Query         gi|254781067|ref|YP_003065480.1| elongation factor P [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 189
No_of_seqs    126 out of 1788
Neff          6.0 
Searched_HMMs 39220
Date          Mon May 30 05:19:03 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781067.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00038 efp translation elon 100.0       0       0  502.4  17.7  189    1-189     1-194 (194)
  2 PRK00529 elongation factor P;  100.0       0       0  495.4  22.0  186    3-188     1-186 (186)
  3 PRK12426 elongation factor P;  100.0       0       0  488.4  21.7  185    3-187     1-185 (185)
  4 PRK04542 elongation factor P;  100.0       0       0  483.4  22.0  186    3-188     1-189 (189)
  5 TIGR02178 yeiP elongation fact 100.0       0       0  360.5  16.6  183    5-187     1-187 (187)
  6 COG0231 Efp Translation elonga 100.0 2.6E-43       0  286.1  15.1  131    1-131     1-131 (131)
  7 PRK03999 translation initiatio 100.0 1.7E-32 4.3E-37  219.9  14.1  120    1-122     1-123 (129)
  8 pfam09285 Elong-fact-P_C Elong  99.9 1.3E-22 3.3E-27  159.3   6.2   56  131-186     1-56  (56)
  9 smart00841 Elong-fact-P_C Elon  99.9 1.5E-22 3.9E-27  158.9   6.2   56  131-186     1-56  (56)
 10 cd05794 S1_EF-P_repeat_2 S1_EF  99.9 2.6E-22 6.7E-27  157.4   6.2   56  131-186     1-56  (56)
 11 cd04470 S1_EF-P_repeat_1 S1_EF  99.8 7.2E-20 1.8E-24  142.5   6.9   61   68-128     1-61  (61)
 12 pfam08207 EFP_N Elongation fac  99.7 1.9E-17 4.8E-22  127.7   7.8   58    5-62      1-58  (58)
 13 pfam01132 EFP Elongation facto  99.7 3.3E-17 8.3E-22  126.3   6.0   55   69-123     1-55  (55)
 14 TIGR00037 eIF_5A translation i  99.6 1.1E-15 2.7E-20  117.0   8.7  113    4-116     7-123 (137)
 15 PTZ00328 eukaryotic initiation  99.4 1.2E-11 3.1E-16   92.1  12.7  115    4-118    23-149 (166)
 16 KOG3271 consensus               99.2 1.7E-10 4.4E-15   85.1   9.4  121    5-125    22-150 (156)
 17 cd04467 S1_aIF5A S1_aIF5A: Arc  96.9  0.0017 4.3E-08   42.2   5.0   53   67-121     1-53  (57)
 18 COG1499 NMD3 NMD protein affec  96.7   0.024 6.2E-07   35.1   9.6  104    7-126   245-352 (355)
 19 cd04463 S1_EF_like S1_EF_like:  96.0  0.0077   2E-07   38.2   3.7   54   70-124     1-54  (55)
 20 cd04463 S1_EF_like S1_EF_like:  95.0   0.045 1.1E-06   33.5   4.8   36  151-186    11-55  (55)
 21 pfam01287 eIF-5a Eukaryotic el  92.6    0.37 9.4E-06   27.9   5.6   60   66-125     1-68  (69)
 22 PRK08463 acetyl-CoA carboxylas  81.2     4.9 0.00012   21.0   6.1   65   70-140   272-344 (478)
 23 PRK08591 acetyl-CoA carboxylas  79.2     2.8 7.1E-05   22.5   3.7   26   70-96    272-297 (449)
 24 TIGR00514 accC acetyl-CoA carb  77.1    0.98 2.5E-05   25.3   0.9   73   71-150   274-355 (451)
 25 KOG0238 consensus               74.4     7.5 0.00019   19.9   4.9   69   70-138   268-356 (670)
 26 cd04468 S1_eIF5A S1_eIF5A: Euk  68.2     9.3 0.00024   19.3   4.2   50   67-116     1-53  (69)
 27 KOG0267 consensus               63.5      13 0.00034   18.4   5.5  161    5-172   137-313 (825)
 28 PRK08654 pyruvate carboxylase   61.6      14 0.00036   18.2   6.4   26   70-96    272-297 (497)
 29 PRK12833 acetyl-CoA carboxylas  59.9      14 0.00035   18.3   3.8   27   70-96    274-301 (458)
 30 COG1153 FwdD Formylmethanofura  58.2     6.2 0.00016   20.4   1.7   32   66-97     16-47  (128)
 31 pfam00900 Ribosomal_S4e Riboso  55.6      18 0.00046   17.6   4.4   37  146-182    36-73  (74)
 32 cd02779 MopB_CT_Arsenite-Ox Th  52.3      10 0.00026   19.1   2.1   14  107-120    47-60  (115)
 33 cd02789 MopB_CT_FmdC-FwdD The   52.1     9.7 0.00025   19.2   2.0   55   45-120     4-58  (106)
 34 cd02792 MopB_CT_Formate-Dh-Na-  48.5      12  0.0003   18.7   1.9   32   78-121    32-63  (122)
 35 TIGR02102 pullulan_Gpos pullul  48.4      13 0.00033   18.4   2.1   19  119-137  1008-1026(1164)
 36 cd02791 MopB_CT_Nitrate-R-NapA  46.5      14 0.00035   18.3   2.0   30   79-120    33-62  (122)
 37 cd02780 MopB_CT_Tetrathionate_  45.9      14 0.00036   18.2   2.0   31   79-121    28-58  (143)
 38 cd02785 MopB_CT_4 The MopB_CT_  45.1      14 0.00036   18.2   1.9   16  106-121    45-60  (124)
 39 TIGR01591 Fdh-alpha formate de  45.0      13 0.00034   18.3   1.7   23  166-188   623-646 (694)
 40 pfam00498 FHA FHA domain. The   44.6      27 0.00069   16.5   4.0   55   61-115    12-66  (67)
 41 cd02790 MopB_CT_Formate-Dh_H F  44.4      15 0.00038   18.1   1.9   31   79-121    33-63  (116)
 42 PRK13480 3'-5' exoribonuclease  43.9      27  0.0007   16.4   5.6   57    1-62      1-57  (314)
 43 cd02777 MopB_CT_DMSOR-like The  42.8      18 0.00046   17.6   2.1   17  106-122    47-63  (127)
 44 PRK06111 acetyl-CoA carboxylas  41.4      28 0.00071   16.4   2.9   27   70-96    272-298 (449)
 45 PRK05586 biotin carboxylase; V  40.0      32 0.00081   16.1   5.8   97   70-173   272-377 (447)
 46 cd02786 MopB_CT_3 The MopB_CT_  38.7      21 0.00053   17.2   1.9   32   79-122    29-60  (116)
 47 pfam02941 FeThRed_A Ferredoxin  38.5      21 0.00054   17.1   2.0   30  106-135    24-57  (67)
 48 PRK08462 biotin carboxylase; V  38.4      34 0.00086   15.9   6.4   97   69-174   273-379 (446)
 49 cd00508 MopB_CT_Fdh-Nap-like T  38.3      21 0.00054   17.1   1.9   31   78-120    32-62  (120)
 50 cd02776 MopB_CT_Nitrate-R-NarG  38.3      23 0.00058   17.0   2.1   30  106-135    44-78  (141)
 51 TIGR01540 portal_PBSX phage po  38.1      11 0.00028   18.8   0.5   21  166-186   169-189 (386)
 52 cd02778 MopB_CT_Thiosulfate-R-  36.8      24 0.00061   16.8   2.0   31   79-121    28-58  (123)
 53 cd02793 MopB_CT_DMSOR-BSOR-TMA  36.2      26 0.00067   16.5   2.1   17  106-122    46-62  (129)
 54 pfam01568 Molydop_binding Moly  35.1      25 0.00065   16.7   1.9   15  107-121    44-58  (110)
 55 KOG1708 consensus               35.1      23  0.0006   16.9   1.7   52  118-184   122-173 (236)
 56 cd02781 MopB_CT_Acetylene-hydr  34.9      26 0.00066   16.6   1.9   15  107-121    47-61  (130)
 57 PRK03955 hypothetical protein;  33.6      29 0.00074   16.3   2.0   16  167-182   111-126 (132)
 58 cd02775 MopB_CT Molybdopterin-  33.1      27  0.0007   16.5   1.8   15  107-121    37-51  (101)
 59 PRK07178 acetyl-CoA carboxylas  32.2      42  0.0011   15.3   7.4   96   71-174   272-376 (471)
 60 cd02782 MopB_CT_1 The MopB_CT_  31.1      34 0.00086   15.9   2.0   16  107-122    47-62  (129)
 61 cd02794 MopB_CT_DmsA-EC The Mo  31.0      34 0.00088   15.8   2.0   17  106-122    43-59  (121)
 62 TIGR01363 strep_his_triad stre  29.4      39   0.001   15.5   2.1   75    6-87    122-206 (376)
 63 TIGR02087 LEUD_arch 3-isopropy  25.7      46  0.0012   15.1   1.9   19  166-184   108-126 (159)
 64 TIGR01196 edd phosphogluconate  25.4      42  0.0011   15.3   1.6   16  168-183   546-561 (614)
 65 TIGR01017 rpsD_bact ribosomal   25.2      56  0.0014   14.5   2.9   27  154-180   126-153 (217)
 66 TIGR02517 type_II_gspD general  24.9      51  0.0013   14.8   2.0   36  142-177   558-595 (697)
 67 PRK06302 acetyl-CoA carboxylas  24.8      31 0.00079   16.1   0.9   14  165-178    99-112 (155)
 68 pfam08968 DUF1885 Domain of un  24.7      47  0.0012   15.0   1.8   52   73-124    59-124 (128)
 69 TIGR03479 DMSO_red_II_alp DMSO  24.5      50  0.0013   14.8   1.9   22  167-188   823-844 (912)
 70 cd00060 FHA Forkhead associate  23.5      60  0.0015   14.3   3.7   56   61-116    36-92  (102)
 71 PRK03947 prefoldin subunit alp  23.4      61  0.0015   14.3   3.1   46  142-187    47-92  (141)
 72 pfam11871 DUF3391 Domain of un  23.0      57  0.0014   14.5   1.9   21    2-22      3-23  (127)
 73 PRK08166 NADH dehydrogenase su  23.0      50  0.0013   14.8   1.7   23  166-188   800-822 (858)
 74 COG3173 Predicted aminoglycosi  22.8      62  0.0016   14.3   2.7   19    9-27    205-223 (321)
 75 TIGR01348 PDHac_trf_long pyruv  22.3      64  0.0016   14.2   2.3   23  143-165   230-253 (655)
 76 PRK08493 NADH dehydrogenase su  21.6      58  0.0015   14.5   1.8   23  166-188   759-781 (819)
 77 COG0243 BisC Anaerobic dehydro  21.3      67  0.0017   14.1   2.0   21  168-188   685-705 (765)
 78 smart00359 PUA Putative RNA-bi  21.2      67  0.0017   14.1   2.9   33  155-187    18-50  (77)
 79 PRK13532 nitrate reductase; Pr  21.1      61  0.0016   14.3   1.8   23  166-188   756-778 (828)
 80 smart00166 UBX Domain present   20.7      49  0.0012   14.9   1.2   48   35-87      3-50  (80)
 81 pfam10709 DUF2511 Protein of u  20.5      69  0.0018   14.0   4.2   56   65-120    34-89  (110)
 82 pfam00789 UBX UBX domain. This  20.1      71  0.0018   13.9   2.1   49   35-86      3-51  (81)

No 1  
>TIGR00038 efp translation elongation factor P; InterPro: IPR011768   Members of this family possess translation elongation factor activity. They have been shown to stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro, possibly indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity) . This family does not include members of IPR011897 from INTERPRO, an EFP-like protein of certain gammaproteobacteria.; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=502.38  Aligned_cols=189  Identities=35%  Similarity=0.620  Sum_probs=187.7

Q ss_pred             CC-EEEHHHCCCCCEEEE-CCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEE
Q ss_conf             92-366432167758998-8937999998753688876389999998246871001342787200101056405789961
Q gi|254781067|r    1 MV-KVIASAVRKGNVLDV-DGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQD   78 (189)
Q Consensus         1 m~-~i~an~lk~G~~i~~-dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~d   78 (189)
                      || ++.+|+||+|..|.. ||+||+|++++|+|||||+||+|+|||||+||++++++||++|++|.|++++..|||||.|
T Consensus         1 MA~~~~s~d~r~Gl~i~~~~G~~~~VvE~~fvKpGkG~AfVR~Klk~L~tG~v~~~tFk~Gd~~e~~~i~~~~mqylYkD   80 (194)
T TIGR00038         1 MAEMISSNDFRKGLKILLIDGEPYRVVENEFVKPGKGQAFVRTKLKNLRTGAVVEKTFKAGDKVEQANIEEKTMQYLYKD   80 (194)
T ss_pred             CCCEEEEECCCCCCEEEECCCEEEEEEECCCCCCCCCCCEEEEEEEECCCCCEEEEECCCCCCCCCCEEEEEEEEEEEEC
T ss_conf             97405520456885387229838999812457875666166766531358848999417668635416764334477706


Q ss_pred             CCEEEEEECCCCCCCCCCHHH---HHHHHHHCCCCCEEEEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEE
Q ss_conf             988999946887643211543---00133201378615689766777440158749999998285421310247700089
Q gi|254781067|r   79 QEGFHFMNPETYDQVTVSEEV---IGDQKVYFQEGMEVKLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAI  155 (189)
Q Consensus        79 g~~~~FMd~etyeqi~i~~~~---ig~~~~fL~eg~~v~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~  155 (189)
                      ||.|+|||++||||++|+.+.   |||+.+||.|+++|+|.+|+|++|+|+||++|.|+|++||||+|||||++++|||+
T Consensus        81 gd~~vFMD~etyeQ~~~~~~~sanl~d~~kfl~e~~~v~v~~~~~~~l~v~lP~~V~levVetepg~KGDTa~~g~KpA~  160 (194)
T TIGR00038        81 GDQYVFMDLETYEQISLDAKQSANLGDEAKFLLEEMEVSVVLYNDEILGVELPNLVELEVVETEPGVKGDTATGGTKPAT  160 (194)
T ss_pred             CCEEEECCCCCHHHEECCCCCCCCCHHHHCCCCCCCEEEEEEECCEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCEE
T ss_conf             97688667886555311611154520110023566338999768948413078725789987588974663678604558


Q ss_pred             EECCCEEECCCCCCCCCEEEEECCCCCEEHHCCC
Q ss_conf             9379599847401688799998899724021029
Q gi|254781067|r  156 LSNDIRTTVPPHINIGDDIVILTEDNSYVERVKK  189 (189)
Q Consensus       156 letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~Rakk  189 (189)
                      |+||++|+||+||++||+|+|||+||||++|+|+
T Consensus       161 L~TG~vV~VPlFv~~Gd~i~v~T~~geY~eR~k~  194 (194)
T TIGR00038       161 LETGAVVKVPLFVNEGDKIKVNTRDGEYVERVKK  194 (194)
T ss_pred             ECCCCEEECCEEEEECCEEEEECCCCCHHCCCCC
T ss_conf             6168688254054208889892577731100269


No 2  
>PRK00529 elongation factor P; Validated
Probab=100.00  E-value=0  Score=495.42  Aligned_cols=186  Identities=38%  Similarity=0.645  Sum_probs=184.6

