Query gi|254780417|ref|YP_003064830.1| transcriptional regulator CarD family protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 188
No_of_seqs 115 out of 1553
Neff 7.7
Searched_HMMs 39220
Date Sun May 29 18:02:37 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780417.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1329 Transcriptional regula 100.0 2.4E-37 6.2E-42 260.4 13.0 164 11-174 2-165 (166)
2 PRK10689 transcription-repair 99.9 2.5E-22 6.3E-27 163.9 9.1 147 12-174 475-621 (1148)
3 TIGR00580 mfd transcription-re 99.8 4.3E-21 1.1E-25 155.9 8.0 147 12-174 381-529 (997)
4 COG1197 Mfd Transcription-repa 99.8 2.8E-20 7.1E-25 150.7 10.7 146 13-174 470-615 (1139)
5 pfam02559 CarD_TRCF CarD-like/ 99.8 1.2E-18 3.2E-23 140.1 7.4 98 13-123 1-98 (98)
6 PRK06330 transcript cleavage f 93.1 0.093 2.4E-06 31.6 3.1 94 13-110 306-428 (906)
7 TIGR01073 pcrA ATP-dependent D 88.8 0.35 9E-06 27.9 2.7 45 8-56 756-801 (811)
8 PRK10917 ATP-dependent DNA hel 85.4 2 5.1E-05 23.0 4.9 33 143-175 247-279 (677)
9 COG1747 Uncharacterized N-term 85.2 0.76 1.9E-05 25.7 2.7 96 13-111 287-410 (711)
10 pfam12073 DUF3553 Protein of u 80.3 1.4 3.5E-05 24.1 2.4 21 14-34 1-24 (52)
11 TIGR00643 recG ATP-dependent D 79.9 2 5.2E-05 22.9 3.2 41 131-175 288-329 (721)
12 pfam09871 DUF2098 Uncharacteri 77.5 2.2 5.6E-05 22.7 2.8 24 14-37 3-27 (91)
13 TIGR00032 argG argininosuccina 75.2 1.4 3.7E-05 23.9 1.3 28 23-50 268-295 (420)
14 COG1200 RecG RecG-like helicas 74.0 7.3 0.00019 19.4 6.0 33 143-175 252-284 (677)
15 TIGR01075 uvrD DNA helicase II 63.5 4.2 0.00011 21.0 1.6 25 9-33 688-712 (741)
16 COG4014 Uncharacterized protei 62.8 6.4 0.00016 19.8 2.5 26 15-40 10-36 (97)
17 COG4709 Predicted membrane pro 61.2 8.7 0.00022 18.9 2.9 52 129-180 23-76 (195)
18 PRK08115 ribonucleotide-diphos 49.9 15 0.00039 17.4 2.6 32 5-36 49-88 (857)
19 TIGR02062 RNase_B exoribonucle 49.6 7.4 0.00019 19.4 1.0 21 1-21 112-132 (664)
20 KOG0463 consensus 48.9 19 0.00048 16.7 3.0 61 3-67 359-421 (641)
21 KOG3091 consensus 48.2 19 0.00048 16.8 2.9 37 135-171 389-426 (508)
22 pfam00924 MS_channel Mechanose 47.5 22 0.00056 16.3 3.9 23 12-35 57-79 (203)
23 KOG3038 consensus 44.4 24 0.00062 16.0 3.0 48 13-61 198-247 (264)
24 cd00320 cpn10 Chaperonin 10 Kd 39.6 23 0.00059 16.1 2.3 29 13-49 57-85 (93)
25 COG3264 Small-conductance mech 39.3 29 0.00074 15.5 4.9 24 12-36 659-682 (835)
26 PRK00364 groES co-chaperonin G 38.4 26 0.00066 15.8 2.4 30 12-49 57-86 (95)
27 COG0137 ArgG Argininosuccinate 36.3 11 0.00028 18.2 0.2 28 22-49 250-277 (403)
28 PHA02142 putative RNA ligase 35.8 13 0.00034 17.7 0.6 12 11-22 41-52 (366)
29 PRK10334 mechanosensitive chan 35.0 34 0.00087 15.1 5.0 42 12-63 128-169 (285)
30 PRK10754 quinone oxidoreductas 34.4 35 0.00088 15.0 2.5 23 12-34 77-99 (327)
31 PRK05886 yajC preprotein trans 34.1 35 0.0009 15.0 3.1 35 12-54 37-71 (108)
32 KOG3858 consensus 33.7 20 0.0005 16.6 1.1 42 9-52 33-77 (233)
33 pfam00166 Cpn10 Chaperonin 10 32.9 34 0.00087 15.1 2.3 16 11-26 54-69 (92)
34 pfam09513 consensus 32.6 16 0.00041 17.1 0.6 12 11-22 35-46 (356)
35 PRK10188 DNA-binding transcrip 30.6 40 0.001 14.6 2.9 44 129-172 178-222 (240)
36 TIGR02890 spore_yteA sporulati 26.8 20 0.00052 16.5 0.2 43 129-171 40-82 (167)
37 PRK03999 translation initiatio 24.3 52 0.0013 13.9 2.8 31 7-38 4-34 (129)
38 cd05834 HDGF_related The PWWP 24.3 52 0.0013 13.9 2.9 49 12-63 1-53 (83)
39 PRK05370 argininosuccinate syn 24.3 27 0.00069 15.7 0.5 20 13-32 190-209 (447)
40 TIGR00996 Mtu_fam_mce virulenc 24.0 52 0.0013 13.9 2.8 113 14-128 46-176 (304)
41 pfam02699 YajC Preprotein tran 23.7 53 0.0014 13.8 3.2 32 12-51 36-67 (83)
42 TIGR02817 adh_fam_1 zinc-bindi 23.6 35 0.00088 15.0 0.9 11 13-23 81-91 (338)
43 PRK11465 hypothetical protein; 23.4 54 0.0014 13.8 3.6 37 12-49 572-610 (741)
44 PRK13870 transcriptional regul 23.1 55 0.0014 13.8 3.7 44 129-172 172-216 (234)
45 pfam11373 DUF3175 Protein of u 23.0 55 0.0014 13.8 4.9 43 108-150 42-84 (86)
46 cd04714 BAH_BAHCC1 BAH, or Bro 22.8 55 0.0014 13.7 2.7 24 12-35 2-31 (121)
47 PRK04527 argininosuccinate syn 22.6 31 0.0008 15.3 0.6 15 93-107 121-135 (397)
48 PRK00409 recombination and DNA 22.2 57 0.0014 13.7 3.8 45 11-64 632-677 (780)
49 pfam01426 BAH BAH domain. This 21.9 58 0.0015 13.6 2.9 26 13-38 2-33 (119)
50 pfam00877 NLPC_P60 NlpC/P60 fa 21.0 60 0.0015 13.5 2.1 17 9-25 46-62 (105)
51 pfam11626 Rap1_C Rap1 - C term 20.2 63 0.0016 13.4 2.7 49 70-121 5-56 (68)
No 1
>COG1329 Transcriptional regulators, similar to M. xanthus CarD [Transcription]
Probab=100.00 E-value=2.4e-37 Score=260.44 Aligned_cols=164 Identities=49% Similarity=0.780 Sum_probs=160.5
Q ss_pred HHHCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCCCHHHHHHHHHCCCCCC
Q ss_conf 53138998697487850999767898648730253022024888569980520121045433441024678985078664
Q gi|254780417|r 11 RQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKAR 90 (188)
Q Consensus 11 ~~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~~~e~~~l~~~l~~~~~ 90 (188)
+.+|++||.||||.||||.|.+|++++|+|..++||+|.+..++|+++||+.+++.+|+|++++.+.++.+++.+...+.
T Consensus 2 ~~~FkiGd~VVYP~HGvG~I~~Ieeke~~Ge~~~yyVI~f~~~dm~v~VP~~ka~~~GlR~v~~~~~l~~~~~vlq~~~~ 81 (166)
T COG1329 2 QMAFKIGDHVVYPAHGVGIIQAIEEKEIAGETLEYYVIDFPQSDMTVMVPVAKADSVGLRPVVDQEELDRALQVLQGGER 81 (166)
T ss_pred CCCCCCCCEEEECCCCCEEEEHHHHHHHCCCEEEEEEEEECCCCCEEEEECCCHHHCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf 86342799888358766530056677625852489999973788289856451554277333236779999999844675
Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 46655038999999985168999999999999841010000012689999999999977467748998999999999850
Q gi|254780417|r 91 VKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLS 170 (188)
Q Consensus 91 ~~~~~~~~R~~~~~~~lksgd~~~~a~vik~L~~~~~~k~l~~~e~~~l~~A~~~L~~Efa~~l~i~~eea~~~I~~~L~ 170 (188)
....+|++|++.|.++++|||+.++|+|+|+||+++..|+|+++|+++|+.|+++|.+|++++++++.++|..+|.+.|.
