Query         gi|254780547|ref|YP_003064960.1| OmpA/MotB [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 160
No_of_seqs    126 out of 4755
Neff          8.2 
Searched_HMMs 39220
Date          Sun May 29 22:30:04 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780547.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK09967 putative outer membra 100.0 1.2E-40 2.8E-45  256.0  12.4  154    1-154     1-158 (160)
  2 TIGR02802 Pal_lipo peptidoglyc 100.0 2.8E-41 1.4E-45  259.6   8.1  103   51-153     1-104 (104)
  3 PRK10802 peptidoglycan-associa 100.0 2.7E-39 6.9E-44  248.1  13.6  105   49-153    68-173 (173)
  4 PRK10510 putative outer membra 100.0 2.6E-37 6.6E-42  236.6  11.8  106   49-154   111-217 (219)
  5 COG2885 OmpA Outer membrane pr 100.0 4.9E-36 1.2E-40  229.2  10.1  111   45-155    78-189 (190)
  6 PRK10808 outer membrane protei 100.0 2.3E-33 5.8E-38  213.7  10.3  111   47-157   221-343 (347)
  7 PRK09038 flagellar motor prote 100.0 5.9E-31 1.5E-35  199.8   8.1  106   48-153   135-244 (285)
  8 cd07185 OmpA_C-like Peptidogly 100.0   3E-30 7.6E-35  195.7   9.3  104   50-153     2-106 (106)
  9 TIGR03350 type_VI_ompA type VI 100.0 3.4E-30 8.7E-35  195.3   8.5  113   41-153    21-137 (137)
 10 PRK06742 flagellar motor prote 100.0 5.4E-29 1.4E-33  188.4   9.5  106   49-154   114-224 (225)
 11 PRK09040 hypothetical protein; 100.0 6.1E-29 1.6E-33  188.1   9.0  108   47-154    86-203 (215)
 12 PRK06925 flagellar motor prote 100.0 1.2E-28 3.1E-33  186.4   8.4  107   48-154   116-227 (230)
 13 PRK07734 motB flagellar motor  100.0 3.1E-28 7.8E-33  184.0   9.3  107   48-154   140-252 (259)
 14 PRK08944 motB flagellar motor  100.0   4E-28   1E-32  183.4   9.1  108   50-157   182-294 (305)
 15 PRK08126 hypothetical protein;  99.9 1.9E-27   5E-32  179.4  10.7  103   52-154   321-427 (428)
 16 PRK08457 motB flagellar motor   99.9 7.5E-28 1.9E-32  181.8   7.5  106   47-155   116-228 (251)
 17 PRK07033 hypothetical protein;  99.9 4.6E-27 1.2E-31  177.2  11.2  107   52-158   318-428 (429)
 18 PRK09039 hypothetical protein;  99.9 3.6E-27 9.3E-32  177.8   8.8  106   49-154   223-341 (343)
 19 PRK06667 motB flagellar motor   99.9 4.8E-27 1.2E-31  177.1   9.3  105   50-154   127-241 (254)
 20 COG1360 MotB Flagellar motor p  99.9   2E-26   5E-31  173.6   9.3  105   50-154   132-241 (244)
 21 pfam00691 OmpA OmpA family. Th  99.9 3.1E-25 7.9E-30  166.6   8.0   95   53-147     1-97  (97)
 22 PRK09041 motB flagellar motor   99.9 8.4E-24 2.2E-28  158.3   9.1  100   52-153   168-273 (317)
 23 PRK06778 hypothetical protein;  99.9 7.1E-24 1.8E-28  158.7   8.2  100   52-153   154-257 (289)
 24 PRK05996 motB flagellar motor   99.9 3.4E-21 8.6E-26  143.3   9.4  103   52-156   324-430 (431)
 25 PRK12799 motB flagellar motor   99.8 5.1E-19 1.3E-23  130.6   9.2  102   51-154   157-264 (424)
 26 PRK07034 hypothetical protein;  99.6 2.2E-15 5.5E-20  109.6   7.1  104   51-154   386-503 (565)
 27 PRK10834 hypothetical protein;  93.7    0.11 2.7E-06   30.4   4.2  119    1-130     1-123 (239)
 28 pfam09476 Pilus_CpaD Pilus bio  91.1     1.3 3.3E-05   24.1   7.9   77   55-136    45-122 (200)
 29 PRK13731 conjugal transfer sur  82.5     1.4 3.7E-05   23.8   3.2   27    1-27      1-27  (243)
 30 TIGR02522 pilus_cpaD pilus (Ca  81.2     4.7 0.00012   20.8   9.4   76   50-130    45-121 (211)
 31 PRK11087 hypothetical protein;  77.3     5.2 0.00013   20.6   4.7   32    1-32      1-33  (238)
 32 COG5461 Type IV pili component  75.7     6.9 0.00018   19.9   9.3   72   52-130    55-129 (224)
 33 pfam00543 P-II Nitrogen regula  73.6       7 0.00018   19.8   4.5   54  103-156     7-65  (102)
 34 PRK10533 putative lipoprotein;  72.4     7.4 0.00019   19.7   4.4   76    1-76      1-78  (171)
 35 PRK10665 nitrogen regulatory p  69.1     9.9 0.00025   19.0   4.8   54  103-156    10-68  (112)
 36 PRK11917 bifunctional adhesin/  69.0     5.7 0.00014   20.4   3.2   24    1-24      1-24  (259)
 37 PRK13289 nitric oxide dioxygen  62.9     5.5 0.00014   20.4   2.2   29  106-134   370-398 (399)
 38 PRK03002 prsA peptidylprolyl i  61.3     8.2 0.00021   19.4   2.8   24    1-24      1-24  (285)
 39 pfam02698 DUF218 DUF218 domain  60.3      15 0.00038   18.0   4.6   59   62-128    12-71  (148)
 40 KOG0524 consensus               60.1      13 0.00033   18.3   3.7   68   76-157   232-299 (359)
 41 PRK11063 metQ DL-methionine tr  57.8      16 0.00042   17.7   6.5   89    1-89      3-109 (271)
 42 cd07762 CYTH-like_Pase_1 Uncha  57.3      16 0.00041   17.7   3.8   86   49-156    29-127 (180)
 43 PRK02998 prsA peptidylprolyl i  55.9     9.4 0.00024   19.1   2.4   24    1-24      1-25  (283)
 44 TIGR00972 3a0107s01c2 phosphat  55.5      16 0.00042   17.7   3.6   53   49-115   163-215 (248)
 45 COG4116 Uncharacterized protei  54.3       5 0.00013   20.7   0.7   71   50-127    35-118 (193)
 46 COG1908 FrhD Coenzyme F420-red  53.0      20  0.0005   17.2   5.2   52   74-126    48-100 (132)
 47 cd06184 flavohem_like_fad_nad_  52.7      13 0.00032   18.3   2.6   29  103-131   218-246 (247)
 48 pfam06925 MGDG_synth Monogalac  47.4      12 0.00031   18.5   1.8   23  106-128   145-167 (169)
 49 PRK10494 hypothetical protein;  43.7      28  0.0007   16.4   4.8   62   58-127    98-160 (259)
 50 PRK03095 prsA peptidylprolyl i  42.9      22 0.00055   17.0   2.6   20    1-22      1-20  (287)
 51 PRK10684 HCP oxidoreductase, N  42.0      24 0.00062   16.7   2.7   32  107-138   217-248 (335)
 52 PRK01326 prsA foldase protein   41.5      27 0.00068   16.5   2.9   24    1-24      1-24  (310)
 53 pfam02662 FlpD Methyl-viologen  40.1      26 0.00067   16.5   2.6   57   72-129    45-102 (124)
 54 COG1735 Php Predicted metal-de  38.8      33 0.00084   15.9   4.9   66   51-129   136-201 (316)
 55 pfam04954 SIP Siderophore-inte  38.4      26 0.00066   16.5   2.4   26  104-129    89-115 (118)
 56 PRK06193 hypothetical protein;  38.3      34 0.00086   15.9   8.0   81    1-81      1-99  (211)
 57 PRK09859 multidrug efflux syst  37.9      34 0.00087   15.9   3.5   23    1-23      1-23  (385)
 58 pfam00123 Hormone_2 Peptide ho  36.6      20  0.0005   17.2   1.5   28   88-115     1-28  (28)
 59 cd06185 PDR_like Phthalate dio  36.6      26 0.00065   16.6   2.1   25  105-129   187-211 (211)
 60 smart00070 GLUCA Glucagon like  36.4      19 0.00049   17.3   1.4   27   88-114     1-27  (27)
 61 pfam01187 MIF Macrophage migra  35.8      37 0.00094   15.7   8.0   74   54-127     5-98  (114)
 62 PRK09585 anmK anhydro-N-acetyl  35.8      37 0.00094   15.7   3.2   32   97-128    65-96  (366)
 63 COG4195 Phage-related replicat  35.0      31  0.0008   16.1   2.4   80   76-158    96-187 (208)
 64 TIGR02544 III_secr_YscJ type I  35.0      32 0.00081   16.0   2.4   20  108-127   174-195 (203)
 65 PRK05363 putative sulfite oxid  34.7      38 0.00098   15.6   6.1   53   38-98     72-124 (327)
 66 PRK10858 nitrogen regulatory p  34.5      39 0.00099   15.5   4.4   53  103-155    10-67  (112)
 67 PRK05421 hypothetical protein;  33.8      40   0.001   15.5   4.6   58   51-121   147-204 (254)
 68 KOG0739 consensus               33.6      40   0.001   15.4   5.1   99   51-153   192-298 (439)
 69 COG4472 Uncharacterized protei  33.1      41   0.001   15.4   3.0   68   50-119     6-87  (88)
 70 pfam09961 DUF2195 Uncharacteri  32.8      32 0.00082   16.0   2.1   57   94-158    63-119 (121)
 71 cd01525 RHOD_Kc Member of the   32.7      42  0.0011   15.4   2.7   64   46-123    31-95  (105)
 72 PRK07609 CDP-6-deoxy-delta-3,4  32.0      35 0.00088   15.8   2.2   26  106-131   309-334 (337)
 73 cd06189 flavin_oxioreductase N  31.7      28 0.00072   16.3   1.7   24  105-128   201-224 (224)
 74 cd06213 oxygenase_e_transfer_s  31.3      34 0.00087   15.9   2.0   24  105-128   204-227 (227)
 75 cd06211 phenol_2-monooxygenase  31.0      35 0.00089   15.8   2.1   23  106-128   216-238 (238)
 76 pfam01764 Lipase_3 Lipase (cla  30.6      45  0.0012   15.1   6.3   58   69-139    50-109 (141)
 77 cd06212 monooxygenase_like The  30.1      36 0.00091   15.7   2.0   24  105-128   208-231 (232)
 78 pfam08085 Entericidin Enterici  29.8      47  0.0012   15.1   2.5   24    1-24      1-24  (42)
 79 cd06209 BenDO_FAD_NAD Benzoate  29.6      40   0.001   15.4   2.2   24  105-128   204-227 (228)
 80 cd06194 FNR_N-term_Iron_sulfur  28.7      40   0.001   15.4   2.1   24  105-128   198-221 (222)
 81 PRK11872 antC anthranilate dio  28.1      48  0.0012   15.0   2.4   26  106-131   313-338 (340)
 82 PRK13609 diacylglycerol glucos  27.8      51  0.0013   14.9   3.7   48  107-158   156-213 (388)
 83 COG3672 Predicted transglutami  27.1      52  0.0013   14.8   8.6   71   55-125    60-133 (191)
 84 PRK12701 flgH flagellar basal   26.8      53  0.0013   14.8   3.5   22    1-22      1-22  (230)
 85 TIGR02074 PBP_1a_fam penicilli  26.5      54  0.0014   14.7   3.0   60   51-124   123-183 (700)
 86 cd00474 SUI1_eIF1 The SUI1/eIF  26.1      42  0.0011   15.4   1.8   49   66-125    25-76  (77)
 87 TIGR01270 Trp_5_monoox tryptop  26.1      54  0.0014   14.7   3.4   54   18-79    403-456 (499)
 88 PRK13799 unknown domain/N-carb  25.9      55  0.0014   14.7   7.1   77   59-135   207-308 (591)
 89 cd00519 Lipase_3 Lipase (class  25.8      55  0.0014   14.7   6.0   56   71-140   117-173 (229)
 90 PHA00691 hypothetical protein   25.7      55  0.0014   14.6   2.5   40   76-117    18-61  (68)
 91 cd06210 MMO_FAD_NAD_binding Me  25.6      49  0.0013   14.9   2.0   23  106-128   213-235 (236)
 92 cd06198 FNR_like_3 NAD(P) bind  24.9      53  0.0013   14.8   2.1   25  104-128   191-215 (216)
 93 cd06217 FNR_iron_sulfur_bindin  24.6      53  0.0014   14.8   2.1   25  104-128   211-235 (235)
 94 cd06191 FNR_iron_sulfur_bindin  24.6      56  0.0014   14.6   2.2   23  106-128   209-231 (231)
 95 cd06187 O2ase_reductase_like T  24.3      54  0.0014   14.7   2.1   25  104-128   200-224 (224)
 96 cd06215 FNR_iron_sulfur_bindin  24.3      58  0.0015   14.5   2.2   25  104-128   207-231 (231)
 97 cd06214 PA_degradation_oxidore  24.2      53  0.0014   14.7   2.0   23  106-128   218-240 (241)
 98 PRK01741 cell division protein  24.0      45  0.0012   15.1   1.6   21    1-21      1-21  (342)
 99 PRK05464 Na(+)-translocating N  23.6      48  0.0012   15.0   1.7   23  107-129   385-407 (408)
100 pfam12000 DUF3495 Domain of un  22.4      64  0.0016   14.3   3.3   50   83-132    21-80  (172)
101 pfam11713 Peptidase_C80 Peptid  22.4      64  0.0016   14.3   4.5   46   78-127    55-111 (160)
102 PRK06437 hypothetical protein;  22.0      65  0.0017   14.2   3.4   48   81-138     3-50  (67)
103 cd06193 siderophore_interactin  21.6      67  0.0017   14.2   2.4   24  105-128   209-233 (235)
104 PRK10523 lipoprotein involved   21.3      68  0.0017   14.1   3.6   28    1-28      1-28  (234)
105 KOG4569 consensus               20.9      69  0.0018   14.1   7.0   55   70-137   159-215 (336)
106 COG1348 NifH Nitrogenase subun  20.5      61  0.0016   14.4   1.7   29   86-114   140-168 (278)
107 TIGR01854 lipid_A_lpxH UDP-2,3  20.5      42  0.0011   15.3   0.9   21   71-91    184-204 (241)
108 pfam03702 UPF0075 Uncharacteri  20.4      71  0.0018   14.0   3.3   34  101-134   265-298 (363)
109 TIGR01618 phage_P_loop phage n  20.3      71  0.0018   14.0   4.0   78   69-147   127-213 (229)
110 cd06196 FNR_like_1 Ferredoxin   20.1      62  0.0016   14.3   1.7   20  106-125   198-217 (218)

No 1  
>PRK09967 putative outer membrane lipoprotein; Provisional
Probab=100.00  E-value=1.2e-40  Score=255.95  Aligned_cols=154  Identities=18%  Similarity=0.281  Sum_probs=128.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCCC--CCCCCCCCCHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             90369999999999986502456666656--6554444201256787520310022047522432479999999843025
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDNLDTKIS--SPDTVLNESSLQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEK   78 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~   78 (160)
                      |.++.+..++.++.+++.|........+.  ..........+.+++...+++.|||+||++.|+|+++..|++++.+|++
T Consensus         1 m~k~~~~~~l~~~l~lsgC~s~~~~~t~~~~~~~~~~~~~~t~~~~~~g~~d~V~Fd~d~~~L~~~s~~~L~~~A~~L~~   80 (160)
T PRK09967          1 MIKHLVAPLIFTSLILTGCQSPQGKFTPEQVAAMQSYGFTESAGDWSLGLSDAILFAKNDYKLLPESQQQIQTMAAKLAS   80 (160)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             90789999999999998458999998989988887437522354314489983792699501199899999999999997


Q ss_pred             CE-EEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCC-CCCEEEEEEEECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             60-5899997226653333200111337999999998528-9860699997074489899878779842991899997
Q gi|254780547|r   79 HD-CDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARG-ISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus        79 ~~-~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~G-i~~~ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      ++ .+|.|+||||++|+++||+.||++||++|++||+..| |+++||.++|||+++|+++|++++||++||||||+|.
T Consensus        81 ~p~~~v~I~GHTD~~G~~~yN~~LS~rRA~aV~~~l~~~g~i~~~ri~~~g~Ge~~Pv~~n~t~~gra~NRRVeivit  158 (160)
T PRK09967         81 TGLTHARMDGHTDNYGEDSYNEGLSLKRANVVADAWAMGGQIPRSNLTTQGLGKKYPIASNKTAQGRAENRRVAVVIT  158 (160)
T ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCCCCHHHHHHCCCEEEEEE
T ss_conf             899629998747998998999999999999999999853785443589996465673889969899987699899983


No 2  
>TIGR02802 Pal_lipo peptidoglycan-associated lipoprotein; InterPro: IPR014169   Members in this entry represent the peptidoglycan-associated lipoprotein (Pal or OprL) protein of the Tol-Pal system. The system appears to be involved both in the maintenance of outer membrane integrity and in the import of certain organic molecules as nutrients. Members of this family contain a hydrodrophobic lipoprotein signal sequence, a conserved N-terminal cleavage and modification site, a poorly conserved low-complexity region, together comprising about 65 amino acids, and a well-conserved C-terminal domain. The entry represents only the conserved C-terminal domain..
Probab=100.00  E-value=2.8e-41  Score=259.55  Aligned_cols=103  Identities=45%  Similarity=0.734  Sum_probs=99.9

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCE-EEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC
Q ss_conf             002204752243247999999984302560-5899997226653333200111337999999998528986069999707
Q gi|254780547|r   51 SVFFDTSSYSIRPADIQVLSNLGSWLEKHD-CDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYG  129 (160)
Q Consensus        51 ~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~-~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G  129 (160)
                      .|||+||++.|++++++.|+..|.||++|| .+|.|+||||++||+|||++|+++||+||++||+..||+++||++++||
T Consensus         1 ~vyF~~D~~~l~~e~~~~l~~hA~~L~~~p~~~V~iEGH~DERGTrEYNlALGeRRA~AV~~yL~~~GV~~~q~~~vSYG   80 (104)
T TIGR02802         1 RVYFDFDSSDLKSEAQAILDAHAQYLKKNPSVRVTIEGHTDERGTREYNLALGERRANAVKDYLQAKGVSASQIETVSYG   80 (104)
T ss_pred             CEECCCCHHHCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECC
T ss_conf             94323581431779999999989999867993788863078888877777788999999999999738961100463026


Q ss_pred             CCCCCCCCCCHHHHHCCCEEEEEE
Q ss_conf             448989987877984299189999
Q gi|254780547|r  130 KEMPSVYGHDEDAYAKNRRAIVFL  153 (160)
Q Consensus       130 ~~~P~~~~~~~~~~~~NRRVei~i  153 (160)
                      |++|++.++||++|+|||||+|++
T Consensus        81 kErP~~~G~~E~~wakNRR~~~vy  104 (104)
T TIGR02802        81 KERPAALGHDEAAWAKNRRAVLVY  104 (104)
T ss_pred             CCCCCCCCCCHHHHHHCCCCCCCC
T ss_conf             656877898857775405310049


No 3  
>PRK10802 peptidoglycan-associated outer membrane lipoprotein; Provisional
Probab=100.00  E-value=2.7e-39  Score=248.07  Aligned_cols=105  Identities=45%  Similarity=0.736  Sum_probs=100.7

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHCCC-EEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             3100220475224324799999998430256-058999972266533332001113379999999985289860699997
Q gi|254780547|r   49 GDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTS  127 (160)
Q Consensus        49 ~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~-~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g  127 (160)
                      .+.|||+||+++|+++++..|+.++.||+.| ..+|.|+||||++|+++||+.||++||++|++||+..||+++||+++|
T Consensus        68 ~~~vyFdfd~~~l~~~~~~~L~~~a~~L~~~p~~~v~i~GhtD~~Gt~eYN~~Ls~rRA~aV~~yL~~~GV~~~ri~~vs  147 (173)
T PRK10802         68 NNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVS  147 (173)
T ss_pred             CCEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHEEEEE
T ss_conf             99799158852169989999999999999889917999874699884999999999999999999998499989968987


Q ss_pred             ECCCCCCCCCCCHHHHHCCCEEEEEE
Q ss_conf             07448989987877984299189999
Q gi|254780547|r  128 YGKEMPSVYGHDEDAYAKNRRAIVFL  153 (160)
Q Consensus       128 ~G~~~P~~~~~~~~~~~~NRRVei~i  153 (160)
                      |||++|++.++++++|++||||||+.
T Consensus       148 yGee~P~~~~~~e~~~~~NRR~~~vY  173 (173)
T PRK10802        148 YGKEKPAVLGHDEAAYAKNRRAVLVY  173 (173)
T ss_pred             ECCCCCCCCCCCHHHHHHCCCEEEEC
T ss_conf             66657689893988998769778869


