Query 028639
Match_columns 206
No_of_seqs 121 out of 187
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 14:39:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028639.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028639hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2351 RNA polymerase II, fou 100.0 2.3E-39 5.1E-44 259.8 6.6 112 91-204 3-114 (134)
2 COG5250 RPB4 RNA polymerase II 100.0 3.1E-30 6.6E-35 206.4 7.2 113 91-204 4-118 (138)
3 smart00657 RPOL4c DNA-directed 99.9 1.9E-26 4.2E-31 181.4 8.8 98 104-204 1-98 (118)
4 PRK14981 DNA-directed RNA poly 99.9 7.2E-23 1.6E-27 160.7 7.7 85 109-202 8-92 (112)
5 PF03874 RNA_pol_Rpb4: RNA pol 99.8 2.8E-21 6.1E-26 149.4 7.0 93 112-204 1-100 (117)
6 COG1460 Uncharacterized protei 99.0 8.7E-10 1.9E-14 87.9 7.7 82 109-200 9-91 (114)
7 KOG4168 Predicted RNA polymera 95.0 0.087 1.9E-06 44.1 6.6 97 108-204 6-113 (149)
8 PF09999 DUF2240: Uncharacteri 38.7 45 0.00098 27.8 3.8 42 142-183 85-127 (144)
9 KOG4479 Transcription factor e 35.3 37 0.00079 26.4 2.5 36 161-200 36-72 (92)
10 TIGR03279 cyano_FeS_chp putati 34.4 42 0.00091 32.6 3.4 63 136-204 188-252 (433)
11 COG3612 Uncharacterized protei 32.1 69 0.0015 27.3 3.9 43 142-184 91-133 (157)
12 CHL00181 cbbX CbbX; Provisiona 31.6 2.1E+02 0.0046 25.6 7.2 79 111-195 194-283 (287)
13 PRK13740 conjugal transfer pro 28.0 2E+02 0.0044 21.5 5.3 51 112-168 16-66 (70)
14 PF11116 DUF2624: Protein of u 26.3 1.2E+02 0.0025 23.4 4.0 55 144-198 17-79 (85)
15 PRK10945 gene expression modul 25.3 78 0.0017 23.8 2.7 35 146-181 7-41 (72)
16 PRK10391 oriC-binding nucleoid 24.4 99 0.0022 23.2 3.1 33 147-180 3-36 (71)
17 PF02023 SCAN: SCAN domain; I 22.1 2.7E+02 0.0059 21.1 5.3 66 133-200 13-83 (95)
18 PHA03056 putative myristoylate 20.9 1.7E+02 0.0038 24.7 4.3 75 113-187 13-110 (165)
19 PRK07075 isochorismate-pyruvat 20.4 2.7E+02 0.0059 21.3 5.1 39 110-159 5-43 (101)
No 1
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=100.00 E-value=2.3e-39 Score=259.83 Aligned_cols=112 Identities=36% Similarity=0.444 Sum_probs=106.3
Q ss_pred cccccCccccccCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 028639 91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSL 170 (206)
Q Consensus 91 ~~~eEdaaeLkLG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL 170 (206)
..+||||++|+||+||. +++|||+|||++||+++.++++ .++|+..++++||+||++|+++||||+|+++|.+||.+|
T Consensus 3 g~~EEdAa~lk~g~EFe-~~~~L~~sEa~lllE~~~~q~~-rs~d~~~~~s~Vf~kTl~Y~~~FsRfKn~etv~avr~iL 80 (134)
T KOG2351|consen 3 GEEEEDAAELKLGKEFE-TADALMLSEARLLLEHRLEQRR-RSEDDESEMSDVFKKTLQYLDRFSRFKNRETVRAVRTIL 80 (134)
T ss_pred chhhccHHhccccHHHH-HHHHHHHHHHHHHHHHHHHHHh-hcccccchHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 46899999999999998 9999999999999999998874 367888999999999999999999999999999999999
Q ss_pred HhCCCCcchhhhhhccCCCCHHHHHHhhcccccc
Q 028639 171 SEHGVTDGEICVIANICPETVEEAYAIVPSLKVW 204 (206)
Q Consensus 171 ~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~~ 204 (206)
...+||+||+|||+||||+|+||||+|||||+.-
T Consensus 81 s~~~lhkFE~A~lgnLcpetaEEAkaLvPSL~nk 114 (134)
T KOG2351|consen 81 SGKGLHKFEVAQLGNLCPETAEEAKALVPSLENK 114 (134)
T ss_pred hhCCcchhhHHHHhccCcccHHHHHHhccccccc
Confidence 9999999999999999999999999999999864
No 2
>COG5250 RPB4 RNA polymerase II, fourth largest subunit [Transcription]
Probab=99.96 E-value=3.1e-30 Score=206.43 Aligned_cols=113 Identities=24% Similarity=0.304 Sum_probs=99.6
Q ss_pred cccccCccccccCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHH--HHHHHHHHHhcCCCCCHHHHHHHHH
Q 028639 91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVS--FDKGLLYAKTHSHFTNPQAVKGLFQ 168 (206)
Q Consensus 91 ~~~eEdaaeLkLG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~v--f~KTleYv~rFSkfkn~Esv~aVRe 168 (206)
+..||||++|+|||||+ |.+.||++||+++|+....+++..-...+...++| |++|+.|++.|+||++.+.+.++|.
