 28.9 27 0.00069 17.7 1.2 45 97-141 95-140 (324)
28 TIGR02814 pfaD_fam PfaD family 27.9 22 0.00057 18.2 0.6 18 63-80 361-378 (449)
29 COG1476 Predicted transcriptio 26.1 64 0.0016 15.4 3.0 31 112-142 9-39 (68)
30 PRK13501 transcriptional activ 26.1 45 0.0011 16.3 1.9 40 96-137 172-212 (290)
31 KOG4414 consensus 26.1 29 0.00074 17.5 0.9 30 5-39 2-31 (197)
32 KOG2530 consensus 25.8 25 0.00065 17.8 0.6 22 12-33 258-279 (483)
33 pfam04545 Sigma70_r4 Sigma-70, 25.2 53 0.0014 15.9 2.1 30 111-140 14-43 (50)
34 PRK13500 transcriptional activ 24.7 52 0.0013 15.9 2.0 30 107-136 211-241 (312)
35 pfam04645 DUF603 Protein of un 24.5 45 0.0012 16.3 1.7 57 116-175 18-74 (181)
36 PRK05231 homoserine kinase; Pr 24.4 34 0.00086 17.1 1.0 125 19-158 5-144 (319)
37 TIGR01362 KDO8P_synth 3-deoxy- 23.8 39 0.001 16.7 1.3 18 158-175 103-120 (279)
38 KOG0289 consensus 22.8 38 0.00098 16.7 1.0 17 50-66 35-51 (506)
39 KOG3832 consensus 22.7 34 0.00086 17.1 0.7 26 5-30 31-58 (319)
40 smart00342 HTH_ARAC helix_turn 22.7 51 0.0013 16.0 1.7 22 12-33 42-63 (84)
41 PRK03902 manganese transport t 22.4 75 0.0019 15.0 2.8 56 101-156 6-62 (142)
42 TIGR02983 SigE-fam_strep RNA p 22.4 46 0.0012 16.3 1.4 27 111-137 123-149 (165)
43 TIGR02643 T_phosphoryl thymidi 22.4 31 0.0008 17.3 0.5 25 17-48 12-36 (440)
44 cd00090 HTH_ARSR Arsenical Res 22.3 76 0.0019 14.9 3.2 30 107-137 11-40 (78)
45 PRK10371 DNA-binding transcrip 22.3 63 0.0016 15.4 2.1 71 107-181 196-291 (302)
46 PRK12544 RNA polymerase sigma 22.2 76 0.0019 14.9 2.8 36 106-141 154-189 (207)
47 pfam00685 Sulfotransfer_1 Sulf 22.0 36 0.00091 16.9 0.8 12 7-18 9-20 (254)
48 COG4989 Predicted oxidoreducta 21.8 39 0.00099 16.7 0.9 22 106-132 245-266 (298)
49 pfam07750 GcrA GcrA cell cycle 21.7 36 0.00091 16.9 0.7 13 19-31 17-29 (162)
50 PRK02251 putative septation in 21.3 66 0.0017 15.3 2.0 33 90-124 7-57 (84)
51 pfam00325 Crp Bacterial regula 21.3 48 0.0012 16.2 1.3 16 21-36 3-18 (32)
52 smart00103 ALBUMIN serum album 20.8 75 0.0019 14.9 2.2 29 107-135 145-173 (187)
53 pfam03339 Pox_L3_FP4 Poxvirus 20.7 34 0.00086 17.1 0.4 42 96-137 204-247 (319)
54 pfam00242 DNA_pol_viral_N DNA 20.5 73 0.0019 15.1 2.1 42 55-100 84-132 (379)
55 PRK11512 DNA-binding transcrip 20.3 83 0.0021 14.7 3.3 46 108-153 45-93 (144)
56 PRK05294 carB carbamoyl phosph 20.2 71 0.0018 15.1 2.0 25 116-140 490-514 (1063)
57 cd06405 PB1_Mekk2_3 The PB1 do 20.0 60 0.0015 15.5 1.6 22 154-175 46-67 (79)
No 1
>COG3820 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=0 Score=627.32 Aligned_cols=189 Identities=67% Similarity=1.033 Sum_probs=176.9
Q ss_pred CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHEEEECCHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCEE-CC
Q ss_conf 98868861345430242043479999967087120511112414638961147401278489999997616487704-03
Q gi|254780800|r 1 MCQRPLMPKASAVWLIDNTSLSFDQIAEFCGLHLLEVMAIADGESLQGIKGFNLISSGQLSAEEIALGEKDKNYKLK-IS 79 (192)
Q Consensus 1 M~~~pLMPkATAvWLvdNT~LtF~QIa~FC~lH~LEVq~IADGeva~gi~g~dPi~~gqLt~eEI~~ce~d~~~~L~-l~ 79 (192)
|+++|||||||||||||||+|||+|||+|||||+|||+||||||||+||+|+|||.+||||||||+|||+||+++|+ +.
T Consensus 1 ~~~~~lmpkatavwlvdNTsLsF~QIA~FCglHplEvk~iADGE~aq~IkGldPI~~GQLtreEi~rae~dP~~~lk~l~ 80 (230)
T COG3820 1 MATQLLMPKATAVWLVDNTSLSFDQIADFCGLHPLEVKGIADGEVAQGIKGLDPIANGQLTREEIARAEKDPNYRLKILS 80 (230)
T ss_pred CCCCCCCCCCEEEEEEECCCCCHHHHHHHHCCCCCEEEEECCCHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHCC
T ss_conf 97444566643799871663259999988476801133102614541455788413575169999865249324444305
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCHHHCCC
Q ss_conf 66433442243556534203311571799999984245584243466438758999996288877012683773322564
Q gi|254780800|r 80 KPKSYILESTKKKKRYTPVSKRQDRPNAILWLIRNYPRLKDAQISHLVGTTGSTIEQIRNRTHWNTANLVPMDPVTLGLC 159 (192)
Q Consensus 80 ~~~~~~~~~~~Kg~kYTPlSkRqDkPdAI~WLiknhPeL~D~QI~KLiGTTK~TI~sIRdRtHWN~~Ni~P~DPV~LGLC 159 (192)
.+++.++++++|||||||+||||||||||+||++|||||+|+||+|||||||.||++||+|||||++||+|+|||+||||
T Consensus 81 ~p~~~~~~~kkk~prYTPvsrRQDrP~AI~Wl~rnhPelkDaQIskliGTTK~TIeqiR~RtHWNsani~p~DPVtLGlc 160 (230)
T COG3820 81 SPKVELPESKKKGPRYTPVSRRQDRPDAILWLLRNHPELKDAQISKLIGTTKSTIEQIRTRTHWNSANITPMDPVTLGLC 160 (230)
T ss_pred CCCCCCCCCCCCCCCCCCCHHCCCCCCCEEHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEH
T ss_conf 75111661100388767602204785211047424864017899999732188899997631233146761796114200
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 89999999999730121245545554205012
Q gi|254780800|r 160 AQIDLDREIEKCSKNTEAKYNKAVDDISTPFS 191 (192)
Q Consensus 160 sQ~dLd~av~KA~~~~~~~~~~~~~~~s~p~~ 191 (192)
||+|||..|++|++... .....+....|++
T Consensus 161 sQidLd~~Veras~~r~--~~~e~~~TL~pAs 190 (230)
T COG3820 161 SQIDLDKEVERASRGRP--TAKELGPTLLPAS 190 (230)
T ss_pred HHHHHHHHHHHHCCCCC--CCCCCCCCCCCHH
T ss_conf 01005889987447999--9788887426535
No 2
>pfam06242 DUF1013 Protein of unknown function (DUF1013). Family of uncharacterized proteins found in Proteobacteria.
