Query         gi|254780140|ref|YP_003064553.1| putative ABC transporter, substrate-binding protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 452
No_of_seqs    295 out of 2333
Neff          11.7
Searched_HMMs 39220
Date          Sun May 22 13:16:50 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780140.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG1463 Ttg2C ABC-type transpo 100.0   8E-27   2E-31  205.7  22.4  126    1-128     1-128 (359)
  2 TIGR00996 Mtu_fam_mce virulenc  99.9 3.9E-20 9.9E-25  158.9  19.5  122   10-132     2-130 (304)
  3 PRK10807 paraquat-inducible pr  99.8 9.9E-18 2.5E-22  142.0  19.1   89   32-122    36-138 (546)
  4 pfam02470 MCE mce related prot  99.5 6.1E-13 1.5E-17  108.5   9.9   79   37-117     1-80  (80)
  5 COG3008 PqiB Paraquat-inducibl  99.2 2.9E-10 7.4E-15   89.7   9.4  111    3-122    18-142 (553)
  6 PRK10807 paraquat-inducible pr  99.1   4E-10   1E-14   88.8   9.8   69   35-105   154-224 (546)
  7 COG3008 PqiB Paraquat-inducibl  98.6   2E-08 5.1E-13   76.8   3.5   64   39-104   162-227 (553)
  8 PRK09793 methyl-accepting prot  98.1 0.00089 2.3E-08   44.3  25.1   29  410-438   485-513 (533)
  9 smart00283 MA Methyl-accepting  98.0  0.0016   4E-08   42.5  25.7   75  253-329    79-153 (262)
 10 KOG0994 consensus               97.8  0.0039   1E-07   39.8  22.5   33  405-437  1695-1727(1758)
 11 pfam00015 MCPsignal Methyl-acc  97.5  0.0099 2.5E-07   36.9  21.6   71  255-327    30-100 (213)
 12 COG0840 Tar Methyl-accepting c  97.3   0.015 3.8E-07   35.7  25.3   62  265-328   236-297 (408)
 13 KOG0994 consensus               97.2   0.018 4.5E-07   35.2  21.7   11   51-61   1323-1333(1758)
 14 pfam00015 MCPsignal Methyl-acc  96.9   0.033 8.3E-07   33.3  18.6   26  405-430   186-211 (213)
 15 PRK09793 methyl-accepting prot  96.3   0.085 2.2E-06   30.4  25.9   25  406-430   488-512 (533)
 16 TIGR00996 Mtu_fam_mce virulenc  96.0    0.12 3.1E-06   29.3  14.2   14   51-64     28-41  (304)
 17 COG1463 Ttg2C ABC-type transpo  95.4    0.19   5E-06   27.9  15.8   38  245-282   184-221 (359)
 18 COG0840 Tar Methyl-accepting c  94.5    0.34 8.8E-06   26.2  25.3   21  333-353   278-298 (408)
 19 COG1511 Predicted membrane pro  92.7    0.66 1.7E-05   24.2  17.3   63   12-80     18-86  (780)
 20 pfam06009 Laminin_II Laminin D  88.1     1.7 4.2E-05   21.4  13.3   73  369-451    54-128 (140)
 21 PRK06531 yajC preprotein trans  87.2    0.47 1.2E-05   25.2   2.4   55   14-74      5-59  (120)
 22 TIGR03545 conserved hypothetic  86.3     2.1 5.3E-05   20.7  11.8   17    9-25      7-23  (554)
 23 TIGR00739 yajC preprotein tran  85.5    0.72 1.8E-05   23.9   2.7   39   49-92     35-73  (86)
 24 PRK03598 hypothetical protein;  82.0     3.1 7.9E-05   19.5   5.0   59    7-76      4-62  (331)
 25 KOG0971 consensus               78.4       4  0.0001   18.7  23.8   24  406-429   521-544 (1243)
 26 PRK05585 yajC preprotein trans  76.1    0.81 2.1E-05   23.6   0.2   37   48-91     50-86  (107)
 27 PRK05886 yajC preprotein trans  74.4     2.4 6.1E-05   20.2   2.3   37   49-92     36-72  (108)
 28 PRK04778 septation ring format  74.2     5.1 0.00013   17.9  24.1   12   64-75     49-60  (569)
 29 COG1862 YajC Preprotein transl  71.4     3.4 8.8E-05   19.2   2.5   25   48-72     40-64  (97)
 30 pfam02699 YajC Preprotein tran  70.4     3.2 8.3E-05   19.3   2.2   37   48-91     34-70  (83)
 31 pfam06160 EzrA Septation ring   68.2     6.9 0.00018   17.0  24.0   11   64-74     45-55  (559)
 32 COG0497 RecN ATPase involved i  64.9       8  0.0002   16.6  12.3   10  107-116   119-128 (557)
 33 pfam01601 Corona_S2 Coronaviru  64.3     8.2 0.00021   16.5  11.0   21  341-361   299-319 (609)
 34 pfam07889 DUF1664 Protein of u  61.6     9.1 0.00023   16.2  11.7   52  372-431    73-124 (126)
 35 PRK11166 chemotaxis regulator   60.2     9.6 0.00024   16.0  15.6   59  363-421   105-165 (214)
 36 pfam09177 Syntaxin-6_N Syntaxi  60.0     9.7 0.00025   16.0   7.5   32  405-436    39-70  (95)
 37 pfam04085 MreC rod shape-deter  59.5     9.8 0.00025   16.0   7.0   42   47-93     20-61  (153)
 38 PRK13415 flagella biosynthesis  58.7      10 0.00026   15.9   5.0   34   18-56     84-117 (216)
 39 pfam06103 DUF948 Bacterial pro  58.5      10 0.00026   15.8   9.8   23  370-392    47-69  (90)
 40 TIGR02169 SMC_prok_A chromosom  58.0      10 0.00027   15.8  26.8   41   32-73     75-117 (1202)
 41 PRK11633 hypothetical protein;  57.9      10 0.00027   15.8   3.3   27    1-27      1-27  (218)
 42 TIGR02168 SMC_prok_B chromosom  55.2      12 0.00029   15.5  28.7   29   36-65     74-102 (1191)
 43 COG4477 EzrA Negative regulato  53.6      12 0.00031   15.3  23.3   23    7-29      3-25  (570)
 44 pfam04582 Reo_sigmaC Reovirus   53.1      12 0.00032   15.2  13.2   10  426-435   142-151 (326)
 45 pfam09890 DUF2117 Uncharacteri  51.6      11 0.00027   15.7   2.1   24   47-70     89-112 (209)
 46 KOG0250 consensus               51.1      13 0.00034   15.0  25.1   25   65-92     39-63  (1074)
 47 pfam06008 Laminin_I Laminin Do  50.7      13 0.00034   15.0  21.7   15  412-426   242-256 (263)
 48 PRK10692 hypothetical protein;  48.5     1.2 3.1E-05   22.4  -3.2   66    1-71      1-69  (92)
 49 COG2715 SpmA Uncharacterized m  47.3      15 0.00039   14.6   2.4   10    6-15      3-12  (206)
 50 COG3556 Predicted membrane pro  46.9      15 0.00037   14.7   2.2   17    8-24     81-97  (150)
 51 TIGR02876 spore_yqfD sporulati  45.7     9.1 0.00023   16.2   1.0   47    7-55     86-135 (406)
 52 COG1256 FlgK Flagellar hook-as  45.2      16 0.00042   14.4  11.6   58  142-199   131-188 (552)
 53 smart00503 SynN Syntaxin N-ter  45.0      16 0.00042   14.4  13.3   24  371-394    47-70  (117)
 54 pfam12273 RCR Chitin synthesis  42.0      18 0.00046   14.1   2.3   22    7-29      2-23  (124)
 55 pfam05667 DUF812 Protein of un  39.9      20  0.0005   13.9  22.1   25  407-431   448-472 (536)
 56 COG1792 MreC Cell shape-determ  39.4      20  0.0005   13.8   5.1   41   47-92    139-179 (284)
 57 pfam07427 consensus             38.7      20 0.00052   13.8   4.4   38   54-91     37-77  (126)
 58 PRK04192 V-type ATP synthase s  38.0      21 0.00053   13.7   2.2   37   33-75     42-78  (585)
 59 PRK09379 membrane-bound transc  38.0      21 0.00053   13.7   6.3   22    1-22      1-22  (303)
 60 pfam02874 ATP-synt_ab_N ATP sy  37.3      21 0.00054   13.6   2.5   13   48-60     55-67  (69)
 61 PRK06793 fliI flagellum-specif  35.9      22 0.00057   13.5   3.2   24   38-62     63-86  (432)
 62 pfam11694 DUF3290 Protein of u  35.8      22 0.00057   13.4   3.8   27    4-30     14-40  (149)
 63 KOG1352 consensus               34.6      23  0.0006   13.3   2.5   43   28-76     54-96  (618)
 64 COG1155 NtpA Archaeal/vacuolar  34.5      23  0.0006   13.3   3.0   31   33-65     40-70  (588)
 65 pfam11025 GP40 Glycoprotein GP  33.8      24 0.00061   13.2   2.4   56   24-89     12-70  (165)
 66 pfam10762 DUF2583 Protein of u  33.4     1.9 4.8E-05   21.0  -4.1   67    1-71      1-69  (89)
 67 TIGR00304 TIGR00304 conserved   33.2      25 0.00063   13.2   3.5   56    7-65      6-62  (93)
 68 TIGR03496 FliI_clade1 flagella  32.1      26 0.00065   13.0   3.4   25   39-64     45-69  (411)
 69 TIGR02545 ATP_syn_fliI flagell  31.9      26 0.00066   13.0   2.7   27   35-62     51-77  (439)
 70 PRK04570 cell division protein  31.7      19 0.00049   13.9   0.8   17    4-20      3-19  (244)
 71 pfam06024 DUF912 Nucleopolyhed  31.6      26 0.00066   13.0   3.6   27    5-31     61-87  (101)
 72 pfam06092 DUF943 Enterobacteri  31.4      26 0.00067   13.0   2.2   93    1-116     1-96  (155)
 73 PRK13922 rod shape-determining  31.3      26 0.00067   13.0   6.8   42   47-93    135-176 (264)
 74 pfam07423 DUF1510 Protein of u  31.2      26 0.00068   12.9   2.8   26    3-28     10-36  (214)
 75 PRK10859 putative transglycosy  31.0      18 0.00047   14.0   0.7   28    3-30      4-31  (507)
 76 pfam05239 PRC PRC-barrel domai  30.8      27 0.00069   12.9   3.8   24   54-77     10-34  (77)
 77 PRK10900 consensus              30.2      27  0.0007   12.8   7.9   43   47-94    140-182 (346)
 78 cd00319 Ribosomal_S12_like Rib  30.1      28  0.0007   12.8   2.1   25   38-62     45-69  (95)
 79 pfam05531 NPV_P10 Nucleopolyhe  30.1      28  0.0007   12.8   8.6   12  417-428    49-60  (75)
 80 TIGR02817 adh_fam_1 zinc-bindi  28.7      26 0.00066   13.0   1.1   12   90-101    46-57  (338)
 81 PRK10334 mechanosensitive chan  27.5      30 0.00078   12.5   1.9   23   51-74    129-151 (285)
 82 PRK07960 fliI flagellum-specif  27.4      31 0.00078   12.5   3.1   11   48-58     84-94  (455)
 83 COG2815 Uncharacterized protei  27.1      31 0.00079   12.5   1.5   53   48-102    30-85  (303)
 84 TIGR02222 chap_CsaA export-rel  27.1      31 0.00079   12.5   1.9   50   62-112     8-62  (107)
 85 pfam03597 CcoS Cytochrome oxid  27.1      31 0.00079   12.5   2.8   28    7-35      4-31  (45)
 86 TIGR02302 aProt_lowcomp conser  27.0      31 0.00079   12.5   8.4   31   75-105   192-237 (899)
 87 TIGR02861 SASP_H small acid-so  26.6      27 0.00069   12.9   0.9   32   56-90     16-47  (59)
 88 KOG2196 consensus               25.8      33 0.00083   12.3  12.9   26  336-361   181-206 (254)
 89 pfam12606 RELT Tumour necrosis  25.7      33 0.00084   12.3   2.1   20    7-26      4-23  (50)
 90 pfam09980 DUF2214 Predicted me  24.6      34 0.00087   12.2   3.4   18    8-25     81-98  (150)
 91 PRK10270 hypothetical protein;  23.9      35  0.0009   12.1   5.4   17    1-18      1-17  (340)
 92 PRK06945 flgK flagellar hook-a  23.5      36 0.00092   12.0  12.8   60  138-197   124-183 (649)
 93 pfam04585 consensus             22.5      37 0.00095   11.9   4.5   39    3-45     26-64  (218)
 94 PRK12714 flgK flagellar hook-a  22.3      38 0.00096   11.9  13.9   53  141-193   126-178 (624)
 95 PRK05464 Na(+)-translocating N  22.2      38 0.00097   11.9   3.5   36    8-43      4-39  (408)
 96 pfam11057 Cortexin Cortexin of  22.1      38 0.00097   11.8   3.4   49    2-56     26-75  (81)
 97 KOG3491 consensus               22.1      38 0.00097   11.8   2.8   21    6-26     38-58  (65)
 98 PRK10559 p-hydroxybenzoic acid  22.1      38 0.00097   11.8   7.1   12   65-76     55-66  (310)
 99 pfam03100 CcmE CcmE. CcmE is t  21.8      39 0.00098   11.8   4.3   48   52-111    47-95  (130)
100 PRK06665 flgK flagellar hook-a  21.6      39 0.00099   11.8  13.8   60  138-197   135-194 (628)
101 COG1580 FliL Flagellar basal b  21.3      39   0.001   11.7   2.7   27    4-30     16-42  (159)
102 PRK08455 fliL flagellar basal   21.3      40   0.001   11.7   2.6   12    8-19     22-33  (180)
103 COG3190 FliO Flagellar biogene  21.3      40   0.001   11.7   6.0   44    8-57     27-71  (137)
104 PRK02118 V-type ATP synthase s  21.1      40   0.001   11.7   3.1   23  429-451   410-432 (432)
105 COG3111 Periplasmic protein wi  21.1      40   0.001   11.7   6.7   44   47-92     49-93  (128)
106 PRK13836 conjugal transfer pro  20.7      41   0.001   11.6   4.6   40    2-45     27-66  (220)
107 PRK02870 heat shock protein Ht  20.5      41   0.001   11.6   3.8   28    3-30     22-49  (338)
108 pfam07172 GRP Glycine rich pro  20.3      41  0.0011   11.6   3.6   16    1-17      1-16  (91)
109 pfam05751 FixH FixH. This fami  20.3      34 0.00087   12.2   0.4   20    7-26      6-25  (146)
110 TIGR01043 ATP_syn_A_arch ATP s  20.2      42  0.0011   11.6   2.5   18   52-70    123-140 (584)
111 PRK05696 fliL flagellar basal   20.2      42  0.0011   11.6   2.7   23    7-29     18-41  (168)
112 PRK11901 hypothetical protein;  20.1      42  0.0011   11.6   2.5   12    9-20     41-52  (329)

