Query 023523
Match_columns 281
No_of_seqs 125 out of 160
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 04:42:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023523.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023523hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2652 RNA polymerase II tran 100.0 1.6E-34 3.5E-39 270.5 16.8 205 1-247 2-216 (348)
2 PF03153 TFIIA: Transcription 100.0 4.8E-30 1E-34 233.3 5.7 193 8-242 1-207 (375)
3 COG5149 TOA1 Transcription ini 99.6 1.3E-15 2.9E-20 139.9 6.0 55 1-55 1-55 (293)
4 KOG1924 RhoA GTPase effector D 61.6 32 0.0007 37.9 7.8 14 8-21 422-435 (1102)
5 COG5352 Uncharacterized protei 60.2 8.6 0.00019 34.4 2.9 46 29-82 2-51 (169)
6 KOG1924 RhoA GTPase effector D 57.8 1.6E+02 0.0036 32.8 12.2 7 13-19 459-465 (1102)
7 PF10593 Z1: Z1 domain; Inter 42.3 58 0.0013 29.6 5.4 45 5-49 38-82 (239)
8 PF05347 Complex1_LYR: Complex 40.5 1.2E+02 0.0026 20.9 6.1 43 5-47 2-58 (59)
9 PTZ00098 phosphoethanolamine N 39.7 80 0.0017 28.3 5.7 43 6-50 207-249 (263)
10 PF03978 Borrelia_REV: Borreli 39.6 30 0.00065 31.1 3.0 39 8-48 47-88 (160)
11 cd08780 Death_TRADD Death Doma 37.9 25 0.00055 28.9 2.1 31 13-44 30-60 (90)
12 PRK05685 fliS flagellar protei 35.1 38 0.00083 28.0 2.8 40 6-45 84-124 (132)
13 PF05555 DUF762: Coxiella burn 31.5 45 0.00098 31.6 2.9 37 2-38 59-96 (248)
14 COG5467 Uncharacterized conser 31.0 82 0.0018 26.5 4.0 19 14-32 63-81 (104)
15 PF07345 DUF1476: Domain of un 30.1 47 0.001 27.5 2.5 34 14-48 65-98 (103)
16 COG3514 Uncharacterized protei 29.0 41 0.0009 27.9 2.0 24 25-48 57-83 (93)
17 PF12296 HsbA: Hydrophobic sur 28.6 1.1E+02 0.0025 23.7 4.4 22 21-42 90-111 (124)
18 TIGR00208 fliS flagellar biosy 27.9 55 0.0012 27.0 2.6 39 6-46 80-121 (124)
19 cd03409 Chelatase_Class_II Cla 27.8 49 0.0011 24.4 2.1 21 30-50 75-95 (101)
20 PF01152 Bac_globin: Bacterial 27.3 1.4E+02 0.0031 23.1 4.7 29 15-43 83-111 (120)
21 PF13232 Complex1_LYR_1: Compl 25.3 2.5E+02 0.0054 19.8 6.5 33 17-49 26-60 (61)
22 KOG2616 Pyridoxalphosphate-dep 24.7 68 0.0015 30.8 2.9 39 15-57 136-175 (266)
23 PF12010 DUF3502: Domain of un 24.5 1.3E+02 0.0028 24.9 4.2 34 14-48 99-132 (134)
24 PF02561 FliS: Flagellar prote 23.9 63 0.0014 25.9 2.2 40 6-46 78-119 (122)
25 TIGR00064 ftsY signal recognit 23.6 1.4E+02 0.0031 27.3 4.7 35 13-47 2-36 (272)
26 PF05402 PqqD: Coenzyme PQQ sy 22.4 2.1E+02 0.0046 20.0 4.5 34 14-50 32-65 (68)
27 TIGR02698 CopY_TcrY copper tra 22.3 1.9E+02 0.0042 23.8 4.8 22 25-46 97-118 (130)
28 PF01985 CRS1_YhbY: CRS1 / Yhb 21.8 92 0.002 23.9 2.6 19 27-45 24-42 (84)
29 PF07750 GcrA: GcrA cell cycle 21.1 46 0.001 28.9 1.0 24 29-52 2-25 (162)
No 1
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=100.00 E-value=1.6e-34 Score=270.51 Aligned_cols=205 Identities=35% Similarity=0.534 Sum_probs=169.3
Q ss_pred CCCChhhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhcccccC-CCCCCCCCCCCCCCccccccCCCC
Q 023523 1 MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDR-TSAPKQPAPGGPITPVHDLNVPYE 79 (281)
Q Consensus 1 MSNs~VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSgAaifp-d~AP~pP~P~gpitPVhdLnvPye 79 (281)
|+++.|++||++||+|||++||++|+|+||||+||.|||++||+||+|+|++-++ +..+.+..|. ....| ++|++
T Consensus 2 ~~~~~v~kvY~~VIeDVI~~vRe~F~~~GiDeqvL~eLk~lWe~Kl~qs~~~~~~~d~~s~~~p~~--~~q~~--~~~~~ 77 (348)
T KOG2652|consen 2 ASTNTVSKVYESVIEDVINNVREDFLENGIDEQVLSELKNLWETKLIQSGVATFPWDRESNQRPPP--GVQLH--HVPLQ 77 (348)
T ss_pred CcccchHHHHHHHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHHHHhhcccccCcccccccCCCC--ccccc--Ccccc
Confidence 6778999999999999999999999999999999999999999999999999543 3333221111 22344 56666
Q ss_pred C-CCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCcccCCCCCCCCC--CCCCCCCCCCCC
Q 023523 80 G-TEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPG-TADNSTYNIPTGSSDYP--TPASDSGGNTEA 155 (281)
Q Consensus 80 ~-teeyetPtAemlfPPtplqtp~qtplp~~~~~~~~~~~~~~~~~~g-~~~~~myniptg~s~yp--~~~~~~g~~~~~ 155 (281)
. +..+.+|+ +||.+++|++..++|+ | .+..|+|||+.++++|+ +|....+.|.