No 4  
>PRK10510 putative outer membrane lipoprotein; Provisional
Probab=100.00  E-value=2.6e-37  Score=236.57  Aligned_cols=106  Identities=26%  Similarity=0.415  Sum_probs=101.6

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHCCCE-EEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             31002204752243247999999984302560-58999972266533332001113379999999985289860699997
Q gi|254780547|r   49 GDSVFFDTSSYSIRPADIQVLSNLGSWLEKHD-CDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTS  127 (160)
Q Consensus        49 ~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~-~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g  127 (160)
                      +..|+|++||+.|+|+++..|+.++.+|++++ .+|.|+||||++|+++||+.||++||++|++||+++||+++||.+.|
T Consensus       111 p~~I~F~~dsa~l~p~~~~~L~~vA~~L~~yp~~~V~I~GHTD~~G~~~yN~~LS~~RA~aV~~yL~~~GV~~~Ri~~~G  190 (219)
T PRK10510        111 PNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVVGYTDSTGSHDLNMRLSQQRADSVASALITQGVDASRIRTQG  190 (219)
T ss_pred             CCCCEEECCCHHCCHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHEEEEE
T ss_conf             88856618852129678999999999999889927999987689671999999999999999999998599956489998


Q ss_pred             ECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             074489899878779842991899997
Q gi|254780547|r  128 YGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       128 ~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      |||++|+++|+|+++|++||||||.|.
T Consensus       191 ~Ge~~Pia~n~t~~gra~NRRVEI~i~  217 (219)
T PRK10510        191 LGPANPIASNSTAEGKAQNRRVEITLS  217 (219)
T ss_pred             ECCCCCCCCCCCHHHHHHCCCEEEEEE
T ss_conf             766577899939778985398899995


No 5  
>COG2885 OmpA Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]
Probab=100.00  E-value=4.9e-36  Score=229.18  Aligned_cols=111  Identities=34%  Similarity=0.540  Sum_probs=104.2

Q ss_pred             HHHHCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCE-EEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             752031002204752243247999999984302560-5899997226653333200111337999999998528986069
Q gi|254780547|r   45 SSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHD-CDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRM  123 (160)
Q Consensus        45 ~~~~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~-~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri  123 (160)
                      .......|+|++||+.|+|+++..|+.++.+|++++ .+|.|+||||++|+++||+.||++||++|++||++.||++++|
T Consensus        78 ~~~~~~~v~F~~ds~~l~p~~~~~L~~~a~~L~~~p~~~i~V~GHTD~~Gs~~yN~~LS~rRA~aV~~~L~~~Gv~~~~i  157 (190)
T COG2885          78 ILNLPNDVLFDFDSSVLKPKAQATLDELAKYLKKNPITRILVEGHTDSTGSDEYNQALSERRAEAVADYLVSQGVVADRI  157 (190)
T ss_pred             HCCCCCEEEECCCCHHHCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCE
T ss_conf             00145406835883443989999999999999878997799975578879867876888999999999999849970117


Q ss_pred             EEEEECCCCCCCCCCCHHHHHCCCEEEEEEEE
Q ss_conf             99970744898998787798429918999971
Q gi|254780547|r  124 KVTSYGKEMPSVYGHDEDAYAKNRRAIVFLKG  155 (160)
Q Consensus       124 ~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~~  155 (160)
                      .++|||+++|+++|+|++||++||||||.|..
T Consensus       158 ~~~G~G~~~Pia~n~t~~gra~NRRVei~i~~  189 (190)
T COG2885         158 STVGYGEEKPIASNATEEGRAKNRRVEIKISP  189 (190)
T ss_pred             EEEECCCCCCCCCCCCCHHCCCCCCEEEEEEC
T ss_conf             89861645777889780010346747898627


No 6  
>PRK10808 outer membrane protein A; Reviewed
Probab=100.00  E-value=2.3e-33  Score=213.72  Aligned_cols=111  Identities=27%  Similarity=0.453  Sum_probs=101.8

Q ss_pred             HHCCEEEEECCCCCCCHHHHHHHHHHHHHHCC--C-EEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             20310022047522432479999999843025--6-05899997226653333200111337999999998528986069
Q gi|254780547|r   47 SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEK--H-DCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRM  123 (160)
Q Consensus        47 ~~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~--~-~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri  123 (160)
                      .+...|+|+|||++|+|++++.|+.++..|.+  + ..+|.|.||||+.|+++||+.||++||++|++||+++||+++||
T Consensus       221 tl~s~v~F~fdss~l~p~~~~~L~~~~~~l~~~~~~~~~i~v~GhtD~~G~~~yN~~LS~~RA~~V~~~l~~~Gi~~~~i  300 (347)
T PRK10808        221 TLKSDVLFNFNKATLKPEGQQALDQLYSQLSNLDPKDGSVVVLGYTDRIGSDAYNQALSERRAQSVVDYLISKGIPADKI  300 (347)
T ss_pred             CCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHE
T ss_conf             12442255157020586689999999999974587765189998369988878879999999999999999869984518


Q ss_pred             EEEEECCCCCCCCCCCHHHH---------HCCCEEEEEEEECC
Q ss_conf             99970744898998787798---------42991899997136
Q gi|254780547|r  124 KVTSYGKEMPSVYGHDEDAY---------AKNRRAIVFLKGCR  157 (160)
Q Consensus       124 ~~~g~G~~~P~~~~~~~~~~---------~~NRRVei~i~~~~  157 (160)
                      .+.|+||++|+++|.++++|         +.||||||.|+|.+
T Consensus       301 ~~~g~Ge~~pva~n~~~~~~~~~~li~c~a~nRRVei~v~g~~  343 (347)
T PRK10808        301 SARGMGESNPVTGNTCDNVKPRAALIDCLAPDRRVEIEVKGIK  343 (347)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCCHHHCCCCCCCEEEEEEEEE
T ss_conf             9998646688888977022443000102478873899998798


No 7  
>PRK09038 flagellar motor protein MotD; Reviewed
Probab=99.97  E-value=5.9e-31  Score=199.77  Aligned_cols=106  Identities=20%  Similarity=0.389  Sum_probs=98.7

Q ss_pred             HCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCC--CCCCC--CCHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             031002204752243247999999984302560589999722665--33332--00111337999999998528986069
Q gi|254780547|r   48 VGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADEL--GSRNS--SIALGLRRAYAVFNYFVARGISASRM  123 (160)
Q Consensus        48 ~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~--Gs~~y--N~~LS~~RA~aV~~~L~~~Gi~~~ri  123 (160)
                      +.+.++|+.||++|+|++++.|+.++..|+..+.+|.|+||||+.  .+..|  ||+||..||.+|+.||+..||+++||
T Consensus       135 l~~~~lF~~GSA~L~~~~~~lL~~ia~~L~~~~n~I~I~GHTD~~Pi~~~~~~sNWeLSaaRA~aV~r~L~~~Gi~p~Rl  214 (285)
T PRK09038        135 INSSLLFGSGDALLSDEAFAILEKVAEVLKPFPNPIHVEGFTDNVPIATAQFPSNWELSAARAASVVRLLADDGVAPSRL  214 (285)
T ss_pred             ECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHE
T ss_conf             56886868884324987999999999999843872899985788765556678648999999999999999759996787


Q ss_pred             EEEEECCCCCCCCCCCHHHHHCCCEEEEEE
Q ss_conf             999707448989987877984299189999
Q gi|254780547|r  124 KVTSYGKEMPSVYGHDEDAYAKNRRAIVFL  153 (160)
Q Consensus       124 ~~~g~G~~~P~~~~~~~~~~~~NRRVei~i  153 (160)
                      .++|||+.+|+++|+|+++|++||||||+|
T Consensus       215 ~~~Gygd~~P~~~N~t~egRa~NRRVeIvI  244 (285)
T PRK09038        215 AAVGYGEFQPVADNDTAEGRARNRRVVLVI  244 (285)
T ss_pred             EEEEECCCCCCCCCCCCHHHHHCCCEEEEE
T ss_conf             998765787689994800253078769999


No 8  
>cd07185 OmpA_C-like Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA. OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli outer membrane protein OmpA, the Escherichia coli lipoprotein PAL, Neisseria meningitdis RmpM, which interact with the outer membrane, as well as the Escherichia coli motor protein MotB, and the Vibrio flagellar motor proteins PomB and MotY, which interact with the inner membrane.
Probab=99.97  E-value=3e-30  Score=195.67  Aligned_cols=104  Identities=35%  Similarity=0.553  Sum_probs=99.8

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHHCCCE-EEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             1002204752243247999999984302560-589999722665333320011133799999999852898606999970
Q gi|254780547|r   50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKHD-CDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus        50 ~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~-~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      ..|||++||+.|++.+...|+.++.+|+.++ .+|.|.||||+.|+.+||+.||++||++|++||++.|+++++|.+.||
T Consensus         2 ~~v~F~~~s~~l~~~~~~~L~~ia~~l~~~~~~~v~v~GhtD~~G~~~~N~~LS~~RA~~V~~~L~~~Gi~~~ri~~~g~   81 (106)
T cd07185           2 ITIYFDFGSAELTPEAKPLLDKLAEVLKKNPDAKIRIEGHTDSRGSDAYNQELSERRAEAVADYLVSKGVDASRITAVGY   81 (106)
T ss_pred             EEEEECCCCCEECHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHEEEEEE
T ss_conf             89996899776198899999999999985899379999984899998998999999999999999984999899899997


Q ss_pred             CCCCCCCCCCCHHHHHCCCEEEEEE
Q ss_conf             7448989987877984299189999
Q gi|254780547|r  129 GKEMPSVYGHDEDAYAKNRRAIVFL  153 (160)
Q Consensus       129 G~~~P~~~~~~~~~~~~NRRVei~i  153 (160)
                      |+++|+.++.+++++++||||||++
T Consensus        82 G~~~p~~~~~~~~~~~~NRRVei~~  106 (106)
T cd07185          82 GESRPIASNDTEEGRAKNRRVEIVI  106 (106)
T ss_pred             CCCCCCCCCCCHHHHHHCCCEEEEC
T ss_conf             5557689990988998559889969


No 9  
>TIGR03350 type_VI_ompA type VI secretion system OmpA/MotB family protein. The flagellar motor protein MotB and the Gram-negative bacterial outer membrane protein OmpA share a region of sequence homology. This model describes a domain found fused to type VI secretion system homologs of the type IV system protein DotU (see model TIGR03349), with OmpA/MotB homology.
Probab=99.96  E-value=3.4e-30  Score=195.34  Aligned_cols=113  Identities=21%  Similarity=0.273  Sum_probs=102.9

Q ss_pred             HHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCC----CCCHHHHHHHHHHHHHHHHC
Q ss_conf             56787520310022047522432479999999843025605899997226653333----20011133799999999852
Q gi|254780547|r   41 QEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRN----SSIALGLRRAYAVFNYFVAR  116 (160)
Q Consensus        41 ~~~~~~~~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~Gs~~----yN~~LS~~RA~aV~~~L~~~  116 (160)
                      .+...+.++..++|++||+.|+|+++..|++++..|+..+..|.|+||||+.+...    .||+||.+||.+|.+||++.
T Consensus        21 ~~~v~l~l~~~~lF~~gsa~L~~~~~~~L~~va~~L~~~~~~I~I~GHTD~~~~~~~~~~~N~~LS~~RA~aV~~~L~~~  100 (137)
T TIGR03350        21 GDRSVVRLRGDELFASGSAEVRADFEPLLDRIAKALAAVPGRITVVGHTDNVPIRTSRFPSNWHLSEARAKAVADVLAQG  100 (137)
T ss_pred             CCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             99999995798718899632098799999999999970998599999838987778775104679999999999999972


Q ss_pred             CCCCEEEEEEEECCCCCCCCCCCHHHHHCCCEEEEEE
Q ss_conf             8986069999707448989987877984299189999
Q gi|254780547|r  117 GISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL  153 (160)
Q Consensus       117 Gi~~~ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i  153 (160)
                      |++++||.+.|||+++|+++|+++++|++||||||+|
T Consensus       101 Gi~~~rl~~~g~G~~~P~~~n~~~~~r~~NRRVEI~i  137 (137)
T TIGR03350       101 GVPAGRVRAEGRGDSEPIASNATAAGRAQNRRVEIDV  137 (137)
T ss_pred             CCCHHEEEEEECCCCCCCCCCCCHHHHHHCCEEEEEC
T ss_conf             9972408997012778679993977997549089979


No 10 
>PRK06742 flagellar motor protein MotS; Reviewed
Probab=99.96  E-value=5.4e-29  Score=188.38  Aligned_cols=106  Identities=23%  Similarity=0.456  Sum_probs=97.6

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCC--CCC--CCCCHHHHHHHHHHHHHHHH-CCCCCEEE
Q ss_conf             31002204752243247999999984302560589999722665--333--32001113379999999985-28986069
Q gi|254780547|r   49 GDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADEL--GSR--NSSIALGLRRAYAVFNYFVA-RGISASRM  123 (160)
Q Consensus        49 ~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~--Gs~--~yN~~LS~~RA~aV~~~L~~-~Gi~~~ri  123 (160)
                      .+.++|+.||++|+|++++.|+.+++.|+..+..|.|+||||+.  .+.  ..||+||..||.+|.+||++ .||+++|+
T Consensus       114 ~~~~lF~~Gsa~l~p~~~~~L~~la~~l~~~~~~I~I~GHTD~~pi~~~~~~sNWeLSsaRA~~V~r~l~~~~gi~~~rl  193 (225)
T PRK06742        114 VDNLIFDTGDANVKPEAKEIISQLVGFFQSVPNPIVVEGHTDSRPIHNDKFPSNWELSSARAANMIHHLIEVYNVDDKRL  193 (225)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEE
T ss_conf             78777689843239669999999999996599708999967887666778886499999999999999998369993148


Q ss_pred             EEEEECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             9997074489899878779842991899997
Q gi|254780547|r  124 KVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       124 ~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      .++|||+.+|+.+|+|+++|++||||||+|+
T Consensus       194 ~~~Gygd~~P~~~n~t~e~ra~NRRVeI~i~  224 (225)
T PRK06742        194 AAVGYADTKPVVPNDSPQNWEKNRRVVIYIK  224 (225)
T ss_pred             EEEEECCCCCCCCCCCHHHHHHCCCEEEEEE
T ss_conf             9986557761799949446853796699983


No 11 
>PRK09040 hypothetical protein; Provisional
Probab=99.96  E-value=6.1e-29  Score=188.10  Aligned_cols=108  Identities=28%  Similarity=0.428  Sum_probs=96.5

Q ss_pred             HHCCEEEEECCCCCCCHHHHHHHHHHHHHHCC----CEEEEEEEEECCCC----CCCCC--CCHHHHHHHHHHHHHHHHC
Q ss_conf             20310022047522432479999999843025----60589999722665----33332--0011133799999999852
Q gi|254780547|r   47 SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEK----HDCDFLIEGHADEL----GSRNS--SIALGLRRAYAVFNYFVAR  116 (160)
Q Consensus        47 ~~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~----~~~~i~I~GhtD~~----Gs~~y--N~~LS~~RA~aV~~~L~~~  116 (160)
                      .+...++|+.||+.|.|+++..|++++..|+.    ++..|.|+||||+.    ++..|  ||+||.+||.+|.+||++.
T Consensus        86 ~i~~~vlF~~gsa~L~p~~~~~L~~ia~~L~~~~~~~~~~i~V~GhTD~~pi~~~~~~f~sNw~LS~~RA~~V~~~L~~~  165 (215)
T PRK09040         86 GISGSVLFALNSDQLQPEGRELLKSLAGPLAAYLRARDEILMVSGFTDDQPVRAGNRRFADNWELSAQRALTVTRALIDA  165 (215)
T ss_pred             ECCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             60564367689640083269999999999998744798659987348997676778888978999999999999999986


Q ss_pred             CCCCEEEEEEEECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             89860699997074489899878779842991899997
Q gi|254780547|r  117 GISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       117 Gi~~~ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      ||+++||.+.|||+++|+++|+|+++|++||||||.+=
T Consensus       166 gv~~~rl~~~g~G~~~P~~~n~t~~~ra~NRRVeI~~~  203 (215)
T PRK09040        166 GVPASSVFAAAFGSEQPVSSNADEEGRAKNRRVEIAPV  203 (215)
T ss_pred             CCCHHHEEEEEECCCCCCCCCCCHHHHHHCCCEEEEEE
T ss_conf             99978958988657687899949889987698789984


No 12 
>PRK06925 flagellar motor protein MotS; Reviewed
Probab=99.95  E-value=1.2e-28  Score=186.36  Aligned_cols=107  Identities=25%  Similarity=0.410  Sum_probs=97.3

Q ss_pred             HCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCC--CCC--CCCHHHHHHHHHHHHHHHH-CCCCCEE
Q ss_conf             0310022047522432479999999843025605899997226653--333--2001113379999999985-2898606
Q gi|254780547|r   48 VGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELG--SRN--SSIALGLRRAYAVFNYFVA-RGISASR  122 (160)
Q Consensus        48 ~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~G--s~~--yN~~LS~~RA~aV~~~L~~-~Gi~~~r  122 (160)
                      +.+.++|+.||++|+++++..|+.++..|+..+..|.|+||||+..  +..  .||+||..||.+|.+||++ .||+++|
T Consensus       116 l~~~~lF~~Gsa~l~~~~~~~L~~ia~~l~~~~~~I~V~GHTD~~p~~~~~~~sNWeLS~aRA~~V~~~li~~~gi~~~r  195 (230)
T PRK06925        116 LQEAVLFDTGEADVLKNAEPLLHKIAVLLKTIPNDIQVEGHTDSRPISTYRYPSNWELSAARASSVIRYFTSKEKLDSSR  195 (230)
T ss_pred             ECCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf             68987878896534877999999999999739963899874487655556788538999999999999999835998467


Q ss_pred             EEEEEECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             99997074489899878779842991899997
Q gi|254780547|r  123 MKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       123 i~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      +.++|||+.+|+++|+|+++|++||||||+|.
T Consensus       196 l~~~Gygd~~P~~~n~t~e~ra~NRRVeI~i~  227 (230)
T PRK06925        196 FIAVGYADTKPVKDNKTEEHMKENRRVEIVIK  227 (230)
T ss_pred             EEEEEECCCCCCCCCCCCCHHHCCCCEEEEEE
T ss_conf             89987657874899958320321886799984


No 13 
>PRK07734 motB flagellar motor protein MotB; Reviewed
Probab=99.95  E-value=3.1e-28  Score=184.02  Aligned_cols=107  Identities=21%  Similarity=0.402  Sum_probs=96.1

Q ss_pred             HCCEEEEECCCCCCCHHHHHHHHHHHHHHC-CCEEEEEEEEECCCC--CCCCC--CCHHHHHHHHHHHHHHHH-CCCCCE
Q ss_conf             031002204752243247999999984302-560589999722665--33332--001113379999999985-289860
Q gi|254780547|r   48 VGDSVFFDTSSYSIRPADIQVLSNLGSWLE-KHDCDFLIEGHADEL--GSRNS--SIALGLRRAYAVFNYFVA-RGISAS  121 (160)
Q Consensus        48 ~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~-~~~~~i~I~GhtD~~--Gs~~y--N~~LS~~RA~aV~~~L~~-~Gi~~~  121 (160)
                      +.+.++|+.||+.|+|+++..|..++..|. .++..|.|+||||+.  .+..|  ||+||..||.+|.+||+. .|++++
T Consensus       140 l~~~~lF~~GsA~l~~~~~~lL~~ia~~l~~~~~~~I~V~GHTD~~Pi~~~~~~sNWeLSaaRA~sV~~~L~~~~gi~~~  219 (259)
T PRK07734        140 ILDNILFDSGKADVRLEDLPLAKEMSNLLVSNPPRNITISGHTDNVPIANAQFASNWELSVMRAVNFMQVLLENKELDPE  219 (259)
T ss_pred             ECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             53776668898756977999999999999857996389998557766667767644899999999999999981699956


Q ss_pred             EEEEEEECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             699997074489899878779842991899997
Q gi|254780547|r  122 RMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       122 ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      ++.+.|||+.+|+++|+|+++|++||||||+|=
T Consensus       220 rl~v~G~gd~~Pi~~n~t~egra~NRRVeI~il  252 (259)
T PRK07734        220 KFSAKGYGEYKPIASNDTAEGRAKNRRVEVLIL  252 (259)
T ss_pred             EEEEEEECCCCCCCCCCCCCHHHCCCCEEEEEE
T ss_conf             799998557874899969201421786799995


No 14 
>PRK08944 motB flagellar motor protein MotB; Reviewed
Probab=99.95  E-value=4e-28  Score=183.38  Aligned_cols=108  Identities=23%  Similarity=0.329  Sum_probs=97.7