T Consensus 82 e~~~~ws~R~k~~~~klksGdi~~~AevvrdL~r~~~qr~l~~~Er~ll~~A~~~l~~Ela~~e~i~~~ea~~~l~~~l~ 161 (166)
T COG1329 82 EKPTMWSRRYKENEEKLKSGDIIDIAEVVRDLYRRDKQRELSYSERRLLEKALQILAGELALAEGISEEEAKTFLDEVLA 161 (166)
T ss_pred CCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 56553789999888776147737899999999986405589968999999999999999999955999999999999755
Q ss_pred CCCC
Q ss_conf 4675
Q gi|254780417|r 171 SKSS 174 (188)
Q Consensus 171 ~~~~ 174 (188)
++++
T Consensus 162 ~~~~ 165 (166)
T COG1329 162 SKSE 165 (166)
T ss_pred HHCC
T ss_conf 2127
No 2
>PRK10689 transcription-repair coupling factor; Provisional
Probab=99.88 E-value=2.5e-22 Score=163.92 Aligned_cols=147 Identities=18% Similarity=0.274 Sum_probs=111.1
Q ss_pred HHCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCCCHHHHHHHHHCCCCCCC
Q ss_conf 31389986974878509997678986487302530220248885699805201210454334410246789850786644
Q gi|254780417|r 12 QGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARV 91 (188)
Q Consensus 12 ~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~~~e~~~l~~~l~~~~~~ 91 (188)
.++++||||||.+||||+|.|+++++++|..+||+.|+|. +++++||||++.+.+..|...+.... -++.|++
T Consensus 475 ~eL~~GDyVVH~dHGIGrY~GL~~iev~G~~~DyL~LeYa-~~DkLYVPVeqL~lIsKY~G~~~~~p--~LdKLGg---- 547 (1148)
T PRK10689 475 AELHPGQPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYA-NDAKLYVPVSSLHLISRYAGGAEENA--PLHKLGG---- 547 (1148)
T ss_pred HHCCCCCEECCCCCCEEEEECCEEEEECCCCCCEEEEEEC-CCCEEEEEHHHHCCEEECCCCCCCCC--CCCCCCC----
T ss_conf 7678898622112575676041898408822225999976-99869856798221421148999887--6110256----
Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf 66550389999999851689999999999998410100000126899999999999774677489989999999998504
Q gi|254780417|r 92 KRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSS 171 (188)
Q Consensus 92 ~~~~~~~R~~~~~~~lksgd~~~~a~vik~L~~~~~~k~l~~~e~~~l~~A~~~L~~Efa~~l~i~~eea~~~I~~~L~~ 171 (188)
..|.++.+.-++++ ..-..++++-...|...++.++....- .+..|++.|+|.+|.||..|++.|..||++
T Consensus 548 --~~W~k~K~Kakk~i----~diA~eLl~lYA~R~~~~G~af~~d~~---~~~eFe~~FpyeET~DQl~AI~eV~~DMes 618 (1148)
T PRK10689 548 --DAWSRARQKAAEKV----RDVAAELLDIYAQRAAKEGFAFKHDRE---QYQLFCDSFPFETTPDQAQAINAVLSDMCQ 618 (1148)
T ss_pred --CHHHHHHHHHHHHH----HHHHHHHHHHHHHHHCCCCCCCCCCHH---HHHHHHHCCCCCCCHHHHHHHHHHHHHHHC
T ss_conf --25899999999999----999999999999872056886789849---999999609997876899999999877638
Q ss_pred CCC
Q ss_conf 675
Q gi|254780417|r 172 KSS 174 (188)
Q Consensus 172 ~~~ 174 (188)
+.|
T Consensus 619 ~~P 621 (1148)
T PRK10689 619 PLA 621 (1148)
T ss_pred CCC
T ss_conf 867
No 3
>TIGR00580 mfd transcription-repair coupling factor; InterPro: IPR004576 All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by TcrF, which releases RNAP and the truncated transcript. The TcrF may replace RNAP at the lesion site and then recruit the UvrA/B/C repair system.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=99.84 E-value=4.3e-21 Score=155.92 Aligned_cols=147 Identities=16% Similarity=0.229 Sum_probs=109.4
Q ss_pred HHCCCCCEEECCCCCCEEEEEEEE-EEECCCCHHHEEEECCCCCCE-EEEECCCHHHCCCCCCCCCHHHHHHHHHCCCCC
Q ss_conf 313899869748785099976789-864873025302202488856-998052012104543344102467898507866
Q gi|254780417|r 12 QGFRTGEHIVYPAHGVGTITEIKE-QEVAGMKLEFFVIAFDKDKMC-LKVPVGKAIDIGMRKLSEAHFVERALKLVRGKA 89 (188)
Q Consensus 12 ~~FkvGD~VVy~~~GVg~i~~I~~-~~i~g~~~eyy~L~~~~~~~~-l~vPv~~~~~~~~R~~~~~~e~~~l~~~l~~~~ 89 (188)
.+.++||+|||-+||||+|.||+. .++.|..+||+.|.|. ++.+ ||||+++.+.+..|...+..... ++.|
T Consensus 381 ~~L~~Gd~VVH~~hGIG~F~~l~~~~~~~g~~~DYL~l~Ya-~~~k~LyvPve~~~li~rY~G~~~~~p~--L~kL---- 453 (997)
T TIGR00580 381 NELKPGDYVVHKDHGIGKFLGLEKKLKVLGIERDYLVLEYA-GEDKKLYVPVEQLDLISRYVGGEGKNPE--LDKL---- 453 (997)
T ss_pred HCCCCCCEEEECCCCCCEEHHHHHHHHHCCCCCCEEEEEEC-CCCCEEEECCCHHHHHHHHCCCCCCCCC--CCCC----
T ss_conf 03799887775335850214223214424765241244402-7786686033124455332067889764--1027----
Q ss_pred CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 44665503899999998516899999999999984101000001268999999999997746774899899999999985
Q gi|254780417|r 90 RVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNL 169 (188)
Q Consensus 90 ~~~~~~~~~R~~~~~~~lksgd~~~~a~vik~L~~~~~~k~l~~~e~~~l~~A~~~L~~Efa~~l~i~~eea~~~I~~~L 169 (188)
.+.-|...+++.+..-..-..++|.-...|...++..+.... ..+..|++.|+|.+|.||..|++.|.+||
T Consensus 454 ------Gg~~W~~~K~kv~~~v~~iA~~Li~lyA~R~~~~G~af~~D~---e~~~~Fe~~FPfeeT~DQ~~AI~eik~Dm 524 (997)
T TIGR00580 454 ------GGKSWEKTKAKVKKSVKEIAAKLIELYAKRKASKGHAFPPDD---EWQAEFEDSFPFEETPDQLKAIEEIKADM 524 (997)
T ss_pred ------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCH---HHHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf ------838899999999999999999999999987515898898880---89999998387889778999999999974
Q ss_pred HCCCC
Q ss_conf 04675
Q gi|254780417|r 170 SSKSS 174 (188)
Q Consensus 170 ~~~~~ 174 (188)
.++.|
T Consensus 525 ~~~~~ 529 (997)
T TIGR00580 525 ESPRP 529 (997)
T ss_pred CCCCC
T ss_conf 06898
No 4
>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]
Probab=99.84 E-value=2.8e-20 Score=150.72 Aligned_cols=146 Identities=15% Similarity=0.234 Sum_probs=108.6
Q ss_pred HCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCCCHHHHHHHHHCCCCCCCC
Q ss_conf 13899869748785099976789864873025302202488856998052012104543344102467898507866446
Q gi|254780417|r 13 GFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVK 92 (188)
Q Consensus 13 ~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~~~e~~~l~~~l~~~~~~~ 92 (188)
+.++||+|||.+||||+|.|+++++++|..++|+.|+|. +++++||||++.+.+..|...+.+.. -++.|+
T Consensus 470 eL~~Gd~VVH~~HGIGrflgl~tl~~~g~~~dyL~l~Ya-~~dkLyVPVeql~lisrY~g~~~~~p--~L~kLG------ 540 (1139)
T COG1197 470 ELKPGDYVVHIDHGIGRFLGLETLEVGGIERDYLELEYA-GEDKLYVPVEQLHLISRYVGASDEAP--KLHKLG------ 540 (1139)
T ss_pred HCCCCCEEEECCCCCEEEEEEEEEECCCCCCCEEEEEEC-CCCEEEEEHHHHHHHHHCCCCCCCCC--CCCCCC------
T ss_conf 378898477515771344204898618876314899976-99738977778567764468998877--542347------
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 65503899999998516899999999999984101000001268999999999997746774899899999999985046
Q gi|254780417|r 93 RTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSSK 172 (188)
Q Consensus 93 ~~~~~~R~~~~~~~lksgd~~~~a~vik~L~~~~~~k~l~~~e~~~l~~A~~~L~~Efa~~l~i~~eea~~~I~~~L~~~ 172 (188)
...|+++. ++++..-..-.+++|+-...|+..++..+....-+ +..|++.|+|.+|.||..|++.|..||.++
T Consensus 541 ~~~W~k~K----~K~~~~v~diA~eLi~lyA~R~~~~G~af~~d~~~---q~~F~~~FPyeET~DQl~AI~eVk~DM~~~ 613 (1139)
T COG1197 541 GGAWKKAK----AKARKKVRDIAAELIKLYAKRQAKKGFAFPPDTEW---QEEFEASFPYEETPDQLKAIEEVKRDMESG 613 (1139)
T ss_pred CHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHH---HHHHHHCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 47789999----99999999999999999998730568787998589---999985499857878999999999886069
Q ss_pred CC
Q ss_conf 75
Q gi|254780417|r 173 SS 174 (188)
Q Consensus 173 ~~ 174 (188)
.|
T Consensus 614 kp 615 (1139)
T COG1197 614 KP 615 (1139)
T ss_pred CC
T ss_conf 86
No 5
>pfam02559 CarD_TRCF CarD-like/TRCF domain. CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG, to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase.