T Consensus 78 ~~~~~~~~Pa---~~~~~~q~~~~~~~l~------------------~~~~~~s~~~i~~~~t~~~~~~P~~q~~~N~-- 134 (348)
T KOG2652|consen 78 SATANLATPA---VFPGAPQQTPAGVPLP------------------GLSGHLSKANIPLPSTATNGQHPSQQVNVNS-- 134 (348)
T ss_pred cccccccCCc---cccccccccCcCccCc------------------cccccccccCccccccccCCcCccccccccc--
Confidence 5 56887777 8889999999998888 7 78899999999999998 6666666655
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCccccceeeeecCc-----cccccCCCCCCcccceeecccccccccCCCcCCCCCCc
Q 023523 156 KSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGR-----DEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGY 230 (281)
Q Consensus 156 k~~~grp~~ym~~~pspw~~~~~~l~vdvnvayvegr-----de~~rg~s~~~~tqdff~~~sgkrkr~d~~~~y~~g~~ 230 (281)
-++.|+|.| .|.|.+.|+.- + ||.+| .+..+|..+++.||+-|.-++| |+.+-.-+|.+++
T Consensus 135 ----~q~~p~~~p-~s~~~~~q~s~--~----~v~~~~~ip~~~p~~~~~~~~~tqq~~~~~~g--~~pq~~~~~~~~~- 200 (348)
T KOG2652|consen 135 ----TQPVPALSP-WSLQLNTQKSQ--Q----TVLQQSAIPPSGPVDGNHNQPVTQQILVPPGG--KSPQSSFHYINLN- 200 (348)
T ss_pred ----cCCCcCcCc-ccccccccccc--c----cccccccccccCcccccccCccccccccCCCC--CCcccccceeccC-
Confidence 577889999 99999766643 3 89999 8999999999999999988777 7888888888887
Q ss_pred ccccCCCCCCchhhHHH
Q 023523 231 NIPQQDGAGDAMSEIFE 247 (281)
Q Consensus 231 ~ipqqdga~d~~~~~~~ 247 (281)
|||++|+++...++..
T Consensus 201 -~~q~~~s~nd~~~~~~ 216 (348)
T KOG2652|consen 201 -IPQVDGSENDVEQIDG 216 (348)
T ss_pred -Cccccccccccccccc
Confidence 9999999998877665
No 2
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=99.96 E-value=4.8e-30 Score=233.34 Aligned_cols=193 Identities=28% Similarity=0.392 Sum_probs=44.0
Q ss_pred HhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhcccccC-CCCCCCCCCCCCCCccccccCCCCCCCCCCC
Q 023523 8 MVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDR-TSAPKQPAPGGPITPVHDLNVPYEGTEEYET 86 (281)
Q Consensus 8 kVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSgAaifp-d~AP~pP~P~gpitPVhdLnvPye~teeyet 86 (281)
|||++||+|||++||+||+|+||||+||+|||++||+||+++||+.|+ ++.+.++.+. +.+|...