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCC--CCCCC--CCHHHHHHHHHHHHHHHH-CCCCCEEEE
Q ss_conf             1002204752243247999999984302560589999722665--33332--001113379999999985-289860699
Q gi|254780547|r   50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADEL--GSRNS--SIALGLRRAYAVFNYFVA-RGISASRMK  124 (160)
Q Consensus        50 ~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~--Gs~~y--N~~LS~~RA~aV~~~L~~-~Gi~~~ri~  124 (160)
                      +..+|+.||+.|+|.+++.|+.++..|+..+.+|.|+||||+.  .+..|  ||+||..||.+|+.||+. .|++++||.
T Consensus       182 d~~lF~~GSa~l~p~~~~lL~~ia~~l~~~~n~I~I~GHTD~~p~~~~~~~sNWeLSaaRA~~v~r~L~~~~gi~~~rl~  261 (305)
T PRK08944        182 EKGSFPSGSAFLQPKFKPLVRKIGELLKDVPGIITVSGHTDNMPISSELYRSNWDLSSARAVAVAHELLKVKGFDPSRLK  261 (305)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEE
T ss_conf             87675788642487689999999999973896279974157776655567874899999999999999980698943489


Q ss_pred             EEEECCCCCCCCCCCHHHHHCCCEEEEEEEECC
Q ss_conf             997074489899878779842991899997136
Q gi|254780547|r  125 VTSYGKEMPSVYGHDEDAYAKNRRAIVFLKGCR  157 (160)
Q Consensus       125 ~~g~G~~~P~~~~~~~~~~~~NRRVei~i~~~~  157 (160)
                      ++|||+.+|+++|+++++|++||||||+|---+
T Consensus       262 v~G~ad~~Pl~~n~t~e~ra~NRRVeI~il~~~  294 (305)
T PRK08944        262 VVGMADTQPLVPNDSPENRARNRRVEISIEQGK  294 (305)
T ss_pred             EEEECCCCCCCCCCCHHHHHCCCCEEEEEECCC
T ss_conf             998657874899978013411887799993798


No 15 
>PRK08126 hypothetical protein; Provisional
Probab=99.95  E-value=1.9e-27  Score=179.38  Aligned_cols=103  Identities=20%  Similarity=0.309  Sum_probs=96.9

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCC--CCCCC--CCHHHHHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             02204752243247999999984302560589999722665--33332--001113379999999985289860699997
Q gi|254780547|r   52 VFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADEL--GSRNS--SIALGLRRAYAVFNYFVARGISASRMKVTS  127 (160)
Q Consensus        52 v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~--Gs~~y--N~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g  127 (160)
                      -+|..||+.|+|++.+.|.+++..|++-+-+|.|+||||+.  .+..|  ||.||..||.+|.++|...|++++||.+.|
T Consensus       321 ~lF~sGsA~l~p~~~pll~rIa~~l~~~~G~I~V~GHTDn~Pi~s~~f~SNw~LS~aRA~~V~~~L~~~~~~~~R~~a~G  400 (428)
T PRK08126        321 AMFAPGGATVNPAMGPLINKIAREIARVPGKVTVTGHTDNQPIRSAQFASNLVLSEERATQVAQMLQSAGVPASRLEAVG  400 (428)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
T ss_conf             88787761106447999999999983799818998858998887888797499999999999999985599976368872


Q ss_pred             ECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             074489899878779842991899997
Q gi|254780547|r  128 YGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       128 ~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      +|+++|+++|+|++||++||||||+|.
T Consensus       401 ~gd~~Pia~N~T~~gRa~NRRVEI~l~  427 (428)
T PRK08126        401 KGDADPVGDNRTPQGRAQNRRVEITVA  427 (428)
T ss_pred             ECCCCCCCCCCCHHHHHHCCCEEEEEE
T ss_conf             178899999989556753582478950


No 16 
>PRK08457 motB flagellar motor protein MotB; Reviewed
Probab=99.95  E-value=7.5e-28  Score=181.79  Aligned_cols=106  Identities=24%  Similarity=0.391  Sum_probs=92.5

Q ss_pred             HHCCEEEEECCCCCCC-HHHHHHHHHHHHHHCCC--EEEEEEEEECCCC--CCCCC--CCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             2031002204752243-24799999998430256--0589999722665--33332--0011133799999999852898
Q gi|254780547|r   47 SVGDSVFFDTSSYSIR-PADIQVLSNLGSWLEKH--DCDFLIEGHADEL--GSRNS--SIALGLRRAYAVFNYFVARGIS  119 (160)
Q Consensus        47 ~~~~~v~F~~~s~~L~-~~~~~~L~~ia~~l~~~--~~~i~I~GhtD~~--Gs~~y--N~~LS~~RA~aV~~~L~~~Gi~  119 (160)
                      .+.+.++|+.||++|. +.....|+.++..|+..  ..+|.|+||||+.  .+..|  ||+||..||.+|..||+..||+
T Consensus       116 ~l~~~~lF~~GsA~l~~~~~~~~L~~ia~il~~lp~~~~I~V~GHTD~~Pi~~~~f~SNWELSaaRA~~V~r~Li~~Gi~  195 (251)
T PRK08457        116 KLPSNLLFENGSAEIINQDMMLYLKRIAKIIQKLPKRVKIEVRGYTDNSPLNKTRYKSSYELAANRAYNVMKVLIQYGIN  195 (251)
T ss_pred             EECCCCCCCCCCCEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             80687545798801168039999999999998489974599871589997777888873999999999999999985998


Q ss_pred             CEEEEEEEECCCCCCCCCCCHHHHHCCCEEEEEEEE
Q ss_conf             606999970744898998787798429918999971
Q gi|254780547|r  120 ASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLKG  155 (160)
Q Consensus       120 ~~ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~~  155 (160)
                      |+||.++|||+.+|+++|   ++|++||||||+|.-
T Consensus       196 p~Rl~a~Gygd~~Pi~~N---e~ra~NRRVeI~i~~  228 (251)
T PRK08457        196 PNRLSFSSYGSNNPIAPN---ENRLKNNRVEIFFKV  228 (251)
T ss_pred             HHHEEEEEECCCCCCCCC---CCHHHCCCEEEEEEC
T ss_conf             789789853278879899---765563957999942


No 17 
>PRK07033 hypothetical protein; Provisional
Probab=99.95  E-value=4.6e-27  Score=177.24  Aligned_cols=107  Identities=23%  Similarity=0.238  Sum_probs=98.7

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCC--CCCCC--CCHHHHHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             02204752243247999999984302560589999722665--33332--001113379999999985289860699997
Q gi|254780547|r   52 VFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADEL--GSRNS--SIALGLRRAYAVFNYFVARGISASRMKVTS  127 (160)
Q Consensus        52 v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~--Gs~~y--N~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g  127 (160)
                      -+|+.||++|++++...|.+++..|++-+.+|.|+||||+.  .+..|  ||+||..||.+|.++|...|++++|+.++|
T Consensus       318 ~lF~sGsa~l~~~~~~ll~~ia~~l~~~~g~i~V~GHTDn~Pi~s~~f~SNw~LS~aRA~~V~~~l~~~~~~~~R~~a~G  397 (429)
T PRK07033        318 GLFASASTSVRDRYQPVLLRVADALNQVKGNVLVTGYSDNRPIRTARFPSNWHLSQARAQAVRALLAARLGDPERVTAEG  397 (429)
T ss_pred             CCCCCCCHHHCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
T ss_conf             88788661008668999999999984799808998838998887788897599999999999999986499977379976


Q ss_pred             ECCCCCCCCCCCHHHHHCCCEEEEEEEECCC
Q ss_conf             0744898998787798429918999971368
Q gi|254780547|r  128 YGKEMPSVYGHDEDAYAKNRRAIVFLKGCRA  158 (160)
Q Consensus       128 ~G~~~P~~~~~~~~~~~~NRRVei~i~~~~~  158 (160)
                      +|+++|+++|+|+++|++||||||+|=..-|
T Consensus       398 ~gd~~Pia~N~t~~gRa~NRRVEI~ll~~p~  428 (429)
T PRK07033        398 RGDSDPVAPNDSPEGRARNRRVEITLMVAPG  428 (429)
T ss_pred             ECCCCCCCCCCCHHHHHHCCCEEEEEECCCC
T ss_conf             3788888989882347546817999963899


No 18 
>PRK09039 hypothetical protein; Validated
Probab=99.94  E-value=3.6e-27  Score=177.81  Aligned_cols=106  Identities=27%  Similarity=0.442  Sum_probs=94.5

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHCC-----C---EEEEEEEEECCCC-----CCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             310022047522432479999999843025-----6---0589999722665-----33332001113379999999985
Q gi|254780547|r   49 GDSVFFDTSSYSIRPADIQVLSNLGSWLEK-----H---DCDFLIEGHADEL-----GSRNSSIALGLRRAYAVFNYFVA  115 (160)
Q Consensus        49 ~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~-----~---~~~i~I~GhtD~~-----Gs~~yN~~LS~~RA~aV~~~L~~  115 (160)
                      +..|+|+.||++|.|+++..|++++..+.+     |   +.-|.|+||||+.     |...+||+||..||.+|..||+.
T Consensus       223 ~SevLF~~gsa~l~~~gk~~l~~ia~~l~~i~~~Ip~~i~wilrVeGHTD~~pi~~~~~f~sNweLS~~RA~sV~~~L~~  302 (343)
T PRK09039        223 QSEVLFPTGSAELNPEGQAEIAKLAAALIQLAKEIPPEINWVLRVDGHTDNVPLSGTGRFRDNWELSSARAISVVKYLIA  302 (343)
T ss_pred             CCCCCCCCCCCHHCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             03323168840106658999999999999987637501461377504577878888999997599999999999999997


Q ss_pred             CCCCCEEEEEEEECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             289860699997074489899878779842991899997
Q gi|254780547|r  116 RGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       116 ~Gi~~~ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      .|+||+|+.+.|||+.+|++++++++++++||||||.+.
T Consensus       303 ~gv~~~rl~a~G~g~~~Pl~~~~t~e~ra~NRRIEiklt  341 (343)
T PRK09039        303 LGVPANRLVAAGFGEYQPLDPGDTPEARARNRRIELKLT  341 (343)
T ss_pred             CCCCHHHEEEECCCCCCCCCCCCCHHHHHHCCCEEEEEC
T ss_conf             699888936520466788999959657973795579827


No 19 
>PRK06667 motB flagellar motor protein MotB; Validated
Probab=99.94  E-value=4.8e-27  Score=177.13  Aligned_cols=105  Identities=24%  Similarity=0.385  Sum_probs=92.6

Q ss_pred             CEEEEECCCCCCC-HHHHHHHHHHHHHHCC---CEEEEEEEEECCCCCC-----CCCCCHHHHHHHHHHHHHHHHCC-CC
Q ss_conf             1002204752243-2479999999843025---6058999972266533-----33200111337999999998528-98
Q gi|254780547|r   50 DSVFFDTSSYSIR-PADIQVLSNLGSWLEK---HDCDFLIEGHADELGS-----RNSSIALGLRRAYAVFNYFVARG-IS  119 (160)
Q Consensus        50 ~~v~F~~~s~~L~-~~~~~~L~~ia~~l~~---~~~~i~I~GhtD~~Gs-----~~yN~~LS~~RA~aV~~~L~~~G-i~  119 (160)
                      +.++|+.|+++|. +++++.|..++..+..   .+..|.|+||||+.-.     ...||+||..||.+|..||++.| |+
T Consensus       127 ~~~lF~~gsa~l~~~~~~~~l~~l~~il~~~~~~~~~I~VeGHTD~~pi~~~~~~~sNWeLSsaRA~~V~~~l~~~g~i~  206 (254)
T PRK06667        127 SDAFFYPGSADVKLEENRDLIQKLASFIGFLDLAGYNFRIEGHTDNVDVNPEGAWKSNWELSGARAVNMLEYILNYEDQS  206 (254)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             68561799731264748999999999998456757428999437877668788888628899999999999999817999


Q ss_pred             CEEEEEEEECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             60699997074489899878779842991899997
Q gi|254780547|r  120 ASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       120 ~~ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      +.|+.+.|||+.+|+++|+|+++|++||||||+|-
T Consensus       207 ~~rl~v~Gygd~~P~~~n~t~e~ra~NRRVeI~Il  241 (254)
T PRK06667        207 ESWFEVSGFGGSRPLATDDTPEGRAYNRRIDIVIL  241 (254)
T ss_pred             CCEEEEEEECCCCCCCCCCCHHHHHHCCCEEEEEE
T ss_conf             54599985458876899959668840897699995


No 20 
>COG1360 MotB Flagellar motor protein [Cell motility and secretion]
Probab=99.94  E-value=2e-26  Score=173.56  Aligned_cols=105  Identities=29%  Similarity=0.443  Sum_probs=96.1

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHHCCCEE-EEEEEEECCCC---CCCCCCCHHHHHHHHHHHHHHHHCC-CCCEEEE
Q ss_conf             10022047522432479999999843025605-89999722665---3333200111337999999998528-9860699
Q gi|254780547|r   50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKHDC-DFLIEGHADEL---GSRNSSIALGLRRAYAVFNYFVARG-ISASRMK  124 (160)
Q Consensus        50 ~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~-~i~I~GhtD~~---Gs~~yN~~LS~~RA~aV~~~L~~~G-i~~~ri~  124 (160)
                      +..+|+.+++.+.++.+..|.+++..|...+. .|.|+||||++   ++...||+||..||.+|.++|++.| ++++++.
T Consensus       132 ~~~~F~~gsa~~~~~~~~~l~~ia~~l~~~~~~~I~I~GHTDn~p~~~~~~sNWeLS~aRA~~v~~~L~~~g~~~~~~~~  211 (244)
T COG1360         132 DSLMFASGSAVVQPEFRDLLLKIAKLLADIPNGNIRIEGHTDNVPIKGSFYSNWELSAARAQSVVRVLINGGLVEAKRLS  211 (244)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEE
T ss_conf             44464677521276679999999999872679828998658997667788850888999999999999974899856689


Q ss_pred             EEEECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             997074489899878779842991899997
Q gi|254780547|r  125 VTSYGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       125 ~~g~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      +.|||+++|+++|+|+++|++||||||.|.
T Consensus       212 ~~G~gd~~Pva~n~t~~~ra~NRRVeI~i~  241 (244)
T COG1360         212 VVGYADTRPLADNDTAEGRAKNRRVEILIL  241 (244)
T ss_pred             EEECCCCCCCCCCCCHHHHHHCCEEEEEEE
T ss_conf             971254776788988134765783799983


No 21 
>pfam00691 OmpA OmpA family. The Pfam entry also includes MotB and related proteins which are not included in the Prosite family.
Probab=99.92  E-value=3.1e-25  Score=166.63  Aligned_cols=95  Identities=36%  Similarity=0.531  Sum_probs=90.9

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCCC--EEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECC
Q ss_conf             220475224324799999998430256--058999972266533332001113379999999985289860699997074
Q gi|254780547|r   53 FFDTSSYSIRPADIQVLSNLGSWLEKH--DCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGK  130 (160)
Q Consensus        53 ~F~~~s~~L~~~~~~~L~~ia~~l~~~--~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G~  130 (160)
                      +|++||+.|+++++..|+.++.+|+.+  ..+|.|+||||..|+..||+.||.+||++|++||++.||+++||.+.|||+
T Consensus         1 ~F~~~s~~L~~~~~~~L~~~a~~l~~~~~~~~v~I~GhtD~~g~~~~N~~LS~~RA~~V~~~L~~~Gv~~~ri~~~g~G~   80 (97)
T pfam00691         1 LFDPGSAELTAEARETLDRLAEVLKAPELKIAIKIEGHTDSRGSAKYNWELSARRAQAVANYLVNHGIPPSRISVEGYGE   80 (97)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHEEEEEECC
T ss_conf             99998121398999999999999971899728999999899998889999999999999999998599978989988757


Q ss_pred             CCCCCCCCCHHHHHCCC
Q ss_conf             48989987877984299
Q gi|254780547|r  131 EMPSVYGHDEDAYAKNR  147 (160)
Q Consensus       131 ~~P~~~~~~~~~~~~NR  147 (160)
                      ++|+.++.+++++++||
T Consensus        81 ~~Pi~~~~~~~~r~~NR   97 (97)
T pfam00691        81 SQPLASNDSDEGRAKNR   97 (97)
T ss_pred             CCCCCCCCCHHHHHHCC
T ss_conf             68889992999997475


No 22 
>PRK09041 motB flagellar motor protein MotB; Validated
Probab=99.90  E-value=8.4e-24  Score=158.32  Aligned_cols=100  Identities=22%  Similarity=0.261  Sum_probs=90.5

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCC---CC-C-CCCHHHHHHHHHHHHHHHHCCCCCEEEE-E
Q ss_conf             022047522432479999999843025605899997226653---33-3-2001113379999999985289860699-9
Q gi|254780547|r   52 VFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELG---SR-N-SSIALGLRRAYAVFNYFVARGISASRMK-V  125 (160)
Q Consensus        52 v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~G---s~-~-yN~~LS~~RA~aV~~~L~~~Gi~~~ri~-~  125 (160)
                      .+|+.||+.|+|.+++.|..++..|+..+.+|.|+||||++.   +. . .||+||..||.+|+.+|+..||+++||. +
T Consensus       168 ~mF~sGSA~l~p~~~~lL~~Ia~vL~~~~n~I~I~GHTD~~P~~~~~~~~SNWeLSaaRA~aarr~L~~~Gl~~~Ri~~V  247 (317)
T PRK09041        168 PMFATGSAEVEPYMRDILREIAPVLNDVPNRISLSGHTDATPYAGGEKGYSNWELSADRANASRRELVAGGMDEGKVLRV  247 (317)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHEEEE
T ss_conf             67678866458889999999999997257856998755877756788889951558999999999999849997687899


Q ss_pred             EEECCCCCCCCCCCHHHHHCCCEEEEEE
Q ss_conf             9707448989987877984299189999
Q gi|254780547|r  126 TSYGKEMPSVYGHDEDAYAKNRRAIVFL  153 (160)
Q Consensus       126 ~g~G~~~P~~~~~~~~~~~~NRRVei~i  153 (160)
                      +||++.+|+.+++...  +.||||||+|
T Consensus       248 ~G~AD~~Pl~~~dP~~--a~NRRI~I~v  273 (317)
T PRK09041        248 VGLASTMLLDKKDPLN--PVNRRISIVV  273 (317)
T ss_pred             EEECCCCCCCCCCCCC--CCCCCEEEEE
T ss_conf             9835677589999876--5468579999


No 23 
>PRK06778 hypothetical protein; Validated
Probab=99.90  E-value=7.1e-24  Score=158.75  Aligned_cols=100  Identities=21%  Similarity=0.305  Sum_probs=89.4

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCC--CCCC-CCCHHHHHHHHHHHHHHHHCCCCCEEE-EEEE
Q ss_conf             02204752243247999999984302560589999722665--3333-200111337999999998528986069-9997
Q gi|254780547|r   52 VFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADEL--GSRN-SSIALGLRRAYAVFNYFVARGISASRM-KVTS  127 (160)
Q Consensus        52 v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~--Gs~~-yN~~LS~~RA~aV~~~L~~~Gi~~~ri-~~~g  127 (160)
                      .+|+.||+.|+|.++..|..++..|+..+.+|.|+||||+.  .+.. .||+||..||.+|+.+|+..|++++|| .+.|
T Consensus       154 ~mF~~GSa~l~p~~~~lL~~ia~vL~~~~n~I~I~GHTD~~Pi~~~~ySNWELSa~RA~avrr~L~~~Gl~~~ri~~V~G  233 (289)
T PRK06778        154 NMFERGSAQIMPFFKRLLVELAPVFDSLDNKIIITGHTDAMAYKNNIYNNWNLSGDRALSARRVLEEAGMPEDKVMQVSA  233 (289)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHEEEEEE
T ss_conf             78288987568789999999999986289538997405777777888996066899999999999985999768889998


Q ss_pred             ECCCCCCCCCCCHHHHHCCCEEEEEE
Q ss_conf             07448989987877984299189999
Q gi|254780547|r  128 YGKEMPSVYGHDEDAYAKNRRAIVFL  153 (160)
Q Consensus       128 ~G~~~P~~~~~~~~~~~~NRRVei~i  153 (160)
                      |++..|+.+++..  .+.||||||+|
T Consensus       234 ~Ad~~p~~~~dP~--~~~NRRI~I~v  257 (289)
T PRK06778        234 MADQMLLDAKNPQ--SAGNRRIEIMV  257 (289)
T ss_pred             ECCCCCCCCCCCC--CCCCCCEEEEE
T ss_conf             4577778999987--65468579999


No 24 
>PRK05996 motB flagellar motor protein MotB; Validated
Probab=99.85  E-value=3.4e-21  Score=143.28  Aligned_cols=103  Identities=22%  Similarity=0.364  Sum_probs=92.5

