Query         gi|254780361|ref|YP_003064774.1| ribosomal protein L32 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 61
No_of_seqs    118 out of 665
Neff          4.8 
Searched_HMMs 39220
Date          Sun May 29 15:44:28 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780361.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK12286 rpmF 50S ribosomal pr 100.0 1.4E-29 3.5E-34  175.7   4.4   59    1-59      1-59  (59)
  2 TIGR01031 rpmF_bact ribosomal   99.9 5.9E-29 1.5E-33  172.4   3.1   55    2-56      1-56  (56)
  3 COG0333 RpmF Ribosomal protein  99.9   9E-27 2.3E-31  161.0   3.8   57    1-57      1-57  (57)
  4 PRK01110 rpmF 50S ribosomal pr  99.9 3.2E-26 8.2E-31  158.1   4.2   56    1-57      1-56  (56)
  5 pfam01783 Ribosomal_L32p Ribos  99.9 4.1E-24   1E-28  147.0   3.9   56    2-57      1-56  (56)
  6 KOG4080 consensus               98.4 3.5E-08 8.9E-13   63.6  -0.2   46    1-46     63-112 (176)
  7 CHL00152 rpl32 ribosomal prote  97.3 5.9E-05 1.5E-09   46.7   0.4   23    1-23      1-23  (53)
  8 PRK08271 anaerobic ribonucleos  93.7   0.032 8.2E-07   32.3   1.6   28   21-48    561-589 (625)
  9 PRK05654 acetyl-CoA carboxylas  92.3   0.041   1E-06   31.8   0.5   23   27-49     30-58  (288)
 10 PRK07111 anaerobic ribonucleos  91.1   0.079   2E-06   30.3   0.8   28   20-47    640-667 (703)
 11 TIGR00354 polC DNA polymerase   90.8    0.12   3E-06   29.4   1.5   23   25-48    677-699 (1173)
 12 CHL00174 accD acetyl-CoA carbo  90.7   0.059 1.5E-06   31.0  -0.1   23   27-49     48-76  (305)
 13 COG1645 Uncharacterized Zn-fin  90.4    0.23 5.8E-06   27.9   2.7   27   28-57     29-58  (131)
 14 PRK08579 anaerobic ribonucleos  89.9    0.12   3E-06   29.4   0.9   29   19-47    558-587 (623)
 15 PRK13130 H/ACA RNA-protein com  89.7    0.11 2.7E-06   29.6   0.5   21   27-48      5-25  (54)
 16 PRK08270 anaerobic ribonucleos  88.5    0.16 4.1E-06   28.7   0.7   28   20-47    618-645 (681)
 17 PRK00420 hypothetical protein;  88.3    0.21 5.3E-06   28.1   1.2   20   28-47     20-43  (107)
 18 COG2888 Predicted Zn-ribbon RN  87.6    0.33 8.5E-06   27.0   1.9   23   26-48     26-58  (61)
 19 COG2260 Predicted Zn-ribbon RN  87.4    0.24 6.1E-06   27.8   1.0   21   27-48      5-25  (59)
 20 PRK08665 ribonucleotide-diphos  85.9    0.42 1.1E-05   26.5   1.7   22   27-49    705-730 (733)
 21 COG1545 Predicted nucleic-acid  85.6    0.41   1E-05   26.6   1.5   30   20-49     20-52  (140)
 22 TIGR00515 accD acetyl-CoA carb  85.1    0.31   8E-06   27.2   0.7   25   25-49     31-61  (292)
 23 TIGR01384 TFS_arch transcripti  84.4     0.5 1.3E-05   26.1   1.5   20   29-48      2-28  (111)
 24 PRK07418 acetolactate synthase  83.6    0.56 1.4E-05   25.9   1.4   30   19-48    583-613 (615)
 25 pfam05876 Terminase_GpA Phage   81.7     1.1 2.8E-05   24.4   2.3   22   27-48    200-237 (552)
 26 pfam10571 UPF0547 Uncharacteri  81.0     0.6 1.5E-05   25.7   0.8   21   29-49      2-23  (26)
 27 PRK12380 hydrogenase nickel in  80.0     1.4 3.6E-05   23.7   2.4   30   23-52     66-98  (113)
 28 pfam09538 FYDLN_acid Protein o  80.0     0.7 1.8E-05   25.4   0.8   21   28-48     10-34  (104)
 29 COG0777 AccD Acetyl-CoA carbox  79.9     1.4 3.5E-05   23.8   2.3   24   26-49     27-56  (294)
 30 PRK12366 replication factor A;  79.7     2.2 5.5E-05   22.8   3.3   31   26-56    532-565 (649)
 31 PRK00564 hypA hydrogenase nick  78.8     1.9 4.8E-05   23.1   2.8   28   23-50     67-98  (117)
 32 PRK08938 DNA topoisomerase I;   78.7     1.3 3.4E-05   23.9   2.0   26   23-48    654-686 (692)
 33 pfam07282 Transposase_35 Putat  78.0     1.2   3E-05   24.1   1.5   29   26-54     27-60  (69)
 34 COG0675 Transposase and inacti  77.7       1 2.6E-05   24.5   1.1   30   25-54    307-336 (364)
 35 COG1594 RPB9 DNA-directed RNA   77.4     1.7 4.3E-05   23.4   2.2   22   27-48      2-30  (113)
 36 cd01675 RNR_III Class III ribo  76.7       1 2.6E-05   24.5   0.9   26   23-48    514-540 (555)
 37 COG1998 RPS31 Ribosomal protei  76.4       1 2.6E-05   24.5   0.9   20   29-48     21-45  (51)
 38 PRK04023 DNA polymerase II lar  76.2       1 2.6E-05   24.5   0.8   25   27-51    645-669 (1128)
 39 PRK09263 anaerobic ribonucleos  76.2       1 2.5E-05   24.5   0.7   28   20-47    634-666 (711)
 40 PRK00423 tfb transcription ini  75.8     1.5 3.9E-05   23.6   1.6   33   25-57      9-47  (310)
 41 PRK07562 ribonucleotide-diphos  74.9     1.7 4.4E-05   23.3   1.7   23   29-51   1149-1175(1177)
 42 smart00661 RPOL9 RNA polymeras  74.0     2.3   6E-05   22.6   2.2   20   29-48      2-28  (52)
 43 PRK03681 hypA hydrogenase nick  73.8     3.4 8.6E-05   21.8   2.9   30   23-52     66-99  (114)
 44 PRK04179 rpl37e 50S ribosomal   73.6     1.6   4E-05   23.5   1.2   27   24-50     14-42  (62)
 45 TIGR01374 soxD sarcosine oxida  72.9     1.1 2.9E-05   24.3   0.3   11   27-37      1-11  (85)
 46 PRK10220 hypothetical protein;  72.2     1.7 4.3E-05   23.3   1.1   23   26-48      2-28  (111)
 47 PRK03824 hypA hydrogenase nick  71.8     3.4 8.6E-05   21.8   2.5   29   23-51     66-118 (135)
 48 COG1326 Uncharacterized archae  70.7     1.4 3.5E-05   23.8   0.4   24   27-50      6-40  (201)
 49 pfam01155 HypA Hydrogenase exp  69.9     4.3 0.00011   21.2   2.8   28   23-50     65-95  (112)
 50 PRK09521 exosome complex RNA-b  69.8     3.8 9.7E-05   21.5   2.5   29   27-55    150-181 (187)
 51 TIGR00340 zpr1_rel zinc finger  68.6       5 0.00013   20.9   2.9   40   21-61      9-49  (168)
 52 pfam08274 PhnA_Zn_Ribbon PhnA   68.2     2.3 5.9E-05   22.6   1.1   22   27-48      2-27  (30)
 53 PRK00762 hypA hydrogenase nick  68.0     3.8 9.7E-05   21.5   2.2   29   23-52     66-104 (124)
 54 pfam04135 Nop10p Nucleolar RNA  66.5     2.3 5.9E-05   22.6   0.8   21   27-48      5-25  (53)
 55 pfam03833 PolC_DP2 DNA polymer  66.3     3.2 8.2E-05   21.9   1.5   22   26-48    628-649 (852)
 56 COG4888 Uncharacterized Zn rib  65.9     6.4 0.00016   20.3   3.0   26   24-49     19-55  (104)
 57 pfam09297 zf-NADH-PPase NADH p  65.8     2.6 6.5E-05   22.4   0.9   21   28-48      4-29  (32)
 58 TIGR02300 FYDLN_acid conserved  65.0     3.1 7.8E-05   22.0   1.2   22   27-48      9-34  (157)
 59 pfam12172 DUF35_N Rubredoxin-l  64.9     2.9 7.4E-05   22.1   1.1   22   26-47     10-32  (37)
 60 pfam09332 Mcm10 Mcm10 replicat  62.8     4.5 0.00012   21.1   1.7   26   25-50    285-315 (346)
 61 PRK05978 hypothetical protein;  62.5     2.8 7.2E-05   22.2   0.6   29   21-49     28-62  (149)
 62 KOG2879 consensus               62.2     3.6 9.1E-05   21.7   1.1   22   26-48    238-260 (298)
 63 PRK08332 ribonucleotide-diphos  62.2     4.8 0.00012   21.0   1.7   24   27-50   1712-1744(1748)
 64 PRK06556 vitamin B12-dependent  61.4     4.9 0.00012   20.9   1.7   22   29-51    930-955 (957)
 65 COG1656 Uncharacterized conser  60.0     5.2 0.00013   20.8   1.6   30   24-53     94-145 (165)
 66 pfam08271 TF_Zn_Ribbon TFIIB z  58.5       5 0.00013   20.9   1.3   29   29-57      2-36  (40)
 67 pfam03367 zf-ZPR1 ZPR1 zinc-fi  58.2      11 0.00028   19.1   3.1   29   28-57      2-46  (160)
 68 COG5349 Uncharacterized protei  57.5     3.3 8.5E-05   21.8   0.3   23   26-48     20-48  (126)
 69 PRK00432 30S ribosomal protein  57.0     5.5 0.00014   20.7   1.3   29   20-48     12-49  (54)
 70 TIGR00201 comF comF family pro  57.0     4.6 0.00012   21.1   0.9   19   30-48      1-20  (207)
 71 PRK00241 nudC NADH pyrophospha  56.7     5.4 0.00014   20.7   1.3   22   27-48    100-126 (257)
 72 COG1328 NrdD Oxygen-sensitive   54.7     6.2 0.00016   20.4   1.3   33   17-50    631-665 (700)
 73 PRK10436 hypothetical protein;  54.4     6.4 0.00016   20.3   1.3   27   29-55    354-398 (461)
 74 PRK06450 threonine synthase; V  52.8     7.1 0.00018   20.1   1.4   20   28-47      4-24  (336)
 75 smart00709 Zpr1 Duplicated dom  52.7      17 0.00043   18.1   3.2   23   34-57     23-45  (160)
 76 COG1592 Rubrerythrin [Energy p  52.3     9.4 0.00024   19.4   1.9   31   21-51    128-160 (166)
 77 TIGR02487 NrdD anaerobic ribon  51.6     6.2 0.00016   20.4   0.9   31   18-48    581-617 (655)
 78 COG2816 NPY1 NTP pyrophosphohy  51.5     7.1 0.00018   20.1   1.2   23   27-49    111-138 (279)
 79 pfam06906 DUF1272 Protein of u  51.5     2.3 5.9E-05   22.6  -1.3   19   28-47     30-48  (57)
 80 pfam09862 DUF2089 Protein of u  50.8      12 0.00031   18.8   2.3   19   30-48      1-20  (113)
 81 pfam01907 Ribosomal_L37e Ribos  50.7     4.9 0.00013   20.9   0.3   27   26-52     14-42  (54)
 82 cd00729 rubredoxin_SM Rubredox  50.7     9.4 0.00024   19.4   1.7   24   27-50      2-28  (34)
 83 COG1405 SUA7 Transcription ini  50.1     8.5 0.00022   19.7   1.4   29   28-56      2-36  (285)
 84 TIGR00373 TIGR00373 conserved   49.4     3.6 9.1E-05   21.7  -0.6   45    3-48     87-138 (168)
 85 TIGR02264 gmx_para_CXXCG Myxoc  49.1     6.5 0.00017   20.3   0.7   22   14-35     18-39  (247)
 86 PRK05580 primosome assembly pr  49.0      13 0.00034   18.7   2.2   19   29-47    433-451 (699)
 87 COG1096 Predicted RNA-binding   48.9      15 0.00037   18.4   2.5   29   27-55    149-180 (188)
 88 PRK08620 DNA topoisomerase III  48.9      12 0.00031   18.8   2.1   13   26-38    608-620 (726)