Probab=99.76 E-value=1.2e-18 Score=140.12 Aligned_cols=98 Identities=36% Similarity=0.566 Sum_probs=84.8
Q ss_pred HCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCCCHHHHHHHHHCCCCCCCC
Q ss_conf 13899869748785099976789864873025302202488856998052012104543344102467898507866446
Q gi|254780417|r 13 GFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVK 92 (188)
Q Consensus 13 ~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~~~e~~~l~~~l~~~~~~~ 92 (188)
+|++||+||||+||||+|.||++++++|..++||+|+|.++ +++|||+++.+.++ |.+.+.+++ ..++.|.+.
T Consensus 1 ~~~~GD~VVh~~~Gvg~~~gi~~~~~~~~~~~y~~l~y~~~-~~l~vPv~~~~~i~-ry~~~~~~~-~~l~~L~~~---- 73 (98)
T pfam02559 1 MLKVGDYVVHPDHGVGRFEGIETIEVGGEKREYYVLEYADG-DKLYVPVDQLDLIG-RYIGSEDEV-PVLDKLGGG---- 73 (98)
T ss_pred CCCCCCEEECCCCCCEEEEEEEEEEECCCCCEEEEEEECCC-CEEEEEHHHHHHHH-CCCCCCCCC-CHHHHCCCH----
T ss_conf 99999999777996489968899830891437999996599-88998778876750-376888875-322212856----
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf 6550389999999851689999999999998
Q gi|254780417|r 93 RTMWSRRAQEYDAKINSGDLIAIAEVVRDLH 123 (188)
Q Consensus 93 ~~~~~~R~~~~~~~lksgd~~~~a~vik~L~ 123 (188)
.|++|.+ ++++++...++++++.++
T Consensus 74 --~W~~rk~----k~k~~~~~~a~ell~~~a 98 (98)
T pfam02559 74 --TWKKRKR----KIKSGDIDIAAELLRLLA 98 (98)
T ss_pred --HHHHHHH----HHHHHHHHHHHHHHHHCC
T ss_conf --5899999----999789999999999619
No 6
>PRK06330 transcript cleavage factor/unknown domain fusion protein; Validated
Probab=93.09 E-value=0.093 Score=31.58 Aligned_cols=94 Identities=18% Similarity=0.261 Sum_probs=53.2
Q ss_pred HCCCCCEEECCCCCCEEEEEEEE----EEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCC-CHHHHHHHH----
Q ss_conf 13899869748785099976789----864873025302202488856998052012104543344-102467898----
Q gi|254780417|r 13 GFRTGEHIVYPAHGVGTITEIKE----QEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSE-AHFVERALK---- 83 (188)
Q Consensus 13 ~FkvGD~VVy~~~GVg~i~~I~~----~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~-~~e~~~l~~---- 83 (188)
.|.+|.||.|.+-|||+|..+.. .+|..+.....-++.. ++.+.|.... -+..++.+. ++++.+.+.
T Consensus 306 ~fd~g~~v~h~~wgvg~i~~~~~~gI~IDF~~K~~H~ms~~ma---~taL~~L~kd-hi~VlK~~~~Ke~l~~~i~edp~ 381 (906)
T PRK06330 306 VFDTGNFVYHRTWGVGKITSISDNGIFVDFVSKRGHKLSIQMA---ITALKPLKRE-HIWVLKAIEPKEELVELFKNDIE 381 (906)
T ss_pred EECCCCEEEEEECCCCEEEEECCCCEEEEECCCCCCCCCHHHH---HHHCCCCCCC-CEEHHHHHCCHHHHHHHHHHCHH
T ss_conf 4304867898404653234566874698600156773469999---9860536712-16422430537999999874969
Q ss_pred --------HCCC------------CCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf --------5078------------66446655038999999985168
Q gi|254780417|r 84 --------LVRG------------KARVKRTMWSRRAQEYDAKINSG 110 (188)
Q Consensus 84 --------~l~~------------~~~~~~~~~~~R~~~~~~~lksg 110 (188)
...+ ........|+.||...+..|+..
T Consensus 382 ~~lk~~ikSf~n~~~lk~IK~ELv~~li~~~eWskWW~kaKkiLKKn 428 (906)
T PRK06330 382 WALKVIIKSYKNRMDLKDIKSELVPSLLTQSEWSKWWNKAKQILKKN 428 (906)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC
T ss_conf 99999999732404288899998762179888899999999998438
No 7
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA; InterPro: IPR005751 The DNA helicase PcrA is found mainly in Gram-positive bacteria and belongs to a superfamily of helicases, together with Rep and UvrD helicases from Escherichia coli. The action of the 3'5' bacterial DNA helicase is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilising the duplex and separating the two strands in an active process .; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=88.84 E-value=0.35 Score=27.85 Aligned_cols=45 Identities=22% Similarity=0.321 Sum_probs=31.7
Q ss_pred HHHHHHCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCC-CCCE
Q ss_conf 334531389986974878509997678986487302530220248-8856
Q gi|254780417|r 8 DAMRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDK-DKMC 56 (188)
Q Consensus 8 ~~~~~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~-~~~~ 56 (188)
+.....+.+||.|.|-..|+|.|.+| .-.|...+ +.+.|+. -+.+
T Consensus 756 ~~~~~~w~vGDrv~H~~fG~GTVv~v---~G~G~~~e-l~i~FP~P~gvK 801 (811)
T TIGR01073 756 GGDTLSWAVGDRVSHKKFGVGTVVSV---KGKGDDAE-LDIAFPSPIGVK 801 (811)
T ss_pred CCCCEEEECCCCCCCCCCCEEEEEEE---EECCCCCC-EEEECCCCCCHH
T ss_conf 65632440586103430000589888---50555751-254267885412
No 8
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=85.36 E-value=2 Score=23.01 Aligned_cols=33 Identities=12% Similarity=0.158 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCC
Q ss_conf 999997746774899899999999985046753
Q gi|254780417|r 143 LNRMVREIAAVNSISEPEAINLIEVNLSSKSSK 175 (188)
Q Consensus 143 ~~~L~~Efa~~l~i~~eea~~~I~~~L~~~~~~ 175 (188)
...|.+.|+|.||.+|..|++.|..||.++.|-
T Consensus 247 ~~~~~~~LPF~LT~~Q~~~~~ei~~dl~~~~~m 279 (677)
T PRK10917 247 LKKFLASLPFELTGAQKRVVAEILADLASPKPM 279 (677)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf 999998099988988999999999876599542
No 9
>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]
Probab=85.17 E-value=0.76 Score=25.71 Aligned_cols=96 Identities=13% Similarity=0.224 Sum_probs=57.6
Q ss_pred HCCCCCEEECCCCCCEEEEEEE-----EEEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCCCHHHHHHHH----
Q ss_conf 1389986974878509997678-----9864873025302202488856998052012104543344102467898----
Q gi|254780417|r 13 GFRTGEHIVYPAHGVGTITEIK-----EQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALK---- 83 (188)
Q Consensus 13 ~FkvGD~VVy~~~GVg~i~~I~-----~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~~~e~~~l~~---- 83 (188)
.|..|.+|.|-.-|||+|.|+. ..+|.|......-+.- ......|....+--.+|.+...++......
T Consensus 287 ~f~eGnFVfHqtWgVG~i~~VsfqqkvlidF~~~rah~I~fem---A~saL~pLs~edi~vlk~v~~~d~laa~arkdpe 363 (711)
T COG1747 287 HFDEGNFVFHQTWGVGEIMGVSFQQKVLIDFEGRRAHDISFEM---AFSALQPLSKEDIFVLKRVGDPDDLAAFARKDPE 363 (711)
T ss_pred EECCCCEEEECCCCCCEEEECCCCCCEEEEEHHHHHHHHHHHH---HHHHHCCCCCCCEEHHHHCCCHHHHHHHHHHCHH
T ss_conf 0124755886155520012104666446650212433523999---9987276773334166640897889999850959
Q ss_pred --------HCCCC-----------CCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf --------50786-----------64466550389999999851689
Q gi|254780417|r 84 --------LVRGK-----------ARVKRTMWSRRAQEYDAKINSGD 111 (188)
Q Consensus 84 --------~l~~~-----------~~~~~~~~~~R~~~~~~~lksgd 111 (188)
.++.+ ......+|+.+++.-+.+||.+.