T Consensus 4 ~~~ee~aa~lklg~efe-~ed~l~lsEAr~lie~~l~~rrretn~~e~~s~dvk~~k~T~~Yl~~F~Rfkd~e~~~a~~~ 82 (138)
T COG5250 4 AIFEEDAAQLKLGPEFE-NEDMLMLSEARYLIEGQLERRRRETNGAEFRSNDVKVFKSTLGYLDDFCRFKDKEVAEALRT 82 (138)
T ss_pred hHhhhhHHHhhcCcccc-chHHHHHHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 46899999999999998 99999999999999998877642211223344454 9999999999999999999999999
Q ss_pred HHHhCCCCcchhhhhhccCCCCHHHHHHhhcccccc
Q 028639 169 SLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVW 204 (206)
Q Consensus 169 lL~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~~ 204 (206)
+|...|+|+|||||+++|||+++||||+|||||..-
T Consensus 83 ~L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nk 118 (138)
T COG5250 83 TLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNK 118 (138)
T ss_pred HHccCCcchhhHHHhhccccccHHHHHhhccccccc
Confidence 999999999999999999999999999999999763
No 3
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=99.93 E-value=1.9e-26 Score=181.38 Aligned_cols=98 Identities=29% Similarity=0.404 Sum_probs=87.2
Q ss_pred cccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhh
Q 028639 104 QELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVI 183 (206)
Q Consensus 104 ~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqL 183 (206)
++|. |++|||||||++||+.+++.. .+.++..+++.++++|++|+++|+++++++++.+++++|..++||+||+|||
T Consensus 1 ~~f~-~a~~L~n~Ev~~ll~~k~~~~--~~~~~~~~l~~v~~~tl~Yl~~~~~~~~~e~i~~~~~~L~~~~L~k~E~~~i 77 (118)
T smart00657 1 PEFK-NATCLTNSEVQLLLELKRQSK--ESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVRTLLKSKKLHKFEIAQL 77 (118)
T ss_pred CCcc-chhHhHHHHHHHHHHHHHHhh--ccccccchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCCHHHHHHH
Confidence 4787 999999999999999654432 2344556678999999999999999999999999999999999999999999
Q ss_pred hccCCCCHHHHHHhhcccccc
Q 028639 184 ANICPETVEEAYAIVPSLKVW 204 (206)
Q Consensus 184 aNLcPeTaEEAKALIPSL~~~ 204 (206)
+||||.|++||++|||||++.