 89 COG1779 C4-type Zn-finger prot  48.1      18 0.00045   18.0   2.8   34   26-60     13-62  (201)
 90 pfam12230 PRP21_like_P Pre-mRN  48.1      11 0.00028   19.1   1.7   18   21-38    156-173 (223)
 91 TIGR02605 CxxC_CxxC_SSSS putat  42.3      11 0.00027   19.2   0.9   20   20-39     19-39  (43)
 92 COG2126 RPL37A Ribosomal prote  41.9      14 0.00036   18.5   1.5   30   24-53     13-44  (61)
 93 pfam07754 DUF1610 Domain of un  41.8     8.7 0.00022   19.6   0.4   11   41-51     11-21  (26)
 94 KOG2907 consensus               41.3     9.7 0.00025   19.4   0.6   14   28-41     75-88  (116)
 95 PRK07219 DNA topoisomerase I;   40.8      19 0.00048   17.9   2.0   28   26-53    715-751 (769)
 96 pfam09526 DUF2387 Probable met  40.7      23 0.00059   17.4   2.4   27   26-52      7-42  (61)
 97 PRK12495 hypothetical protein;  39.8     8.6 0.00022   19.6   0.1   28   21-48     34-66  (221)
 98 COG1066 Sms Predicted ATP-depe  39.6      20 0.00052   17.7   2.0   27   25-51      5-32  (456)
 99 pfam08792 A2L_zn_ribbon A2L zi  39.6      13 0.00033   18.7   1.0   23   26-48      2-29  (33)
100 pfam02150 RNA_POL_M_15KD RNA p  39.0     9.1 0.00023   19.5   0.1   22   27-48      1-28  (35)
101 COG1885 Uncharacterized protei  38.9      14 0.00035   18.6   1.0   36   26-61     48-86  (115)
102 PRK11032 hypothetical protein;  38.5      19  0.0005   17.8   1.8   27   22-48    119-150 (160)
103 pfam07295 DUF1451 Protein of u  38.2      24 0.00061   17.3   2.2   27   22-48    109-140 (148)
104 TIGR01405 polC_Gram_pos DNA po  37.6      10 0.00026   19.3   0.2   12   36-47    738-749 (1264)
105 COG5257 GCD11 Translation init  37.5      18 0.00045   18.0   1.4   26   23-48     53-80  (415)
106 PRK05452 anaerobic nitric oxid  37.5      15 0.00038   18.4   1.0   34   26-61    424-477 (479)
107 PRK00448 polC DNA polymerase I  37.3      12  0.0003   18.9   0.5   20   29-48    909-940 (1436)
108 COG1198 PriA Primosomal protei  36.6      17 0.00043   18.1   1.2   20   28-47    463-482 (730)
109 cd01121 Sms Sms (bacterial rad  36.2      17 0.00043   18.1   1.1   23   29-51      2-25  (372)
110 COG1439 Predicted nucleic acid  35.7      18 0.00046   17.9   1.2   22   22-43    148-169 (177)
111 PTZ00073 60S ribosomal protein  35.5      13 0.00033   18.7   0.5   25   25-49     14-40  (89)
112 COG4260 Membrane protease subu  34.8      11 0.00028   19.1  -0.0   21   27-47    315-341 (345)
113 pfam06677 Auto_anti-p27 Sjogre  33.5      25 0.00064   17.2   1.7   20   28-47     18-41  (41)
114 pfam01873 eIF-5_eIF-2B Domain   33.0      37 0.00095   16.3   2.5   25   24-48     90-122 (125)
115 PRK00418 zinc-binding protein;  32.5      26 0.00067   17.1   1.7   16   23-38      2-17  (62)
116 cd00350 rubredoxin_like Rubred  32.0      22 0.00057   17.5   1.2   20   29-48      3-25  (33)
117 pfam09567 RE_MamI MamI restric  31.7      11 0.00027   19.2  -0.5   25   25-49     86-111 (350)
118 PRK11823 DNA repair protein Ra  31.6      38 0.00096   16.3   2.3   28   25-52      5-33  (454)
119 pfam01927 DUF82 Protein of unk  30.6      29 0.00073   16.9   1.6   29   25-53     88-138 (146)
120 TIGR00612 ispG_gcpE 4-hydroxy-  30.6      28 0.00071   17.0   1.5   15   21-35    525-539 (633)
121 PRK11788 hypothetical protein;  30.4      35  0.0009   16.4   2.0   29   21-49    348-377 (389)
122 PRK12496 hypothetical protein;  30.2      23 0.00059   17.4   1.0   21   28-48    130-153 (166)
123 KOG3352 consensus               30.0      17 0.00042   18.2   0.3   12   43-54    136-148 (153)
124 smart00653 eIF2B_5 domain pres  29.9      39   0.001   16.2   2.2   25   24-48     77-109 (110)
125 COG0375 HybF Zn finger protein  29.6      32 0.00082   16.6   1.7   25   24-48     67-94  (115)
126 pfam04551 GcpE GcpE protein. I  29.3      26 0.00067   17.1   1.2   14   23-36    252-265 (345)
127 TIGR02443 TIGR02443 conserved   28.7      31 0.00079   16.7   1.5   25   26-50      8-41  (63)
128 COG2995 PqiA Uncharacterized p  28.7      30 0.00078   16.8   1.4   31   18-48      9-46  (418)
129 TIGR00686 phnA alkylphosphonat  28.6      24 0.00062   17.3   0.9   23   27-49      2-28  (111)
130 COG2093 DNA-directed RNA polym  28.4      17 0.00043   18.1   0.1   18   30-47      7-25  (64)
131 pfam06044 DRP Dam-replacing fa  28.3      23 0.00059   17.4   0.8   21   27-47     31-60  (254)
132 PRK00366 ispG 4-hydroxy-3-meth  28.2      28 0.00071   17.0   1.2   15   22-36    262-276 (367)
133 PRK06260 threonine synthase; V  28.1      26 0.00067   17.1   1.0   20   28-47      4-26  (400)
134 TIGR00107 deoD purine nucleosi  27.9      23  0.0006   17.4   0.7   12   44-55     44-55  (234)
135 COG1996 RPC10 DNA-directed RNA  27.3      33 0.00085   16.6   1.4   22   27-48      6-32  (49)
136 pfam04035 consensus             26.9      30 0.00077   16.8   1.2   27   30-56      4-36  (60)
137 TIGR02772 Ku_bact Ku protein;   26.6      28  0.0007   17.0   0.9   20   29-48     35-54  (271)
138 COG1997 RPL43A Ribosomal prote  26.6      41   0.001   16.1   1.8   24   25-48     33-61  (89)
139 COG4640 Predicted membrane pro  26.5      27 0.00069   17.0   0.8   21   28-48      2-23  (465)
140 COG1867 TRM1 N2,N2-dimethylgua  26.5      37 0.00095   16.3   1.6   38   11-48    223-265 (380)
141 pfam10005 DUF2248 Uncharacteri  26.4      33 0.00084   16.6   1.3   19   30-48      2-21  (340)
142 pfam09889 DUF2116 Uncharacteri  26.4      21 0.00053   17.6   0.3   10   39-48      2-11  (59)
143 TIGR00368 TIGR00368 Mg chelata  26.1      25 0.00064   17.2   0.6   22   19-40    274-298 (505)
144 cd00789 KU_like Ku-core domain  26.0      55  0.0014   15.4   2.3   19   29-47     33-51  (256)
145 COG4311 SoxD Sarcosine oxidase  25.5      30 0.00076   16.8   0.9   10   26-35      2-11  (97)
146 COG3677 Transposase and inacti  25.4      29 0.00075   16.8   0.9   21   28-48     31-61  (129)
147 KOG0506 consensus               25.2      15 0.00037   18.4  -0.7   31   20-50    382-419 (622)
148 KOG1705 consensus               25.1      38 0.00097   16.3   1.4   29   28-56     28-61  (110)
149 TIGR00143 hypF [NiFe] hydrogen  25.0      32 0.00081   16.7   1.0   19   41-59    175-198 (799)
150 COG1273 Ku-homolog [Replicatio  25.0      37 0.00094   16.3   1.3   16   32-47     39-54  (278)
151 COG1571 Predicted DNA-binding   25.0      25 0.00063   17.2   0.4   27   29-55    352-383 (421)
152 pfam00798 Arena_glycoprot Aren  25.0      26 0.00066   17.1   0.5   13   38-51    453-470 (473)
153 TIGR02349 DnaJ_bact chaperone   24.9      64  0.0016   15.1   2.9   32   27-58    214-249 (386)
154 PRK10996 thioredoxin 2; Provis  24.9      30 0.00077   16.8   0.9   10   27-36      2-11  (139)
155 pfam09723 CxxC_CxxC_SSSS Zinc   24.7      45  0.0011   15.9   1.7   16   40-55     26-41  (42)
156 smart00834 CxxC_CXXC_SSSS Puta  24.3      42  0.0011   16.0   1.5   26   29-55      7-40  (41)
157 COG4530 Uncharacterized protei  24.2      29 0.00074   16.9   0.7   23   26-48      8-34  (129)
158 CHL00018 rpoC1 RNA polymerase   24.1      30 0.00077   16.8   0.7   20   28-48     67-92  (668)
159 pfam04475 DUF555 Protein of un  23.9      38 0.00098   16.2   1.2   36   25-60     45-83  (102)
160 PRK12336 translation initiatio  23.7      66  0.0017   15.0   2.4   26   24-49     95-128 (201)
161 cd00202 ZnF_GATA Zinc finger D  23.7      16  0.0004   18.3  -0.8   11   39-49     20-30  (54)
162 pfam06676 DUF1178 Protein of u  23.4      27 0.00068   17.1   0.3   24   18-41     23-46  (145)
163 PRK07591 threonine synthase; V  23.2      48  0.0012   15.7   1.6   25   23-47     14-41  (422)
164 smart00531 TFIIE Transcription  23.0      25 0.00065   17.2   0.2   27   22-48     94-131 (147)
165 PHA00732 hypothetical protein   22.8      24 0.00061   17.3  -0.0   11   26-36     26-36  (79)
166 PRK03922 hypothetical protein;  22.4      42  0.0011   16.0   1.2   36   25-60     47-85  (113)
167 COG2051 RPS27A Ribosomal prote  22.0      64  0.0016   15.1   2.0   31   27-57     19-60  (67)
168 KOG1729 consensus               22.0      19 0.00049   17.8  -0.6   27   21-48    162-193 (288)
169 COG0492 TrxB Thioredoxin reduc  21.7      56  0.0014   15.4   1.7   20   39-58    130-150 (305)
170 TIGR02827 RNR_anaer_Bdell anae  21.3      48  0.0012   15.7   1.3   28   21-48    577-605 (638)
171 TIGR00269 TIGR00269 conserved   21.3      18 0.00047   17.9  -0.8   23   26-48     80-102 (106)
172 PRK05778 2-oxoglutarate ferred  21.1      27  0.0007   17.0   0.0   13   37-49     15-27  (306)
173 COG3058 FdhE Uncharacterized p  20.9      16 0.00042   18.2  -1.2   11   26-36    184-194 (308)
174 pfam02591 DUF164 Putative zinc  20.7      49  0.0012   15.7   1.2   11   25-35     44-54  (56)
175 KOG3134 consensus               20.7      35 0.00088   16.5   0.5   14   24-37     21-34  (225)
176 PRK08351 DNA-directed RNA poly  20.5      48  0.0012   15.7   1.2   27   29-56      5-37  (61)
177 pfam09535 Gmx_para_CXXCG Prote  20.4      41   0.001   16.1   0.8   24   12-35     13-36  (237)
178 pfam09884 DUF2111 Uncharacteri  20.4      66  0.0017   15.0   1.9   17   41-57     48-64  (84)
179 COG4307 Uncharacterized protei  20.4      32 0.00082   16.6   0.3   22   28-49      4-26  (349)