T Consensus 364 wAikviiks~~~~nlKeIK~ELVpsli~e~dWnsWsqkAK~ilKk~t 410 (711)
T COG1747 364 WAIKVIIKSLGPKNLKEIKQELVPSLIPEGDWNSWSQKAKKILKKST 410 (711)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCC
T ss_conf 99999997258766889999888751785012278999999874188
No 10
>pfam12073 DUF3553 Protein of unknown function (DUF3553). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Probab=80.30 E-value=1.4 Score=24.08 Aligned_cols=21 Identities=24% Similarity=0.439 Sum_probs=18.3
Q ss_pred CCCCCEEECCCC---CCEEEEEEE
Q ss_conf 389986974878---509997678
Q gi|254780417|r 14 FRTGEHIVYPAH---GVGTITEIK 34 (188)
Q Consensus 14 FkvGD~VVy~~~---GVg~i~~I~ 34 (188)
|++|++|.||++ |+|+|..+.
T Consensus 1 lePG~~V~~P~~pdWGiGQVQS~I 24 (52)
T pfam12073 1 LEPGMLVRHPDQPDWGVGQVQSNI 24 (52)
T ss_pred CCCCCEEECCCCCCCCCCEEEEEC
T ss_conf 989778768999877700255430
No 11
>TIGR00643 recG ATP-dependent DNA helicase RecG; InterPro: IPR004609 The ATP-dependent DNA helicase RecG 3.6.1 from EC plays a critical role in recombination and DNA repair. It helps to process Holliday junction intermediates to mature products by catalysing branch migration. RecG has DNA unwinding activity characteristic of a DNA helicase with 3' to 5' polarity.; GO: 0004003 ATP-dependent DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=79.92 E-value=2 Score=22.94 Aligned_cols=41 Identities=17% Similarity=0.199 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHHHHHH-HHHHHHCCCHHHHHHHHHHHHHCCCCC
Q ss_conf 001268999999999997-746774899899999999985046753
Q gi|254780417|r 131 KSYSERQLYESALNRMVR-EIAAVNSISEPEAINLIEVNLSSKSSK 175 (188)
Q Consensus 131 l~~~e~~~l~~A~~~L~~-Efa~~l~i~~eea~~~I~~~L~~~~~~ 175 (188)
+...+...+. .+.. .++|.||-+|..|+..|.+||+++.|=
T Consensus 288 ~~~~~~~~l~----k~~~~~LPF~LT~aQ~r~v~EI~~DL~~~~pM 329 (721)
T TIGR00643 288 LNVSENELLE----KFLAKSLPFELTRAQKRVVKEILQDLKSDVPM 329 (721)
T ss_pred EEECHHHHHH----HHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf 1002057999----99985288877677899999999861478753
No 12
>pfam09871 DUF2098 Uncharacterized protein conserved in archaea (DUF2098). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=77.51 E-value=2.2 Score=22.74 Aligned_cols=24 Identities=38% Similarity=0.728 Sum_probs=20.2
Q ss_pred CCCCCEEECCCCC-CEEEEEEEEEE
Q ss_conf 3899869748785-09997678986
Q gi|254780417|r 14 FRTGEHIVYPAHG-VGTITEIKEQE 37 (188)
Q Consensus 14 FkvGD~VVy~~~G-Vg~i~~I~~~~ 37 (188)
-++|++|.|++.| +|+|..|+..+
T Consensus 3 I~vG~~VrY~~TgT~G~V~~ik~e~ 27 (91)
T pfam09871 3 IKVGSYVRYINTGTVGTVKDIKEEN 27 (91)
T ss_pred CEECCEEEECCCCCEEEEEEEEECC
T ss_conf 2116569976799568899989728
No 13
>TIGR00032 argG argininosuccinate synthase; InterPro: IPR001518 Argininosuccinate synthase (6.3.4.5 from EC) (AS) is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate , . In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterised by severe vomiting spells and mental retardation. AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity.; GO: 0004055 argininosuccinate synthase activity, 0005524 ATP binding, 0006526 arginine biosynthetic process.
Probab=75.25 E-value=1.4 Score=23.93 Aligned_cols=28 Identities=25% Similarity=0.313 Sum_probs=24.8
Q ss_pred CCCCCEEEEEEEEEEECCCCHHHEEEEC
Q ss_conf 8785099976789864873025302202
Q gi|254780417|r 23 PAHGVGTITEIKEQEVAGMKLEFFVIAF 50 (188)
Q Consensus 23 ~~~GVg~i~~I~~~~i~g~~~eyy~L~~ 50 (188)
+.|||||+.-|+++-|+=++++.|.-..
T Consensus 268 G~HGvGR~D~iEdR~ig~KSRe~YE~Pg 295 (420)
T TIGR00032 268 GKHGVGRIDIIEDRIIGLKSREIYEAPG 295 (420)
T ss_pred CCCCCCCEEEEEECEECCCCCCHHHHHH
T ss_conf 0078864315330343132454010157
No 14
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=74.03 E-value=7.3 Score=19.40 Aligned_cols=33 Identities=15% Similarity=0.173 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCC
Q ss_conf 999997746774899899999999985046753
Q gi|254780417|r 143 LNRMVREIAAVNSISEPEAINLIEVNLSSKSSK 175 (188)
Q Consensus 143 ~~~L~~Efa~~l~i~~eea~~~I~~~L~~~~~~ 175 (188)
...|.+.++|.||-.|..|++.|..||.++.|-
T Consensus 252 ~~~~~~~LPF~LT~aQ~~vi~EI~~Dl~~~~~M 284 (677)
T COG1200 252 LAKFLAALPFKLTNAQKRVIKEILADLASPVPM 284 (677)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHH
T ss_conf 999998589976789999999998664486666
No 15
>TIGR01075 uvrD DNA helicase II; InterPro: IPR005753 The SOS response is required for efficient nucleotide excision repair (NER) of the major ultraviolet light (UV) induced DNA lesions. The expression of three NER genes, uvrA, uvrB, and uvrD, is upregulated as part of the SOS response. UvrD differs from the others in that it is not involved in lesion recognition but rather in promoting the post-incision steps of NER, including turnover of the UvrBC incision complex . The form of the UvrD helicase with optimal helicase activity is oligomeric with at least two sites for binding the DNA substrate, where one site contacts regions of the 3'-ssDNA tail that are distal from the single-stranded/double-stranded DNA junction.; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=63.49 E-value=4.2 Score=20.96 Aligned_cols=25 Identities=32% Similarity=0.644 Sum_probs=13.9
Q ss_pred HHHHHCCCCCEEECCCCCCEEEEEE
Q ss_conf 3453138998697487850999767
Q gi|254780417|r 9 AMRQGFRTGEHIVYPAHGVGTITEI 33 (188)
Q Consensus 9 ~~~~~FkvGD~VVy~~~GVg~i~~I 33 (188)
..-..|+.|..|-||..|.|.|...
T Consensus 688 ~~y~~~klG~~VrH~kFG~G~ii~~ 712 (741)
T TIGR01075 688 QTYAGFKLGQRVRHPKFGEGTIINV 712 (741)
T ss_pred CCCCCCCCCCCCCCCCCCCEEEEEC
T ss_conf 5446632675122465761169832
No 16
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=62.80 E-value=6.4 Score=19.75 Aligned_cols=26 Identities=31% Similarity=0.648 Sum_probs=20.6
Q ss_pred CCCCEEECCCCC-CEEEEEEEEEEECC
Q ss_conf 899869748785-09997678986487
Q gi|254780417|r 15 RTGEHIVYPAHG-VGTITEIKEQEVAG 40 (188)
Q Consensus 15 kvGD~VVy~~~G-Vg~i~~I~~~~i~g 40 (188)
.+||+|.|.+.| +|+|..|+..+-+.
T Consensus 10 ~VG~avrYvnTgTvgrV~dIkkdEdG~ 36 (97)
T COG4014 10 KVGDAVRYVNTGTVGRVVDIKKDEDGD 36 (97)
T ss_pred HHCCEEEEEECCCEEEEEEEEEECCCC
T ss_conf 433358993069546578877605796
No 17
>COG4709 Predicted membrane protein [Function unknown]
Probab=61.19 E-value=8.7 Score=18.90 Aligned_cols=52 Identities=15% Similarity=0.054 Sum_probs=37.7
Q ss_pred HHCCHHHHHHHHHHHHHH--HHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 000012689999999999--9774677489989999999998504675334432
Q gi|254780417|r 129 PEKSYSERQLYESALNRM--VREIAAVNSISEPEAINLIEVNLSSKSSKTEKST 180 (188)
Q Consensus 129 k~l~~~e~~~l~~A~~~L--~~Efa~~l~i~~eea~~~I~~~L~~~~~~~~~~~ 180 (188)
+...+..+++|+.|.-.= ++|++..||-|++-|.+.+.+.+.+..+..+++.
T Consensus 23 ~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~~~k~~~~~~~~~ 76 (195)
T COG4709 23 REIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERGIKKEEVKPTQK 76 (195)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHHHCCCHHHHCCCCCC
T ss_conf 999999999998650348988999988199999999999871504775267600
No 18
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=49.90 E-value=15 Score=17.35 Aligned_cols=32 Identities=28% Similarity=0.585 Sum_probs=25.8
Q ss_pred HCCHHHHHHCCCCCEEE--------CCCCCCEEEEEEEEE
Q ss_conf 40533453138998697--------487850999767898
Q gi|254780417|r 5 QKRDAMRQGFRTGEHIV--------YPAHGVGTITEIKEQ 36 (188)
Q Consensus 5 ~~~~~~~~~FkvGD~VV--------y~~~GVg~i~~I~~~ 36 (188)
..|..++.-..+||+|| ||..|+|.|.+|.-.