Probab=100.00 E-value=0 Score=505.06 Aligned_cols=140 Identities=63% Similarity=0.984 Sum_probs=137.8
Q ss_pred HHEEEECCHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCEECCCCCCCCCCCCCCCCCCCCHHHHCCCHHHHHHHHHH
Q ss_conf 05111124146389611474012784899999976164877040366433442243556534203311571799999984
Q gi|254780800|r 35 LEVMAIADGESLQGIKGFNLISSGQLSAEEIALGEKDKNYKLKISKPKSYILESTKKKKRYTPVSKRQDRPNAILWLIRN 114 (192)
Q Consensus 35 LEVq~IADGeva~gi~g~dPi~~gqLt~eEI~~ce~d~~~~L~l~~~~~~~~~~~~Kg~kYTPlSkRqDkPdAI~WLikn 114 (192)
||||||||||||+||+|||||++||||+|||+|||+||+++|+|.+++++.+..++||+|||||||||||||||+|||||
T Consensus 1 LEVqgIADGeVa~gI~G~dPI~~gqLT~eEI~rce~d~~~~L~i~~~~~~~~~~k~kg~rYtPlSkRqDrPdAI~WLikn 80 (141)
T pfam06242 1 LEVQGIADGEVAQGIKGLDPIANGQLTREEIERCEKDPNYRLKLSKSKVIVPRRKRKGPRYTPVSKRQDRPDAIAWLLRN 80 (141)
T ss_pred CCEEEECCHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHC
T ss_conf 93014536677668867797003783899999884287668332456442551001456767526514671999999971
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHHHH
Q ss_conf 245584243466438758999996288877012683773322564899999999997301
Q gi|254780800|r 115 YPRLKDAQISHLVGTTGSTIEQIRNRTHWNTANLVPMDPVTLGLCAQIDLDREIEKCSKN 174 (192)
Q Consensus 115 hPeL~D~QI~KLiGTTK~TI~sIRdRtHWN~~Ni~P~DPV~LGLCsQ~dLd~av~KA~~~ 174 (192)
||||+|+||+|||||||+||++||||||||++||+|+|||+||||||+|||++|+||.++
T Consensus 81 hPeL~D~QI~kLiGTTK~TI~~IR~rthWN~~Ni~p~dPV~LGLCsQ~dLd~~v~ka~~~ 140 (141)
T pfam06242 81 HPELSDAQISKLIGTTKTTIEAIRDRSHWNSANIKPRDPVTLGLCSQIDLDAAVEKAAKR 140 (141)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCCEECCCCHHHHHHHHHHHHCC
T ss_conf 670248788887477578899986357444457786998235665799999999998725
No 3
>TIGR00938 thrB_alt homoserine kinase; InterPro: IPR005280 Homoserine kinase is required in the biosynthesis of threonine from aspartate.The member of this family from Pseudomonas aeruginosa was shown by direct assay and complementation to act specifically as a homoserine kinase. .
Probab=71.00 E-value=2.3 Score=24.15 Aligned_cols=108 Identities=19% Similarity=0.249 Sum_probs=61.5
Q ss_pred CCCCHHHHHHHHCCC-----HHHEEEECCHHHHCCCCCCCCCCCC-----CCCHHHHHH-HHHCCCCCEE----CCCCCC
Q ss_conf 434799999670871-----2051111241463896114740127-----848999999-7616487704----036643
Q gi|254780800|r 19 TSLSFDQIAEFCGLH-----LLEVMAIADGESLQGIKGFNLISSG-----QLSAEEIAL-GEKDKNYKLK----ISKPKS 83 (192)
Q Consensus 19 T~LtF~QIa~FC~lH-----~LEVq~IADGeva~gi~g~dPi~~g-----qLt~eEI~~-ce~d~~~~L~----l~~~~~ 83 (192)
|+.||+|+..|-.+- .|.+||||.| |.--|=..+- -||-=|-.. .|.=|.- |. |+...+
T Consensus 5 T~vsD~e~~~FL~GYPDlG~ll~lkGIA~G-----v~NSNYl~tT~~GrYiLTlyE~~~~~EeLPfF-L~L~~hLA~~g~ 78 (312)
T TIGR00938 5 TSVSDEEMEAFLEGYPDLGELLSLKGIAEG-----VENSNYLLTTDKGRYILTLYEKRVKAEELPFF-LELLTHLAERGL 78 (312)
T ss_pred ECCCHHHHHHHHCCCCCCCCHHHCCCCCCC-----CCEECCEEEECCCCEEEEEEEECCCCCCCCHH-HHHHHHHHHCCC
T ss_conf 024189999985337755531000132236-----21003156605873688765201686577108-899999986389
Q ss_pred CCC--CCCCCCCCCCCHHHHCCCHHHHHHHHHHCC-CCCHHHHHHHHCCCHHHHH
Q ss_conf 344--224355653420331157179999998424-5584243466438758999
Q gi|254780800|r 84 YIL--ESTKKKKRYTPVSKRQDRPNAILWLIRNYP-RLKDAQISHLVGTTGSTIE 135 (192)
Q Consensus 84 ~~~--~~~~Kg~kYTPlSkRqDkPdAI~WLiknhP-eL~D~QI~KLiGTTK~TI~ 135 (192)
+++ -+++-|.. +|.=.-||.||-=.++--. ..+-.+=|+-||--+--+.
T Consensus 79 p~a~p~~~~~G~~---~~~L~GkPAaLv~fL~G~s~~~P~~~~c~~~G~~lA~~h 130 (312)
T TIGR00938 79 PVAKPVKSRDGRA---LSSLAGKPAALVEFLKGLSVAKPTAEHCREVGEVLAWMH 130 (312)
T ss_pred CCCCCCCCCCCCH---HHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 9887500025430---222067715666312688778880775367647887898
No 4
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=60.54 E-value=9.8 Score=20.36 Aligned_cols=47 Identities=17% Similarity=0.235 Sum_probs=34.2
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHCC---CCCCCCCCCCCCC
Q ss_conf 9999998424558424346643875899999628---8877012683773
Q gi|254780800|r 107 AILWLIRNYPRLKDAQISHLVGTTGSTIEQIRNR---THWNTANLVPMDP 153 (192)
Q Consensus 107 AI~WLiknhPeL~D~QI~KLiGTTK~TI~sIRdR---tHWN~~Ni~P~DP 153 (192)
.|++.|.++|.++-++|++..|.+++||..+=++ .-|=.-.-.|.|-
T Consensus 14 ~vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~glv~r~~~~~D~ 63 (101)
T smart00347 14 LVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDR 63 (101)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf 99999997699799999999896887999999999458938982189998
No 5
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=56.19 E-value=13 Score=19.66 Aligned_cols=34 Identities=21% Similarity=0.356 Sum_probs=30.0
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 9999998424558424346643875899999628
Q gi|254780800|r 107 AILWLIRNYPRLKDAQISHLVGTTGSTIEQIRNR 140 (192)
Q Consensus 107 AI~WLiknhPeL~D~QI~KLiGTTK~TI~sIRdR 140 (192)
.+++.|..||.++-++|++.++.+++||..+=+|
T Consensus 7 ~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i~~ 40 (59)
T pfam01047 7 HILRILYEHGPLTVSELAEKLGVDRSTVTRVLDR 40 (59)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999469929999999988586549999999
No 6
>PRK09954 hypothetical protein; Provisional
Probab=44.84 E-value=28 Score=17.55 Aligned_cols=12 Identities=17% Similarity=0.080 Sum_probs=6.3
Q ss_pred CCCCCHHHHHHH
Q ss_conf 278489999997
Q gi|254780800|r 57 SGQLSAEEIALG 68 (192)
Q Consensus 57 ~gqLt~eEI~~c 68 (192)
..++|-+.|+..
T Consensus 170 ~~~itp~~l~~~ 181 (362)
T PRK09954 170 LQQLTPQLLNGS 181 (362)
T ss_pred HHHCCHHHHHHH
T ss_conf 433699999999
No 7
>pfam02787 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.
Probab=44.20 E-value=15 Score=19.26 Aligned_cols=24 Identities=33% Similarity=0.619 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 558424346643875899999628
Q gi|254780800|r 117 RLKDAQISHLVGTTGSTIEQIRNR 140 (192)
Q Consensus 117 eL~D~QI~KLiGTTK~TI~sIRdR 140 (192)
-.||.||++|.|.+-..|...|..