No 1  
>COG1463 Ttg2C ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=99.96  E-value=8e-27  Score=205.67  Aligned_cols=126  Identities=30%  Similarity=0.427  Sum_probs=111.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCC
Q ss_conf             9632789999999999999999999986254446--77618999997187567668980789007433798888648886
Q gi|254780140|r    1 MESKNYYTSVGLFVVSILFFSFFSIYWLSRSNQY--DGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYP   78 (452)
Q Consensus         1 m~~~~~~~~vG~fvi~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~   78 (452)
                      |++|.+++++|+|++++++.++++++|+....+.  +...|+++++|+ ++.||.+|+||+|+||+||+|++|.+++ ++
T Consensus         1 m~~r~~~~~v~~f~~~~l~~~~~~~~~~~~~~~~~~~~~~~~v~a~f~-~~~GL~~gs~V~~~GV~VG~V~~I~~~~-~~   78 (359)
T COG1463           1 METRANRVLVGLFLLLGLLAVLLFVLWLATLPGLPGGTGTYTVTAYFD-DAGGLYVGSPVRYRGVKVGKVASISLDP-KP   78 (359)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEC-CCCCCCCCCEEEECCEEEEEEEEEEECC-CC
T ss_conf             986412689999999999999999998610243347788628999841-4457789982699787864486887617-88


Q ss_pred             EEEEEEEEECCCCCCCCCCEEEEEECCCCHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             07999999748972468846999742321023321014653221124678
Q gi|254780140|r   79 NHSLAKALIRPDTPLYPSTTATIRTQGLAGITYIELSTLRKEKKTIFQIA  128 (452)
Q Consensus        79 ~~v~v~~~i~~~~~i~~~~~~~i~~~~l~g~~~i~~~~~~~~~~~l~~~~  128 (452)
                      ..++|.++|+.+++||.++.+.|.+.|++|++||++.|+.+..+.+....
T Consensus        79 ~~~~v~~~id~~~~Ip~~s~A~I~~~gL~G~~yIeL~~~~~~~~~l~~~~  128 (359)
T COG1463          79 NGARVTLEIDSDYPIPADSTASIRTTGLLGEKYIELTPGDAGGPKLRLGA  128 (359)
T ss_pred             CEEEEEEEECCCCCCCCCCEEEEECCCCHHHHEEEECCCCCCCCCCCCCC
T ss_conf             70699999658950578746887306530543366347988866567899


No 2  
>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=99.87  E-value=3.9e-20  Score=158.86  Aligned_cols=122  Identities=18%  Similarity=0.181  Sum_probs=96.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCC---CCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEE--ECCCCCEEEEEE
Q ss_conf             9999999999999999986254446---77618999997187567668980789007433798888--648886079999
Q gi|254780140|r   10 VGLFVVSILFFSFFSIYWLSRSNQY---DGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLF--LDQEYPNHSLAK   84 (452)
Q Consensus        10 vG~fvi~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~--l~~~~~~~v~v~   84 (452)
                      +++|.++.+++++++.+.+...+++   +...|+|+++|+ ++.||.+|+.|+|+||+||+|++|.  ..+++..+++|.
T Consensus         2 ~~~~~~v~~~~v~~~~~~~~~~p~~~~~g~~~~t~~a~f~-~~~gl~~G~~V~~~Gv~VG~V~~i~~i~~~~~~~~~~v~   80 (304)
T TIGR00996         2 LGVVAVVVLALVVVLAVVFLRLPFTLGFGPGTYTVYAYFT-DAGGLYPGSKVRVRGVEVGKVTAIEEIPRGGNGAGVRVT   80 (304)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEC-CCCCCCCCCEEEEEEEEEEEEEEEEECCCCCCCCEEEEE
T ss_conf             7899999999999999998510221255788505899862-244758998038843330056432122788887678999


Q ss_pred             EEECCCCCCCCCCEEEEEECCCCHHHHHHCCCCCC--CCCCCCCCCCCCC
Q ss_conf             99748972468846999742321023321014653--2211246787777
Q gi|254780140|r   85 ALIRPDTPLYPSTTATIRTQGLAGITYIELSTLRK--EKKTIFQIATERN  132 (452)
Q Consensus        85 ~~i~~~~~i~~~~~~~i~~~~l~g~~~i~~~~~~~--~~~~l~~~~~~~~  132 (452)
                      |.+++++.||.+++|.|.+..++|.+||++.|+..  ..+.|.++..+.-
T Consensus        81 ~~~~~~~~iP~~~~A~I~~~~l~G~~~veL~pp~~p~~~~~L~~g~~I~~  130 (304)
T TIGR00996        81 FSLDRSVTIPANATAAIRSTTLLGSRYVELTPPKGPSGGPRLSDGGVIPL  130 (304)
T ss_pred             EEECCCEECCCCCEEEEECCCEEEEEEEEEECCCCCCCCCCCCCCCEECC
T ss_conf             97067732377207887303303423577633888988896975876444


No 3  
>PRK10807 paraquat-inducible protein B; Provisional
Probab=99.81  E-value=9.9e-18  Score=141.98  Aligned_cols=89  Identities=21%  Similarity=0.261  Sum_probs=73.4

Q ss_pred             CCCCCCEEEEEEEECCCCCCCCCC-CEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCC--CCCCCCEEEEEEC----
Q ss_conf             446776189999971875676689-807890074337988886488860799999974897--2468846999742----
Q gi|254780140|r   32 NQYDGPMAEVIIRIPGSVDGLSTD-SSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDT--PLYPSTTATIRTQ----  104 (452)
Q Consensus        32 ~~~~~~~~~~~~~f~~~v~GL~~g-spV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~--~i~~~~~~~i~~~----  104 (452)
                      ..|..++..+.+.|+ ++.||.+| ++|+|+||.||+|++|.|.+|. .+|.|.++++++.  .+..++++|+...    
T Consensus        36 ~~~~~~Gp~Iti~f~-~a~Gi~aGkT~ikyr~V~VG~V~~v~ls~d~-~~V~v~a~l~~~~~~~l~~dtrFWvV~Pri~~  113 (546)
T PRK10807         36 YHYSHQGPEVTLITT-NAEGIEGGKTTIKSRSVDVGVVESATLTDDL-THVEIKARLNSGMEKLLHKDTVFWVVKPQIGR  113 (546)
T ss_pred             HHHHHCCCEEEEEEC-CCCCCCCCCEEEEECCCCEEEEEEEEECCCC-CEEEEEEEECHHHHHHHHCCCEEEEEECEECC
T ss_conf             999826986999976-8788656964689758617899799988876-72899999887688774238769998020246


Q ss_pred             -------CCCHHHHHHCCCCCCCCC
Q ss_conf             -------321023321014653221
Q gi|254780140|r  105 -------GLAGITYIELSTLRKEKK  122 (452)
Q Consensus       105 -------~l~g~~~i~~~~~~~~~~  122 (452)
                             .|+.+.||.+.||....+
T Consensus       114 ~gvsGL~TLlSG~YI~~~pG~~~~~  138 (546)
T PRK10807        114 EGISGLGTLLSGAYIELQPGSKGSK  138 (546)
T ss_pred             CCCCCCCCCCCCCEEEEECCCCCCC
T ss_conf             6766744102433299706999971


No 4  
>pfam02470 MCE mce related protein. This family of proteins contains the mce (mammalian cell entry) proteins from Mycobacterium tuberculosis. The archetype (Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage. This family contains proteins of unknown function from other bacteria.
Probab=99.46  E-value=6.1e-13  Score=108.46  Aligned_cols=79  Identities=30%  Similarity=0.442  Sum_probs=72.2

Q ss_pred             CEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCC-CCCCCCEEEEEECCCCHHHHHHCC
Q ss_conf             6189999971875676689807890074337988886488860799999974897-246884699974232102332101
Q gi|254780140|r   37 PMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDT-PLYPSTTATIRTQGLAGITYIELS  115 (452)
Q Consensus        37 ~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~-~i~~~~~~~i~~~~l~g~~~i~~~  115 (452)
                      ++|++++.|+ ++.||.+|+||+|+|++||+|++|.+.++. ..+.+.+.+++++ ++|.++.+.+.+.+++|++|+++.
T Consensus         1 ~~~~i~~~f~-~~~Gl~~gs~V~~~Gv~VG~V~~i~~~~~~-~~v~v~~~i~~~~~~i~~~s~a~i~~~~llG~~~i~i~   78 (80)
T pfam02470         1 RGYTVTAYFD-DAGGLEVGAPVRYRGVPVGRVTSIDLDPDG-GGVRVTLRIDPDVVVIPKDSRAGIRSLGLLGEKYIALD   78 (80)
T ss_pred             CCEEEEEEEC-CCCCCCCCCEEEECCEEEEEEEEEEECCCC-CEEEEEEEECCCCCCCCCCCEEEEEECCCCCCEEEEEE
T ss_conf             9859999987-878988989899999899999899982899-88999999958976979995999986983532689985


Q ss_pred             CC
Q ss_conf             46
Q gi|254780140|r  116 TL  117 (452)
Q Consensus       116 ~~  117 (452)
                      ||
T Consensus        79 ~g   80 (80)
T pfam02470        79 PG   80 (80)
T ss_pred             CC
T ss_conf             88


No 5  
>COG3008 PqiB Paraquat-inducible protein B [General function prediction only]
Probab=99.16  E-value=2.9e-10  Score=89.69  Aligned_cols=111  Identities=17%  Similarity=0.216  Sum_probs=81.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCCCC-CEEEEEEEEEEEEEEEEECCCCCEEE
Q ss_conf             32789999999999999999999986254446776189999971875676689-80789007433798888648886079
Q gi|254780140|r    3 SKNYYTSVGLFVVSILFFSFFSIYWLSRSNQYDGPMAEVIIRIPGSVDGLSTD-SSVRFNGIPVGRIVGLFLDQEYPNHS   81 (452)
Q Consensus         3 ~~~~~~~vG~fvi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~v~GL~~g-spV~~~Gv~VG~V~~I~l~~~~~~~v   81 (452)
                      ++--++|+=-||-    ++++..+|+.   .+..++..+.+.| .|+.|+..| +||+|+||.||.|++|.|..|- .+|
T Consensus        18 r~~SpiWllPivA----l~igawL~~~---~~~~~G~~Itl~f-~saeGIeaGKT~Iry~gvdVG~V~~v~LsdDl-~~V   88 (553)
T COG3008          18 RRISPIWLLPIVA----LLIGAWLLFQ---HVQDRGPEITLTF-ESAEGIEAGKTPIRYQGVDVGVVTDIKLSDDL-KGV   88 (553)
T ss_pred             CCCCCHHHHHHHH----HHHHHHHHHH---HHHHCCCEEEEEE-CCCCCCCCCCCEEEECCEEEEEEEEEEECCCC-CCE
T ss_conf             5778068999999----9999999999---9970497599995-47666214860588513136678898853676-616


Q ss_pred             EEEEEECCCC--CCCCCCEEEEEE-----------CCCCHHHHHHCCCCCCCCC
Q ss_conf             9999974897--246884699974-----------2321023321014653221
Q gi|254780140|r   82 LAKALIRPDT--PLYPSTTATIRT-----------QGLAGITYIELSTLRKEKK  122 (452)
Q Consensus        82 ~v~~~i~~~~--~i~~~~~~~i~~-----------~~l~g~~~i~~~~~~~~~~  122 (452)
                      .|+.+++++.  .++.|+++|+..           ..|+++.||.+.||....+
T Consensus        89 ~V~a~i~~da~~~L~~dT~FWvVkPr~slaGiSGLdtLlSG~YI~lqPG~~~~~  142 (553)
T COG3008          89 EVTAQINSDAKDLLREDTRFWVVKPRASLAGISGLDTLLSGNYIGLQPGKKGEA  142 (553)
T ss_pred             EEEEEECHHHHHHHHCCCEEEEEECCCCCCCCCCCCHHHCCCEEEECCCCCCCC
T ss_conf             999996864888753285799982564545665400231473488667888886


No 6  
>PRK10807 paraquat-inducible protein B; Provisional
Probab=99.15  E-value=4e-10  Score=88.76  Aligned_cols=69  Identities=19%  Similarity=0.083  Sum_probs=54.4

Q ss_pred             CCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEE--EEEEECCCCCCCCCCEEEEEECC
Q ss_conf             776189999971875676689807890074337988886488860799--99997489724688469997423
Q gi|254780140|r   35 DGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSL--AKALIRPDTPLYPSTTATIRTQG  105 (452)
Q Consensus        35 ~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~--v~~~i~~~~~i~~~~~~~i~~~~  105 (452)
                      +.++.++...- ++.+.|.+|+||+|||++||+|++..|++++.+ +.  +++.-.++..|+.++++|-.+.-
T Consensus       154 ~~~G~~~~L~a-~~~gsl~~GsPV~yr~i~VG~V~~~~l~~~~~~-v~~~~fI~apYd~lV~~~trFW~~SGi  224 (546)
T PRK10807        154 DAKGIRVILDS-KKAGQLSPGDPVLFRGYRVGSVETSTFDPQKRN-MSYQLFINAPYDRLVTSNVRFWKDSGI  224 (546)
T ss_pred             CCCCEEEEEEE-CCCCCCCCCCCEEECCCEEEEEEEEEECCCCCE-EEEEEEECCCHHHHCCCCCEEEECCCE
T ss_conf             99956999995-898987799960677935778989998888998-999999837045330579777754554


No 7  
>COG3008 PqiB Paraquat-inducible protein B [General function prediction only]
Probab=98.65  E-value=2e-08  Score=76.80  Aligned_cols=64  Identities=16%  Similarity=0.171  Sum_probs=49.0

Q ss_pred             EEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEE--EEECCCCCCCCCCEEEEEEC
Q ss_conf             8999997187567668980789007433798888648886079999--99748972468846999742
Q gi|254780140|r   39 AEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAK--ALIRPDTPLYPSTTATIRTQ  104 (452)
Q Consensus        39 ~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~--~~i~~~~~i~~~~~~~i~~~  104 (452)
                      -++... .++.+.|.+|+||+||+++||+|++-+|++++.+ |.+.  |+-.++-.+.+++++|-.+.
T Consensus       162 L~i~L~-a~dlGsL~~GspVyfr~i~VGqV~sy~~d~d~~~-V~i~vfI~~py~~lV~~~sRFWn~SG  227 (553)
T COG3008         162 LRIHLD-AKDLGSLNVGSPVYFRKIPVGQVESYQFDPDKQG-VTIQVFIEAPYDRLVKKDSRFWNVSG  227 (553)
T ss_pred             CEEEEE-CCCCCCCCCCCEEEEECEEEEEEEEEEECCCCCE-EEEEEEECCHHHHHHCCCCEEEECCC
T ss_conf             089984-6755776789804880104301788877677884-79999955737666235754652214


No 8  
>PRK09793 methyl-accepting protein IV; Provisional
Probab=98.14  E-value=0.00089  Score=44.27  Aligned_cols=29  Identities=7%  Similarity=0.125  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCHHHHHC
Q ss_conf             99999999999999999999878888611
Q gi|254780140|r  410 NLVRKLQETVNHFDDCLNNFERNPQDIVW  438 (452)
Q Consensus       410 ~~~~~~~~~~~~l~~~~~~l~~~p~~li~  438 (452)
                      ..+++...+..+|.+....|..-..++-.
T Consensus       485 a~vee~a~aa~~L~~~a~~L~~~V~~Fkl  513 (533)
T PRK09793        485 SLVEEAAVATEQLANQADHLSSRVAVFTL  513 (533)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHEEC
T ss_conf             99999999999999999999999854124


No 9  
>smart00283 MA Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). Thought to undergo reversible methylation in response to attractants or repellants during bacterial chemotaxis.
Probab=98.00  E-value=0.0016  Score=42.52  Aligned_cols=75  Identities=9%  Similarity=0.201  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             55544444431012577898889889999987755323332223333210145677777765543322211122344
Q gi|254780140|r  253 FVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKII  329 (452)
Q Consensus       253 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  329 (452)
                      +......+......+......+.++.++.+  +-.+++.+.+.+.+.....+....+.++...............+.
T Consensus        79 ~~~~~~~l~~~~~~I~~i~~~I~~Ia~QTn--LLALNAaIEAARAGE~GrGFAVVA~EIr~LA~~t~~a~~~I~~~i  153 (262)
T smart00283       79 AVSAVEELEESSDEIGEIVSVIDDIADQTN--LLALNAAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLI  153 (262)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999999987--777516888875487786489999999999999999999999999