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCC--CCCCC-CCHHHHHHHHHHHHHHHHCCCCCEEE-EEEE
Q ss_conf             02204752243247999999984302560589999722665--33332-00111337999999998528986069-9997
Q gi|254780547|r   52 VFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADEL--GSRNS-SIALGLRRAYAVFNYFVARGISASRM-KVTS  127 (160)
Q Consensus        52 v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~--Gs~~y-N~~LS~~RA~aV~~~L~~~Gi~~~ri-~~~g  127 (160)
                      -+|+.||+.++|.....|..|+..|...+.+|.|.||||++  .+..| ||+||..||++.+..|+..|++++|| .++|
T Consensus       324 ~MF~~GSA~p~p~~~~lL~~Ia~vL~~~pn~I~I~GHTDa~Pf~~~~y~NWeLSa~RA~aARr~L~~gGl~~~RI~rV~G  403 (431)
T PRK05996        324 GMFAIGSAVPRAELVLAMEKIGQLLAEQPGAVIIRGHTDARPFKSATYDNWRLSTARAQMAYYMLVRGGLDEKRILRVEG  403 (431)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHEEEEEE
T ss_conf             88477977568899999999999996389817998756887777889984211189999999999985998546667887


Q ss_pred             ECCCCCCCCCCCHHHHHCCCEEEEEEEEC
Q ss_conf             07448989987877984299189999713
Q gi|254780547|r  128 YGKEMPSVYGHDEDAYAKNRRAIVFLKGC  156 (160)
Q Consensus       128 ~G~~~P~~~~~~~~~~~~NRRVei~i~~~  156 (160)
                      |+..+|+.+.+...  +.||||||.||.-
T Consensus       404 ~ADr~p~~~~dP~a--~~NRRIeILlr~~  430 (431)
T PRK05996        404 YADRRPKLPNDPNA--AANRRIEILIQAK  430 (431)
T ss_pred             ECCCCCCCCCCCCC--CCCCEEEEEEECC
T ss_conf             13567688899988--6457489997058


No 25 
>PRK12799 motB flagellar motor protein MotB; Reviewed
Probab=99.79  E-value=5.1e-19  Score=130.63  Aligned_cols=102  Identities=22%  Similarity=0.326  Sum_probs=90.4

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCC----CCCCC-CCHHHHHHHHHHHHHHHHCCCCCEEE-E
Q ss_conf             002204752243247999999984302560589999722665----33332-00111337999999998528986069-9
Q gi|254780547|r   51 SVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADEL----GSRNS-SIALGLRRAYAVFNYFVARGISASRM-K  124 (160)
Q Consensus        51 ~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~----Gs~~y-N~~LS~~RA~aV~~~L~~~Gi~~~ri-~  124 (160)
                      +-+|+.||+.|.|.++..|..++..|++-+.+|.|.||||+.    |...| ||+||..||++.+..|+..|++.++| .
T Consensus       157 RPMF~~GSA~l~Py~rdIL~aIApvLn~vPNkIsISGHTDA~PYa~G~~gYSNWELSADRANAARReLvaGGm~e~KvlR  236 (424)
T PRK12799        157 RPMFKMGSAQVEPYMRDILRAIAPILNDIPNKLSLSGHTDDLPYARGERGYSNWELSADRANASRRELLAGGLDEGKILR  236 (424)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEE
T ss_conf             97601277757889999999999998658983488631688555689988765622366687999999976898113678


Q ss_pred             EEEECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             997074489899878779842991899997
Q gi|254780547|r  125 VTSYGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       125 ~~g~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                      ++|+..+-|+...+..  .+.|||+.|+|=
T Consensus       237 VvGmAst~~ld~~~p~--~PvNRRISIiVL  264 (424)
T PRK12799        237 VVGMASTMRLKEQASD--DPVNRRISILVL  264 (424)
T ss_pred             EEECCCCCCCCCCCCC--CCCCCEEEEEEE
T ss_conf             9851213414667999--854365789996


No 26 
>PRK07034 hypothetical protein; Provisional
Probab=99.60  E-value=2.2e-15  Score=109.65  Aligned_cols=104  Identities=22%  Similarity=0.291  Sum_probs=88.4

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCC--CCC--CCCHHHHHHHHHHHHHHHHCCCC-----C-
Q ss_conf             0022047522432479999999843025605899997226653--333--20011133799999999852898-----6-
Q gi|254780547|r   51 SVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELG--SRN--SSIALGLRRAYAVFNYFVARGIS-----A-  120 (160)
Q Consensus        51 ~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~G--s~~--yN~~LS~~RA~aV~~~L~~~Gi~-----~-  120 (160)
                      .=.|+.+++.|.++++..+..+...+..-+-.++|.||||++-  +.+  .|+.||+.||..|++.|.+.-.+     + 
T Consensus       386 DGaF~~g~A~l~~~f~~nieRLG~A~ApwpGdleViGHTD~rPiRss~fp~N~~LSeARA~~VAD~lR~s~~~~~~~~~~  465 (565)
T PRK07034        386 DGAFDVGKANVRADFMHNIERLGLAFAPWPGDLEVIGHTDSRPIRTSEFPDNQALSEARARNVADELRKTALPGGARAPE  465 (565)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCH
T ss_conf             87644341203698898899986763688886577514788764378898407678888878999999853435445712


Q ss_pred             ----EEEEEEEECCCCCCCCCCCHHHHHCCCEEEEEEE
Q ss_conf             ----0699997074489899878779842991899997
Q gi|254780547|r  121 ----SRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK  154 (160)
Q Consensus       121 ----~ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~  154 (160)
                          ..|+.+|.|+.+|++.+.|++++..||||+|.-+
T Consensus       466 ~~~QR~i~~~GrGd~~Pldt~~T~~~~~RNRRVDiLWK  503 (565)
T PRK07034        466 NAVQRNIEYSGRGDAQPIDTAKTAAAYERNRRVDVLWK  503 (565)
T ss_pred             HHHHHHEEEECCCCCCCCCCCCHHHHHHHCCCCEEEEE
T ss_conf             66652000004788886654005777752653015665


No 27 
>PRK10834 hypothetical protein; Provisional
Probab=93.70  E-value=0.11  Score=30.39  Aligned_cols=119  Identities=12%  Similarity=0.180  Sum_probs=65.2

Q ss_pred             CCHHHHHHHHH--HHHHHHHHCCCCCCCCCCCCCCCCC-CCHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             90369999999--9999865024566666566554444-20125678752031002204752243247999999984302
Q gi|254780547|r    1 MQYSTIFIILS--AITMMSISGIDNLDTKISSPDTVLN-ESSLQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLE   77 (160)
Q Consensus         1 M~~~~i~i~l~--a~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~   77 (160)
                      |.++.++.++.  ++.++.+-+++..-........... ........+..++..-++..|  .+++-...-|+.-++..+
T Consensus         1 m~Krl~~~~~~~~~~~~~~i~~~d~wv~~~~~~~iy~~i~~vP~~~valVLGtak~~~~G--~pn~~~~~RldaA~~LY~   78 (239)
T PRK10834          1 MLKRVFYSLLVLIGLLLLTVLGLDRWMSWKTAPYIYDELQDLPYRQVGVVLGTAKYYRTG--VINQYYRYRIQGAINAYN   78 (239)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCHHHCCCCCEEEEECCCCCCCCC--CCCHHHHHHHHHHHHHHH
T ss_conf             979999999999999999999987988544067542687477987569994576467899--819899999999999998


Q ss_pred             CCE-EEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECC
Q ss_conf             560-58999972266533332001113379999999985289860699997074
Q gi|254780547|r   78 KHD-CDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGK  130 (160)
Q Consensus        78 ~~~-~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G~  130 (160)
                      +.. .+|.+.|..   ++..||.--      +-++||+++|||++.|..-..|=
T Consensus        79 ~GKv~~iLvSGDn---~~~~YnEp~------~Mk~~Li~~GVP~e~I~~D~AGf  123 (239)
T PRK10834         79 SGKVNYLLLSGDN---ALQSYNEPM------TMRKDLIAAGVDPADIVLDYAGF  123 (239)
T ss_pred             CCCCCEEEECCCC---CCCCCCCHH------HHHHHHHHCCCCHHHEECCCCCC
T ss_conf             6997489866899---988898289------99999998599899950566765


No 28 
>pfam09476 Pilus_CpaD Pilus biogenesis CpaD protein (pilus_cpaD). Proteins in this entry consist of a pilus biogenesis protein, CpaD, from Caulobacter, and homologues in other bacteria, including three in the root nodule bacterium Bradyrhizobium japonicum. The molecular function of the homologues is not known.
Probab=91.09  E-value=1.3  Score=24.09  Aligned_cols=77  Identities=10%  Similarity=0.124  Sum_probs=55.8

Q ss_pred             ECCCCCCCHHHHHHHHHHHHHHC-CCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCC
Q ss_conf             04752243247999999984302-56058999972266533332001113379999999985289860699997074489
Q gi|254780547|r   55 DTSSYSIRPADIQVLSNLGSWLE-KHDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMP  133 (160)
Q Consensus        55 ~~~s~~L~~~~~~~L~~ia~~l~-~~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G~~~P  133 (160)
                      ..+...|++..+..|..++.-.. .....|.|.=...     .-|..-+.+=+..|+..|...||++.+|.+..|-...|
T Consensus        45 ~~~~~~Lt~~qr~~l~~f~~~~~~~g~g~i~I~~Psg-----s~n~~aa~~~~~~ir~~l~~~Gv~~~~I~~~~y~~~~~  119 (200)
T pfam09476        45 GPGRGGLTASQRARLAGFAARYGRRGAGPLVIDVPSG-----SPNARAASALSAEVRALLAAAGVPPSNISVRAYDAAGA  119 (200)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCC-----CCCHHHHHHHHHHHHHHHHHCCCCHHHEEECCCCCCCC
T ss_conf             6888988999999999999998456886189975899-----86357899999999999998599843155422577787


Q ss_pred             CCC
Q ss_conf             899
Q gi|254780547|r  134 SVY  136 (160)
Q Consensus       134 ~~~  136 (160)
                      ...
T Consensus       120 ~~~  122 (200)
T pfam09476       120 RAP  122 (200)
T ss_pred             CCC
T ss_conf             888


No 29 
>PRK13731 conjugal transfer surface exclusion protein TraT; Provisional
Probab=82.45  E-value=1.4  Score=23.82  Aligned_cols=27  Identities=15%  Similarity=0.367  Sum_probs=22.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             903699999999999865024566666
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDNLDTK   27 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~~~~~   27 (160)
                      |+.++++++..+++++.+++|......
T Consensus         1 m~~kk~~~~~~~~~~l~lsGC~a~~ta   27 (243)
T PRK13731          1 MKTKKLMMVALVSSTLALSGCGAMSTA   27 (243)
T ss_pred             CCHHHHHHHHHHHHHHHHCCHHHHHHH
T ss_conf             933775799999999997156876778


No 30 
>TIGR02522 pilus_cpaD pilus (Caulobacter type) biogenesis lipoprotein CpaD; InterPro: IPR013361    Proteins in this entry consist of a pilus biogenesis protein, CpaD, from Caulobacter, and homologues in other bacteria, including three in the root nodule bacterium Bradyrhizobium japonicum. The molecular function of the homologues is not known..
Probab=81.18  E-value=4.7  Score=20.85  Aligned_cols=76  Identities=13%  Similarity=0.168  Sum_probs=54.6

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHH-HHHCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             100220475224324799999998-4302560589999722665333320011133799999999852898606999970
Q gi|254780547|r   50 DSVFFDTSSYSIRPADIQVLSNLG-SWLEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus        50 ~~v~F~~~s~~L~~~~~~~L~~ia-~~l~~~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      ..++-..+..-|+++.++.|..++ .|.+..-..|.|.=|.   ||  .|..=+..=+...+..|...||.+.+|..+.|
T Consensus        45 ~~l~v~~~~~Gl~a~~~~~l~~~l~~~~~~~~~~l~~~~p~---GS--aN~~aa~~~~~e~~~~l~~~Gv~a~~iV~~~~  119 (211)
T TIGR02522        45 IDLLVAPGDRGLSASQQDQLLGFLKDWSRASAQTLVVVIPS---GS--ANEAAAEAMAAEIRRVLAASGVGARNIVKVVY  119 (211)
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCC---CC--HHHHHHHHHHHHHHHHHHHCCCCCHHEEEECC
T ss_conf             34554488876798889999999999863058537897588---87--54688999999999999965997204177445


Q ss_pred             CC
Q ss_conf             74
Q gi|254780547|r  129 GK  130 (160)
Q Consensus       129 G~  130 (160)
                      -.
T Consensus       120 ~~  121 (211)
T TIGR02522       120 RA  121 (211)
T ss_pred             CC
T ss_conf             57


No 31 
>PRK11087 hypothetical protein; Provisional
Probab=77.26  E-value=5.2  Score=20.58  Aligned_cols=32  Identities=9%  Similarity=0.109  Sum_probs=14.5

Q ss_pred             CCHHHHHHH-HHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             903699999-99999986502456666656655
Q gi|254780547|r    1 MQYSTIFII-LSAITMMSISGIDNLDTKISSPD   32 (160)
Q Consensus         1 M~~~~i~i~-l~a~~~~~~~~~~~~~~~~~~~~   32 (160)
                      ||++.+.|+ |.+++....+.+....+.+..|.
T Consensus         1 ~~~~~~~~~~~~~l~~~~~~~~~~a~~~p~~p~   33 (238)
T PRK11087          1 MKLKVLALAALLGLSASLLAMAAQAAELPDFPH   33 (238)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCHHHCCCCCCCE
T ss_conf             930499999999987766324344347999987


No 32 
>COG5461 Type IV pili component [Cell motility and secretion]
Probab=75.74  E-value=6.9  Score=19.88  Aligned_cols=72  Identities=14%  Similarity=0.220  Sum_probs=51.3

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHH-HHCC--CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             02204752243247999999984-3025--60589999722665333320011133799999999852898606999970
Q gi|254780547|r   52 VFFDTSSYSIRPADIQVLSNLGS-WLEK--HDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus        52 v~F~~~s~~L~~~~~~~L~~ia~-~l~~--~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      +....+.+-|+...++.|..++. |...  ..+.|.|-+     ||  -|..-+.+=++.++..|...||++.||.+++|
T Consensus        55 ipi~~gds~Lt~sqrd~lrgf~~~y~s~~a~~l~i~ip~-----gs--~n~~tA~~m~~eir~~l~~~Gv~~~ri~~~~y  127 (224)
T COG5461          55 IPILKGDSGLTASQRDRLRGFLDRYSSASADALHIQIPS-----GS--ANEVTASRMAKEIRRLLAGSGVDRARIRVVNY  127 (224)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEECCC-----CC--CCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEE
T ss_conf             023247654435588999999987643257716998158-----98--42577899999999999864888460589973


Q ss_pred             CC
Q ss_conf             74
Q gi|254780547|r  129 GK  130 (160)
Q Consensus       129 G~  130 (160)
                      -.
T Consensus       128 ~a  129 (224)
T COG5461         128 DA  129 (224)
T ss_pred             CC
T ss_conf             34


No 33 
>pfam00543 P-II Nitrogen regulatory protein P-II. P-II modulates the activity of glutamine synthetase.
Probab=73.56  E-value=7  Score=19.84  Aligned_cols=54  Identities=7%  Similarity=0.041  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHCCCCCEE-EEEEEECCCCCCCCCCCHHH----HHCCCEEEEEEEEC
Q ss_conf             33799999999852898606-99997074489899878779----84299189999713
Q gi|254780547|r  103 LRRAYAVFNYFVARGISASR-MKVTSYGKEMPSVYGHDEDA----YAKNRRAIVFLKGC  156 (160)
Q Consensus       103 ~~RA~aV~~~L~~~Gi~~~r-i~~~g~G~~~P~~~~~~~~~----~~~NRRVei~i~~~  156 (160)
                      -.|.+.|++.|.+.|++.=- ..+.|+|..+....-.....    .-.-+++|++++.-
T Consensus         7 p~kl~~v~~AL~~~G~~g~Tv~~v~G~G~q~g~~~~~~g~~~~~~~~pK~~ieivv~d~   65 (102)
T pfam00543         7 PEKLDEVKEALEKAGVPGMTVTEVKGRGRQKGHTEIYRGAEYYVEFLPKVKIEIVVPDE   65 (102)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCEECCCEEEECCCCEEEEEEEECHH
T ss_conf             89999999999977998589998289767777441541623571314215999998738


No 34 
>PRK10533 putative lipoprotein; Provisional
Probab=72.44  E-value=7.4  Score=19.70  Aligned_cols=76  Identities=16%  Similarity=0.093  Sum_probs=40.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCC-EEE-EECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             90369999999999986502456666656655444420125678752031-002-20475224324799999998430
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDNLDTKISSPDTVLNESSLQEQFSSSVGD-SVF-FDTSSYSIRPADIQVLSNLGSWL   76 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~v~-F~~~s~~L~~~~~~~L~~ia~~l   76 (160)
                      |+++.+.++++...++++|++-+..-+..+.......+.-.+..+..+-+ ++. =..+.+.|+|-..+.|..+....
T Consensus         1 Mr~~~~~ll~PlallLSACttV~Pa~kd~gsRs~~CveGGPD~VAqqFYD~riq~~~~~~a~lRPylS~~L~~~L~~a   78 (171)
T PRK10533          1 MRYSKLALLLPCALLLSACTTVTPAYKDNGSRSGPCVEGGPDSVAQQFYDYRIQHRSNDIAALRPYLSDKLATLLSDA   78 (171)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHH
T ss_conf             986203899999999987224761143037765554158920899998887302255652542524578999999998


No 35 
>PRK10665 nitrogen regulatory protein P-II 2; Provisional
Probab=69.09  E-value=9.9  Score=18.96  Aligned_cols=54  Identities=11%  Similarity=0.059  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHCCCCCE-EEEEEEECCCCCCCCC---CCHH-HHHCCCEEEEEEEEC
Q ss_conf             3379999999985289860-6999970744898998---7877-984299189999713
Q gi|254780547|r  103 LRRAYAVFNYFVARGISAS-RMKVTSYGKEMPSVYG---HDED-AYAKNRRAIVFLKGC  156 (160)
Q Consensus       103 ~~RA~aV~~~L~~~Gi~~~-ri~~~g~G~~~P~~~~---~~~~-~~~~NRRVei~i~~~  156 (160)
                      -.|.+.|++.|.+.|++.= -..+.|+|.+.....-   .... ..---+|+||++.+-
T Consensus        10 p~kl~~vk~aL~~~G~~g~Tv~~V~G~G~q~g~~~~~rg~~~~~~~~pKv~ieivv~D~   68 (112)
T PRK10665         10 PFKLEDVREALSSIGIQGLTVTEVKGFGRQKGHAELYRGAEYSVNFLPKVKIDVAIADD   68 (112)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEECEEECCCCCCCCCCCCCCCCCCCCCEEEEEEEECHH
T ss_conf             99999999999978997399984868756887553314651021521226999999728


No 36 
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=68.99  E-value=5.7  Score=20.36  Aligned_cols=24  Identities=13%  Similarity=0.257  Sum_probs=18.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             903699999999999865024566
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDNL   24 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~~   24 (160)
                      |+|+..++.++++++.+|......
T Consensus         1 m~~~~~l~~~~~~~l~~~~~~~~~   24 (259)
T PRK11917          1 MVFRKSLLKLAVFALGACVAFSNA   24 (259)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             942799999999999999863452


No 37 
>PRK13289 nitric oxide dioxygenase; Provisional
Probab=62.89  E-value=5.5  Score=20.45  Aligned_cols=29  Identities=14%  Similarity=0.194  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEEECCCCCC
Q ss_conf             99999999852898606999970744898
Q gi|254780547|r  106 AYAVFNYFVARGISASRMKVTSYGKEMPS  134 (160)
Q Consensus       106 A~aV~~~L~~~Gi~~~ri~~~g~G~~~P~  134 (160)
                      -++|++.|.+.||++++|....||..+.+
T Consensus       370 m~av~~~L~~~GVp~~~Ih~E~FGP~~~l  398 (399)
T PRK13289        370 MQFVAKQLLDLGVPEERIHYEFFGPAKVL  398 (399)
T ss_pred             HHHHHHHHHHCCCCHHHEEEECCCCCHHC
T ss_conf             99999999977997899788335880411


No 38 
>PRK03002 prsA peptidylprolyl isomerase; Reviewed
Probab=61.33  E-value=8.2  Score=19.43  Aligned_cols=24  Identities=29%  Similarity=0.441  Sum_probs=20.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             903699999999999865024566
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDNL   24 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~~   24 (160)
                      |+++.++++.++++++.+++|...
T Consensus         1 mkkK~i~~~~~~~svl~LaaC~~~   24 (285)
T PRK03002          1 MRGKHIFIITALISILMLSACGQK   24 (285)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             960189999999999999984579


No 39 
>pfam02698 DUF218 DUF218 domain. This large family of proteins contains several highly conserved charged amino acids, suggesting this may be an enzymatic domain (Bateman A pers. obs). The family includes SanA, which is involved in Vancomycin resistance. This protein may be involved in murein synthesis.
Probab=60.28  E-value=15  Score=17.97  Aligned_cols=59  Identities=17%  Similarity=0.219  Sum_probs=38.1

