Query         043253
Match_columns 230
No_of_seqs    253 out of 2054
Neff          8.7 
Searched_HMMs 46136
Date          Fri Mar 29 03:01:51 2013
Command       hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043253.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043253hhsearch_cdd -cpu 12 -v 0 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG0207 Cation transport ATPas  99.4 3.9E-12 8.4E-17  118.5  15.0  140   30-185    70-216 (951)
  2 PRK10671 copA copper exporting  99.4 2.4E-11 5.1E-16  117.0  15.9  149   29-183     3-164 (834)
  3 KOG0207 Cation transport ATPas  99.3 1.3E-11 2.9E-16  115.0  12.0  135   36-187     2-141 (951)
  4 PF00403 HMA:  Heavy-metal-asso  99.2 7.7E-11 1.7E-15   76.9   8.4   59   32-91      1-62  (62)
  5 PF00403 HMA:  Heavy-metal-asso  99.2 9.2E-11   2E-15   76.5   7.5   57  122-179     3-62  (62)
  6 COG2608 CopZ Copper chaperone   99.1 4.2E-10 9.2E-15   75.5   8.7   66   28-94      1-69  (71)
  7 COG2608 CopZ Copper chaperone   99.1 9.8E-10 2.1E-14   73.7   7.9   63  120-183     5-70  (71)
  8 KOG1603 Copper chaperone [Inor  98.7 8.5E-08 1.8E-12   64.6   8.6   66  117-183     4-70  (73)
  9 KOG4656 Copper chaperone for s  98.4 8.3E-07 1.8E-11   69.9   7.1   69  119-188     8-76  (247)
 10 KOG1603 Copper chaperone [Inor  98.4 2.6E-06 5.7E-11   57.3   7.9   64   28-93      4-68  (73)
 11 KOG4656 Copper chaperone for s  98.3 5.9E-06 1.3E-10   65.2   8.8   69   27-97      5-73  (247)
 12 PLN02957 copper, zinc superoxi  98.0 3.6E-05 7.8E-10   63.7   8.9   71  118-189     6-76  (238)
 13 COG2217 ZntA Cation transport   97.8 6.4E-05 1.4E-09   71.0   7.6   64   29-94      2-69  (713)
 14 PRK10671 copA copper exporting  97.7 8.5E-05 1.8E-09   72.0   7.2   62  120-184     5-67  (834)
 15 PLN02957 copper, zinc superoxi  97.7 0.00043 9.4E-09   57.3   9.9   67   29-97      6-72  (238)
 16 COG2217 ZntA Cation transport   97.6 0.00014 3.1E-09   68.7   7.0   60  121-182     6-69  (713)
 17 TIGR00003 copper ion binding p  97.3  0.0034 7.3E-08   38.8   8.7   61   30-91      3-66  (68)
 18 TIGR00003 copper ion binding p  97.0  0.0078 1.7E-07   37.1   7.7   58  122-180     7-67  (68)
 19 PRK11033 zntA zinc/cadmium/mer  96.2   0.024 5.3E-07   54.5   9.0   65   28-93     52-117 (741)
 20 PRK11033 zntA zinc/cadmium/mer  95.3   0.049 1.1E-06   52.4   6.8   60  123-183    59-119 (741)
 21 TIGR02052 MerP mercuric transp  86.4     7.3 0.00016   25.7   8.1   59  123-182    29-90  (92)
 22 TIGR02052 MerP mercuric transp  81.1      13 0.00028   24.4   9.0   61   31-92     25-88  (92)
 23 COG4888 Uncharacterized Zn rib  76.7     2.2 4.8E-05   30.1   2.2   22    1-22      1-22  (104)
 24 PF10999 DUF2839:  Protein of u  74.3     1.4   3E-05   28.9   0.7   19    1-20      1-19  (68)
 25 PRK13748 putative mercuric red  71.7      20 0.00044   33.2   8.0   63  123-186     6-70  (561)
 26 PRK13748 putative mercuric red  67.4      39 0.00084   31.3   8.9   61   33-94      4-66  (561)
 27 COG2177 FtsX Cell division pro  64.0      82  0.0018   27.0   9.5   87   34-151    66-152 (297)
 28 COG1888 Uncharacterized protei  57.2      45 0.00098   23.2   5.4   51  132-183    21-79  (97)
 29 cd00371 HMA Heavy-metal-associ  55.6      30 0.00066   18.3   6.3   54  124-178     5-60  (63)
 30 PF01206 TusA:  Sulfurtransfera  52.2      56  0.0012   20.9   5.3   52   32-93      2-55  (70)
 31 PF02680 DUF211:  Uncharacteriz  52.2      58  0.0013   22.8   5.4   49  132-181    19-75  (95)
 32 PRK14054 methionine sulfoxide   48.1      48   0.001   26.0   5.1   45  129-173    10-76  (172)
 33 COG1888 Uncharacterized protei  41.8 1.2E+02  0.0026   21.2   5.8   50   44-94     22-78  (97)
 34 PF02680 DUF211:  Uncharacteriz  40.1      81  0.0018   22.1   4.6   63   29-93      5-75  (95)
 35 PRK10553 assembly protein for   40.0 1.2E+02  0.0027   20.8   5.9   43  131-173    18-61  (87)
 36 PRK11018 hypothetical protein;  37.8 1.2E+02  0.0026   20.1   5.6   53   31-93      9-63  (78)
 37 PF01883 DUF59:  Domain of unkn  37.7      57  0.0012   21.0   3.5   30  121-150    37-72  (72)
 38 PRK14892 putative transcriptio  33.1      20 0.00043   25.4   0.7    9    1-9       1-9   (99)
 39 PF03927 NapD:  NapD protein;    32.5 1.6E+02  0.0034   19.7   6.4   43  130-173    15-58  (79)
 40 PRK14054 methionine sulfoxide   30.8 1.2E+02  0.0026   23.7   4.9   46   40-85     10-76  (172)
 41 PRK13014 methionine sulfoxide   30.2      97  0.0021   24.6   4.2   45  129-173    15-81  (186)
 42 cd03420 SirA_RHOD_Pry_redox Si  30.2 1.5E+02  0.0033   19.0   4.7   51   33-93      2-54  (69)
 43 PF13732 DUF4162:  Domain of un  30.2 1.6E+02  0.0035   19.3   5.0   44  139-185    26-71  (84)
 44 PRK00058 methionine sulfoxide   30.0 1.3E+02  0.0027   24.6   4.9   27  129-155    52-78  (213)
 45 cd03421 SirA_like_N SirA_like_  28.7 1.6E+02  0.0034   18.6   5.1   48  125-183     6-55  (67)
 46 PRK05528 methionine sulfoxide   27.6      61  0.0013   25.0   2.6   45  129-173     8-69  (156)
 47 PF09580 Spore_YhcN_YlaJ:  Spor  25.6   2E+02  0.0043   22.1   5.4   31  130-160    75-105 (177)
 48 COG0425 SirA Predicted redox p  25.3 1.2E+02  0.0026   20.3   3.5   54   30-92      5-60  (78)
 49 PF14492 EFG_II:  Elongation Fa  25.2   2E+02  0.0044   18.8   4.6   51  131-181    17-72  (75)
 50 cd02410 archeal_CPSF_KH The ar  24.0 3.1E+02  0.0068   20.9   5.8   57  131-188    54-117 (145)
 51 PF01625 PMSR:  Peptide methion  21.3 1.1E+02  0.0024   23.4   3.1   27  129-155     7-33  (155)
 52 cd03423 SirA SirA (also known   21.1 2.4E+02  0.0051   18.0   5.4   52   33-94      2-55  (69)
 53 TIGR00401 msrA methionine-S-su  20.8   1E+02  0.0022   23.5   2.7   28  129-156     7-34  (149)