Q ss_pred             EEEHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEE
Q ss_conf             36643216775899889379999987536888763899999982468710013427872001010564057899619889
Q gi|254781067|r    3 KVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGF   82 (189)
Q Consensus         3 ~i~an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~   82 (189)
                      |++||+||+|++|++||+||+|++++|++||||+||+|+|||||.||+++++||+++|++|.|+++++++||||.||+.|
T Consensus         1 Mi~~~~ik~G~~i~~~g~~~~V~~~~~~kpgkg~A~~~~klknl~tG~~~e~~f~s~d~ve~a~~~~~~~qylY~dg~~~   80 (186)
T PRK00529          1 MISANDFRPGNVIELDGEPWVVLEFEHVKPGKGQAFVRVKLKNLLTGKVVEKTFKAGDKVERADVERKEMQYLYFDGEMY   80 (186)
T ss_pred             CCCHHHCCCCCEEEECCEEEEEEEEEEECCCCCCEEEEEEEEECCCCCEEEEEECCCCEEEEEEEEEEEEEEEEECCCCE
T ss_conf             98568667878999999999999988873888952899999982789748999858977788689634569999779953


Q ss_pred             EEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCCEE
Q ss_conf             99946887643211543001332013786156897667774401587499999982854213102477000899379599
Q gi|254781067|r   83 HFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRT  162 (189)
Q Consensus        83 ~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i  162 (189)
                      +|||++||||++|+++++|++.+||+||++|.+.+|+|+||+|+||++|+|+|++|+|++|||||++++|||+||||++|
T Consensus        81 ~FMd~etyEQi~l~~~~ig~~~~~L~e~~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~vKGdTas~~~KpA~letG~~v  160 (186)
T PRK00529         81 VFMDTETYEQIEVPAEQVGDAAKFLKEGMEVTVTFYNGEPISVELPNTVELEVTETEPGVKGDTASGGTKPATLETGAVV  160 (186)
T ss_pred             EEECCCCCCCEECCHHHHHHHHHHHCCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCEEEECCCCEE
T ss_conf             99769974114347889777887423797899999899998555898599999988996444456788661998289999


Q ss_pred             ECCCCCCCCCEEEEECCCCCEEHHCC
Q ss_conf             84740168879999889972402102
Q gi|254781067|r  163 TVPPHINIGDDIVILTEDNSYVERVK  188 (189)
Q Consensus       163 ~VP~FI~~Gd~IkV~T~~g~Y~~Rak  188 (189)
                      +||+||++||+|+||||+|+|++|||
T Consensus       161 ~VP~FI~~Gd~IkVdT~~geYv~RaK  186 (186)
T PRK00529        161 QVPLFINEGEKIKVDTRTGEYVSRAK  186 (186)
T ss_pred             EECCCCCCCCEEEEECCCCEEEHHCC
T ss_conf             83883218999999899976800249


No 3  
>PRK12426 elongation factor P; Provisional
Probab=100.00  E-value=0  Score=488.35  Aligned_cols=185  Identities=23%  Similarity=0.484  Sum_probs=183.4

Q ss_pred             EEEHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEE
Q ss_conf             36643216775899889379999987536888763899999982468710013427872001010564057899619889
Q gi|254781067|r    3 KVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGF   82 (189)
Q Consensus         3 ~i~an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~   82 (189)
                      |++||+||+|++|+++|+||+|++++|++||||+||+|+|||||.||+++++||+++|++|.|+++++++||||.||+.|
T Consensus         1 Mi~~n~lk~G~~i~~~g~~~~V~~~~h~kpGkg~a~v~~klknl~tG~~~e~tf~s~ekve~a~~~~~~~qyLY~dg~~~   80 (185)
T PRK12426          1 MVLSSQLSVGMFISTKDGLYKVVSVSKVTGPKGESFIKVSLQAADSDVIVERNFKAGQEVKEAQFEPRNLEYLYLEDDSY   80 (185)
T ss_pred             CCCHHHCCCCCEEEECCEEEEEEEEEECCCCCCCEEEEEEEEECCCCCEEEEEECCCCEEEEEEEEEEEEEEEEECCCEE
T ss_conf             97456257888999999899999976137999850899999983789989988989999978889887889999789838


Q ss_pred             EEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCCEE
Q ss_conf             99946887643211543001332013786156897667774401587499999982854213102477000899379599
Q gi|254781067|r   83 HFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRT  162 (189)
Q Consensus        83 ~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i  162 (189)
                      +|||++||||++|+++.+|++.+||+||++|+++||+++||+|+||++|+|+|++|+|++||||+++++|||+||||++|
T Consensus        81 ~FMd~etyEQ~~v~~~~lg~~~~~L~e~~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~~kg~t~s~~~KpA~leTG~~I  160 (185)
T PRK12426         81 LFLDLGNYEKIYIPKEIMKDNFLFLKAGVTVSALVYDNTVFSVELPHFLELMVSKTDFPGDSLSLSGGAKKALLETGVEV  160 (185)
T ss_pred             EEECCCCCCCEECCHHHCCHHHHHHCCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEECCCCEE
T ss_conf             99579983317814556003565303786699999188389988899799999989999678535787250898189999


Q ss_pred             ECCCCCCCCCEEEEECCCCCEEHHC
Q ss_conf             8474016887999988997240210
Q gi|254781067|r  163 TVPPHINIGDDIVILTEDNSYVERV  187 (189)
Q Consensus       163 ~VP~FI~~Gd~IkV~T~~g~Y~~Ra  187 (189)
                      +||+||++||+|+||||+|+|++|+
T Consensus       161 ~VP~FI~~Gd~IkVdT~~g~Yv~RV  185 (185)
T PRK12426        161 LVPPFVEIGDVIKVDTRTCEYIQRV  185 (185)
T ss_pred             EECCCCCCCCEEEEECCCCEEEECC
T ss_conf             8188402999999989987577059


No 4  
>PRK04542 elongation factor P; Provisional
Probab=100.00  E-value=0  Score=483.36  Aligned_cols=186  Identities=26%  Similarity=0.512  Sum_probs=182.3

Q ss_pred             EEEHHHCCCCCEEEECCEEEEEEEEEEECCC--CCCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECC
Q ss_conf             3664321677589988937999998753688--87638999999824687100134278720010105640578996198
Q gi|254781067|r    3 KVIASAVRKGNVLDVDGKLYIVLVAKNFHPG--KGTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQE   80 (189)
Q Consensus         3 ~i~an~lk~G~~i~~dg~~~~V~~~~~~kpg--kg~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~   80 (189)
                      |++||+||+|++|++||+||+|++++|++||  +|+|++|+|||||+||+++++||+++|+||.|+++++++||||.||+
T Consensus         1 M~~a~dik~G~~i~~~g~~~~V~~~~~~kpg~r~g~~~~r~klKnl~tG~~~e~tf~~~d~ve~a~ve~~~~qyLY~dg~   80 (189)
T PRK04542          1 MPKASEIKKGMAVEYNGKLLLVKDIERSSPQGRGGATLYKMRFYDVRTGLKVEERFKGDDILDTVTLTRRQVTFSYVDGD   80 (189)
T ss_pred             CCCHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCCEEEEEEEEECCCCCEEEEEECCCCEEEEEEEEEEEEEEEEECCC
T ss_conf             98556367988999999899999999888998886169999997627898899998699999887886788899995899


Q ss_pred             EEEEEECCCCCCCCCCHHHHHHHHHHCCCCCE-EEEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECC
Q ss_conf             89999468876432115430013320137861-56897667774401587499999982854213102477000899379
Q gi|254781067|r   81 GFHFMNPETYDQVTVSEEVIGDQKVYFQEGME-VKLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSND  159 (189)
Q Consensus        81 ~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~-v~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~letG  159 (189)
                      .|+|||++||||++|+++++|++.+||+||++ |.+++|+|+||+|+||++|+|+|++|||++||||+++++|||+||||
T Consensus        81 ~~~FMd~etyEQi~l~~~~vg~~~~~L~e~~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~vKGdTas~~~K~AtletG  160 (189)
T PRK04542         81 EYVFMDNEDYTPYTFTKDQIEEELLFIPEGTPGMQVLTVDGQPVALELPQTVDLEIVETAPSIKGASASARTKPATLSTG  160 (189)
T ss_pred             EEEEEECCCHHHEEECHHHHHHHHHHHHCCCEEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCEEEECCC
T ss_conf             17999699833265278995118765126998999999899789998898399999988996445357888760998289


Q ss_pred             CEEECCCCCCCCCEEEEECCCCCEEHHCC
Q ss_conf             59984740168879999889972402102
Q gi|254781067|r  160 IRTTVPPHINIGDDIVILTEDNSYVERVK  188 (189)
Q Consensus       160 ~~i~VP~FI~~Gd~IkV~T~~g~Y~~Rak  188 (189)
                      ++|+||+||++||+|+||||+|+|++||+
T Consensus       161 ~~I~VPlFI~~Gd~IkVdT~~g~Yv~RAn  189 (189)
T PRK04542        161 LVIQVPEYISTGEKIRINTAERKFMGRAD  189 (189)
T ss_pred             CEEEECCCCCCCCEEEEECCCCEEHHHCC
T ss_conf             99982884039999999899873611269


No 5  
>TIGR02178 yeiP elongation factor P-like protein YeiP; InterPro: IPR011897    This entry represents homologs of elongation factor P (IPR011768 from INTERPRO) and probably are translation factors. Member of this family are found only in some gammaproteobacteria, including Escherichia coli (YeiP) and Vibrio cholerae..
Probab=100.00  E-value=0  Score=360.45  Aligned_cols=183  Identities=28%  Similarity=0.552  Sum_probs=178.6

Q ss_pred             EHHHCCCCCEEEECCEEEEEEEEEEECC-CCCCC-EEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEE
Q ss_conf             6432167758998893799999875368-88763-899999982468710013427872001010564057899619889
Q gi|254781067|r    5 IASAVRKGNVLDVDGKLYIVLVAKNFHP-GKGTP-ITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGF   82 (189)
Q Consensus         5 ~an~lk~G~~i~~dg~~~~V~~~~~~kp-gkg~a-~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~   82 (189)
                      .|||||||++|+++|+.|+|-|++..+| |||++ .+|+.+.++.||.++|.+|+++|-++-|.+.||++.|+|.||+.|
T Consensus         1 kAsE~KKG~~~~yngktllikDI~~~sP~gRGg~~~yk~r~~dv~tG~kveerfk~Dd~ldtVel~rR~~sFSY~DG~ey   80 (187)
T TIGR02178         1 KASELKKGSVVEYNGKTLLIKDIEVSSPQGRGGAVLYKLRMSDVRTGSKVEERFKADDVLDTVELLRREVSFSYVDGEEY   80 (187)
T ss_pred             CCCCCCCCEEEEECCCEEEEEEEEECCCCCCCCCEEEEEEEEECCCCCEEEECCCCCCEEEEEEEEECEEEEEEECCCEE
T ss_conf             95421124389835987889865542899876233888998656878524201076722311121100046777637506


Q ss_pred             EEEECCCCCCCCCCHHHHHHHHHHCCCC-CE-EEEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCC
Q ss_conf             9994688764321154300133201378-61-568976677744015874999999828542131024770008993795
Q gi|254781067|r   83 HFMNPETYDQVTVSEEVIGDQKVYFQEG-ME-VKLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDI  160 (189)
Q Consensus        83 ~FMd~etyeqi~i~~~~ig~~~~fL~eg-~~-v~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~letG~  160 (189)
                      +|||.|+|..|++.+|.++|.+.|+.|| |. |+|++||+.+++++||++|+|+|.+|+|.+||.|||+++|||+|.||+
T Consensus        81 VFmd~eDYTpYtf~kd~Iedellfi~EgG~~gm~V~l~Dg~~vAleLPq~V~leiveT~P~iKGasAs~R~KPA~l~TGl  160 (187)
T TIGR02178        81 VFMDEEDYTPYTFDKDEIEDELLFISEGGLSGMSVLLIDGEAVALELPQSVELEIVETDPEIKGASASKRPKPAKLITGL  160 (187)
T ss_pred             EEECCCCCCCCCCCHHHHCCCCCEECCCCCCCCEEEEECCCHHHHHCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             83058788742577445001000205577688679998130042318874589988479998453247788886115652


Q ss_pred             EEECCCCCCCCCEEEEECCCCCEEHHC
Q ss_conf             998474016887999988997240210
Q gi|254781067|r  161 RTTVPPHINIGDDIVILTEDNSYVERV  187 (189)
Q Consensus       161 ~i~VP~FI~~Gd~IkV~T~~g~Y~~Ra  187 (189)
                      +||||.||.+||+|.|||+++.|++||
T Consensus       161 vv~VPEYi~tGerI~in~~er~fmgRA  187 (187)
T TIGR02178       161 VVQVPEYITTGERILINTEERKFMGRA  187 (187)
T ss_pred             EEECCCCCCCCCEEEEECCCCCCCCCC
T ss_conf             786776238998699962457656889


No 6  
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=2.6e-43  Score=286.13  Aligned_cols=131  Identities=36%  Similarity=0.661  Sum_probs=129.5

Q ss_pred             CCEEEHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECC
Q ss_conf             92366432167758998893799999875368887638999999824687100134278720010105640578996198
Q gi|254781067|r    1 MVKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQE   80 (189)
Q Consensus         1 m~~i~an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~   80 (189)
                      |+++++|+||+|++|.+||+||+|++++|+|||||+|++|+++|||.||++.+.+|+++|++|.|.++++++||||.||+
T Consensus         1 ~~~i~~~~lr~G~~i~~dg~~~~V~~~~~~KpGKg~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q~lY~dg~   80 (131)
T COG0231           1 MAMISASELRKGLYIVIDGEPYVVVEISHVKPGKGGAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQYLYIDGD   80 (131)
T ss_pred             CCEEEHHHCCCCCEEEECCEEEEEEEEEECCCCCCCCEEEEEEEECCCCCEEEEEECCCCEEEEEEEEEEEEEEEECCCC
T ss_conf             94056777268779998996899999787269999857999999845898999997578889886996005699994899


Q ss_pred             EEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEECCCCEE
Q ss_conf             899994688764321154300133201378615689766777440158749
Q gi|254781067|r   81 GFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVEVPRHV  131 (189)
Q Consensus        81 ~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~lP~~v  131 (189)
                      .|+|||++||||++++.+.+||.++||+||++|++++|+|++++|+||++|
T Consensus        81 ~~~FMD~etyeq~~v~~~~~~d~~~~l~eg~~v~v~~~~g~~i~v~lP~~v  131 (131)
T COG0231          81 FYVFMDLETYEQYELPKDQIGDAAKFLKEGMEVEVLLYNGEPIAVELPNFV  131 (131)
T ss_pred             EEEECCCCCCEEEEECHHHHHHHHHHCCCCCEEEEEEECCEEEEEECCCCC
T ss_conf             589814898268996402414588635799899999999999999889879


No 7  
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00  E-value=1.7e-32  Score=219.86  Aligned_cols=120  Identities=25%  Similarity=0.305  Sum_probs=113.2

Q ss_pred             CCE--EEHHHCCCCCEEEECCEEEEEEEEEEECCCC-CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEE
Q ss_conf             923--6643216775899889379999987536888-7638999999824687100134278720010105640578996
Q gi|254781067|r    1 MVK--VIASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQ   77 (189)
Q Consensus         1 m~~--i~an~lk~G~~i~~dg~~~~V~~~~~~kpgk-g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~   77 (189)
                      |++  ++|++||+|..|+++|+||+|++++|+|||| |+|++|++++||+||++.+.+|++++++|.|.++++++||||.
T Consensus         1 m~~~~i~~~dlK~G~~i~idg~pckVve~~~sKpGKHG~Akvr~~~~~i~tG~k~e~~~~~~~kve~p~i~kk~~Q~l~~   80 (129)
T PRK03999          1 MSKKQVEVGELKEGSYVVIDGEPCRIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVAPVDAKVEVPIIEKRTGQVLSI   80 (129)
T ss_pred             CCCCEEEHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCEEEEEECCCCEEECCEEEEEEEEEEEE
T ss_conf             97222678992689999999985999998886499985369999999646797899988798805646698768899995