T Consensus 49 ~~kd~~~~~~~~gd~v~~~~k~dp~~p~~~~g~~~~~~~~ 88 (857)
T PRK08115 49 SFKDTEKKTLAEGDFVVLTIKYDPKFPARGLGTILGLDWG 88 (857)
T ss_pred CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEECCC
T ss_conf 0145321445568889998347999876672379973277
No 19
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804 This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process.
Probab=49.57 E-value=7.4 Score=19.36 Aligned_cols=21 Identities=19% Similarity=0.436 Sum_probs=14.5
Q ss_pred CCHHHCCHHHHHHCCCCCEEE
Q ss_conf 973340533453138998697
Q gi|254780417|r 1 MTFQQKRDAMRQGFRTGEHIV 21 (188)
Q Consensus 1 ~~~~~~~~~~~~~FkvGD~VV 21 (188)
+..|.+|+..-.+|+.||+||
T Consensus 112 i~a~~~ks~~~a~fqeGDWvV 132 (664)
T TIGR02062 112 IKARAKKSLNEAEFQEGDWVV 132 (664)
T ss_pred CHHHHCCCCCCCCCCCCCEEE
T ss_conf 011304786202134677246
No 20
>KOG0463 consensus
Probab=48.89 E-value=19 Score=16.74 Aligned_cols=61 Identities=16% Similarity=0.275 Sum_probs=40.5
Q ss_pred HHHCCHHHHHHCCCCCEEECCCCCCEEEEEEEEEEECCC--CHHHEEEECCCCCCEEEEECCCHHHC
Q ss_conf 334053345313899869748785099976789864873--02530220248885699805201210
Q gi|254780417|r 3 FQQKRDAMRQGFRTGEHIVYPAHGVGTITEIKEQEVAGM--KLEFFVIAFDKDKMCLKVPVGKAIDI 67 (188)
Q Consensus 3 ~~~~~~~~~~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~--~~eyy~L~~~~~~~~l~vPv~~~~~~ 67 (188)
++.-.|.++.+|++.| +|-.-|||.|..=.. +.|. -.+++.|-+-.++.-+-+|+.+++.-
T Consensus 359 R~~~~E~~PAeFQIDD--~Y~VpGVGTvvSGT~--L~GtIrLND~LlLGPd~~G~F~pI~iKSIHRK 421 (641)
T KOG0463 359 RRQLNENDPAEFQIDD--IYWVPGVGTVVSGTL--LSGTIRLNDILLLGPDSNGDFMPIPIKSIHRK 421 (641)
T ss_pred CCCCCCCCCCCEEECC--EEECCCCCEEEECCE--EEEEEEECCEEEECCCCCCCEEEEEHHHHHHC
T ss_conf 4566657973035222--485178522764225--52157752278866788887645345664540
No 21
>KOG3091 consensus
Probab=48.18 E-value=19 Score=16.76 Aligned_cols=37 Identities=11% Similarity=0.171 Sum_probs=20.0
Q ss_pred HHHHHHHHH-HHHHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf 689999999-9999774677489989999999998504
Q gi|254780417|r 135 ERQLYESAL-NRMVREIAAVNSISEPEAINLIEVNLSS 171 (188)
Q Consensus 135 e~~~l~~A~-~~L~~Efa~~l~i~~eea~~~I~~~L~~ 171 (188)
.+|+|+-+. .-..+--.++|++++|+.-..++..+..
T Consensus 389 s~RiLRv~ikqeilr~~G~~L~~~EE~Lr~Kldtll~~ 426 (508)
T KOG3091 389 SHRILRVMIKQEILRKRGYALTPDEEELRAKLDTLLAQ 426 (508)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf 99999999999998604876896589999999999987
No 22
>pfam00924 MS_channel Mechanosensitive ion channel. Two members of this protein family from M. jannaschii have been functionally characterized. Both proteins form mechanosensitive (MS) ion channels upon reconstitution into liposomes and functional examination by the patch-clamp technique. Therefore this family are likely to also be MS channel proteins.
Probab=47.51 E-value=22 Score=16.32 Aligned_cols=23 Identities=26% Similarity=0.408 Sum_probs=19.1
Q ss_pred HHCCCCCEEECCCCCCEEEEEEEE
Q ss_conf 313899869748785099976789
Q gi|254780417|r 12 QGFRTGEHIVYPAHGVGTITEIKE 35 (188)
Q Consensus 12 ~~FkvGD~VVy~~~GVg~i~~I~~ 35 (188)
+.|++||+|.-+++ -|.|++|.-
T Consensus 57 ~pf~vGD~I~i~~~-~G~V~~I~~ 79 (203)
T pfam00924 57 KPFKIGDWIEIGDV-EGTVEDIGI 79 (203)
T ss_pred CCEECCCEEEECCE-EEEEEEEEC
T ss_conf 76224868999998-899999765
No 23
>KOG3038 consensus
Probab=44.40 E-value=24 Score=16.04 Aligned_cols=48 Identities=21% Similarity=0.317 Sum_probs=24.6
Q ss_pred HCCCCCEE--ECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEEC
Q ss_conf 13899869--74878509997678986487302530220248885699805
Q gi|254780417|r 13 GFRTGEHI--VYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPV 61 (188)
Q Consensus 13 ~FkvGD~V--Vy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv 61 (188)
.|.+|..| |||.. -|-|.+|....-..-...||+|.+-++...-+.|+
T Consensus 198 ~fpp~~~VLA~YP~T-TcFY~aiVh~tp~d~s~~y~vlffD~~ee~g~~pp 247 (264)
T KOG3038 198 LFPPGTIVLAVYPGT-TCFYKAIVHSTPRDGSCDYYVLFFDDEEEDGVSPP 247 (264)
T ss_pred CCCCCCEEEEECCCC-CEEEEEEEECCCCCCCCCCEEEEECCCCCCCCCCC
T ss_conf 789997799975886-23544576437877877522564057433467997
No 24
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=39.61 E-value=23 Score=16.15 Aligned_cols=29 Identities=14% Similarity=0.581 Sum_probs=18.8
Q ss_pred HCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEE
Q ss_conf 1389986974878509997678986487302530220
Q gi|254780417|r 13 GFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIA 49 (188)
Q Consensus 13 ~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~ 49 (188)
..++||+|+|+.++-..| ++.|. +|+++.
T Consensus 57 ~vk~GD~Vl~~~~~g~~i------~~~~~--~y~ii~ 85 (93)
T cd00320 57 SVKVGDKVLFPKYAGTEV------KLDGE--EYLILR 85 (93)
T ss_pred CCCCCCEEEECCCCCEEE------EECCE--EEEEEE
T ss_conf 665799999867686099------99999--999999
No 25
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=39.27 E-value=29 Score=15.51 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=20.0
Q ss_pred HHCCCCCEEECCCCCCEEEEEEEEE
Q ss_conf 3138998697487850999767898
Q gi|254780417|r 12 QGFRTGEHIVYPAHGVGTITEIKEQ 36 (188)
Q Consensus 12 ~~FkvGD~VVy~~~GVg~i~~I~~~ 36 (188)
+.||+||+|.-++ .-|.|..|..+
T Consensus 659 rpvkvGD~It~g~-~~G~V~~I~vR 682 (835)
T COG3264 659 RPVKVGDTVTIGT-VSGTVRKISVR 682 (835)
T ss_pred CCCCCCCEEEECC-CEEEEEEEEEE
T ss_conf 5735677799878-24899998755
No 26
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=38.42 E-value=26 Score=15.84 Aligned_cols=30 Identities=7% Similarity=0.376 Sum_probs=18.8
Q ss_pred HHCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEE
Q ss_conf 31389986974878509997678986487302530220
Q gi|254780417|r 12 QGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIA 49 (188)
Q Consensus 12 ~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~ 49 (188)
-..++||+|+|+.++--+ .++.|.. |+++.
T Consensus 57 ~~vk~GD~V~~~~~~g~~------v~~~g~~--y~li~ 86 (95)
T PRK00364 57 LDVKVGDKVLFGKYAGTE------VKIDGEE--YLILR 86 (95)
T ss_pred CCCCCCCEEEECCCCCEE------EEECCEE--EEEEE
T ss_conf 877879999985768759------9989928--99999
No 27
>COG0137 ArgG Argininosuccinate synthase [Amino acid transport and metabolism]
Probab=36.25 E-value=11 Score=18.21 Aligned_cols=28 Identities=25% Similarity=0.305 Sum_probs=21.0
Q ss_pred CCCCCCEEEEEEEEEEECCCCHHHEEEE
Q ss_conf 4878509997678986487302530220
Q gi|254780417|r 22 YPAHGVGTITEIKEQEVAGMKLEFFVIA 49 (188)
Q Consensus 22 y~~~GVg~i~~I~~~~i~g~~~eyy~L~ 49 (188)
-+.|||||+.-|+++-++=+++++|.-.