T Consensus 1 kvY~~VI~dVI~~vr~dF~~~Gvde~vL~eLk~~We~KL~qs~v~~~~~d~~~~~~~~~--------~~~p~~~------ 66 (375)
T PF03153_consen 1 KVYESVIDDVINNVREDFEEEGVDEQVLQELKQLWESKLSQSGVADFPWDPPPAPPPPP--------PQQPQPP------ 66 (375)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHH-SS--TTGGGG---------------------------
T ss_pred CcHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcCCccCCCCcccCCCccc--------ccCCCCc------
Confidence 799999999999999999999999999999999999999999999665 5444321111 1111111
Q ss_pred CCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCcccCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCC
Q 023523 87 PTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPG-TADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSY 165 (281)
Q Consensus 87 PtAemlfPPtplqtp~qtplp~~~~~~~~~~~~~~~~~~g-~~~~~myniptg~s~yp~~~~~~g~~~~~k~~~grp~~y 165 (281)
+.+++++.+++ +++++ . ...+.++++|++.+.+..+......+. + .+++.++
T Consensus 67 ----~~~~~~~~~~~-~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~--~~~~~~i 119 (375)
T PF03153_consen 67 ----QSTPPSPSQQP-QAPQA------------------IPQGQSQQQNQPSSMSNSNPPATFSTPPG--Q--VPAPPTI 119 (375)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ----ccCCCCCCCCc-ccccc------------------cCCCCccccccccccCcCCCcccccCCCc--c--cCCCCCc
Confidence 55566666666 55555 3 455677888888777633322222111 2 2678888
Q ss_pred CCCCCCCCCCCCCCccccceeeeecCccccccCCCCCCcccceeeccccccc-----------ccCCCcCCCCCCc-ccc
Q 023523 166 MPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRK-----------REDFPAQYHNGGY-NIP 233 (281)
Q Consensus 166 m~~~pspw~~~~~~l~vdvnvayvegrde~~rg~s~~~~tqdff~~~sgkrk-----------r~d~~~~y~~g~~-~ip 233 (281)
+++ +..|++.+.+..+..+.++..++....+....+++++.|+.+.+.+++ +.....++..|.. .++
T Consensus 120 q~~-pG~~~~~~~P~~~~~~~~~~~~~~~~aqq~~~qq~~q~~g~~aa~q~~~~~qq~q~~~~~~~~~~~~~~~~~~~~~ 198 (375)
T PF03153_consen 120 QQP-PGQQYQVQVPSMNNQPPGNQQIAQQPAQQRAAQQLQQPYGQPAAQQISQQQQQQQPQQQQQQQQQQQQPGQQVQQQ 198 (375)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cCC-CccccCcccCCccCCcccccccccccccccccccccccccccccccCCccccccccccccccccccccCCCccCCC
Confidence 888 999999898988899999999999999999999999999999999999 6777778877775 358
Q ss_pred cCCCCCCch
Q 023523 234 QQDGAGDAM 242 (281)
Q Consensus 234 qqdga~d~~ 242 (281)
|.||++|..
T Consensus 199 Qtdga~d~~ 207 (375)
T PF03153_consen 199 QTDGAGDSE 207 (375)
T ss_dssp ---------
T ss_pred cccCCCCcc
Confidence 899999985
No 3
>COG5149 TOA1 Transcription initiation factor IIA, large chain [Transcription]
Probab=99.59 E-value=1.3e-15 Score=139.86 Aligned_cols=55 Identities=38% Similarity=0.631 Sum_probs=53.9
Q ss_pred CCCChhhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhcccccC
Q 023523 1 MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDR 55 (281)
Q Consensus 1 MSNs~VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSgAaifp 55 (281)
|||+.|++||+.||.|||+++|+||++.|||+++|+|||.+||+||.+++|+.|+
T Consensus 1 msns~~~~vy~~vi~~vi~~~r~dfe~~gvdd~tlrelqnlwq~kl~~t~vatf~ 55 (293)
T COG5149 1 MSNSIVGEVYHHVILDVIANSRSDFEENGVDDATLRELQNLWQSKLVATDVATFP 55 (293)
T ss_pred CCcchhhHHHHHHHHHHHHHhhhHHHhcCccHHHHHHHHHHHHHhhhhheeeecc
Confidence 9999999999999999999999999999999999999999999999999999776
No 4
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=61.60 E-value=32 Score=37.95 Aligned_cols=14 Identities=36% Similarity=0.686 Sum_probs=8.4
Q ss_pred HhHHHHHHHHHHhh
Q 023523 8 MVYIRVIEDVISKV 21 (281)
Q Consensus 8 kVYrsVIEDVIn~V 21 (281)
.-|-.+||+.|..|
T Consensus 422 pqYykLIEecISqI 435 (1102)
T KOG1924|consen 422 PQYYKLIEECISQI 435 (1102)
T ss_pred HHHHHHHHHHHHHH
Confidence 44666666666554
No 5
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.17 E-value=8.6 Score=34.43 Aligned_cols=46 Identities=15% Similarity=0.208 Sum_probs=30.7
Q ss_pred CCChHHHHHHHHHHHHHHHHhccc-ccC---CCCCCCCCCCCCCCccccccCCCCCCC
Q 023523 29 GPGESVLNELQGIWEMKMIQAGVI-IDR---TSAPKQPAPGGPITPVHDLNVPYEGTE 82 (281)
Q Consensus 29 GVDEqVLqELKqlWE~KLsQSgAa-ifp---d~AP~pP~P~gpitPVhdLnvPye~te 82 (281)
.+.+.-.+-||++|-+-|++|.++ +.- .+| -|-.||-|-|+-.+..