No 10 
>KOG0994 consensus
Probab=97.76  E-value=0.0039  Score=39.77  Aligned_cols=33  Identities=18%  Similarity=0.317  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH
Q ss_conf             899999999999999999999999987888861
Q gi|254780140|r  405 LNDIQNLVRKLQETVNHFDDCLNNFERNPQDIV  437 (452)
Q Consensus       405 ~~~~~~~~~~~~~~~~~l~~~~~~l~~~p~~li  437 (452)
                      .....+++.+.++.+..|+++-...+++-+.|.
T Consensus      1695 ~~eA~~Ll~~a~~kl~~l~dLe~~y~~~~~~L~ 1727 (1758)
T KOG0994        1695 RTEAEKLLGQANEKLDRLKDLELEYLRNEQALE 1727 (1758)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999989988888750368899


No 11 
>pfam00015 MCPsignal Methyl-accepting chemotaxis protein (MCP) signaling domain. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.
Probab=97.46  E-value=0.0099  Score=36.95  Aligned_cols=71  Identities=6%  Similarity=0.147  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5444444310125778988898899999877553233322233332101456777777655433222111223
Q gi|254780140|r  255 KSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQK  327 (452)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  327 (452)
                      .....+.....++...+..+.++.++.+-+  .+++.+.+.+.+.....+....+.++...............
T Consensus        30 ~~i~~L~~~s~~I~~i~~~I~~IA~QTNLL--ALNAaIEAARAGE~GrGFAVVA~EVR~LA~~t~~st~~I~~  100 (213)
T pfam00015        30 ETMEELETSSKKISDIISVIDEIAFQTNLL--ALNAAIEAARAGEQGRGFAVVADEVRKLAERSAQAAKEIEA  100 (213)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999998999999999899988898--99999999750668996088999999999988899999999


No 12 
>COG0840 Tar Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]
Probab=97.30  E-value=0.015  Score=35.67  Aligned_cols=62  Identities=8%  Similarity=0.172  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1257789888988999998775532333222333321014567777776554332221112234
Q gi|254780140|r  265 HDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKI  328 (452)
Q Consensus       265 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  328 (452)
                      .++......+..+.++.+  +-.+++.+.+.+..+....+....+.++...............+
T Consensus       236 ~~I~~i~~~I~~IAeQTN--LLALNAaIEAARAGE~GrGFaVVAdEVR~LA~~s~~st~~I~~~  297 (408)
T COG0840         236 QEIEEITSVINSIAEQTN--LLALNAAIEAARAGEAGRGFAVVADEVRKLAERSADSAKEIGLL  297 (408)
T ss_pred             HHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             789999999999999998--89888999998577678884146998999999989899999999


No 13 
>KOG0994 consensus
Probab=97.24  E-value=0.018  Score=35.21  Aligned_cols=11  Identities=18%  Similarity=-0.049  Sum_probs=4.7

Q ss_pred             CCCCCCEEEEE
Q ss_conf             76689807890
Q gi|254780140|r   51 GLSTDSSVRFN   61 (452)
Q Consensus        51 GL~~gspV~~~   61 (452)
                      -+.+.++|--+
T Consensus      1323 ~~~l~s~~~~s 1333 (1758)
T KOG0994        1323 SRELASLVDQS 1333 (1758)
T ss_pred             HHCCCCHHHHH
T ss_conf             31334303466


No 14 
>pfam00015 MCPsignal Methyl-accepting chemotaxis protein (MCP) signaling domain. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.
Probab=96.94  E-value=0.033  Score=33.33  Aligned_cols=26  Identities=12%  Similarity=0.317  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999999999999999998
Q gi|254780140|r  405 LNDIQNLVRKLQETVNHFDDCLNNFE  430 (452)
Q Consensus       405 ~~~~~~~~~~~~~~~~~l~~~~~~l~  430 (452)
                      ..++....+++.....+|...+..|+
T Consensus       186 ~~~~~~~~~~l~~~a~~L~~~v~~Fk  211 (213)
T pfam00015       186 VEESAAAAETLEEQAEELTASVAQFR  211 (213)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999999999999999987111


No 15 
>PRK09793 methyl-accepting protein IV; Provisional
Probab=96.30  E-value=0.085  Score=30.40  Aligned_cols=25  Identities=12%  Similarity=0.283  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999998
Q gi|254780140|r  406 NDIQNLVRKLQETVNHFDDCLNNFE  430 (452)
Q Consensus       406 ~~~~~~~~~~~~~~~~l~~~~~~l~  430 (452)
                      .+......++.+....|...+..|+
T Consensus       488 ee~a~aa~~L~~~a~~L~~~V~~Fk  512 (533)
T PRK09793        488 EEAAVATEQLANQADHLSSRVAVFT  512 (533)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHEE
T ss_conf             9999999999999999999985412


No 16 
>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=95.98  E-value=0.12  Score=29.34  Aligned_cols=14  Identities=7%  Similarity=0.209  Sum_probs=6.0

Q ss_pred             CCCCCCEEEEEEEE
Q ss_conf             76689807890074
Q gi|254780140|r   51 GLSTDSSVRFNGIP   64 (452)
Q Consensus        51 GL~~gspV~~~Gv~   64 (452)
                      |..++.+++|.=++
T Consensus        28 ~~g~~~~t~~a~f~   41 (304)
T TIGR00996        28 GFGPGTYTVYAYFT   41 (304)
T ss_pred             CCCCCCEEEEEEEC
T ss_conf             55788505899862


No 17 
>COG1463 Ttg2C ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=95.42  E-value=0.19  Score=27.90  Aligned_cols=38  Identities=5%  Similarity=0.208  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             33333445555444444310125778988898899999
Q gi|254780140|r  245 NIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKID  282 (452)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  282 (452)
                      ++.++...+.+..+.+...+..+......+......++
T Consensus       184 ~l~~~~~~ln~~~~~i~~~i~~l~~~~~~~~~~~~~l~  221 (359)
T COG1463         184 NLAQFTDALNARDGDIGALIANLNQLLDSLAAASDQLD  221 (359)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999870342389999999999999997789999


No 18 
>COG0840 Tar Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]
Probab=94.45  E-value=0.34  Score=26.15  Aligned_cols=21  Identities=14%  Similarity=0.379  Sum_probs=7.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             006888865798999999999
Q gi|254780140|r  333 NTIENITSNLNDSSQKFAELM  353 (452)
Q Consensus       333 ~~~~~~~~~l~~~~~~v~~~~  353 (452)
                      ..+..+..+...+..++..+.
T Consensus       278 dEVR~LA~~s~~st~~I~~~i  298 (408)
T COG0840         278 DEVRKLAERSADSAKEIGLLI  298 (408)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             989999999898999999999


No 19 
>COG1511 Predicted membrane protein [Function unknown]
Probab=92.72  E-value=0.66  Score=24.16  Aligned_cols=63  Identities=13%  Similarity=0.169  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCE--EEEEEEECCCCCCCCCCCEEEEEE--EEEEE--EEEEEECCCCCEE
Q ss_conf             999999999999999862544467761--899999718756766898078900--74337--9888864888607
Q gi|254780140|r   12 LFVVSILFFSFFSIYWLSRSNQYDGPM--AEVIIRIPGSVDGLSTDSSVRFNG--IPVGR--IVGLFLDQEYPNH   80 (452)
Q Consensus        12 ~fvi~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~f~~~v~GL~~gspV~~~G--v~VG~--V~~I~l~~~~~~~   80 (452)
                      +++++++.++...+.|+.-...|....  ..+-+...+.-      -+..|+|  +.+|.  |..+.-+++.+++
T Consensus        18 li~~i~i~vip~ly~~~~i~s~~dpy~~~~~lpVAVVNeD------kg~t~~Gk~~~iG~~~V~~L~kn~~~~w~   86 (780)
T COG1511          18 LIPIIAILVLPSLYAFFFLGALWDPYGNTSKLPVAVVNED------KGATFNGKKVNIGDDLVKTLKKNKSLDWH   86 (780)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECC------CCCCCCCCEEEHHHHHHHHHCCCCCCCEE
T ss_conf             9999999999989999973245786667888946998577------66664775110789999986068898628


No 20 
>pfam06009 Laminin_II Laminin Domain II. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure.
Probab=88.05  E-value=1.7  Score=21.37  Aligned_cols=73  Identities=8%  Similarity=0.124  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCC--CCCCCCC
Q ss_conf             99999999999999999999999999999986464289999999999999999999999998788886118--8877745
Q gi|254780140|r  369 FKDAQRAMHTFRDTSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHFDDCLNNFERNPQDIVWG--REKGSVK  446 (452)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~p~~li~g--~~~~~~~  446 (452)
                      ..++...+..+...++.+...+.++......   ....++..-+++       +++.+..-++-.+++-+|  -+..|+.
T Consensus        54 l~~a~~~V~~L~~~a~~L~dkl~~l~~~~~~---~~~~~ls~ni~~-------ik~~I~~AR~~An~Ikv~~~f~~~~~~  123 (140)
T pfam06009        54 VDDAGRSVRKLEKLAPDLLDKLKPLKQLEVA---NQSRTLSRNISR-------IKELIAQARKAANSIKVSVSFDGDSGL  123 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHH-------HHHHHHHHHHHHHHEEEEEEECCCCEE
T ss_conf             9999978999999889999998999987000---246689878999-------999999999998850021355798334


Q ss_pred             CCCCC
Q ss_conf             42689
Q gi|254780140|r  447 IYKPK  451 (452)
Q Consensus       447 ~~~~~  451 (452)
                      +|||.
T Consensus       124 e~~~p  128 (140)
T pfam06009       124 ELRPP  128 (140)
T ss_pred             EECCC
T ss_conf             41695


No 21 
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=87.16  E-value=0.47  Score=25.22  Aligned_cols=55  Identities=11%  Similarity=0.172  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEEC
Q ss_conf             9999999999999862544467761899999718756766898078900743379888864
Q gi|254780140|r   14 VVSILFFSFFSIYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLD   74 (452)
Q Consensus        14 vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~l~   74 (452)
                      .|+.++++++++||+-+- .--++..+-     +-.+.|++|+.|.-.|=-.|+|.+|.-+
T Consensus         5 ~iim~vv~~~~~ffmiRp-QkK~qke~q-----~ml~~L~kGdeVvTiGGl~G~V~~Vd~e   59 (120)
T PRK06531          5 TIIMFVVMLGLIFFMQRQ-QKKQAQERQ-----NQLNAIQKGDEVVTIGGLFGTVDEVDTE   59 (120)
T ss_pred             HHHHHHHHHHHHHHEECH-HHHHHHHHH-----HHHHHCCCCCEEEECCCCEEEEEEEECC
T ss_conf             899999999999860374-889999999-----9997257999899789828999999278


No 22 
>TIGR03545 conserved hypothetical protein TIGR03545. This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.
Probab=86.28  E-value=2.1  Score=20.71  Aligned_cols=17  Identities=6%  Similarity=0.377  Sum_probs=7.5

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999
Q gi|254780140|r    9 SVGLFVVSILFFSFFSI   25 (452)
Q Consensus         9 ~vG~fvi~~~~~~~~~~   25 (452)
                      ++|+|++++++++++++
T Consensus         7 li~f~~v~a~I~~~~~~   23 (554)
T TIGR03545         7 LIAFLIVVAVILALLYF   23 (554)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             89999999999999999


No 23 
>TIGR00739 yajC preprotein translocase, YajC subunit; InterPro: IPR003849   This entry describes proteins of unknown function..
Probab=85.53  E-value=0.72  Score=23.93  Aligned_cols=39  Identities=13%  Similarity=0.144  Sum_probs=27.5

Q ss_pred             CCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCC
Q ss_conf             56766898078900743379888864888607999999748972
Q gi|254780140|r   49 VDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTP   92 (452)
Q Consensus        49 v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~~   92 (452)
                      .++|++|+.|.-.|==+|+|++|.=..     -.+.+++.++..
T Consensus        35 ~~~L~KGd~V~T~gGi~G~V~~i~e~~-----~~i~i~~~~~t~   73 (86)
T TIGR00739        35 IESLKKGDKVLTIGGIIGTVTKIAENT-----NNIVIELNDNTE   73 (86)
T ss_pred             HHCCCCCCEEEECCCEEEEEEEEECCC-----CEEEEEECCCCE
T ss_conf             852799778998388389998852388-----678999879948


No 24 
>PRK03598 hypothetical protein; Provisional
Probab=81.95  E-value=3.1  Score=19.47  Aligned_cols=59  Identities=17%  Similarity=0.213  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEECCC
Q ss_conf             9999999999999999999986254446776189999971875676689807890074337988886488
Q gi|254780140|r    7 YTSVGLFVVSILFFSFFSIYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQE   76 (452)
Q Consensus         7 ~~~vG~fvi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~   76 (452)
                      ++++++.+++.+++.+++++|+....   ....+...++        .+..|.+.-=-=|+|++|.....
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~g~v--------e~~~V~vs~~v~G~V~~v~V~eG   62 (331)
T PRK03598          4 PVVIGLAVVALVAVGAGGWWWYQSRQ---DNGLTLYGNV--------DIRTVNLSFRVGGRLASLAVDEG   62 (331)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHEEECC---CCCEEEEEEE--------EEEEEEECCCCCEEEEEEECCCC
T ss_conf             38999999999999999765214057---8860357999--------99999991327759999986897


No 25 
>KOG0971 consensus
Probab=78.41  E-value=4  Score=18.69  Aligned_cols=24  Identities=29%  Similarity=0.527  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999
Q gi|254780140|r  406 NDIQNLVRKLQETVNHFDDCLNNF  429 (452)
Q Consensus       406 ~~~~~~~~~~~~~~~~l~~~~~~l  429 (452)
                      -|...++-.+++.+..|++.+..+
T Consensus       521 yDrdqTI~KfRelva~Lqdqlqe~  544 (1243)
T KOG0971         521 YDRDQTIKKFRELVAHLQDQLQEL  544 (1243)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             637889999999999999999998


No 26 
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=76.09  E-value=0.81  Score=23.56  Aligned_cols=37  Identities=22%  Similarity=0.317  Sum_probs=26.5

Q ss_pred             CCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCC
Q ss_conf             75676689807890074337988886488860799999974897
Q gi|254780140|r   48 SVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDT   91 (452)
Q Consensus        48 ~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~   91 (452)
                      =.+.|++|+.|.-.|=-.|+|.+|.   +  .  .+.+++.++.
T Consensus        50 m~~~L~~Gd~VvT~gGi~G~I~~v~---d--~--~v~leia~gv   86 (107)
T PRK05585         50 MLSSLAKGDEVVTNGGIIGKVTKVS---E--D--FVIIELNDDT   86 (107)
T ss_pred             HHHHCCCCCEEEECCCCEEEEEEEE---C--C--EEEEEECCCC
T ss_conf             9984589999998998589999997---9--9--8999988995


No 27 
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=74.45  E-value=2.4  Score=20.24  Aligned_cols=37  Identities=19%  Similarity=0.208  Sum_probs=26.5