T Consensus 250 ag~hGvGRiD~vEnR~vG~KSRevYE~P 277 (403)
T COG0137 250 AGRHGVGRIDIVENRLVGIKSREVYEAP 277 (403)
T ss_pred HHHCCCCCHHEEEHHEEEEECCHHCCCC
T ss_conf 7445876031132200112021002482
No 28
>PHA02142 putative RNA ligase
Probab=35.79 E-value=13 Score=17.68 Aligned_cols=12 Identities=42% Similarity=0.899 Sum_probs=10.3
Q ss_pred HHHCCCCCEEEC
Q ss_conf 531389986974
Q gi|254780417|r 11 RQGFRTGEHIVY 22 (188)
Q Consensus 11 ~~~FkvGD~VVy 22 (188)
+.+|++||.|||
T Consensus 41 kgefk~GD~~Vy 52 (366)
T PHA02142 41 KGEFRVGDDCVY 52 (366)
T ss_pred CCCCCCCCEEEE
T ss_conf 786235997999
No 29
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=34.99 E-value=34 Score=15.08 Aligned_cols=42 Identities=24% Similarity=0.363 Sum_probs=28.0
Q ss_pred HHCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCC
Q ss_conf 3138998697487850999767898648730253022024888569980520
Q gi|254780417|r 12 QGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGK 63 (188)
Q Consensus 12 ~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~ 63 (188)
+.|++||+|--+.+ -|.|++|.-+. -.|+- .++..+++|=..
T Consensus 128 rpf~vGD~I~i~g~-~G~V~~I~lr~--------T~lrt-~Dg~~v~IPNs~ 169 (285)
T PRK10334 128 RPFRAGEYVDLGGV-AGTVLSVQIFS--------TTMRT-ADGKIIVIPNGK 169 (285)
T ss_pred CCCCCCCEEEECCE-EEEEEEEEEEE--------EEEEC-CCCCEEEEECHH
T ss_conf 88147976999999-99999988679--------99986-899789963288
No 30
>PRK10754 quinone oxidoreductase, NADPH-dependent; Provisional
Probab=34.43 E-value=35 Score=15.04 Aligned_cols=23 Identities=17% Similarity=0.611 Sum_probs=17.7
Q ss_pred HHCCCCCEEECCCCCCEEEEEEE
Q ss_conf 31389986974878509997678
Q gi|254780417|r 12 QGFRTGEHIVYPAHGVGTITEIK 34 (188)
Q Consensus 12 ~~FkvGD~VVy~~~GVg~i~~I~ 34 (188)
..|++||.|++...+.|-+.+..
T Consensus 77 ~~~~vGdrV~~~~~~~G~~aey~ 99 (327)
T PRK10754 77 KHIKVGDRVVYAQSALGAYSSVH 99 (327)
T ss_pred CCCCCCCEEEECCCCCCCCEEEE
T ss_conf 64789998866667873654699
No 31
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=34.12 E-value=35 Score=15.00 Aligned_cols=35 Identities=11% Similarity=0.135 Sum_probs=25.4
Q ss_pred HHCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCC
Q ss_conf 3138998697487850999767898648730253022024888
Q gi|254780417|r 12 QGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDK 54 (188)
Q Consensus 12 ~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~ 54 (188)
.+.++||.|+-..-=.|+|.++. -++..|+...+-
T Consensus 37 ~sL~~Gd~VvT~~Gl~GtV~~v~--------dd~v~lEiApGv 71 (108)
T PRK05886 37 ESLQPGDRVHTTSGLQATIVGIT--------DDTVDLEIAPGV 71 (108)
T ss_pred HHCCCCCEEEECCCCEEEEEEEC--------CCEEEEEECCCC
T ss_conf 83689998997898289999971--------887999976995
No 32
>KOG3858 consensus
Probab=33.68 E-value=20 Score=16.63 Aligned_cols=42 Identities=19% Similarity=0.408 Sum_probs=26.1
Q ss_pred HHHHHCCCCCEEECCCCCCEEEEEEEEEEEC-CCC--HHHEEEECCC
Q ss_conf 3453138998697487850999767898648-730--2530220248
Q gi|254780417|r 9 AMRQGFRTGEHIVYPAHGVGTITEIKEQEVA-GMK--LEFFVIAFDK 52 (188)
Q Consensus 9 ~~~~~FkvGD~VVy~~~GVg~i~~I~~~~i~-g~~--~eyy~L~~~~ 52 (188)
+-...|..||+|||++-| =+..|.--... +.. .|||+|.-+.
T Consensus 33 SSNp~F~~~d~vI~v~ig--D~ldIiCP~~e~~~~~~~E~yilYmV~ 77 (233)
T KOG3858 33 SSNPRFRRGDYVIYVQIG--DYLDIICPHYEEGGPEGYEYYILYMVS 77 (233)
T ss_pred CCCCCEECCCCEEEECCC--CEEEEECCCCCCCCCCCCEEEEEEEEC
T ss_conf 789652168846985259--889897888879988762499999957
No 33
>pfam00166 Cpn10 Chaperonin 10 Kd subunit. This family contains GroES and Gp31-like chaperonins. Gp31 is a functional co-chaperonin that is required for the folding and assembly of Gp23, a major capsid protein, during phage morphogenesis.
Probab=32.90 E-value=34 Score=15.06 Aligned_cols=16 Identities=13% Similarity=0.520 Sum_probs=13.1
Q ss_pred HHHCCCCCEEECCCCC
Q ss_conf 5313899869748785
Q gi|254780417|r 11 RQGFRTGEHIVYPAHG 26 (188)
Q Consensus 11 ~~~FkvGD~VVy~~~G 26 (188)
....++||+|+|+.++
T Consensus 54 p~~vk~GD~Vl~~~~~ 69 (92)
T pfam00166 54 PLEVKVGDKVLFPKYA 69 (92)
T ss_pred CCCCCCCCEEEECCCC
T ss_conf 5755419999987758
No 34
>pfam09513 consensus
Probab=32.62 E-value=16 Score=17.15 Aligned_cols=12 Identities=33% Similarity=0.814 Sum_probs=8.3
Q ss_pred HHHCCCCCEEEC
Q ss_conf 531389986974
Q gi|254780417|r 11 RQGFRTGEHIVY 22 (188)
Q Consensus 11 ~~~FkvGD~VVy 22 (188)
+-+|++||.|||
T Consensus 35 Kge~k~GD~~Vy 46 (356)
T pfam09513 35 KGEYRVGDPAVY 46 (356)
T ss_pred CCCCCCCCEEEE
T ss_conf 786136997999
No 35
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=30.58 E-value=40 Score=14.62 Aligned_cols=44 Identities=23% Similarity=0.093 Sum_probs=38.2
Q ss_pred HHCCHHHHHHHH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 000012689999-99999997746774899899999999985046
Q gi|254780417|r 129 PEKSYSERQLYE-SALNRMVREIAAVNSISEPEAINLIEVNLSSK 172 (188)
Q Consensus 129 k~l~~~e~~~l~-~A~~~L~~Efa~~l~i~~eea~~~I~~~L~~~ 172 (188)
.+|+..|...|. .|+..-..|+|..|++++..|.-.|.+.+.+=
T Consensus 178 ~~LT~RE~E~L~W~A~GKTs~EIa~IL~ISe~TV~fHl~na~~KL 222 (240)
T PRK10188 178 MNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKF 222 (240)
T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 889989999999997799999999883999999999999999995
No 36
>TIGR02890 spore_yteA sporulation protein, yteA family; InterPro: IPR014240 This entry contains predicted regulatory proteins that are found in nearly every species of the endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria), with the exception of Clostridium perfringens. Some (but not all) of these proteins contain an unusual DksA/TraR C4-type zinc finger, where only one of the four key Cys residues is conserved. All members of this entry share an additional C-terminal domain. The function of proteins in this family is unknown. YteA is found in mature spores of Bacillus subtilis and its expression appeasr to be regulated by sigma-K ..