Q ss_pred             ECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEE
Q ss_conf             198899994688764321154300133201378615689766777
Q gi|254781067|r   78 DQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVA  122 (189)
Q Consensus        78 dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~  122 (189)
                      +|+.|+|||+|||||+++|.+  .+...+|++|++|.++-..|+-
T Consensus        81 ~gd~~~fMD~etyE~~elp~~--~e~~~~l~~G~eV~~~~a~G~~  123 (129)
T PRK03999         81 MGDTVQLMDLETYETFEVPIP--EELKDKIEPGVEVEYWEAMGRR  123 (129)
T ss_pred             CCCEEEEECCCCCEEEEECCC--HHHHHHCCCCCEEEEEEECCEE
T ss_conf             699999975999426770199--8998505399879999828937


No 8  
>pfam09285 Elong-fact-P_C Elongation factor P, C-terminal. Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology.
Probab=99.87  E-value=1.3e-22  Score=159.35  Aligned_cols=56  Identities=38%  Similarity=0.588  Sum_probs=55.1

Q ss_pred             EEEEEEECCCCCCCCCCCCCEEEEEEECCCEEECCCCCCCCCEEEEECCCCCEEHH
Q ss_conf             99999982854213102477000899379599847401688799998899724021
Q gi|254781067|r  131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER  186 (189)
Q Consensus       131 v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~R  186 (189)
                      |+|+|++|+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++|
T Consensus         1 V~l~V~etep~vKG~Ta~~~~K~A~letG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R   56 (56)
T pfam09285         1 VELEVVETEPGVKGDTASSGTKPATLETGAEVQVPLFIEEGEKIKVDTRTGEYVSR   56 (56)
T ss_pred             CEEEEEECCCCCCCCCCCCCCCEEEECCCCEEECCCCCCCCCEEEEECCCCEEECC
T ss_conf             98999978985235345777342898389899838740489999998998858778


No 9  
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=99.87  E-value=1.5e-22  Score=158.88  Aligned_cols=56  Identities=41%  Similarity=0.577  Sum_probs=55.1

Q ss_pred             EEEEEEECCCCCCCCCCCCCEEEEEEECCCEEECCCCCCCCCEEEEECCCCCEEHH
Q ss_conf             99999982854213102477000899379599847401688799998899724021
Q gi|254781067|r  131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER  186 (189)
Q Consensus       131 v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~R  186 (189)
                      |+|+|++|+|++||||+++++|||+||||++||||+||++||+|+|||++|+|++|
T Consensus         1 V~l~V~etep~vKG~Tas~~~K~A~letG~~i~VP~FI~~Gd~I~IdT~~g~Y~~R   56 (56)
T smart00841        1 VELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFINEGDKIKVDTRTGEYVSR   56 (56)
T ss_pred             CEEEEEECCCCCCCCCCCCCCCEEEECCCCEEECCCCCCCCCEEEEECCCCEEECC
T ss_conf             98999978997335455786031898489899838740389999998999858778


No 10 
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P 
Probab=99.86  E-value=2.6e-22  Score=157.43  Aligned_cols=56  Identities=39%  Similarity=0.586  Sum_probs=55.1

Q ss_pred             EEEEEEECCCCCCCCCCCCCEEEEEEECCCEEECCCCCCCCCEEEEECCCCCEEHH
Q ss_conf             99999982854213102477000899379599847401688799998899724021
Q gi|254781067|r  131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER  186 (189)
Q Consensus       131 v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~R  186 (189)
                      |+|+|++|+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++|
T Consensus         1 v~l~V~etep~~kG~Tas~~~K~A~letG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R   56 (56)
T cd05794           1 VELEVTETEPGVKGDTASSGTKPATLETGAEVQVPLFIKEGEKIKVDTRTGEYVER   56 (56)
T ss_pred             CEEEEEECCCCCCCCCCCCCCCEEEECCCCEEECCCCCCCCCEEEEECCCCEEECC
T ss_conf             98999988986335445777452897389999848740489999998998848678


No 11 
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P 
Probab=99.80  E-value=7.2e-20  Score=142.52  Aligned_cols=61  Identities=39%  Similarity=0.840  Sum_probs=60.0

Q ss_pred             CCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEECCC
Q ss_conf             5640578996198899994688764321154300133201378615689766777440158
Q gi|254781067|r   68 EDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVEVP  128 (189)
Q Consensus        68 e~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~lP  128 (189)
                      +++++||||.||+.|+|||++||||++|+++.+|++.+||+||++|.+.+|+|+||+|+||
T Consensus         1 e~~~~qyLY~dg~~~~FMd~etyEQi~v~~~~igd~~~~L~e~~~v~i~~~~~~~i~i~lP   61 (61)
T cd04470           1 EEREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVELP   61 (61)
T ss_pred             CCCEEEEEEECCCEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEEECC
T ss_conf             9831699896899089954886412216677863278635589899999989998988895


No 12 
>pfam08207 EFP_N Elongation factor P (EF-P) KOW-like domain.
Probab=99.72  E-value=1.9e-17  Score=127.71  Aligned_cols=58  Identities=31%  Similarity=0.678  Sum_probs=56.6

Q ss_pred             EHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCE
Q ss_conf             6432167758998893799999875368887638999999824687100134278720
Q gi|254781067|r    5 IASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQV   62 (189)
Q Consensus         5 ~an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekv   62 (189)
                      +|||||+|++|++||+||+|++++|++||||+|++|+|||||.||+++|++|+++|+|
T Consensus         1 ~a~elkkG~~i~~~g~l~~V~~~~~~~pgkg~a~~~~klknl~tG~~~e~~f~~~dkv   58 (58)
T pfam08207         1 SASDLKKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLRTGAKVEKTFKSGDKV   58 (58)
T ss_pred             CHHHCCCCCEEEECCEEEEEEEEEEECCCCCCEEEEEEEEECCCCCEEEEEECCCCCC
T ss_conf             9425459879999999999999888759998538999988625698999888788739


No 13 
>pfam01132 EFP Elongation factor P (EF-P) OB domain.
Probab=99.69  E-value=3.3e-17  Score=126.25  Aligned_cols=55  Identities=36%  Similarity=0.803  Sum_probs=53.6

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEE
Q ss_conf             6405789961988999946887643211543001332013786156897667774
Q gi|254781067|r   69 DQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVAL  123 (189)
Q Consensus        69 ~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i  123 (189)
                      ++++||||.||+.|||||++||||++|+++.+|++.+||+||++|.+.+|+|+||
T Consensus         1 ~~~~qylY~dg~~~~FMd~etyEQi~i~~~~ig~~~~~L~e~~~v~v~~~~~~~i   55 (55)
T pfam01132         1 RREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVTVLFYNGEPI   55 (55)
T ss_pred             CCCEEEEEECCCCEEEEECCCCEEEECCHHHHCCHHHHCCCCCEEEEEEECCEEC
T ss_conf             9846999948991899618975067638789672887587999999999999999


No 14 
>TIGR00037 eIF_5A translation initiation factor eIF-5A; InterPro: IPR001884   Translation initiation factor 5A (IF-5A) is reported to be involved in the first step of peptide bond formation in translation, to be involved in cell-cycle regulation and to be a cofactor for the Rev and Rex transactivator proteins of human immunodeficiency virus-1 and T-cell leukaemia virus I, respectively , , . IF-5A contains an unusual amino acid, hypusine N-epsilon-(4-aminobutyl-2-hydroxy)lysine), that is required for its function. The first step in the post-translational modification of lysine to hypusine is catalyzed by the enzyme deoxyhypusine synthase, the structure of which has been reported.    The crystal structure of IF-5A from the archaeon Pyrobaculum aerophilum has been determined to 1.75 A. Unmodified P. aerophilum IF-5A is found to be a beta structure with two domains and three separate hydrophobic cores. The lysine (Lys42) that is post-translationally modified by deoxyhypusine synthase is found at one end of the IF-5A molecule in a turn between beta strands beta4 and beta5; this lysine residue is freely solvent accessible. The C-terminal domain is found to be homologous to the cold-shock protein CspA of E. coli, which has a well characterised RNA-binding fold, suggesting that IF-5A is involved in RNA binding . ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation.
Probab=99.64  E-value=1.1e-15  Score=116.96  Aligned_cols=113  Identities=27%  Similarity=0.274  Sum_probs=98.6

Q ss_pred             EEHHHCCCCCEEEECCEEEEEEEEEEECCCC-CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEE
Q ss_conf             6643216775899889379999987536888-763899999982468710013427872001010564057899619889
Q gi|254781067|r    4 VIASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGF   82 (189)
Q Consensus         4 i~an~lk~G~~i~~dg~~~~V~~~~~~kpgk-g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~   82 (189)
                      +..+.||+|.++.+||+||.|++.+.+|||| |+|.+|+..-.++++++.+.--+++.++|.+.++|+++|.|-.+|+..
T Consensus         7 v~v~~Lr~g~yVvIdg~PC~IvdiS~SkpGKHG~AKar~~aigIF~~~K~e~v~P~~~k~~VPiv~r~~~Q~l~i~g~~~   86 (137)
T TIGR00037         7 VEVSALRVGGYVVIDGEPCKIVDISTSKPGKHGHAKARVVAIGIFDGQKREFVSPVTSKVEVPIVDRREAQVLAIMGGVV   86 (137)
T ss_pred             EEEEECCCCCEEEECCCCCEEEECCCCCCCCCCCCEEEEEEEECCCCCCEEEECCCCCCEEECEEECCCCEEEEECCCEE
T ss_conf             46345124866887686760676131498986752789988612266542101775562141437367503888618837


Q ss_pred             EEEECCCCCCCCCCHH--HHHHHHHHCC-CCCEEEEE
Q ss_conf             9994688764321154--3001332013-78615689
Q gi|254781067|r   83 HFMNPETYDQVTVSEE--VIGDQKVYFQ-EGMEVKLL  116 (189)
Q Consensus        83 ~FMd~etyeqi~i~~~--~ig~~~~fL~-eg~~v~i~  116 (189)
                      -+||++|||.++++.-  -++|...-=. ||-.+-|.
T Consensus        87 qLMdl~tyet~e~~~PeGEL~d~l~~g~DEGkDLmV~  123 (137)
T TIGR00037        87 QLMDLETYETFELPIPEGELGDSLEEGFDEGKDLMVE  123 (137)
T ss_pred             EEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             8632788730220278775734300013666022034


No 15 
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=99.39  E-value=1.2e-11  Score=92.10  Aligned_cols=115  Identities=21%  Similarity=0.344  Sum_probs=96.7

Q ss_pred             EEHHHCCCCCEEEECCEEEEEEEEEEECCCC-CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECC--
Q ss_conf             6643216775899889379999987536888-7638999999824687100134278720010105640578996198--
Q gi|254781067|r    4 VIASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQE--   80 (189)
Q Consensus         4 i~an~lk~G~~i~~dg~~~~V~~~~~~kpgk-g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~--   80 (189)
                      +.++.||+|..+.++|.||+|++...+|+|| |.|.+++-..+|.||++.+...+++++++.+.+.+.++|.+-.+++  
T Consensus        23 ~q~~~lrkgg~vvikgrPCkVv~~stSKtGKHGhAK~~lvgiDIFtgkk~ed~~Ps~hn~~vP~V~r~~yqli~I~dd~d  102 (166)
T PTZ00328         23 LPAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPNED  102 (166)
T ss_pred             EECCCEEECCEEEECCCCEEEEEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCCCCCCCEEECCEEEEEEECCCCC
T ss_conf             68661338899998885418999884679866630467898861468666788605786225678802879986315666


Q ss_pred             -----EEEEEEC--CCCCCCCCCHH-HHHHHHH-HCCCCCEEEEEEE
Q ss_conf             -----8999946--88764321154-3001332-0137861568976
Q gi|254781067|r   81 -----GFHFMNP--ETYDQVTVSEE-VIGDQKV-YFQEGMEVKLLIH  118 (189)
Q Consensus        81 -----~~~FMd~--etyeqi~i~~~-~ig~~~~-fL~eg~~v~i~~~  118 (189)
                           ...+|+.  ++-|.+.||.+ -++...+ -..+|-++.+...
T Consensus       103 ~~~~G~lsLm~e~G~~k~Dlklp~~~~l~~~I~~~f~~gk~~~vtVl  149 (166)
T PTZ00328        103 PSLPAHLSLMDDEGESREDLDMPPDAALATQIKEQFDSGKEVLVVVV  149 (166)
T ss_pred             CCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             55541599996899823576389827999999999867990999998


No 16 
>KOG3271 consensus
Probab=99.19  E-value=1.7e-10  Score=85.07  Aligned_cols=121  Identities=18%  Similarity=0.228  Sum_probs=101.2

Q ss_pred             EHHHCCCCCEEEECCEEEEEEEEEEECCCC-CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEEE
Q ss_conf             643216775899889379999987536888-7638999999824687100134278720010105640578996198899
Q gi|254781067|r    5 IASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGFH   83 (189)
Q Consensus         5 ~an~lk~G~~i~~dg~~~~V~~~~~~kpgk-g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~~   83 (189)
                      .++.||++-++.++|.||+|++...+|.|| |.|.+.+-..+|.||++.+--.+++++++++.++|.++|.+-.+++...
T Consensus        22 q~salrkNG~vviK~rpckivEmSTsKtGKHGhAKvh~vaidifTgkk~edI~psthnmdVp~vkr~~yqLidIsd~~~s  101 (156)
T KOG3271          22 QCSALRKNGHVVIKGRPCKIVEMSTSKTGKHGHAKVHIVAIDIFTGKKLEDICPSTHNMDVPVVKRVDYQLIDISDGYLS  101 (156)
T ss_pred             HHHHEEECCEEEECCCCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCEEE
T ss_conf             22212317889973887369984512377677417899999964376425535777750147635010489973288489


Q ss_pred             EEECCCC--CCCCCCHHHHHHHHHHCCCCC-EEEEE----EECCEEEEE
Q ss_conf             9946887--643211543001332013786-15689----766777440
Q gi|254781067|r   84 FMNPETY--DQVTVSEEVIGDQKVYFQEGM-EVKLL----IHEGVALSV  125 (189)
Q Consensus        84 FMd~ety--eqi~i~~~~ig~~~~fL~eg~-~v~i~----~~~~~~i~i  125 (189)
                      ||+.+.+  +.+-+|..-+|+++.-=-|+. .+.+.    ++++..+++
T Consensus       102 l~~~sG~~kdDlklp~~el~~~i~~~~e~g~dl~v~Vlsa~gee~~~a~  150 (156)
T KOG3271         102 LMTDSGETKDDLKLPEGELGNQIRQGFEEGKDLLVTVLSAMGEEAAVAP  150 (156)
T ss_pred             EECCCCCCCHHCCCCCHHHHHHHHHHHCCCCCEEEEEHHHHCHHHHEEE
T ss_conf             8868997120004764157899998642687279997564170443242


No 17 
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=96.92  E-value=0.0017  Score=42.23  Aligned_cols=53  Identities=25%  Similarity=0.251  Sum_probs=42.7

Q ss_pred             ECCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCE
Q ss_conf             0564057899619889999468876432115430013320137861568976677
Q gi|254781067|r   67 VEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGV  121 (189)
Q Consensus        67 ie~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~  121 (189)
                      ++|+..|.+-..|+....||+||||.++++..  .+...=|.+|.+|.-.-..|+
T Consensus         1 Iekk~gQVlsi~G~~vQlMD~etYeTfe~~ip--ee~~~~l~~G~eVeY~e~mG~   53 (57)
T cd04467           1 IERKTGQVLSIMGDVVQLMDLETYETFEVPIP--EEIKDKLEPGKEVEYWESMGK   53 (57)
T ss_pred             CCCCEEEEEEECCCEEEEEECCCCEEEEEECC--HHHHHCCCCCCEEEEEEECCC
T ss_conf             96521269997598379850666111776588--788724679974988311583