T Consensus 78 ~Nl~P~s~~E~~~lI~sl~~r 98 (118)
T smart00657 78 GNLRPETAEEAQLLIPSLEER 98 (118)
T ss_pred hCCCCCCHHHHHHHhhhhhcc
Confidence 999999999999999999843
No 4
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=99.88 E-value=7.2e-23 Score=160.73 Aligned_cols=85 Identities=24% Similarity=0.278 Sum_probs=76.2
Q ss_pred ccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhhhccCC
Q 028639 109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICP 188 (206)
Q Consensus 109 na~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqLaNLcP 188 (206)
+.+|||++||+.||+++.+.+ ++++++++|++|+++|++++..++.+.+++++...+||+|++|+|+||||
T Consensus 8 ~e~~lt~sEa~~iL~~~~~~~---------els~~~~ktl~y~~kFsk~~~e~a~elve~L~~~~~l~e~~a~~I~nL~P 78 (112)
T PRK14981 8 EEEYITIAEAKEILSEIEEER---------ELSYELRRTLDYLNRFSKLDPEDAEELVEELLELEKMKEKTAVKIADILP 78 (112)
T ss_pred hcccccHHHHHHHHHHHHhcc---------chhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHccCCCHHHHHHHHhcCC
Confidence 567999999999999876541 67899999999999999998777777788888887899999999999999
Q ss_pred CCHHHHHHhhcccc
Q 028639 189 ETVEEAYAIVPSLK 202 (206)
Q Consensus 189 eTaEEAKALIPSL~ 202 (206)
+|+||||+||||+.
T Consensus 79 ~~~dElrai~~~~~ 92 (112)
T PRK14981 79 ETRDELRAIFAKER 92 (112)
T ss_pred CCHHHHHHHHHHhc
Confidence 99999999999994
No 5
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=99.84 E-value=2.8e-21 Score=149.39 Aligned_cols=93 Identities=33% Similarity=0.402 Sum_probs=77.0
Q ss_pred cccHHHHHHHHHHHHHHHhhh-------cCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhhh
Q 028639 112 CLMDCEAAHILEGIQEQMALL-------SADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIA 184 (206)
Q Consensus 112 cLslsEV~lILe~~~e~~~~~-------s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqLa 184 (206)
||||+||..||+++.+..+.. ...+..+++.++.+|++|+++|+++.+++++..+++.|..++|++||++||+
T Consensus 1 ~Lsn~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi~ 80 (117)
T PF03874_consen 1 LLSNYEVLQILEKRREEQKNKSKKKQKNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELREELKKFGLTEFEILQII 80 (117)
T ss_dssp EE-HHHHHHHHHHHHHHHHCHCHHHHHHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHHHHTTSTS-HHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHHHHhcccCCHHHHHHHh
Confidence 799999999999665543211 1345667889999999999999999999999999999999999999999999
Q ss_pred ccCCCCHHHHHHhhcccccc
Q 028639 185 NICPETVEEAYAIVPSLKVW 204 (206)
Q Consensus 185 NLcPeTaEEAKALIPSL~~~ 204 (206)
||||.|++|+++|||+++..
T Consensus 81 Nl~P~~~~El~~ii~~~~~r 100 (117)
T PF03874_consen 81 NLRPTTAVELRAIIESLESR 100 (117)
T ss_dssp HH--SSHHHHHHHSTTGTTT
T ss_pred cCCCCCHHHHHHHHHHhccC
Confidence 99999999999999999853
No 6
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=99.03 E-value=8.7e-10 Score=87.87 Aligned_cols=82 Identities=22% Similarity=0.307 Sum_probs=63.3
Q ss_pred ccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHH-HHHHHHhCCCCcchhhhhhccC
Q 028639 109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKG-LFQSLSEHGVTDGEICVIANIC 187 (206)
Q Consensus 109 na~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~a-VRelL~~~gL~kFEIAqLaNLc 187 (206)
+-+.+|++||+.||..+ ....++++.++.||+|+++|+++. |+.++. |.+++.-.++.+-=++-|++||
T Consensus 9 e~~yiti~Eak~il~~~---------~~~~eL~y~~~~al~y~~kFakld-pe~a~e~veEL~~i~~~~e~~avkIadI~ 78 (114)
T COG1460 9 EEKYITISEAKKILSKV---------EREEELTYEQREALEYAEKFAKLD-PEKARELVEELLSIVKMSEKIAVKIADIM 78 (114)
T ss_pred hccCccHHHHHHHHHHh---------cccccchHHHHHHHHHHHHHhcCC-HHHHHHHHHHHHhhccccHHHHHHHHHhC
Confidence 44689999999999877 234467899999999999999998 666655 5555555555333344499999
Q ss_pred CCCHHHHHHhhcc
Q 028639 188 PETVEEAYAIVPS 200 (206)
Q Consensus 188 PeTaEEAKALIPS 200 (206)
|+|.+|.|+++-.