T Consensus 2 nWtdERve~LkKLWseGLSASQIAaQLGGVsRnA--------VIGKVHRL~lsgR~~~ 51 (169)
T COG5352 2 NWTDERVETLKKLWSEGLSASQIAAQLGGVSRNA--------VIGKVHRLGLSGRAKP 51 (169)
T ss_pred CchHHHHHHHHHHHHcccCHHHHHHHhcCcchhh--------hheeeeeccccccCCc
Confidence 345666788999999999999887 222 121 1556777766655543
No 6
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=57.80 E-value=1.6e+02 Score=32.82 Aligned_cols=7 Identities=14% Similarity=0.676 Sum_probs=3.0
Q ss_pred HHHHHHH
Q 023523 13 VIEDVIS 19 (281)
Q Consensus 13 VIEDVIn 19 (281)
+||+.|+
T Consensus 459 liD~~vd 465 (1102)
T KOG1924|consen 459 LIDKMVD 465 (1102)
T ss_pred HHHHHHH
Confidence 3444443
No 7
>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases. This domain is found associated with a helicase domain of superfamily type II [].
Probab=42.33 E-value=58 Score=29.58 Aligned_cols=45 Identities=20% Similarity=0.322 Sum_probs=36.0
Q ss_pred hhhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHh
Q 023523 5 ATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQA 49 (281)
Q Consensus 5 ~VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQS 49 (281)
.+-+-+...|++.++.++.+..+.--+...+.+|+++|++.....
T Consensus 38 ~~h~~~~~~I~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 82 (239)
T PF10593_consen 38 DVHEQVADWIEEYLNELKKALRYNDDDPEELNELRELWEEDFEPT 82 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHHhhhh
Confidence 345667788888899999998887766666999999999887643
No 8
>PF05347 Complex1_LYR: Complex 1 protein (LYR family); InterPro: IPR008011 This family of short proteins includes proteins from the NADH-ubiquinone oxidoreductase complex I. The family includes the B14 subunit from bovine NADH-ubiquinone oxidoreductase B14 subunit Q02366 from SWISSPROT, and the B22 subunit from the human enzyme Q9Y6M9 from SWISSPROT. The family has been named LYR after a highly conserved tripeptide motif close to the N terminus of these proteins. Members of this family also found in yeast which do contain this complex. In these organisms they are believed to be be required for iron-sulphur custer biogenesis.
Probab=40.55 E-value=1.2e+02 Score=20.87 Aligned_cols=43 Identities=19% Similarity=0.269 Sum_probs=30.8
Q ss_pred hhhHhHHHHHHH------------HHHhhHHHHHhCC--CChHHHHHHHHHHHHHHH
Q 023523 5 ATGMVYIRVIED------------VISKVRDEFVNNG--PGESVLNELQGIWEMKMI 47 (281)
Q Consensus 5 ~VskVYrsVIED------------VIn~VReDFeeeG--VDEqVLqELKqlWE~KLs 47 (281)
.|-++|++++.. +.+.||+.|..+= -|..-+++|-+.++..|.
T Consensus 2 ~vl~LYR~lLR~~~~~~~~~~r~~~~~~iR~~Fr~n~~~~d~~~I~~~l~~g~~~l~ 58 (59)
T PF05347_consen 2 RVLSLYRQLLRAARSFPDDSEREYIRAEIRQEFRKNRNETDPEKIEELLKKGEEELE 58 (59)
T ss_pred hHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhc
Confidence 355677766543 4567888898766 478888888888887764
No 9
>PTZ00098 phosphoethanolamine N-methyltransferase; Provisional
Probab=39.67 E-value=80 Score=28.31 Aligned_cols=43 Identities=16% Similarity=0.199 Sum_probs=32.4
Q ss_pred hhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhc
Q 023523 6 TGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAG 50 (281)
Q Consensus 6 VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSg 50 (281)
+...|..+.+.+. .-|++|.+. +.+..++.|+..|+.|+...+
T Consensus 207 ~~~~~~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ 249 (263)
T PTZ00098 207 WLELLQVELKKLE-EKKEEFLKL-YSEKEYNSLKDGWTRKIKDTK 249 (263)
T ss_pred HHHHHHHHHHHHH-HhHHHHHHh-cCHHHHHHHHHHHHHHHHHhh
Confidence 3455665555444 448889886 999999999999999987654
No 10
>PF03978 Borrelia_REV: Borrelia burgdorferi REV protein; InterPro: IPR007126 This family consists of several REV proteins from Borrelia burgdorferi (Lyme disease spirochete) and Borrelia garinii. The function of REV is unknown although it has been shown that the gene is induced during the ingesting of host blood suggesting a role in the metabolic activation of borreliae to adapt to physiological stimuli [].
Probab=39.62 E-value=30 Score=31.06 Aligned_cols=39 Identities=18% Similarity=0.274 Sum_probs=25.2
Q ss_pred HhHHHHHHHHHHhhHHHHHhCC---CChHHHHHHHHHHHHHHHH
Q 023523 8 MVYIRVIEDVISKVRDEFVNNG---PGESVLNELQGIWEMKMIQ 48 (281)
Q Consensus 8 kVYrsVIEDVIn~VReDFeeeG---VDEqVLqELKqlWE~KLsQ 48 (281)
..|...-+ =|+..+++|.+.| +.+ -|.+|+.+|++||..