Q ss_pred             CCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCC
Q ss_conf             56766898078900743379888864888607999999748972
Q gi|254780140|r   49 VDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTP   92 (452)
Q Consensus        49 v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~~   92 (452)
                      ...|.+|+.|.-.|=-.|+|++|.   +    -.|.+++-+++.
T Consensus        36 ~~sL~~Gd~VvT~~Gl~GtV~~v~---d----d~v~lEiApGv~   72 (108)
T PRK05886         36 HESLQPGDRVHTTSGLQATIVGIT---D----DTVDLEIAPGVV   72 (108)
T ss_pred             HHHCCCCCEEEECCCCEEEEEEEC---C----CEEEEEECCCCE
T ss_conf             983689998997898289999971---8----879999769958


No 28 
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=74.23  E-value=5.1  Score=17.94  Aligned_cols=12  Identities=17%  Similarity=0.207  Sum_probs=6.2

Q ss_pred             EEEEEEEEEECC
Q ss_conf             433798888648
Q gi|254780140|r   64 PVGRIVGLFLDQ   75 (452)
Q Consensus        64 ~VG~V~~I~l~~   75 (452)
                      .+++|..+.+.+
T Consensus        49 el~kvk~L~l~G   60 (569)
T PRK04778         49 ELEKVKKLNLTG   60 (569)
T ss_pred             HHHHHHCCCCCC
T ss_conf             999888086770


No 29 
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=71.42  E-value=3.4  Score=19.16  Aligned_cols=25  Identities=20%  Similarity=0.157  Sum_probs=21.6

Q ss_pred             CCCCCCCCCEEEEEEEEEEEEEEEE
Q ss_conf             7567668980789007433798888
Q gi|254780140|r   48 SVDGLSTDSSVRFNGIPVGRIVGLF   72 (452)
Q Consensus        48 ~v~GL~~gspV~~~Gv~VG~V~~I~   72 (452)
                      -.+.|.+|+.|--.|=-+|+|++|.
T Consensus        40 ml~sL~kGD~VvT~gGi~G~V~~v~   64 (97)
T COG1862          40 LLNSLKKGDEVVTIGGIVGTVTKVG   64 (97)
T ss_pred             HHHHCCCCCEEEECCCEEEEEEEEE
T ss_conf             9974568998997587399999970


No 30 
>pfam02699 YajC Preprotein translocase subunit. See.
Probab=70.37  E-value=3.2  Score=19.33  Aligned_cols=37  Identities=19%  Similarity=0.127  Sum_probs=26.5

Q ss_pred             CCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCC
Q ss_conf             75676689807890074337988886488860799999974897
Q gi|254780140|r   48 SVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDT   91 (452)
Q Consensus        48 ~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~   91 (452)
                      =.+.|++|+.|.-.|=-.|+|.+|.   +  .  .+.+++.++.
T Consensus        34 m~~~L~~Gd~VvT~gGi~G~V~~i~---~--~--~v~lei~~gv   70 (83)
T pfam02699        34 MLSSLKKGDEVVTIGGIHGKIVKVD---D--D--TVVLEIADGV   70 (83)
T ss_pred             HHHHCCCCCEEEECCCEEEEEEEEE---C--C--EEEEEECCCC
T ss_conf             9985789999998997199999997---9--9--9999988993


No 31 
>pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.
Probab=68.15  E-value=6.9  Score=17.03  Aligned_cols=11  Identities=18%  Similarity=0.292  Sum_probs=5.9

Q ss_pred             EEEEEEEEEEC
Q ss_conf             43379888864
Q gi|254780140|r   64 PVGRIVGLFLD   74 (452)
Q Consensus        64 ~VG~V~~I~l~   74 (452)
                      .+++|..+.+.
T Consensus        45 el~kvk~L~l~   55 (559)
T pfam06160        45 ELSKVKKLNLT   55 (559)
T ss_pred             HHHHHHCCCCC
T ss_conf             99998829897


No 32 
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=64.88  E-value=8  Score=16.60  Aligned_cols=10  Identities=20%  Similarity=0.348  Sum_probs=4.2

Q ss_pred             CHHHHHHCCC
Q ss_conf             1023321014
Q gi|254780140|r  107 AGITYIELST  116 (452)
Q Consensus       107 ~g~~~i~~~~  116 (452)
                      +|...++|.+
T Consensus       119 l~~~Li~IHG  128 (557)
T COG0497         119 LGQLLIDIHG  128 (557)
T ss_pred             HHHHHEEEEC
T ss_conf             9976601226


No 33 
>pfam01601 Corona_S2 Coronavirus S2 glycoprotein. The coronavirus spike glycoprotein forms the characteristic 'corona' after which the group is named. The Spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 pfam01600 and S2.
Probab=64.30  E-value=8.2  Score=16.53  Aligned_cols=21  Identities=19%  Similarity=0.441  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             579899999999999987640
Q gi|254780140|r  341 NLNDSSQKFAELMSKINNISA  361 (452)
Q Consensus       341 ~l~~~~~~v~~~~~~id~~~~  361 (452)
                      +..+.+..+.++..++|.+.+
T Consensus       299 nFgAISssI~dIy~RLD~leA  319 (609)
T pfam01601       299 NFGAISSSIQDIYSRLDALEA  319 (609)
T ss_pred             HCCHHHHHHHHHHHHHHHHHH
T ss_conf             302156789999998887776


No 34 
>pfam07889 DUF1664 Protein of unknown function (DUF1664). The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=61.56  E-value=9.1  Score=16.20  Aligned_cols=52  Identities=19%  Similarity=0.316  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999864642899999999999999999999999987
Q gi|254780140|r  372 AQRAMHTFRDTSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHFDDCLNNFER  431 (452)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~  431 (452)
                      +...+++.....+.+...+.++...++.+        ..-++.++..+..|..-+..+|.
T Consensus        73 vd~kld~~~eis~~i~~eV~e~~~~~~~i--------~~D~~~v~~~v~~Le~Ki~~ie~  124 (126)
T pfam07889        73 LDDKLDEQKEISESTRDEVTEIREDLSNI--------GEDVKSVQQAVEGLEGKLDSIEY  124 (126)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             53219999999999999999999649988--------76999999999989999988860


No 35 
>PRK11166 chemotaxis regulator CheZ; Provisional
Probab=60.19  E-value=9.6  Score=16.04  Aligned_cols=59  Identities=10%  Similarity=0.278  Sum_probs=33.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2236799999999999999999999999999--9999986464289999999999999999
Q gi|254780140|r  363 KENNSLFKDAQRAMHTFRDTSEKINRYIPSI--GNNLQNFSQSGLNDIQNLVRKLQETVNH  421 (452)
Q Consensus       363 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~  421 (452)
                      .+...+..+...-+..+......++..+.+|  +..+++.+++....+-.+++++...+-.
T Consensus       105 ~efr~L~~~t~~fL~~~~~~t~~~~~~L~EImmAQDFQDLTGQVIkkVi~lv~~vE~~Lv~  165 (214)
T PRK11166        105 ADARELVTDTRQFLRDVPQHTSFTNAQLLEIMMAQDFQDLTGQVIKKMMDVVQEIEQQLLM  165 (214)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999998687699999999999998254687899999999999999999999


No 36 
>pfam09177 Syntaxin-6_N Syntaxin 6, N-terminal. Members of this family, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport.
Probab=59.99  E-value=9.7  Score=16.01  Aligned_cols=32  Identities=13%  Similarity=0.426  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHH
Q ss_conf             89999999999999999999999998788886
Q gi|254780140|r  405 LNDIQNLVRKLQETVNHFDDCLNNFERNPQDI  436 (452)
Q Consensus       405 ~~~~~~~~~~~~~~~~~l~~~~~~l~~~p~~l  436 (452)
                      ..++...++.+...+.+|..++.-.+++|.++
T Consensus        39 ~~eL~~~l~~i~w~LeDLe~aV~~ve~np~kf   70 (95)
T pfam09177        39 TKELRNALESIEWDLEDLEEAVSVVEANPEKF   70 (95)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCC
T ss_conf             99999999999989999999999998392304


No 37 
>pfam04085 MreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.
Probab=59.53  E-value=9.8  Score=15.96  Aligned_cols=42  Identities=24%  Similarity=0.222  Sum_probs=30.8

Q ss_pred             CCCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCCC
Q ss_conf             87567668980789007433798888648886079999997489724
Q gi|254780140|r   47 GSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTPL   93 (452)
Q Consensus        47 ~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~~i   93 (452)
                      +...|+++|+||...+--||+|.++..     ....|.+-.+++..+
T Consensus        20 G~~~Gi~~g~~Vi~~~GlVG~V~~v~~-----~~S~V~li~d~~~~i   61 (153)
T pfam04085        20 GSKDGVEKGMPVINEKGLVGQVTEVSK-----NTSRVLLLTDTNHKV   61 (153)
T ss_pred             CCHHCCCCCCEEEECCCCEEEEEEECC-----CEEEEEECCCCCCEE
T ss_conf             704189799989949920999999899-----889999861576289


No 38 
>PRK13415 flagella biosynthesis protein FliZ; Provisional
Probab=58.68  E-value=10  Score=15.86  Aligned_cols=34  Identities=24%  Similarity=0.533  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCCCCC
Q ss_conf             999999999862544467761899999718756766898
Q gi|254780140|r   18 LFFSFFSIYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDS   56 (452)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~v~GL~~gs   56 (452)
                      ++++.+++-|++..++++.....+     .+.+|...|.
T Consensus        84 i~Liy~llkfl~kr~~~~~~~~~i-----~~lGGtslG~  117 (216)
T PRK13415         84 IFLIYALVKWLNKRNRLLKPFQYV-----ENIGGTSVGQ  117 (216)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCHH-----HHCCCCCCCC
T ss_conf             999999999986521033555234-----5226744578


No 39 
>pfam06103 DUF948 Bacterial protein of unknown function (DUF948). This family consists of bacterial sequences several of which are thought to be general stress proteins.
Probab=58.49  E-value=10  Score=15.84  Aligned_cols=23  Identities=9%  Similarity=0.140  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999
Q gi|254780140|r  370 KDAQRAMHTFRDTSEKINRYIPS  392 (452)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~~  392 (452)
                      .+..+.+.+.+...+.++..+..
T Consensus        47 ~et~~lL~ktN~L~~DVn~K~~~   69 (90)
T pfam06103        47 TETEDLLAKTNVLLEDVNGKVET   69 (90)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999888899999989997


No 40 
>TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression .    This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent ..
Probab=58.00  E-value=10  Score=15.79  Aligned_cols=41  Identities=20%  Similarity=0.055  Sum_probs=23.3

Q ss_pred             CCCCCCEEEEEEEECCCCCCCCCCCEEEEE--EEEEEEEEEEEE
Q ss_conf             446776189999971875676689807890--074337988886
Q gi|254780140|r   32 NQYDGPMAEVIIRIPGSVDGLSTDSSVRFN--GIPVGRIVGLFL   73 (452)
Q Consensus        32 ~~~~~~~~~~~~~f~~~v~GL~~gspV~~~--Gv~VG~V~~I~l   73 (452)
                      +.-.....+|.++|.++... .+.+.|.-.  .=.||.|.++.+
T Consensus        75 ~~~~~~ea~V~v~F~nd~~~-~prsqvttaaGsenv~~vde~~v  117 (1202)
T TIGR02169        75 NAKSADEAEVTVTFKNDDGK-FPRSQVTTAAGSENVLEVDELEV  117 (1202)
T ss_pred             CCCCCCEEEEEEEEECCCCC-CCCCCCCCCCCCCCCCCCCCEEE
T ss_conf             68899689898887227875-87310000224444442243589


No 41 
>PRK11633 hypothetical protein; Provisional
Probab=57.93  E-value=10  Score=15.78  Aligned_cols=27  Identities=26%  Similarity=0.110  Sum_probs=20.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             963278999999999999999999998
Q gi|254780140|r    1 MESKNYYTSVGLFVVSILFFSFFSIYW   27 (452)
Q Consensus         1 m~~~~~~~~vG~fvi~~~~~~~~~~~~   27 (452)
                      |+++..+=+||..||.+++.+|+=.++
T Consensus         1 M~s~~k~RLVGaiVLValaVIfLP~l~   27 (218)
T PRK11633          1 MASKFQNRLVGTIVLVALGVIVLPGLL   27 (218)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             937888888979999999999321652


No 42 
>TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome.
Probab=55.18  E-value=12  Score=15.48  Aligned_cols=29  Identities=24%  Similarity=0.363  Sum_probs=11.8

Q ss_pred             CCEEEEEEEECCCCCCCCCCCEEEEEEEEE
Q ss_conf             761899999718756766898078900743
Q gi|254780140|r   36 GPMAEVIIRIPGSVDGLSTDSSVRFNGIPV   65 (452)
Q Consensus        36 ~~~~~~~~~f~~~v~GL~~gspV~~~Gv~V   65 (452)
                      -..-.|...| ||.+|+-+|-=..|.=|.|
T Consensus        74 ~~~AeV~L~f-dN~d~~l~~~y~~y~Ei~i  102 (1191)
T TIGR02168        74 LSLAEVELVF-DNSDGLLPGQYADYSEISI  102 (1191)
T ss_pred             CCEEEEEEEE-ECCCCCCHHHHCCCCEEEE
T ss_conf             7700689888-5588835121136771789


No 43 
>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]
Probab=53.56  E-value=12  Score=15.30  Aligned_cols=23  Identities=17%  Similarity=0.248  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999999862
Q gi|254780140|r    7 YTSVGLFVVSILFFSFFSIYWLS   29 (452)
Q Consensus         7 ~~~vG~fvi~~~~~~~~~~~~~~   29 (452)
                      |++||+.||..++.++++++.-.
T Consensus         3 ~liv~llVilv~~~~~g~~lRkk   25 (570)
T COG4477           3 YLIVALLVILVAAYAVGYLLRKK   25 (570)
T ss_pred             EHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             34999999999999999999973


No 44 
>pfam04582 Reo_sigmaC Reovirus sigma C capsid protein.
Probab=53.06  E-value=12  Score=15.25  Aligned_cols=10  Identities=10%  Similarity=0.438  Sum_probs=3.2

Q ss_pred             HHHHHHCHHH
Q ss_conf             9999878888
Q gi|254780140|r  426 LNNFERNPQD  435 (452)
Q Consensus       426 ~~~l~~~p~~  435 (452)
                      +..+++..+.
T Consensus       142 is~Le~Rv~a  151 (326)
T pfam04582       142 ITDLEQRVKS  151 (326)
T ss_pred             HHHHHHHHHH
T ss_conf             8779999988


No 45 
>pfam09890 DUF2117 Uncharacterized protein conserved in archaea (DUF2117). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=51.64  E-value=11  Score=15.70  Aligned_cols=24  Identities=21%  Similarity=0.493  Sum_probs=21.6

Q ss_pred             CCCCCCCCCCEEEEEEEEEEEEEE
Q ss_conf             875676689807890074337988
Q gi|254780140|r   47 GSVDGLSTDSSVRFNGIPVGRIVG   70 (452)
Q Consensus        47 ~~v~GL~~gspV~~~Gv~VG~V~~   70 (452)
                      .-+.|..+|.++..+|+-||+.++
T Consensus        89 R~i~Gv~pGE~I~VNGiVIG~a~s  112 (209)
T pfam09890        89 RRISGVFPGENIMVNGIVIGKATS  112 (209)
T ss_pred             EEEEEECCCCCEEEEEEEEEEECC
T ss_conf             999600899947994189988648


No 46 
>KOG0250 consensus
Probab=51.11  E-value=13  Score=15.04  Aligned_cols=25  Identities=20%  Similarity=0.202  Sum_probs=13.4