No 18 
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=96.73  E-value=0.024  Score=35.15  Aligned_cols=104  Identities=25%  Similarity=0.424  Sum_probs=76.5

Q ss_pred             HHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCEE--EEE--ECCCEEEEEEEECCEE
Q ss_conf             321677589988937999998753688876389999998246871001342787200--101--0564057899619889
Q gi|254781067|r    7 SAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVE--RAF--VEDQRFQFLYQDQEGF   82 (189)
Q Consensus         7 n~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekve--~~~--ie~~~~qylY~dg~~~   82 (189)
                      -++++|.++.++|..+.++...    |+     .+.++++.|+...+.++.-...-+  .+.  -+-+.+.+.-.+.+..
T Consensus       245 p~~~~gDiV~~~~~~~~~v~~~----~~-----~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~~~~~~~vvs~~~~~~  315 (355)
T COG1499         245 PEFRPGDIVSVRGRQLVLVRSI----GK-----GIVVLDLETGEPVEITWSVYKRNEGKVAVKEPRLKKAVVVSRDPSAI  315 (355)
T ss_pred             CCCCCCCEEEECCCEEEEEEEE----CC-----CEEEEECCCCCCCCCCHHHCCCCCCEEEECCCCCEEEEEEECCCCEE
T ss_conf             8879887899779738999993----68-----44898556587033675450067641552145526899996588803


Q ss_pred             EEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEEC
Q ss_conf             99946887643211543001332013786156897667774401
Q gi|254781067|r   83 HFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVE  126 (189)
Q Consensus        83 ~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~  126 (189)
                      .|||++|||-+++...       =|.+|.+|.+..+.+....++
T Consensus       316 ~v~d~et~e~~~~~~~-------~~~~g~~v~v~~~~~~~~~~~  352 (355)
T COG1499         316 QVLDPETYEARTVKGP-------SLEEGDEVKVFKVRGRNYVVE  352 (355)
T ss_pred             EEEECCEEEEEECCCC-------CCCCCCEEEEEEECCEEEEEE
T ss_conf             8970553898861688-------778997899999804387610


No 19 
>cd04463 S1_EF_like S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication.
Probab=96.01  E-value=0.0077  Score=38.20  Aligned_cols=54  Identities=24%  Similarity=0.184  Sum_probs=34.1

Q ss_pred             CEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEE
Q ss_conf             4057899619889999468876432115430013320137861568976677744
Q gi|254781067|r   70 QRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALS  124 (189)
Q Consensus        70 ~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~  124 (189)
                      +++|+||..++..+|||.++||+..++.-.--. .-++.+|+.+.+..+.|+.+.
T Consensus         1 ~e~qVLd~q~~~~~~Md~e~~~~~~~p~~~~~~-~E~f~~G~~vlv~~~~Gq~~~   54 (55)
T cd04463           1 RELQVLDIQGSKPVTMDLETYEVVQVPPPVDQS-FESFEPGEVVLVDTRTGQYVG   54 (55)
T ss_pred             CCCEEEECCCCEEEEEEEEEEEEEECCCCCCCC-CCCCCCCEEEEEECCCCCEEC
T ss_conf             950688106872389871213677238985644-223489608999746662743


No 20 
>cd04463 S1_EF_like S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication.
Probab=95.05  E-value=0.045  Score=33.51  Aligned_cols=36  Identities=25%  Similarity=0.394  Sum_probs=30.9

Q ss_pred             EEEEEEEC--CCEEECCCCC-------CCCCEEEEECCCCCEEHH
Q ss_conf             00089937--9599847401-------688799998899724021
Q gi|254781067|r  151 YKPAILSN--DIRTTVPPHI-------NIGDDIVILTEDNSYVER  186 (189)
Q Consensus       151 ~K~A~let--G~~i~VP~FI-------~~Gd~IkV~T~~g~Y~~R  186 (189)
                      .++++++.  +-+.+||+++       +.|..|.+++++|+|+.+
T Consensus        11 ~~~~~Md~e~~~~~~~p~~~~~~~E~f~~G~~vlv~~~~Gq~~~v   55 (55)
T cd04463          11 SKPVTMDLETYEVVQVPPPVDQSFESFEPGEVVLVDTRTGQYVGV   55 (55)
T ss_pred             CEEEEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEECCCCCEECC
T ss_conf             723898712136772389856442234896089997466627439


No 21 
>pfam01287 eIF-5a Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold. eIF5A, previously thought to be an initiation factor, has been shown to be required for peptide chain elongation in yeast.
Probab=92.57  E-value=0.37  Score=27.90  Aligned_cols=60  Identities=23%  Similarity=0.376  Sum_probs=41.3

Q ss_pred             EECCCEEEEEEEECC-EEEEEEC--CCCCCCCCCHHHHHHHHH-HCCCCCEEEEEEE----CCEEEEE
Q ss_conf             105640578996198-8999946--887643211543001332-0137861568976----6777440
Q gi|254781067|r   66 FVEDQRFQFLYQDQE-GFHFMNP--ETYDQVTVSEEVIGDQKV-YFQEGMEVKLLIH----EGVALSV  125 (189)
Q Consensus        66 ~ie~~~~qylY~dg~-~~~FMd~--etyeqi~i~~~~ig~~~~-fL~eg~~v~i~~~----~~~~i~i  125 (189)
                      .+.|+.+|.+..++| ....||.  +++|.+.+|..-+++..+ -+.+|.++.+.++    +..++++
T Consensus         1 ~V~r~eyQli~I~~Dg~lsLMde~g~t~eDl~lP~~~l~~eI~~~~~~Gk~~~V~v~~amGee~ii~~   68 (69)
T pfam01287         1 NVKRTEYQLIDISGDGFLSLMDEDGETKEDLKLPEGELGEEIKEKFEEGKEVLVTVLSAMGEEKIVAV   68 (69)
T ss_pred             CCCCCEEEEEEECCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEEEHHCCEEEEEEC
T ss_conf             96322148986668863776648898831466994689999999986799389999042881335762


No 22 
>PRK08463 acetyl-CoA carboxylase; Validated
Probab=81.16  E-value=4.9  Score=21.03  Aligned_cols=65  Identities=20%  Similarity=0.190  Sum_probs=37.6

Q ss_pred             CEEEEEEEECCEEEEEECCCCCCCCCC-------HHHHHHHHHHCCCCCEEEEEEECCEEEEECC-CCEEEEEEEECCC
Q ss_conf             405789961988999946887643211-------5430013320137861568976677744015-8749999998285
Q gi|254781067|r   70 QRFQFLYQDQEGFHFMNPETYDQVTVS-------EEVIGDQKVYFQEGMEVKLLIHEGVALSVEV-PRHVVFTVIDTEP  140 (189)
Q Consensus        70 ~~~qylY~dg~~~~FMd~etyeqi~i~-------~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~l-P~~v~l~V~~t~p  140 (189)
                      -.++|||.+.+.|+||...+==|++=+       .|++..+.. +..|..+.+.-.     .+.+ -..+++.|.--+|
T Consensus       272 GTvEFL~d~~~~fyFlEmNtRlQVEHpVTE~vTGvDLV~~Qi~-iA~G~~L~~~q~-----~i~~~GhAIE~RI~AEdp  344 (478)
T PRK08463        272 GTIEFLLDDYNNFYFMEMNTRIQVEHGVTEEITGIDLIVRQIR-IAAGEILDLEQS-----DIKPRGFAIEARITAENV  344 (478)
T ss_pred             CEEEEEECCCCCEEEEEEECCCCCCCCCCCEECCCCHHHHHHH-HHCCCCCCCCCC-----CCCCCCEEEEEEEECCCC
T ss_conf             3389888389978999607554556654110038868999999-867998885400-----346674599999851477


No 23 
>PRK08591 acetyl-CoA carboxylase biotin carboxylase subunit; Validated
Probab=79.19  E-value=2.8  Score=22.53  Aligned_cols=26  Identities=31%  Similarity=0.464  Sum_probs=19.4

Q ss_pred             CEEEEEEEECCEEEEEECCCCCCCCCC
Q ss_conf             405789961988999946887643211
Q gi|254781067|r   70 QRFQFLYQDQEGFHFMNPETYDQVTVS   96 (189)
Q Consensus        70 ~~~qylY~dg~~~~FMd~etyeqi~i~   96 (189)
                      -.++|||. ++.|+||...|==|++=|
T Consensus       272 GTvEFL~d-~~~fyFlEmNtRlQVEHp  297 (449)
T PRK08591        272 GTIEFLYE-NGEFYFIEMNTRIQVEHP  297 (449)
T ss_pred             EEEEEEEE-CCEEEEEEEECCCCCCCC
T ss_conf             03899997-890899962434124565


No 24 
>TIGR00514 accC acetyl-CoA carboxylase, biotin carboxylase; InterPro: IPR004549   This family represents the biotin carboxylase subunit found usually as a component of acetyl-CoA carboxylase. Acetyl-CoA carboxylase (6.4.1.2 from EC) is a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase (6.3.4.14 from EC), and two subunits of carboxyl transferase in a 2:2 complex. In the first step of long-chain fatty acid synthesis, biotin carboxylase catalyses the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-coA. Homologous domains are found in eukaryotic forms of acetyl-CoA carboxylase and in a number of other carboxylases (e.g. pyruvate carboxylase). In some systems, the biotin carboxyl carrier protein and this protein (biotin carboxylase) may be shared by different carboxyltransferases. However, this model is not intended to identify the biotin carboxylase domain of propionyl-coA carboxylase. The model should hit the full length of proteins, except for chloroplast transit peptides in plants. If it hits a domain only of a longer protein, there may be a problem with the identification.; GO: 0016874 ligase activity.
Probab=77.15  E-value=0.98  Score=25.31  Aligned_cols=73  Identities=21%  Similarity=0.259  Sum_probs=45.0

Q ss_pred             EEEEEEEECCE-EEEEECCCCCCCCCC-------HHHHHHHHHHCCCCCEEEEEEECCEEEEECC-CCEEEEEEEECCCC
Q ss_conf             05789961988-999946887643211-------5430013320137861568976677744015-87499999982854
Q gi|254781067|r   71 RFQFLYQDQEG-FHFMNPETYDQVTVS-------EEVIGDQKVYFQEGMEVKLLIHEGVALSVEV-PRHVVFTVIDTEPS  141 (189)
Q Consensus        71 ~~qylY~dg~~-~~FMd~etyeqi~i~-------~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~l-P~~v~l~V~~t~p~  141 (189)
                      +++|||...+. ||||.+.|==|+|=|       -|+|.+|.+ +..|+++.+-  ++.   |.| =..++|.| .||..
T Consensus       274 TvEFLld~~~~rFYFmEMNTRIQVEHPVTEmvtGvDL~keQir-vA~G~~L~~k--Qe~---v~~~GHaieCRI-NAEDP  346 (451)
T TIGR00514       274 TVEFLLDKNGQRFYFMEMNTRIQVEHPVTEMVTGVDLIKEQIR-VAAGEKLSLK--QED---VKLRGHAIECRI-NAEDP  346 (451)
T ss_pred             EEEEEEECCCCEEEEEEECCEEEEEECCEEEEECHHHHHHHHH-HHCCCCCCCC--CCE---EEEEEEEEEEEE-CCCCC
T ss_conf             1688862588735776517602111032014600257888998-7378956643--114---799988998651-45587


Q ss_pred             CCCCCCCCC
Q ss_conf             213102477
Q gi|254781067|r  142 SKGQTVTAS  150 (189)
Q Consensus       142 ~kG~t~~~~  150 (189)
                      .|+=+=|.+
T Consensus       347 ~~~F~PsPG  355 (451)
T TIGR00514       347 IKNFLPSPG  355 (451)
T ss_pred             CCCCCCCCC
T ss_conf             877868885


No 25 
>KOG0238 consensus
Probab=74.40  E-value=7.5  Score=19.88  Aligned_cols=69  Identities=17%  Similarity=0.140  Sum_probs=40.4

Q ss_pred             CEEEEEEEECCEEEEEECCCCCCCCCC-------HHHHHHHH--------HHCC-----CCCEEEEEEECCEEEEECCCC
Q ss_conf             405789961988999946887643211-------54300133--------2013-----786156897667774401587
Q gi|254781067|r   70 QRFQFLYQDQEGFHFMNPETYDQVTVS-------EEVIGDQK--------VYFQ-----EGMEVKLLIHEGVALSVEVPR  129 (189)
Q Consensus        70 ~~~qylY~dg~~~~FMd~etyeqi~i~-------~~~ig~~~--------~fL~-----eg~~v~i~~~~~~~i~i~lP~  129 (189)
                      -.++|++...++|+||.+.|-=|++-|       .|++.+++        ++-+     .|--+....|-+.|.+--||.
T Consensus       268 GTVEFi~D~~~~FyFmEmNTRLQVEHPvTEmItg~DLVewqiRvA~ge~lp~~q~ei~l~GhafE~RiyAEdp~~~f~P~  347 (670)
T KOG0238         268 GTVEFIVDSKDNFYFMEMNTRLQVEHPVTEMITGTDLVEWQIRVAAGEPLPLKQEEIPLNGHAFEARIYAEDPYKGFLPS  347 (670)
T ss_pred             CEEEEEECCCCCEEEEEEECEEEECCCCHHHCCCHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEEEECCCCCCCCCC
T ss_conf             44999983788579998402253036416321222789999998649999977020136454789998500775467778


Q ss_pred             EEEEEEEEC
Q ss_conf             499999982
Q gi|254781067|r  130 HVVFTVIDT  138 (189)
Q Consensus       130 ~v~l~V~~t  138 (189)
                      .=-|.-..+
T Consensus       348 ~G~L~~~~~  356 (670)
T KOG0238         348 AGRLVYYSF  356 (670)
T ss_pred             CCCCEEECC
T ss_conf             741112026


No 26 
>cd04468 S1_eIF5A S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the oligonucleotides-binding fold (OB fold) which binds RNA. Moreover, eIF5A prefers binding to the actively translating ribosome. This evidence suggests that eIF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=68.22  E-value=9.3  Score=19.32  Aligned_cols=50  Identities=24%  Similarity=0.410  Sum_probs=36.4

Q ss_pred             ECCCEEEEEEEECCEEEEEEC--CCCCCCCCCHHHHHHHHH-HCCCCCEEEEE
Q ss_conf             056405789961988999946--887643211543001332-01378615689
Q gi|254781067|r   67 VEDQRFQFLYQDQEGFHFMNP--ETYDQVTVSEEVIGDQKV-YFQEGMEVKLL  116 (189)
Q Consensus        67 ie~~~~qylY~dg~~~~FMd~--etyeqi~i~~~~ig~~~~-fL~eg~~v~i~  116 (189)
                      +.|.++|.+..+++....|+.  ++-|.+.+|..-+|...+ -.-+|-.+.+.
T Consensus         1 V~R~eYqLidIdDGflsLm~d~G~~keDlklP~~elg~~I~~~f~~gk~~~Vt   53 (69)
T cd04468           1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKFDEGKDVLVT   53 (69)
T ss_pred             CCHHHEEEEEECCCCEEEECCCCCCHHCCCCCCHHHHHHHHHHHHCCCCEEEE
T ss_conf             94131589841156200356899832125699479999999997679918999


No 27 
>KOG0267 consensus
Probab=63.48  E-value=13  Score=18.40  Aligned_cols=161  Identities=16%  Similarity=0.195  Sum_probs=97.8