No 1  
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=99.42  E-value=3.9e-12  Score=118.49  Aligned_cols=140  Identities=23%  Similarity=0.350  Sum_probs=120.2

Q ss_pred             EEEEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCC--CHHHHHHHHHHhCCCceeecCCCCCCCCCCC
Q 043253           30 DIVLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKA--EPSKVIERIRKKYSTNAELISPKPKTNNGED  106 (230)
Q Consensus        30 ~~~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~--~~~~i~~~i~~~~G~~~~~~~~~~~~~~~~~  106 (230)
                      +-.|++ ||+|.+|++.|++.++.++|+.++.+.+......+.+++.  .+..+.+.+++. ||.+.+++.....     
T Consensus        70 ~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~-gf~a~~i~~~~~~-----  143 (951)
T KOG0207|consen   70 KCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDL-GFSAELIESVNGN-----  143 (951)
T ss_pred             eeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhc-CccceehhcccCC-----
Confidence            667899 9999999999999999999999999999999999998863  888999999966 9998876543211     


Q ss_pred             CCCCCCCCCceeEEEEec-cccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEE---eeCCHHHHHHHHHHhcCCceEE
Q 043253          107 KKEPQKKQPQVKVVILKM-YMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVK---GEFDPPKLAEAITKRLGKFVEI  182 (230)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~-gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~---~~~~~~~i~~~i~~~~G~~a~~  182 (230)
                               .....++.+ ||.|.+|+.+|+..|.+++||.++++++.++++.|.   ..+++.++++.|. ..|+.+.+
T Consensus       144 ---------~~~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie-~~~~~~~~  213 (951)
T KOG0207|consen  144 ---------SNQKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIE-ETGFEASV  213 (951)
T ss_pred             ---------CCCcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHH-hhccccee
Confidence                     013445655 999999999999999999999999999999999986   5578999999999 59998877


Q ss_pred             ccc
Q 043253          183 VKE  185 (230)
Q Consensus       183 ~~~  185 (230)
                      ...
T Consensus       214 ~~~  216 (951)
T KOG0207|consen  214 RPY  216 (951)
T ss_pred             eec
Confidence            653


No 2  
>PRK10671 copA copper exporting ATPase; Provisional
Probab=99.35  E-value=2.4e-11  Score=116.98  Aligned_cols=149  Identities=21%  Similarity=0.370  Sum_probs=110.2

Q ss_pred             eEEEEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCCCHHHHHHHHHHhCCCceeecCCCCCC--CCCC
Q 043253           29 EDIVLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKAEPSKVIERIRKKYSTNAELISPKPKT--NNGE  105 (230)
Q Consensus        29 ~~~~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~~~~~i~~~i~~~~G~~~~~~~~~~~~--~~~~  105 (230)
                      .+..|.| ||+|++|+.+|++++.+++||..+.+++.  +..+... .+.+.+...+++. ||.+...+.....  ....
T Consensus         3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~-~~~~~i~~~i~~~-Gy~~~~~~~~~~~~~~~~~   78 (834)
T PRK10671          3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGT-ASAEALIETIKQA-GYDASVSHPKAKPLTESSI   78 (834)
T ss_pred             eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEec-CCHHHHHHHHHhc-CCccccccccccccccccc
Confidence            5688999 99999999999999999999999999994  4555554 4788999999977 9998764321100  0000


Q ss_pred             CC--CCCC----C---CCCceeEEEE-eccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEeeCCHHHHHHHHHHh
Q 043253          106 DK--KEPQ----K---KQPQVKVVIL-KMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKGEFDPPKLAEAITKR  175 (230)
Q Consensus       106 ~~--~~~~----~---~~~~~~~~~~-~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~~~~~~~i~~~i~~~  175 (230)
                      +.  ....    +   .... ....+ +.||+|.+|+..+++.+..++||..+.+++.++++.+....+.+++...++ .
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~-~~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~-~  156 (834)
T PRK10671         79 PSEALTAASEELPAATADDD-DSQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVE-K  156 (834)
T ss_pred             CchhhhhhhhhccccccCcC-ceEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHH-h
Confidence            00  0000    0   0001 12334 459999999999999999999999999999999988875567788888899 5


Q ss_pred             cCCceEEc
Q 043253          176 LGKFVEIV  183 (230)
Q Consensus       176 ~G~~a~~~  183 (230)
                      +||.+.+.
T Consensus       157 ~Gy~a~~~  164 (834)
T PRK10671        157 AGYGAEAI  164 (834)
T ss_pred             cCCCcccc
Confidence            99987644


No 3  
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=99.33  E-value=1.3e-11  Score=115.03  Aligned_cols=135  Identities=26%  Similarity=0.435  Sum_probs=115.8

Q ss_pred             eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCC-CHHHHHHHHHHhCCCceeecCCCCCCCCCCCCCCCCCCC
Q 043253           36 YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKA-EPSKVIERIRKKYSTNAELISPKPKTNNGEDKKEPQKKQ  114 (230)
Q Consensus        36 gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~-~~~~i~~~i~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~  114 (230)
                      ||+|..|.+.|+.+++..+|+.++.+++.++.++|.++.. +++.+.+.|++. ||++.+.+.....             
T Consensus         2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~-gf~~~~~~~~~~~-------------   67 (951)
T KOG0207|consen    2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDM-GFEASLLSDSEIT-------------   67 (951)
T ss_pred             CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcc-cceeeecccCccc-------------
Confidence            7999999999999999999999999999999999998742 899999999987 9999875442210             


Q ss_pred             CceeEEEEec-cccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEE---eeCCHHHHHHHHHHhcCCceEEccccc
Q 043253          115 PQVKVVILKM-YMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVK---GEFDPPKLAEAITKRLGKFVEIVKEEA  187 (230)
Q Consensus       115 ~~~~~~~~~~-gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~---~~~~~~~i~~~i~~~~G~~a~~~~~~~  187 (230)
                        ..+.++.+ ||+|.+|+..|++.|++..|+.++.+.+......+.   ..++++.+.+.++ ..||.+++.....
T Consensus        68 --~~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie-~~gf~a~~i~~~~  141 (951)
T KOG0207|consen   68 --ASKCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIE-DLGFSAELIESVN  141 (951)
T ss_pred             --cceeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHH-hcCccceehhccc
Confidence              12345555 999999999999999999999999999999999986   4578899999999 5999998876544


No 4  
>PF00403 HMA:  Heavy-metal-associated domain;  InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures.  These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases [].  A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding.  Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.23  E-value=7.7e-11  Score=76.88  Aligned_cols=59  Identities=36%  Similarity=0.567  Sum_probs=53.8

Q ss_pred             EEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCC--CHHHHHHHHHHhCCCc
Q 043253           32 VLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKA--EPSKVIERIRKKYSTN   91 (230)
Q Consensus        32 ~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~--~~~~i~~~i~~~~G~~   91 (230)
                      +|.| ||+|++|+++|+++|.+++||.++.+|+.++++.|.++..  +++.|.++|+++ ||+
T Consensus         1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~-Gy~   62 (62)
T PF00403_consen    1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKA-GYE   62 (62)
T ss_dssp             EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHT-TSE
T ss_pred             CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHh-CcC
Confidence            4889 9999999999999999999999999999999999998742  568999999987 984


No 5  
>PF00403 HMA:  Heavy-metal-associated domain;  InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures.  These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases [].  A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding.  Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.20  E-value=9.2e-11  Score=76.50  Aligned_cols=57  Identities=33%  Similarity=0.522  Sum_probs=51.3