T Consensus 47 ~~yknyk~-ki~eLke~lK~~~NAElee-kll~lq~lfq~Kl~a 88 (160)
T PF03978_consen 47 EAYKNYKK-KINELKEDLKDVSNAELEE-KLLKLQKLFQDKLEA 88 (160)
T ss_pred HHHHHHHH-HHHHHHHHHHHhhhHHHHH-HHHHHHHHHHHHHHH
Confidence 34444332 3677888888876 444 455699999987654
No 11
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into s
Probab=37.87 E-value=25 Score=28.91 Aligned_cols=31 Identities=16% Similarity=0.203 Sum_probs=26.4
Q ss_pred HHHHHHHhhHHHHHhCCCChHHHHHHHHHHHH
Q 023523 13 VIEDVISKVRDEFVNNGPGESVLNELQGIWEM 44 (281)
Q Consensus 13 VIEDVIn~VReDFeeeGVDEqVLqELKqlWE~ 44 (281)
+-|-.|++|..++..+|+.|+|.|-|++ |..
T Consensus 30 l~d~~ID~I~~~y~r~gL~EqvyQ~L~~-W~~ 60 (90)
T cd08780 30 LRDPAIDNLAYEYDREGLYEQAYQLLRR-FIQ 60 (90)
T ss_pred cchhHHHHHHhhcccccHHHHHHHHHHH-HHH
Confidence 4567799999999999999999997774 765
No 12
>PRK05685 fliS flagellar protein FliS; Validated
Probab=35.12 E-value=38 Score=28.03 Aligned_cols=40 Identities=18% Similarity=0.338 Sum_probs=27.5
Q ss_pred hhHhHHHHHHHHHHhh-HHHHHhCCCChHHHHHHHHHHHHH
Q 023523 6 TGMVYIRVIEDVISKV-RDEFVNNGPGESVLNELQGIWEMK 45 (281)
Q Consensus 6 VskVYrsVIEDVIn~V-ReDFeeeGVDEqVLqELKqlWE~K 45 (281)
..++|..++..++... +.|.+.-.--..+|++|+..|++=
T Consensus 84 L~~LY~y~~~~L~~A~~~~d~~~l~ev~~il~~LreaW~~i 124 (132)
T PRK05685 84 LSALYDYMIRRLLEANLRNDVQAIDEVEGLLREIKEAWKQI 124 (132)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999886543 333333223357899999999873
No 13
>PF05555 DUF762: Coxiella burnetii protein of unknown function (DUF762); InterPro: IPR008481 This family consists several of several uncharacterised proteins from the bacterium Coxiella burnetii. C. burnetii is the causative agent of the Q fever disease.
Probab=31.47 E-value=45 Score=31.58 Aligned_cols=37 Identities=24% Similarity=0.371 Sum_probs=30.0
Q ss_pred CCChhhHhHHHHHHHHHHhhHHHHHhCC-CChHHHHHH
Q 023523 2 ATSATGMVYIRVIEDVISKVRDEFVNNG-PGESVLNEL 38 (281)
Q Consensus 2 SNs~VskVYrsVIEDVIn~VReDFeeeG-VDEqVLqEL 38 (281)
|++...+|=..=|+++|..|+..|.-+| +||.|++=+
T Consensus 59 S~~~Lpkl~i~~i~~sIk~v~n~FKk~GLkde~i~nYI 96 (248)
T PF05555_consen 59 SNRDLPKLPIPNIDNSIKYVKNEFKKHGLKDENISNYI 96 (248)
T ss_pred ccCCCccCchhHHHHHHHHHHHHHHHhccchHHHHHHH
Confidence 3445556777889999999999999999 899998843
No 14
>COG5467 Uncharacterized conserved protein [Function unknown]
Probab=30.98 E-value=82 Score=26.51 Aligned_cols=19 Identities=37% Similarity=0.510 Sum_probs=16.5
Q ss_pred HHHHHHhhHHHHHhCCCCh
Q 023523 14 IEDVISKVRDEFVNNGPGE 32 (281)
Q Consensus 14 IEDVIn~VReDFeeeGVDE 32 (281)
-+||.++||.||...||..
T Consensus 63 deDV~RKv~~D~daAGVs~ 81 (104)
T COG5467 63 DEDVFRKVREDLDAAGVST 81 (104)
T ss_pred cHHHHHHHHHhcccccccc
Confidence 4799999999999999854
No 15
>PF07345 DUF1476: Domain of unknown function (DUF1476); InterPro: IPR009945 This family consists of several hypothetical bacterial proteins of around 100 residues in length. Members of this family are found in Bradyrhizobium, Rhizobium, Brucella and Caulobacter species. The function of this family is unknown.; PDB: 2KZC_A 2LL0_A.