Q ss_pred             EHHHCC-CCCEEEECCEEEEEEEEEEECCCC----CCCEEEEEEEECCCCCCEEEEECCCC-CEEEEEECCCEEEEEEEE
Q ss_conf             643216-775899889379999987536888----76389999998246871001342787-200101056405789961
Q gi|254781067|r    5 IASAVR-KGNVLDVDGKLYIVLVAKNFHPGK----GTPITQVEMRRISDGVKVSNRWRTTE-QVERAFVEDQRFQFLYQD   78 (189)
Q Consensus         5 ~an~lk-~G~~i~~dg~~~~V~~~~~~kpgk----g~a~v~~klknL~tG~~~e~~f~~~e-kve~~~ie~~~~qylY~d   78 (189)
                      ...|+| +|....++|-++.|--.++.--||    |+--.-+++=++.-|+.+ ..|++.+ ++..++  -.+..||-.-
T Consensus       137 ~iwD~Rk~Gc~~~~~s~~~vv~~l~lsP~Gr~v~~g~ed~tvki~d~~agk~~-~ef~~~e~~v~sle--~hp~e~Lla~  213 (825)
T KOG0267         137 KIWDIRKKGCSHTYKSHTRVVDVLRLSPDGRWVASGGEDNTVKIWDLTAGKLS-KEFKSHEGKVQSLE--FHPLEVLLAP  213 (825)
T ss_pred             EEHHHHCCCCEEEECCCCCEEEEEEECCCCCEEECCCCCCEEEEECCCCCCCC-CCCCCCCCCCCCCC--CCCHHHHHCC
T ss_conf             11000004742450587632577753699706610688654562034432002-22566655510134--6823542166


Q ss_pred             C---CEEEEEECCCCCCCCCCHHHHHH--HHHHCCCCCEE----EEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCC
Q ss_conf             9---88999946887643211543001--33201378615----689766777440158749999998285421310247
Q gi|254781067|r   79 Q---EGFHFMNPETYDQVTVSEEVIGD--QKVYFQEGMEV----KLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTA  149 (189)
Q Consensus        79 g---~~~~FMd~etyeqi~i~~~~ig~--~~~fL~eg~~v----~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~  149 (189)
                      |   ...-|-|+|+||-|.-.+-...+  ...|-.+|+.+    ++.+-+..    .--.+|...+..+||...|+++..
T Consensus       214 Gs~d~tv~f~dletfe~I~s~~~~~~~v~~~~fn~~~~~~~~G~q~sl~~~~----~a~ah~~~~~~~~Ep~~~~~~vqs  289 (825)
T KOG0267         214 GSSDRTVRFWDLETFEVISSGKPETDGVRSLAFNPDGKIVLSGEQISLSESR----TASAHVRKTLARWEPEMDGAVVQS  289 (825)
T ss_pred             CCCCCEEEEECCCEEEEEECCCCCCCCCEEEEECCCCEEEECCCHHHHHHHH----CCCCEEECCCCCCCCCCCCCEEEE
T ss_conf             7777506643141368861268755772221016874032047503222221----033102101245564424522444


Q ss_pred             C-EEEEEEECCCEEECCCCCCCCC
Q ss_conf             7-0008993795998474016887
Q gi|254781067|r  150 S-YKPAILSNDIRTTVPPHINIGD  172 (189)
Q Consensus       150 ~-~K~A~letG~~i~VP~FI~~Gd  172 (189)
                      . .|+..+--|-.=+.--|+..++
T Consensus       290 ~~~~ek~v~v~~d~~~ln~~~s~~  313 (825)
T KOG0267         290 NSHKEKVVAVGRDPQDLNAFSSKV  313 (825)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             377542001345743100210355


No 28 
>PRK08654 pyruvate carboxylase subunit A; Validated
Probab=61.61  E-value=14  Score=18.19  Aligned_cols=26  Identities=31%  Similarity=0.450  Sum_probs=19.1

Q ss_pred             CEEEEEEEECCEEEEEECCCCCCCCCC
Q ss_conf             405789961988999946887643211
Q gi|254781067|r   70 QRFQFLYQDQEGFHFMNPETYDQVTVS   96 (189)
Q Consensus        70 ~~~qylY~dg~~~~FMd~etyeqi~i~   96 (189)
                      -++||||. ++.|+||...+==|.+-+
T Consensus       272 GTVEFl~d-~g~fyFlEmNtRlQVEHp  297 (497)
T PRK08654        272 GTVEFLYS-NGNFYFLEMNTRLQVEHP  297 (497)
T ss_pred             CEEEEEEE-CCEEEEEEEECCCCCCCC
T ss_conf             32799874-883999961244224554


No 29 
>PRK12833 acetyl-CoA carboxylase biotin carboxylase subunit; Provisional
Probab=59.86  E-value=14  Score=18.27  Aligned_cols=27  Identities=26%  Similarity=0.460  Sum_probs=19.5

Q ss_pred             CEEEEEEEE-CCEEEEEECCCCCCCCCC
Q ss_conf             405789961-988999946887643211
Q gi|254781067|r   70 QRFQFLYQD-QEGFHFMNPETYDQVTVS   96 (189)
Q Consensus        70 ~~~qylY~d-g~~~~FMd~etyeqi~i~   96 (189)
                      -.++|||.+ .+.|+||...+==|.+-+
T Consensus       274 gTvEFl~d~~~~~fyFlEvNtRlQVEH~  301 (458)
T PRK12833        274 GTLEYLFDDARGEFYFIEMNTRIQVEHP  301 (458)
T ss_pred             EEEEEEEECCCCCEEEEEEECCCCCCCC
T ss_conf             0266678658896899962136444442


No 30 
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=58.15  E-value=6.2  Score=20.42  Aligned_cols=32  Identities=31%  Similarity=0.375  Sum_probs=23.7

Q ss_pred             EECCCEEEEEEEECCEEEEEECCCCCCCCCCH
Q ss_conf             10564057899619889999468876432115
Q gi|254781067|r   66 FVEDQRFQFLYQDQEGFHFMNPETYDQVTVSE   97 (189)
Q Consensus        66 ~ie~~~~qylY~dg~~~~FMd~etyeqi~i~~   97 (189)
                      .++.-...=.|.+-..+.-||+++++|.-+++
T Consensus        16 aie~gK~~~~Y~~a~a~~~inp~D~~~Lgv~E   47 (128)
T COG1153          16 AIEGGKFTDEYFNACAVCEINPEDMKQLGVSE   47 (128)
T ss_pred             HHHCCCCHHHHHHHEEEEEECHHHHHHHCCCC
T ss_conf             22236325666301058997999999848876


No 31 
>pfam00900 Ribosomal_S4e Ribosomal family S4e.
Probab=55.55  E-value=18  Score=17.56  Aligned_cols=37  Identities=24%  Similarity=0.305  Sum_probs=30.0

Q ss_pred             CCCCCEEEEEEECCCEEECC-CCCCCCCEEEEECCCCC
Q ss_conf             02477000899379599847-40168879999889972
Q gi|254781067|r  146 TVTASYKPAILSNDIRTTVP-PHINIGDDIVILTEDNS  182 (189)
Q Consensus       146 t~~~~~K~A~letG~~i~VP-~FI~~Gd~IkV~T~~g~  182 (189)
                      ++.++--...+.-|-.|.+| .-++.||.++|+..+++
T Consensus        36 ~~kgG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~k   73 (74)
T pfam00900        36 TVKGGKPQLNLHDGRNIRYPDPDYKTGDTLVIDLPTQK   73 (74)
T ss_pred             EECCCEEEEEECCCCEEEECCCCCCCCCEEEEECCCCC
T ss_conf             90399389995487589827898226999999877783


No 32 
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=52.25  E-value=10  Score=19.09  Aligned_cols=14  Identities=21%  Similarity=0.313  Sum_probs=5.6

Q ss_pred             CCCCCEEEEEEECC
Q ss_conf             13786156897667
Q gi|254781067|r  107 FQEGMEVKLLIHEG  120 (189)
Q Consensus       107 L~eg~~v~i~~~~~  120 (189)
                      |++|..|.+.--.|
T Consensus        47 I~~Gd~V~v~s~rG   60 (115)
T cd02779          47 LKNGDLVEVYNDYG   60 (115)
T ss_pred             CCCCCEEEEECCCE
T ss_conf             99989999987990


No 33 
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the  C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=52.11  E-value=9.7  Score=19.20  Aligned_cols=55  Identities=22%  Similarity=0.290  Sum_probs=31.5

Q ss_pred             ECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECC
Q ss_conf             8246871001342787200101056405789961988999946887643211543001332013786156897667
Q gi|254781067|r   45 RISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG  120 (189)
Q Consensus        45 nL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~  120 (189)
                      .|.||+.+++    +.     .+++...-=.|.+-..|.+|+++++..+-+            .+|..|.+.--.|
T Consensus         4 iL~TGRti~q----g~-----~m~~~~~~~~y~~~~a~~~i~P~D~~~lGi------------~~Gd~V~v~s~~G   58 (106)
T cd02789           4 ILNSGRTIDQ----GR-----IIEGGNKLTYEVDACAYCEINPEDYKLLGK------------PEGDKVKVTSEFG   58 (106)
T ss_pred             EECCCCHHHH----HH-----HHHCCCCCHHHCCCCEEEEECHHHHHHCCC------------CCCCEEEEECCCE
T ss_conf             9824754755----75-----200768732321666499989999998098------------9999999987987


No 34 
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a  functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=48.48  E-value=12  Score=18.68  Aligned_cols=32  Identities=22%  Similarity=0.162  Sum_probs=16.2

Q ss_pred             ECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCE
Q ss_conf             19889999468876432115430013320137861568976677
Q gi|254781067|r   78 DQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGV  121 (189)
Q Consensus        78 dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~  121 (189)
                      ..+.|++|++++=+..            =|.+|..|.|.--.|.
T Consensus        32 ~pe~~v~i~p~dA~~l------------gi~dGd~V~v~s~~G~   63 (122)
T cd02792          32 QPEMFVEISPELAAER------------GIKNGDMVWVSSPRGK   63 (122)
T ss_pred             CCCCEEEECHHHHHHC------------CCCCCCEEEEECCCEE
T ss_conf             9998999999999874------------9988988999889989


No 35 
>TIGR02102 pullulan_Gpos pullulanase, extracellular; InterPro: IPR011838    Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. In contrast, a glycogen debranching enzyme such GlgX, homologous to this family, can release glucose at alpha,1-6 linkages from glycogen first subjected to limit degradation by phosphorylase. Characterised members of this family include a surface-located pullulanase from Streptococcus pneumoniae  and an extracellular bifunctional amylase/pullulanase with C-terminal pullulanase activity ..
Probab=48.40  E-value=13  Score=18.41  Aligned_cols=19  Identities=21%  Similarity=0.163  Sum_probs=8.2

Q ss_pred             CCEEEEECCCCEEEEEEEE
Q ss_conf             6777440158749999998
Q gi|254781067|r  119 EGVALSVEVPRHVVFTVID  137 (189)
Q Consensus       119 ~~~~i~i~lP~~v~l~V~~  137 (189)
                      ..+-|.++-=+.++++|-+
T Consensus      1008 ~~~~l~ldpLTa~v~~Vg~ 1026 (1164)
T TIGR02102      1008 TKEGLKLDPLTAVVVRVGE 1026 (1164)
T ss_pred             ECCCEEECCCEEEEEEECC
T ss_conf             1033156141579998557


No 36 
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=46.49  E-value=14  Score=18.27  Aligned_cols=30  Identities=23%  Similarity=0.400  Sum_probs=14.4

Q ss_pred             CCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECC
Q ss_conf             988999946887643211543001332013786156897667
Q gi|254781067|r   79 QEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG  120 (189)
Q Consensus        79 g~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~  120 (189)
                      .+.++.|++++-+..-            |.||..|.|.--.|
T Consensus        33 pe~~v~inp~dA~~~g------------i~dgd~V~v~s~~G   62 (122)
T cd02791          33 PEPYVEIHPEDAARLG------------LKEGDLVRVTSRRG   62 (122)
T ss_pred             CCCEEEECHHHHHHCC------------CCCCCEEEEECCCE
T ss_conf             9978999999998869------------98999999984880


No 37 
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=45.88  E-value=14  Score=18.20  Aligned_cols=31  Identities=23%  Similarity=0.379  Sum_probs=17.5

Q ss_pred             CCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCE
Q ss_conf             9889999468876432115430013320137861568976677
Q gi|254781067|r   79 QEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGV  121 (189)
Q Consensus        79 g~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~  121 (189)
                      .++|+.|++++=++            .=|++|..|.|.--.|.
T Consensus        28 pen~v~inp~dA~~------------~Gi~~Gd~V~v~s~~G~   58 (143)
T cd02780          28 PENPVWINPEDAAK------------LGIKTGDRVRVVTPGGS   58 (143)
T ss_pred             CCCEEEECHHHHHH------------CCCCCCCEEEEECCCEE
T ss_conf             99859999999998------------69998999999879857


No 38 
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=45.15  E-value=14  Score=18.21  Aligned_cols=16  Identities=19%  Similarity=0.169  Sum_probs=8.3

Q ss_pred             HCCCCCEEEEEEECCE
Q ss_conf             0137861568976677
Q gi|254781067|r  106 YFQEGMEVKLLIHEGV  121 (189)
Q Consensus       106 fL~eg~~v~i~~~~~~  121 (189)
                      =|++|..|.+.---|+
T Consensus        45 GI~dgd~V~v~n~rG~   60 (124)
T cd02785          45 GIAHGDLVEVYNDRGS   60 (124)
T ss_pred             CCCCCCEEEEECCCEE
T ss_conf             9999999999859999


No 39 
>TIGR01591 Fdh-alpha formate dehydrogenase, alpha subunit; InterPro: IPR006478   This group of sequences describe a subset of formate dehydrogenase alpha chains found mainly in the archaea but also in alpha and gamma proteobacteria and a small number of Gram-positive bacteria. The alpha chain contains domains for molybdopterin dinucleotide binding and molybdopterin oxidoreductase. The holo-enzyme also contains beta and gamma subunits. The enzyme catalyzes the oxidation of formate (produced from pyruvate during anaerobic growth) to carbon dioxide with the concomitant release of two electrons and two protons. The enzyme's purpose is to allow growth on formate in some circumstances  and, in the case of FdhH in gamma proteobacteria, to pass electrons to hydrogenase (by which process acid is neutralized) . The alpha subunit of a version of nitrate reductase is closely related.; GO: 0008863 formate dehydrogenase activity, 0015942 formate metabolic process, 0009326 formate dehydrogenase complex.
Probab=44.95  E-value=13  Score=18.35  Aligned_cols=23  Identities=22%  Similarity=0.200  Sum_probs=19.7

Q ss_pred             CCCCCCCEEEEECCCC-CEEHHCC
Q ss_conf             4016887999988997-2402102
Q gi|254781067|r  166 PHINIGDDIVILTEDN-SYVERVK  188 (189)
Q Consensus       166 ~FI~~Gd~IkV~T~~g-~Y~~Rak  188 (189)
                      +=|+.||.|+|.+|.| +-.-||+
T Consensus       623 lgI~dgd~V~V~Sr~GG~~~~rA~  646 (694)
T TIGR01591       623 LGIKDGDLVKVKSRRGGEITLRAK  646 (694)
T ss_pred             CCCCCCCEEEEEECCCCCEEEEEE
T ss_conf             588356778998414710143441


No 40 
>pfam00498 FHA FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
Probab=44.56  E-value=27  Score=16.50  Aligned_cols=55  Identities=15%  Similarity=0.272  Sum_probs=37.9