T Consensus 71 GFSD~~IA~l~~~~e~~Ir~~R~~ 94 (122)
T pfam02787 71 GFSDAQIAKLLGVTEEEVRKLRKE 94 (122)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999899998839869999999998
No 8
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=43.37 E-value=15 Score=19.28 Aligned_cols=22 Identities=23% Similarity=0.463 Sum_probs=15.4
Q ss_pred HHHHHHHHCCCCCHHHHHHHHC
Q ss_conf 9999998424558424346643
Q gi|254780800|r 107 AILWLIRNYPRLKDAQISHLVG 128 (192)
Q Consensus 107 AI~WLiknhPeL~D~QI~KLiG 128 (192)
...||++.+..++-.+|++..|
T Consensus 35 iamyL~r~~~~~s~~~IG~~fg 56 (60)
T smart00760 35 IAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred HHHHHHHHHHCCCHHHHHHHHC
T ss_conf 9999999986799999999977
No 9
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=42.54 E-value=18 Score=18.71 Aligned_cols=18 Identities=17% Similarity=0.298 Sum_probs=8.2
Q ss_pred CCHHHHHHHHCCCHHHHH
Q ss_conf 584243466438758999
Q gi|254780800|r 118 LKDAQISHLVGTTGSTIE 135 (192)
Q Consensus 118 L~D~QI~KLiGTTK~TI~ 135 (192)
|+-.++++.+|-.--+.+
T Consensus 237 lsl~~LA~~~~~S~R~le 254 (328)
T COG4977 237 LSLEELADRAGLSRRQLE 254 (328)
T ss_pred CCHHHHHHHHCCCHHHHH
T ss_conf 689999999687887899
No 10
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=41.61 E-value=18 Score=18.74 Aligned_cols=38 Identities=24% Similarity=0.404 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHCCCCCHHHHHHHHCCCHHH------HHHHHCCC
Q ss_conf 5717999999842455842434664387589------99996288
Q gi|254780800|r 103 DRPNAILWLIRNYPRLKDAQISHLVGTTGST------IEQIRNRT 141 (192)
Q Consensus 103 DkPdAI~WLiknhPeL~D~QI~KLiGTTK~T------I~sIRdRt 141 (192)
|=|...+=-.|.+ --||.||++++|+|-.+ |.++|...
T Consensus 489 ~~~~e~L~~aK~l-GFSD~~iA~~~~~~~~~~~~~~~vR~~R~~~ 532 (1089)
T TIGR01369 489 ELDKELLRKAKKL-GFSDAQIARLVNVTEAESIEELEVRKLRKEL 532 (1089)
T ss_pred CCCHHHHHHHHHC-CCCHHHHHHHHCCCHHHCCCHHHHHHHHHHC
T ss_conf 4898899998641-8887899998689744420068999999846
No 11
>cd05131 RasGAP_IQGAP2 IQGAP2 is a member of the IQGAP family that contains a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeat, a single WW domain, four IQ motifs which mediate interactions with calmodulin, and a Ras-GTPase-activating protein (GAP)-related domain that binds Rho family GTPases. IQGAP2 and IQGAP3 play important roles in the regulation of the cytoskeleton for axon outgrowth in hippocampal neurons and are thought to stay in a common regulatory pathway. The results of RNA interference studies indicated that IQGAP3 partially compensates functions of IQGAP2, but has lesser ability than IQGAP2 to promote axon outgrowth in hippocampal neuron. Morevover, IQGAP2 is required for the cadherin-mediated cell-to-cell adhesion in Xenopus laevis embryos.
Probab=40.33 E-value=22 Score=18.20 Aligned_cols=48 Identities=19% Similarity=0.364 Sum_probs=32.8
Q ss_pred CCCHHHHHH--------HHHHCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCHHHCCC
Q ss_conf 157179999--------9984245584243466438758999996288877012683773322564
Q gi|254780800|r 102 QDRPNAILW--------LIRNYPRLKDAQISHLVGTTGSTIEQIRNRTHWNTANLVPMDPVTLGLC 159 (192)
Q Consensus 102 qDkPdAI~W--------LiknhPeL~D~QI~KLiGTTK~TI~sIRdRtHWN~~Ni~P~DPV~LGLC 159 (192)
-.=|.+|-| +.+.||+-++.+|+++||.- +=-| |-|-+-+.|.. .|++
T Consensus 142 ~~iPygiR~ick~i~~~l~~kFP~a~~~~il~vvG~~------~~~r-yinPaIvsPe~---f~ii 197 (339)
T cd05131 142 DLIPYGMRYIAKVLKNSLHEKFPDATEDELLKIVGNL------LYYR-YMNPAIVAPDG---FDII 197 (339)
T ss_pred HHCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH------HHHH-HHHHHHCCCHH---CCCC
T ss_conf 7489999999999999999778999778899999999------9999-73016148411---2830
No 12
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=37.63 E-value=31 Score=17.27 Aligned_cols=33 Identities=15% Similarity=0.312 Sum_probs=28.9
Q ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 999998424558424346643875899999628
Q gi|254780800|r 108 ILWLIRNYPRLKDAQISHLVGTTGSTIEQIRNR 140 (192)
Q Consensus 108 I~WLiknhPeL~D~QI~KLiGTTK~TI~sIRdR 140 (192)
-.++++.+-+|+-.+|+..+|.+-+||.+.--|
T Consensus 138 ~v~~Lr~~~~ls~~EIA~~l~~s~~tVk~~l~R 170 (191)
T PRK12520 138 RVFMMREWLELETEEICKELQITATNLWVMLYR 170 (191)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999993899999999989499999999999
No 13
>pfam11762 Arabinose_Iso_C L-arabinose isomerase C-terminal domain. This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <= L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme. This is a C-terminal non catalytic domain.
Probab=37.35 E-value=16 Score=19.14 Aligned_cols=23 Identities=13% Similarity=0.388 Sum_probs=18.7
Q ss_pred HHHCCCCHHHHHHHHCCCHHHEE
Q ss_conf 42043479999967087120511
Q gi|254780800|r 16 IDNTSLSFDQIAEFCGLHLLEVM 38 (192)
Q Consensus 16 vdNT~LtF~QIa~FC~lH~LEVq 38 (192)
|=.+++|.+|+.+||.|.-+|.-
T Consensus 91 v~S~~~~~e~~~d~A~~~giE~v 113 (115)
T pfam11762 91 VFSQAVTTEQLEDFAEMAGIELV 113 (115)
T ss_pred EEECCCCHHHHHHHHHHHCCEEE
T ss_conf 88836899999999998798898
No 14
>KOG0237 consensus
Probab=37.04 E-value=15 Score=19.24 Aligned_cols=44 Identities=30% Similarity=0.464 Sum_probs=35.4
Q ss_pred HHHHCCCC---HHHHHHHHCCCHHH----------EEEECCHHHHCCCCCCCCCCCC
Q ss_conf 24204347---99999670871205----------1111241463896114740127
Q gi|254780800|r 15 LIDNTSLS---FDQIAEFCGLHLLE----------VMAIADGESLQGIKGFNLISSG 58 (192)
Q Consensus 15 LvdNT~Lt---F~QIa~FC~lH~LE----------Vq~IADGeva~gi~g~dPi~~g 58 (192)
-|+|+.++ |+++++||.-|-.+ |-||+|--...||.-|-|-.-+
T Consensus 46 ~~~~~dI~~~d~~ala~f~~e~~I~lVvvGPE~PL~~Gl~~~l~~~gi~~FGPs~~a 102 (788)
T KOG0237 46 KVPNLDISVADFEALASFCKEHNINLVVVGPELPLVAGLADVLRSAGIPCFGPSKQA 102 (788)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHHHHCCCCCEECCHHHH
T ss_conf 375565576559999999987462189978732654235666640585101743777
No 15
>pfam03376 Adeno_E3B Adenovirus E3B protein.
Probab=36.24 E-value=16 Score=19.08 Aligned_cols=18 Identities=17% Similarity=0.567 Sum_probs=15.9
Q ss_pred HHHHCCCCCHHHHHHHHC
Q ss_conf 998424558424346643
Q gi|254780800|r 111 LIRNYPRLKDAQISHLVG 128 (192)
Q Consensus 111 LiknhPeL~D~QI~KLiG 128 (192)
-.|+|||-.|.||++|.+
T Consensus 72 Y~rHhPqYrn~~iA~LL~ 89 (90)
T pfam03376 72 YLRHHPQYRNQNVARLLR 89 (90)
T ss_pred HHHCCCCCCCHHHHHHHC
T ss_conf 886281004868999864
No 16
>cd00015 ALBUMIN Albumin domain, contains five or six internal disulphide bonds; albuminoid superfamily includes alpha-fetoprotein which binds various cations, fatty acids and bilirubin; vitamin D-binding protein which binds to vitamin D, its metabolites, and fatty acids; alpha-albumin which binds water, cations (such as Ca2+, Na+ and K+), fatty acids, hormones, bilirubin and drugs; and afamin of which little is known; these belong to a multigene family with highly conserved intron/exon organization and encoded protein structures; evolutionary comparisons strongly support vitamin D-binding protein as the original gene in this group with subsequent local duplications generating the remaining genes in the cluster
Probab=35.50 E-value=29 Score=17.51 Aligned_cols=28 Identities=14% Similarity=0.140 Sum_probs=22.0
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHH
Q ss_conf 9999998424558424346643875899
Q gi|254780800|r 107 AILWLIRNYPRLKDAQISHLVGTTGSTI 134 (192)
Q Consensus 107 AI~WLiknhPeL~D~QI~KLiGTTK~TI 134 (192)
-++.+.|.||++++.+|-++...-...+
T Consensus 138 flye~~rrhP~~~~~~ll~~a~~y~~~l 165 (185)
T cd00015 138 FLYEYSRRHPELSVPELLRLAKEYEELL 165 (185)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf 9999997288888999999999999999
No 17
>pfam08299 Bac_DnaA_C domain.