No 1  
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=99.95  E-value=1.4e-29  Score=175.75  Aligned_cols=59  Identities=47%  Similarity=0.733  Sum_probs=57.8

Q ss_pred             CCCCCCCCCHHCCCCHHHHHCCCCCCEEECCCCCCEEEEEEEECCCCCCCCEEEEEEEC
Q ss_conf             97887887610017412231026883788789978244046425778676879643423
Q gi|254780361|r    1 MAVPKRKTSPSKRGMRRSADALTPPAYVEDKKSGELRRPHHVDMKTGLYRGRQVFVLKT   59 (61)
Q Consensus         1 MAVPKrK~S~sr~~~RRsh~~l~~p~l~~c~~cG~~~~~H~vc~~cG~YkGr~Vi~~~~   59 (61)
                      |||||+|+|+||+++|||||+|++|+|+.||+||++++||+||++||||+|||||++++
T Consensus         1 MAvPKrk~Sksr~~~RRsh~~~~~~~~~~C~~CG~~~~~H~vC~~CG~Y~Gr~Vi~~~~   59 (59)
T PRK12286          1 MAVPKRKTSKSRKRKRRAHDKLKAPGLVECPNCGELKLPHRVCPSCGYYKGREVVEVEK   59 (59)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEECCCCCEECCEEEEEECC
T ss_conf             98775656741451110140125872457889998654777889898199998764259