Probab=26.76 E-value=20 Score=16.53 Aligned_cols=43 Identities=21% Similarity=0.072 Sum_probs=31.4
Q ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf 0000126899999999999774677489989999999998504
Q gi|254780417|r 129 PEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSS 171 (188)
Q Consensus 129 k~l~~~e~~~l~~A~~~L~~Efa~~l~i~~eea~~~I~~~L~~ 171 (188)
-.||.+|..--+.|=.++..|=-++|.--...-...|+.+|.+
T Consensus 40 gELS~YDNHPaD~ATElyEReKD~AL~~~~~~~L~~Ie~AL~~ 82 (167)
T TIGR02890 40 GELSSYDNHPADLATELYEREKDIALKEHEKRELREIEHALQK 82 (167)
T ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 1100136885334430457753268899999999889999999
No 37
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=24.31 E-value=52 Score=13.91 Aligned_cols=31 Identities=16% Similarity=0.234 Sum_probs=24.7
Q ss_pred CHHHHHHCCCCCEEECCCCCCEEEEEEEEEEE
Q ss_conf 53345313899869748785099976789864
Q gi|254780417|r 7 RDAMRQGFRTGEHIVYPAHGVGTITEIKEQEV 38 (188)
Q Consensus 7 ~~~~~~~FkvGD~VVy~~~GVg~i~~I~~~~i 38 (188)
+.++...++.|.+|++-.. .|+|.++..-.-
T Consensus 4 ~~i~~~dlK~G~~i~idg~-pckVve~~~sKp 34 (129)
T PRK03999 4 KQVEVGELKEGSYVVIDGE-PCRIVEISKSKP 34 (129)
T ss_pred CEEEHHHCCCCCEEEECCE-EEEEEEEEEECC
T ss_conf 2267899268999999998-599999888649
No 38
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=24.31 E-value=52 Score=13.91 Aligned_cols=49 Identities=10% Similarity=0.160 Sum_probs=31.9
Q ss_pred HHCCCCCEEECCCCC----CEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCC
Q ss_conf 313899869748785----0999767898648730253022024888569980520
Q gi|254780417|r 12 QGFRTGEHIVYPAHG----VGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGK 63 (188)
Q Consensus 12 ~~FkvGD~VVy~~~G----Vg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~ 63 (188)
.+|++||.|-=-..| -|+|....... ..... |.+.+++....-.|++.+
T Consensus 1 ~~f~vGDlVwaK~kGyP~WPa~I~~~~~~~--~~~~k-~~V~FfGt~~~a~v~~~~ 53 (83)
T cd05834 1 KQFKAGDLVFAKVKGYPAWPARVDEPEDWK--PPGKK-YPVYFFGTHETAFLKPED 53 (83)
T ss_pred CCCCCCCEEEEECCCCCCCCCEECCCCCCC--CCCCE-EEEEEEECCCEEEECHHH
T ss_conf 987679799982478999980230633368--76777-899995079779874899
No 39
>PRK05370 argininosuccinate synthase; Validated
Probab=24.29 E-value=27 Score=15.74 Aligned_cols=20 Identities=10% Similarity=0.300 Sum_probs=9.8
Q ss_pred HCCCCCEEECCCCCCEEEEE
Q ss_conf 13899869748785099976
Q gi|254780417|r 13 GFRTGEHIVYPAHGVGTITE 32 (188)
Q Consensus 13 ~FkvGD~VVy~~~GVg~i~~ 32 (188)
.|.+...+.|..|.-|..+.
T Consensus 190 ~YSiD~NLwg~S~Egg~LEd 209 (447)
T PRK05370 190 AYSTDSNMLGATHEAKDLEH 209 (447)
T ss_pred CCCCCCCCCCCCCCCCCCCC
T ss_conf 85336330132344444567
No 40
>TIGR00996 Mtu_fam_mce virulence factor Mce family protein; InterPro: IPR005693 Mycobacterial species are usually slender, curved rods with a unique cell wall of complex waxes and glycolipids. They are resistant to acids, alkalis and dehydration, and are very slow to grow in vitro. The human pathogenic Mycobacteria (Mycobacterium tuberculosis and Mycobacterium leprae) are becoming resistant to conventional treatments and, together with HIV-related diseases, are fast posing a global health threat. An essential requirement, particularly of M. tuberculosis, is to gain entrance to, and to resist, the hostile intra-cellular environment of epithelial cells . The genome of M. tuberculosis contains four mammalian cell entry (mce) operons , which are widely distributed in both pathogenic and non-pathogenic mycobacteria suggesting that the presence of these putative virulence genes is not an indicator for the pathogenicity of the bacilli. At the 5' end of the transcriptional unit are two genes that have evolved from a tandem duplication, and whose products resemble YrbE, a conserved hypothetical protein found in Escherichia. coli, Haemophilus influenzae and Porphyra purpurea. All of the YrbE proteins, including the eight from M. tuberculosis, are probable integral membrane proteins with six TM alpha helices. The next six genes in each operon, the mce genes, are related, their products ranging in size from 275 to 564 amino acid residues. The corresponding protein sequences contain a number of highly conserved motifs that define a 24- member family with a common organization. Twenty of these proteins have a strongly hydrophobic segment at the NH2-terminal end that could span the lipid bilayer whereas the remaining four, all of which correspond to the seventh gene in their respective operons, mce1E to mce4E, are probably lipoprotein precursors. In all 24 cases the COOH-terminal domain of the mce proteins is predicted to be exposed on the external face of the cytoplasmic membrane . The ability to gain entry and resist the antimicrobial intracellular environment of mammalian cells is an essential virulence property of M. tuberculosis. This property is conferred by Mce1A, the third gene of operon 1, which when expressed in Escherichia coli conferred the ability to invade HeLa cells. The recombinant protein when used to coat latex spheres also promoted their uptake into HeLa cells. N-terminus deletion constructs of Mce1A identified a domain located between amino acid positions 106 and 163 that was needed for this cell uptake activity. Mce1A contains hydrophobic stretches at the N-terminus predictive of a signal sequence, and colloidal gold immunoelectron microscopy indicated that the corresponding native protein is expressed on the surface of M. tuberculosis. Recombinant Mce2A, which had the highest level of identity (67%) to Mce1A, was unable to promote the association of microspheres with HeLa cells and an mce-deletion mutant in Mycobacterium bovis greatly impaired the ability of the microbe to infect epithelial cells in vitro. Although the exact function of Mce1A is still unknown, it appears to serve as an effector molecule expressed on the surface of M. tuberculosis that is capable of eliciting plasma membrane perturbations in non-phagocytic mammalian cells . The distribution of the mce operons in both pathogenic and non-pathogenic mycobacteria suggests that the presence of these putative virulence genes is not an indicator for the pathogenicity of the bacilli - it may be that pathogenicity is determined by their expression , . The members of this family represent all 24 genes associated with the four mammalian cell entry operons of M. tuberculosis and their homologs in other Actinomycetales.; GO: 0009405 pathogenesis.
Probab=23.99 E-value=52 Score=13.87 Aligned_cols=113 Identities=15% Similarity=0.146 Sum_probs=74.3
Q ss_pred CCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCCCHHHHHH------------
Q ss_conf 38998697487850999767898648730253022024888569980520121045433441024678------------
Q gi|254780417|r 14 FRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERA------------ 81 (188)
Q Consensus 14 FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~~~e~~~l------------ 81 (188)
...|+.|-|-.--||+|..|+.+.-.|. .....+.+.-+. ...||.+-...++=-.++...-++=.
T Consensus 46 l~~G~~V~~~Gv~VG~V~~i~~i~~~~~-~~~~~v~~~~~~-~~~iP~~~~A~I~~~~l~G~~~veL~pp~~p~~~~~L~ 123 (304)
T TIGR00996 46 LYPGSKVRVRGVEVGKVTAIEEIPRGGN-GAGVRVTFSLDR-SVTIPANATAAIRSTTLLGSRYVELTPPKGPSGGPRLS 123 (304)
T ss_pred CCCCCEEEEEEEEEEEEEEEEECCCCCC-CCEEEEEEEECC-CEECCCCCEEEEECCCEEEEEEEEEECCCCCCCCCCCC
T ss_conf 5899803884333005643212278888-767899997067-73237720788730330342357763388898889697
Q ss_pred -HHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHH-----HHHHHHHHHHHHHH
Q ss_conf -985078664466550389999999851689999-----99999999841010
Q gi|254780417|r 82 -LKLVRGKARVKRTMWSRRAQEYDAKINSGDLIA-----IAEVVRDLHRTDSQ 128 (188)
Q Consensus 82 -~~~l~~~~~~~~~~~~~R~~~~~~~lksgd~~~-----~a~vik~L~~~~~~ 128 (188)
-..++-........|..-.......+...++.. +-.++..++.-=.+
T Consensus 124 ~g~~I~~~~T~~~~~~~~ll~~~~~~l~~l~~~~~~~gpl~~~l~~~~~al~G 176 (304)
T TIGR00996 124 DGGVIPLARTSVPLEIDDLLGSLTRLLNGLDPEKQPKGPLNAILNALAEALAG 176 (304)
T ss_pred CCCEECCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf 58764443687665289999999999850583335667089999999998638
No 41
>pfam02699 YajC Preprotein translocase subunit. See.
Probab=23.71 E-value=53 Score=13.84 Aligned_cols=32 Identities=16% Similarity=0.300 Sum_probs=23.5
Q ss_pred HHCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECC
Q ss_conf 3138998697487850999767898648730253022024
Q gi|254780417|r 12 QGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFD 51 (188)
Q Consensus 12 ~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~ 51 (188)
.+.++||.|+-..==.|+|.++. .++.+|+..
T Consensus 36 ~~L~~Gd~VvT~gGi~G~V~~i~--------~~~v~lei~ 67 (83)
T pfam02699 36 SSLKKGDEVVTIGGIHGKIVKVD--------DDTVVLEIA 67 (83)
T ss_pred HHCCCCCEEEECCCEEEEEEEEE--------CCEEEEEEC
T ss_conf 85789999998997199999997--------999999988
No 42
>TIGR02817 adh_fam_1 zinc-binding alcohol dehydrogenase family protein; InterPro: IPR014182 Members of this entry form a distinct subset of the larger family of oxidoreductases that includes zinc-binding alcohol dehydrogenases and NADPH:quinone reductases. Some current members of this entry carry designations as putative alginate lyase, however none have been characterised as such..