Probab=35.02 E-value=24 Score=17.99 Aligned_cols=29 Identities=21% Similarity=0.429 Sum_probs=22.0
Q ss_pred HHHHHHHHCCCCCHHHHHHHHC-CCHHHHH
Q ss_conf 9999998424558424346643-8758999
Q gi|254780800|r 107 AILWLIRNYPRLKDAQISHLVG-TTGSTIE 135 (192)
Q Consensus 107 AI~WLiknhPeL~D~QI~KLiG-TTK~TI~ 135 (192)
...||++.+-.++-.+|++..| -.-.||-
T Consensus 35 iamyL~r~~t~~s~~~IG~~fg~RdHsTVi 64 (70)
T pfam08299 35 IAMYLLRELTNLSLPEIGEIFGGRDHTTVL 64 (70)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCCCHHHH
T ss_conf 999999998679999999993899737999
No 18
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=34.77 E-value=43 Score=16.41 Aligned_cols=33 Identities=9% Similarity=0.188 Sum_probs=26.3
Q ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 999998424558424346643875899999628
Q gi|254780800|r 108 ILWLIRNYPRLKDAQISHLVGTTGSTIEQIRNR 140 (192)
Q Consensus 108 I~WLiknhPeL~D~QI~KLiGTTK~TI~sIRdR 140 (192)
+.+|..+.|.++-.++++.+|..++|+..+=||
T Consensus 37 L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ld~ 69 (144)
T PRK03573 37 LHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999997398989999999979878369999999
No 19
>cd05133 RasGAP_IQGAP1 IQGAP1 is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. Mammalian IQGAP1 protein is the best characterized member of the IQGAP family, and contains several protein-interacting domains. Human IQGAP1 is most similar to mouse Iqgap1 (94% identity) and has 62% identity to human IQGAP2. IQGAP1 binds and cross-links actin filaments in vitro and has been implicated in Ca2+/calmodulin signaling, E-cadherin-dependent cell adhesion, cell motility, and invasion. Yeast IQGAP homologues have a role in the recruitment of actin filaments, are components of the spindle pole body, and are required for actomyosin ring assembly and cytokinesis. Furthermore, IQGAP1 over-expression has also been detected in gastric and colorectal carcinomas and gastric cancer cell lines.
Probab=33.45 E-value=34 Score=17.09 Aligned_cols=47 Identities=15% Similarity=0.315 Sum_probs=31.7
Q ss_pred CCHHHHHHHHH--------HCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCHHHCCC
Q ss_conf 57179999998--------4245584243466438758999996288877012683773322564
Q gi|254780800|r 103 DRPNAILWLIR--------NYPRLKDAQISHLVGTTGSTIEQIRNRTHWNTANLVPMDPVTLGLC 159 (192)
Q Consensus 103 DkPdAI~WLik--------nhPeL~D~QI~KLiGTTK~TI~sIRdRtHWN~~Ni~P~DPV~LGLC 159 (192)
.=|.+|-|++| .||+-++.+|+++||.-= =.-|-|-+-..|.. .|++
T Consensus 143 ~iPygiR~ick~l~~~l~~kFP~a~~~~il~vvG~f~-------~~ryinPaIvsPe~---f~iv 197 (360)
T cd05133 143 KIPYGMRFIAKVLKDSLHEKFPDAGEDELLKIVGNLL-------YYRYMNPAIVAPDA---FDII 197 (360)
T ss_pred HCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH-------HHHHCCHHCCCCHH---CCCC
T ss_conf 5888999999999999997689997788999999999-------99860004068411---2811
No 20
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=31.09 E-value=37 Score=16.81 Aligned_cols=20 Identities=20% Similarity=0.277 Sum_probs=11.7
Q ss_pred HHHHHCCCCHHHHHHHHCCC
Q ss_conf 02420434799999670871
Q gi|254780800|r 14 WLIDNTSLSFDQIAEFCGLH 33 (192)
Q Consensus 14 WLvdNT~LtF~QIa~FC~lH 33 (192)
||-.+-.++..++|+.++.-
T Consensus 15 ~L~~~g~v~v~eLa~~~~VS 34 (252)
T PRK10681 15 ALKRSDKLHLKDAAALLGVS 34 (252)
T ss_pred HHHHCCCEEHHHHHHHHCCC
T ss_conf 99986979999999887979
No 21
>TIGR02739 TraF type-F conjugative transfer system pilin assembly protein TraF; InterPro: IPR014110 This entry includes TraF; a protein that is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically in the F-type system. TraF has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm . Unlike the related protein TrbB (IPR014109 from INTERPRO), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulphide isomerase by complementation of an Escherichia coli DsbA defect . The protein is believed to be involved in pilin assembly . Even more closely related than TrbB is a clade of genes (IPR014111 from INTERPRO), which do contain the CXXC motif, but it is unclear whether these are involved in type-F conjugation systems per se..
Probab=30.75 E-value=31 Score=17.35 Aligned_cols=23 Identities=26% Similarity=0.430 Sum_probs=16.9
Q ss_pred CCCCHHHCCCCHHHHHHHHHHHH
Q ss_conf 37733225648999999999973
Q gi|254780800|r 150 PMDPVTLGLCAQIDLDREIEKCS 172 (192)
Q Consensus 150 P~DPV~LGLCsQ~dLd~av~KA~ 172 (192)
-..||.-||.||.||++-+-.+.
T Consensus 240 ~~~PlAYGf~Sqd~L~~ri~~V~ 262 (270)
T TIGR02739 240 KMSPLAYGFISQDELKERILNVL 262 (270)
T ss_pred CEEEEEHHHCCHHHHHHHHHHHC
T ss_conf 22010010204889999999853
No 22
>pfam05917 DUF874 Helicobacter pylori protein of unknown function (DUF874). This family consists of several hypothetical proteins specific to Helicobacter pylori. The function of this family is unknown.
Probab=30.61 E-value=25 Score=17.90 Aligned_cols=14 Identities=36% Similarity=0.681 Sum_probs=6.2
Q ss_pred HHHHCCCHHHHHHH
Q ss_conf 03311571799999
Q gi|254780800|r 98 VSKRQDRPNAILWL 111 (192)
Q Consensus 98 lSkRqDkPdAI~WL 111 (192)
-||...+|+-|.|+
T Consensus 89 kskq~~~~NqinW~ 102 (417)
T pfam05917 89 KSKQAEHENQINWF 102 (417)
T ss_pred HHHHCCCCCCHHHH
T ss_conf 45420475511077
No 23
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=30.23 E-value=38 Score=16.79 Aligned_cols=55 Identities=24% Similarity=0.265 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCC--------CCCCCHHHCCCCHHHHHHHHHHH
Q ss_conf 55842434664387589999962888770126--------83773322564899999999997
Q gi|254780800|r 117 RLKDAQISHLVGTTGSTIEQIRNRTHWNTANL--------VPMDPVTLGLCAQIDLDREIEKC 171 (192)
Q Consensus 117 eL~D~QI~KLiGTTK~TI~sIRdRtHWN~~Ni--------~P~DPV~LGLCsQ~dLd~av~KA 171 (192)
-++-.+|++++||++-.|.+|-.|.-=|+..- .-.-||..-+=.-.||.++-...
T Consensus 19 G~tQ~eIA~~lgTSraNvs~iEk~A~eNIekAreTl~~~~~l~Apv~i~i~~GtDl~~iP~~v 81 (139)
T PRK03975 19 GLTQQEIADILGTSRANISIIEKRARENIEKARNTLAFWNTLNAPVQVTIPAGTDLFEIPKII 81 (139)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHH
T ss_conf 897999999977328899999999999999999999999966898899967999288828999
No 24
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=29.73 E-value=52 Score=15.92 Aligned_cols=34 Identities=26% Similarity=0.309 Sum_probs=28.5
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 9999998424558424346643875899999628
Q gi|254780800|r 107 AILWLIRNYPRLKDAQISHLVGTTGSTIEQIRNR 140 (192)
Q Consensus 107 AI~WLiknhPeL~D~QI~KLiGTTK~TI~sIRdR 140 (192)
.....++++-+++-.+|+...|.+-+||.+.-.|
T Consensus 16 r~vl~l~y~~~~s~~EIa~~lgis~~tVk~~l~r 49 (55)
T cd06171 16 REVILLRFGEGLSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 8989999980999999999989599999999999
No 25
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=29.08 E-value=31 Score=17.32 Aligned_cols=20 Identities=25% Similarity=0.642 Sum_probs=17.2
Q ss_pred HHHHCCCCCHHHHHHHHCCC
Q ss_conf 99842455842434664387
Q gi|254780800|r 111 LIRNYPRLKDAQISHLVGTT 130 (192)
Q Consensus 111 LiknhPeL~D~QI~KLiGTT 130 (192)
+...+|+++.+.|+|++|..