T Consensus 79 P~t~~ElRsIla~ 91 (114)
T COG1460 79 PRTPDELRSILAK 91 (114)
T ss_pred CCCHHHHHHHHHH
Confidence 9999999998743
No 7
>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]
Probab=95.00 E-value=0.087 Score=44.10 Aligned_cols=97 Identities=18% Similarity=0.204 Sum_probs=69.0
Q ss_pred cccccccHHHHHHHHHHHHHHHhh----hcCC-----CCCCchHHHHHHHHHHHhcC--CCCCHHHHHHHHHHHHhCCCC
Q 028639 108 KNAKCLMDCEAAHILEGIQEQMAL----LSAD-----PTIKIPVSFDKGLLYAKTHS--HFTNPQAVKGLFQSLSEHGVT 176 (206)
Q Consensus 108 ena~cLslsEV~lILe~~~e~~~~----~s~d-----~~~~~s~vf~KTleYv~rFS--kfkn~Esv~aVRelL~~~gL~ 176 (206)
.+.-.|++-||...|+....+... ..+. .-.+++-+...|+.|+..-. .-.+.|.+.++-.-|..++|+
T Consensus 6 ar~a~LtnyEVl~fL~el~~~n~~~~k~s~r~~~Q~~~~~~l~ti~~et~kYls~~~n~~~qt~E~i~el~~k~~~fkLt 85 (149)
T KOG4168|consen 6 ARNAALTNYEVLQFLNELECMNEEADKSSHRLGAQNILQNDLPTITYETLKYLSDNKNASTQTNESIIELITKLKSFKLT 85 (149)
T ss_pred hhHHHhhhHHHHHHHHHhhhhhhhhhhhhhhhhcccccccccchhHHHHHHHHhcCcccccccHHHHHHHHHHhccccch
Confidence 455689999999999876521110 0011 11236678889999998755 333466777777777788999
Q ss_pred cchhhhhhccCCCCHHHHHHhhcccccc
Q 028639 177 DGEICVIANICPETVEEAYAIVPSLKVW 204 (206)
Q Consensus 177 kFEIAqLaNLcPeTaEEAKALIPSL~~~ 204 (206)
+-|+-||.|+.|-++=|...+|--+++.
T Consensus 86 KAE~LqiiN~rPss~vel~~~iE~~eeR 113 (149)
T KOG4168|consen 86 KAEILQIINLRPSSSVELYLIIEEVEER 113 (149)
T ss_pred HHHHHHHhccCcchHHHHHHHHHHHHHh
Confidence 9999999999999998888887655443
No 8
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=38.67 E-value=45 Score=27.75 Aligned_cols=42 Identities=19% Similarity=0.278 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCC-CCcchhhhh
Q 028639 142 VSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHG-VTDGEICVI 183 (206)
Q Consensus 142 ~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~g-L~kFEIAqL 183 (206)
.+|.+.++|+-.=..+.-.+.+.+|.+.-.+++ +-..|+|.+
T Consensus 85 ~~fe~ild~ia~~~g~~~~evv~~in~~q~~~~~~l~~e~aal 127 (144)
T PF09999_consen 85 DPFERILDYIAAKTGIEKQEVVAEINELQEELGGLLDPEAAAL 127 (144)
T ss_pred cHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCCHHHHHH
Confidence 579999999999999988999999999777776 668887764
No 9
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=35.31 E-value=37 Score=26.40 Aligned_cols=36 Identities=28% Similarity=0.316 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhCCCCcchhhh-hhccCCCCHHHHHHhhcc
Q 028639 161 QAVKGLFQSLSEHGVTDGEICV-IANICPETVEEAYAIVPS 200 (206)