Q ss_pred             EeccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEee---CCHHHHHHHHHHhcCCc
Q 043253          122 LKMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKGE---FDPPKLAEAITKRLGKF  179 (230)
Q Consensus       122 ~~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~~---~~~~~i~~~i~~~~G~~  179 (230)
                      .+.||+|++|+.+|+++|.+++||.++.+|+.+++++|...   .++++|.++|+ ++||+
T Consensus         3 ~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~-~~Gy~   62 (62)
T PF00403_consen    3 KVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE-KAGYE   62 (62)
T ss_dssp             EEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH-HTTSE
T ss_pred             EECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH-HhCcC
Confidence            34599999999999999999999999999999999999844   45699999999 59995


No 6  
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.14  E-value=4.2e-10  Score=75.46  Aligned_cols=66  Identities=26%  Similarity=0.404  Sum_probs=58.7

Q ss_pred             ceEEEEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccC--CCHHHHHHHHHHhCCCceee
Q 043253           28 VEDIVLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEK--AEPSKVIERIRKKYSTNAEL   94 (230)
Q Consensus        28 ~~~~~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~--~~~~~i~~~i~~~~G~~~~~   94 (230)
                      |.+..|.+ ||+|.+|+.+|+++|..++||.++.+++..+...|.++.  .+.+.|..+|.++ ||.+..
T Consensus         1 ~~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~a-Gy~~~~   69 (71)
T COG2608           1 MMKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDA-GYKVEE   69 (71)
T ss_pred             CceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHc-CCCeee
Confidence            34678999 999999999999999999999999999999888888875  3889999999988 997653


No 7  
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.06  E-value=9.8e-10  Score=73.67  Aligned_cols=63  Identities=30%  Similarity=0.491  Sum_probs=54.6

Q ss_pred             EEEeccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEE--e-eCCHHHHHHHHHHhcCCceEEc
Q 043253          120 VILKMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVK--G-EFDPPKLAEAITKRLGKFVEIV  183 (230)
Q Consensus       120 ~~~~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~--~-~~~~~~i~~~i~~~~G~~a~~~  183 (230)
                      .+.+.||+|.+|+..|+++|.+++||.++.+++..+.+.|.  + ..+.++|.++|. .+||.+..+
T Consensus         5 ~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aGy~~~~~   70 (71)
T COG2608           5 TLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAGYKVEEI   70 (71)
T ss_pred             EEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcCCCeeec
Confidence            34455999999999999999999999999999999777776  4 579999999999 599987643


No 8  
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.75  E-value=8.5e-08  Score=64.62  Aligned_cols=66  Identities=45%  Similarity=0.824  Sum_probs=59.4

Q ss_pred             eeEEEEeccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEeeCCHHHHHHHHHHhcC-CceEEc
Q 043253          117 VKVVILKMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKGEFDPPKLAEAITKRLG-KFVEIV  183 (230)
Q Consensus       117 ~~~~~~~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~~~~~~~i~~~i~~~~G-~~a~~~  183 (230)
                      .....+.++|+|.+|..+|.+.|..+.||.++.++...++++|.+.+++..+++.|+ +.| ..+..+
T Consensus         4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~-k~~~k~~~~~   70 (73)
T KOG1603|consen    4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLK-KTGGKRAELW   70 (73)
T ss_pred             ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHH-hcCCCceEEe
Confidence            355678889999999999999999999999999999999999998899999999999 577 666655


No 9  
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.42  E-value=8.3e-07  Score=69.94  Aligned_cols=69  Identities=19%  Similarity=0.396  Sum_probs=63.4

Q ss_pred             EEEEeccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEeeCCHHHHHHHHHHhcCCceEEcccccc
Q 043253          119 VVILKMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKGEFDPPKLAEAITKRLGKFVEIVKEEAA  188 (230)
Q Consensus       119 ~~~~~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~~~~~~~i~~~i~~~~G~~a~~~~~~~~  188 (230)
                      ...|.+.|+|.+|++.|+..|..++||.+++|++..+.+.|.+...+..|...|+ ..|.+|.+.....+
T Consensus         8 ~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le-~tGr~Avl~G~G~p   76 (247)
T KOG4656|consen    8 EAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLE-NTGRDAVLRGAGKP   76 (247)
T ss_pred             eEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHH-hhChheEEecCCch
Confidence            4577889999999999999999999999999999999999998889999999999 69999998876555


No 10 
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.38  E-value=2.6e-06  Score=57.30  Aligned_cols=64  Identities=41%  Similarity=0.802  Sum_probs=56.1

Q ss_pred             ceEEEEEEeecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCCCHHHHHHHHHHhCC-Ccee
Q 043253           28 VEDIVLQVYMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKAEPSKVIERIRKKYS-TNAE   93 (230)
Q Consensus        28 ~~~~~~~vgm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~~~~~i~~~i~~~~G-~~~~   93 (230)
                      +....+.+.|+|.+|..+|.+.|..+.||.++.++...++++|.+. .++..+++.+.+. | ....
T Consensus         4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~-~~p~~vl~~l~k~-~~k~~~   68 (73)
T KOG1603|consen    4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGN-VDPVKLLKKLKKT-GGKRAE   68 (73)
T ss_pred             ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEe-cCHHHHHHHHHhc-CCCceE
Confidence            3556777799999999999999999999999999999999999998 7999999999875 4 4443


No 11 
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.28  E-value=5.9e-06  Score=65.21  Aligned_cols=69  Identities=25%  Similarity=0.475  Sum_probs=60.9

Q ss_pred             cceEEEEEEeecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCCCHHHHHHHHHHhCCCceeecCC
Q 043253           27 RVEDIVLQVYMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKAEPSKVIERIRKKYSTNAELISP   97 (230)
Q Consensus        27 ~~~~~~~~vgm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~~~~~i~~~i~~~~G~~~~~~~~   97 (230)
                      ...+.+|.|.|+|.+|++.|+..|..++||.++.+++..+.+.|... ..+..|...++. +|.++.+...
T Consensus         5 ~~~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts-~p~s~i~~~le~-tGr~Avl~G~   73 (247)
T KOG4656|consen    5 DTYEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETS-VPPSEIQNTLEN-TGRDAVLRGA   73 (247)
T ss_pred             CceeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEcc-CChHHHHHHHHh-hChheEEecC
Confidence            45678899999999999999999999999999999999999999886 588899999985 4988877543


No 12 
>PLN02957 copper, zinc superoxide dismutase
Probab=98.01  E-value=3.6e-05  Score=63.68  Aligned_cols=71  Identities=24%  Similarity=0.469  Sum_probs=60.9

Q ss_pred             eEEEEeccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEeeCCHHHHHHHHHHhcCCceEEccccccc
Q 043253          118 KVVILKMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKGEFDPPKLAEAITKRLGKFVEIVKEEAAK  189 (230)
Q Consensus       118 ~~~~~~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~~~~~~~i~~~i~~~~G~~a~~~~~~~~~  189 (230)
                      +.+.+.++|+|.+|+..|++.|..++||..+.+++..+++.|........+...|+ ++||.+.+++...++
T Consensus         6 ~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe-~~Gy~a~~~~~~~~~   76 (238)
T PLN02957          6 LLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALE-QTGRKARLIGQGDPE   76 (238)
T ss_pred             EEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHH-HcCCcEEEecCCCcc
Confidence            34455569999999999999999999999999999999999986667888999999 599999887765554


No 13 
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.80  E-value=6.4e-05  Score=71.01  Aligned_cols=64  Identities=25%  Similarity=0.541  Sum_probs=55.9

Q ss_pred             eEEEEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCC--C-HHHHHHHHHHhCCCceee
Q 043253           29 EDIVLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKA--E-PSKVIERIRKKYSTNAEL   94 (230)
Q Consensus        29 ~~~~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~--~-~~~i~~~i~~~~G~~~~~   94 (230)
                      .+..|.+ ||+|++|+.+|+ +|.+++||..+.+|+.++++.+.++..  + .+.+...++.. ||.+..
T Consensus         2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~-gy~~~~   69 (713)
T COG2217           2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKA-GYSARL   69 (713)
T ss_pred             ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhc-Cccccc
Confidence            3567999 999999999999 999999999999999999999998742  4 67889999877 997653