Q ss_pred             CHHHHHHHHHHHHHHCC-CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             32479999999843025-60589999722665333320011133799999999852898606999970
Q gi|254780547|r   62 RPADIQVLSNLGSWLEK-HDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus        62 ~~~~~~~L~~ia~~l~~-~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      .|....-++.-+...++ +..+|.+.|-.     ...+   ...-|+..++||++.|||+++|.....
T Consensus        12 ~~~~~~R~~~a~~l~~~g~~~~ii~sGg~-----~~~~---~~~ea~~~~~~l~~~gvp~~~I~~e~~   71 (148)
T pfam02698        12 SPALAARLDAAAELYRAGPAPRIIVSGGA-----GGGE---PVSEAEVMRRYLVELGVPAEAILLEPQ   71 (148)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCEEEEECCC-----CCCC---CCCHHHHHHHHHHHCCCCHHHEECCCC
T ss_conf             87799999999999980999889984898-----8888---878999999999986989999774556


No 40 
>KOG0524 consensus
Probab=60.15  E-value=13  Score=18.32  Aligned_cols=68  Identities=18%  Similarity=0.190  Sum_probs=45.9

Q ss_pred             HCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCHHHHHCCCEEEEEEEE
Q ss_conf             02560589999722665333320011133799999999852898606999970744898998787798429918999971
Q gi|254780547|r   76 LEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLKG  155 (160)
Q Consensus        76 l~~~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~~  155 (160)
                      +..++..|.|.+|+-           +-.-+-..++.|.+.|++++-|..++   -+|++...-...-.|-+|+.++=+|
T Consensus       232 ier~G~~iTivt~Sr-----------~v~~~leAA~~L~~~Gvs~EVInlrS---irP~D~~tI~~Sv~KT~~lvtVe~~  297 (359)
T KOG0524         232 IEREGTHITIVTYSR-----------MVGHCLEAAETLVAKGVSAEVINLRS---IRPFDIETIGASVKKTNRLVTVEEG  297 (359)
T ss_pred             EEECCCCEEEEEECH-----------HHHHHHHHHHHHHHCCCCCEEEEEEC---CCCCCHHHHHHHHHHHCEEEEEECC
T ss_conf             661588469998502-----------58999999999986698803674102---4765589999887650538998345


Q ss_pred             CC
Q ss_conf             36
Q gi|254780547|r  156 CR  157 (160)
Q Consensus       156 ~~  157 (160)
                      .+
T Consensus       298 ~p  299 (359)
T KOG0524         298 WP  299 (359)
T ss_pred             CC
T ss_conf             66


No 41 
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=57.79  E-value=16  Score=17.72  Aligned_cols=89  Identities=16%  Similarity=0.167  Sum_probs=39.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC--C-CCCCCCHHHHHHH----HHHCC---EEEE-ECC-------CCCCC
Q ss_conf             9036999999999998650245666665665--5-4444201256787----52031---0022-047-------52243
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDNLDTKISSP--D-TVLNESSLQEQFS----SSVGD---SVFF-DTS-------SYSIR   62 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~----~~~~~---~v~F-~~~-------s~~L~   62 (160)
                      |++++++.+.+.+..+.+++|.........-  . .........+...    ...+-   -+.| ++.       .-+|+
T Consensus         3 ~~~k~~~~~~~l~~~l~l~gCg~~~~~~~~ikVG~~~gp~~ei~e~~~~~~~ek~G~~veiv~FsDy~~pN~AL~~G~iD   82 (271)
T PRK11063          3 FKFKTFAAVGALIGSLALVGCGQDEKDPNHIKVGVIVGAEQQVAEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDID   82 (271)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHHCCCCC
T ss_conf             02999999999999997500589856798189984689879999998888886079768999936832155898679844


Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEEEEEC
Q ss_conf             247999999984302560589999722
Q gi|254780547|r   63 PADIQVLSNLGSWLEKHDCDFLIEGHA   89 (160)
Q Consensus        63 ~~~~~~L~~ia~~l~~~~~~i~I~Ght   89 (160)
                      ....|...-+..+-++++..+...|.|
T Consensus        83 aN~fQH~~yL~~~nk~~g~~L~~v~~~  109 (271)
T PRK11063         83 ANAFQHKPYLDQQIKDRGYKLVAVGNT  109 (271)
T ss_pred             HHHHHCHHHHHHHHHHCCCCEEEEEEE
T ss_conf             234557999999999779957998667


No 42 
>cd07762 CYTH-like_Pase_1 Uncharacterized subgroup 1 of the CYTH-like superfamily. Enzymes belonging to the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) superfamily hydrolyze triphosphate-containing substrates, require metal cations as cofactors, and have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB) and from thiamine triphosphatase. Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions. Proteins of this subgroup
Probab=57.33  E-value=16  Score=17.74  Aligned_cols=86  Identities=17%  Similarity=0.297  Sum_probs=51.1

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHC--CCEEEEEEEEECCCCCCCCCCCHHHHHHHH-----------HHHHHHHH
Q ss_conf             31002204752243247999999984302--560589999722665333320011133799-----------99999985
Q gi|254780547|r   49 GDSVFFDTSSYSIRPADIQVLSNLGSWLE--KHDCDFLIEGHADELGSRNSSIALGLRRAY-----------AVFNYFVA  115 (160)
Q Consensus        49 ~~~v~F~~~s~~L~~~~~~~L~~ia~~l~--~~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~-----------aV~~~L~~  115 (160)
                      +.+.||++..-.|+...      .+--++  +....+.+-.=. ..|.-++|..|+...|.           .|.++|.+
T Consensus        29 Q~N~YfDT~~~~Lk~~~------~aLRIR~~~~~~elTLK~p~-~~g~lE~~~~l~~~~a~~~i~~~~~~~~~I~~~L~~  101 (180)
T cd07762          29 QTNYYFDTPDFALKKKH------SALRIREKEGKAELTLKVPQ-EVGLLETNQPLTLEEAEKLIKGGTLPEGEILDKLKE  101 (180)
T ss_pred             EEEEEEECCCHHHHHCC------CEEEEEECCCEEEEEEECCC-CCCCEEEECCCCHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             73898888856677487------06899972983799985787-668468824588899999986178996699999999


Q ss_pred             CCCCCEEEEEEEECCCCCCCCCCCHHHHHCCCEEEEEEEEC
Q ss_conf             28986069999707448989987877984299189999713
Q gi|254780547|r  116 RGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLKGC  156 (160)
Q Consensus       116 ~Gi~~~ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~~~  156 (160)
                      .||+++.+...|.               -.+.|.|.-..||
T Consensus       102 ~~i~~~~l~~~G~---------------ltT~R~e~~~~~g  127 (180)
T cd07762         102 LGIDPSELKLFGS---------------LTTIRAEIPYEGG  127 (180)
T ss_pred             HCCCHHHEEEEEE---------------EEEEEEEEECCCE
T ss_conf             2999789899510---------------5889999973897


No 43 
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=55.90  E-value=9.4  Score=19.10  Aligned_cols=24  Identities=17%  Similarity=0.264  Sum_probs=15.6

Q ss_pred             CCHHHHHHHHH-HHHHHHHHCCCCC
Q ss_conf             90369999999-9999865024566
Q gi|254780547|r    1 MQYSTIFIILS-AITMMSISGIDNL   24 (160)
Q Consensus         1 M~~~~i~i~l~-a~~~~~~~~~~~~   24 (160)
                      |+.+++++.+. +++++++++|...
T Consensus         1 Mkkkk~~~~~~~~~~~l~LaaC~s~   25 (283)
T PRK02998          1 MKKKKLFIGTIISCVVLALSACGSS   25 (283)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             9358999999999999999866899


No 44 
>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein; InterPro: IPR005670   This is a family of phosphate transport system permease proteins.; GO: 0005315 inorganic phosphate transmembrane transporter activity, 0015114 phosphate transmembrane transporter activity, 0006817 phosphate transport, 0016020 membrane.
Probab=55.50  E-value=16  Score=17.69  Aligned_cols=53  Identities=15%  Similarity=0.230  Sum_probs=44.0

Q ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             3100220475224324799999998430256058999972266533332001113379999999985
Q gi|254780547|r   49 GDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVA  115 (160)
Q Consensus        49 ~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~  115 (160)
                      |+-++||-=.|.|+|-+-..++++...|+++ ++|+|+=|-             .+-|.-|.+|-.-
T Consensus       163 PeVlLlDEPTSALDPIaT~~IEeLi~eLk~~-YTivIVTHn-------------MqQA~RiSD~tAF  215 (248)
T TIGR00972       163 PEVLLLDEPTSALDPIATGKIEELIQELKKK-YTIVIVTHN-------------MQQAARISDRTAF  215 (248)
T ss_pred             CCEECCCCCCCCCCHHHHHHHHHHHHHHHHC-CEEEEEECC-------------HHHHHHHHHHHHH
T ss_conf             8521057888757877899999999987652-979988177-------------5678999999988


No 45 
>COG4116 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.30  E-value=5  Score=20.71  Aligned_cols=71  Identities=15%  Similarity=0.280  Sum_probs=47.3

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHHCC--CEEEEEEEEECCCCCCCCCCCHHHHHHHHH-----------HHHHHHHC
Q ss_conf             10022047522432479999999843025--605899997226653333200111337999-----------99999852
Q gi|254780547|r   50 DSVFFDTSSYSIRPADIQVLSNLGSWLEK--HDCDFLIEGHADELGSRNSSIALGLRRAYA-----------VFNYFVAR  116 (160)
Q Consensus        50 ~~v~F~~~s~~L~~~~~~~L~~ia~~l~~--~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~a-----------V~~~L~~~  116 (160)
                      .+-||+++.-.|+..      ..|-.++.  +.+.+.+.-- -.+|.-+||+.||.+-|..           |.+.|.+.
T Consensus        35 tN~YiDT~dF~LKek------~~ALRIR~~e~~~elTLK~P-~~vGllEynq~Ls~e~a~~~l~~~~~P~g~v~d~l~~~  107 (193)
T COG4116          35 TNHYIDTDDFKLKEK------KSALRIRTKENQYELTLKVP-AKVGLLEYNQILSLEEAKLALISANLPEGEVLDILEKL  107 (193)
T ss_pred             EEEEECCCCHHHHHH------HCCEEEEEECCEEEEEECCC-HHCCCHHHCCCCCHHHHHHHHHCCCCCCCHHHHHHHHC
T ss_conf             223332742101330------00036776055689995483-12274111310337799987411689950899999983


Q ss_pred             CCCCEEEEEEE
Q ss_conf             89860699997
Q gi|254780547|r  117 GISASRMKVTS  127 (160)
Q Consensus       117 Gi~~~ri~~~g  127 (160)
                      ||+.+.|.+.|
T Consensus       108 gI~~~~l~~~G  118 (193)
T COG4116         108 GIKDSALQVFG  118 (193)
T ss_pred             CCCHHHHHHHH
T ss_conf             99878877511


No 46 
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=52.95  E-value=20  Score=17.25  Aligned_cols=52  Identities=23%  Similarity=0.174  Sum_probs=32.0

Q ss_pred             HHHCCCEEEEEEEEEC-CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             4302560589999722-6653333200111337999999998528986069999
Q gi|254780547|r   74 SWLEKHDCDFLIEGHA-DELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVT  126 (160)
Q Consensus        74 ~~l~~~~~~i~I~Ght-D~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~  126 (160)
                      ..+++----|.|.|-- ++ =...+--.+..+|++.+++.|-+.||.++|+...
T Consensus        48 ~Al~~GaDGV~v~GC~~ge-CHy~~GN~ka~rR~~~lke~l~elgie~eRv~~~  100 (132)
T COG1908          48 KALRKGADGVLVAGCKIGE-CHYISGNYKAKRRMELLKELLKELGIEPERVRVL  100 (132)
T ss_pred             HHHHCCCCEEEEECCCCCC-EEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             9997389868993441561-2330166479999999999999948884427899


No 47 
>cd06184 flavohem_like_fad_nad_binding FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The hemoglobin domain adopts a globin fold with an embedded heme molecule. Flavohemoglobins also have a C-terminal reductase domain with bindiing sites for FAD and NAD(P)H. This domain catalyzes the conversion of NO + O2 + NAD(P)H to NO3- + NAD(P)+.  Instead of the oxygen transport function of hemoglobins, flavohemoglobins seem to act in NO dioxygenation and NO signalling.
Probab=52.69  E-value=13  Score=18.34  Aligned_cols=29  Identities=24%  Similarity=0.276  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEEECCC
Q ss_conf             33799999999852898606999970744
Q gi|254780547|r  103 LRRAYAVFNYFVARGISASRMKVTSYGKE  131 (160)
Q Consensus       103 ~~RA~aV~~~L~~~Gi~~~ri~~~g~G~~  131 (160)
                      ..=.++|.+.|.+.|+++++|....||..
T Consensus       218 ~~mi~~~~~~L~~~Gv~~~~I~~E~FgP~  246 (247)
T cd06184         218 VPFMQAVREGLKALGVPAERIHYEVFGPG  246 (247)
T ss_pred             HHHHHHHHHHHHHCCCCHHHEEEEEECCC
T ss_conf             99999999999976997895999000898


No 48 
>pfam06925 MGDG_synth Monogalactosyldiacylglycerol (MGDG) synthase. This family represents a conserved region of approximately 180 residues within plant and bacterial monogalactosyldiacylglycerol (MGDG) synthase (EC:2.4.1.46). In Arabidopsis, there are two types of MGDG synthase which differ in their N-terminal portion: type A and type B.
Probab=47.40  E-value=12  Score=18.46  Aligned_cols=23  Identities=30%  Similarity=0.358  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             99999999852898606999970
Q gi|254780547|r  106 AYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       106 A~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      .+.+++.|+++||++++|.+.|.
T Consensus       145 ~ee~~~~l~~~Gi~~~kI~vtGI  167 (169)
T pfam06925       145 SKEVKKEALEKGIDPSNIKVTGI  167 (169)
T ss_pred             CHHHHHHHHHCCCCHHHEEEECC
T ss_conf             99999999985999889788374


No 49 
>PRK10494 hypothetical protein; Provisional
Probab=43.66  E-value=28  Score=16.39  Aligned_cols=62  Identities=8%  Similarity=0.049  Sum_probs=37.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHCC-CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             522432479999999843025-6058999972266533332001113379999999985289860699997
Q gi|254780547|r   58 SYSIRPADIQVLSNLGSWLEK-HDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTS  127 (160)
Q Consensus        58 s~~L~~~~~~~L~~ia~~l~~-~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g  127 (160)
                      +..+...+.+-|..-+...+. +..+|++.|-.     ..+|. .  .-|+..++++++.||++++|....
T Consensus        98 ~~~~~~~a~~Rl~~g~~L~r~~~~~~li~SGG~-----~~~~~-~--sea~~~~~~~~~lGv~~~~I~~e~  160 (259)
T PRK10494         98 SSNLINNSLPRLNEGIRLWRANPGAKLIFTGGV-----AKTNT-V--STAEVGARVAQSLGVPREDIITLD  160 (259)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC-----CCCCC-C--CHHHHHHHHHHHCCCCHHHEEECC
T ss_conf             444446489999999999983899839996887-----88899-9--899999999998399989915256


No 50 
>PRK03095 prsA peptidylprolyl isomerase; Reviewed
Probab=42.93  E-value=22  Score=17.01  Aligned_cols=20  Identities=20%  Similarity=0.381  Sum_probs=11.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9036999999999998650245
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGID   22 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~   22 (160)
                      |++..+.  +++++++++++|.
T Consensus         1 MKK~~la--~~~~svl~LaaC~   20 (287)
T PRK03095          1 MKKAMLA--LAATSVIALSACG   20 (287)
T ss_pred             CCHHHHH--HHHHHHHHHHHCC
T ss_conf             9078999--9999999998516


No 51 
>PRK10684 HCP oxidoreductase, NADH-dependent; Provisional
Probab=41.97  E-value=24  Score=16.72  Aligned_cols=32  Identities=16%  Similarity=-0.027  Sum_probs=26.6

Q ss_pred             HHHHHHHHHCCCCCEEEEEEEECCCCCCCCCC
Q ss_conf             99999998528986069999707448989987
Q gi|254780547|r  107 YAVFNYFVARGISASRMKVTSYGKEMPSVYGH  138 (160)
Q Consensus       107 ~aV~~~L~~~Gi~~~ri~~~g~G~~~P~~~~~  138 (160)
                      +++++.|.+.|+++++|....|+...+.....
T Consensus       217 ~a~~~~l~~~Gv~~~~ih~E~F~~~~~~~~~~  248 (335)
T PRK10684        217 DWVEQEVKALGVTADRFFKEKFFTPDEVAEAA  248 (335)
T ss_pred             HHHHHHHHHCCCCHHHEEEEECCCCCCCCCCC
T ss_conf             99999999849988997975568998666678


No 52 
>PRK01326 prsA foldase protein PrsA; Reviewed
Probab=41.48  E-value=27  Score=16.46  Aligned_cols=24  Identities=8%  Similarity=0.155  Sum_probs=18.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             903699999999999865024566
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDNL   24 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~~   24 (160)
                      |+++.++.++.+++++.+++|...
T Consensus         1 MKKKl~~~~~~~~svl~LaaCs~~   24 (310)
T PRK01326          1 MKKKLIAGAVTLLSVATLAACSKT   24 (310)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             908899999999999999871699


No 53 
>pfam02662 FlpD Methyl-viologen-reducing hydrogenase, delta subunit. This family consist of methyl-viologen-reducing hydrogenase, delta subunit / heterodisulphide reductase. No specific functions have been assigned to this subunit. The aligned region corresponds to almost the entire delta chain sequence and contains 4 conserved cysteine residues. However, in two Archaeoglobus sequences this region corresponds to only the C-terminus of these proteins.
Probab=40.15  E-value=26  Score=16.51  Aligned_cols=57  Identities=21%  Similarity=0.195  Sum_probs=33.7

Q ss_pred             HHHHHCCCEEEEEEEE-ECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC
Q ss_conf             9843025605899997-226653333200111337999999998528986069999707
Q gi|254780547|r   72 LGSWLEKHDCDFLIEG-HADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYG  129 (160)
Q Consensus        72 ia~~l~~~~~~i~I~G-htD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G  129 (160)
                      +...+.+----|.|.| |..+=-...-| ...++|...+++.|...|++++|+...-..
T Consensus        45 il~A~~~GADGV~V~GC~~GdChy~~Gn-~~a~~Rv~~~~~~L~~~Gi~~~Rv~~~~vs  102 (124)
T pfam02662        45 ILKALEKGADGVLVLGCHPGDCHYLKGN-EKARRRVEKVKELLEELGIEPERLRFFWVS  102 (124)
T ss_pred             HHHHHHCCCCEEEEECCCCCCCCCCHHH-HHHHHHHHHHHHHHHHCCCCHHHEEEEEEC
T ss_conf             9999986999799947888887672646-999999999999999839985684888966


No 54 
>COG1735 Php Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]
Probab=38.75  E-value=33  Score=15.94  Aligned_cols=66  Identities=12%  Similarity=0.149  Sum_probs=47.3

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC
Q ss_conf             0022047522432479999999843025605899997226653333200111337999999998528986069999707
Q gi|254780547|r   51 SVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYG  129 (160)
Q Consensus        51 ~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G  129 (160)
                      .|-|..++..++|.-...|...|..-++.  ++-|.-||          .++. .|-.+.+.|.+.|++++++.+-=++
T Consensus       136 iIk~~~~~~~iTp~Eek~lrAaA~A~~~T--g~Pi~tHt----------~~gt-~g~eq~~il~~egvdl~~v~igH~d  201 (316)
T COG1735         136 IIKEAGGSPAITPLEEKSLRAAARAHKET--GAPISTHT----------PAGT-MGLEQLRILAEEGVDLRKVSIGHMD  201 (316)
T ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHHHHC--CCCEEEEC----------CCHH-HHHHHHHHHHHCCCCHHHEEEECCC
T ss_conf             46642576667989999999999986411--89717734----------4003-0199999999729986673673258


No 55 
>pfam04954 SIP Siderophore-interacting protein.
Probab=38.45  E-value=26  Score=16.55  Aligned_cols=26  Identities=15%  Similarity=0.212  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHH-CCCCCEEEEEEEEC
Q ss_conf             379999999985-28986069999707
Q gi|254780547|r  104 RRAYAVFNYFVA-RGISASRMKVTSYG  129 (160)
Q Consensus       104 ~RA~aV~~~L~~-~Gi~~~ri~~~g~G  129 (160)
                      .-+..++++|.. .|++.++|.+.||=
T Consensus        89 ~~~r~lR~~l~~~~g~~~~~i~~~gYW  115 (118)
T pfam04954        89 GAVRALRRHLRNERGLPREQVYASGYW  115 (118)
T ss_pred             HHHHHHHHHHHHHHCCCHHHEEEEEEC
T ss_conf             899999999998539997993899854