T Consensus 20 ~~~~~P~~~~~eiSk~lg~~ 39 (72)
T cd01388 20 VLQEYPLKENRAISKILGDR 39 (72)
T ss_pred HHHHCCCCCHHHHHHHHHHH
T ss_conf 99888899889999999999
No 26
>pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
Probab=29.00 E-value=54 Score=15.83 Aligned_cols=32 Identities=25% Similarity=0.386 Sum_probs=24.7
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999984245584243466438758999996
Q gi|254780800|r 107 AILWLIRNYPRLKDAQISHLVGTTGSTIEQIR 138 (192)
Q Consensus 107 AI~WLiknhPeL~D~QI~KLiGTTK~TI~sIR 138 (192)
..+.+++++-+++-.+|++..|.+-+||.+--
T Consensus 16 r~~~~l~~~~~~s~~eIA~~lg~s~~tVk~~l 47 (54)
T pfam08281 16 REVFLLRYLEGLSYAEIAELLGISEGTVKSRL 47 (54)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 98968799878599999999894999999999
No 27
>pfam11199 DUF2891 Protein of unknown function (DUF2891). This is a bacterial family of uncharacterized proteins.
Probab=28.90 E-value=27 Score=17.65 Aligned_cols=45 Identities=18% Similarity=0.296 Sum_probs=34.6
Q ss_pred CHHHHCCCHHHHHHHHHHCCCCCHHH-HHHHHCCCHHHHHHHHCCC
Q ss_conf 20331157179999998424558424-3466438758999996288
Q gi|254780800|r 97 PVSKRQDRPNAILWLIRNYPRLKDAQ-ISHLVGTTGSTIEQIRNRT 141 (192)
Q Consensus 97 PlSkRqDkPdAI~WLiknhPeL~D~Q-I~KLiGTTK~TI~sIRdRt 141 (192)
|-++--+||.+.+||++-+-||.-.. -..+-++.++-.+.|.+|.
T Consensus 95 ~~~~~FERpYGwAWlL~L~~EL~~~~~a~~w~~~l~PL~~~i~~r~ 140 (324)
T pfam11199 95 PGNASFERPYGWAWLLKLAAELRRWDQAARWAEALEPLADLIVERL 140 (324)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7668884865599999999999972888899986208999999999
No 28
>TIGR02814 pfaD_fam PfaD family protein; InterPro: IPR014179 The protein PfaD is part of a four-gene locus, similar to polyketide biosynthesis systems, which is responsible for omega-3 polyunsaturated fatty acid biosynthesis in several high pressure and/or cold-adapted bacteria. Several other members of the entry are found in loci presumed to act in polyketide biosyntheses per se..
Probab=27.85 E-value=22 Score=18.15 Aligned_cols=18 Identities=28% Similarity=0.353 Sum_probs=15.4
Q ss_pred HHHHHHHHCCCCCEECCC
Q ss_conf 999997616487704036
Q gi|254780800|r 63 EEIALGEKDKNYKLKISK 80 (192)
Q Consensus 63 eEI~~ce~d~~~~L~l~~ 80 (192)
+||+|.|.||++|+-|.+
T Consensus 361 a~i~rAe~dPKhkMALvF 378 (449)
T TIGR02814 361 AEIERAERDPKHKMALVF 378 (449)
T ss_pred HHHHHHHHCCCHHHHHHH
T ss_conf 799998627760057898
No 29
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=26.08 E-value=64 Score=15.39 Aligned_cols=31 Identities=26% Similarity=0.354 Sum_probs=26.7
Q ss_pred HHHCCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 9842455842434664387589999962888
Q gi|254780800|r 112 IRNYPRLKDAQISHLVGTTGSTIEQIRNRTH 142 (192)
Q Consensus 112 iknhPeL~D~QI~KLiGTTK~TI~sIRdRtH 142 (192)
+|+.--++-.+.++.+|-++-||.+|-+..|
T Consensus 9 ~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky 39 (68)
T COG1476 9 LRAELGLTQEELAKLVGVSRQTIIAIEKGKY 39 (68)
T ss_pred HHHHHCCCHHHHHHHCCCCHHHHHHHHCCCC
T ss_conf 9998285899999991957999999991798
No 30
>PRK13501 transcriptional activator RhaR; Provisional
Probab=26.06 E-value=45 Score=16.33 Aligned_cols=40 Identities=15% Similarity=0.150 Sum_probs=25.2
Q ss_pred CCHHHHCCCHHHHHHHHHHCC-CCCHHHHHHHHCCCHHHHHHH
Q ss_conf 420331157179999998424-558424346643875899999
Q gi|254780800|r 96 TPVSKRQDRPNAILWLIRNYP-RLKDAQISHLVGTTGSTIEQI 137 (192)
Q Consensus 96 TPlSkRqDkPdAI~WLiknhP-eL~D~QI~KLiGTTK~TI~sI 137 (192)
.|-+.|-|+ .+.|+-.|+. .++-+++++..|.++..+..+
T Consensus 172 ~~~~~~~~~--i~~~i~~~~~~~~~l~~lA~~~~lS~~~lsrl 212 (290)
T PRK13501 172 LPDGEQLDL--IMSALQQSLGAYFDMADFCHKNQLVERSLKQL 212 (290)
T ss_pred CCCHHHHHH--HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 884689999--99999997468999999999969899999999
No 31
>KOG4414 consensus
Probab=26.06 E-value=29 Score=17.49 Aligned_cols=30 Identities=40% Similarity=0.625 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHEEE
Q ss_conf 88613454302420434799999670871205111
Q gi|254780800|r 5 PLMPKASAVWLIDNTSLSFDQIAEFCGLHLLEVMA 39 (192)
Q Consensus 5 pLMPkATAvWLvdNT~LtF~QIa~FC~lH~LEVq~ 39 (192)
||-|.|-|. .+.||+.|+|-|.--+||+-|
T Consensus 2 ~la~m~Eal-----aA~SFdKi~D~Cdn~~Lea~~ 31 (197)
T KOG4414 2 DLAPMAEAL-----AAFSFDKIADICDNLELEAAG 31 (197)
T ss_pred CCHHHHHHH-----HHHHHHHHHHHHHHHHHCCCC
T ss_conf 842888988-----864288999886135540557
No 32
>KOG2530 consensus
Probab=25.80 E-value=25 Score=17.82 Aligned_cols=22 Identities=36% Similarity=0.635 Sum_probs=14.6
Q ss_pred HHHHHHHCCCCHHHHHHHHCCC
Q ss_conf 4302420434799999670871
Q gi|254780800|r 12 AVWLIDNTSLSFDQIAEFCGLH 33 (192)
Q Consensus 12 AvWLvdNT~LtF~QIa~FC~lH 33 (192)
--|++=|++|+|-|..+||.|-
T Consensus 258 ~~~~~lN~als~~qLs~~~~l~ 279 (483)
T KOG2530 258 NKWLKLNKALSLSQLSQECSLY 279 (483)
T ss_pred HHHHHHHHHHHHHHHHHHCCEE
T ss_conf 7788888777788775300234
No 33
>pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.