No 14 
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.71  E-value=8.5e-05  Score=72.05  Aligned_cols=62  Identities=18%  Similarity=0.335  Sum_probs=53.0

Q ss_pred             EEEe-ccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEeeCCHHHHHHHHHHhcCCceEEcc
Q 043253          120 VILK-MYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKGEFDPPKLAEAITKRLGKFVEIVK  184 (230)
Q Consensus       120 ~~~~-~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~~~~~~~i~~~i~~~~G~~a~~~~  184 (230)
                      ..+. .||+|++|+.+|+++|.+++||..+.+++  ++.+|....+.+.+.+.++ .+||.+....
T Consensus         5 ~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~--~~~~v~~~~~~~~i~~~i~-~~Gy~~~~~~   67 (834)
T PRK10671          5 IDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSI--TEAHVTGTASAEALIETIK-QAGYDASVSH   67 (834)
T ss_pred             EEEEECCcccHHHHHHHHHHHhcCCCcceEEEee--eEEEEEecCCHHHHHHHHH-hcCCcccccc
Confidence            3444 49999999999999999999999999999  4566666678899999999 5999988754


No 15 
>PLN02957 copper, zinc superoxide dismutase
Probab=97.67  E-value=0.00043  Score=57.25  Aligned_cols=67  Identities=27%  Similarity=0.437  Sum_probs=57.4

Q ss_pred             eEEEEEEeecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCCCHHHHHHHHHHhCCCceeecCC
Q 043253           29 EDIVLQVYMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKAEPSKVIERIRKKYSTNAELISP   97 (230)
Q Consensus        29 ~~~~~~vgm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~~~~~i~~~i~~~~G~~~~~~~~   97 (230)
                      +++.|.++|+|.+|+..|++.|..++||..+.+++..+++.|.+. .....+...++.. ||.+.++..
T Consensus         6 ~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~-~~~~~I~~aIe~~-Gy~a~~~~~   72 (238)
T PLN02957          6 LLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS-SPVKAMTAALEQT-GRKARLIGQ   72 (238)
T ss_pred             EEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec-CCHHHHHHHHHHc-CCcEEEecC
Confidence            455677799999999999999999999999999999999999875 5777888888876 999876544


No 16 
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.62  E-value=0.00014  Score=68.72  Aligned_cols=60  Identities=23%  Similarity=0.447  Sum_probs=52.5

Q ss_pred             EEeccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEe---eCC-HHHHHHHHHHhcCCceEE
Q 043253          121 ILKMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKG---EFD-PPKLAEAITKRLGKFVEI  182 (230)
Q Consensus       121 ~~~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~---~~~-~~~i~~~i~~~~G~~a~~  182 (230)
                      +...||+|++|+.+|+ +|.+++||.++.+|+.++++.|..   ..+ .+.+...++ ..||.+..
T Consensus         6 l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~gy~~~~   69 (713)
T COG2217           6 LSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAGYSARL   69 (713)
T ss_pred             EeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcCccccc
Confidence            4455999999999999 999999999999999999999872   344 689999999 69998765


No 17 
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.32  E-value=0.0034  Score=38.84  Aligned_cols=61  Identities=25%  Similarity=0.380  Sum_probs=48.3

Q ss_pred             EEEEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccC--CCHHHHHHHHHHhCCCc
Q 043253           30 DIVLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEK--AEPSKVIERIRKKYSTN   91 (230)
Q Consensus        30 ~~~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~--~~~~~i~~~i~~~~G~~   91 (230)
                      +..+.+ |++|..|+..++..+....++....+++....+.+.++.  .+...+...+... ||.
T Consensus         3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-g~~   66 (68)
T TIGR00003         3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDA-GYE   66 (68)
T ss_pred             EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHc-CCC
Confidence            456889 999999999999999999999999999999998888742  2455555555544 664


No 18 
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=96.96  E-value=0.0078  Score=37.11  Aligned_cols=58  Identities=31%  Similarity=0.424  Sum_probs=47.3

Q ss_pred             EeccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEe---eCCHHHHHHHHHHhcCCce
Q 043253          122 LKMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKG---EFDPPKLAEAITKRLGKFV  180 (230)
Q Consensus       122 ~~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~---~~~~~~i~~~i~~~~G~~a  180 (230)
                      .+.|+.|..|+..++..+...+++..+.+++....+.+..   ......+...+. ..||.+
T Consensus         7 ~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~   67 (68)
T TIGR00003         7 QVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYEV   67 (68)
T ss_pred             EECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCCc
Confidence            3449999999999999999999999999999999988862   245666767777 488753


No 19 
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.24  E-value=0.024  Score=54.45  Aligned_cols=65  Identities=23%  Similarity=0.372  Sum_probs=52.4

Q ss_pred             ceEEEEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCCCHHHHHHHHHHhCCCcee
Q 043253           28 VEDIVLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKAEPSKVIERIRKKYSTNAE   93 (230)
Q Consensus        28 ~~~~~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~~~~~i~~~i~~~~G~~~~   93 (230)
                      ..+..+.+ ||+|++|+..++..+..++|+.++.+++.+.++.+.++......+...+... ||.+.
T Consensus        52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~-Gy~a~  117 (741)
T PRK11033         52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKA-GFSLR  117 (741)
T ss_pred             CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhc-ccccc
Confidence            34667889 9999999999999999999999999999999988876532235566666655 88764


No 20 
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=95.28  E-value=0.049  Score=52.43  Aligned_cols=60  Identities=18%  Similarity=0.322  Sum_probs=48.8

Q ss_pred             eccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEee-CCHHHHHHHHHHhcCCceEEc
Q 043253          123 KMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKGE-FDPPKLAEAITKRLGKFVEIV  183 (230)
Q Consensus       123 ~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~~-~~~~~i~~~i~~~~G~~a~~~  183 (230)
                      ..||+|.+|+.++++.+..++||.++.+++.++++.+... ...+.+...++ ..||.+...
T Consensus        59 V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~-~~Gy~a~~~  119 (741)
T PRK11033         59 VSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQ-KAGFSLRDE  119 (741)
T ss_pred             ECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHH-hcccccccc
Confidence            4499999999999999999999999999999999887621 12266777888 599986543


No 21 
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=86.37  E-value=7.3  Score=25.66  Aligned_cols=59  Identities=22%  Similarity=0.303  Sum_probs=43.9

Q ss_pred             eccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEe---eCCHHHHHHHHHHhcCCceEE
Q 043253          123 KMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKG---EFDPPKLAEAITKRLGKFVEI  182 (230)
Q Consensus       123 ~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~---~~~~~~i~~~i~~~~G~~a~~  182 (230)
                      ..++.|..|...++..+...+++....+++......+..   ......+...+. ..||.+++
T Consensus        29 ~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~~   90 (92)
T TIGR02052        29 VPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPSSL   90 (92)
T ss_pred             ECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCeEe
Confidence            349999999999999999999988888888887765541   234555556667 48887543


No 22 
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=81.08  E-value=13  Score=24.40  Aligned_cols=61  Identities=21%  Similarity=0.356  Sum_probs=42.3

Q ss_pred             EEEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccC--CCHHHHHHHHHHhCCCce
Q 043253           31 IVLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEK--AEPSKVIERIRKKYSTNA   92 (230)
Q Consensus        31 ~~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~--~~~~~i~~~i~~~~G~~~   92 (230)
                      ..+.+ ++.|..|...++..+...+++.....++......+....  .....+...+... |+..
T Consensus        25 ~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-g~~~   88 (92)
T TIGR02052        25 VTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDA-GYPS   88 (92)
T ss_pred             EEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhc-CCCe
Confidence            35668 999999999999999999998888888777776665321  2344443444433 6654