No 2  
>TIGR01031 rpmF_bact ribosomal protein L32; InterPro: IPR002677   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 , .   Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene }.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=99.95  E-value=5.9e-29  Score=172.39  Aligned_cols=55  Identities=51%  Similarity=0.724  Sum_probs=53.3

Q ss_pred             CCCCCCCCHHCCCCHHHHH-CCCCCCEEECCCCCCEEEEEEEECCCCCCCCEEEEE
Q ss_conf             7887887610017412231-026883788789978244046425778676879643
Q gi|254780361|r    2 AVPKRKTSPSKRGMRRSAD-ALTPPAYVEDKKSGELRRPHHVDMKTGLYRGRQVFV   56 (61)
Q Consensus         2 AVPKrK~S~sr~~~RRsh~-~l~~p~l~~c~~cG~~~~~H~vc~~cG~YkGr~Vi~   56 (61)
                      ||||+|+|+||+++||||+ +|++|+|++||||||+++|||||++||||+|+|||+
T Consensus         1 AVPkrk~Sksr~~~RRsh~~Kl~~~~~v~C~~CGe~~~pHrvC~~CG~Y~g~~V~~   56 (56)
T TIGR01031         1 AVPKRKTSKSRKRKRRSHDAKLTAPTLVVCPNCGEYKLPHRVCPSCGYYKGRQVLE   56 (56)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCEECC
T ss_conf             98887888544367312100112457542677888535502028888647511059


No 3  
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=99.93  E-value=9e-27  Score=160.95  Aligned_cols=57  Identities=54%  Similarity=0.775  Sum_probs=55.9

Q ss_pred             CCCCCCCCCHHCCCCHHHHHCCCCCCEEECCCCCCEEEEEEEECCCCCCCCEEEEEE
Q ss_conf             978878876100174122310268837887899782440464257786768796434
Q gi|254780361|r    1 MAVPKRKTSPSKRGMRRSADALTPPAYVEDKKSGELRRPHHVDMKTGLYRGRQVFVL   57 (61)
Q Consensus         1 MAVPKrK~S~sr~~~RRsh~~l~~p~l~~c~~cG~~~~~H~vc~~cG~YkGr~Vi~~   57 (61)
                      |||||+|+|+||+++||+||+|++|++++|++||++++|||||+.||||+|++|+++
T Consensus         1 MAVPkrktSksrr~~RRsh~~l~~~~~~~c~~cG~~~l~Hrvc~~cg~Y~g~~v~~~   57 (57)
T COG0333           1 MAVPKRKTSKSRRRMRRSHDALKAPTLSVCPNCGEYKLPHRVCLKCGYYKGRQVIEK   57 (57)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCCCEECCCCCCEECCCEECCCCCCCCCEEECCC
T ss_conf             987755678556110445676517663035678860157547486776256474029


No 4  
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=99.92  E-value=3.2e-26  Score=158.07  Aligned_cols=56  Identities=59%  Similarity=0.843  Sum_probs=54.4