Q ss_pred             EEEEEEEEECCCCCEEEEEEEEECCCCC
Q ss_conf             3379888864888607999999748972
Q gi|254780140|r   65 VGRIVGLFLDQEYPNHSLAKALIRPDTP   92 (452)
Q Consensus        65 VG~V~~I~l~~~~~~~v~v~~~i~~~~~   92 (452)
                      .|+|.+|.|.   +....-.+.|+.+.+
T Consensus        39 sG~I~sI~L~---NFMCHsnL~IeFg~~   63 (1074)
T KOG0250          39 SGKIESIHLT---NFMCHSNLLIEFGPR   63 (1074)
T ss_pred             CCEEEEEEEE---EECCCCCCEECCCCC
T ss_conf             3638999975---210333541025887


No 47 
>pfam06008 Laminin_I Laminin Domain I. coiled-coil structure. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure.
Probab=50.69  E-value=13  Score=15.00  Aligned_cols=15  Identities=7%  Similarity=0.140  Sum_probs=4.7

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999999
Q gi|254780140|r  412 VRKLQETVNHFDDCL  426 (452)
Q Consensus       412 ~~~~~~~~~~l~~~~  426 (452)
                      +.+.+..+...+.+.
T Consensus       242 L~~a~~~L~~a~~ll  256 (263)
T pfam06008       242 LATGRDSLDQANLLL  256 (263)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999887999999999


No 48 
>PRK10692 hypothetical protein; Provisional
Probab=48.51  E-value=1.2  Score=22.37  Aligned_cols=66  Identities=17%  Similarity=0.256  Sum_probs=34.8

Q ss_pred             CCCHHHHHHHHH-HHHHHHHHHHHHHHH--HCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEE
Q ss_conf             963278999999-999999999999998--62544467761899999718756766898078900743379888
Q gi|254780140|r    1 MESKNYYTSVGL-FVVSILFFSFFSIYW--LSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGL   71 (452)
Q Consensus         1 m~~~~~~~~vG~-fvi~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I   71 (452)
                      |++|.... +|= |..++++..++.+-+  +.....+.  -..+.+.  .+.-|+.+|+-+++.|-+||-=+.|
T Consensus         1 MKrk~a~~-lGN~lM~lGm~~Mv~~igysi~~~~~~l~--lP~f~~~--~al~~IFiGAl~WLaGARi~GrE~v   69 (92)
T PRK10692          1 MKRKNASL-LGNVLMGLGLVVMVVGVGYSILNQLPQFN--LPQFFAH--GAILSIFVGALLWLAGARVGGREQV   69 (92)
T ss_pred             CCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHH--HHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf             97304668-64699999899999999999997365678--6089987--5799999999999923632562366


No 49 
>COG2715 SpmA Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]
Probab=47.35  E-value=15  Score=14.65  Aligned_cols=10  Identities=30%  Similarity=0.633  Sum_probs=3.8

Q ss_pred             HHHHHHHHHH
Q ss_conf             8999999999
Q gi|254780140|r    6 YYTSVGLFVV   15 (452)
Q Consensus         6 ~~~~vG~fvi   15 (452)
                      ||+|+|+|++
T Consensus         3 N~iW~~f~lv   12 (206)
T COG2715           3 NYIWLAFFLV   12 (206)
T ss_pred             CHHHHHHHHH
T ss_conf             0479999999


No 50 
>COG3556 Predicted membrane protein [Function unknown]
Probab=46.87  E-value=15  Score=14.74  Aligned_cols=17  Identities=29%  Similarity=0.387  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999
Q gi|254780140|r    8 TSVGLFVVSILFFSFFS   24 (452)
Q Consensus         8 ~~vG~fvi~~~~~~~~~   24 (452)
                      +++|+|++.++..+.-.
T Consensus        81 aKmglFvlvgLlSi~PT   97 (150)
T COG3556          81 AKMGLFVLVGLLSIIPT   97 (150)
T ss_pred             HHHHHHHHHHHHHCCCH
T ss_conf             99889999999851531


No 51 
>TIGR02876 spore_yqfD sporulation protein YqfD; InterPro: IPR010690   This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis (P54469 from SWISSPROT) is known to be essential for efficient sporulation although its exact function is unknown ..
Probab=45.73  E-value=9.1  Score=16.20  Aligned_cols=47  Identities=11%  Similarity=0.240  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCC--CCCCCC-CEEEEEEEECCCCCCCCCC
Q ss_conf             999999999999999999998625--444677-6189999971875676689
Q gi|254780140|r    7 YTSVGLFVVSILFFSFFSIYWLSR--SNQYDG-PMAEVIIRIPGSVDGLSTD   55 (452)
Q Consensus         7 ~~~vG~fvi~~~~~~~~~~~~~~~--~~~~~~-~~~~~~~~f~~~v~GL~~g   55 (452)
                      -+++|+|++.+++.++..++|.=.  ...... ..|.+....  +-.|+++|
T Consensus        86 ~~~~G~L~f~~~~~~lS~fiW~IdvrI~g~~~~~~~~i~~~L--~~~G~k~G  135 (406)
T TIGR02876        86 GILIGILLFLAIVYLLSTFIWKIDVRITGVKGETEYEIRKEL--KEMGIKPG  135 (406)
T ss_pred             CHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCHHHHHHHH--HHCCCCCC
T ss_conf             076689999999998617558999997279997789999999--85587568


No 52 
>COG1256 FlgK Flagellar hook-associated protein [Cell motility and secretion]
Probab=45.17  E-value=16  Score=14.42  Aligned_cols=58  Identities=14%  Similarity=0.303  Sum_probs=28.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1112221101222332211000001122223344566543222110012334567888
Q gi|254780140|r  142 SGINYFISNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDK  199 (452)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i~~  199 (452)
                      .....++..++.+...+......+...-.++...+...+..+..+...+++....+..
T Consensus       131 a~r~~vl~~a~~l~~~in~~~~~L~~l~~~i~~~I~~~V~~vNsLl~qIa~lN~qI~~  188 (552)
T COG1256         131 AARQAVLSKAQTLVNQINNTYEQLTDLRKDINAEIAATVDEVNSLLKQIADLNKQIRK  188 (552)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999989999999999888689999999999999999999999997


No 53 
>smart00503 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p
Probab=44.97  E-value=16  Score=14.40  Aligned_cols=24  Identities=8%  Similarity=0.266  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999
Q gi|254780140|r  371 DAQRAMHTFRDTSEKINRYIPSIG  394 (452)
Q Consensus       371 ~~~~~~~~~~~~~~~~~~~~~~~~  394 (452)
                      ++......+...+..+...+..+.
T Consensus        47 ~l~~~~~~i~~~a~~ik~~Lk~l~   70 (117)
T smart00503       47 KLERLIDDIKRLAKEIRAKLKELE   70 (117)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             998789999999999999999987


No 54 
>pfam12273 RCR Chitin synthesis regulation, resistance to Congo red. RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5.
Probab=42.03  E-value=18  Score=14.10  Aligned_cols=22  Identities=18%  Similarity=0.617  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999999862
Q gi|254780140|r    7 YTSVGLFVVSILFFSFFSIYWLS   29 (452)
Q Consensus         7 ~~~vG~fvi~~~~~~~~~~~~~~   29 (452)
                      |++..+||++.|++ |+++.++.
T Consensus         2 Wv~fav~i~~~~i~-~f~~~~~n   23 (124)
T pfam12273         2 WVLFAIFIIALLIL-FFLTARIN   23 (124)
T ss_pred             EEEHHHHHHHHHHH-HHHHHHHH
T ss_conf             11089999999999-99999873


No 55 
>pfam05667 DUF812 Protein of unknown function (DUF812). This family consists of several eukaryotic proteins of unknown function.
Probab=39.86  E-value=20  Score=13.87  Aligned_cols=25  Identities=12%  Similarity=0.371  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999987
Q gi|254780140|r  407 DIQNLVRKLQETVNHFDDCLNNFER  431 (452)
Q Consensus       407 ~~~~~~~~~~~~~~~l~~~~~~l~~  431 (452)
                      ||.+.+.+.+....+++.+.+.++|
T Consensus       448 dI~KIl~DTR~LQkeiN~~~~~L~R  472 (536)
T pfam05667       448 DIDKILSDTRSLQKEINNITGKLDR  472 (536)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999888888840


No 56 
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=39.42  E-value=20  Score=13.83  Aligned_cols=41  Identities=29%  Similarity=0.325  Sum_probs=29.6

Q ss_pred             CCCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCC
Q ss_conf             8756766898078900743379888864888607999999748972
Q gi|254780140|r   47 GSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTP   92 (452)
Q Consensus        47 ~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~~   92 (452)
                      ++-.|+.+|.||-..|--||+|+.+.-     ...+|.+.-|....
T Consensus       139 Gs~~GV~~~~~Vi~~~GLVG~V~~V~~-----~tS~V~Lltd~~~~  179 (284)
T COG1792         139 GSNDGIKKGMPVVAEGGLVGKVVEVSK-----NTSRVLLLTDVNSK  179 (284)
T ss_pred             CCCCCCCCCCEEEECCCCEEEEEEECC-----CEEEEEEEECCCCC
T ss_conf             755686689647966831899999727-----65699984246610


No 57 
>pfam07427 consensus
Probab=38.74  E-value=20  Score=13.76  Aligned_cols=38  Identities=11%  Similarity=0.145  Sum_probs=28.5

Q ss_pred             CCCEEEEEEEEEEEEEEE---EECCCCCEEEEEEEEECCCC
Q ss_conf             898078900743379888---86488860799999974897
Q gi|254780140|r   54 TDSSVRFNGIPVGRIVGL---FLDQEYPNHSLAKALIRPDT   91 (452)
Q Consensus        54 ~gspV~~~Gv~VG~V~~I---~l~~~~~~~v~v~~~i~~~~   91 (452)
                      .+-.|+++||+||.=...   .+.++..+.+.+...++.+.
T Consensus        37 v~y~v~mNgv~ig~G~~~~~~~i~~~s~~tv~v~t~idn~~   77 (126)
T pfam07427        37 LKADIYMNGVKIGEGRILKGATIQPKSRGTVKVSLTLDNSK   77 (126)
T ss_pred             EEEEEEECCEEEEEEEECCCEEECCCCEEEEEEEEEEECCC
T ss_conf             28999999999864686021897899759999999980432


No 58 
>PRK04192 V-type ATP synthase subunit A; Provisional
Probab=37.98  E-value=21  Score=13.68  Aligned_cols=37  Identities=19%  Similarity=0.335  Sum_probs=23.4

Q ss_pred             CCCCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEECC
Q ss_conf             4677618999997187567668980789007433798888648
Q gi|254780140|r   33 QYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQ   75 (452)
Q Consensus        33 ~~~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~l~~   75 (452)
                      .+.++...+.+ | ++.+||.+|+||.+.|-    .-++.+.|
T Consensus        42 ~i~gd~a~iQV-y-E~T~Gl~~G~~V~~TG~----pLsV~LGp   78 (585)
T PRK04192         42 RVRGDEASIQV-Y-EETSGIKPGEPVEFTGE----PLSVELGP   78 (585)
T ss_pred             EEECCEEEEEE-C-CCCCCCCCCCEEEECCC----CEEEEECH
T ss_conf             99499899996-6-68889999898884799----44988676


No 59 
>PRK09379 membrane-bound transcriptional regulator LytR; Provisional
Probab=37.98  E-value=21  Score=13.68  Aligned_cols=22  Identities=23%  Similarity=0.211  Sum_probs=12.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9632789999999999999999
Q gi|254780140|r    1 MESKNYYTSVGLFVVSILFFSF   22 (452)
Q Consensus         1 m~~~~~~~~vG~fvi~~~~~~~   22 (452)
                      |+.|.-.+.+++++++.++...
T Consensus         1 ~KKkil~~i~~v~~vlll~~g~   22 (303)
T PRK09379          1 MKKKILFWILGIIGVLIIGGGI   22 (303)
T ss_pred             CCCEEEHHHHHHHHHHHHHHHH
T ss_conf             9826603699999999999999


No 60 
>pfam02874 ATP-synt_ab_N ATP synthase alpha/beta family, beta-barrel domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.
Probab=37.29  E-value=21  Score=13.61  Aligned_cols=13  Identities=38%  Similarity=0.549  Sum_probs=5.2

Q ss_pred             CCCCCCCCCEEEE
Q ss_conf             7567668980789
Q gi|254780140|r   48 SVDGLSTDSSVRF   60 (452)
Q Consensus        48 ~v~GL~~gspV~~   60 (452)
                      +..||+.|++|+.
T Consensus        55 ~t~Gl~~G~~V~~   67 (69)
T pfam02874        55 GTDGLSRGDEVKR   67 (69)
T ss_pred             CCCCCCCCCEEEC
T ss_conf             8677538999982


No 61 
>PRK06793 fliI flagellum-specific ATP synthase; Validated
Probab=35.88  E-value=22  Score=13.46  Aligned_cols=24  Identities=8%  Similarity=0.177  Sum_probs=16.4

Q ss_pred             EEEEEEEECCCCCCCCCCCEEEEEE
Q ss_conf             1899999718756766898078900
Q gi|254780140|r   38 MAEVIIRIPGSVDGLSTDSSVRFNG   62 (452)
Q Consensus        38 ~~~~~~~f~~~v~GL~~gspV~~~G   62 (452)
                      ...+.+.| ++..||..|+.|+..|
T Consensus        63 ~~v~l~p~-~~~~gi~~G~~V~~~g   86 (432)
T PRK06793         63 ENNMLLPF-EQTEKVCYGDSVTLIA   86 (432)
T ss_pred             CEEEEEEC-CCCCCCCCCCEEEECC
T ss_conf             93999988-7877889999999799


No 62 
>pfam11694 DUF3290 Protein of unknown function (DUF3290). This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=35.79  E-value=22  Score=13.45  Aligned_cols=27  Identities=11%  Similarity=0.321  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             278999999999999999999998625
Q gi|254780140|r    4 KNYYTSVGLFVVSILFFSFFSIYWLSR   30 (452)
Q Consensus         4 ~~~~~~vG~fvi~~~~~~~~~~~~~~~   30 (452)
                      ..+++++++++++.++++++++.++..
T Consensus        14 ~~~~~~~~i~~~~l~~li~~~~~Y~r~   40 (149)
T pfam11694        14 TQNWLRYILIIILLVVIIIFAFKYLRH   40 (149)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             888999999999999999999999985


No 63 
>KOG1352 consensus
Probab=34.55  E-value=23  Score=13.31  Aligned_cols=43  Identities=21%  Similarity=0.342  Sum_probs=29.3

Q ss_pred             HCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEECCC
Q ss_conf             6254446776189999971875676689807890074337988886488
Q gi|254780140|r   28 LSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQE   76 (452)
Q Consensus        28 ~~~~~~~~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~   76 (452)
                      .+..-++.++.-++.+|  +.-+||.+|+||.--|-+    -++.|.|.
T Consensus        54 vGEiIrlegD~aTIQVY--EeTsG~tVgDpvlrTgkP----LsvELGPG   96 (618)
T KOG1352          54 VGEIIRLEGDMATIQVY--EETSGLTVGDPVLRTGKP----LSVELGPG   96 (618)
T ss_pred             CEEEEEECCCEEEEEEE--ECCCCCCCCCCHHHCCCC----CEEEECCC
T ss_conf             00005861760379998--124885148704315885----15762753


No 64 
>COG1155 NtpA Archaeal/vacuolar-type H+-ATPase subunit A [Energy production and conversion]
Probab=34.53  E-value=23  Score=13.31  Aligned_cols=31  Identities=19%  Similarity=0.391  Sum_probs=14.3