No 23 
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=76.71  E-value=2.2  Score=30.11  Aligned_cols=22  Identities=32%  Similarity=0.410  Sum_probs=15.9

Q ss_pred             CCccccceeeeecCCCCCcccc
Q 043253            1 MGERKNRRKKINVPQNQGDEDK   22 (230)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~   22 (230)
                      ||.|+++|+++-.+-.|..+..
T Consensus         1 MG~rr~krr~~ik~~~~~L~k~   22 (104)
T COG4888           1 MGRRRRKRRKIIKRRPQVLPKT   22 (104)
T ss_pred             CCcccccccccCcccCccCCce
Confidence            8998888887777666655543


No 24 
>PF10999 DUF2839:  Protein of unknown function (DUF2839);  InterPro: IPR021262  This bacterial family of unknown function appear to be restricted to Cyanobacteria. 
Probab=74.33  E-value=1.4  Score=28.95  Aligned_cols=19  Identities=37%  Similarity=0.616  Sum_probs=12.4

Q ss_pred             CCccccceeeeecCCCCCcc
Q 043253            1 MGERKNRRKKINVPQNQGDE   20 (230)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~   20 (230)
                      |||+|||+.. ++|.....+
T Consensus         1 MGEAKRRke~-Gl~pr~~k~   19 (68)
T PF10999_consen    1 MGEAKRRKEL-GLPPRYKKE   19 (68)
T ss_pred             Ccchhhhhhc-cCCCccCCc
Confidence            9999988766 444444333


No 25 
>PRK13748 putative mercuric reductase; Provisional
Probab=71.71  E-value=20  Score=33.22  Aligned_cols=63  Identities=21%  Similarity=0.394  Sum_probs=48.8

Q ss_pred             eccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEe--eCCHHHHHHHHHHhcCCceEEcccc
Q 043253          123 KMYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKG--EFDPPKLAEAITKRLGKFVEIVKEE  186 (230)
Q Consensus       123 ~~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~--~~~~~~i~~~i~~~~G~~a~~~~~~  186 (230)
                      ..++.|.+|..+++..+..++++....+++......+..  ......+...+. ..|+.......+
T Consensus         6 i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~-~~g~~~~~~~~~   70 (561)
T PRK13748          6 ITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA-GLGYRATLADAP   70 (561)
T ss_pred             ECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH-HcCCeeeccCcc
Confidence            448999999999999999999999999999888866652  234556666677 588887666553


No 26 
>PRK13748 putative mercuric reductase; Provisional
Probab=67.39  E-value=39  Score=31.34  Aligned_cols=61  Identities=23%  Similarity=0.402  Sum_probs=44.8

Q ss_pred             EEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccC-CCHHHHHHHHHHhCCCceee
Q 043253           33 LQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEK-AEPSKVIERIRKKYSTNAEL   94 (230)
Q Consensus        33 ~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~-~~~~~i~~~i~~~~G~~~~~   94 (230)
                      +.+ +|.|.+|...++..+...+++....+++......+.+.. .+...+...+... |+....
T Consensus         4 i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~-g~~~~~   66 (561)
T PRK13748          4 LKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGL-GYRATL   66 (561)
T ss_pred             EEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHc-CCeeec
Confidence            568 999999999999999999998888888888877766431 2444554555543 776543


No 27 
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=64.02  E-value=82  Score=27.00  Aligned_cols=87  Identities=15%  Similarity=0.210  Sum_probs=54.7

Q ss_pred             EEeecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCCCHHHHHHHHHHhCCCceeecCCCCCCCCCCCCCCCCCC
Q 043253           34 QVYMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKAEPSKVIERIRKKYSTNAELISPKPKTNNGEDKKEPQKK  113 (230)
Q Consensus        34 ~vgm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~~~~~i~~~i~~~~G~~~~~~~~~~~~~~~~~~~~~~~~  113 (230)
                      +++.+ ..|+..+++.+...+||.++++-             +.++..+.+.+..|+. ........+            
T Consensus        66 ~~~~~-~~~~~~v~~~i~~~~gV~~v~~~-------------sre~~l~~L~~~lg~~-~~~~l~~nP------------  118 (297)
T COG2177          66 QIDAD-QDDAALVREKIEGIPGVKSVRFI-------------SREEALKELQPWLGFG-ALLMLDENP------------  118 (297)
T ss_pred             ecCCC-hHHHHHHHHHHhcCCCcceEEEe-------------CHHHHHHHHHHHcCch-hhhcCCCCC------------
Confidence            33444 78999999999999999877642             5555555555555775 211111000            


Q ss_pred             CCceeEEEEeccccCcccHHHHHHHHhccCCeeEEEee
Q 043253          114 QPQVKVVILKMYMHCEGCARDIKKNIARIDGVLTVEPD  151 (230)
Q Consensus       114 ~~~~~~~~~~~gm~C~~C~~~i~~~L~~~~GV~~v~v~  151 (230)
                        -..  .+++-.+-+.=...+.++|+.++||.+|.-+
T Consensus       119 --LP~--~~vV~~~~p~~~~~i~~~l~~l~gV~~V~~~  152 (297)
T COG2177         119 --LPD--VFVVTPDDPPQVKAIAAALRDLPGVAEVDDD  152 (297)
T ss_pred             --CCc--eEEEEeCCCccHHHHHHHHHcCccceehhcc
Confidence              011  2233333366788999999999999887644


No 28 
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=57.20  E-value=45  Score=23.18  Aligned_cols=51  Identities=18%  Similarity=0.388  Sum_probs=35.0

Q ss_pred             HHHHHHHHhccCCeeEEEeec-----CCCeE--EEE-eeCCHHHHHHHHHHhcCCceEEc
Q 043253          132 ARDIKKNIARIDGVLTVEPDM-----SKSQV--TVK-GEFDPPKLAEAITKRLGKFVEIV  183 (230)
Q Consensus       132 ~~~i~~~L~~~~GV~~v~v~~-----~~~~~--~V~-~~~~~~~i~~~i~~~~G~~a~~~  183 (230)
                      .-.+-..|++++||..|.+.+     .+..+  +|. ..++-++|.+.|+ ..|..++-+
T Consensus        21 ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSi   79 (97)
T COG1888          21 IVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSI   79 (97)
T ss_pred             HHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeeh
Confidence            445566788889888776653     33333  444 4689999999999 498765433


No 29 
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=55.60  E-value=30  Score=18.33  Aligned_cols=54  Identities=35%  Similarity=0.604  Sum_probs=36.2

Q ss_pred             ccccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEEee--CCHHHHHHHHHHhcCC
Q 043253          124 MYMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVKGE--FDPPKLAEAITKRLGK  178 (230)
Q Consensus       124 ~gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~~~--~~~~~i~~~i~~~~G~  178 (230)
                      .++.|..|...+...+....++....+++......+...  .....+...+. ..|+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~   60 (63)
T cd00371           5 EGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE-DAGY   60 (63)
T ss_pred             CCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH-HcCC
Confidence            477899999999999888889877777777666555421  24444434444 3444


No 30 
>PF01206 TusA:  Sulfurtransferase TusA;  InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=52.25  E-value=56  Score=20.88  Aligned_cols=52  Identities=10%  Similarity=0.054  Sum_probs=35.6

Q ss_pred             EEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccCC-CHHHHHHHHHHhCCCcee
Q 043253           32 VLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEKA-EPSKVIERIRKKYSTNAE   93 (230)
Q Consensus        32 ~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~~-~~~~i~~~i~~~~G~~~~   93 (230)
                      ++.+ |+.|+...-.+.++|..++.-         +.+.|..++. ....+...+... ||...
T Consensus         2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~-g~~~~   55 (70)
T PF01206_consen    2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEEN-GYEVV   55 (70)
T ss_dssp             EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHH-TEEEE
T ss_pred             EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHC-CCEEE
Confidence            4677 999999999999999987543         3344544422 456677777766 98754