Q ss_pred             CCCCCCCCCHHCCCCHHHHHCCCCCCEEECCCCCCEEEEEEEECCCCCCCCEEEEEE
Q ss_conf             978878876100174122310268837887899782440464257786768796434
Q gi|254780361|r    1 MAVPKRKTSPSKRGMRRSADALTPPAYVEDKKSGELRRPHHVDMKTGLYRGRQVFVL   57 (61)
Q Consensus         1 MAVPKrK~S~sr~~~RRsh~~l~~p~l~~c~~cG~~~~~H~vc~~cG~YkGr~Vi~~   57 (61)
                      |||||+|+|+||+++|||||+|++|+|+.|++||++++||+||+. |||+||+||++
T Consensus         1 MAVPKrK~Sksr~~~RRsh~kl~~p~~~~c~~~g~~~lpH~v~~~-G~YkGr~Vi~k   56 (56)
T PRK01110          1 MAVPKRKTSKSKRRMRRSHWKLTAPTLSVDKTTGEYHLPHHVSLK-GYYKGRKVIPK   56 (56)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEECCC-CCCCCEEEECC
T ss_conf             987656577000656422101368854489899986567778899-84989881219


No 5  
>pfam01783 Ribosomal_L32p Ribosomal L32p protein family.
Probab=99.89  E-value=4.1e-24  Score=147.03  Aligned_cols=56  Identities=48%  Similarity=0.664  Sum_probs=54.6

Q ss_pred             CCCCCCCCHHCCCCHHHHHCCCCCCEEECCCCCCEEEEEEEECCCCCCCCEEEEEE
Q ss_conf             78878876100174122310268837887899782440464257786768796434
Q gi|254780361|r    2 AVPKRKTSPSKRGMRRSADALTPPAYVEDKKSGELRRPHHVDMKTGLYRGRQVFVL   57 (61)
Q Consensus         2 AVPKrK~S~sr~~~RRsh~~l~~p~l~~c~~cG~~~~~H~vc~~cG~YkGr~Vi~~   57 (61)
                      ||||+|+|+||+++||+||+|++++|+.||+||+++++|+||++||||+|++|++.
T Consensus         1 AVPKrr~Sksr~~~Rrs~~~~~~~~l~~c~~cg~~~l~H~vc~~cg~Y~gr~v~~~   56 (56)
T pfam01783         1 AVPKRKTSKSRKRKRRAHWKLKAPNLVECPNCGELKLPHRVCPSCGYYKGRQVIEK   56 (56)
T ss_pred             CCCCCCCCCHHCCCCCCCCCCCCCCEEECCCCCCCCCCCEECCCCCEECCEEEECC
T ss_conf             98766676010622223402358754588899985358778898980999983319


No 6  
>KOG4080 consensus
Probab=98.42  E-value=3.5e-08  Score=63.59  Aligned_cols=46  Identities=26%  Similarity=0.349  Sum_probs=39.3

Q ss_pred             CCCCCCCCCHHCCCCHHHH---HCCCCCC-EEECCCCCCEEEEEEEECCC
Q ss_conf             9788788761001741223---1026883-78878997824404642577
Q gi|254780361|r    1 MAVPKRKTSPSKRGMRRSA---DALTPPA-YVEDKKSGELRRPHHVDMKT   46 (61)
Q Consensus         1 MAVPKrK~S~sr~~~RRsh---~~l~~p~-l~~c~~cG~~~~~H~vc~~c   46 (61)
                      |||||.|+|..++.+|+-.   ..|.... |..||.||..++.|++|+.|
T Consensus        63 lAVPK~r~S~eK~~kRk~~~~~k~Lk~k~nl~~CP~CGh~k~a~~LC~~C  112 (176)
T KOG4080          63 LAVPKKRTSKEKKVKRKFLYTRKLLKPKDNLNTCPACGHIKPAHTLCDYC  112 (176)
T ss_pred             EECCCCCCCHHHHHHHHCCCCCCCCCCHHCCCCCCCCCCCCCCCCCHHHH
T ss_conf             96365544125555553167602143200224375457644145207999


No 7  
>CHL00152 rpl32 ribosomal protein L32; Validated
Probab=97.29  E-value=5.9e-05  Score=46.70  Aligned_cols=23  Identities=43%  Similarity=0.579  Sum_probs=20.9

Q ss_pred             CCCCCCCCCHHCCCCHHHHHCCC
Q ss_conf             97887887610017412231026
Q gi|254780361|r    1 MAVPKRKTSPSKRGMRRSADALT   23 (61)
Q Consensus         1 MAVPKrK~S~sr~~~RRsh~~l~   23 (61)
                      |||||+|+|+|+++.|.+.|+-.
T Consensus         1 MAVPKKRtS~sKk~iRk~~WK~K   23 (53)
T CHL00152          1 MAVPKKRTSKSKKRIRKNIWKKK   23 (53)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             99884322068888999999988


No 8  
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=93.68  E-value=0.032  Score=32.35  Aligned_cols=28  Identities=7%  Similarity=-0.100  Sum_probs=22.7

Q ss_pred             CCCCCCEEECCCCCCE-EEEEEEECCCCC
Q ss_conf             0268837887899782-440464257786
Q gi|254780361|r   21 ALTPPAYVEDKKSGEL-RRPHHVDMKTGL   48 (61)
Q Consensus        21 ~l~~p~l~~c~~cG~~-~~~H~vc~~cG~   48 (61)
                      .-..|++++|++||.+ .--|..||.||-
T Consensus       561 ~titp~fsiC~~chgy~~Ge~~~CP~CG~  589 (625)
T PRK08271        561 FAINVKITICNEGHAIDKRTGKRCPVCGS  589 (625)
T ss_pred             EEECCCEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             99576713788999885776883989989


No 9  
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=92.34  E-value=0.041  Score=31.81  Aligned_cols=23  Identities=17%  Similarity=0.135  Sum_probs=19.1

Q ss_pred             EEECCCCCCEEE------EEEEECCCCCC
Q ss_conf             788789978244------04642577867
Q gi|254780361|r   27 YVEDKKSGELRR------PHHVDMKTGLY   49 (61)
Q Consensus        27 l~~c~~cG~~~~------~H~vc~~cG~Y   49 (61)
                      -+.||+||+...      ..+|||+|||+
T Consensus        30 W~kCp~C~~~i~~~dL~~n~~VCp~C~~H   58 (288)
T PRK05654         30 WTKCPSCGQVLYRKELEANLNVCPKCGHH   58 (288)
T ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCCCCC
T ss_conf             22287765035099999838789299798


No 10 
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=91.06  E-value=0.079  Score=30.30  Aligned_cols=28  Identities=14%  Similarity=-0.123  Sum_probs=23.3

Q ss_pred             HCCCCCCEEECCCCCCEEEEEEEECCCC
Q ss_conf             1026883788789978244046425778
Q gi|254780361|r   20 DALTPPAYVEDKKSGELRRPHHVDMKTG   47 (61)
Q Consensus        20 ~~l~~p~l~~c~~cG~~~~~H~vc~~cG   47 (61)
                      +.-..|.++.|+.||-...-|..||.||
T Consensus       640 Y~~in~~~~~C~~CGy~~~~~~~CP~CG  667 (703)
T PRK07111        640 YGSINHPVDYCKNCGYYGVINDKCPKCG  667 (703)
T ss_pred             EEEECCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             6996899765788998288778291997