Probab=25.20 E-value=53 Score=15.89 Aligned_cols=30 Identities=23% Similarity=0.329 Sum_probs=25.1
Q ss_pred HHHHCCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 998424558424346643875899999628
Q gi|254780800|r 111 LIRNYPRLKDAQISHLVGTTGSTIEQIRNR 140 (192)
Q Consensus 111 LiknhPeL~D~QI~KLiGTTK~TI~sIRdR 140 (192)
.++++-+++-.+|++..|.+..+|.++-.|
T Consensus 14 ~l~y~~~~t~~EIA~~lgis~~~V~~~~~r 43 (50)
T pfam04545 14 VLRFGEGLTLEEIGERLGISRERVRQIEKR 43 (50)
T ss_pred HHHCCCCCHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 987068824999999989799999999999
No 34
>PRK13500 transcriptional activator RhaR; Provisional
Probab=24.70 E-value=52 Score=15.94 Aligned_cols=30 Identities=10% Similarity=0.075 Sum_probs=19.2
Q ss_pred HHHHHHHHCCC-CCHHHHHHHHCCCHHHHHH
Q ss_conf 99999984245-5842434664387589999
Q gi|254780800|r 107 AILWLIRNYPR-LKDAQISHLVGTTGSTIEQ 136 (192)
Q Consensus 107 AI~WLiknhPe-L~D~QI~KLiGTTK~TI~s 136 (192)
.|.||-.|+-| ++-.++|...|-...+...
T Consensus 211 ll~~l~~~~~ep~~l~~lA~~~~lS~r~L~R 241 (312)
T PRK13500 211 LITRLAASLKSPFALDKFCDEASCSERVLRQ 241 (312)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999998744999899999897889999999
No 35
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=24.51 E-value=45 Score=16.30 Aligned_cols=57 Identities=12% Similarity=0.264 Sum_probs=39.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf 455842434664387589999962888770126837733225648999999999973012
Q gi|254780800|r 116 PRLKDAQISHLVGTTGSTIEQIRNRTHWNTANLVPMDPVTLGLCAQIDLDREIEKCSKNT 175 (192)
Q Consensus 116 PeL~D~QI~KLiGTTK~TI~sIRdRtHWN~~Ni~P~DPV~LGLCsQ~dLd~av~KA~~~~ 175 (192)
.-|+|++|++-.|....-|-..|++ |-+.+-.+..---+- .++..|+..+..+-++.
T Consensus 18 G~L~D~eIA~~LGVsr~nV~kmRqK--wes~~dsv~edsrvT-isEdtf~~ll~~t~~s~ 74 (181)
T pfam04645 18 GSLSDAEIAKELGVSRVNVWRMRQK--WESGEDSVNEDSRVT-ISEDTFEHLLIQTFQSE 74 (181)
T ss_pred CCCCHHHHHHHHCCHHHHHHHHHHH--HHHCCCCCCCCCCEE-ECHHHHHHHHHHHHHHH
T ss_conf 7875799999978309999999999--981278855567300-03724999999999999
No 36
>PRK05231 homoserine kinase; Provisional
Probab=24.44 E-value=34 Score=17.09 Aligned_cols=125 Identities=21% Similarity=0.232 Sum_probs=64.3
Q ss_pred CCCCHHHHHHHHCC----CHHHEEEECCHHHHCCCCCCCCCCCC--------CCCHHHHHHHHHCCCCCEECCCCCCCCC
Q ss_conf 43479999967087----12051111241463896114740127--------8489999997616487704036643344
Q gi|254780800|r 19 TSLSFDQIAEFCGL----HLLEVMAIADGESLQGIKGFNLISSG--------QLSAEEIALGEKDKNYKLKISKPKSYIL 86 (192)
Q Consensus 19 T~LtF~QIa~FC~l----H~LEVq~IADGeva~gi~g~dPi~~g--------qLt~eEI~~ce~d~~~~L~l~~~~~~~~ 86 (192)
|.||.++|+.|+.- -..+++||+.|=.-....=.- ..| ..+.+|+...- +.-..|.....+.|
T Consensus 5 T~ls~~el~~~l~~Y~lG~l~~~~gI~~GieNTNY~v~T--~~g~yILTifEr~~~~~lpff~---~Lm~~L~~~gipcP 79 (319)
T PRK05231 5 TPVSDDELAAFLAPYDLGELLSLKGIAEGIENSNFFLTT--TQGEYVLTLFERLTAEDLPFFL---ELMQHLAARGLPVP 79 (319)
T ss_pred CCCCHHHHHHHHHHCCCCCCCEECCCCCCCCCCEEEEEE--CCCCEEEEEEECCCHHHCCHHH---HHHHHHHHCCCCCC
T ss_conf 148999999999966999750210646663474289994--5971899996128836552999---99999987899788
Q ss_pred --CCCCCCCCCCCHHHHCCCHHHHH-HHHHHCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCHHHCC
Q ss_conf --22435565342033115717999-9998424558424346643875899999628887701268377332256
Q gi|254780800|r 87 --ESTKKKKRYTPVSKRQDRPNAIL-WLIRNYPRLKDAQISHLVGTTGSTIEQIRNRTHWNTANLVPMDPVTLGL 158 (192)
Q Consensus 87 --~~~~Kg~kYTPlSkRqDkPdAI~-WLiknhPeL~D~QI~KLiGTTK~TI~sIRdRtHWN~~Ni~P~DPV~LGL 158 (192)
-..+.|.....+ .+||-+|. ||=-.+++..+..-|+-||..=-- -|=-..+.....|-.+|+
T Consensus 80 ~Pi~~~~G~~i~~l---~gKpa~L~~fL~G~~~~~~~~~~c~~iG~~LA~-------lH~a~~~f~~~r~n~~~~ 144 (319)
T PRK05231 80 APLARRDGELLGTL---AGKPAAIVTFLEGKHPRAPTAAHCAEVGEMLAR-------MHLAGRDFPLERPNLRSL 144 (319)
T ss_pred CEEECCCCCCHHHH---CCEEEEEEEECCCCCCCCCCHHHHHHHHHHHHH-------HHHCCCCCCCCCCCCCCH
T ss_conf 36788998755785---690489998258988799999999999999999-------665216798668888986
No 37
>TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase; InterPro: IPR006269 These sequences describe 2-dehydro-3-deoxyphosphooctonate aldolase. Alternate names include 3-deoxy-d-manno-octulosonic acid 8-phosphate and KDO-8 phosphate synthetase. It catalyzes the aldol condensation of phosphoenolpyruvate with D-arabinose 5-phosphate. phosphoenolpyruvate + D-arabinose 5-phosphate + H_2O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide. ; GO: 0008676 3-deoxy-8-phosphooctulonate synthase activity, 0008152 metabolic process, 0005737 cytoplasm.
Probab=23.81 E-value=39 Score=16.67 Aligned_cols=18 Identities=39% Similarity=0.416 Sum_probs=14.7
Q ss_pred CCCHHHHHHHHHHHHHHH
Q ss_conf 648999999999973012
Q gi|254780800|r 158 LCAQIDLDREIEKCSKNT 175 (192)
Q Consensus 158 LCsQ~dLd~av~KA~~~~ 175 (192)
||.|.||=.|+.+.++=.
T Consensus 103 LCRQTDLl~AaA~TG~iv 120 (279)
T TIGR01362 103 LCRQTDLLVAAAKTGKIV 120 (279)
T ss_pred HHHHHHHHHHHHHCCCEE
T ss_conf 211468999998239868
No 38
>KOG0289 consensus
Probab=22.82 E-value=38 Score=16.75 Aligned_cols=17 Identities=35% Similarity=0.475 Sum_probs=14.8
Q ss_pred CCCCCCCCCCCCHHHHH
Q ss_conf 11474012784899999
Q gi|254780800|r 50 KGFNLISSGQLSAEEIA 66 (192)
Q Consensus 50 ~g~dPi~~gqLt~eEI~ 66 (192)
-|.|||.++.|+.|||-
T Consensus 35 ~G~DPIt~~pLs~eelV 51 (506)
T KOG0289 35 TGKDPITNEPLSIEELV 51 (506)
T ss_pred CCCCCCCCCCCCHHHEE
T ss_conf 08998779967889905
No 39
>KOG3832 consensus
Probab=22.70 E-value=34 Score=17.08 Aligned_cols=26 Identities=38% Similarity=0.604 Sum_probs=21.0
Q ss_pred CCCCHH--HHHHHHHHCCCCHHHHHHHH
Q ss_conf 886134--54302420434799999670
Q gi|254780800|r 5 PLMPKA--SAVWLIDNTSLSFDQIAEFC 30 (192)
Q Consensus 5 pLMPkA--TAvWLvdNT~LtF~QIa~FC 30 (192)
.-|||| ||-||+--|-|+|--.-.|.
T Consensus 31 lalpkafatagwllsi~ll~fl~fmsfm 58 (319)
T KOG3832 31 LALPKAFATAGWLLSITLLTFLAFMSFM 58 (319)
T ss_pred CCCHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf 2250767532099999999999999999
No 40
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=22.67 E-value=51 Score=15.99 Aligned_cols=22 Identities=36% Similarity=0.415 Sum_probs=13.3
Q ss_pred HHHHHHHCCCCHHHHHHHHCCC
Q ss_conf 4302420434799999670871
Q gi|254780800|r 12 AVWLIDNTSLSFDQIAEFCGLH 33 (192)
Q Consensus 12 AvWLvdNT~LtF~QIa~FC~lH 33 (192)
|..++.++..+..+||..||..