Q ss_pred             CCCCCEEEEEEEECCCCCCCCCCCEEEEEEEEE
Q ss_conf             467761899999718756766898078900743
Q gi|254780140|r   33 QYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPV   65 (452)
Q Consensus        33 ~~~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~V   65 (452)
                      +..++...+.+|  +.-+||.+|.||..-|-+.
T Consensus        40 ~i~gd~a~iQVy--E~T~Gi~~Ge~V~~Tg~pL   70 (588)
T COG1155          40 RIEGNRATIQVY--EDTAGIRPGEKVENTGRPL   70 (588)
T ss_pred             EEECCEEEEEEE--EECCCCCCCCEEECCCCCE
T ss_conf             985876899999--6058999998321279822


No 65 
>pfam11025 GP40 Glycoprotein GP40 of Cryptosporidium. This family is highly conserved in Cryptosporidium spp. Many members are annotated as being a 60 kDa glycoprotein.
Probab=33.79  E-value=24  Score=13.23  Aligned_cols=56  Identities=5%  Similarity=0.181  Sum_probs=30.8

Q ss_pred             HHHHHCCCCCCC---CCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECC
Q ss_conf             999862544467---761899999718756766898078900743379888864888607999999748
Q gi|254780140|r   24 SIYWLSRSNQYD---GPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRP   89 (452)
Q Consensus        24 ~~~~~~~~~~~~---~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~   89 (452)
                      +++||+......   --.|+++. -  .+.|-..-+|=++.    |.|+++.|...+   -.|.|.++-
T Consensus        12 FVMWFgeGtPvaTlKCG~YTiVY-A--P~k~~tdPaPrYIS----GeV~sVtFeksd---~TvkIkv~g   70 (165)
T pfam11025        12 FVMWFGEGTPVATLKCGGYTIVY-A--PIKDQTDPAPRYIS----GEVTSVTFEKSD---NTVKIKVNG   70 (165)
T ss_pred             EEEEECCCCEEEEEEECCEEEEE-C--CCCCCCCCCCCEEE----CCEEEEEEECCC---CEEEEEECC
T ss_conf             89994389553588648989997-0--35789898872350----516788885378---649999889


No 66 
>pfam10762 DUF2583 Protein of unknown function (DUF2583). Some members in this family of proteins are annotated as YchH however currently no function is known.
Probab=33.44  E-value=1.9  Score=20.96  Aligned_cols=67  Identities=15%  Similarity=0.161  Sum_probs=34.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHH--HHCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEE
Q ss_conf             96327899999999999999999999--862544467761899999718756766898078900743379888
Q gi|254780140|r    1 MESKNYYTSVGLFVVSILFFSFFSIY--WLSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGL   71 (452)
Q Consensus         1 m~~~~~~~~vG~fvi~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I   71 (452)
                      |++|...++=-+|..++++..++.+-  .++....+.-+  .+.+.  .+.-|+.+|+-+++.|-+||-=+.|
T Consensus         1 MKRk~a~~lGN~lMglGm~~Mv~gigy~i~s~i~~L~lp--~~~~~--gal~~IFiGAl~WL~GARigGrE~V   69 (89)
T pfam10762         1 MKRKNAAILGNVLMGLGLVTMVVGVGYSILAQVPQFNLP--QFFAH--GALLSIFVGALLWLVGARIGGREEV   69 (89)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH--HHHHH--HHHHHHHHHHHHHHHCCCCCCCHHH
T ss_conf             985202030259999889999999999999855247971--99986--4899999999999954654571035


No 67 
>TIGR00304 TIGR00304 conserved hypothetical protein TIGR00304; InterPro: IPR002849 This archaebacterial protein family has no known function. The proteins are predicted to contain two transmembrane helices..
Probab=33.16  E-value=25  Score=13.16  Aligned_cols=56  Identities=13%  Similarity=0.238  Sum_probs=30.5

Q ss_pred             HHHHHHH-HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEEEE
Q ss_conf             9999999-9999999999999862544467761899999718756766898078900743
Q gi|254780140|r    7 YTSVGLF-VVSILFFSFFSIYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPV   65 (452)
Q Consensus         7 ~~~vG~f-vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~V   65 (452)
                      .+..|+| ++.|+...++...|........ .+.+-..  .+.-..=+....|+|.||-.
T Consensus         6 ~I~lG~~li~~G~~~~~lg~~l~~~~e~~r-eyerrri--sE~~~~~k~~~~V~~~GvV~   62 (93)
T TIGR00304         6 LILLGIILIVIGFLLVFLGLALEAESEDER-EYERRRI--SEKRKSDKDKEEVKYGGVVM   62 (93)
T ss_pred             EHHHHHHHHHHHHHHHHHHHHHCCCCCCHH-HHHHHHC--CCCCCCCCCCCCEEECCEEE
T ss_conf             034418999999999998654313542123-4543202--46877677410310146587


No 68 
>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=32.07  E-value=26  Score=13.04  Aligned_cols=25  Identities=20%  Similarity=0.262  Sum_probs=16.5

Q ss_pred             EEEEEEECCCCCCCCCCCEEEEEEEE
Q ss_conf             89999971875676689807890074
Q gi|254780140|r   39 AEVIIRIPGSVDGLSTDSSVRFNGIP   64 (452)
Q Consensus        39 ~~~~~~f~~~v~GL~~gspV~~~Gv~   64 (452)
                      ..+...| ++..||..|++|++.|-+
T Consensus        45 ~v~l~~~-~~~~Gi~~G~~V~~tg~~   69 (411)
T TIGR03496        45 RVLLMPL-EDVEGLRPGARVFPLEGP   69 (411)
T ss_pred             EEEEEEC-CCCCCCCCCCEEEECCCC
T ss_conf             7999986-688788889999978996


No 69 
>TIGR02545 ATP_syn_fliI flagellar protein export ATPase FliI; InterPro: IPR013379    FliI proteins are involved in bacterial flagellum systems, acting to drive protein export for flagellar biosynthesis. The most closely related proteins are the YscN proteins of bacterial type III secretion systems.; GO: 0016887 ATPase activity, 0001539 ciliary or flagellar motility, 0009296 flagellum biogenesis, 0009288 flagellin-based flagellum.
Probab=31.87  E-value=26  Score=13.02  Aligned_cols=27  Identities=11%  Similarity=0.175  Sum_probs=20.1

Q ss_pred             CCCEEEEEEEECCCCCCCCCCCEEEEEE
Q ss_conf             7761899999718756766898078900
Q gi|254780140|r   35 DGPMAEVIIRIPGSVDGLSTDSSVRFNG   62 (452)
Q Consensus        35 ~~~~~~~~~~f~~~v~GL~~gspV~~~G   62 (452)
                      |...+.+.+-| +.+.|+.+|++|...|
T Consensus        51 F~~~~~~lmP~-~~~~Gi~~G~~V~~~~   77 (439)
T TIGR02545        51 FEGDRVILMPY-EPLEGIRPGDRVFLLG   77 (439)
T ss_pred             ECCCEEEEEEC-CCCCCCCCCCEEEECC
T ss_conf             73883698644-6555624576578634


No 70 
>PRK04570 cell division protein ZipA; Provisional
Probab=31.69  E-value=19  Score=13.94  Aligned_cols=17  Identities=12%  Similarity=0.434  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             27899999999999999
Q gi|254780140|r    4 KNYYTSVGLFVVSILFF   20 (452)
Q Consensus         4 ~~~~~~vG~fvi~~~~~   20 (452)
                      -...++||+|+++++++
T Consensus         3 ~~~~lri~i~~~g~llv   19 (244)
T PRK04570          3 DMAMIRIGILIAGLLLV   19 (244)
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             32589999999999884


No 71 
>pfam06024 DUF912 Nucleopolyhedrovirus protein of unknown function (DUF912). This family consists of several Nucleopolyhedrovirus proteins of unknown function.
Probab=31.64  E-value=26  Score=13.00  Aligned_cols=27  Identities=15%  Similarity=0.371  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             789999999999999999999986254
Q gi|254780140|r    5 NYYTSVGLFVVSILFFSFFSIYWLSRS   31 (452)
Q Consensus         5 ~~~~~vG~fvi~~~~~~~~~~~~~~~~   31 (452)
                      .+.+|+|+..+.++++++..+++|-..
T Consensus        61 ~~~ili~ll~~~~ilvlly~IyYFVIL   87 (101)
T pfam06024        61 GNIILIGLLAFFCVLVLLYAIYYFVIL   87 (101)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHEE
T ss_conf             245899999999999999999986236


No 72 
>pfam06092 DUF943 Enterobacterial putative membrane protein (DUF943). This family consists of several hypothetical putative membrane proteins from Escherichia coli, Yersinia pestis and Salmonella typhi.
Probab=31.44  E-value=26  Score=12.97  Aligned_cols=93  Identities=15%  Similarity=0.231  Sum_probs=42.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEE
Q ss_conf             96327899999999999999999999862544467761899999718756766898078900743379888864888607
Q gi|254780140|r    1 MESKNYYTSVGLFVVSILFFSFFSIYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNH   80 (452)
Q Consensus         1 m~~~~~~~~vG~fvi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~   80 (452)
                      |..|.+.+++++|.++++     +++|...      +.++++....++  +   .+.|..+-+|+=.=.+|..=.+..  
T Consensus         1 Mk~k~~~il~~l~L~~~~-----y~~W~~~------rPVeIi~Vh~~~--~---~~~IlV~~fP~TD~gKI~WW~~Nk--   62 (155)
T pfam06092         1 MKKKSIKILVALFLLGSI-----YLLWMTL------RPVEIVAVHQDN--G---SSDILVRNFPITDKGKINWWLENK--   62 (155)
T ss_pred             CCCHHHEEHHHHHHHHHH-----HHHHHHC------CCEEEEEEEECC--C---EEEEEEECCCCCCCCHHHHHHHHH--
T ss_conf             972021005999999999-----9987535------866999997069--7---368998048867622403988759--


Q ss_pred             EEEEEEECCCCCCCCCC---EEEEEECCCCHHHHHHCCC
Q ss_conf             99999974897246884---6999742321023321014
Q gi|254780140|r   81 SLAKALIRPDTPLYPST---TATIRTQGLAGITYIELST  116 (452)
Q Consensus        81 v~v~~~i~~~~~i~~~~---~~~i~~~~l~g~~~i~~~~  116 (452)
                          -.+...+.+|...   .+.|..-. .|+.|..+.+
T Consensus        63 ----~~Lk~KY~iP~~~~~g~f~I~iwd-fGdGY~~~~~   96 (155)
T pfam06092        63 ----DMLKAKYGIPKPASDGFFSITIWD-FGDGYKDYEP   96 (155)
T ss_pred             ----HHHHHHCCCCCCCCCCCEEEEEEE-CCCCCCCCCC
T ss_conf             ----999976599998778838999997-2787144677


No 73 
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=31.27  E-value=26  Score=12.95  Aligned_cols=42  Identities=31%  Similarity=0.385  Sum_probs=30.0

Q ss_pred             CCCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCCC
Q ss_conf             87567668980789007433798888648886079999997489724
Q gi|254780140|r   47 GSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTPL   93 (452)
Q Consensus        47 ~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~~i   93 (452)
                      +.-.|+.+|.||.-.+--||+|.++..     ....|.+-.|++..+
T Consensus       135 G~~~Gi~~g~~Vi~~~GlVG~V~~v~~-----~~s~V~li~d~~~~v  176 (264)
T PRK13922        135 GSNDGVKKGMPVVDPGGLVGRVIEVSP-----NTSRVLLLTDPNSAV  176 (264)
T ss_pred             CCCCCCCCCCEEEECCCCEEEEEEECC-----CEEEEEEEECCCCCE
T ss_conf             776787689879977853799999537-----717999998799716


No 74 
>pfam07423 DUF1510 Protein of unknown function (DUF1510). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=31.20  E-value=26  Score=12.95  Aligned_cols=26  Identities=4%  Similarity=-0.093  Sum_probs=11.3

Q ss_pred             CHHHHHHHHHHHHHHHH-HHHHHHHHH
Q ss_conf             32789999999999999-999999986
Q gi|254780140|r    3 SKNYYTSVGLFVVSILF-FSFFSIYWL   28 (452)
Q Consensus         3 ~~~~~~~vG~fvi~~~~-~~~~~~~~~   28 (452)
                      +|.|-++=.+|.|..++ +++++.++|
T Consensus        10 Rk~n~vLNiaI~iV~llIiiva~~lf~   36 (214)
T pfam07423        10 RKINRVLNIAIGIVVVLIIIVAYQLFF   36 (214)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHEEE
T ss_conf             645345579999999999997664023


No 75 
>PRK10859 putative transglycosylase; Provisional
Probab=31.04  E-value=18  Score=14.04  Aligned_cols=28  Identities=21%  Similarity=0.358  Sum_probs=18.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             3278999999999999999999998625
Q gi|254780140|r    3 SKNYYTSVGLFVVSILFFSFFSIYWLSR   30 (452)
Q Consensus         3 ~~~~~~~vG~fvi~~~~~~~~~~~~~~~   30 (452)
                      -|.||+.+|+..++..+.++..+.|...
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~   31 (507)
T PRK10859          4 LKINYLFIGIVTLLLAAALWPSIPWFGK   31 (507)
T ss_pred             CEEEHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             1210128999999999997205888998


No 76 
>pfam05239 PRC PRC-barrel domain. The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain.
Probab=30.76  E-value=27  Score=12.90  Aligned_cols=24  Identities=17%  Similarity=0.299  Sum_probs=17.4

Q ss_pred             CCCEEEEE-EEEEEEEEEEEECCCC
Q ss_conf             89807890-0743379888864888
Q gi|254780140|r   54 TDSSVRFN-GIPVGRIVGLFLDQEY   77 (452)
Q Consensus        54 ~gspV~~~-Gv~VG~V~~I~l~~~~   77 (452)
                      .|.+|+=. |-.+|+|.+|.++...
T Consensus        10 ~G~~V~~~~G~~lG~V~Dv~id~~~   34 (77)
T pfam05239        10 IGLEVYTEDGEKLGKVKDVVIDEGE   34 (77)
T ss_pred             ECCEEECCCCCEEEEEEEEEEECCC
T ss_conf             4888799999999899999997899


No 77 
>PRK10900 consensus
Probab=30.21  E-value=27  Score=12.83  Aligned_cols=43  Identities=23%  Similarity=0.207  Sum_probs=30.6

Q ss_pred             CCCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCCCC
Q ss_conf             875676689807890074337988886488860799999974897246
Q gi|254780140|r   47 GSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTPLY   94 (452)
Q Consensus        47 ~~v~GL~~gspV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~~i~   94 (452)
                      ++-.|+.+|.||-=..=-||+|.++..     ...+|.+-.|.+..||
T Consensus       140 Gs~dGV~~GqpVid~~GLVGqV~~V~~-----~sSrVlLItD~~~aIP  182 (346)
T PRK10900        140 GSVNGVYEGQPVISDKGVVGQVVAVAK-----LTSRVLLICDATHALP  182 (346)
T ss_pred             CCCCCCCCCCEEEECCCCEEEEEEECC-----CEEEEEEEECCCCCCE
T ss_conf             665787589868707986799999668-----6489999646877643


No 78 
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of  prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=30.14  E-value=28  Score=12.83  Aligned_cols=25  Identities=36%  Similarity=0.385  Sum_probs=10.5

Q ss_pred             EEEEEEEECCCCCCCCCCCEEEEEE
Q ss_conf             1899999718756766898078900
Q gi|254780140|r   38 MAEVIIRIPGSVDGLSTDSSVRFNG   62 (452)
Q Consensus        38 ~~~~~~~f~~~v~GL~~gspV~~~G   62 (452)
                      ...+.+|+|+.-.-|+.-+-|.++|
T Consensus        45 g~~vtayIPG~gh~lqeh~~VLvrG   69 (95)
T cd00319          45 GYEVTAYIPGEGHNLQEHSVVLIRG   69 (95)
T ss_pred             CCEEEEECCCCCCCCCCCCEEEEEC
T ss_conf             9899998288987754378899948