No 11 
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=90.83  E-value=0.12  Score=29.43  Aligned_cols=23  Identities=17%  Similarity=-0.038  Sum_probs=19.3

Q ss_pred             CCEEECCCCCCEEEEEEEECCCCC
Q ss_conf             837887899782440464257786
Q gi|254780361|r   25 PAYVEDKKSGELRRPHHVDMKTGL   48 (61)
Q Consensus        25 p~l~~c~~cG~~~~~H~vc~~cG~   48 (61)
                      .+...||+||...+ ..+||.||.
T Consensus       677 i~~~~CP~Cgk~s~-~~~Cp~CG~  699 (1173)
T TIGR00354       677 IAIAKCPSCGKESL-YRVCPVCGE  699 (1173)
T ss_pred             ECCCCCCCCCCCCE-EEECCCCCC
T ss_conf             50121887664000-014577885


No 12 
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=90.68  E-value=0.059  Score=30.96  Aligned_cols=23  Identities=13%  Similarity=0.147  Sum_probs=19.1

Q ss_pred             EEECCCCCCEE------EEEEEECCCCCC
Q ss_conf             78878997824------404642577867
Q gi|254780361|r   27 YVEDKKSGELR------RPHHVDMKTGLY   49 (61)
Q Consensus        27 l~~c~~cG~~~------~~H~vc~~cG~Y   49 (61)
                      -++||+|++..      ....|||+|||+
T Consensus        48 W~KCp~C~~~iy~kdLe~Nl~VCp~C~~H   76 (305)
T CHL00174         48 WVQCENCYGLNYKKFLKSKMNICEQCGYH   76 (305)
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCCCCCC
T ss_conf             65498766224599999839899299799


No 13 
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=90.39  E-value=0.23  Score=27.92  Aligned_cols=27  Identities=22%  Similarity=0.082  Sum_probs=20.3

Q ss_pred             EECCCCCCEEEEEE---EECCCCCCCCEEEEEE
Q ss_conf             88789978244046---4257786768796434
Q gi|254780361|r   28 VEDKKSGELRRPHH---VDMKTGLYRGRQVFVL   57 (61)
Q Consensus        28 ~~c~~cG~~~~~H~---vc~~cG~YkGr~Vi~~   57 (61)
                      ..||.||.|-..+.   +||.||+   +.++..
T Consensus        29 ~hCp~Cg~PLF~KdG~v~CPvC~~---~~~~v~   58 (131)
T COG1645          29 KHCPKCGTPLFRKDGEVFCPVCGY---REVVVE   58 (131)
T ss_pred             HHCCCCCCCCEEECCEEECCCCCC---EEEEEE
T ss_conf             448655883163089587777776---677764


No 14 
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=89.92  E-value=0.12  Score=29.39  Aligned_cols=29  Identities=14%  Similarity=-0.015  Sum_probs=21.6

Q ss_pred             HHCCCCCCEEECCCCCC-EEEEEEEECCCC
Q ss_conf             31026883788789978-244046425778
Q gi|254780361|r   19 ADALTPPAYVEDKKSGE-LRRPHHVDMKTG   47 (61)
Q Consensus        19 h~~l~~p~l~~c~~cG~-~~~~H~vc~~cG   47 (61)
                      .+.-..|.+..|++||- ..--|..||.||
T Consensus       558 ~Y~~in~~~d~C~~CGy~~~g~~~~CP~CG  587 (623)
T PRK08579        558 VYWSYTPAITVCNRCGRSTTGLYTRCPRCG  587 (623)
T ss_pred             CEEEECCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             579958888335889981777765590996


No 15 
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=89.70  E-value=0.11  Score=29.63  Aligned_cols=21  Identities=14%  Similarity=0.017  Sum_probs=18.4

Q ss_pred             EEECCCCCCEEEEEEEECCCCC
Q ss_conf             7887899782440464257786
Q gi|254780361|r   27 YVEDKKSGELRRPHHVDMKTGL   48 (61)
Q Consensus        27 l~~c~~cG~~~~~H~vc~~cG~   48 (61)
                      |..|++||.+.| --+||.||-
T Consensus         5 irkC~~Cg~YTL-~~~CP~CG~   25 (54)
T PRK13130          5 IRKCPKCGRYTL-KETCPECGG   25 (54)
T ss_pred             HHHCCCCCCEEC-CCCCCCCCC
T ss_conf             651863564303-252866887


No 16 
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=88.47  E-value=0.16  Score=28.69  Aligned_cols=28  Identities=25%  Similarity=0.233  Sum_probs=21.5

Q ss_pred             HCCCCCCEEECCCCCCEEEEEEEECCCC
Q ss_conf             1026883788789978244046425778
Q gi|254780361|r   20 DALTPPAYVEDKKSGELRRPHHVDMKTG   47 (61)
Q Consensus        20 ~~l~~p~l~~c~~cG~~~~~H~vc~~cG   47 (61)
                      +.-..|.+..|+.||-..--|..||.||
T Consensus       618 Y~tin~~~~~C~~CGy~~ge~~~CP~CG  645 (681)
T PRK08270        618 YITITPTFSICPKHGYLAGEHEFCPKCG  645 (681)
T ss_pred             EEEECCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             4985898786788997778867493998


No 17 
>PRK00420 hypothetical protein; Validated
Probab=88.33  E-value=0.21  Score=28.11  Aligned_cols=20  Identities=15%  Similarity=-0.165  Sum_probs=17.2

Q ss_pred             EECCCCCCEEEEE----EEECCCC
Q ss_conf             8878997824404----6425778
Q gi|254780361|r   28 VEDKKSGELRRPH----HVDMKTG   47 (61)
Q Consensus        28 ~~c~~cG~~~~~H----~vc~~cG   47 (61)
                      ..||.||.|-..+    -+||+||
T Consensus        20 ~~C~~Cg~plf~~k~G~~~Cp~cg   43 (107)
T PRK00420         20 KHCPVCGLPLFELKDGEVVCPNHG   43 (107)
T ss_pred             HHCCCCCCCEEECCCCCEECCCCC
T ss_conf             137657984057489877689898


No 18 
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=87.65  E-value=0.33  Score=27.03  Aligned_cols=23  Identities=17%  Similarity=0.031  Sum_probs=15.5

Q ss_pred             CEEECCCCCCEEEE----------EEEECCCCC
Q ss_conf             37887899782440----------464257786
Q gi|254780361|r   26 AYVEDKKSGELRRP----------HHVDMKTGL   48 (61)
Q Consensus        26 ~l~~c~~cG~~~~~----------H~vc~~cG~   48 (61)
                      ..-.|||||+...-          -.+||+|||
T Consensus        26 v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF   58 (61)
T COG2888          26 VKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF   58 (61)
T ss_pred             EEEECCCCCCEEEEHHHHHHHCCCCEECCCCCC
T ss_conf             086489998242410566877499447887675


No 19 
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=87.39  E-value=0.24  Score=27.80  Aligned_cols=21  Identities=14%  Similarity=-0.075  Sum_probs=17.9