Q ss_pred             CEEEEEECCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEE
Q ss_conf             2001010564057899619889999468876432115430013320137861568
Q gi|254781067|r   61 QVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKL  115 (189)
Q Consensus        61 kve~~~ie~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i  115 (189)
                      .++...+.++-+.+.+.++..|+..|..+-.-..++...++...--|.+|..+.+
T Consensus        12 ~l~~~~iSr~Ha~i~~~~~~~~~i~Dl~S~nGt~vNg~~i~~~~~~L~~GD~i~i   66 (67)
T pfam00498        12 VLDDPSVSRRHAEIRYDGGGRFYLEDLGSTNGTFVNGQRLGPEPVRLKDGDVIRL   66 (67)
T ss_pred             EECCCCCCHHHEEEEEECCCEEEEEECCCCCCEEECCEECCCCCEECCCCCEEEE
T ss_conf             9898360702499999249869999799886859999996788769999999984


No 41 
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a  Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=44.45  E-value=15  Score=18.07  Aligned_cols=31  Identities=23%  Similarity=0.448  Sum_probs=14.7

Q ss_pred             CCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCE
Q ss_conf             9889999468876432115430013320137861568976677
Q gi|254781067|r   79 QEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGV  121 (189)
Q Consensus        79 g~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~  121 (189)
                      .+.|+.|++++-+..-            |++|..|.|.--.|.
T Consensus        33 pep~v~i~p~dA~~lG------------i~~Gd~V~v~s~~G~   63 (116)
T cd02790          33 PEEYVEINPEDAKRLG------------IEDGEKVRVSSRRGS   63 (116)
T ss_pred             CCCEEEECHHHHHHCC------------CCCCCEEEEECCCEE
T ss_conf             9988998999998859------------988998999879989


No 42 
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=43.94  E-value=27  Score=16.44  Aligned_cols=57  Identities=16%  Similarity=0.310  Sum_probs=44.1

Q ss_pred             CCEEEHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCE
Q ss_conf             92366432167758998893799999875368887638999999824687100134278720
Q gi|254781067|r    1 MVKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQV   62 (189)
Q Consensus         1 m~~i~an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekv   62 (189)
                      ||+ .-++++.|..+.   ..|.|.+.+..+.-.|.+|.++.|++ .||.+--+-|..++..
T Consensus         1 m~~-~i~~l~~G~~v~---~~~lv~~~~~~~tknG~~Yl~l~L~D-~tG~I~ak~W~~~~~~   57 (314)
T PRK13480          1 MMK-GIENLEVGESVD---HFLLIKSATKGVASNGKPFLTLILQD-KSGDIEAKLWDVSKED   57 (314)
T ss_pred             CCC-CHHHCCCCCEEE---EEEEEEECHHHCCCCCCCEEEEEEEC-CCCEEEEEECCCCHHH
T ss_conf             965-141089998888---99999871433189998147999983-7876889967898666


No 43 
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR),  trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=42.80  E-value=18  Score=17.56  Aligned_cols=17  Identities=18%  Similarity=0.331  Sum_probs=9.3

Q ss_pred             HCCCCCEEEEEEECCEE
Q ss_conf             01378615689766777
Q gi|254781067|r  106 YFQEGMEVKLLIHEGVA  122 (189)
Q Consensus       106 fL~eg~~v~i~~~~~~~  122 (189)
                      =|.+|..|.+.--.|++
T Consensus        47 gI~dGd~V~v~n~~G~i   63 (127)
T cd02777          47 GIKDGDIVRVFNDRGAV   63 (127)
T ss_pred             CCCCCCEEEEECCCCEE
T ss_conf             99898999998789649


No 44 
>PRK06111 acetyl-CoA carboxylase biotin carboxylase subunit; Validated
Probab=41.39  E-value=28  Score=16.41  Aligned_cols=27  Identities=30%  Similarity=0.420  Sum_probs=21.0

Q ss_pred             CEEEEEEEECCEEEEEECCCCCCCCCC
Q ss_conf             405789961988999946887643211
Q gi|254781067|r   70 QRFQFLYQDQEGFHFMNPETYDQVTVS   96 (189)
Q Consensus        70 ~~~qylY~dg~~~~FMd~etyeqi~i~   96 (189)
                      -.++|||.++..|+||...+==|++-+
T Consensus       272 gTvEFl~d~~~~fyFlEvNtRlQVEHp  298 (449)
T PRK06111        272 GTIEFLVDNQKNFYFLEMNTRLQVEHP  298 (449)
T ss_pred             EEEEEEEECCCCEEEEEEECCCCCCCC
T ss_conf             689999948986899953435444664


No 45 
>PRK05586 biotin carboxylase; Validated
Probab=40.01  E-value=32  Score=16.06  Aligned_cols=97  Identities=14%  Similarity=0.247  Sum_probs=47.4

Q ss_pred             CEEEEEEEECCEEEEEECCCCCCCCCC-------HHHHHHHHHHCCCCCEEEEEEECCEEEEEC-CCCEEEEEEEECCCC
Q ss_conf             405789961988999946887643211-------543001332013786156897667774401-587499999982854
Q gi|254781067|r   70 QRFQFLYQDQEGFHFMNPETYDQVTVS-------EEVIGDQKVYFQEGMEVKLLIHEGVALSVE-VPRHVVFTVIDTEPS  141 (189)
Q Consensus        70 ~~~qylY~dg~~~~FMd~etyeqi~i~-------~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~-lP~~v~l~V~~t~p~  141 (189)
                      -.++|||..++.|+||...+==|++=+       .|++..+. .+..|..+...  .+   .|. -...+++.| ++|..
T Consensus       272 GTvEFl~d~~~~fyFlEvNtRlQVEH~VTE~vtGvDLV~~Qi-~iA~G~~L~~~--q~---~i~~~GhAIe~Ri-~AEdp  344 (447)
T PRK05586        272 GTIEFLLDKDGNFYFMEMNTRIQVEHPITEMITGVDLVKEQI-KIAYGEKLSIT--QE---DIKINGHAIECRI-NAEDP  344 (447)
T ss_pred             CEEEEEECCCCCEEEEEEECCCCCCCCCEEECCCCCHHHHHH-HHHCCCCCCCC--CC---CCCCCCEEEEEEE-ECCCC
T ss_conf             247888758997899933435555664110003776899999-98679999977--01---0787856999982-14578


Q ss_pred             CCC-CCCCCCEEEEEEECCCEEECCCCCCCCCE
Q ss_conf             213-10247700089937959984740168879
Q gi|254781067|r  142 SKG-QTVTASYKPAILSNDIRTTVPPHINIGDD  173 (189)
Q Consensus       142 ~kG-~t~~~~~K~A~letG~~i~VP~FI~~Gd~  173 (189)
                      .++ -.+++.-..-..-+|--|.|-..+..|+.
T Consensus       345 ~~~f~Ps~G~i~~~~~P~g~gvRvDt~~~~G~~  377 (447)
T PRK05586        345 ENGFMPCPGKIEELYIPGGLGVRLDSAIYSGYT  377 (447)
T ss_pred             CCCCCCCCCEEEEEECCCCCCEEEECCCCCCCC
T ss_conf             878505875665897699998898787458796


No 46 
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=38.75  E-value=21  Score=17.18  Aligned_cols=32  Identities=16%  Similarity=0.158  Sum_probs=16.8

Q ss_pred             CCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEE
Q ss_conf             98899994688764321154300133201378615689766777
Q gi|254781067|r   79 QEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVA  122 (189)
Q Consensus        79 g~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~  122 (189)
                      ++.+++|++++-++            .=|++|..|.+.---|++
T Consensus        29 ~~p~v~i~p~DA~~------------~GI~dGd~V~v~n~~G~v   60 (116)
T cd02786          29 GEPTLLIHPADAAA------------RGIADGDLVVVFNDRGSV   60 (116)
T ss_pred             CCCEEEECHHHHHH------------CCCCCCCEEEEECCCEEE
T ss_conf             99869999999988------------599999999997899899


No 47 
>pfam02941 FeThRed_A Ferredoxin thioredoxin reductase variable alpha chain.
Probab=38.54  E-value=21  Score=17.12  Aligned_cols=30  Identities=27%  Similarity=0.351  Sum_probs=21.6

Q ss_pred             HCCCCCE----EEEEEECCEEEEECCCCEEEEEE
Q ss_conf             0137861----56897667774401587499999
Q gi|254781067|r  106 YFQEGME----VKLLIHEGVALSVEVPRHVVFTV  135 (189)
Q Consensus       106 fL~eg~~----v~i~~~~~~~i~i~lP~~v~l~V  135 (189)
                      |=..||+    =.+..|+|+|||..||-.|.+.+
T Consensus        24 fDl~G~eGeV~~~v~~wkGr~ISanlP~~V~F~~   57 (67)
T pfam02941        24 FDLKGMEGEIKQYVGDWKGRPISANLPFKVQFSK   57 (67)
T ss_pred             CCCCCCEEEEEEEEECCCCCEECCCCCEEEEECH
T ss_conf             4446777777567631369695699879999800


No 48 
>PRK08462 biotin carboxylase; Validated
Probab=38.38  E-value=34  Score=15.91  Aligned_cols=97  Identities=19%  Similarity=0.221  Sum_probs=45.8

Q ss_pred             CCEEEEEEEE-CCEEEEEECCCCCCCCCC-------HHHHHHHHHHCCCCCEEEEEEECCEEEEECC-CCEEEEEEEECC
Q ss_conf             6405789961-988999946887643211-------5430013320137861568976677744015-874999999828
Q gi|254781067|r   69 DQRFQFLYQD-QEGFHFMNPETYDQVTVS-------EEVIGDQKVYFQEGMEVKLLIHEGVALSVEV-PRHVVFTVIDTE  139 (189)
Q Consensus        69 ~~~~qylY~d-g~~~~FMd~etyeqi~i~-------~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~l-P~~v~l~V~~t~  139 (189)
                      --.+||||.. ++.|+||...+==|++=+       -|++..+.. +..|..+    .+...  +.+ -..+++.|.--+
T Consensus       273 aGTvEFl~d~~~~~fyFlE~NtRlQVEH~VTE~vtGiDLV~~Qi~-iA~G~~l----~~q~~--i~~~GhaIe~Ri~AEd  345 (446)
T PRK08462        273 AGTFEFLLDSNMKDFYFMEMNTRLQVEHTVSEMVSGLDLIEWMIK-IAEGEEL----PSQES--IKLKGHAIECRITAED  345 (446)
T ss_pred             CCEEEEEECCCCCEEEEEEEECCCCEECCCCCCCCCCCHHHHHHH-HHCCCCC----CCCCC--CCCCCEEEEEEEECCC
T ss_conf             433899980799718999743342100111122148779999999-8679998----75666--6726434223420458


Q ss_pred             CCCCCCCCC-CCEEEEEEECCCEEECCCCCCCCCEE
Q ss_conf             542131024-77000899379599847401688799
Q gi|254781067|r  140 PSSKGQTVT-ASYKPAILSNDIRTTVPPHINIGDDI  174 (189)
Q Consensus       140 p~~kG~t~~-~~~K~A~letG~~i~VP~FI~~Gd~I  174 (189)
                      |  ..-.-+ +.-..-..-+|.-|.|-.++..|+.|
T Consensus       346 p--~~F~Ps~G~i~~~~~P~g~gvRvDt~~~~G~~v  379 (446)
T PRK08462        346 P--KKFYPSPGKITKWIAPGGRNVRMDSHAYAGYVV  379 (446)
T ss_pred             C--CCCCCCCEEEEEEECCCCCCEEEECCCCCCCEE
T ss_conf             7--767998758878987999998963887785987


No 49 
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex  and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=38.32  E-value=21  Score=17.13  Aligned_cols=31  Identities=23%  Similarity=0.375  Sum_probs=15.8

Q ss_pred             ECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECC
Q ss_conf             1988999946887643211543001332013786156897667
Q gi|254781067|r   78 DQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG  120 (189)
Q Consensus        78 dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~  120 (189)
                      ..+.++.|++++-++.-            |++|..|.|.--.|
T Consensus        32 ~pep~v~~~p~dA~~lg------------i~~Gd~V~v~s~~G   62 (120)
T cd00508          32 APEPFVEIHPEDAARLG------------IKDGDLVRVSSRRG   62 (120)
T ss_pred             CCCCEEEECHHHHHHCC------------CCCCCEEEEECCCE
T ss_conf             99988999999998859------------99999999981773


No 50 
>cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=38.28  E-value=23  Score=16.95  Aligned_cols=30  Identities=27%  Similarity=0.402  Sum_probs=14.0

Q ss_pred             HCCCCCEEEEEEECCE-----EEEECCCCEEEEEE
Q ss_conf             0137861568976677-----74401587499999
Q gi|254781067|r  106 YFQEGMEVKLLIHEGV-----ALSVEVPRHVVFTV  135 (189)
Q Consensus       106 fL~eg~~v~i~~~~~~-----~i~i~lP~~v~l~V  135 (189)
                      =++||.-|.+.--.|.     .++=.+|.-+++.=
T Consensus        44 GI~DgD~Vev~N~~G~v~arA~Vs~rip~G~v~my   78 (141)
T cd02776          44 GIKDNDWVEVFNDNGVVVARAKVSPRIPRGTVFMY   78 (141)
T ss_pred             CCCCCCEEEEECCCCEEEEEEEECCCCCCCEEEEE
T ss_conf             99889999998489259999998998799989997


No 51 
>TIGR01540 portal_PBSX phage portal protein, PBSX family; InterPro: IPR006430   This group of sequences, from phage and prophage, represent one of several distantly related families of portal proteins. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average molecular weight of 40-90 kDa. This family shows clear homology to sequences represented by IPR006427 from INTERPRO..
Probab=38.10  E-value=11  Score=18.84  Aligned_cols=21  Identities=24%  Similarity=0.327  Sum_probs=17.5

Q ss_pred             CCCCCCCEEEEECCCCCEEHH
Q ss_conf             401688799998899724021
Q gi|254781067|r  166 PHINIGDDIVILTEDNSYVER  186 (189)
Q Consensus       166 ~FI~~Gd~IkV~T~~g~Y~~R  186 (189)
                      .||+.+|-+|.|-|||||+.-
T Consensus       169 ~F~~~~dp~kmdirtGeyvnt  189 (386)
T TIGR01540       169 IFIELPDPIKMDIRTGEYVNT  189 (386)
T ss_pred             EEEECCCCCEEECCCCHHHHH
T ss_conf             986168974121134226787


No 52 
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=36.80  E-value=24  Score=16.80  Aligned_cols=31  Identities=26%  Similarity=0.392  Sum_probs=14.6

Q ss_pred             CCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCE
Q ss_conf             9889999468876432115430013320137861568976677
Q gi|254781067|r   79 QEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGV  121 (189)
Q Consensus        79 g~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~  121 (189)
                      .+.++.|++++=+..            =|++|..|.|.--.|.
T Consensus        28 ~~~~v~inp~dA~~~------------Gi~dGd~V~v~s~~G~   58 (123)
T cd02778          28 PENTLWINPETAARL------------GIKDGDRVEVSSARGK   58 (123)
T ss_pred             CCCEEEECHHHHHHC------------CCCCCCEEEEECCCEE
T ss_conf             998899999999984------------9999999999889968


No 53 
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR),  trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=36.18  E-value=26  Score=16.54  Aligned_cols=17  Identities=18%  Similarity=0.305  Sum_probs=10.1

Q ss_pred             HCCCCCEEEEEEECCEE
Q ss_conf             01378615689766777
Q gi|254781067|r  106 YFQEGMEVKLLIHEGVA  122 (189)
Q Consensus       106 fL~eg~~v~i~~~~~~~  122 (189)
                      =|++|..|.|.--.|++
T Consensus        46 GI~dGd~V~V~n~rG~v   62 (129)
T cd02793          46 GIADGDIVRVFNDRGAC   62 (129)
T ss_pred             CCCCCCEEEEECCCCEE
T ss_conf             99898999998889569