Q Consensus 161 Esv~aVRelL~~~gL~kFEIAq-LaNLcPeTaEEAKALIPS 200 (206)
+--..+|+++...|+..|.+-| +|-+.|+ ||+|+|-
T Consensus 36 ~ik~mcrniimEkG~~n~tvdqL~AeitPk----aRaLVPd 72 (92)
T KOG4479|consen 36 DIKEMCRNIIMEKGVDNITVDQLAAEITPK----ARALVPD 72 (92)
T ss_pred HHHHHHHHHHHHhccccccHHHHHHHhCch----hhhhchH
Confidence 3444588999988998899888 6677785 7888884
No 10
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase. Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Probab=34.37 E-value=42 Score=32.63 Aligned_cols=63 Identities=16% Similarity=0.141 Sum_probs=42.3
Q ss_pred CCCCchHHHHHHHHHHHhcCC--CCCHHHHHHHHHHHHhCCCCcchhhhhhccCCCCHHHHHHhhcccccc
Q 028639 136 PTIKIPVSFDKGLLYAKTHSH--FTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVW 204 (206)
Q Consensus 136 ~~~~~s~vf~KTleYv~rFSk--fkn~Esv~aVRelL~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~~ 204 (206)
|..+.-+.+.+|+.++..|.. +..-.++.-| =-||++|=- -+-.|.|-|.|+|+..|.-+++|
T Consensus 188 PGiNDg~~L~~Ti~dL~~~~~~~~P~v~S~avV-----PVGlTk~R~-~l~~l~~~~~e~A~~vi~~ie~~ 252 (433)
T TIGR03279 188 PGINDGKHLERTLRDLAQFHDGDWPTVLSVAVV-----PVGLTRFRP-EEDELTPVTPECARRVIAQVEAL 252 (433)
T ss_pred CCcCCHHHHHHHHHHHHhhcccCCCceeEEEEE-----ccccccCCC-CCCCCccCCHHHHHHHHHHHHHH
Confidence 555666788888888888754 3322332221 137777743 37788999999999999777655
No 11
>COG3612 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.14 E-value=69 Score=27.27 Aligned_cols=43 Identities=19% Similarity=0.166 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhhh
Q 028639 142 VSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIA 184 (206)
Q Consensus 142 ~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqLa 184 (206)
.+|.+.||.+--=.++.-+|.|.+|+++.++.+|-.|-+|.|+
T Consensus 91 ~~~driLDa~aA~g~~~rqe~Va~vn~~qe~l~lvtf~~aaLi 133 (157)
T COG3612 91 PSFDRILDAAAASGKLDRQEAVAEVNSLQENLGLVTFQTAALI 133 (157)
T ss_pred chHHHHHHHHHHhcCccHHHHHHHHHHHHHHhcceehHHHHHH
Confidence 4799999999999999999999999999999998899887754
No 12
>CHL00181 cbbX CbbX; Provisional
Probab=31.55 E-value=2.1e+02 Score=25.57 Aligned_cols=79 Identities=14% Similarity=0.024 Sum_probs=47.8
Q ss_pred ccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh-----------CCCCcch
Q 028639 111 KCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSE-----------HGVTDGE 179 (206)
Q Consensus 111 ~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~-----------~gL~kFE 179 (206)
..++..|...|++...++.. ... .......-++|+.+-......-.++.||+++++ .+.....