No 56 
>PRK06193 hypothetical protein; Provisional
Probab=38.26  E-value=34  Score=15.89  Aligned_cols=81  Identities=11%  Similarity=0.150  Sum_probs=47.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHH--------------HHHCCEEEEECCC----CCCC
Q ss_conf             903699999999999865024566666566554444201256787--------------5203100220475----2243
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDNLDTKISSPDTVLNESSLQEQFS--------------SSVGDSVFFDTSS----YSIR   62 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~v~F~~~s----~~L~   62 (160)
                      |+...+++.|.++.+++.|+...................+-..+.              ...++...|+.+.    -.|+
T Consensus         1 ~~~~~~~~~l~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ll~~L~~GG~vl~~RHa~a~pg~gDp~~f~l~dCsTQRnLs   80 (211)
T PRK06193          1 MRAAALLCALLVAALLAGCGRESAANQNPDFEDKLSTKDLLASLQKGGYVIYFRHAATDKDYADQATPELDDCSTQRQLS   80 (211)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             91799999999999942522001243582155405859999999719989999767778999998888843022447878


Q ss_pred             HHHHHHHHHHHHHHCCCEE
Q ss_conf             2479999999843025605
Q gi|254780547|r   63 PADIQVLSNLGSWLEKHDC   81 (160)
Q Consensus        63 ~~~~~~L~~ia~~l~~~~~   81 (160)
                      .+.++.=..+..+++++..
T Consensus        81 ~~Gr~qA~~iG~~~~~~~I   99 (211)
T PRK06193         81 AEGRQQAKAIGEAFRALDI   99 (211)
T ss_pred             HHHHHHHHHHHHHHHHCCC
T ss_conf             8999999999999998599


No 57 
>PRK09859 multidrug efflux system protein MdtE; Provisional
Probab=37.93  E-value=34  Score=15.86  Aligned_cols=23  Identities=13%  Similarity=0.138  Sum_probs=10.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             90369999999999986502456
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDN   23 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~   23 (160)
                      ||+++.+++...+..+.+++|..
T Consensus         1 m~~k~~~li~ll~~~~lL~gC~~   23 (385)
T PRK09859          1 MNRRRKLLIPLLFCGAMLTACDD   23 (385)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             98206789999999999953799


No 58 
>pfam00123 Hormone_2 Peptide hormone. This family contains glucagon, GIP, secretin and VIP.
Probab=36.61  E-value=20  Score=17.23  Aligned_cols=28  Identities=21%  Similarity=0.193  Sum_probs=24.6

Q ss_pred             ECCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             2266533332001113379999999985
Q gi|254780547|r   88 HADELGSRNSSIALGLRRAYAVFNYFVA  115 (160)
Q Consensus        88 htD~~Gs~~yN~~LS~~RA~aV~~~L~~  115 (160)
                      |+|.+=+.+|+.-|.+.+|+-..++|++
T Consensus         1 HadGtFTsdysk~l~~~~ak~fl~~L~~   28 (28)
T pfam00123         1 HADGTFTSDYSKLLDQLAAKKFLQWLMN   28 (28)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9876202579999988889999999749


No 59 
>cd06185 PDR_like Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal  ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur [2Fe-2S] cluster domain. Although structurally homologous to FNR, PDR binds FMN rather than FAD in it's FNR-like domain. Electron transfer between pyrimidines and iron-sulfur clusters (Rieske center [2Fe-2S]) or heme groups is mediated by flavins in respiration, photosynthesis, and oxygenase systems. Type I dioxygenase systems, including the hydroxylate phthalate system, have 2 components, a monomeric reductase consisting of a flavin and a 2Fe-2S center and a multimeric oxygenase. In contrast to other Rieske dioxygenases the ferredoxin like domain is C-, not N-terminal.
Probab=36.58  E-value=26  Score=16.58  Aligned_cols=25  Identities=20%  Similarity=0.171  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEEEEC
Q ss_conf             7999999998528986069999707
Q gi|254780547|r  105 RAYAVFNYFVARGISASRMKVTSYG  129 (160)
Q Consensus       105 RA~aV~~~L~~~Gi~~~ri~~~g~G  129 (160)
                      --++|.+.|.+.||++++|....|+
T Consensus       187 m~~a~~~~L~~~Gv~~~~Ih~E~Fa  211 (211)
T cd06185         187 MMDAVRAAAAALGWPEARLHFERFA  211 (211)
T ss_pred             HHHHHHHHHHHCCCCHHHEEEEECC
T ss_conf             9999999999869988995865288


No 60 
>smart00070 GLUCA Glucagon like hormones.
Probab=36.36  E-value=19  Score=17.32  Aligned_cols=27  Identities=22%  Similarity=0.192  Sum_probs=23.4

Q ss_pred             ECCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             226653333200111337999999998
Q gi|254780547|r   88 HADELGSRNSSIALGLRRAYAVFNYFV  114 (160)
Q Consensus        88 htD~~Gs~~yN~~LS~~RA~aV~~~L~  114 (160)
                      |+|.+-+.+|+.-|.+.+|+-..++|+
T Consensus         1 HadG~Fts~ysk~l~~~aak~fl~~L~   27 (27)
T smart00070        1 HADGTFTSDYSKYLDQLAAKKFLQWLM   27 (27)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             998740014899999999999999869


No 61 
>pfam01187 MIF Macrophage migration inhibitory factor (MIF).
Probab=35.84  E-value=37  Score=15.66  Aligned_cols=74  Identities=16%  Similarity=0.218  Sum_probs=42.7

Q ss_pred             EECC--CCCCCHHHHHHHHH-HHHHHCCCEEEEEEEEECCCC----CCCC------------CCCHHHHHHHHHHHHHHH
Q ss_conf             2047--52243247999999-984302560589999722665----3333------------200111337999999998
Q gi|254780547|r   54 FDTS--SYSIRPADIQVLSN-LGSWLEKHDCDFLIEGHADEL----GSRN------------SSIALGLRRAYAVFNYFV  114 (160)
Q Consensus        54 F~~~--s~~L~~~~~~~L~~-ia~~l~~~~~~i~I~GhtD~~----Gs~~------------yN~~LS~~RA~aV~~~L~  114 (160)
                      +.+|  ...+..+....|.. +++.|.+|...|.|.-..|..    |+.+            .+-+.-.+-+.++-++|.
T Consensus         5 i~TNv~~~~~~~~f~~~ls~~la~~lgKPe~yv~V~v~~~~~m~fgGs~eP~a~~~l~siG~l~~~~n~~~s~~l~~~l~   84 (114)
T pfam01187         5 IDTNLPANSVPAGLEKRLTAALAKALGKPADRIAVHIRPGQAMVFGGSTDPCAVCSIKSIGVVGAEQNRSHSALLFKFLT   84 (114)
T ss_pred             EECCCCCHHCCHHHHHHHHHHHHHHHCCCHHEEEEEEECCCEEEECCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHH
T ss_conf             98679822256899999999999986898362999992897189668899779999998678998999999999999999


Q ss_pred             H-CCCCCEEEEEEE
Q ss_conf             5-289860699997
Q gi|254780547|r  115 A-RGISASRMKVTS  127 (160)
Q Consensus       115 ~-~Gi~~~ri~~~g  127 (160)
                      + .||+++||-+.=
T Consensus        85 ~~LgI~~~RiyI~F   98 (114)
T pfam01187        85 KELGLPKDRIYIRF   98 (114)
T ss_pred             HHCCCCCCEEEEEE
T ss_conf             86297946499999


No 62 
>PRK09585 anmK anhydro-N-acetylmuramic acid kinase; Reviewed
Probab=35.81  E-value=37  Score=15.66  Aligned_cols=32  Identities=25%  Similarity=0.187  Sum_probs=18.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             20011133799999999852898606999970
Q gi|254780547|r   97 SSIALGLRRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus        97 yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      .|..|++.=|++|.+++.+.++++..|..+|+
T Consensus        65 l~~~~~~~~~~~i~~~i~~~~~~~~~id~Ig~   96 (366)
T PRK09585         65 LDRALGRLFAEAVNALLAEAGLSPEDIDAIGS   96 (366)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEC
T ss_conf             99999999999999999984998036328975


No 63 
>COG4195 Phage-related replication protein [General function prediction only]
Probab=34.96  E-value=31  Score=16.06  Aligned_cols=80  Identities=18%  Similarity=0.160  Sum_probs=46.1

Q ss_pred             HCCCEEEEEEEEECCCCCCCCCCC--HHHHHHHHHHHHHHHHCCCCCEEE----EEEEECCCCCCCCCCCHHH------H
Q ss_conf             025605899997226653333200--111337999999998528986069----9997074489899878779------8
Q gi|254780547|r   76 LEKHDCDFLIEGHADELGSRNSSI--ALGLRRAYAVFNYFVARGISASRM----KVTSYGKEMPSVYGHDEDA------Y  143 (160)
Q Consensus        76 l~~~~~~i~I~GhtD~~Gs~~yN~--~LS~~RA~aV~~~L~~~Gi~~~ri----~~~g~G~~~P~~~~~~~~~------~  143 (160)
                      ..++++.|-+.||.|-.  ...-|  -+-.+||......|...|.+++-.    ...|.-+.+++..+.+..+      +
T Consensus        96 ~~~h~~vis~HGy~~~~--~~~~lvGG~dR~~aa~i~~~L~~aGF~a~L~~~~~~LaG~hpnNi~Nr~~~g~~iQLE~s~  173 (208)
T COG4195          96 VSDHDYVISLHGYADIE--SKQTLVGGTDRELAAHIARALQLAGFSAELANSKHRLAGLHPNNIVNRGKTGLSIQLEIST  173 (208)
T ss_pred             HCCCCEEEEECCCCCCC--CCEEEECCCCHHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEEH
T ss_conf             40562799851435788--7615654745899999999986078537764499767777866522235567436887617


Q ss_pred             HCCCEEEEEEEECCC
Q ss_conf             429918999971368
Q gi|254780547|r  144 AKNRRAIVFLKGCRA  158 (160)
Q Consensus       144 ~~NRRVei~i~~~~~  158 (160)
                      . -||.-+..-||++
T Consensus       174 ~-~r~~lf~~f~~~~  187 (208)
T COG4195         174 E-QRRALFTTFGLKG  187 (208)
T ss_pred             H-HHHCCCCCCCCCC
T ss_conf             6-4302004755466


No 64 
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family; InterPro: IPR003282 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia.   The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell  and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis . However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself, type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.    One of the outer membrane protein subunit families, termed "K" here for nomenclature purposes, aids in the structural assembly of the invasion complex . It is also described as a lipoprotein. Members of this family include the Salmonella PrgK and SsaJ genes, MxiJ from Shigella, YscJ from Yersinia, and from the plant enteropathogens NolT (Rhizobium) and HrcJ Erwinia). The flagellar M-ring protein FliF also shares a low level of similarity, presumably due to evolution of the type III secretion system from the flagellar biosynthetic pathway.; GO: 0009306 protein secretion.
Probab=34.95  E-value=32  Score=16.05  Aligned_cols=20  Identities=10%  Similarity=0.182  Sum_probs=10.2

Q ss_pred             HHHHHHHH--CCCCCEEEEEEE
Q ss_conf             99999985--289860699997
Q gi|254780547|r  108 AVFNYFVA--RGISASRMKVTS  127 (160)
Q Consensus       108 aV~~~L~~--~Gi~~~ri~~~g  127 (160)
                      -+|..+..  .|++-++|+++-
T Consensus       174 ~IK~Lv~~Si~gL~Yd~vSVvl  195 (203)
T TIGR02544       174 KIKRLVANSIPGLAYDNVSVVL  195 (203)
T ss_pred             HHHHHHHHHCCCCCCCCEEEEE
T ss_conf             2689998603788716568998


No 65 
>PRK05363 putative sulfite oxidase subunit YedY; Reviewed
Probab=34.74  E-value=38  Score=15.56  Aligned_cols=53  Identities=15%  Similarity=0.257  Sum_probs=33.8

Q ss_pred             CHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCC
Q ss_conf             0125678752031002204752243247999999984302560589999722665333320
Q gi|254780547|r   38 SSLQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSS   98 (160)
Q Consensus        38 ~~~~~~~~~~~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~Gs~~yN   98 (160)
                      ..+....+...++  |++||+.+=+|.      ..|..|+-.+-+|.|.|..+.-++-++.
T Consensus        72 ~~T~~~~vTtYNN--FYEFGt~K~dp~------~~A~~l~t~PWtv~IdG~V~kP~~~d~d  124 (327)
T PRK05363         72 PLTPEKDVTTYNN--FYEFGTDKADPA------RNAGSLKTRPWTVKIDGEVEKPGTLDLD  124 (327)
T ss_pred             CCCCHHHHHEECC--EEEECCCCCCHH------HHHHHCCCCCCEEEEEECCCCCCCCCHH
T ss_conf             8898788403110--266057767577------8875167888559984011678513899


No 66 
>PRK10858 nitrogen regulatory protein P-II 1; Provisional
Probab=34.51  E-value=39  Score=15.54  Aligned_cols=53  Identities=9%  Similarity=0.055  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHHCCCCCE-EEEEEEECCCCCCCCC---C-CHHHHHCCCEEEEEEEE
Q ss_conf             3379999999985289860-6999970744898998---7-87798429918999971
Q gi|254780547|r  103 LRRAYAVFNYFVARGISAS-RMKVTSYGKEMPSVYG---H-DEDAYAKNRRAIVFLKG  155 (160)
Q Consensus       103 ~~RA~aV~~~L~~~Gi~~~-ri~~~g~G~~~P~~~~---~-~~~~~~~NRRVei~i~~  155 (160)
                      ..|-+.|++.|.+.|++.= -..+.|+|.+.....-   . .....---+++||++..
T Consensus        10 p~kl~~vk~aL~~~G~~g~Tv~~V~G~G~q~g~~~~~rg~~~~~~~~pK~~ieivv~d   67 (112)
T PRK10858         10 PFKLDDVREALAEVGITGMTVTEVKGFGRQKGHTELYRGAEYMVDFLPKVKIEIVVPD   67 (112)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEECEEECCCCCCCCCCCCCCEEECCCCEEEEEEEECH
T ss_conf             9999999999997899739999577874588855431365204122310599999678


No 67 
>PRK05421 hypothetical protein; Provisional
Probab=33.78  E-value=40  Score=15.47  Aligned_cols=58  Identities=14%  Similarity=0.264  Sum_probs=45.4

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCE
Q ss_conf             00220475224324799999998430256058999972266533332001113379999999985289860
Q gi|254780547|r   51 SVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISAS  121 (160)
Q Consensus        51 ~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~  121 (160)
                      .|.|.++-    .+...+|+.+...|+.|.--|++.|        ++| .=|.+|...+.+++.+.|+..-
T Consensus       147 aINF~~g~----~~y~~QL~~l~~~i~~H~GPvI~AG--------DFN-tWs~~R~~~l~~~~~~~gL~ev  204 (254)
T PRK05421        147 AINFSVGV----DVYSKQLEPIGDQIAHHSGPIILAG--------DFN-TWSRKRMNALKRFARELGLKEV  204 (254)
T ss_pred             EEEEECCH----HHHHHHHHHHHHHHHHCCCCEEEEC--------CCC-CCCHHHHHHHHHHHHHCCCCEE
T ss_conf             67665156----9999999999999984899879844--------533-0139999999999997698087


No 68 
>KOG0739 consensus
Probab=33.60  E-value=40  Score=15.45  Aligned_cols=99  Identities=20%  Similarity=0.238  Sum_probs=56.8

Q ss_pred             EEEEECCCCCCCHH----HHHHHHHHHHHHCCCEEEEEEEEECCCC-CCCCCCCHHHHHHHHHHHHHHHH-CCC--CCEE
Q ss_conf             00220475224324----7999999984302560589999722665-33332001113379999999985-289--8606
Q gi|254780547|r   51 SVFFDTSSYSIRPA----DIQVLSNLGSWLEKHDCDFLIEGHADEL-GSRNSSIALGLRRAYAVFNYFVA-RGI--SASR  122 (160)
Q Consensus        51 ~v~F~~~s~~L~~~----~~~~L~~ia~~l~~~~~~i~I~GhtD~~-Gs~~yN~~LS~~RA~aV~~~L~~-~Gi--~~~r  122 (160)
                      .-||...|++|-..    +....+.+-++-+.+...|+-.---|+. |++.-|..=+.+|-++  ++|++ .||  +.+-
T Consensus       192 STFFSvSSSDLvSKWmGESEkLVknLFemARe~kPSIIFiDEiDslcg~r~enEseasRRIKT--EfLVQMqGVG~d~~g  269 (439)
T KOG0739         192 STFFSVSSSDLVSKWMGESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENESEASRRIKT--EFLVQMQGVGNDNDG  269 (439)
T ss_pred             CCEEEEEHHHHHHHHHCCHHHHHHHHHHHHHHCCCCEEEEEHHHHHCCCCCCCCHHHHHHHHH--HHHHHHHCCCCCCCC
T ss_conf             706873017889987321799999999998734994798634444326887771177777777--888764066658886


Q ss_pred             EEEEEECCCCCCCCCCCHHHHHCCCEEEEEE
Q ss_conf             9999707448989987877984299189999
Q gi|254780547|r  123 MKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL  153 (160)
Q Consensus       123 i~~~g~G~~~P~~~~~~~~~~~~NRRVei~i  153 (160)
                      +-+-  |.++---.-++.--|...+|+-|-+
T Consensus       270 vLVL--gATNiPw~LDsAIRRRFekRIYIPL  298 (439)
T KOG0739         270 VLVL--GATNIPWVLDSAIRRRFEKRIYIPL  298 (439)
T ss_pred             EEEE--ECCCCCHHHHHHHHHHHHCCEECCC
T ss_conf             4897--2378843677999987650230108


No 69 
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.08  E-value=41  Score=15.40  Aligned_cols=68  Identities=21%  Similarity=0.132  Sum_probs=43.1

Q ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHHCCCEE--EEEEEEECCCCCCCCC----CCHHHHH----H----HHHHHHHHHH
Q ss_conf             10022047522432479999999843025605--8999972266533332----0011133----7----9999999985
Q gi|254780547|r   50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKHDC--DFLIEGHADELGSRNS----SIALGLR----R----AYAVFNYFVA  115 (160)
Q Consensus        50 ~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~--~i~I~GhtD~~Gs~~y----N~~LS~~----R----A~aV~~~L~~  115 (160)
                      .++.|+++. ..+.+-+..|..+-..|...++  -=.|.||- -.|.++|    |-+=++=    |    -+-|+.||..
T Consensus         6 ~T~~f~~~d-~~~~~v~e~L~~VY~sL~ekGYNpiNQiVGYl-lSGDPaYIpr~ndARn~IRk~eRDeIvEElvk~YLk~   83 (88)
T COG4472           6 ETMRFDVGD-SDKKDVKETLNDVYNSLEEKGYNPINQIVGYL-LSGDPAYIPRYNDARNQIRKLERDEIVEELVKYYLKG   83 (88)
T ss_pred             CEEEEECCC-CHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH-CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             325655688-70889999999999999872787287788440-1489644676210899999874889999999999851


Q ss_pred             CCCC
Q ss_conf             2898
Q gi|254780547|r  116 RGIS  119 (160)
Q Consensus       116 ~Gi~  119 (160)
                      .|++
T Consensus        84 ~~~~   87 (88)
T COG4472          84 NGKD   87 (88)
T ss_pred             CCCC
T ss_conf             5789


No 70 
>pfam09961 DUF2195 Uncharacterized protein conserved in bacteria (DUF2195). This domain, found in various hypothetical bacterial proteins, has no known function.
Probab=32.82  E-value=32  Score=16.00  Aligned_cols=57  Identities=14%  Similarity=0.074  Sum_probs=38.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCHHHHHCCCEEEEEEEECCC
Q ss_conf             33320011133799999999852898606999970744898998787798429918999971368
Q gi|254780547|r   94 SRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLKGCRA  158 (160)
Q Consensus        94 s~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G~~~P~~~~~~~~~~~~NRRVei~i~~~~~  158 (160)
                      |.-.+..+|..++..++..|++.-++-.+-...    +-|++   ++.+...||+|.+.+ ||..
T Consensus        63 SAL~~Y~s~v~~~~g~~~~LQ~G~~~~~~~~~r----tl~LA---sd~~l~~dr~v~l~l-gCa~  119 (121)
T pfam09961        63 SALVRYQSLVEFARGSRLVLQEGLFNLAKSQGR----TLPLA---TDAALVFDGRLALRL-GCAP  119 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCE----EEEEE---CCHHHHCCCEEEEEE-ECCC
T ss_conf             899999999887277899999760665415864----79975---374451387079998-3577


No 71 
>cd01525 RHOD_Kc Member of the Rhodanese Homology Domain superfamily. Included in this CD are the rhodanese-like domains found C-terminal of the serine/threonine protein kinases catalytic (S_TKc) domain and the Tre-2, BUB2p, Cdc16p (TBC) domain. The putative active site Cys residue is not present in this CD.
Probab=32.69  E-value=42  Score=15.36  Aligned_cols=64  Identities=17%  Similarity=0.247  Sum_probs=40.7