No 54 
>pfam01568 Molydop_binding Molydopterin dinucleotide binding domain. This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules.
Probab=35.08  E-value=25  Score=16.66  Aligned_cols=15  Identities=20%  Similarity=0.355  Sum_probs=8.7

Q ss_pred             CCCCCEEEEEEECCE
Q ss_conf             137861568976677
Q gi|254781067|r  107 FQEGMEVKLLIHEGV  121 (189)
Q Consensus       107 L~eg~~v~i~~~~~~  121 (189)
                      |.+|..|.+.--.|+
T Consensus        44 i~~Gd~V~v~s~~G~   58 (110)
T pfam01568        44 IKDGDLVEVTSRRGS   58 (110)
T ss_pred             CCCCCEEEEECCCEE
T ss_conf             988999999768989


No 55 
>KOG1708 consensus
Probab=35.05  E-value=23  Score=16.85  Aligned_cols=52  Identities=17%  Similarity=0.273  Sum_probs=32.6

Q ss_pred             ECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCCEEECCCCCCCCCEEEEECCCCCEE
Q ss_conf             6677744015874999999828542131024770008993795998474016887999988997240
Q gi|254781067|r  118 HEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYV  184 (189)
Q Consensus       118 ~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~  184 (189)
                      +.|.++-.+-|-++.-.|.=-+|.-.          .-.|-+.     -|-+.|++|+|+||+|.-+
T Consensus       122 ~pgtivk~EaPlhvsk~VmLvdp~d~----------q~te~~w-----r~~e~GekVRvstrSG~iI  173 (236)
T KOG1708         122 EPGTIVKSEAPLHVSKQVMLVDPEDD----------QPTEVEW-----RFTEDGEKVRVSTRSGRII  173 (236)
T ss_pred             CCCEEEEECCCCEEECCEEEECCCCC----------CCCEEEE-----EECCCCCEEEEEECCCCCC
T ss_conf             88627750377234040698773236----------7732015-----7747885799983055161


No 56 
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=34.93  E-value=26  Score=16.60  Aligned_cols=15  Identities=20%  Similarity=0.114  Sum_probs=8.1

Q ss_pred             CCCCCEEEEEEECCE
Q ss_conf             137861568976677
Q gi|254781067|r  107 FQEGMEVKLLIHEGV  121 (189)
Q Consensus       107 L~eg~~v~i~~~~~~  121 (189)
                      |++|..|.|.---|+
T Consensus        47 i~~Gd~V~v~s~~G~   61 (130)
T cd02781          47 IADGDWVWVETPRGR   61 (130)
T ss_pred             CCCCCEEEEECCCEE
T ss_conf             999999999848978


No 57 
>PRK03955 hypothetical protein; Reviewed
Probab=33.55  E-value=29  Score=16.30  Aligned_cols=16  Identities=13%  Similarity=0.312  Sum_probs=14.2

Q ss_pred             CCCCCCEEEEECCCCC
Q ss_conf             0168879999889972
Q gi|254781067|r  167 HINIGDDIVILTEDNS  182 (189)
Q Consensus       167 FI~~Gd~IkV~T~~g~  182 (189)
                      .|+.||+|+||+.+|.
T Consensus       111 ~i~~Gd~v~vd~~~G~  126 (132)
T PRK03955        111 ELKDGDRVRVDGDTGT  126 (132)
T ss_pred             CCCCCCEEEEECCCCE
T ss_conf             0479999999689638


No 58 
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a  large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=33.07  E-value=27  Score=16.46  Aligned_cols=15  Identities=20%  Similarity=0.355  Sum_probs=8.2

Q ss_pred             CCCCCEEEEEEECCE
Q ss_conf             137861568976677
Q gi|254781067|r  107 FQEGMEVKLLIHEGV  121 (189)
Q Consensus       107 L~eg~~v~i~~~~~~  121 (189)
                      |++|..|.+.--.+.
T Consensus        37 i~~Gd~v~v~~~~g~   51 (101)
T cd02775          37 IKDGDLVRVESRRGS   51 (101)
T ss_pred             CCCCCEEEEEECCEE
T ss_conf             988999999969858


No 59 
>PRK07178 acetyl-CoA carboxylase; Validated
Probab=32.16  E-value=42  Score=15.29  Aligned_cols=96  Identities=16%  Similarity=0.196  Sum_probs=43.8

Q ss_pred             EEEEEEEECCEEEEEECCCCCCCCCC-------HHHHHHHHHHCCCCCEEEEEEECCEEEEECC-CCEEEEEEEECCCCC
Q ss_conf             05789961988999946887643211-------5430013320137861568976677744015-874999999828542
Q gi|254781067|r   71 RFQFLYQDQEGFHFMNPETYDQVTVS-------EEVIGDQKVYFQEGMEVKLLIHEGVALSVEV-PRHVVFTVIDTEPSS  142 (189)
Q Consensus        71 ~~qylY~dg~~~~FMd~etyeqi~i~-------~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~l-P~~v~l~V~~t~p~~  142 (189)
                      .++|||.+ +.|+||...+==|++=+       -|++..+. .+..|..+...  ++ .  +.+ -..+++.| ++|...
T Consensus       272 TvEFlv~~-~~~yFlEvNtRlQVEH~VTE~vtGiDLV~~Qi-~iA~G~~L~~~--q~-~--i~~~GhAIe~Ri-~AEDp~  343 (471)
T PRK07178        272 TVEFLLAD-GEVYFMEMNTRVQVEHTITEEITGIDIVREQI-RIASGLPLSVK--QE-D--IQHRGFALQFRI-NAEDPK  343 (471)
T ss_pred             EEEEEEEC-CCEEEEECCCCCCCCCCHHHHHHCCCHHHHHH-HHHCCCCCCCC--CC-C--CCCCCCEEEEEE-ECCCCC
T ss_conf             69999867-94799832466655542136661675899999-98679978831--02-4--455885899998-513776


Q ss_pred             CCC-CCCCCEEEEEEECCCEEECCCCCCCCCEE
Q ss_conf             131-02477000899379599847401688799
Q gi|254781067|r  143 KGQ-TVTASYKPAILSNDIRTTVPPHINIGDDI  174 (189)
Q Consensus       143 kG~-t~~~~~K~A~letG~~i~VP~FI~~Gd~I  174 (189)
                      ++= .+.+.-..-..-.|--|.+-..+..|+.|
T Consensus       344 ~~F~Ps~G~i~~~~~P~g~gvR~Dt~~~~G~~v  376 (471)
T PRK07178        344 NNFLPSFGKITRYYAPGGPGVRTDTAIYTGYTI  376 (471)
T ss_pred             CCCCCCCCEEEEEECCCCCCEEEECCCCCCCEE
T ss_conf             686568725778976999988986677688961


No 60 
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.06  E-value=34  Score=15.88  Aligned_cols=16  Identities=19%  Similarity=0.397  Sum_probs=9.6

Q ss_pred             CCCCCEEEEEEECCEE
Q ss_conf             1378615689766777
Q gi|254781067|r  107 FQEGMEVKLLIHEGVA  122 (189)
Q Consensus       107 L~eg~~v~i~~~~~~~  122 (189)
                      |++|..|.|.---|.+
T Consensus        47 i~~Gd~V~v~s~~G~~   62 (129)
T cd02782          47 LADGDKVRVTSAAGSV   62 (129)
T ss_pred             CCCCCEEEEECCCEEE
T ss_conf             9899999998698479


No 61 
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a  predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=30.99  E-value=34  Score=15.84  Aligned_cols=17  Identities=18%  Similarity=0.262  Sum_probs=10.1

Q ss_pred             HCCCCCEEEEEEECCEE
Q ss_conf             01378615689766777
Q gi|254781067|r  106 YFQEGMEVKLLIHEGVA  122 (189)
Q Consensus       106 fL~eg~~v~i~~~~~~~  122 (189)
                      =|.+|..|.|.---|++
T Consensus        43 gi~dGd~V~v~n~~G~i   59 (121)
T cd02794          43 GIKDGDRVLVFNDRGKV   59 (121)
T ss_pred             CCCCCCEEEEECCCCEE
T ss_conf             99899999998199069


No 62 
>TIGR01363 strep_his_triad streptococcal histidine triad protein; InterPro: IPR006270   The sequences represented in this group are identified by a domain which consists of the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Additional copies of the repeats are found in more poorly conserved regions. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice . .
Probab=29.42  E-value=39  Score=15.48  Aligned_cols=75  Identities=20%  Similarity=0.307  Sum_probs=43.3

Q ss_pred             HHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCC--EEEEEECCC--------EEEEE
Q ss_conf             43216775899889379999987536888763899999982468710013427872--001010564--------05789
Q gi|254781067|r    6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQ--VERAFVEDQ--------RFQFL   75 (189)
Q Consensus         6 an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ek--ve~~~ie~~--------~~qyl   75 (189)
                      .|||+-|-+|.++|+.|.=|     |+|.-+-.+|+|-  =+...+.+.+-...++  -..+.+..+        ..|==
T Consensus       122 vNEi~~GYVIKV~G~YYVYL-----K~aa~~~NiRTK~--~I~~Q~~~~~~~~~~~Glaqvahl~~~~~~AV~~A~~QGR  194 (376)
T TIGR01363       122 VNEIKGGYVIKVNGKYYVYL-----KDAAHADNIRTKE--EIARQKQERSKEAKEKGLAQVAHLSKREDAAVAEARRQGR  194 (376)
T ss_pred             EEEECCCEEEEECCEEEEEE-----CCCCCCCCCCHHH--HHHHHHHHHHHHHHCCCEEEHHHHCHHHHHHHHHHHHCCC
T ss_conf             02203866898858188961-----7212210130178--9999987433433225401011203246789999984788


Q ss_pred             EEECCEEEEEEC
Q ss_conf             961988999946
Q gi|254781067|r   76 YQDQEGFHFMNP   87 (189)
Q Consensus        76 Y~dg~~~~FMd~   87 (189)
                      |+-+|+|+|--.
T Consensus       195 YTTDDGYIF~a~  206 (376)
T TIGR01363       195 YTTDDGYIFNAS  206 (376)
T ss_pred             CCCCCCCEECCH
T ss_conf             104576222712


No 63 
>TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011827   3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus .     This entry is most closely related to the 3-isopropylmalate dehydratase IPR004431 from INTERPRO. It also includes members, which cluster with other genes of leucine biosynthesis.    The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex.
Probab=25.72  E-value=46  Score=15.08  Aligned_cols=19  Identities=21%  Similarity=0.240  Sum_probs=13.9

Q ss_pred             CCCCCCCEEEEECCCCCEE
Q ss_conf             4016887999988997240
Q gi|254781067|r  166 PHINIGDDIVILTEDNSYV  184 (189)
Q Consensus       166 ~FI~~Gd~IkV~T~~g~Y~  184 (189)
                      .-++.||.|.||-++|+=+
T Consensus       108 e~~~dGD~V~vdl~~geir  126 (159)
T TIGR02087       108 ELIKDGDEVEVDLEKGEIR  126 (159)
T ss_pred             EEECCCCEEEEECCCCEEE
T ss_conf             0213788789975766088


No 64 
>TIGR01196 edd phosphogluconate dehydratase; InterPro: IPR004786   Two dehydratases, dihydroxy-acid dehydratase (gene ilvD or ILV3) and 6-phosphogluconate dehydratase (gene edd) have been shown to be evolutionary related . Dihydroxy-acid dehydratase catalyzes the fourth step in the biosynthesis of isoleucine and valine, the dehydratation of 2,3-dihydroxy-isovaleic acid into alpha-ketoisovaleric acid. 6-Phosphogluconate dehydratase catalyzes the first step in the Entner-Doudoroff pathway, the dehydratation of 6-phospho-D-gluconate into 6-phospho-2-dehydro-3-deoxy-D-gluconate. Another protein containing this signature is the Escherichia coli hypothetical protein yjhG. The N-terminal part of the proteins contains a cysteine that could be involved in the binding of a 2Fe-2S iron-sulphur cluster .    This family defines the 6-phosphogluconate dehydratases.; GO: 0004456 phosphogluconate dehydratase activity, 0009255 Entner-Doudoroff pathway.
Probab=25.39  E-value=42  Score=15.33  Aligned_cols=16  Identities=25%  Similarity=0.219  Sum_probs=13.7

Q ss_pred             CCCCCEEEEECCCCCE
Q ss_conf             1688799998899724
Q gi|254781067|r  168 INIGDDIVILTEDNSY  183 (189)
Q Consensus       168 I~~Gd~IkV~T~~g~Y  183 (189)
                      |+.||.|+||--+|+-
T Consensus       546 irdGD~iR~D~~nG~L  561 (614)
T TIGR01196       546 IRDGDLIRVDAVNGEL  561 (614)
T ss_pred             EECCCEEEECCCCCEE
T ss_conf             6238788980778804


No 65 
>TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=25.15  E-value=56  Score=14.54  Aligned_cols=27  Identities=30%  Similarity=0.426  Sum_probs=18.7

Q ss_pred             EEEECCCEEECCCC-CCCCCEEEEECCC
Q ss_conf             89937959984740-1688799998899
Q gi|254781067|r  154 AILSNDIRTTVPPH-INIGDDIVILTED  180 (189)
Q Consensus       154 A~letG~~i~VP~F-I~~Gd~IkV~T~~  180 (189)
                      .++=||-.|..|.| +++||.|.|--.+
T Consensus       126 hi~vNGk~VdIPSy~v~~Gd~i~ikEk~  153 (217)
T TIGR01017       126 HILVNGKKVDIPSYQVRPGDIISIKEKS  153 (217)
T ss_pred             EEEECCEEECCCEEEECCCCEEEEEECC
T ss_conf             0787981852240670799889981032


No 66 
>TIGR02517 type_II_gspD general secretion pathway protein D; InterPro: IPR013356    In Gram-negative bacteria, proteins that have first crossed the inner member by Sec-dependent protein transport can be exported across the outer membrane by type II secretion (also referred to as the main terminal branch of the general secretion pathway). Members of this family are general secretion pathway protein D. In Yersinia enterocolitica, a second member of this family is part of a novel second type II secretion system specifically associated with virulence (See ). This family is closely homologous to the type IV pilus outer membrane secretin PilQ (IPR013355 from INTERPRO) and to the type III secretion system pore YscC/HrcC (IPR003522 from INTERPRO).; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex, 0019867 outer membrane.
Probab=24.90  E-value=51  Score=14.80  Aligned_cols=36  Identities=22%  Similarity=0.348  Sum_probs=26.3

Q ss_pred             CCCCCCCCCEEEEEE-ECCCEEECCCCCC-CCCEEEEE
Q ss_conf             213102477000899-3795998474016-88799998
Q gi|254781067|r  142 SKGQTVTASYKPAIL-SNDIRTTVPPHIN-IGDDIVIL  177 (189)
Q Consensus       142 ~kG~t~~~~~K~A~l-etG~~i~VP~FI~-~Gd~IkV~  177 (189)
                      +.+++.++.+....- ++|++++|=|+|. +|+.|+.+
T Consensus       558 ~~~~~~~n~f~t~~r~~vG~~L~v~PqIn~eg~~v~L~  595 (697)
T TIGR02517       558 GTGGTNANPFNTVERKDVGIKLKVTPQINGEGGTVRLE  595 (697)
T ss_pred             EEECCCCCEEEEEEEEEEEEEEEEEEEEECCCCEEEEE
T ss_conf             63054553143016887228998887783799869999


No 67 
>PRK06302 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=24.84  E-value=31  Score=16.12  Aligned_cols=14  Identities=29%  Similarity=0.662  Sum_probs=10.3