Probab=30.14 E-value=47 Score=27.55 Aligned_cols=34 Identities=26% Similarity=0.349 Sum_probs=21.5
Q ss_pred HHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHH
Q 023523 14 IEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQ 48 (281)
Q Consensus 14 IEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQ 48 (281)
-+|||++|+.||...||+.+ ..+|+..-...|.+
T Consensus 65 dedv~~kv~~DL~a~gv~~~-~~~iR~km~~~l~~ 98 (103)
T PF07345_consen 65 DEDVLRKVRADLAAAGVDVS-EAEIRAKMDELLAE 98 (103)
T ss_dssp TTHHHHHHHHHHTTTS-----HHHHHHHHHHCHHH
T ss_pred HHHHHHHHHHHHHHccCCCC-HHHHHHHHHHHHHH
Confidence 36999999999999997654 34555544444443
No 16
>COG3514 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.05 E-value=41 Score=27.85 Aligned_cols=24 Identities=17% Similarity=0.374 Sum_probs=19.5
Q ss_pred HHhCCCChHHHHHHHH---HHHHHHHH
Q 023523 25 FVNNGPGESVLNELQG---IWEMKMIQ 48 (281)
Q Consensus 25 FeeeGVDEqVLqELKq---lWE~KLsQ 48 (281)
+..--||.+||+-+|. .||++|.+
T Consensus 57 ~vslRiDaDVle~fra~GkGwQtRiN~ 83 (93)
T COG3514 57 LVSLRIDADVLEKFRAGGKGWQTRINA 83 (93)
T ss_pred eeeeEecHHHHHHHHcCCccHHHHHHH
Confidence 4445589999999995 79999975
No 17
>PF12296 HsbA: Hydrophobic surface binding protein A; InterPro: IPR021054 Hydrophobic surface binding proteins are typically between 171 to 275 amino acids in length. Although the HsbA amino acid sequence suggests that HsbA may be hydrophilic, HsbA adsorbed to hydrophobic PBSA (Polybutylene succinate-co-adipate) surfaces in the presence of NaCl or CaCl2. When HsbA was adsorbed on the hydrophobic PBSA surfaces, it promoted PBSA degradation via the CutL1 polyesterase. CutL1 interacts directly with HsbA attached to the hydrophobic QCM electrode surface. These results suggest that when HsbA is adsorbed onto the PBSA surface, it recruits CutL1, and that when CutL1 is accumulated on the PBSA surface, it stimulates PBSA degradation []. This entry is also characterised by a antigenic cell wall galactomannoprotein in Aspergillus fumigatus, which is a protein of 284 amino acid residues. It contains a serine- and threonine-rich region for O glycosylation, a signal peptide, and a putative glycosylphosphatidyl inositol attachment signal sequence. Ultrastructural analysis showed that the protein is present in the cell walls of hyphae and conidia []. ; PDB: 3L1N_A.
Probab=28.58 E-value=1.1e+02 Score=23.71 Aligned_cols=22 Identities=23% Similarity=0.229 Sum_probs=17.9
Q ss_pred hHHHHHhCCCChHHHHHHHHHH
Q 023523 21 VRDEFVNNGPGESVLNELQGIW 42 (281)
Q Consensus 21 VReDFeeeGVDEqVLqELKqlW 42 (281)
=|..|+..|++..|+..|+.+=
T Consensus 90 Kk~~f~~~g~~~~v~~~L~~l~ 111 (124)
T PF12296_consen 90 KKPAFDAAGLCSVVRADLQDLK 111 (124)
T ss_dssp THHHHHHTT-HHHHHHHHHHHH
T ss_pred hHHHHHHcCCcHHHHHHHHHHH
Confidence 3678999999999999998763
No 18
>TIGR00208 fliS flagellar biosynthetic protein FliS. The function of this protein in flagellar biosynthesis is unknown, but appears to be regulatory. The member of this family in Vibrio parahaemolyticus is designated FlaJ (creating a synonym for FliS) and was shown essential for flagellin biosynthesis.
Probab=27.93 E-value=55 Score=26.97 Aligned_cols=39 Identities=10% Similarity=0.298 Sum_probs=26.3
Q ss_pred hhHhHHHHHHHHHHhhHH-HHHhCCCC--hHHHHHHHHHHHHHH
Q 023523 6 TGMVYIRVIEDVISKVRD-EFVNNGPG--ESVLNELQGIWEMKM 46 (281)
Q Consensus 6 VskVYrsVIEDVIn~VRe-DFeeeGVD--EqVLqELKqlWE~KL 46 (281)
...+|..++...+..... |-+. +| ..+|.+|+..|++=+
T Consensus 80 L~~LY~y~~~~L~~An~~~d~~~--l~ev~~~l~~Lr~aW~e~~ 121 (124)
T TIGR00208 80 LGALYDYMYRRLVQANIKNDTSK--LAEVEGYVRDFRDAWKEAI 121 (124)
T ss_pred HHHHHHHHHHHHHHHHhhCCHHH--HHHHHHHHHHHHHHHHHHh
Confidence 348999999888654433 2221 33 357999999998744
No 19
>cd03409 Chelatase_Class_II Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. Excluded from this family are the ATP-dependent heterotrimeric chelatases (class I) and the multifunctional homodimeric enzymes with dehydrogenase and chelatase activities (class III).