Q ss_pred             EEECCCCCCEEEEEEEECCCCC
Q ss_conf             7887899782440464257786
Q gi|254780361|r   27 YVEDKKSGELRRPHHVDMKTGL   48 (61)
Q Consensus        27 l~~c~~cG~~~~~H~vc~~cG~   48 (61)
                      +-.|++||.+++. -.||.||-
T Consensus         5 ~rkC~~cg~YTLk-e~Cp~CG~   25 (59)
T COG2260           5 IRKCPKCGRYTLK-EKCPVCGG   25 (59)
T ss_pred             HHCCCCCCCEEEC-CCCCCCCC
T ss_conf             4317678814611-33778887


No 20 
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=85.95  E-value=0.42  Score=26.48  Aligned_cols=22  Identities=18%  Similarity=0.137  Sum_probs=16.8

Q ss_pred             EEECCCCCCEEEEEE----EECCCCCC
Q ss_conf             788789978244046----42577867
Q gi|254780361|r   27 YVEDKKSGELRRPHH----VDMKTGLY   49 (61)
Q Consensus        27 l~~c~~cG~~~~~H~----vc~~cG~Y   49 (61)
                      ...||+||+. +-|.    +|.+|||=
T Consensus       705 ~~~CP~CG~~-l~~~eGC~~C~~CGyS  730 (733)
T PRK08665        705 RGACPECGSI-LEHEEGCAVCHSCGYS  730 (733)
T ss_pred             CCCCCCCCCE-EEECCCCCCCCCCCCC
T ss_conf             8979999874-7876898727778998


No 21 
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=85.57  E-value=0.41  Score=26.58  Aligned_cols=30  Identities=23%  Similarity=0.146  Sum_probs=21.0

Q ss_pred             HCCCCCC--EEECCCCCCE-EEEEEEECCCCCC
Q ss_conf             1026883--7887899782-4404642577867
Q gi|254780361|r   20 DALTPPA--YVEDKKSGEL-RRPHHVDMKTGLY   49 (61)
Q Consensus        20 ~~l~~p~--l~~c~~cG~~-~~~H~vc~~cG~Y   49 (61)
                      +.|....  -+.|++||.. .-|+..|+.||.=
T Consensus        20 ~~l~~~kl~g~kC~~CG~v~~PPr~~Cp~C~~~   52 (140)
T COG1545          20 KGLKEGKLLGTKCKKCGRVYFPPRAYCPKCGSE   52 (140)
T ss_pred             HHHHHCEEEEEECCCCCCEECCCCCCCCCCCCC
T ss_conf             401317087868378981881982338788997


No 22 
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit; InterPro: IPR000438 Fatty acid synthesis involves a set of reactions, commencing with carboxylation of acetyl-CoA to malonyl-CoA. This is an irreversible reaction, catalysed by the acetyl-CoA carboxylase complex (6.4.1.2 from EC); a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps:   Biotin carrier protein + ATP + HCO_3^- = Carboxybiotin carrier protein + ADP + P_i  Carboxybiotin carrier protein + Acetyl-CoA = Malonyl-CoA + Biotin carrier protein   In the first step, biotin carboxylase catalyses the carboxylation of the carrier protein to form an intermediate. Next, the transcarboxylase complex transfers the carboxyl group from the intermediate to acetyl-CoA forming malonyl-CoA.; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=85.11  E-value=0.31  Score=27.18  Aligned_cols=25  Identities=24%  Similarity=0.275  Sum_probs=19.9

Q ss_pred             CCEEECCCCCC------EEEEEEEECCCCCC
Q ss_conf             83788789978------24404642577867
Q gi|254780361|r   25 PAYVEDKKSGE------LRRPHHVDMKTGLY   49 (61)
Q Consensus        25 p~l~~c~~cG~------~~~~H~vc~~cG~Y   49 (61)
                      -..++||.|+.      ...--.||++|||-
T Consensus        31 g~wtKCp~C~~~~Y~keL~~n~~VC~~C~hH   61 (292)
T TIGR00515        31 GVWTKCPKCGQLLYTKELQRNLSVCLKCDHH   61 (292)
T ss_pred             CCEECCCHHHHHHHHHHHHCCCEECCCCCCC
T ss_conf             7300144243443466530355574237987


No 23 
>TIGR01384 TFS_arch transcription factor S; InterPro: IPR006288   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.   These sequences are the archaeal DNA-directed RNA polymerase, subunit M (also known as transcription factor S), a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase . ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=84.40  E-value=0.5  Score=26.12  Aligned_cols=20  Identities=30%  Similarity=0.192  Sum_probs=13.6

Q ss_pred             ECCCCCCEEEE-------EEEECCCCC
Q ss_conf             87899782440-------464257786
Q gi|254780361|r   29 EDKKSGELRRP-------HHVDMKTGL   48 (61)
Q Consensus        29 ~c~~cG~~~~~-------H~vc~~cG~   48 (61)
                      .||.||.+.+|       -.+|+.|||
T Consensus         2 FCPKCgs~M~P~K~~Gkn~~~C~~CGY   28 (111)
T TIGR01384         2 FCPKCGSLMVPDKKNGKNKYKCRKCGY   28 (111)
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCCC
T ss_conf             878669715854306950116288887


No 24 
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=83.57  E-value=0.56  Score=25.86  Aligned_cols=30  Identities=17%  Similarity=0.144  Sum_probs=22.9

Q ss_pred             HHCCCCCCEEECCCCCCEE-EEEEEECCCCC
Q ss_conf             3102688378878997824-40464257786
Q gi|254780361|r   19 ADALTPPAYVEDKKSGELR-RPHHVDMKTGL   48 (61)
Q Consensus        19 h~~l~~p~l~~c~~cG~~~-~~H~vc~~cG~   48 (61)
                      |..+.......|++||... -.|+-||+||.
T Consensus       583 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  613 (615)
T PRK07418        583 HPELAQAAEIYCSNCGTKNPSTHKFCPECGT  613 (615)
T ss_pred             CCCCCCCCEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             8541324531058888888633553642267


No 25 
>pfam05876 Terminase_GpA Phage terminase large subunit (GpA). This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities.
Probab=81.70  E-value=1.1  Score=24.36  Aligned_cols=22  Identities=27%  Similarity=0.265  Sum_probs=15.3

Q ss_pred             EEECCCCCC----------------EEEEEEEECCCCC
Q ss_conf             788789978----------------2440464257786
Q gi|254780361|r   27 YVEDKKSGE----------------LRRPHHVDMKTGL   48 (61)
Q Consensus        27 l~~c~~cG~----------------~~~~H~vc~~cG~   48 (61)
                      .+.||.||+                +...+.+|+.||.
T Consensus       200 ~vpCPhCg~~q~l~~~~l~w~~~~~p~~a~y~C~~Cg~  237 (552)
T pfam05876       200 YVPCPHCGEEQELRWERLKWDKGEAPETARYVCPHCGC  237 (552)
T ss_pred             EEECCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCCC
T ss_conf             86898999865550054664799985534998988988


No 26 
>pfam10571 UPF0547 Uncharacterized protein family UPF0547. This domain contains a zinc-ribbon motif.
Probab=80.96  E-value=0.6  Score=25.71  Aligned_cols=21  Identities=10%  Similarity=-0.002  Sum_probs=16.9