T Consensus 42 a~~~L~~~~~~i~~ia~~~Gy~ 63 (84)
T smart00342 42 ARRLLRDTDLSVTEIALRVGFS 63 (84)
T ss_pred HHHHHHCCCCHHHHHHHHCCCC
T ss_conf 9999985763499998881999
No 41
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=22.43 E-value=75 Score=14.96 Aligned_cols=56 Identities=13% Similarity=0.084 Sum_probs=37.2
Q ss_pred HCCCHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHH-HHHCCCCCCCCCCCCCCCHHH
Q ss_conf 11571799999984245584243466438758999-996288877012683773322
Q gi|254780800|r 101 RQDRPNAILWLIRNYPRLKDAQISHLVGTTGSTIE-QIRNRTHWNTANLVPMDPVTL 156 (192)
Q Consensus 101 RqDkPdAI~WLiknhPeL~D~QI~KLiGTTK~TI~-sIRdRtHWN~~Ni~P~DPV~L 156 (192)
..|==-+|+.|.......+-+.|++..|.+++||. .|+.=.-=+.-+-.|-..|.|
T Consensus 6 ~EdYLe~Iy~L~~~~~~vr~~dIA~~L~Vs~~SVs~mikkL~~~Glv~~~~y~~i~L 62 (142)
T PRK03902 6 MEDYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEKYRGLVL 62 (142)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEECCCCCEEE
T ss_conf 999999999998258971299999997899533999999999879924558987568
No 42
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor . The protein appears to include a paralogous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives..
Probab=22.41 E-value=46 Score=16.26 Aligned_cols=27 Identities=22% Similarity=0.534 Sum_probs=23.8
Q ss_pred HHHHCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 998424558424346643875899999
Q gi|254780800|r 111 LIRNYPRLKDAQISHLVGTTGSTIEQI 137 (192)
Q Consensus 111 LiknhPeL~D~QI~KLiGTTK~TI~sI 137 (192)
.++||-.||+.||+.-.|.--.||.|=
T Consensus 123 VLRY~eDlSe~~~A~~LG~SvGTVKS~ 149 (165)
T TIGR02983 123 VLRYYEDLSEAEVAEVLGISVGTVKSR 149 (165)
T ss_pred EEECCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf 320457898689998819993228998
No 43
>TIGR02643 T_phosphoryl thymidine phosphorylase; InterPro: IPR013465 Thymidine phosphorylase (alternate name: pyrimidine phosphorylase) 2.4.2.4 from EC is involved, in E. coli and other Proteobacteria, in (deoxy)nucleotide degradation. It is often encoded in an operon together with a deoxyribose-phosphate aldolase, a phosphopentomutase and a purine nucleoside phosphorylase. In many other lineages, the corresponding enzyme is designated pyrimidine-nucleoside phosphorylase (2.4.2.2 from EC); the naming convention here follows standard literature practice.; GO: 0009032 thymidine phosphorylase activity.
Probab=22.37 E-value=31 Score=17.27 Aligned_cols=25 Identities=40% Similarity=0.591 Sum_probs=20.6
Q ss_pred HHCCCCHHHHHHHHCCCHHHEEEECCHHHHCC
Q ss_conf 20434799999670871205111124146389
Q gi|254780800|r 17 DNTSLSFDQIAEFCGLHLLEVMAIADGESLQG 48 (192)
Q Consensus 17 dNT~LtF~QIa~FC~lH~LEVq~IADGeva~g 48 (192)
|+.+|+-..|+.| |+||.||.|+-|
T Consensus 12 D~~~Ls~~eI~~F-------i~G~~~~~vseG 36 (440)
T TIGR02643 12 DGLSLSDAEIAAF-------INGVTDGSVSEG 36 (440)
T ss_pred CCCCCCHHHHHHH-------HHHHCCCCCCHH
T ss_conf 7888898899999-------852037884468
No 44
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=22.29 E-value=76 Score=14.95 Aligned_cols=30 Identities=27% Similarity=0.400 Sum_probs=26.3
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9999998424558424346643875899999
Q gi|254780800|r 107 AILWLIRNYPRLKDAQISHLVGTTGSTIEQI 137 (192)
Q Consensus 107 AI~WLiknhPeL~D~QI~KLiGTTK~TI~sI 137 (192)
.|+.++...| ++-+||++.+|.+.+||..-
T Consensus 11 ~Il~~L~~~~-~~~~eia~~l~is~~~vs~h 40 (78)
T cd00090 11 RILRLLLEGP-LTVSELAERLGLSQSTVSRH 40 (78)
T ss_pred HHHHHHHHCC-CCHHHHHHHHCCCHHHHHHH
T ss_conf 9999998489-06999987778487899999
No 45
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=22.26 E-value=63 Score=15.44 Aligned_cols=71 Identities=17% Similarity=0.225 Sum_probs=41.9
Q ss_pred HHHHHHHHCC-CCCHHHHHHHHCCCHHHHHHH----------------H--------CCCCCCCCCCCCCCCHHHCCCCH
Q ss_conf 9999998424-558424346643875899999----------------6--------28887701268377332256489
Q gi|254780800|r 107 AILWLIRNYP-RLKDAQISHLVGTTGSTIEQI----------------R--------NRTHWNTANLVPMDPVTLGLCAQ 161 (192)
Q Consensus 107 AI~WLiknhP-eL~D~QI~KLiGTTK~TI~sI----------------R--------dRtHWN~~Ni~P~DPV~LGLCsQ 161 (192)
-+.|+-.||- +|+-.+||+.+|-.+.....+ | -.|..++..|. ...|+.+.
T Consensus 196 il~YI~~hY~e~IsL~diA~~~~lS~~y~sr~FKk~tG~T~~~YL~~~Rl~~A~~LL~~Td~sIteIA----~~~GF~n~ 271 (302)
T PRK10371 196 MLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIA----LTAGFRSS 271 (302)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHH----HHHCCCCH
T ss_conf 99999998289999999998979599999999999989099999999999999999874899899999----99589987
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999973012124554
Q gi|254780800|r 162 IDLDREIEKCSKNTEAKYNK 181 (192)
Q Consensus 162 ~dLd~av~KA~~~~~~~~~~ 181 (192)
.-+.+.-.|.-+-.+.+-.+
T Consensus 272 s~F~r~FKk~~G~TP~eYRK 291 (302)
T PRK10371 272 SRFYSTFGKYVGMSPQQYRK 291 (302)
T ss_pred HHHHHHHHHHHCCCHHHHHH
T ss_conf 99999999887909899998
No 46
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.21 E-value=76 Score=14.94 Aligned_cols=36 Identities=22% Similarity=0.355 Sum_probs=30.9
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf 799999984245584243466438758999996288
Q gi|254780800|r 106 NAILWLIRNYPRLKDAQISHLVGTTGSTIEQIRNRT 141 (192)
Q Consensus 106 dAI~WLiknhPeL~D~QI~KLiGTTK~TI~sIRdRt 141 (192)
....++++++-+++-.+|+...|.|-+||.+.-.|.
T Consensus 154 ~R~vl~Lr~~eglS~~EIAe~Lgis~~tVks~L~RA 189 (207)
T PRK12544 154 YARVFMMREFIELETPEICHNEDLTVSNLNVMLYRS 189 (207)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999999999819999999999797999999999999
No 47
>pfam00685 Sulfotransfer_1 Sulfotransferase domain.
Probab=21.97 E-value=36 Score=16.92 Aligned_cols=12 Identities=33% Similarity=0.803 Sum_probs=7.0
Q ss_pred CCHHHHHHHHHH
Q ss_conf 613454302420
Q gi|254780800|r 7 MPKASAVWLIDN 18 (192)
Q Consensus 7 MPkATAvWLvdN 18 (192)
+||.---||-.-
T Consensus 9 yPKSGnTWlr~i 20 (254)
T pfam00685 9 YPKSGTTWLQEI 20 (254)
T ss_pred CCCHHHHHHHHH
T ss_conf 998679999999
No 48
>COG4989 Predicted oxidoreductase [General function prediction only]
Probab=21.85 E-value=39 Score=16.71 Aligned_cols=22 Identities=41% Similarity=0.759 Sum_probs=17.2
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHH
Q ss_conf 799999984245584243466438758
Q gi|254780800|r 106 NAILWLIRNYPRLKDAQISHLVGTTGS 132 (192)
Q Consensus 106 dAI~WLiknhPeL~D~QI~KLiGTTK~ 132 (192)
=||+||+|+ | +++.-.|||+|.