Q ss_pred             CCCCCCCCEEEEEC
Q ss_conf             74016887999988
Q gi|254781067|r  165 PPHINIGDDIVILT  178 (189)
Q Consensus       165 P~FI~~Gd~IkV~T  178 (189)
                      |+||+.||+|+...
T Consensus        99 ~pFV~vGd~V~~Gq  112 (155)
T PRK06302         99 PPFVEVGDTVKEGQ  112 (155)
T ss_pred             CCCCCCCCEECCCC
T ss_conf             97424686724898


No 68 
>pfam08968 DUF1885 Domain of unknown function (DUF1885). This domain is found in a set of hypothetical proteins produced by bacteria of the Bacillus genus.
Probab=24.72  E-value=47  Score=15.02  Aligned_cols=52  Identities=17%  Similarity=0.432  Sum_probs=37.7

Q ss_pred             EEEEEECCEEEEE-------ECCCCCCCCCCHHH-HHHH------HHHCCCCCEEEEEEECCEEEE
Q ss_conf             7899619889999-------46887643211543-0013------320137861568976677744
Q gi|254781067|r   73 QFLYQDQEGFHFM-------NPETYDQVTVSEEV-IGDQ------KVYFQEGMEVKLLIHEGVALS  124 (189)
Q Consensus        73 qylY~dg~~~~FM-------d~etyeqi~i~~~~-ig~~------~~fL~eg~~v~i~~~~~~~i~  124 (189)
                      -||-.+++.|.-|       ..++|=|+.||... .||.      .+||.--++=++.+|+|+.+-
T Consensus        59 l~L~~~~~rY~~I~vgVg~e~~~sfIqi~LP~~AT~GDKgKANEfckfLAK~l~geL~LFNGRtmy  124 (128)
T pfam08968        59 LYLQSDHDRYNGIYIGVGTEGEQTFIQISLPPTATFGDKGKANEFSKFLAKKLEGELQLFNGRTMY  124 (128)
T ss_pred             EEECCCCCCEEEEEEEECCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCEEEEECCEEEE
T ss_conf             998047875505999635678715799988999877762227689999999741015775470798


No 69 
>TIGR03479 DMSO_red_II_alp DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane.
Probab=24.45  E-value=50  Score=14.85  Aligned_cols=22  Identities=23%  Similarity=0.347  Sum_probs=19.7

Q ss_pred             CCCCCCEEEEECCCCCEEHHCC
Q ss_conf             0168879999889972402102
Q gi|254781067|r  167 HINIGDDIVILTEDNSYVERVK  188 (189)
Q Consensus       167 FI~~Gd~IkV~T~~g~Y~~Rak  188 (189)
                      =|+.||.|+|-++.|+-.-||+
T Consensus       823 GI~dGD~V~V~N~~G~v~~~A~  844 (912)
T TIGR03479       823 GIKDGDQVRIFNDLAEFEAMAK  844 (912)
T ss_pred             CCCCCCEEEEECCCEEEEEEEE
T ss_conf             9986999999869989999999


No 70 
>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53,  Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
Probab=23.55  E-value=60  Score=14.35  Aligned_cols=56  Identities=13%  Similarity=0.225  Sum_probs=41.9

Q ss_pred             CEEEEEECCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHH-HHCCCCCEEEEE
Q ss_conf             20010105640578996198899994688764321154300133-201378615689
Q gi|254781067|r   61 QVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQK-VYFQEGMEVKLL  116 (189)
Q Consensus        61 kve~~~ie~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~-~fL~eg~~v~i~  116 (189)
                      .+....+.++.+.+.|.+...++++|..+=.-..|+...+.... .-|.+|..+.+-
T Consensus        36 ~l~~~~iSr~Ha~i~~~~~~~~~~~d~~S~nGt~vn~~~~~~~~~~~L~~gd~i~lG   92 (102)
T cd00060          36 VLDDPSVSRRHAVIRYDGDGGVVLIDLGSTNGTFVNGQRVSPGEPVRLRDGDVIRLG   92 (102)
T ss_pred             EECCCCCCHHHEEEEECCCCEEEEEECCCCCCEEECCEECCCCCCEECCCCCEEEEC
T ss_conf             918976482358999938706999989987468999999679960698999999999


No 71 
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=23.44  E-value=61  Score=14.33  Aligned_cols=46  Identities=11%  Similarity=0.063  Sum_probs=36.2

Q ss_pred             CCCCCCCCCEEEEEEECCCEEECCCCCCCCCEEEEECCCCCEEHHC
Q ss_conf             2131024770008993795998474016887999988997240210
Q gi|254781067|r  142 SKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVERV  187 (189)
Q Consensus       142 ~kG~t~~~~~K~A~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~Ra  187 (189)
                      +++-...+..+...+.=|..+-||.-|...|+|.||--+|=|++|-
T Consensus        47 l~~L~~~~~~~e~lvplg~~~~v~~~i~~~~kvlV~iG~g~~vE~~   92 (141)
T PRK03947         47 LEELKGAGEEKETLVPIGAGSFVKAKIKDPDKVIVSLGAGYSAEKD   92 (141)
T ss_pred             HHHHHCCCCCCEEEEECCCCEEEEEEECCCCEEEEECCCCEEEEEC
T ss_conf             9975347999638896588728788846888689983898699975


No 72 
>pfam11871 DUF3391 Domain of unknown function (DUF3391). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is typically between 122 to 139 amino acids in length. This domain is found associated with pfam01966.
Probab=23.01  E-value=57  Score=14.51  Aligned_cols=21  Identities=14%  Similarity=0.222  Sum_probs=16.0

Q ss_pred             CEEEHHHCCCCCEEEECCEEE
Q ss_conf             236643216775899889379
Q gi|254781067|r    2 VKVIASAVRKGNVLDVDGKLY   22 (189)
Q Consensus         2 ~~i~an~lk~G~~i~~dg~~~   22 (189)
                      .+|..++|+.||+|.-=+.+|
T Consensus         3 ~kI~v~~L~vGMyV~~l~~~W   23 (127)
T pfam11871         3 KKIPVSQLQVGMYVSLLDRSW   23 (127)
T ss_pred             EEEEHHHCCCCCEEEECCCCC
T ss_conf             077799957761898678775


No 73 
>PRK08166 NADH dehydrogenase subunit G; Validated
Probab=23.00  E-value=50  Score=14.82  Aligned_cols=23  Identities=13%  Similarity=0.177  Sum_probs=19.1

Q ss_pred             CCCCCCCEEEEECCCCCEEHHCC
Q ss_conf             40168879999889972402102
Q gi|254781067|r  166 PHINIGDDIVILTEDNSYVERVK  188 (189)
Q Consensus       166 ~FI~~Gd~IkV~T~~g~Y~~Rak  188 (189)
                      +=|+.||.|+|.++.|+..-+|+
T Consensus       800 lGI~dGd~V~V~SrrG~v~~~a~  822 (858)
T PRK08166        800 LGVNAGTRVSFSYDGQTVRLPVR  822 (858)
T ss_pred             CCCCCCCEEEEEECCEEEEEEEE
T ss_conf             59999798999969999999999


No 74 
>COG3173 Predicted aminoglycoside phosphotransferase [General function prediction only]
Probab=22.81  E-value=62  Score=14.26  Aligned_cols=19  Identities=32%  Similarity=0.214  Sum_probs=5.9

Q ss_pred             CCCCCEEEECCEEEEEEEE
Q ss_conf             1677589988937999998
Q gi|254781067|r    9 VRKGNVLDVDGKLYIVLVA   27 (189)
Q Consensus         9 lk~G~~i~~dg~~~~V~~~   27 (189)
                      ++.||+|..++.|-=|+++
T Consensus       205 ~~~gNlii~~~~~~gVlDw  223 (321)
T COG3173         205 YRPGNLIIDPGRPTGVLDW  223 (321)
T ss_pred             CCCCCEEEECCCEEEEEEC
T ss_conf             5568788728972589965


No 75 
>TIGR01348 PDHac_trf_long pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006256   This group of sequences are a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and percent identity (UPGMA) trees. Members contain two or three copies of the lipoyl-binding domain. Escherichia coli AceF is included in this set while mitochondrial and some other bacterial forms are excluded.  dihydrolipoyllysine-residue acetyltransferase E2 component of pyruvate dehydrogenase complex; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006096 glycolysis, 0045254 pyruvate dehydrogenase complex.
Probab=22.29  E-value=64  Score=14.19  Aligned_cols=23  Identities=35%  Similarity=0.434  Sum_probs=14.3

Q ss_pred             CCCCCCCCEEEEEEECC-CEEECC
Q ss_conf             13102477000899379-599847
Q gi|254781067|r  143 KGQTVTASYKPAILSND-IRTTVP  165 (189)
Q Consensus       143 kG~t~~~~~K~A~letG-~~i~VP  165 (189)
                      =|||++..+=-.|||+. .++.||
T Consensus       230 vGDtV~~~QslItLE~DKA~~EvP  253 (655)
T TIGR01348       230 VGDTVSADQSLITLESDKASMEVP  253 (655)
T ss_pred             CCCEECCCCCEEEEECCEEEEEEC
T ss_conf             377764788678870671478746


No 76 
>PRK08493 NADH dehydrogenase subunit G; Validated
Probab=21.58  E-value=58  Score=14.46  Aligned_cols=23  Identities=17%  Similarity=0.380  Sum_probs=19.5

Q ss_pred             CCCCCCCEEEEECCCCCEEHHCC
Q ss_conf             40168879999889972402102
Q gi|254781067|r  166 PHINIGDDIVILTEDNSYVERVK  188 (189)
Q Consensus       166 ~FI~~Gd~IkV~T~~g~Y~~Rak  188 (189)
                      +=|+.||.|+|.++.|+-.-||+
T Consensus       759 lgi~dGd~V~v~S~~G~I~~~v~  781 (819)
T PRK08493        759 LNLKDGDRVTLKKEEEELTGSVR  781 (819)
T ss_pred             CCCCCCCEEEEEECCEEEEEEEE
T ss_conf             39999997999979858999999


No 77 
>COG0243 BisC Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]
Probab=21.27  E-value=67  Score=14.08  Aligned_cols=21  Identities=24%  Similarity=0.254  Sum_probs=15.9

Q ss_pred             CCCCCEEEEECCCCCEEHHCC
Q ss_conf             168879999889972402102
Q gi|254781067|r  168 INIGDDIVILTEDNSYVERVK  188 (189)
Q Consensus       168 I~~Gd~IkV~T~~g~Y~~Rak  188 (189)
                      |+.||.|+|-++.|+-..||+
T Consensus       685 I~~GD~V~V~~~rG~v~~~a~  705 (765)
T COG0243         685 IKDGDLVRVENRRGEVEARAK  705 (765)
T ss_pred             CCCCCEEEEEECCCEEEEEEE
T ss_conf             977998999908977999999


No 78 
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=21.24  E-value=67  Score=14.06  Aligned_cols=33  Identities=24%  Similarity=0.121  Sum_probs=24.2

Q ss_pred             EEECCCEEECCCCCCCCCEEEEECCCCCEEHHC
Q ss_conf             993795998474016887999988997240210
Q gi|254781067|r  155 ILSNDIRTTVPPHINIGDDIVILTEDNSYVERV  187 (189)
Q Consensus       155 ~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~Ra  187 (189)
                      -|--.-.+.|..-++.||.|.|-+++|+.+.|.
T Consensus        18 sll~~GI~~v~g~f~~gd~V~i~~~~g~~ia~G   50 (77)
T smart00359       18 SLLAPGVVRVDGGIKEGDVVVIVDEKGEPLGIG   50 (77)
T ss_pred             CCCCCCEEEECCCCCCCCEEEEECCCCCEEEEE
T ss_conf             706463186828727999999998999999999


No 79 
>PRK13532 nitrate reductase; Provisional
Probab=21.12  E-value=61  Score=14.30  Aligned_cols=23  Identities=17%  Similarity=0.401  Sum_probs=18.8

Q ss_pred             CCCCCCCEEEEECCCCCEEHHCC
Q ss_conf             40168879999889972402102
Q gi|254781067|r  166 PHINIGDDIVILTEDNSYVERVK  188 (189)
Q Consensus       166 ~FI~~Gd~IkV~T~~g~Y~~Rak  188 (189)
                      +=|+.||.|+|.++-|+-.-||+
T Consensus       756 ~GI~~GD~V~V~S~RG~v~~~~~  778 (828)
T PRK13532        756 RGLRRGDEVKVVSRRGEVKSRVE  778 (828)
T ss_pred             CCCCCCCEEEEEECCEEEEEEEE
T ss_conf             59999799999809889999999


No 80 
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=20.70  E-value=49  Score=14.91  Aligned_cols=48  Identities=15%  Similarity=0.321  Sum_probs=30.4

Q ss_pred             CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEEEEEEC
Q ss_conf             76389999998246871001342787200101056405789961988999946
Q gi|254781067|r   35 GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGFHFMNP   87 (189)
Q Consensus        35 g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~~FMd~   87 (189)
                      ..+-+|++   |-+|+.+..+|.++|.+..+.-=-.  +-+..+.+.|.++-+
T Consensus         3 ~~~~iqiR---lpdG~~l~~~F~~~dtl~~v~~fV~--~~~~~~~~~f~L~t~   50 (80)
T smart00166        3 DQCRLQIR---LPDGSRLVRRFPSSDTLRTVYEFVS--AALTDGNDPFTLNSP   50 (80)
T ss_pred             CCEEEEEE---ECCCCEEEEECCCCCHHHHHHHHHH--HCCCCCCCCEEEEEC
T ss_conf             74799999---1999989998389783999999998--647789950899738


No 81 
>pfam10709 DUF2511 Protein of unknown function (DUF2511). This family is conserved in bacteria. The function is not known.
Probab=20.50  E-value=69  Score=13.97  Aligned_cols=56  Identities=7%  Similarity=-0.028  Sum_probs=37.6

Q ss_pred             EEECCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECC
Q ss_conf             01056405789961988999946887643211543001332013786156897667
Q gi|254781067|r   65 AFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG  120 (189)
Q Consensus        65 ~~ie~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~  120 (189)
                      =.+.+.+++..-..|..++.+|+.|..||.++.-.-......=..+..+++..-+|
T Consensus        34 WpftrEevmL~Cr~g~alfViN~sTl~qYpLN~iA~~q~ksgk~~~~~id~i~~dd   89 (110)
T pfam10709        34 WPFTREEVMLQCRNGNALFVANGSTLMQYPLNGVAESQGKSGKVPYQPIDVIWLDD   89 (110)
T ss_pred             CCCCCHHEEEEEECCCEEEEECCCCHHHCCCHHHHHHHHHCCCCCCCCCCEEECCC
T ss_conf             87520306999826987999877500323623899998764775578677375279


No 82 
>pfam00789 UBX UBX domain. This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.
Probab=20.06  E-value=71  Score=13.91  Aligned_cols=49  Identities=16%  Similarity=0.435  Sum_probs=28.3

Q ss_pred             CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEEEEEE
Q ss_conf             7638999999824687100134278720010105640578996198899994
Q gi|254781067|r   35 GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGFHFMN   86 (189)
Q Consensus        35 g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~~FMd   86 (189)
                      +...+++.+| |-+|+.+..+|.++|++..+.-=-.  +.++.+...|.++-
T Consensus         3 ~~~~t~I~iR-lpdG~r~~r~F~~~~tl~~v~~fV~--~~~~~~~~~f~L~t   51 (81)
T pfam00789         3 AEDVCRLQIR-LPDGSRLVRRFNSSDPLQDVYDFVD--SNRYDDDEPFSLNT   51 (81)
T ss_pred             CCCEEEEEEE-CCCCCEEEEEECCCCCHHHHHHHHH--HHCCCCCCCEEEEE
T ss_conf             9982899999-8999889999089983999999999--70879997689984


Done!