Probab=23.55 E-value=35 Score=15.04 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=5.4
Q ss_pred HCCCCCEEECC
Q ss_conf 13899869748
Q gi|254780417|r 13 GFRTGEHIVYP 23 (188)
Q Consensus 13 ~FkvGD~VVy~ 23 (188)
.||+||-|-|-
T Consensus 81 LFKpGDeVwYA 91 (338)
T TIGR02817 81 LFKPGDEVWYA 91 (338)
T ss_pred EECCCCEEEEC
T ss_conf 10278755754
No 43
>PRK11465 hypothetical protein; Provisional
Probab=23.36 E-value=54 Score=13.80 Aligned_cols=37 Identities=19% Similarity=0.365 Sum_probs=25.7
Q ss_pred HHCCCCCEEECCCCCCEEEEEEEEEEEC--CCCHHHEEEE
Q ss_conf 3138998697487850999767898648--7302530220
Q gi|254780417|r 12 QGFRTGEHIVYPAHGVGTITEIKEQEVA--GMKLEFFVIA 49 (188)
Q Consensus 12 ~~FkvGD~VVy~~~GVg~i~~I~~~~i~--g~~~eyy~L~ 49 (188)
++|.+||+|--+.+ -|.|+++.-+.+. +....+.++.
T Consensus 572 d~~~vGD~V~vgg~-~GtVE~islRs~~LRd~~G~~h~IP 610 (741)
T PRK11465 572 NGMNTGDLVTIGPL-TGTVERMSIRSVGVRQDTGAYHIIP 610 (741)
T ss_pred CCCCCCCEEEECCC-EEEEEEEEEEEEEEECCCCCEEEEE
T ss_conf 24377998998893-5899999748999987998789974
No 44
>PRK13870 transcriptional regulator TraR; Provisional
Probab=23.13 E-value=55 Score=13.77 Aligned_cols=44 Identities=14% Similarity=0.043 Sum_probs=38.3
Q ss_pred HHCCHHHHHHHH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 000012689999-99999997746774899899999999985046
Q gi|254780417|r 129 PEKSYSERQLYE-SALNRMVREIAAVNSISEPEAINLIEVNLSSK 172 (188)
Q Consensus 129 k~l~~~e~~~l~-~A~~~L~~Efa~~l~i~~eea~~~I~~~L~~~ 172 (188)
..|+..|...|. .|...-..|+|.+|++++..|.-.|.+.+.+=
T Consensus 172 ~~LT~RE~E~L~W~A~GKT~~EIA~ILgISe~TV~fHl~na~~KL 216 (234)
T PRK13870 172 AWLDPKEATYLRWIAVGMTMEEIADVEGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 679979999999997899899999997988999999999999995
No 45
>pfam11373 DUF3175 Protein of unknown function (DUF3175). This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=23.04 E-value=55 Score=13.76 Aligned_cols=43 Identities=12% Similarity=0.125 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf 1689999999999998410100000126899999999999774
Q gi|254780417|r 108 NSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREI 150 (188)
Q Consensus 108 ksgd~~~~a~vik~L~~~~~~k~l~~~e~~~l~~A~~~L~~Ef 150 (188)
+.+.+++-|--.-+.|.-+.++.|+..-+..|+.|.+.|-.-|
T Consensus 42 RK~~pf~SAMSML~FYINRAG~~L~~~rr~~Le~AKdeLR~~f 84 (86)
T pfam11373 42 RKGTPFQSAMSMLNFYINRAGRNLPKTQRATLERAKDELRKAF 84 (86)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 4577189999999999983014389999999999999999984
No 46
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=22.78 E-value=55 Score=13.72 Aligned_cols=24 Identities=25% Similarity=0.523 Sum_probs=18.6
Q ss_pred HHCCCCCEEECCCCC------CEEEEEEEE
Q ss_conf 313899869748785------099976789
Q gi|254780417|r 12 QGFRTGEHIVYPAHG------VGTITEIKE 35 (188)
Q Consensus 12 ~~FkvGD~VVy~~~G------Vg~i~~I~~ 35 (188)
+.|++||.|.--+.| ||+|..|-+
T Consensus 2 ~v~~vGD~V~i~~~~~~~~p~Ig~I~~iw~ 31 (121)
T cd04714 2 EIIRVGDCVLFKSPGRPSLPYVARIESLWE 31 (121)
T ss_pred CEEECCCEEEEECCCCCCCCEEEEEEEEEE
T ss_conf 879679999995899999999999999999
No 47
>PRK04527 argininosuccinate synthase; Provisional
Probab=22.62 E-value=31 Score=15.32 Aligned_cols=15 Identities=7% Similarity=-0.321 Sum_probs=6.3
Q ss_pred CCCCHHHHHHHHHHH
Q ss_conf 655038999999985
Q gi|254780417|r 93 RTMWSRRAQEYDAKI 107 (188)
Q Consensus 93 ~~~~~~R~~~~~~~l 107 (188)
..|...|.+..-..+
T Consensus 121 kGNDQvRFe~~~~al 135 (397)
T PRK04527 121 MGNDQVRFDLAVKAL 135 (397)
T ss_pred CCCCHHHHHHHHHHC
T ss_conf 787025677688863
No 48
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=22.20 E-value=57 Score=13.65 Aligned_cols=45 Identities=22% Similarity=0.427 Sum_probs=28.8
Q ss_pred HHHCCCCCEEECCCCC-CEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCCH
Q ss_conf 5313899869748785-09997678986487302530220248885699805201
Q gi|254780417|r 11 RQGFRTGEHIVYPAHG-VGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKA 64 (188)
Q Consensus 11 ~~~FkvGD~VVy~~~G-Vg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~ 64 (188)
...|++||.|-+.+.| .|+|.++. |.. .+.+.. +.+++-||....
T Consensus 632 ~~~~~~Gd~V~v~~~~~~G~V~~i~-----~~~--~~~V~~--g~~k~~v~~~~l 677 (780)
T PRK00409 632 KEELKVGDEVKYLSLGQKGEVLSIP-----DNK--EAIVQA--GIMKMKVPLSDL 677 (780)
T ss_pred CCCCCCCCEEEECCCCCEEEEEEEC-----CCC--EEEEEE--CCEEEEEEHHHC
T ss_conf 7799999989985799679999986-----998--199997--976999779993
No 49
>pfam01426 BAH BAH domain. This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.
Probab=21.94 E-value=58 Score=13.62 Aligned_cols=26 Identities=27% Similarity=0.487 Sum_probs=19.1
Q ss_pred HCCCCCEEECCCCC------CEEEEEEEEEEE
Q ss_conf 13899869748785------099976789864
Q gi|254780417|r 13 GFRTGEHIVYPAHG------VGTITEIKEQEV 38 (188)
Q Consensus 13 ~FkvGD~VVy~~~G------Vg~i~~I~~~~i 38 (188)
.|.+||+|.-.+.. ||+|..|-...-
T Consensus 2 ~~~vGD~V~v~~~~~~~~~~i~rI~~i~~~~~ 33 (119)
T pfam01426 2 TYSVGDFVLVEPDDAGEPPYVGRIEEIFEDKD 33 (119)
T ss_pred EEECCCEEEEECCCCCCCCEEEEEEEEEECCC
T ss_conf 79369999997599999879999989999099
No 50
>pfam00877 NLPC_P60 NlpC/P60 family. The function of this domain is unknown. It is found in several lipoproteins.
Probab=21.04 E-value=60 Score=13.50 Aligned_cols=17 Identities=6% Similarity=0.192 Sum_probs=12.9
Q ss_pred HHHHHCCCCCEEECCCC
Q ss_conf 34531389986974878
Q gi|254780417|r 9 AMRQGFRTGEHIVYPAH 25 (188)
Q Consensus 9 ~~~~~FkvGD~VVy~~~ 25 (188)
....+.++||.|.+...
T Consensus 46 v~~~~~~~GDLvFf~~~ 62 (105)
T pfam00877 46 IPKSEPQRGDLVFFGTG 62 (105)
T ss_pred CCHHHCCCCCEEEECCC
T ss_conf 47899898788997789
No 51
>pfam11626 Rap1_C Rap1 - C terminal domain. This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C terminal domain.
Probab=20.19 E-value=63 Score=13.39 Aligned_cols=49 Identities=14% Similarity=0.217 Sum_probs=32.8
Q ss_pred CCCCCCHHHHHHHHHCCCCC---CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 43344102467898507866---44665503899999998516899999999999
Q gi|254780417|r 70 RKLSEAHFVERALKLVRGKA---RVKRTMWSRRAQEYDAKINSGDLIAIAEVVRD 121 (188)
Q Consensus 70 R~~~~~~e~~~l~~~l~~~~---~~~~~~~~~R~~~~~~~lksgd~~~~a~vik~ 121 (188)
..-+....++.+++.|.... .....-|... -.+.|.+++..++..+++-
T Consensus 5 ~t~~~p~lA~~vl~~L~~g~GIP~n~pGIWT~e---DDe~L~~~d~~~i~~l~kK 56 (68)
T pfam11626 5 CTSYDPSQADKVLEDLRDGKGIPDNVPGIWTKE---DDECLESNDGRDIERLEKK 56 (68)
T ss_pred CCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCC---CHHHHHCCCHHHHHHHHHH
T ss_conf 213788799999999980799999999867523---3899974888999999998
Done!