T Consensus 245 VaiAWllR~-P----a~~~PiiGt~~~ 266 (298)
T COG4989 245 VAIAWLLRH-P----AKPQPIIGTGNL 266 (298)
T ss_pred HHHHHHHHC-C----CCCCCEECCCCH
T ss_conf 999999967-6----756541057988
No 49
>pfam07750 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery.
Probab=21.69 E-value=36 Score=16.93 Aligned_cols=13 Identities=46% Similarity=0.419 Sum_probs=7.5
Q ss_pred CCCCHHHHHHHHC
Q ss_conf 4347999996708
Q gi|254780800|r 19 TSLSFDQIAEFCG 31 (192)
Q Consensus 19 T~LtF~QIa~FC~ 31 (192)
-.||--|||.--|
T Consensus 17 eGlSaSqIA~~LG 29 (162)
T pfam07750 17 EGLSASQIAAQLG 29 (162)
T ss_pred CCCCHHHHHHHHC
T ss_conf 5365999999976
No 50
>PRK02251 putative septation inhibitor protein; Reviewed
Probab=21.27 E-value=66 Score=15.32 Aligned_cols=33 Identities=27% Similarity=0.711 Sum_probs=20.0
Q ss_pred CCCCCCCCHHHHCCCH------------------HHHHHHHHHCCCCCHHHHH
Q ss_conf 3556534203311571------------------7999999842455842434
Q gi|254780800|r 90 KKKKRYTPVSKRQDRP------------------NAILWLIRNYPRLKDAQIS 124 (192)
Q Consensus 90 ~Kg~kYTPlSkRqDkP------------------dAI~WLiknhPeL~D~QI~ 124 (192)
+|...|||-..++... -+++|+|-+| |+.+|+.
T Consensus 7 RKK~~~t~~~~~~~~~~~~~~P~W~~p~m~~lm~iGL~Wivv~Y--is~~~~P 57 (84)
T PRK02251 7 RKKQDYTPPPSREAKKGTKVNPRWFAPVMVALMIIGLIWLVVYY--VTSGSLP 57 (84)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH--HCCCCCC
T ss_conf 57877889964445666789984089999999999899984531--1368778
No 51
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=21.27 E-value=48 Score=16.17 Aligned_cols=16 Identities=31% Similarity=0.465 Sum_probs=8.6
Q ss_pred CCHHHHHHHHCCCHHH
Q ss_conf 4799999670871205
Q gi|254780800|r 21 LSFDQIAEFCGLHLLE 36 (192)
Q Consensus 21 LtF~QIa~FC~lH~LE 36 (192)
+|-..||+||||-..-
T Consensus 3 msrqdIadylGlt~ET 18 (32)
T pfam00325 3 MSRQEIADYLGLTRET 18 (32)
T ss_pred CCHHHHHHHHCCHHHH
T ss_conf 6588999984725999
No 52
>smart00103 ALBUMIN serum albumin.
Probab=20.79 E-value=75 Score=14.95 Aligned_cols=29 Identities=21% Similarity=0.283 Sum_probs=22.4
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHH
Q ss_conf 99999984245584243466438758999
Q gi|254780800|r 107 AILWLIRNYPRLKDAQISHLVGTTGSTIE 135 (192)
Q Consensus 107 AI~WLiknhPeL~D~QI~KLiGTTK~TI~ 135 (192)
-++=+.|+||++++.||-++...-...++
T Consensus 145 fl~e~~rrhP~~~~~~ll~~a~~y~~~l~ 173 (187)
T smart00103 145 FLYELSRRHPELSEPQLLRVAKEYEALLE 173 (187)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf 99999961888989999999999999999
No 53
>pfam03339 Pox_L3_FP4 Poxvirus L3/FP4 protein.
Probab=20.69 E-value=34 Score=17.09 Aligned_cols=42 Identities=19% Similarity=0.210 Sum_probs=32.4
Q ss_pred CCHHHHCCCHH--HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 42033115717--9999998424558424346643875899999
Q gi|254780800|r 96 TPVSKRQDRPN--AILWLIRNYPRLKDAQISHLVGTTGSTIEQI 137 (192)
Q Consensus 96 TPlSkRqDkPd--AI~WLiknhPeL~D~QI~KLiGTTK~TI~sI 137 (192)
-++++|.-.+- =+-|++|||-+|-+-|-..+--+-|+||..-
T Consensus 204 ~~la~r~~e~~nYFfEW~I~NHl~lLsk~~~difkikkk~~t~~ 247 (319)
T pfam03339 204 DTLATRNLESTNYFFEWFIRNHFELLSRQCLDIFKIKKKYITTP 247 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHEEEEHHCCCC
T ss_conf 27776320226899999998798774103422522331002566
No 54
>pfam00242 DNA_pol_viral_N DNA polymerase (viral) N-terminal domain.
Probab=20.48 E-value=73 Score=15.05 Aligned_cols=42 Identities=21% Similarity=0.405 Sum_probs=30.2
Q ss_pred CCCCCCCHHHHHHHHH-------CCCCCEECCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf 0127848999999761-------648770403664334422435565342033
Q gi|254780800|r 55 ISSGQLSAEEIALGEK-------DKNYKLKISKPKSYILESTKKKKRYTPVSK 100 (192)
Q Consensus 55 i~~gqLt~eEI~~ce~-------d~~~~L~l~~~~~~~~~~~~Kg~kYTPlSk 100 (192)
+..--|..+-|.+|+. |++++||++.+.--.|+ --+|-||.|
T Consensus 84 fp~iHl~~diin~c~q~~gpltvnekRrlKli~PArF~Pk----stkYfPl~k 132 (379)
T pfam00242 84 FPDIHLHEDIINKCEQFVGPLTVNEKRRLKLIMPARFYPK----STKYFPLDK 132 (379)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCCCHHCCEEEECCCCCCCC----CCCCCCCCC
T ss_conf 7420002889987675247654120004024133220567----530244013
No 55
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=20.27 E-value=83 Score=14.69 Aligned_cols=46 Identities=15% Similarity=0.279 Sum_probs=33.2
Q ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHCC---CCCCCCCCCCCCC
Q ss_conf 999998424558424346643875899999628---8877012683773
Q gi|254780800|r 108 ILWLIRNYPRLKDAQISHLVGTTGSTIEQIRNR---THWNTANLVPMDP 153 (192)
Q Consensus 108 I~WLiknhPeL~D~QI~KLiGTTK~TI~sIRdR---tHWN~~Ni~P~DP 153 (192)
++--+..++.++-+++++++|.++.||..+=+| .-|-.---.|.|=
T Consensus 45 vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ldrLe~~GlI~R~~~p~Dr 93 (144)
T PRK11512 45 VLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDK 93 (144)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC
T ss_conf 9999998699799999999788887899999999978796635798776
No 56
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=20.16 E-value=71 Score=15.11 Aligned_cols=25 Identities=28% Similarity=0.551 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 4558424346643875899999628
Q gi|254780800|r 116 PRLKDAQISHLVGTTGSTIEQIRNR 140 (192)
Q Consensus 116 PeL~D~QI~KLiGTTK~TI~sIRdR 140 (192)
=-.+|.||++|.|++-..|...|..
T Consensus 490 ~GFSD~~IA~l~~~~~~~Vr~~R~~ 514 (1063)
T PRK05294 490 LGFSDARIAKLLGVTEDEVRKLRKE 514 (1063)
T ss_pred HCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 0998599998849999999999998
No 57
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f
Probab=20.04 E-value=60 Score=15.54 Aligned_cols=22 Identities=36% Similarity=0.439 Sum_probs=17.2
Q ss_pred HHHCCCCHHHHHHHHHHHHHHH
Q ss_conf 3225648999999999973012
Q gi|254780800|r 154 VTLGLCAQIDLDREIEKCSKNT 175 (192)
Q Consensus 154 V~LGLCsQ~dLd~av~KA~~~~ 175 (192)
+..-|-+|.|||+||+--.++.
T Consensus 46 L~IPl~~Q~DLDkAiellD~s~ 67 (79)
T cd06405 46 LLIPLKNQEDLDRAIELLDRSP 67 (79)
T ss_pred EEEECCCHHHHHHHHHHHCCCC
T ss_conf 7886256777899999870592
Done!