No 31 
>PF02680 DUF211:  Uncharacterized ArCR, COG1888;  InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=52.18  E-value=58  Score=22.84  Aligned_cols=49  Identities=22%  Similarity=0.464  Sum_probs=34.1

Q ss_pred             HHHHHHHHhccCCeeEEEeec-----CCCeEEE--Ee-eCCHHHHHHHHHHhcCCceE
Q 043253          132 ARDIKKNIARIDGVLTVEPDM-----SKSQVTV--KG-EFDPPKLAEAITKRLGKFVE  181 (230)
Q Consensus       132 ~~~i~~~L~~~~GV~~v~v~~-----~~~~~~V--~~-~~~~~~i~~~i~~~~G~~a~  181 (230)
                      .-.+-..|..++||..+.+..     .+..+.|  +| .++.+.+.++|+ .+|-.+.
T Consensus        19 i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IH   75 (95)
T PF02680_consen   19 IVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIH   75 (95)
T ss_dssp             HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEE
T ss_pred             HHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEE
Confidence            556778899999998887663     3444444  44 489999999999 4885543


No 32 
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=48.12  E-value=48  Score=25.98  Aligned_cols=45  Identities=18%  Similarity=0.353  Sum_probs=34.5

Q ss_pred             cccHHHHHHHHhccCCeeEEEeecCCCe-------------------EEEE---eeCCHHHHHHHHH
Q 043253          129 EGCARDIKKNIARIDGVLTVEPDMSKSQ-------------------VTVK---GEFDPPKLAEAIT  173 (230)
Q Consensus       129 ~~C~~~i~~~L~~~~GV~~v~v~~~~~~-------------------~~V~---~~~~~~~i~~~i~  173 (230)
                      .+|=+.++..+..++||.++.+-++++.                   +.|.   ..++.++|++..=
T Consensus        10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~   76 (172)
T PRK14054         10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF   76 (172)
T ss_pred             cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence            4588888999999999999999988775                   3444   4567778877554


No 33 
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=41.84  E-value=1.2e+02  Score=21.16  Aligned_cols=50  Identities=20%  Similarity=0.277  Sum_probs=33.7

Q ss_pred             HHHHHHHhCCCCceEEEEEc-----cC--CEEEEeccCCCHHHHHHHHHHhCCCceee
Q 043253           44 TKVAHCLHGFDGVEKVKLDR-----AN--NKVIVSGEKAEPSKVIERIRKKYSTNAEL   94 (230)
Q Consensus        44 ~~Ie~~l~~~~gv~~v~v~~-----~~--~~~~v~~~~~~~~~i~~~i~~~~G~~~~~   94 (230)
                      --+...|++++||..+.+.+     .+  -++++.+.+.+.+++.+.|++. |.-.+.
T Consensus        22 ve~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~-Gg~IHS   78 (97)
T COG1888          22 VELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEEL-GGAIHS   78 (97)
T ss_pred             HHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHc-CCeeee
Confidence            34556788888887765443     23  3445667667999999999977 765543


No 34 
>PF02680 DUF211:  Uncharacterized ArCR, COG1888;  InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=40.08  E-value=81  Score=22.14  Aligned_cols=63  Identities=17%  Similarity=0.322  Sum_probs=38.8

Q ss_pred             eEEEEEE-eecchhhHHHHHHHHhCCCCceEEEEEc-----cCCEE--EEeccCCCHHHHHHHHHHhCCCcee
Q 043253           29 EDIVLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDR-----ANNKV--IVSGEKAEPSKVIERIRKKYSTNAE   93 (230)
Q Consensus        29 ~~~~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~-----~~~~~--~v~~~~~~~~~i~~~i~~~~G~~~~   93 (230)
                      .++.|.+ -- -..-.-.+...|++++||..+.+.+     .+..+  ++.++..+.+.+.++|++. |-..+
T Consensus         5 rRlVLDVlKP-~~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~-Gg~IH   75 (95)
T PF02680_consen    5 RRLVLDVLKP-HEPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEEL-GGVIH   75 (95)
T ss_dssp             EEEEEEEEEE-SSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHT-T-EEE
T ss_pred             eEEEEEeecC-CCCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHc-CCeEE
Confidence            4445555 22 2233445678899999998876553     33333  4556656999999999977 75443


No 35 
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=39.95  E-value=1.2e+02  Score=20.80  Aligned_cols=43  Identities=21%  Similarity=0.238  Sum_probs=31.9

Q ss_pred             cHHHHHHHHhccCCeeEEEeecCCCeEEEE-eeCCHHHHHHHHH
Q 043253          131 CARDIKKNIARIDGVLTVEPDMSKSQVTVK-GEFDPPKLAEAIT  173 (230)
Q Consensus       131 C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~-~~~~~~~i~~~i~  173 (230)
                      =...+.+.|..++|++-...+...+++.|+ ...+.+.+.+.|.
T Consensus        18 ~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~   61 (87)
T PRK10553         18 RISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE   61 (87)
T ss_pred             HHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence            477899999999999877777677888877 4445665555554


No 36 
>PRK11018 hypothetical protein; Provisional
Probab=37.78  E-value=1.2e+02  Score=20.10  Aligned_cols=53  Identities=13%  Similarity=0.025  Sum_probs=36.5

Q ss_pred             EEEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccC-CCHHHHHHHHHHhCCCcee
Q 043253           31 IVLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEK-AEPSKVIERIRKKYSTNAE   93 (230)
Q Consensus        31 ~~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~-~~~~~i~~~i~~~~G~~~~   93 (230)
                      ..+.+ |+.|+...-+..++|.++..-+         .+.|..++ .....+...+... ||...
T Consensus         9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~G~---------~L~V~~d~~~a~~di~~~~~~~-G~~v~   63 (78)
T PRK11018          9 YRLDMVGEPCPYPAVATLEALPQLKKGE---------ILEVVSDCPQSINNIPLDARNH-GYTVL   63 (78)
T ss_pred             eeEECCCCcCCHHHHHHHHHHHhCCCCC---------EEEEEeCCccHHHHHHHHHHHc-CCEEE
Confidence            56778 9999999999999998875332         33444432 2445666666655 88764


No 37 
>PF01883 DUF59:  Domain of unknown function DUF59;  InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=37.68  E-value=57  Score=21.01  Aligned_cols=30  Identities=17%  Similarity=0.436  Sum_probs=19.3

Q ss_pred             EEeccccCccc------HHHHHHHHhccCCeeEEEe
Q 043253          121 ILKMYMHCEGC------ARDIKKNIARIDGVLTVEP  150 (230)
Q Consensus       121 ~~~~gm~C~~C------~~~i~~~L~~~~GV~~v~v  150 (230)
                      .+...+..++|      ...++.+|..++|+.+++|
T Consensus        37 ~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V   72 (72)
T PF01883_consen   37 SVSLELPTPACPAAEPLREEIREALKALPGVKSVKV   72 (72)
T ss_dssp             EEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred             EEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence            34444444444      4778889999999998875


No 38 
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=33.08  E-value=20  Score=25.42  Aligned_cols=9  Identities=56%  Similarity=1.114  Sum_probs=7.0

Q ss_pred             CCcccccee
Q 043253            1 MGERKNRRK    9 (230)
Q Consensus         1 ~~~~~~~~~    9 (230)
                      ||.|+++|+
T Consensus         1 MGkRk~~~k    9 (99)
T PRK14892          1 MGRRRKKRK    9 (99)
T ss_pred             CCCccccCC
Confidence            898877754


No 39 
>PF03927 NapD:  NapD protein;  InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=32.48  E-value=1.6e+02  Score=19.74  Aligned_cols=43  Identities=16%  Similarity=0.197  Sum_probs=32.5