Q ss_pred             HHHCCEEEEECCCCCCCHHHHHHHHHHHHHHCCC-EEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             5203100220475224324799999998430256-05899997226653333200111337999999998528986069
Q gi|254780547|r   46 SSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRM  123 (160)
Q Consensus        46 ~~~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~-~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri  123 (160)
                      ..+...+..+|++..........+..++ .|+++ +.-|+|.|+..             +.|.....+|++.|.+.--+
T Consensus        31 ghi~~siniPf~~~~~~~~~L~~~~~~~-~Lek~Kgk~VViV~~~g-------------~~a~~fa~~Lvk~Gf~rVcv   95 (105)
T cd01525          31 GHIEGSINIPFSSVFLKEGELEQLPTVP-RLENYKGKIIVIVSHSH-------------KHAALFAAFLVKCGVPRVCI   95 (105)
T ss_pred             CEECCCCCCCCHHHCCCCCCCCCCCCHH-HHHHCCCCEEEEECCCC-------------CCHHHHHHHHHHCCCCEEEE
T ss_conf             6112755057302015544221364258-99975898299988998-------------67999999999849986999


No 72 
>PRK07609 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated
Probab=32.03  E-value=35  Score=15.83  Aligned_cols=26  Identities=27%  Similarity=0.452  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEEECCC
Q ss_conf             99999999852898606999970744
Q gi|254780547|r  106 AYAVFNYFVARGISASRMKVTSYGKE  131 (160)
Q Consensus       106 A~aV~~~L~~~Gi~~~ri~~~g~G~~  131 (160)
                      -+++++.|.+.||++++|....|+..
T Consensus       309 v~a~~~~L~~~Gv~~~~I~~E~F~pa  334 (337)
T PRK07609        309 VYAARDDFVAAGLPAEEFFADAFTSA  334 (337)
T ss_pred             HHHHHHHHHHCCCCHHHEEEEECCCC
T ss_conf             99999999985998899798203470


No 73 
>cd06189 flavin_oxioreductase NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a substrate, rather than a tightly bound prosthetic group as in flavoenzymes; weaker binding is due to the absence of a binding site for the AMP moeity of FAD.
Probab=31.68  E-value=28  Score=16.34  Aligned_cols=24  Identities=21%  Similarity=0.443  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             799999999852898606999970
Q gi|254780547|r  105 RAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       105 RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      =-++|.+.|.+.|+++++|....|
T Consensus       201 m~~~v~~~L~~~Gv~~~~I~~E~F  224 (224)
T cd06189         201 MVYAARDDFVEKGLPEENFFSDAF  224 (224)
T ss_pred             HHHHHHHHHHHCCCCHHHEEECCC
T ss_conf             999999999985998899574119


No 74 
>cd06213 oxygenase_e_transfer_subunit The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate while mono-oxygenases add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with  Rieske type [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate.
Probab=31.27  E-value=34  Score=15.87  Aligned_cols=24  Identities=17%  Similarity=0.238  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             799999999852898606999970
Q gi|254780547|r  105 RAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       105 RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      =.++|++.|.+.||++++|...-|
T Consensus       204 m~~~v~~~L~~~Gv~~~~I~~E~F  227 (227)
T cd06213         204 MIDAAIAVLRALGIAREHIHADRF  227 (227)
T ss_pred             HHHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             999999999985998899797159


No 75 
>cd06211 phenol_2-monooxygenase_like Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use molecular oxygen as a substrate in the microbial degredation of phenol. This protein is encoded by a single gene and uses a tightly bound FAD cofactor in the NAD(P)H dependent conversion of phenol and O2 to catechol and H2O. This group is related to the NAD binding ferredoxin reductases.
Probab=31.01  E-value=35  Score=15.81  Aligned_cols=23  Identities=4%  Similarity=0.060  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             99999999852898606999970
Q gi|254780547|r  106 AYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       106 A~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      .++|++.|.+.|+++++|....|
T Consensus       216 ~~av~~~L~~~Gv~~~~I~~E~F  238 (238)
T cd06211         216 IDACIKTLMQGRLFERDIYYEKF  238 (238)
T ss_pred             HHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             99999999986998899898069


No 76 
>pfam01764 Lipase_3 Lipase (class 3).
Probab=30.57  E-value=45  Score=15.15  Aligned_cols=58  Identities=31%  Similarity=0.491  Sum_probs=38.9

Q ss_pred             HHHHHHHHCC-CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCEEEEEEEECCCCCCCCCCC
Q ss_conf             9999843025-6058999972266533332001113379999999985289-860699997074489899878
Q gi|254780547|r   69 LSNLGSWLEK-HDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGI-SASRMKVTSYGKEMPSVYGHD  139 (160)
Q Consensus        69 L~~ia~~l~~-~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi-~~~ri~~~g~G~~~P~~~~~~  139 (160)
                      +..+.+++++ ++++|.|.||+           |+-.=|.-..-+|...+. +..++....||.  |..-|..
T Consensus        50 ~~~l~~~~~~~~~~~l~itGHS-----------LGGa~A~l~a~~l~~~~~~~~~~~~~~tfg~--Prvgn~~  109 (141)
T pfam01764        50 LEELKRLLEKYPDYKIVVTGHS-----------LGGALASLAAADLAENGLFPSSRIRVVTFGS--PRVGNYA  109 (141)
T ss_pred             HHHHHHHHHHCCCCEEEEEECC-----------HHHHHHHHHHHHHHHHCCCCCCCEEEEEECC--CCCCCHH
T ss_conf             9999999997899769998056-----------5789999999999982567878658999479--9757999


No 77 
>cd06212 monooxygenase_like The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is incorportated into the aromatic compond, while the other is used to form a molecule of water. In contrast dioxygenases add both atoms of oxygen to the substrate.
Probab=30.07  E-value=36  Score=15.73  Aligned_cols=24  Identities=8%  Similarity=0.170  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             799999999852898606999970
Q gi|254780547|r  105 RAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       105 RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      =-++|++.|.+.|+++++|....|
T Consensus       208 m~~~~~~~L~~~Gv~~~~I~~E~F  231 (232)
T cd06212         208 MIDAALPVLEMSGVPPDQIFYDKF  231 (232)
T ss_pred             HHHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             999999999986998899587407


No 78 
>pfam08085 Entericidin Entericidin EcnA/B family. This family consists of the entericidin antidote/toxin peptides. The entericidin locus is activated in stationary phase under high osmolarity conditions by rho-S and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins which can maintain plasmids in bacterial population by means of post-segregational killing.
Probab=29.75  E-value=47  Score=15.07  Aligned_cols=24  Identities=8%  Similarity=0.277  Sum_probs=16.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             903699999999999865024566
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDNL   24 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~~   24 (160)
                      |++..+++.+.+..++.+++|.+.
T Consensus         1 Mk~~~~~~~~l~~~~~~lagCNTv   24 (42)
T pfam08085         1 MKKLIALLLALLLLALVLAGCNTV   24 (42)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             923699999999999998612221


No 79 
>cd06209 BenDO_FAD_NAD Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal ferredoxin at the end fused to an FAD/NADP(P) domain.  In dioxygenase FAD/NAD(P) binding domain, the reductase transfers 2 electrons from NAD(P)H to the oxygenase which insert into an aromatic substrate, an initial step in microbial aerobic degradation of aromatic rings. Flavin oxidoreductases use flavins as substrates, unlike flavoenzymes which have a flavin prosthetic group.
Probab=29.63  E-value=40  Score=15.44  Aligned_cols=24  Identities=17%  Similarity=0.277  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             799999999852898606999970
Q gi|254780547|r  105 RAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       105 RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      =.++|++.|.+.||++++|....|
T Consensus       204 m~~~v~~~L~~~Gv~~~~Ih~E~F  227 (228)
T cd06209         204 MVDAVRSWLDEQGIEPANFYYEKF  227 (228)
T ss_pred             HHHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             999999999986998899388527


No 80 
>cd06194 FNR_N-term_Iron_sulfur_binding Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an N-terminal Iron-Sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second e
Probab=28.70  E-value=40  Score=15.44  Aligned_cols=24  Identities=17%  Similarity=0.146  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             799999999852898606999970
Q gi|254780547|r  105 RAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       105 RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      -.++|+++|.+.|+++++|....|
T Consensus       198 m~~a~~~~L~~~Gv~~~~I~~E~F  221 (222)
T cd06194         198 MVNAVRRRAFLAGAPMKRIYADPF  221 (222)
T ss_pred             HHHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             999999999986997897466011


No 81 
>PRK11872 antC anthranilate dioxygenase reductase; Provisional
Probab=28.07  E-value=48  Score=14.97  Aligned_cols=26  Identities=12%  Similarity=0.216  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEEECCC
Q ss_conf             99999999852898606999970744
Q gi|254780547|r  106 AYAVFNYFVARGISASRMKVTSYGKE  131 (160)
Q Consensus       106 A~aV~~~L~~~Gi~~~ri~~~g~G~~  131 (160)
                      -+++++.|.+.||++++|....|..+
T Consensus       313 v~a~~~~L~~~Gv~~~~I~~E~F~~S  338 (340)
T PRK11872        313 VEAVKQWLDEQALQNYRLYSEKFTQS  338 (340)
T ss_pred             HHHHHHHHHHCCCCHHHEEEEECCCC
T ss_conf             99999999986998899688615388


No 82 
>PRK13609 diacylglycerol glucosyltransferase; Provisional
Probab=27.82  E-value=51  Score=14.87  Aligned_cols=48  Identities=21%  Similarity=0.370  Sum_probs=32.9

Q ss_pred             HHHHHHHHHCCCCCEEEEEEEECCCCCCCCC-----CCHHHH-----HCCCEEEEEEEECCC
Q ss_conf             9999999852898606999970744898998-----787798-----429918999971368
Q gi|254780547|r  107 YAVFNYFVARGISASRMKVTSYGKEMPSVYG-----HDEDAY-----AKNRRAIVFLKGCRA  158 (160)
Q Consensus       107 ~aV~~~L~~~Gi~~~ri~~~g~G~~~P~~~~-----~~~~~~-----~~NRRVei~i~~~~~  158 (160)
                      +.+++.|++.|+++++|.+.|    -|+.+.     +.+..|     ..++++.++.-|..|
T Consensus       156 e~~k~~l~~~Gv~~~kI~vtG----iPVr~~F~~~~~k~~~r~~lgL~~d~~~vLimgGg~G  213 (388)
T PRK13609        156 DHVKEVMVDIGVPAEQIVETG----IPIRSSFELKINPDIIYNKYQLCKNKKILLIVAGAHG  213 (388)
T ss_pred             HHHHHHHHHHCCCHHHEEEEC----CCCCHHHCCCCCHHHHHHHHCCCCCCCEEEEECCHHH
T ss_conf             999999998099888999889----8438787275887899998289987847999766012


No 83 
>COG3672 Predicted transglutaminase-like cysteine proteinase [General    function prediction only]
Probab=27.14  E-value=52  Score=14.80  Aligned_cols=71  Identities=17%  Similarity=0.154  Sum_probs=42.8

Q ss_pred             ECCCCCCCHHHHHHHHHHHHHHCC---CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             047522432479999999843025---60589999722665333320011133799999999852898606999
Q gi|254780547|r   55 DTSSYSIRPADIQVLSNLGSWLEK---HDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKV  125 (160)
Q Consensus        55 ~~~s~~L~~~~~~~L~~ia~~l~~---~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~  125 (160)
                      +.....|+++-...|..+-...+.   +-.-+.|-|..|.=-.+.-+.-=-+.-|..=+..|++.|++++.+.+
T Consensus        60 ~~~~~~Lt~~~~~~L~~VN~~vN~~i~~~tD~e~~G~ed~Wa~P~~~~GDCEDyal~KRr~L~~~G~s~~~Lli  133 (191)
T COG3672          60 DTDPVKLTPDRWAELKRVNASVNTSIKPMTDMEIYGKEDYWAYPVTGAGDCEDYALEKRRRLMEAGVSSSALLI  133 (191)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHEEE
T ss_conf             99720059999999999999872115655215541752345688888666799999999999985998124789


No 84 
>PRK12701 flgH flagellar basal body L-ring protein; Reviewed
Probab=26.77  E-value=53  Score=14.76  Aligned_cols=22  Identities=14%  Similarity=-0.055  Sum_probs=13.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9036999999999998650245
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGID   22 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~   22 (160)
                      |+...+.+++.++.+++.|+..
T Consensus         1 m~r~~~~~~~la~~lL~GC~~~   22 (230)
T PRK12701          1 MNRLNIAVSCLATALLFGCEAL   22 (230)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCC
T ss_conf             9258999999999997556688


No 85 
>TIGR02074 PBP_1a_fam penicillin-binding protein, 1A family; InterPro: IPR011816    Bacterial that synthesize a cell wall of peptidoglycan (murein) generally have several transglycosylases and transpeptidases for the task. This family consists of bifunctional transglycosylase/transpeptidase penicillin-binding proteins (PBP). In the Proteobacteria, this family includes PBP 1A but not the paralogous PBP 1B (IPR011813 from INTERPRO). This family also includes related proteins, often designated PBP 1A, from other bacterial lineages.; GO: 0008233 peptidase activity, 0016763 transferase activity transferring pentosyl groups, 0009252 peptidoglycan biosynthetic process, 0046677 response to antibiotic.
Probab=26.48  E-value=54  Score=14.72  Aligned_cols=60  Identities=18%  Similarity=0.174  Sum_probs=41.0

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCC-CCCEEEE
Q ss_conf             0022047522432479999999843025605899997226653333200111337999999998528-9860699
Q gi|254780547|r   51 SVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARG-ISASRMK  124 (160)
Q Consensus        51 ~v~F~~~s~~L~~~~~~~L~~ia~~l~~~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~G-i~~~ri~  124 (160)
                      ..||.-+=.+|+-.-.+   -||..++.|           +.=+|-+|.+.+++|.+.|.+-..+.| |++++.+
T Consensus       123 ~~YFgK~v~~Ltl~EaA---~LAGlpkaP-----------s~Y~P~~~~e~A~~Rr~~VL~~M~~~G~It~~~~~  183 (700)
T TIGR02074       123 QVYFGKSVNDLTLAEAA---LLAGLPKAP-----------SAYNPFVNPERAKARRNLVLSRMVEEGYITAEEAE  183 (700)
T ss_pred             HHHCCCCHHHCCHHHHH---HHHHHHCCC-----------CCCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             76069776527888999---999861375-----------20276221689999999999999865897899999


No 86 
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA.  Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=26.13  E-value=42  Score=15.36  Aligned_cols=49  Identities=16%  Similarity=0.242  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHCCC---EEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             99999998430256---0589999722665333320011133799999999852898606999
Q gi|254780547|r   66 IQVLSNLGSWLEKH---DCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKV  125 (160)
Q Consensus        66 ~~~L~~ia~~l~~~---~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~  125 (160)
                      ...|..++..|++.   +-.+.           +....|--..-+.|++||.+.|+++++|.+
T Consensus        25 ~~~lk~l~k~LKk~~gcGGtvk-----------~~~IelQGD~R~~i~~~L~~~G~~~~~I~i   76 (77)
T cd00474          25 YADLKKLAKELKKKCACGGTVK-----------DEVIELQGDQRKKIKEFLIKMGFAKDNIKI   76 (77)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEE-----------CCEEEECCCHHHHHHHHHHHCCCCHHHEEE
T ss_conf             8999999999888643880795-----------399998281799999999984997898884


No 87 
>TIGR01270 Trp_5_monoox tryptophan 5-monooxygenase; InterPro: IPR005963    Tryptophan 5-monooxygenase (1.14.16.4 from EC) is a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tyrosine 3-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria. It is the rate-limiting enzyme in the biosynthesis of serotonin in the central nervous system and catalyzes the first step of the synthesis of melatonin in the pineal gland .  L-tryptophan + tetrahydropteridine + O2 = 5-hydroxy-L-tryptophan + dihydropteridine + H2O  ; GO: 0004510 tryptophan 5-monooxygenase activity, 0042427 serotonin biosynthetic process.
Probab=26.08  E-value=54  Score=14.68  Aligned_cols=54  Identities=13%  Similarity=0.210  Sum_probs=32.9

Q ss_pred             HHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             50245666665665544442012567875203100220475224324799999998430256
Q gi|254780547|r   18 ISGIDNLDTKISSPDTVLNESSLQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH   79 (160)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~F~~~s~~L~~~~~~~L~~ia~~l~~~   79 (160)
                      .+-......+.=.|..+..+    |-+...++ .+||.+.|-+   +|+++|+.++.-|++|
T Consensus       403 HA~~~~a~ik~FdP~~v~~q----ECLiTtFQ-~aYF~t~sFE---eA~~~mR~F~~~ikRP  456 (499)
T TIGR01270       403 HALSGKAKIKPFDPEKVCEQ----ECLITTFQ-NAYFYTESFE---EAKEKMREFTKTIKRP  456 (499)
T ss_pred             HHHCCCCEEEECCCCCEECC----CCCEEEEC-CEEEEECCHH---HHHHHHHHHHHHCCCC
T ss_conf             63245753651587400013----40154303-4146407769---9999999999736888


No 88 
>PRK13799 unknown domain/N-carbamoyl-L-amino acid hydrolase fusion protein; Provisional
Probab=25.85  E-value=55  Score=14.66  Aligned_cols=77  Identities=14%  Similarity=0.205  Sum_probs=53.7

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCEE-EEEE----------------------EEECCCC-CCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             22432479999999843025605-8999----------------------9722665-3333200111337999999998
Q gi|254780547|r   59 YSIRPADIQVLSNLGSWLEKHDC-DFLI----------------------EGHADEL-GSRNSSIALGLRRAYAVFNYFV  114 (160)
Q Consensus        59 ~~L~~~~~~~L~~ia~~l~~~~~-~i~I----------------------~GhtD~~-Gs~~yN~~LS~~RA~aV~~~L~  114 (160)
                      ..|+|..+.....+..||++.+. .|.|                      =-|-|.+ -.-.|-=.|+-==+..|.+.|.
T Consensus       207 ~ylt~~h~~~~~~~~~wMr~aG~deV~IDAvGNl~GR~eG~~p~ap~l~~GSHlDTVpnGG~yDG~LGVla~le~v~~L~  286 (591)
T PRK13799        207 TYLSDAHRACANQISDWMRDAGFDEVEIDAVGNVVGRYKAADDDAKTLITGSHYDTVRNGGKYDGREGIFLAIACVKELH  286 (591)
T ss_pred             EECCHHHHHHHHHHHHHHHHCCCCEEEECCCCCEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             96499999999999999998099779986775468880379999988888776036778865771899999999999999


Q ss_pred             HCCCCCE-EEEEEEECCCCCCC
Q ss_conf             5289860-69999707448989
Q gi|254780547|r  115 ARGISAS-RMKVTSYGKEMPSV  135 (160)
Q Consensus       115 ~~Gi~~~-ri~~~g~G~~~P~~  135 (160)
                      +.|+.+. -|++++|.+++..-
T Consensus       287 e~g~~~~~~iEVV~F~dEEGsR  308 (591)
T PRK13799        287 EQGERLPFHFEVIAFAEEEGQR  308 (591)
T ss_pred             HHCCCCCCCEEEEEECCCCCCC
T ss_conf             8099999986999874667766


No 89 
>cd00519 Lipase_3 Lipase (class 3).  Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface.  A typical feature of lipases is "interfacial activation," the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation .  The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure.  A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site.
Probab=25.83  E-value=55  Score=14.65  Aligned_cols=56  Identities=29%  Similarity=0.374  Sum_probs=37.2

Q ss_pred             HHHHHHCC-CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCH
Q ss_conf             99843025-60589999722665333320011133799999999852898606999970744898998787
Q gi|254780547|r   71 NLGSWLEK-HDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDE  140 (160)
Q Consensus        71 ~ia~~l~~-~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G~~~P~~~~~~~  140 (160)
                      .+...+++ ++++|.|.||+           |+-.=|.-..-+|...+ +...+.+..||.  |.+-+..-
T Consensus       117 ~~~~~~~~~p~~~i~vTGHS-----------LGgalA~L~a~~l~~~~-~~~~~~~~tfG~--Prvgn~~f  173 (229)
T cd00519         117 ELKSALKQYPDYKIIVTGHS-----------LGGALASLLALDLRLRG-PGSDVTVYTFGQ--PRVGNAAF  173 (229)
T ss_pred             HHHHHHHHCCCCEEEEECCC-----------CHHHHHHHHHHHHHHHC-CCCCEEEEEECC--CCCCCHHH
T ss_conf             99999987899569996467-----------06899999999999717-999707999479--97578999


No 90 
>PHA00691 hypothetical protein
Probab=25.73  E-value=55  Score=14.64  Aligned_cols=40  Identities=18%  Similarity=0.310  Sum_probs=25.5