Probab=27.83 E-value=49 Score=24.42 Aligned_cols=21 Identities=10% Similarity=-0.143 Sum_probs=14.5
Q ss_pred CChHHHHHHHHHHHHHHHHhc
Q 023523 30 PGESVLNELQGIWEMKMIQAG 50 (281)
Q Consensus 30 VDEqVLqELKqlWE~KLsQSg 50 (281)
+.+++..++++.|++++.+-|
T Consensus 75 ~~~di~~~~~~~~~~~~~~~g 95 (101)
T cd03409 75 VFYDIDSEIGLVRKQVGEPLG 95 (101)
T ss_pred hHHHHHHHHHHHHHhcccccc
Confidence 555777888888877665544
No 20
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=27.26 E-value=1.4e+02 Score=23.12 Aligned_cols=29 Identities=17% Similarity=0.276 Sum_probs=23.8
Q ss_pred HHHHHhhHHHHHhCCCChHHHHHHHHHHH
Q 023523 15 EDVISKVRDEFVNNGPGESVLNELQGIWE 43 (281)
Q Consensus 15 EDVIn~VReDFeeeGVDEqVLqELKqlWE 43 (281)
+-+++..++.+++.||++.+.+++-+..+
T Consensus 83 ~~~~~~~~~al~~~~v~~~~~~~~~~~~~ 111 (120)
T PF01152_consen 83 DRWLELLKQALDELGVPEELIDELLARLE 111 (120)
T ss_dssp HHHHHHHHHHHHHTTCTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 55688889999999999999988776554
No 21
>PF13232 Complex1_LYR_1: Complex1_LYR-like
Probab=25.27 E-value=2.5e+02 Score=19.81 Aligned_cols=33 Identities=15% Similarity=0.155 Sum_probs=26.6
Q ss_pred HHHhhHHHHHhCC--CChHHHHHHHHHHHHHHHHh
Q 023523 17 VISKVRDEFVNNG--PGESVLNELQGIWEMKMIQA 49 (281)
Q Consensus 17 VIn~VReDFeeeG--VDEqVLqELKqlWE~KLsQS 49 (281)
+.+.||+.|..+- -|+.-+++|-+.|+..|...
T Consensus 26 ~~~~ir~~Fr~~~~~td~~~i~~~l~~~~~~L~~l 60 (61)
T PF13232_consen 26 FRRRIRDRFRRNKNVTDPEKIAKLLKEGRKELELL 60 (61)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHc
Confidence 6788999999866 37778888888888888654
No 22
>KOG2616 consensus Pyridoxalphosphate-dependent enzyme/predicted threonine synthase [Amino acid transport and metabolism]
Probab=24.74 E-value=68 Score=30.77 Aligned_cols=39 Identities=18% Similarity=0.412 Sum_probs=31.3
Q ss_pred HHHHHhhHHHHHhCC-CChHHHHHHHHHHHHHHHHhcccccCCC
Q 023523 15 EDVISKVRDEFVNNG-PGESVLNELQGIWEMKMIQAGVIIDRTS 57 (281)
Q Consensus 15 EDVIn~VReDFeeeG-VDEqVLqELKqlWE~KLsQSgAaifpd~ 57 (281)
.+++++.++||..+- -+|.+++-+|++|++ .+-++.|..
T Consensus 136 kel~ekls~dftse~vS~ee~~~ti~k~yes----~~YiLdPHT 175 (266)
T KOG2616|consen 136 KELHEKLSEDFTSERVSNEETTQTIKKIYES----NHYILDPHT 175 (266)
T ss_pred HHHHHHHHHhhhhhhcCcHHHHHHHHHHhcc----CCeeecCch
Confidence 467899999999888 578899999999998 565555533
No 23
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=24.47 E-value=1.3e+02 Score=24.86 Aligned_cols=34 Identities=18% Similarity=0.290 Sum_probs=26.2
Q ss_pred HHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHH
Q 023523 14 IEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQ 48 (281)
Q Consensus 14 IEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQ 48 (281)
.++.+...++...+.|+| .|++|+|+-+..=|.+
T Consensus 99 ~e~~~~~~~~kLk~AGid-kV~~E~QkQlda~~~~ 132 (134)
T PF12010_consen 99 PEEALPEFNEKLKAAGID-KVIAELQKQLDAFLAA 132 (134)
T ss_pred HHHHHHHHHHHHHHhChH-HHHHHHHHHHHHHHHh
Confidence 467788899999999986 4888888876655543
No 24
>PF02561 FliS: Flagellar protein FliS; InterPro: IPR003713 The fliD operon of several bacteria consists of three flagellar genes, fliD, fliS, and fliT, and is transcribed in this order []. In Bacillus subtilis the operon encoding the flagellar proteins FliD, FliS, and FliT is sigma D-dependent [].; GO: 0009296 flagellum assembly, 0009288 bacterial-type flagellum; PDB: 1VH6_A 3IQC_B 3K1I_B 1ORJ_B 1ORY_A.