Q ss_pred             ccHHHHHHHHhccCCeeEEEeecCCCeEEEE-eeCCHHHHHHHHH
Q 043253          130 GCARDIKKNIARIDGVLTVEPDMSKSQVTVK-GEFDPPKLAEAIT  173 (230)
Q Consensus       130 ~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~-~~~~~~~i~~~i~  173 (230)
                      .=...+.++|..++|++-...+.. +++.|+ ...+...+.+.+.
T Consensus        15 ~~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~   58 (79)
T PF03927_consen   15 ERLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID   58 (79)
T ss_dssp             CCHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence            347789999999999976667765 888776 5556677777666


No 40 
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=30.78  E-value=1.2e+02  Score=23.73  Aligned_cols=46  Identities=15%  Similarity=0.226  Sum_probs=33.2

Q ss_pred             hhhHHHHHHHHhCCCCceEEEEEccCCE-------------------EEEeccCC--CHHHHHHHHH
Q 043253           40 DGCATKVAHCLHGFDGVEKVKLDRANNK-------------------VIVSGEKA--EPSKVIERIR   85 (230)
Q Consensus        40 ~~C~~~Ie~~l~~~~gv~~v~v~~~~~~-------------------~~v~~~~~--~~~~i~~~i~   85 (230)
                      ++|=..++..+..++||.++.+-+..+.                   +.|.+|+.  +.+.|+...-
T Consensus        10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~   76 (172)
T PRK14054         10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF   76 (172)
T ss_pred             cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence            4577888888999999999998876654                   56667642  5666665543


No 41 
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=30.22  E-value=97  Score=24.65  Aligned_cols=45  Identities=18%  Similarity=0.324  Sum_probs=32.7

Q ss_pred             cccHHHHHHHHhccCCeeEEEeecCCCe-------------------EEEE---eeCCHHHHHHHHH
Q 043253          129 EGCARDIKKNIARIDGVLTVEPDMSKSQ-------------------VTVK---GEFDPPKLAEAIT  173 (230)
Q Consensus       129 ~~C~~~i~~~L~~~~GV~~v~v~~~~~~-------------------~~V~---~~~~~~~i~~~i~  173 (230)
                      .+|=+.++..+.+++||.++.+-++++.                   +.|.   ..++.++|++.+=
T Consensus        15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff   81 (186)
T PRK13014         15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFF   81 (186)
T ss_pred             cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHH
Confidence            3466777888889999999999988764                   3333   4467788877554


No 42 
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox.    SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210.  This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=30.22  E-value=1.5e+02  Score=18.97  Aligned_cols=51  Identities=8%  Similarity=0.122  Sum_probs=34.6

Q ss_pred             EEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccC-CCHHHHHHHHHHhCCCcee
Q 043253           33 LQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEK-AEPSKVIERIRKKYSTNAE   93 (230)
Q Consensus        33 ~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~-~~~~~i~~~i~~~~G~~~~   93 (230)
                      +.+ |+.|+.-.-...++|.++..-         +.+.|..++ .....+....... ||...
T Consensus         2 lD~rG~~CP~Pvl~~kkal~~l~~G---------~~l~V~~d~~~a~~di~~~~~~~-G~~~~   54 (69)
T cd03420           2 VDACGLQCPGPILKLKKEIDKLQDG---------EQLEVKASDPGFARDAQAWCKST-GNTLI   54 (69)
T ss_pred             cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEECCccHHHHHHHHHHHc-CCEEE
Confidence            456 999999999999999887533         234444432 2455666666655 88765


No 43 
>PF13732 DUF4162:  Domain of unknown function (DUF4162)
Probab=30.17  E-value=1.6e+02  Score=19.26  Aligned_cols=44  Identities=23%  Similarity=0.400  Sum_probs=31.2

Q ss_pred             HhccCCeeEEEeecCCCeEEEE--eeCCHHHHHHHHHHhcCCceEEccc
Q 043253          139 IARIDGVLTVEPDMSKSQVTVK--GEFDPPKLAEAITKRLGKFVEIVKE  185 (230)
Q Consensus       139 L~~~~GV~~v~v~~~~~~~~V~--~~~~~~~i~~~i~~~~G~~a~~~~~  185 (230)
                      |..++||..+... ..+.+.+.  ......+|+..|. ..|. +.-+..
T Consensus        26 l~~~~~v~~v~~~-~~~~~~i~l~~~~~~~~ll~~l~-~~g~-I~~f~~   71 (84)
T PF13732_consen   26 LEELPGVESVEQD-GDGKLRIKLEDEETANELLQELI-EKGI-IRSFEE   71 (84)
T ss_pred             HhhCCCeEEEEEe-CCcEEEEEECCcccHHHHHHHHH-hCCC-eeEEEE
Confidence            7888999988764 34435554  5567788999999 4888 655443


No 44 
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=30.01  E-value=1.3e+02  Score=24.56  Aligned_cols=27  Identities=15%  Similarity=0.291  Sum_probs=22.9

Q ss_pred             cccHHHHHHHHhccCCeeEEEeecCCC
Q 043253          129 EGCARDIKKNIARIDGVLTVEPDMSKS  155 (230)
Q Consensus       129 ~~C~~~i~~~L~~~~GV~~v~v~~~~~  155 (230)
                      ++|-+.++..+.+++||.++.+-++++
T Consensus        52 gGCFWg~E~~F~~l~GV~~t~vGYagG   78 (213)
T PRK00058         52 MGCFWGAERLFWQLPGVYSTAVGYAGG   78 (213)
T ss_pred             ccCcchhHHHHhcCCCEEEEEeeecCC
Confidence            457788888899999999999998855


No 45 
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain.  The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA  (also known as UvrY,  and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA.  A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium.  Moreover, despite a low primary sequence similarity,  the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=28.71  E-value=1.6e+02  Score=18.60  Aligned_cols=48  Identities=15%  Similarity=0.193  Sum_probs=33.7

Q ss_pred             cccCcccHHHHHHHHhccCCeeEEEeecCCCeEEEE--eeCCHHHHHHHHHHhcCCceEEc
Q 043253          125 YMHCEGCARDIKKNIARIDGVLTVEPDMSKSQVTVK--GEFDPPKLAEAITKRLGKFVEIV  183 (230)
Q Consensus       125 gm~C~~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~--~~~~~~~i~~~i~~~~G~~a~~~  183 (230)
                      |+.|+.-.-..+++| .+..-         +.+.|.  ......+|....+ ..||.....
T Consensus         6 G~~CP~P~l~~k~al-~~~~g---------~~l~v~~d~~~s~~~i~~~~~-~~G~~~~~~   55 (67)
T cd03421           6 GLACPQPVIKTKKAL-ELEAG---------GEIEVLVDNEVAKENVSRFAE-SRGYEVSVE   55 (67)
T ss_pred             CCCCCHHHHHHHHHH-hcCCC---------CEEEEEEcChhHHHHHHHHHH-HcCCEEEEE
Confidence            889999999999999 55322         234333  3345578899999 599987543


No 46 
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=27.56  E-value=61  Score=24.99  Aligned_cols=45  Identities=13%  Similarity=0.254  Sum_probs=33.4

Q ss_pred             cccHHHHHHHHhccCCeeEEEeecCCCeE--------------EEE---eeCCHHHHHHHHH
Q 043253          129 EGCARDIKKNIARIDGVLTVEPDMSKSQV--------------TVK---GEFDPPKLAEAIT  173 (230)
Q Consensus       129 ~~C~~~i~~~L~~~~GV~~v~v~~~~~~~--------------~V~---~~~~~~~i~~~i~  173 (230)
                      ++|=+.++..+.+++||.++.+-++++..              .|.   ..++.++|++.+=
T Consensus         8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~   69 (156)
T PRK05528          8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLF   69 (156)
T ss_pred             cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHH
Confidence            46888889999999999999999876432              233   4467788877554