Q ss_pred             HCCC-EEEEEEEEECCCCCCCCCCCH---HHHHHHHHHHHHHHHCC
Q ss_conf             0256-058999972266533332001---11337999999998528
Q gi|254780547|r   76 LEKH-DCDFLIEGHADELGSRNSSIA---LGLRRAYAVFNYFVARG  117 (160)
Q Consensus        76 l~~~-~~~i~I~GhtD~~Gs~~yN~~---LS~~RA~aV~~~L~~~G  117 (160)
                      |++. .+.+.|.|-|.++-...||+.   +|.  |.+-.+||..+-
T Consensus        18 L~K~~~Y~V~vSG~THST~DS~Y~lsda~~~i--A~~R~DYLArk~   61 (68)
T PHA00691         18 LKKSDSYTVFVSGVTHSTSDSTYELSDAESGI--AKARADYLARKL   61 (68)
T ss_pred             EEECCCEEEEEECCCCCCCCCCEECCCHHHHH--HHHHHHHHHHHC
T ss_conf             98278279998624324554201214112147--788778998722


No 91 
>cd06210 MMO_FAD_NAD_binding Methane monooxygenase (MMO) reductase of methanotrophs catalyzes the NADH-dependent hydroxylation of methane to methanol. This multicomponent enzyme mediates electron transfer via a hydroxylase (MMOH), a coupling protein, and a reductase which is comprised of an N-terminal [2Fe-2S] ferredoxin domain, an FAD binding subdomain, and an NADH binding subdomain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. Dioxygenases add both atom of oxygen to the substrate, while mono-oxygenases add one atom to the substrate and one atom to water.
Probab=25.62  E-value=49  Score=14.93  Aligned_cols=23  Identities=13%  Similarity=0.252  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             99999999852898606999970
Q gi|254780547|r  106 AYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       106 A~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      -++|++.|.+.|+++++|....|
T Consensus       213 ~~~~~~~l~~~Gv~~~~I~~E~F  235 (236)
T cd06210         213 VDAAFAAAREAGVPDEQVYLEKF  235 (236)
T ss_pred             HHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             99999999986998899598347


No 92 
>cd06198 FNR_like_3 NAD(P) binding domain of  ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH.
Probab=24.90  E-value=53  Score=14.77  Aligned_cols=25  Identities=24%  Similarity=0.230  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             3799999999852898606999970
Q gi|254780547|r  104 RRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       104 ~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      .-.++|++.|.+.|+++++|....|
T Consensus       191 ~mv~~~~~~L~~~Gv~~~~I~~E~F  215 (216)
T cd06198         191 GMADALEKGLRALGVPARRFHYERF  215 (216)
T ss_pred             HHHHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             9999999999986997898797022


No 93 
>cd06217 FNR_iron_sulfur_binding_3 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap between the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form 
Probab=24.61  E-value=53  Score=14.75  Aligned_cols=25  Identities=12%  Similarity=0.292  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             3799999999852898606999970
Q gi|254780547|r  104 RRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       104 ~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      .-.++|.+.|.+.|+++++|....|
T Consensus       211 ~m~~~v~~~L~~~Gv~~~~I~~E~F  235 (235)
T cd06217         211 AFVEAATRLLLELGVPRDRIRTEAF  235 (235)
T ss_pred             HHHHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             9999999999986997899797269


No 94 
>cd06191 FNR_iron_sulfur_binding Iron-sulfur binding Ferredoxin Reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with a C-terminal iron-sulfur binding cluster domain. FNR was intially identified as a chloroplast reductase activity catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methnae assimilation in a variety of organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in
Probab=24.56  E-value=56  Score=14.61  Aligned_cols=23  Identities=17%  Similarity=0.254  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             99999999852898606999970
Q gi|254780547|r  106 AYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       106 A~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      -++|++.|.+.|+++++|....|
T Consensus       209 ~~~~~~~L~~~Gv~~~~I~~E~F  231 (231)
T cd06191         209 MDAVETALKELGMPPERIHTERF  231 (231)
T ss_pred             HHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             99999999987997898898279


No 95 
>cd06187 O2ase_reductase_like The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate, while mono-oxygenases (aka mixed oxygenases) add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with Rieske type  [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate.
Probab=24.35  E-value=54  Score=14.71  Aligned_cols=25  Identities=20%  Similarity=0.377  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             3799999999852898606999970
Q gi|254780547|r  104 RRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       104 ~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      .--++|++.|.+.||++++|....|
T Consensus       200 ~m~~~v~~~L~~~Gv~~~~i~~E~F  224 (224)
T cd06187         200 AMVDATVDALLARGAPPERIHFDKF  224 (224)
T ss_pred             HHHHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             9999999999986997899798169


No 96 
>cd06215 FNR_iron_sulfur_binding_1 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal portion of the FAD/NAD binding domain contains most of the NADP(H) binding residues and the N-terminal sub-domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. In this ferredoxin like sub-group, the FAD/NAD sub-domains is typically fused to a C-terminal iron-sulfur binding domain. Iron-sulfur pr
Probab=24.28  E-value=58  Score=14.54  Aligned_cols=25  Identities=24%  Similarity=0.247  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             3799999999852898606999970
Q gi|254780547|r  104 RRAYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       104 ~RA~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      .--++|++.|.+.|+++++|....|
T Consensus       207 ~m~~~~~~~L~~~Gv~~~~I~~E~F  231 (231)
T cd06215         207 GFMKAVKSLLAELGFPMSRFHQESF  231 (231)
T ss_pred             HHHHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             9999999999986997897698179


No 97 
>cd06214 PA_degradation_oxidoreductase_like NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like domain with an iron-sulfur binding cluster domain. Ferredoxins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal portion may contain a flavin prosthetic group, as in flavoenzymes, or use flavin as a substrate. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and
Probab=24.24  E-value=53  Score=14.73  Aligned_cols=23  Identities=22%  Similarity=0.276  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf             99999999852898606999970
Q gi|254780547|r  106 AYAVFNYFVARGISASRMKVTSY  128 (160)
Q Consensus       106 A~aV~~~L~~~Gi~~~ri~~~g~  128 (160)
                      -++|.+.|.+.|+++++|....|
T Consensus       218 ~~~~~~~L~~~Gv~~~~I~~E~F  240 (241)
T cd06214         218 MDAVEAALLELGVPAERIHRELF  240 (241)
T ss_pred             HHHHHHHHHHCCCCHHHEEEEEC
T ss_conf             99999999986997899598315


No 98 
>PRK01741 cell division protein ZipA; Provisional
Probab=24.00  E-value=45  Score=15.13  Aligned_cols=21  Identities=29%  Similarity=0.559  Sum_probs=18.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHCC
Q ss_conf             903699999999999865024
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGI   21 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~   21 (160)
                      |.++.|||+++++++.++-..
T Consensus         1 MdLrlILIIvGaIAI~ALL~H   21 (342)
T PRK01741          1 MDLNTILIILGILALVALVAH   21 (342)
T ss_pred             CCCEEHHHHHHHHHHHHHHHH
T ss_conf             971254999999999999985


No 99 
>PRK05464 Na(+)-translocating NADH-quinone reductase subunit F; Provisional
Probab=23.56  E-value=48  Score=15.02  Aligned_cols=23  Identities=17%  Similarity=0.400  Sum_probs=11.3

Q ss_pred             HHHHHHHHHCCCCCEEEEEEEEC
Q ss_conf             99999998528986069999707
Q gi|254780547|r  107 YAVFNYFVARGISASRMKVTSYG  129 (160)
Q Consensus       107 ~aV~~~L~~~Gi~~~ri~~~g~G  129 (160)
                      ++|...|.+.||++++|....||
T Consensus       385 ~Av~~~L~~lGV~~E~I~~D~FG  407 (408)
T PRK05464        385 AAVIKMLKDLGVEDENILLDDFG  407 (408)
T ss_pred             HHHHHHHHHCCCCHHHEEECCCC
T ss_conf             99999999869998996433568


No 100
>pfam12000 DUF3495 Domain of unknown function (DUF3495). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 170 amino acids in length. This domain is found associated with pfam00534. This domain has a single completely conserved residue G that may be functionally important.
Probab=22.42  E-value=64  Score=14.26  Aligned_cols=50  Identities=14%  Similarity=0.125  Sum_probs=31.3

Q ss_pred             EEEEEECCCCCC------CCCCCHHHHHHHHHHHHHHH---HCCCCCEEEE-EEEECCCC
Q ss_conf             999972266533------33200111337999999998---5289860699-99707448
Q gi|254780547|r   83 FLIEGHADELGS------RNSSIALGLRRAYAVFNYFV---ARGISASRMK-VTSYGKEM  132 (160)
Q Consensus        83 i~I~GhtD~~Gs------~~yN~~LS~~RA~aV~~~L~---~~Gi~~~ri~-~~g~G~~~  132 (160)
                      |.+.-|.-.+++      ...+.+....|+++|.+.+.   +.|..|+-|. ..|.||.-
T Consensus        21 V~~~~Y~~~r~~~~~~h~~~~~~E~~~~rg~av~~aa~~L~~~Gf~PDvIi~H~GWGe~L   80 (172)
T pfam12000        21 VRLLRYRPPRGATPGTHPYLRDFEAAVIRGQAVARAARQLRAQGFRPDVIVAHPGWGETL   80 (172)
T ss_pred             EEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHH
T ss_conf             489995689888888783320599999999999999999997499999898758764010


No 101
>pfam11713 Peptidase_C80 Peptidase C80 family. This family belongs to cysteine peptidase family C80.
Probab=22.40  E-value=64  Score=14.26  Aligned_cols=46  Identities=17%  Similarity=0.226  Sum_probs=30.8

Q ss_pred             CCEEEEEEEEECCCCCCCCC-CCHHHHHHHHHHHHHHH--------HC--CCCCEEEEEEE
Q ss_conf             56058999972266533332-00111337999999998--------52--89860699997
Q gi|254780547|r   78 KHDCDFLIEGHADELGSRNS-SIALGLRRAYAVFNYFV--------AR--GISASRMKVTS  127 (160)
Q Consensus        78 ~~~~~i~I~GhtD~~Gs~~y-N~~LS~~RA~aV~~~L~--------~~--Gi~~~ri~~~g  127 (160)
                      ..+.+..+.||-+.    ++ |..|+-.-|+.++..|.        ..  .+.|++|..+|
T Consensus        55 ~gkiRwqlVGHG~~----~~n~~~lag~~a~~La~~l~~~~~~~~~~~~~~~~P~kI~LvG  111 (160)
T pfam11713        55 KGKIRWQFVGHGRD----EFNGPTLGGHTADELANKIASFRDAFLQTYGSNASPKKISLVG  111 (160)
T ss_pred             CCCEEEEEEECCCC----CCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEE
T ss_conf             78657999945866----5678432688999999999999999987534578874789998


No 102
>PRK06437 hypothetical protein; Provisional
Probab=22.02  E-value=65  Score=14.22  Aligned_cols=48  Identities=17%  Similarity=0.304  Sum_probs=35.9

Q ss_pred             EEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCC
Q ss_conf             5899997226653333200111337999999998528986069999707448989987
Q gi|254780547|r   81 CDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGH  138 (160)
Q Consensus        81 ~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G~~~P~~~~~  138 (160)
                      .-|.|.||-        |..+-..+-..|-+.+...|++.++..+.--|+  |+...+
T Consensus         3 ~MI~vkG~~--------~k~i~id~e~~v~Di~k~~~ldee~yvvIvNGs--P~~~D~   50 (67)
T PRK06437          3 AMIRVKGHI--------NKTIEIDHELTVNDIIKDLGLDEEEYVVIVNGS--PVLEDH   50 (67)
T ss_pred             EEEEEECEE--------CEEEEEECCCCHHHHHHHCCCCCCCEEEEECCC--CCCCCC
T ss_conf             799981100--------306984401328789998199921079998698--544445


No 103
>cd06193 siderophore_interacting Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from transferrin and lactoferrin for bacterial uptake, contributing to pathogen virulence. Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hy
Probab=21.59  E-value=67  Score=14.17  Aligned_cols=24  Identities=17%  Similarity=0.319  Sum_probs=20.3

Q ss_pred             HHHHHHHHHHH-CCCCCEEEEEEEE
Q ss_conf             79999999985-2898606999970
Q gi|254780547|r  105 RAYAVFNYFVA-RGISASRMKVTSY  128 (160)
Q Consensus       105 RA~aV~~~L~~-~Gi~~~ri~~~g~  128 (160)
                      =+++++.+|.. .|++.++|.+.||
T Consensus       209 ~~r~lR~~l~~~~g~~r~~i~~~gY  233 (235)
T cd06193         209 AVRALRRHLREERGVPRAQVYASGY  233 (235)
T ss_pred             HHHHHHHHHHHHHCCCHHHEEEEEE
T ss_conf             9999999999851998799489864


No 104
>PRK10523 lipoprotein involved with copper homeostasis and adhesion; Provisional
Probab=21.27  E-value=68  Score=14.13  Aligned_cols=28  Identities=21%  Similarity=0.315  Sum_probs=21.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             9036999999999998650245666665
Q gi|254780547|r    1 MQYSTIFIILSAITMMSISGIDNLDTKI   28 (160)
Q Consensus         1 M~~~~i~i~l~a~~~~~~~~~~~~~~~~   28 (160)
                      |=++.+|.++.++.++++.+|++..+..
T Consensus         1 ~mkk~~~~~~~a~g~~~l~GC~~r~~~~   28 (234)
T PRK10523          1 MMKKAILTALAAVGLFALMGCNNRAEVD   28 (234)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9058999999999999876346654346


No 105
>KOG4569 consensus
Probab=20.88  E-value=69  Score=14.08  Aligned_cols=55  Identities=27%  Similarity=0.405  Sum_probs=38.9

Q ss_pred             HHHHHHHCC-CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CEEEEEEEECCCCCCCCC
Q ss_conf             999843025-60589999722665333320011133799999999852898-606999970744898998
Q gi|254780547|r   70 SNLGSWLEK-HDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYFVARGIS-ASRMKVTSYGKEMPSVYG  137 (160)
Q Consensus        70 ~~ia~~l~~-~~~~i~I~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~~~Gi~-~~ri~~~g~G~~~P~~~~  137 (160)
                      +.+...+.. ++++|.|.||+           |+-.=|.--+.+++..|.. +.++.+..||.  |..-+
T Consensus       159 ~~~~~L~~~~~~~~i~vTGHS-----------LGgAlA~laa~~i~~~~~~~~~~v~v~tFG~--PRvGn  215 (336)
T KOG4569         159 AELRRLIELYPNYSIWVTGHS-----------LGGALASLAALDLVKNGLKTSSPVKVYTFGQ--PRVGN  215 (336)
T ss_pred             HHHHHHHHHCCCCEEEEEECC-----------CCHHHHHHHHHHHHHCCCCCCCCEEEEEECC--CCCCH
T ss_conf             999999986899679994068-----------7089899999999972766566459999169--96954


No 106
>COG1348 NifH Nitrogenase subunit NifH (ATPase) [Inorganic ion transport and metabolism]
Probab=20.54  E-value=61  Score=14.39  Aligned_cols=29  Identities=28%  Similarity=0.181  Sum_probs=10.1

Q ss_pred             EEECCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             97226653333200111337999999998
Q gi|254780547|r   86 EGHADELGSRNSSIALGLRRAYAVFNYFV  114 (160)
Q Consensus        86 ~GhtD~~Gs~~yN~~LS~~RA~aV~~~L~  114 (160)
                      +||+|..---..+.-.|..-|+.+..-+.
T Consensus       140 eg~AdeiyIVtSge~MalYAANNI~kgi~  168 (278)
T COG1348         140 EGYADEIYIVTSGEMMALYAANNIAKGIR  168 (278)
T ss_pred             CCCCCEEEEEECCCHHHHHHHHHHHHHHH
T ss_conf             26663799995683589999889999999


No 107
>TIGR01854 lipid_A_lpxH UDP-2,3-diacylglucosamine hydrolase; InterPro: IPR010138   This entry represents LpxH, or UDP-2,3-diacylglucosamine hydrolase (or pyrophosphatase), which is an essential enzyme in Escherichia coli that catalyses the fourth step in lipid A biosynthesis. This reaction involves pyrophosphate bond hydrolysis of the precursor UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate and UMP . Several Gram-negative bacteria have homologues of LpxH and/or LpxH2, while others have only distant orthologues of LpxH or LpxH2, or lack these enzymes altogether .; GO: 0016462 pyrophosphatase activity, 0009245 lipid A biosynthetic process, 0005737 cytoplasm.
Probab=20.48  E-value=42  Score=15.34  Aligned_cols=21  Identities=24%  Similarity=0.550  Sum_probs=14.0

Q ss_pred             HHHHHHCCCEEEEEEEEECCC
Q ss_conf             998430256058999972266
Q gi|254780547|r   71 NLGSWLEKHDCDFLIEGHADE   91 (160)
Q Consensus        71 ~ia~~l~~~~~~i~I~GhtD~   91 (160)
                      .++..|++++....|-|||-.
T Consensus       184 ~v~~~~~~~~v~~lIHGHTHR  204 (241)
T TIGR01854       184 EVAAVMRRYGVDLLIHGHTHR  204 (241)
T ss_pred             HHHHHHHHCCCCEEECCCCCC
T ss_conf             889999873861430678798


No 108
>pfam03702 UPF0075 Uncharacterized protein family (UPF0075). The proteins is this family are about 370 amino acids long and have no known function.
Probab=20.41  E-value=71  Score=14.02  Aligned_cols=34  Identities=21%  Similarity=0.231  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCC
Q ss_conf             1133799999999852898606999970744898
Q gi|254780547|r  101 LGLRRAYAVFNYFVARGISASRMKVTSYGKEMPS  134 (160)
Q Consensus       101 LS~~RA~aV~~~L~~~Gi~~~ri~~~g~G~~~P~  134 (160)
                      |.+--|+++.+.+...+..+.+|.+.|=|..+|.
T Consensus       265 lt~~ta~sIa~~i~~~~~~~~~iiv~GGG~~N~~  298 (363)
T pfam03702       265 LVELTAVTIVDALLQAGPDCERLLVCGGGARNPL  298 (363)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHH
T ss_conf             9999999999999962899758999788756889


No 109
>TIGR01618 phage_P_loop phage nucleotide-binding protein; InterPro: IPR006505   These sequences represent an uncharacterised family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of these proteins is unknown..
Probab=20.29  E-value=71  Score=14.00  Aligned_cols=78  Identities=15%  Similarity=0.150  Sum_probs=53.7

Q ss_pred             HHHHHHHHCC-CEEEEEEEEECCCCCCCC-----CCCHHHHHHHHHHHHHHHHCCCCCEEEEEEE-ECC--CCCCCCCCC
Q ss_conf             9999843025-605899997226653333-----2001113379999999985289860699997-074--489899878
Q gi|254780547|r   69 LSNLGSWLEK-HDCDFLIEGHADELGSRN-----SSIALGLRRAYAVFNYFVARGISASRMKVTS-YGK--EMPSVYGHD  139 (160)
Q Consensus        69 L~~ia~~l~~-~~~~i~I~GhtD~~Gs~~-----yN~~LS~~RA~aV~~~L~~~Gi~~~ri~~~g-~G~--~~P~~~~~~  139 (160)
                      +-.+...|.+ .+..|...-|-++.+...     ||+.+.+=|++.+=++|--.-|- .||...+ -|+  -+-+.-..+
T Consensus       127 ~~d~~~vl~~l~~~~i~~tAwe~~~~~~~e~G~iy~ry~pdir~kvlN~~lgl~DvV-aRl~~~~~tG~eevRg~~L~~~  205 (229)
T TIGR01618       127 FLDLLTVLKELKNKNIYVTAWEDTNQLSLESGQIYNRYLPDIREKVLNAFLGLTDVV-ARLVKNAKTGEEEVRGFILDPS  205 (229)
T ss_pred             HHHHHHHHHHCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEE-EEEEECCCCCHHHCCCEEECCC
T ss_conf             999999998558987999876566753401146687666775478876550333234-5676568888113132355599


Q ss_pred             HHHHHCCC
Q ss_conf             77984299
Q gi|254780547|r  140 EDAYAKNR  147 (160)
Q Consensus       140 ~~~~~~NR  147 (160)
                      +..+||||
T Consensus       206 ~G~yAKNr  213 (229)
T TIGR01618       206 KGNYAKNR  213 (229)
T ss_pred             CCCCCCCC
T ss_conf             87212110


No 110
>cd06196 FNR_like_1 Ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which varies in orientation with respect to the NAD(P) binding domain. The N-terminal region may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH.
Probab=20.11  E-value=62  Score=14.34  Aligned_cols=20  Identities=10%  Similarity=0.124  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHCCCCCEEEEE
Q ss_conf             99999999852898606999
Q gi|254780547|r  106 AYAVFNYFVARGISASRMKV  125 (160)
Q Consensus       106 A~aV~~~L~~~Gi~~~ri~~  125 (160)
                      -++|++.|.+.|+++++|..
T Consensus       198 ~~~~~~~L~~~Gv~~~~I~~  217 (218)
T cd06196         198 EEAINGALKELGVPEDSIVF  217 (218)
T ss_pred             HHHHHHHHHHCCCCHHHEEE
T ss_conf             99999999986998899883


Done!