Probab=23.90 E-value=63 Score=25.92 Aligned_cols=40 Identities=18% Similarity=0.211 Sum_probs=26.5
Q ss_pred hhHhHHHHHHHHHHhhHHHHHhCCCC--hHHHHHHHHHHHHHH
Q 023523 6 TGMVYIRVIEDVISKVRDEFVNNGPG--ESVLNELQGIWEMKM 46 (281)
Q Consensus 6 VskVYrsVIEDVIn~VReDFeeeGVD--EqVLqELKqlWE~KL 46 (281)
..++|..+++.+++..... .-+.+| ..+|.+|+..|++=.
T Consensus 78 L~~lY~y~~~~L~~A~~~~-d~~~l~~v~~~l~~l~~aW~e~~ 119 (122)
T PF02561_consen 78 LFRLYDYMIRQLVQANLKK-DPERLDEVIRILEELRDAWEEIA 119 (122)
T ss_dssp HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999887754431 112233 367889999998743
No 25
>TIGR00064 ftsY signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.
Probab=23.56 E-value=1.4e+02 Score=27.28 Aligned_cols=35 Identities=11% Similarity=0.210 Sum_probs=29.5
Q ss_pred HHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHH
Q 023523 13 VIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMI 47 (281)
Q Consensus 13 VIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLs 47 (281)
+|+++++.++..+.+.+|+..+.++|-+.=++++.
T Consensus 2 ~~~~~~~~l~~~L~~~dv~~~~~~~i~~~~~~~~~ 36 (272)
T TIGR00064 2 DDEDFFEELEEILLESDVGYEVVEKIIEALKKELK 36 (272)
T ss_pred ccHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHh
Confidence 67899999999999999999999988776665554
No 26
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=22.36 E-value=2.1e+02 Score=20.04 Aligned_cols=34 Identities=12% Similarity=0.270 Sum_probs=16.9
Q ss_pred HHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhc
Q 023523 14 IEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAG 50 (281)
Q Consensus 14 IEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSg 50 (281)
++++++.+.+.| +++...+++==..+-++|.+.|
T Consensus 32 ~~ei~~~l~~~y---~~~~~~~~~dv~~fl~~L~~~g 65 (68)
T PF05402_consen 32 VEEIVDALAEEY---DVDPEEAEEDVEEFLEQLREKG 65 (68)
T ss_dssp HHHHHHHHHHHT---T--HHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHc---CCCHHHHHHHHHHHHHHHHHCc
Confidence 567777777776 5666544332223444444443
No 27
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=22.32 E-value=1.9e+02 Score=23.80 Aligned_cols=22 Identities=9% Similarity=0.143 Sum_probs=18.4
Q ss_pred HHhCCCChHHHHHHHHHHHHHH
Q 023523 25 FVNNGPGESVLNELQGIWEMKM 46 (281)
Q Consensus 25 FeeeGVDEqVLqELKqlWE~KL 46 (281)
+.++.++++-|++|+++++++-
T Consensus 97 ~~~~~ls~eele~L~~li~~~~ 118 (130)
T TIGR02698 97 IEESPLSQTDIEKLEKLLSEKK 118 (130)
T ss_pred HhcCCCCHHHHHHHHHHHHhcc
Confidence 4556799999999999988764
No 28
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=21.78 E-value=92 Score=23.94 Aligned_cols=19 Identities=26% Similarity=0.470 Sum_probs=14.5
Q ss_pred hCCCChHHHHHHHHHHHHH
Q 023523 27 NNGPGESVLNELQGIWEMK 45 (281)
Q Consensus 27 eeGVDEqVLqELKqlWE~K 45 (281)
.+|+.+.|+++++..|+..
T Consensus 24 k~Glt~~vi~~i~~~l~~~ 42 (84)
T PF01985_consen 24 KNGLTDGVIEEIDDALEKH 42 (84)
T ss_dssp TTSS-HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHhC
Confidence 3688899999999988863
No 29
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the 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=21.09 E-value=46 Score=28.90 Aligned_cols=24 Identities=8% Similarity=0.277 Sum_probs=21.1
Q ss_pred CCChHHHHHHHHHHHHHHHHhccc
Q 023523 29 GPGESVLNELQGIWEMKMIQAGVI 52 (281)
Q Consensus 29 GVDEqVLqELKqlWE~KLsQSgAa 52 (281)
.+.+.-++.|+++|.+-|+.+..+
T Consensus 2 ~Wtde~~~~L~~lw~~G~SasqIA 25 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGLSASQIA 25 (162)
T ss_pred CCCHHHHHHHHHHHHcCCCHHHHH
Confidence 478889999999999999888776
Done!