T Consensus 194 ~~~t~~el~~I~~~~l~~~~-----~~l-~~~~~~~L~~~i~~~~~~~~~GNaR~vrn~ve~~~~~~~~r~~~~~~~~~~ 267 (287)
T CHL00181 194 PDYTPEELLQIAKIMLEEQQ-----YQL-TPEAEKALLDYIKKRMEQPLFANARSVRNALDRARMRQANRIFESGGRVLT 267 (287)
T ss_pred CCcCHHHHHHHHHHHHHHhc-----CCC-ChhHHHHHHHHHHHhCCCCCCccHHHHHHHHHHHHHHHHHHHHcCCCCCCC
Confidence 35678899888887765431 111 123466678888875544445556667776652 1222334
Q ss_pred hhhhhccCCCCHHHHH
Q 028639 180 ICVIANICPETVEEAY 195 (206)
Q Consensus 180 IAqLaNLcPeTaEEAK 195 (206)
...|..|+|+++++-+
T Consensus 268 ~~~l~~~~~~d~~~~~ 283 (287)
T CHL00181 268 KADLVTIEAEDILKSR 283 (287)
T ss_pred HHHHhCCCHHHHhHHH
Confidence 5568888888876654
No 13
>PRK13740 conjugal transfer protein TraY; Provisional
Probab=27.97 E-value=2e+02 Score=21.50 Aligned_cols=51 Identities=14% Similarity=0.019 Sum_probs=35.6
Q ss_pred cccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 028639 112 CLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (206)
Q Consensus 112 cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRe 168 (206)
+-...|...+|....++- ....-.++.-+-.||+.+|.-|-|+|.+..+.+
T Consensus 16 ~~Ld~etn~lL~~A~~RS------GRSK~~EA~lRL~DHL~rFpDfy~sei~~e~~~ 66 (70)
T PRK13740 16 LKLDEDTNNKLIEAKERS------GRSKTNEVQIRLRDHLKRFPDFYNSEIFREVAE 66 (70)
T ss_pred EEeCHHHHHHHHHHHHHc------CCcccHHHHHHHHHHHHhCccccchHHhhHhhh
Confidence 344567778887665541 122334788899999999999999977766543
No 14
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=26.26 E-value=1.2e+02 Score=23.37 Aligned_cols=55 Identities=18% Similarity=0.190 Sum_probs=39.3
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcc---h----hhhhhcc-CCCCHHHHHHhh
Q 028639 144 FDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDG---E----ICVIANI-CPETVEEAYAIV 198 (206)
Q Consensus 144 f~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kF---E----IAqLaNL-cPeTaEEAKALI 198 (206)
..-=+.|++.|.--=+++.++.|-.+|....+.-| | +-.|+.+ -|+|+.++..|+
T Consensus 17 ~~eLlkyskqy~i~it~~QA~~I~~~lr~k~inIfn~~~r~~llkeia~iT~p~ta~~vn~Lf 79 (85)
T PF11116_consen 17 AKELLKYSKQYNISITKKQAEQIANILRGKNINIFNEQERKKLLKEIAKITSPQTAKQVNELF 79 (85)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 34456788888888888899999999985543333 2 2235666 788999888876
No 15
>PRK10945 gene expression modulator; Provisional
Probab=25.32 E-value=78 Score=23.78 Aligned_cols=35 Identities=9% Similarity=0.112 Sum_probs=26.9
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhh
Q 028639 146 KGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEIC 181 (206)
Q Consensus 146 KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIA 181 (206)
...+|+-+|-||.+.++.+.|-+-+. +.|+.-|+.
T Consensus 7 tk~dyL~~fRrcss~eTLEkvie~~~-~~L~~~E~~ 41 (72)
T PRK10945 7 TKTDYLMRLRRCQTIDTLERVIEKNK-YELSDDELA 41 (72)
T ss_pred cHHHHHHHHHhcCcHHHHHHHHHHhh-ccCCHHHHH
Confidence 45899999999999999998877654 346665543
No 16
>PRK10391 oriC-binding nucleoid-associated protein; Provisional
Probab=24.36 E-value=99 Score=23.18 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=25.8
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHhCCCCc-chh
Q 028639 147 GLLYAKTHSHFTNPQAVKGLFQSLSEHGVTD-GEI 180 (206)
Q Consensus 147 TleYv~rFSkfkn~Esv~aVRelL~~~gL~k-FEI 180 (206)
.++|+-+|-|+.+.++.+.|-+-+.- .|+. -|+
T Consensus 3 k~eyLlkfRkcss~eTLEkv~e~~~y-~L~~~~e~ 36 (71)
T PRK10391 3 VQDYLLKFRKISSLESLEKLFDHLNY-TLTDDQEI 36 (71)
T ss_pred HHHHHHHHHhcCcHHHHHHHHHHhhc-ccCCHHHH
Confidence 57999999999999999998777643 4665 444
No 17
>PF02023 SCAN: SCAN domain; InterPro: IPR003309 A number of C2H2-zinc finger proteins contain a highly conserved N-terminal motif termed the SCAN domain. The SCAN domain may play an important role in the assembly and function of this newly defined subclass of transcriptional regulators [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3LHR_B 4E6S_A 2FI2_A 1Y7Q_A.