No 79 
>pfam05531 NPV_P10 Nucleopolyhedrovirus P10 protein. This family consists of several nucleopolyhedrovirus P10 proteins which are thought to be involved in the morphogenesis of the polyhedra.
Probab=30.07  E-value=28  Score=12.82  Aligned_cols=12  Identities=8%  Similarity=0.230  Sum_probs=3.8

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780140|r  417 ETVNHFDDCLNN  428 (452)
Q Consensus       417 ~~~~~l~~~~~~  428 (452)
                      .++..++..+++
T Consensus        49 a~L~~l~tkV~~   60 (75)
T pfam05531        49 AQLTTLQTKVTN   60 (75)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 80 
>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=28.66  E-value=26  Score=13.00  Aligned_cols=12  Identities=17%  Similarity=0.188  Sum_probs=4.9

Q ss_pred             CCCCCCCCEEEE
Q ss_conf             972468846999
Q gi|254780140|r   90 DTPLYPSTTATI  101 (452)
Q Consensus        90 ~~~i~~~~~~~i  101 (452)
                      |++|+++..+.-
T Consensus        46 DtKVR~~~~p~~   57 (338)
T TIGR02817        46 DTKVRARVAPEA   57 (338)
T ss_pred             CCCCCCCCCCCC
T ss_conf             600127787688


No 81 
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=27.52  E-value=30  Score=12.52  Aligned_cols=23  Identities=13%  Similarity=0.348  Sum_probs=19.4

Q ss_pred             CCCCCCEEEEEEEEEEEEEEEEEC
Q ss_conf             766898078900743379888864
Q gi|254780140|r   51 GLSTDSSVRFNGIPVGRIVGLFLD   74 (452)
Q Consensus        51 GL~~gspV~~~Gv~VG~V~~I~l~   74 (452)
                      -.++|+-|...|+. |+|++|.+.
T Consensus       129 pf~vGD~I~i~g~~-G~V~~I~lr  151 (285)
T PRK10334        129 PFRAGEYVDLGGVA-GTVLSVQIF  151 (285)
T ss_pred             CCCCCCEEEECCEE-EEEEEEEEE
T ss_conf             81479769999999-999998867


No 82 
>PRK07960 fliI flagellum-specific ATP synthase; Validated
Probab=27.43  E-value=31  Score=12.51  Aligned_cols=11  Identities=27%  Similarity=0.549  Sum_probs=4.2

Q ss_pred             CCCCCCCCCEE
Q ss_conf             75676689807
Q gi|254780140|r   48 SVDGLSTDSSV   58 (452)
Q Consensus        48 ~v~GL~~gspV   58 (452)
                      +..|+.+|++|
T Consensus        84 ~~~Gi~~G~~V   94 (455)
T PRK07960         84 EVEGILPGARV   94 (455)
T ss_pred             CCCCCCCCCEE
T ss_conf             76657999999


No 83 
>COG2815 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.14  E-value=31  Score=12.48  Aligned_cols=53  Identities=17%  Similarity=0.290  Sum_probs=27.2

Q ss_pred             CCCCCCCC---CEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCCCCCCCEEEEE
Q ss_conf             75676689---80789007433798888648886079999997489724688469997
Q gi|254780140|r   48 SVDGLSTD---SSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPDTPLYPSTTATIR  102 (452)
Q Consensus        48 ~v~GL~~g---spV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~~i~~~~~~~i~  102 (452)
                      ++.|+..-   .-++-.|+.|| +.. +.+.+-+...++.-....+..++.++.+.+.
T Consensus        30 ~v~g~~~~~A~~~l~~~~l~v~-~~~-~~s~~~~~g~VI~t~P~~Gt~v~~G~~V~l~   85 (303)
T COG2815          30 NVAGLDEEDAKAELQKAGLEVG-VRE-RESDKVPEGKVIRTDPKAGTVVKQGSKVTLF   85 (303)
T ss_pred             CCCCCCHHHHHHHHHHCCCEEE-EEE-CCCCCCCCCEEEECCCCCCCEECCCCEEEEE
T ss_conf             7677648999999986475353-673-2466689970781489998351378679999


No 84 
>TIGR02222 chap_CsaA export-related chaperone CsaA; InterPro: IPR008231 The CsaA protein is required for SecA-mediated translocation of a subset of proteins , . CsaA and its relatives are typified by the presence of little more than a tRNA-binding motif that adopts an OB-fold. The Aquifex aeolicus member, Trbp111, has been demonstrated to bind tRNA, likely in a structure-specific manner .; GO: 0000049 tRNA binding, 0008565 protein transporter activity, 0015031 protein transport.
Probab=27.12  E-value=31  Score=12.47  Aligned_cols=50  Identities=24%  Similarity=0.195  Sum_probs=32.0

Q ss_pred             EEEEEEEEEEEECCCCCEEEEEEEEECCCCCCC-CCCEEEEEE----CCCCHHHHH
Q ss_conf             074337988886488860799999974897246-884699974----232102332
Q gi|254780140|r   62 GIPVGRIVGLFLDQEYPNHSLAKALIRPDTPLY-PSTTATIRT----QGLAGITYI  112 (452)
Q Consensus        62 Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~~~i~-~~~~~~i~~----~~l~g~~~i  112 (452)
                      -++||||-+....|.. .+--..+.||-+.+|. +.|-|+|..    ..|+|-.-+
T Consensus         8 dlRVGrIv~a~~fPeA-RKPAY~L~vDfG~elG~k~SSAQiT~lY~~E~L~gr~Vv   62 (107)
T TIGR02222         8 DLRVGRIVKAEPFPEA-RKPAYKLEVDFGEELGVKTSSAQITKLYKPEDLVGRLVV   62 (107)
T ss_pred             EECCCCEEEECCCCCC-CCCEEEEEEECCCCCCCCCCHHHHHCCCCCCCCCCCEEE
T ss_conf             3022637861689855-787179997017977741440564123783300197789


No 85 
>pfam03597 CcoS Cytochrome oxidase maturation protein cbb3-type.
Probab=27.07  E-value=31  Score=12.47  Aligned_cols=28  Identities=14%  Similarity=0.121  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             99999999999999999999862544467
Q gi|254780140|r    7 YTSVGLFVVSILFFSFFSIYWLSRSNQYD   35 (452)
Q Consensus         7 ~~~vG~fvi~~~~~~~~~~~~~~~~~~~~   35 (452)
                      ++++++-++++++.++++++-+ +.+.++
T Consensus         4 ~~LIpisl~l~~~~l~~f~Wav-k~gQfD   31 (45)
T pfam03597         4 YLLIPISLLLGAVGLAAFLWAV-KSGQFD   31 (45)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHH-CCCCCC
T ss_conf             6238999999999999999985-058777


No 86 
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302; InterPro: IPR012683    Members of this family are bacterial proteins from the alphaproteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted to be outside the membrane. Bradyrhizobium japonicum contains two tandem copies that are, together, homologous to the single members found in other species. .
Probab=26.98  E-value=31  Score=12.46  Aligned_cols=31  Identities=16%  Similarity=0.187  Sum_probs=21.3

Q ss_pred             CCCCEEEEEEEEECCC---------------CCCCCCCEEEEEECC
Q ss_conf             8886079999997489---------------724688469997423
Q gi|254780140|r   75 QEYPNHSLAKALIRPD---------------TPLYPSTTATIRTQG  105 (452)
Q Consensus        75 ~~~~~~v~v~~~i~~~---------------~~i~~~~~~~i~~~~  105 (452)
                      |-|.++..+++.-..+               ++||..|.+.|+..|
T Consensus       192 P~YTgraPIfLTa~s~~~~~aqekd~~~~~pitvP~gS~l~VR~~G  237 (899)
T TIGR02302       192 PVYTGRAPIFLTAASDKDKGAQEKDTQESDPITVPQGSTLLVRVSG  237 (899)
T ss_pred             CCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEC
T ss_conf             7767888767316444557743467765677357756527888525


No 87 
>TIGR02861 SASP_H small acid-soluble spore protein, H-type; InterPro: IPR012610   This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties .; GO: 0030436 sporulation (sensu Bacteria), 0042601 endospore-forming forespore.
Probab=26.62  E-value=27  Score=12.88  Aligned_cols=32  Identities=25%  Similarity=0.329  Sum_probs=19.3

Q ss_pred             CEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCC
Q ss_conf             80789007433798888648886079999997489
Q gi|254780140|r   56 SSVRFNGIPVGRIVGLFLDQEYPNHSLAKALIRPD   90 (452)
Q Consensus        56 spV~~~Gv~VG~V~~I~l~~~~~~~v~v~~~i~~~   90 (452)
                      .||+|.|.|| -+..+.-  +..+.++|...-+++
T Consensus        16 ~~V~Y~g~PV-~I~~VDt--e~~~~A~i~~l~np~   47 (59)
T TIGR02861        16 INVTYKGVPV-YIEHVDT--EQSGTARIYSLDNPG   47 (59)
T ss_pred             CCEEECCCEE-EEEEECC--CCCCCEEEEECCCCC
T ss_conf             1156669647-9875358--989716887528999


No 88 
>KOG2196 consensus
Probab=25.76  E-value=33  Score=12.31  Aligned_cols=26  Identities=31%  Similarity=0.530  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             88886579899999999999987640
Q gi|254780140|r  336 ENITSNLNDSSQKFAELMSKINNISA  361 (452)
Q Consensus       336 ~~~~~~l~~~~~~v~~~~~~id~~~~  361 (452)
                      .++..+++.....++.+...+|.+..
T Consensus       181 ~nidsqLk~l~~dL~~ii~~lN~~~~  206 (254)
T KOG2196         181 ENIDSQLKRLSEDLKQIIKSLNTMSK  206 (254)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             98999999887459999999872257


No 89 
>pfam12606 RELT Tumour necrosis factor receptor superfamily member 19. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 49 and 288 amino acids in length. There are two completely conserved residues (K and Y) that may be functionally important. The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1.
Probab=25.65  E-value=33  Score=12.30  Aligned_cols=20  Identities=20%  Similarity=0.187  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999
Q gi|254780140|r    7 YTSVGLFVVSILFFSFFSIY   26 (452)
Q Consensus         7 ~~~vG~fvi~~~~~~~~~~~   26 (452)
                      +++|.+|++++++++...-+
T Consensus         4 ~llV~vf~v~gllg~~Ic~~   23 (50)
T pfam12606         4 FLLVPVFFVMGLLGLLICTL   23 (50)
T ss_pred             EEEHHHHHHHHHHHHHHHHH
T ss_conf             43049999999999999999


No 90 
>pfam09980 DUF2214 Predicted membrane protein (DUF2214). This domain, found in various hypothetical bacterial proteins, has no known function.
Probab=24.56  E-value=34  Score=12.16  Aligned_cols=18  Identities=33%  Similarity=0.351  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999
Q gi|254780140|r    8 TSVGLFVVSILFFSFFSI   25 (452)
Q Consensus         8 ~~vG~fvi~~~~~~~~~~   25 (452)
                      +++|+|++.++..+.-++
T Consensus        81 ~K~~lfv~igllSi~PT~   98 (150)
T pfam09980        81 LKVTLFVLIGLLSLYPTI   98 (150)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             999999999999987899


No 91 
>PRK10270 hypothetical protein; Provisional
Probab=23.92  E-value=35  Score=12.08  Aligned_cols=17  Identities=29%  Similarity=0.208  Sum_probs=6.5

Q ss_pred             CCCHHHHHHHHHHHHHHH
Q ss_conf             963278999999999999
Q gi|254780140|r    1 MESKNYYTSVGLFVVSIL   18 (452)
Q Consensus         1 m~~~~~~~~vG~fvi~~~   18 (452)
                      |+ |.-.+++-+++++++
T Consensus         1 Mk-k~~~~~~~l~~~l~i   17 (340)
T PRK10270          1 MK-KVLLIILLLLVVLGI   17 (340)
T ss_pred             CC-HHHHHHHHHHHHHHH
T ss_conf             90-289999999999999


No 92 
>PRK06945 flgK flagellar hook-associated protein FlgK; Validated
Probab=23.47  E-value=36  Score=12.02  Aligned_cols=60  Identities=18%  Similarity=0.333  Sum_probs=28.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             333211122211012223322110000011222233445665432221100123345678
Q gi|254780140|r  138 TATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHI  197 (452)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i  197 (452)
                      |........++..++.+...+......+...-.+....+...+..+......+++....|
T Consensus       124 P~~~a~R~~~~~~a~~L~~~~~~~~~~l~~~~~~~~~~i~~~V~~iN~l~~~Ia~LN~qI  183 (649)
T PRK06945        124 PSDPSARQTALSNAQALASQFNAAGQQYDQLRQGVNTQLTSTVTQINSYTKQIAQLNQQI  183 (649)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             787899999999999999999999999999999999999999999999999999999999


No 93 
>pfam04585 consensus
Probab=22.50  E-value=37  Score=11.89  Aligned_cols=39  Identities=13%  Similarity=0.230  Sum_probs=26.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEE
Q ss_conf             3278999999999999999999998625444677618999997
Q gi|254780140|r    3 SKNYYTSVGLFVVSILFFSFFSIYWLSRSNQYDGPMAEVIIRI   45 (452)
Q Consensus         3 ~~~~~~~vG~fvi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f   45 (452)
                      ...|+-+++++.++..++++++++|.+..   . .-.-|++..
T Consensus        26 qa~nWrl~a~~~L~ia~~~~~g~v~~~~q---s-kivPYVVev   64 (218)
T pfam04585        26 QAQNWRFVGLLSLLIALALVGGLVYQSSQ---S-KFVPYVVEV   64 (218)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHEECCC---C-CEEEEEEEE
T ss_conf             99889999999999999999886405157---8-077699998


No 94 
>PRK12714 flgK flagellar hook-associated protein FlgK; Provisional
Probab=22.31  E-value=38  Score=11.87  Aligned_cols=53  Identities=6%  Similarity=0.255  Sum_probs=24.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21112221101222332211000001122223344566543222110012334
Q gi|254780140|r  141 PSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANN  193 (452)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  193 (452)
                      ......++..++.+...+......+...-.+....+...+..+......+++.
T Consensus       126 ~~~R~~vl~~a~~L~~~~~~~~~~l~~~~~~~~~~i~~~v~~iN~l~~qIa~L  178 (624)
T PRK12714        126 TAERQSMLDSGNSLATRFKQLNGQMDSLSNEVNSGLTSSVDEVNRLTQQIAKI  178 (624)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             79999999999999999999999999999999999999999999999999999


No 95 
>PRK05464 Na(+)-translocating NADH-quinone reductase subunit F; Provisional
Probab=22.20  E-value=38  Score=11.85  Aligned_cols=36  Identities=8%  Similarity=0.229  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEE
Q ss_conf             999999999999999999986254446776189999
Q gi|254780140|r    8 TSVGLFVVSILFFSFFSIYWLSRSNQYDGPMAEVII   43 (452)
Q Consensus         8 ~~vG~fvi~~~~~~~~~~~~~~~~~~~~~~~~~~~~   43 (452)
                      +.+|++++.++++++++++++..........+++.+
T Consensus         4 i~~~~~~f~~~~~~lv~~il~a~~~l~~~g~v~i~i   39 (408)
T PRK05464          4 IILGVVMFTAIVLILVAVILFAKSKLVPSGDVTIKI   39 (408)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEE
T ss_conf             652799999999999999999975215788579998