No 47 
>PF09580 Spore_YhcN_YlaJ:  Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ);  InterPro: IPR019076  This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain. 
Probab=25.63  E-value=2e+02  Score=22.09  Aligned_cols=31  Identities=16%  Similarity=0.220  Sum_probs=28.1

Q ss_pred             ccHHHHHHHHhccCCeeEEEeecCCCeEEEE
Q 043253          130 GCARDIKKNIARIDGVLTVEPDMSKSQVTVK  160 (230)
Q Consensus       130 ~C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~  160 (230)
                      .=+..|.+.+.+++||.++.|-.....+.|.
T Consensus        75 ~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va  105 (177)
T PF09580_consen   75 QLADRIANRVKKVPGVEDATVVVTDDNAYVA  105 (177)
T ss_pred             HHHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence            3688999999999999999999999999875


No 48 
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=25.34  E-value=1.2e+02  Score=20.30  Aligned_cols=54  Identities=17%  Similarity=0.217  Sum_probs=34.7

Q ss_pred             EEEEEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccC-CCHHHHHHHHHHhCCCce
Q 043253           30 DIVLQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEK-AEPSKVIERIRKKYSTNA   92 (230)
Q Consensus        30 ~~~~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~-~~~~~i~~~i~~~~G~~~   92 (230)
                      ...|.+ |+.|+.-...+.++|.+++--         ..+.|..++ .....|........|+..
T Consensus         5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~G---------e~LeV~~ddp~~~~dIp~~~~~~~~~~l   60 (78)
T COG0425           5 DKVLDLRGLRCPGPVVETKKALAKLKPG---------EILEVIADDPAAKEDIPAWAKKEGGHEL   60 (78)
T ss_pred             ceEEeccCCcCCccHHHHHHHHHcCCCC---------CEEEEEecCcchHHHHHHHHHHcCCcEE
Confidence            456888 999999999999999987543         344444432 234455555553423543


No 49 
>PF14492 EFG_II:  Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=25.19  E-value=2e+02  Score=18.80  Aligned_cols=51  Identities=25%  Similarity=0.411  Sum_probs=35.7

Q ss_pred             cHHHHHHHHhcc---CCeeEEEeecCCCeEEEE--eeCCHHHHHHHHHHhcCCceE
Q 043253          131 CARDIKKNIARI---DGVLTVEPDMSKSQVTVK--GEFDPPKLAEAITKRLGKFVE  181 (230)
Q Consensus       131 C~~~i~~~L~~~---~GV~~v~v~~~~~~~~V~--~~~~~~~i~~~i~~~~G~~a~  181 (230)
                      =..++..+|..+   +--..+..|..++.+.|.  |....+-+...|+++.|..++
T Consensus        17 d~~kl~~aL~~l~~eDP~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~   72 (75)
T PF14492_consen   17 DEPKLSEALQKLSEEDPSLRVERDEETGELILSGMGELHLEVLLERLKRRFGVEVE   72 (75)
T ss_dssp             HHHHHHHHHHHHHHH-TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence            345566666555   344478889889998887  778888889999855565544


No 50 
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH).  The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold.  The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.  In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=24.04  E-value=3.1e+02  Score=20.86  Aligned_cols=57  Identities=16%  Similarity=0.169  Sum_probs=39.7

Q ss_pred             cHHHHHHHHhccCCeeEEEeecCCCeEEEE----ee---CCHHHHHHHHHHhcCCceEEcccccc
Q 043253          131 CARDIKKNIARIDGVLTVEPDMSKSQVTVK----GE---FDPPKLAEAITKRLGKFVEIVKEEAA  188 (230)
Q Consensus       131 C~~~i~~~L~~~~GV~~v~v~~~~~~~~V~----~~---~~~~~i~~~i~~~~G~~a~~~~~~~~  188 (230)
                      -...|.+.+-.-.|+.++.++..++.+.|.    +.   -....+.+... ++|+.+.+....+-
T Consensus        54 A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~-~tgW~p~vvRtpPi  117 (145)
T cd02410          54 AIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITR-ETGWAPKVVRTPPI  117 (145)
T ss_pred             HHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHH-HhCCeeEEEecCCC
Confidence            455666667666899999999999999986    11   12233455555 69999888765443


No 51 
>PF01625 PMSR:  Peptide methionine sulfoxide reductase;  InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate.  In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=21.34  E-value=1.1e+02  Score=23.44  Aligned_cols=27  Identities=19%  Similarity=0.464  Sum_probs=23.9

Q ss_pred             cccHHHHHHHHhccCCeeEEEeecCCC
Q 043253          129 EGCARDIKKNIARIDGVLTVEPDMSKS  155 (230)
Q Consensus       129 ~~C~~~i~~~L~~~~GV~~v~v~~~~~  155 (230)
                      .+|=+.++..+.+++||.++.+-++++
T Consensus         7 ~GCFW~~e~~f~~~~GV~~t~vGYagG   33 (155)
T PF01625_consen    7 GGCFWGVEAAFRRLPGVISTRVGYAGG   33 (155)
T ss_dssp             ESSHHHHHHHHHTSTTEEEEEEEEESS
T ss_pred             cCCCeEhHHHHhhCCCEEEEEecccCC
Confidence            468899999999999999999998765


No 52 
>cd03423 SirA SirA (also known as UvrY,  and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA.  A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium.  Moreover, despite a low primary sequence similarity,  the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=21.14  E-value=2.4e+02  Score=18.02  Aligned_cols=52  Identities=6%  Similarity=0.033  Sum_probs=35.0

Q ss_pred             EEE-eecchhhHHHHHHHHhCCCCceEEEEEccCCEEEEeccC-CCHHHHHHHHHHhCCCceee
Q 043253           33 LQV-YMHCDGCATKVAHCLHGFDGVEKVKLDRANNKVIVSGEK-AEPSKVIERIRKKYSTNAEL   94 (230)
Q Consensus        33 ~~v-gm~C~~C~~~Ie~~l~~~~gv~~v~v~~~~~~~~v~~~~-~~~~~i~~~i~~~~G~~~~~   94 (230)
                      +.+ |+.|+.-.-...++|.+++--         +.+.|..++ .....+...+... ||....
T Consensus         2 lD~~G~~CP~P~i~~k~~l~~l~~G---------~~l~V~~dd~~s~~di~~~~~~~-g~~~~~   55 (69)
T cd03423           2 LDTRGLRCPEPVMMLHKKVRKMKPG---------DTLLVLATDPSTTRDIPKFCTFL-GHELLA   55 (69)
T ss_pred             ccccCCcCCHHHHHHHHHHHcCCCC---------CEEEEEeCCCchHHHHHHHHHHc-CCEEEE
Confidence            346 899999999999999887432         233444332 3556677777755 987653


No 53 
>TIGR00401 msrA methionine-S-sulfoxide reductase. This model describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens.
Probab=20.85  E-value=1e+02  Score=23.55  Aligned_cols=28  Identities=21%  Similarity=0.321  Sum_probs=23.4

Q ss_pred             cccHHHHHHHHhccCCeeEEEeecCCCe
Q 043253          129 EGCARDIKKNIARIDGVLTVEPDMSKSQ  156 (230)
Q Consensus       129 ~~C~~~i~~~L~~~~GV~~v~v~~~~~~  156 (230)
                      .+|=+.++..+..++||.++.+-++++.
T Consensus         7 gGCFWg~E~~f~~~~GV~~t~~GYagG~   34 (149)
T TIGR00401         7 GGCFWGVEKYFWLIPGVYSTAVGYTGGY   34 (149)
T ss_pred             cCCchhhHHHHhcCCCEEEEEEeeCCCC
Confidence            4578888888999999999999887653


Done!