Probab=22.10 E-value=2.7e+02 Score=21.13 Aligned_cols=66 Identities=12% Similarity=0.027 Sum_probs=42.5
Q ss_pred cCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhC----CCCcchhhh-hhccCCCCHHHHHHhhcc
Q 028639 133 SADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEH----GVTDGEICV-IANICPETVEEAYAIVPS 200 (206)
Q Consensus 133 s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~----gL~kFEIAq-LaNLcPeTaEEAKALIPS 200 (206)
.-.+.....+++.+-.+++.+.-+- ...+.++|.++|-.. .| +-|+.. +..=.|+|.+||-+|+-.
T Consensus 13 ~~~~~~~p~e~~~rL~~l~~~WL~p-e~~tkeqi~ellvlEQFL~~l-P~e~~~wV~e~~p~s~~ea~~Lae~ 83 (95)
T PF02023_consen 13 QYQEGEGPREFLSRLRELCDRWLQP-EVHTKEQILELLVLEQFLNIL-PPEVQTWVRERKPESAEEAVALAED 83 (95)
T ss_dssp -CCTTTSHHHHHHHHHHHHHHHH-T-TTS-HHHHHHHHHHHHHHHHS--HHHHHHHHTCS-SSHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHHhCcc-ccCcHHHHHHHHHHHHHHHHC-CHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 3345556668888888999888665 344566666665421 24 556555 788899999999998743
No 18
>PHA03056 putative myristoylated protein; Provisional
Probab=20.92 E-value=1.7e+02 Score=24.66 Aligned_cols=75 Identities=17% Similarity=0.218 Sum_probs=42.7
Q ss_pred ccHH-HHHHHHHHHHHHHhh----hcCCCCCCc------------hHHHHHHHH---HHHhcCCCCCHHHHHH-HHHHHH
Q 028639 113 LMDC-EAAHILEGIQEQMAL----LSADPTIKI------------PVSFDKGLL---YAKTHSHFTNPQAVKG-LFQSLS 171 (206)
Q Consensus 113 Lsls-EV~lILe~~~e~~~~----~s~d~~~~~------------s~vf~KTle---Yv~rFSkfkn~Esv~a-VRelL~ 171 (206)
|++- -|.+||+++.+++.. +++++..+. +-+++.-.+ -++.|..-+++++..+ |..+|.
T Consensus 13 lmnkenaemilekivdhivmyisdesrdennpeyidfrnrygdyrsliiksdheFsnLCKd~l~~~~p~T~~~~IK~Il~ 92 (165)
T PHA03056 13 LMNKENAEMILEKIVDHIVMYISDESRDENNPEYIDFRNRYGDYRSLIIKSDHEFVKLCKDHAEKSSPETQQMIIKHIYE 92 (165)
T ss_pred HhchhhHHHHHHHHHHHheeeecccccccCCchheehhhhccchhhhhhhccHHHHHHHHHHHHcCCchHHHHHHHHHHH
Confidence 4444 466788999888753 122221110 012222222 2345666677777776 888888
Q ss_pred hCCCCcchhhh--hhccC
Q 028639 172 EHGVTDGEICV--IANIC 187 (206)
Q Consensus 172 ~~gL~kFEIAq--LaNLc 187 (206)
++.+..-++.- |+|+|
T Consensus 93 qy~IP~S~Vvw~Pia~~c 110 (165)
T PHA03056 93 QYLIPVSEVLLKPMMSMG 110 (165)
T ss_pred HhcCChhHHHHHHHHhhC
Confidence 77777666533 77776
No 19
>PRK07075 isochorismate-pyruvate lyase; Reviewed
Probab=20.42 E-value=2.7e+02 Score=21.33 Aligned_cols=39 Identities=13% Similarity=0.320 Sum_probs=32.4
Q ss_pred cccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCC
Q 028639 110 AKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTN 159 (206)
Q Consensus 110 a~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn 159 (206)
.+|-++.+++.-|+.+.+++. .+|.+=+.|+.+-+++|.
T Consensus 5 ~~~~~L~~lR~~ID~ID~~iv-----------~LL~eR~~~~~~ia~~K~ 43 (101)
T PRK07075 5 EACTGLDDIREAIDRLDRDII-----------AALGRRMQYVKAASRFKP 43 (101)
T ss_pred HHHhhHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhcC
Confidence 479999999999998877653 678888889988888886
Done!