No 96 
>pfam11057 Cortexin Cortexin of kidney. In the middle of cortexin protein there is a single membrane-spanning domain which indicates that this protein may be a membrane protein involved in intracellular or extracellular signalling of the kidney or brain, since it is expressed specifically in the kidneys and brain only. The protein is highly conserved among species. Cortexin is also thought to be important to neurons of both the developing and adult cerebral cortex.
Probab=22.12  E-value=38  Score=11.84  Aligned_cols=49  Identities=18%  Similarity=0.170  Sum_probs=23.8

Q ss_pred             CCHHHHHHHHHHH-HHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCCCCC
Q ss_conf             6327899999999-999999999999862544467761899999718756766898
Q gi|254780140|r    2 ESKNYYTSVGLFV-VSILFFSFFSIYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDS   56 (452)
Q Consensus         2 ~~~~~~~~vG~fv-i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~v~GL~~gs   56 (452)
                      |.|+.+.-||+.. ++++++.-.+-+++-...+-...+++      |-..||..|.
T Consensus        26 EQkt~faFV~ll~ifL~~livRCfrillDPYssmPsStW~------d~~eglekg~   75 (81)
T pfam11057        26 EQKTAFAFVGLLLIFLGLLIVRCFRILLDPYSSMPASSWT------DHKEGLEKGQ   75 (81)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCCCCCHHH------HHHHHHHCCC
T ss_conf             4504679999999999999999999980811038853034------4455443362


No 97 
>KOG3491 consensus
Probab=22.12  E-value=38  Score=11.84  Aligned_cols=21  Identities=29%  Similarity=0.262  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             899999999999999999999
Q gi|254780140|r    6 YYTSVGLFVVSILFFSFFSIY   26 (452)
Q Consensus         6 ~~~~vG~fvi~~~~~~~~~~~   26 (452)
                      -+.++|+||+......++-++
T Consensus        38 gPwLlglFvFVVcGSa~FqII   58 (65)
T KOG3491          38 GPWLLGLFVFVVCGSALFQII   58 (65)
T ss_pred             CHHHHHHHHHHHHCHHHHHHH
T ss_conf             228988899986159999999


No 98 
>PRK10559 p-hydroxybenzoic acid efflux subunit AaeA; Provisional
Probab=22.08  E-value=38  Score=11.84  Aligned_cols=12  Identities=17%  Similarity=0.255  Sum_probs=7.3

Q ss_pred             EEEEEEEEECCC
Q ss_conf             337988886488
Q gi|254780140|r   65 VGRIVGLFLDQE   76 (452)
Q Consensus        65 VG~V~~I~l~~~   76 (452)
                      =|+|+++....+
T Consensus        55 sG~V~eV~V~dn   66 (310)
T PRK10559         55 SGLITQVNVHDN   66 (310)
T ss_pred             CEEEEEEECCCC
T ss_conf             469999991794


No 99 
>pfam03100 CcmE CcmE. CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.
Probab=21.81  E-value=39  Score=11.80  Aligned_cols=48  Identities=13%  Similarity=0.299  Sum_probs=20.9

Q ss_pred             CCCCCEEEEEEEEE-EEEEEEEECCCCCEEEEEEEEECCCCCCCCCCEEEEEECCCCHHHH
Q ss_conf             66898078900743-3798888648886079999997489724688469997423210233
Q gi|254780140|r   52 LSTDSSVRFNGIPV-GRIVGLFLDQEYPNHSLAKALIRPDTPLYPSTTATIRTQGLAGITY  111 (452)
Q Consensus        52 L~~gspV~~~Gv~V-G~V~~I~l~~~~~~~v~v~~~i~~~~~i~~~~~~~i~~~~l~g~~~  111 (452)
                      ...|..+|+.|.-+ |.|   .-+ ++   ..+.+.+...     .....+...|.+.+.|
T Consensus        47 ~~~~~~iRvgG~V~~gSi---~~~-~~---~~~~F~itD~-----~~~i~V~Y~G~lPdlF   95 (130)
T pfam03100        47 APPGRRIRLGGLVEEGSV---VRD-DG---LTVRFVVTDG-----AASVPVRYTGILPDLF   95 (130)
T ss_pred             CCCCCEEEEEEEEECCCE---EEC-CC---CEEEEEEECC-----CCEEEEEEECCCCHHH
T ss_conf             666868999889960867---967-99---7799999848-----9469999947796566


No 100
>PRK06665 flgK flagellar hook-associated protein FlgK; Validated
Probab=21.59  E-value=39  Score=11.77  Aligned_cols=60  Identities=13%  Similarity=0.204  Sum_probs=32.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             333211122211012223322110000011222233445665432221100123345678
Q gi|254780140|r  138 TATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHI  197 (452)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i  197 (452)
                      |........++..++.+...+......+...-.++...+...+..+......+++....|
T Consensus       135 P~~~~~R~~vl~~a~~L~~~~n~~~~~L~~~~~~~n~~i~~~V~~iN~l~~~Ia~LN~qI  194 (628)
T PRK06665        135 PEGLAERQVVLERAQALGERIEDRYRSLERIRDMANDEIEITTEEVNNYLRNIADLNEQI  194 (628)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             688899999999999999999999999999999999999999999999999999999999


No 101
>COG1580 FliL Flagellar basal body-associated protein [Cell motility and secretion]
Probab=21.32  E-value=39  Score=11.73  Aligned_cols=27  Identities=11%  Similarity=0.320  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             278999999999999999999998625
Q gi|254780140|r    4 KNYYTSVGLFVVSILFFSFFSIYWLSR   30 (452)
Q Consensus         4 ~~~~~~vG~fvi~~~~~~~~~~~~~~~   30 (452)
                      +.-++.+.+.+++.++..+++++|++.
T Consensus        16 ~~~~I~liv~ivl~~~a~~~~~~~~~~   42 (159)
T COG1580          16 KSLWILLIVLIVLLALAGAGYFFWFGS   42 (159)
T ss_pred             CEEEHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             511227999999999998888875303


No 102
>PRK08455 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=21.28  E-value=40  Score=11.73  Aligned_cols=12  Identities=25%  Similarity=0.559  Sum_probs=5.1

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780140|r    8 TSVGLFVVSILF   19 (452)
Q Consensus         8 ~~vG~fvi~~~~   19 (452)
                      +.+|+.+++.++
T Consensus        22 Iii~vvvlll~~   33 (180)
T PRK08455         22 IIIGVVVLLLLI   33 (180)
T ss_pred             EEHHHHHHHHHH
T ss_conf             349999999999


No 103
>COG3190 FliO Flagellar biogenesis protein [Cell motility and secretion]
Probab=21.27  E-value=40  Score=11.73  Aligned_cols=44  Identities=16%  Similarity=0.093  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHH-HHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCCCCCE
Q ss_conf             99999999999-999999998625444677618999997187567668980
Q gi|254780140|r    8 TSVGLFVVSIL-FFSFFSIYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDSS   57 (452)
Q Consensus         8 ~~vG~fvi~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~v~GL~~gsp   57 (452)
                      ...+++.++++ ++++|.+..|. ....++....+.+     ..+...|+.
T Consensus        27 ~~gsL~~iL~lil~~~wl~kr~~-~~~~~~~~~~lki-----l~~~~lG~r   71 (137)
T COG3190          27 MFGSLILILALILFLAWLVKRLG-RAPLFKGSSGLKI-----LASRSLGSR   71 (137)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCCEEE-----ECCCCCCCC
T ss_conf             99999999999999999999984-1436786421110-----113544787


No 104
>PRK02118 V-type ATP synthase subunit B; Provisional
Probab=21.10  E-value=40  Score=11.70  Aligned_cols=23  Identities=17%  Similarity=0.149  Sum_probs=16.0

Q ss_pred             HHHCHHHHHCCCCCCCCCCCCCC
Q ss_conf             98788886118887774542689
Q gi|254780140|r  429 FERNPQDIVWGREKGSVKIYKPK  451 (452)
Q Consensus       429 l~~~p~~li~g~~~~~~~~~~~~  451 (452)
                      +..-|..-+..=....+++|.||
T Consensus       410 l~~~~~~~~~~~~~~~~~~~~~~  432 (432)
T PRK02118        410 LAQCFTPEEVGIKEQLIDKYWPK  432 (432)
T ss_pred             HHHCCHHHHHCCCHHHHHHHCCC
T ss_conf             98769998827999999874699


No 105
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=21.09  E-value=40  Score=11.70  Aligned_cols=44  Identities=16%  Similarity=0.015  Sum_probs=28.9

Q ss_pred             CCCCCCCCCCEEEEEEEEEEEEEEEEECC-CCCEEEEEEEEECCCCC
Q ss_conf             87567668980789007433798888648-88607999999748972
Q gi|254780140|r   47 GSVDGLSTDSSVRFNGIPVGRIVGLFLDQ-EYPNHSLAKALIRPDTP   92 (452)
Q Consensus        47 ~~v~GL~~gspV~~~Gv~VG~V~~I~l~~-~~~~~v~v~~~i~~~~~   92 (452)
                      +.+.-+.-+++|.++|--|-|+.+=++-. |..|.  +.++|+...+
T Consensus        49 ~~Ak~~~Dda~V~l~GnIv~qi~~D~y~FrD~sGe--I~VeIdd~~w   93 (128)
T COG3111          49 DQAKTLHDDAWVSLEGNIVRQIGDDRYVFRDASGE--INVDIDDKVW   93 (128)
T ss_pred             HHHHCCCCCCEEEEEEEEEEEECCCEEEEECCCCC--EEEEECCCCC
T ss_conf             87533025984999756777607836999758961--9998160113


No 106
>PRK13836 conjugal transfer protein TrbF; Provisional
Probab=20.70  E-value=41  Score=11.65  Aligned_cols=40  Identities=15%  Similarity=0.326  Sum_probs=23.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEE
Q ss_conf             63278999999999999999999998625444677618999997
Q gi|254780140|r    2 ESKNYYTSVGLFVVSILFFSFFSIYWLSRSNQYDGPMAEVIIRI   45 (452)
Q Consensus         2 ~~~~~~~~vG~fvi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f   45 (452)
                      ...-|+-++|++.++..++.+++++|.+..    +.-..|++..
T Consensus        27 ~qa~nWrl~a~~~L~la~~~~~g~i~~~sq----skvvPYVVeV   66 (220)
T PRK13836         27 KAAAAWRIVGILGLTMAVIGFSYALYLSTQ----VKLVPYIVEV   66 (220)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHEECCC----CCEEEEEEEE
T ss_conf             999888999999999999999886114047----8187599998


No 107
>PRK02870 heat shock protein HtpX; Provisional
Probab=20.47  E-value=41  Score=11.61  Aligned_cols=28  Identities=0%  Similarity=0.129  Sum_probs=16.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             3278999999999999999999998625
Q gi|254780140|r    3 SKNYYTSVGLFVVSILFFSFFSIYWLSR   30 (452)
Q Consensus         3 ~~~~~~~vG~fvi~~~~~~~~~~~~~~~   30 (452)
                      +|+.+++++++++..++.++..++|..+
T Consensus        22 rkT~~ll~~f~~l~~~iG~~v~~~~~~~   49 (338)
T PRK02870         22 LRTRFVIATFLIIFLFIGLLVDAIRIAS   49 (338)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             7689999999999999999999998614


No 108
>pfam07172 GRP Glycine rich protein family. This family of proteins includes several glycine rich proteins as well as two nodulins 16 and 24. The family also contains proteins that are induced in response to various stresses.
Probab=20.30  E-value=41  Score=11.59  Aligned_cols=16  Identities=31%  Similarity=0.553  Sum_probs=10.4

Q ss_pred             CCCHHHHHHHHHHHHHH
Q ss_conf             96327899999999999
Q gi|254780140|r    1 MESKNYYTSVGLFVVSI   17 (452)
Q Consensus         1 m~~~~~~~~vG~fvi~~   17 (452)
                      |-+|+ ++++|+|+.+.
T Consensus         1 MaSKa-~llLglllA~~   16 (91)
T pfam07172         1 MASKA-LLLLGLLLAAV   16 (91)
T ss_pred             CCCHH-HHHHHHHHHHH
T ss_conf             95057-99999999999


No 109
>pfam05751 FixH FixH. This family consists of several Rhizobium FixH like proteins. It has been suggested that suggested that the four proteins FixG, FixH, FixI, and FixS may participate in a membrane-bound complex coupling the FixI cation pump with a redox process catalysed by FixG.
Probab=20.29  E-value=34  Score=12.19  Aligned_cols=20  Identities=20%  Similarity=0.200  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999
Q gi|254780140|r    7 YTSVGLFVVSILFFSFFSIY   26 (452)
Q Consensus         7 ~~~vG~fvi~~~~~~~~~~~   26 (452)
                      ++++|+|.+..++.++..++
T Consensus         6 w~li~~~~~vv~~~~~~v~~   25 (146)
T pfam05751         6 WFLIALFGVVIVVNLTMVYL   25 (146)
T ss_pred             EEHHHHHHHHHHHHHHHHHH
T ss_conf             72287458854068862121


No 110
>TIGR01043 ATP_syn_A_arch ATP synthase archaeal, A subunit; InterPro: IPR005726   ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , .  F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.   A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases . A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore . The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C . A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species.    This entry represents the alpha subunit from the A1 complex of A-ATPases. The A1 complex contains three copies each of subunits alpha (or A) and beta (or B) (IPR005724 from INTERPRO), both of which form the headpiece that participates in nucleotide binding. However, only the alpha subunit is catalytic, the beta subunit being regulatory in function .   More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0016820 hydrolase activity acting on acid anhydrides catalyzing transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0016021 integral to membrane, 0016469 proton-transporting two-sector ATPase complex.
Probab=20.22  E-value=42  Score=11.58  Aligned_cols=18  Identities=17%  Similarity=0.287  Sum_probs=7.9

Q ss_pred             CCCCCEEEEEEEEEEEEEE
Q ss_conf             6689807890074337988
Q gi|254780140|r   52 LSTDSSVRFNGIPVGRIVG   70 (452)
Q Consensus        52 L~~gspV~~~Gv~VG~V~~   70 (452)
                      ++.|+.|. .|--||.|.+
T Consensus       123 v~~Gd~V~-~Gd~~G~V~E  140 (584)
T TIGR01043       123 VKEGDKVE-GGDIIGVVQE  140 (584)
T ss_pred             ECCCCEEC-CCCEEEEECC
T ss_conf             22686434-7615877637


No 111
>PRK05696 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=20.18  E-value=42  Score=11.57  Aligned_cols=23  Identities=9%  Similarity=-0.025  Sum_probs=7.7

Q ss_pred             HHHHHHH-HHHHHHHHHHHHHHHC
Q ss_conf             9999999-9999999999999862
Q gi|254780140|r    7 YTSVGLF-VVSILFFSFFSIYWLS   29 (452)
Q Consensus         7 ~~~vG~f-vi~~~~~~~~~~~~~~   29 (452)
                      .+++++. +++.+++.++++||++
T Consensus        18 Liiii~~~vlll~ggggg~~~~lg   41 (168)
T PRK05696         18 LIIIIVVGVLLALGGGGAAWFFMG   41 (168)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             204799999999999999999955


No 112
>PRK11901 hypothetical protein; Reviewed
Probab=20.10  E-value=42  Score=11.56  Aligned_cols=12  Identities=25%  Similarity=0.744  Sum_probs=4.9

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780140|r    9 SVGLFVVSILFF   20 (452)
Q Consensus         9 ~vG~fvi~~~~~   20 (452)
                      =|||+||+.|++
T Consensus        41 GiGILVLLLLII   52 (329)
T PRK11901         41 GIGILVLLLLII   52 (329)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


Done!