Q ss_pred             ECCCCCCE-EEEEEEECCCCCC
Q ss_conf             87899782-4404642577867
Q gi|254780361|r   29 EDKKSGEL-RRPHHVDMKTGLY   49 (61)
Q Consensus        29 ~c~~cG~~-~~~H~vc~~cG~Y   49 (61)
                      .||+|++. -+.-+.||.|||.
T Consensus         2 ~CP~C~~~vp~~~~~Cp~CG~~   23 (26)
T pfam10571         2 TCPECGAEVPLAAKICPHCGYE   23 (26)
T ss_pred             CCCCCCCCCCHHCCCCCCCCCC
T ss_conf             6875548364003447788855


No 27 
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=79.95  E-value=1.4  Score=23.74  Aligned_cols=30  Identities=13%  Similarity=-0.142  Sum_probs=22.2

Q ss_pred             CCCCEEECCCCCCEE---EEEEEECCCCCCCCE
Q ss_conf             688378878997824---404642577867687
Q gi|254780361|r   23 TPPAYVEDKKSGELR---RPHHVDMKTGLYRGR   52 (61)
Q Consensus        23 ~~p~l~~c~~cG~~~---~~H~vc~~cG~YkGr   52 (61)
                      ..|....|.+||...   ..+-.||.||-+.-+
T Consensus        66 ~~p~~~~C~~C~~~~~~~~~~~~CP~Cgs~~~~   98 (113)
T PRK12380         66 YKPAQAWCWDCSQVVEIHQHDAQCPHCHGERLR   98 (113)
T ss_pred             ECCCEEECCCCCCEEECCCCCCCCCCCCCCCCE
T ss_conf             548579965599987247888839069799649


No 28 
>pfam09538 FYDLN_acid Protein of unknown function (FYDLN_acid). Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=79.95  E-value=0.7  Score=25.36  Aligned_cols=21  Identities=24%  Similarity=0.151  Sum_probs=15.7

Q ss_pred             EECCCCCC----EEEEEEEECCCCC
Q ss_conf             88789978----2440464257786
Q gi|254780361|r   28 VEDKKSGE----LRRPHHVDMKTGL   48 (61)
Q Consensus        28 ~~c~~cG~----~~~~H~vc~~cG~   48 (61)
                      ..||+||.    +.+.-.+||.||.
T Consensus        10 r~c~~c~~~fydl~k~p~~cp~cg~   34 (104)
T pfam09538        10 RTCPTCGKRFYDLNKDPIVCPKCGE   34 (104)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             5478888821127989871899888


No 29 
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=79.94  E-value=1.4  Score=23.84  Aligned_cols=24  Identities=21%  Similarity=0.145  Sum_probs=18.9

Q ss_pred             CEEECCCCCCEEEE------EEEECCCCCC
Q ss_conf             37887899782440------4642577867
Q gi|254780361|r   26 AYVEDKKSGELRRP------HHVDMKTGLY   49 (61)
Q Consensus        26 ~l~~c~~cG~~~~~------H~vc~~cG~Y   49 (61)
                      -.++||.||+..-.      -.|||+|||.
T Consensus        27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h   56 (294)
T COG0777          27 LWTKCPSCGEMLYRKELESNLKVCPKCGHH   56 (294)
T ss_pred             CEEECCCCCCEEEHHHHHHHHHCCCCCCCC
T ss_conf             354778755354688787332326556764


No 30 
>PRK12366 replication factor A; Reviewed
Probab=79.73  E-value=2.2  Score=22.79  Aligned_cols=31  Identities=10%  Similarity=-0.046  Sum_probs=22.4

Q ss_pred             CEEECCCCCCEEEEEE---EECCCCCCCCEEEEE
Q ss_conf             3788789978244046---425778676879643
Q gi|254780361|r   26 AYVEDKKSGELRRPHH---VDMKTGLYRGRQVFV   56 (61)
Q Consensus        26 ~l~~c~~cG~~~~~H~---vc~~cG~YkGr~Vi~   56 (61)
                      -+..||+|+.-.-.-.   +|+.||-+.-..++.
T Consensus       532 ~~~~CP~C~krv~~~e~~y~C~~cGeveP~~ll~  565 (649)
T PRK12366        532 ILTLCPNCRKRVNLVDNKYVCEECGEVEPNELLV  565 (649)
T ss_pred             EEEECCCCCCEEEECCCCEECCCCCCCCCCEEEE
T ss_conf             8972866676056458825277678747764899


No 31 
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=78.82  E-value=1.9  Score=23.08  Aligned_cols=28  Identities=18%  Similarity=0.090  Sum_probs=20.9

Q ss_pred             CCCCEEECCCCCCEEEEE----EEECCCCCCC
Q ss_conf             688378878997824404----6425778676
Q gi|254780361|r   23 TPPAYVEDKKSGELRRPH----HVDMKTGLYR   50 (61)
Q Consensus        23 ~~p~l~~c~~cG~~~~~H----~vc~~cG~Yk   50 (61)
                      ..|....|++||..-.+-    ..||.||-+.
T Consensus        67 ~~p~~~~C~~Cg~~f~~~~~~~~~CP~Cgs~~   98 (117)
T PRK00564         67 DEKVELECKDCSHVFKPNALDYGVCEKCHSKN   98 (117)
T ss_pred             EECCEEECCCCCCEEECCCCCCCCCCCCCCCC
T ss_conf             73878991008998822774068590988999


No 32 
>PRK08938 DNA topoisomerase I; Validated
Probab=78.72  E-value=1.3  Score=23.91  Aligned_cols=26  Identities=12%  Similarity=-0.021  Sum_probs=15.3

Q ss_pred             CCCCEEECCCCCCEEEE-------EEEECCCCC
Q ss_conf             68837887899782440-------464257786
Q gi|254780361|r   23 TPPAYVEDKKSGELRRP-------HHVDMKTGL   48 (61)
Q Consensus        23 ~~p~l~~c~~cG~~~~~-------H~vc~~cG~   48 (61)
                      ..|....||.||.+..-       --+|++|+|
T Consensus       654 ~~p~~~~Cp~Cg~~~~~~~~~~g~~~~C~nc~~  686 (692)
T PRK08938        654 DKPIGRDCPKCGHYLVEKKVKKGKQVQCSNCDY  686 (692)
T ss_pred             CCCCCCCCCCCCCCCEEEECCCCCEEECCCCCC
T ss_conf             887488499999604268557888797899997


No 33 
>pfam07282 Transposase_35 Putative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding.
Probab=77.97  E-value=1.2  Score=24.14  Aligned_cols=29  Identities=14%  Similarity=0.096  Sum_probs=20.0

Q ss_pred             CEEECCCCCCEEEE-----EEEECCCCCCCCEEE
Q ss_conf             37887899782440-----464257786768796
Q gi|254780361|r   26 AYVEDKKSGELRRP-----HHVDMKTGLYRGRQV   54 (61)
Q Consensus        26 ~l~~c~~cG~~~~~-----H~vc~~cG~YkGr~V   54 (61)
                      +-..||.||.....     ...|++||+--.+.+
T Consensus        27 TS~~C~~Cg~~~~~~~~~r~~~C~~Cg~~~~rD~   60 (69)
T pfam07282        27 TSKTCSVCGHKNKESLSGRTFKCPNCGFVADRDV   60 (69)
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCEECCHH
T ss_conf             8642799989986748887898998996899599


No 34 
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=77.67  E-value=1  Score=24.49  Aligned_cols=30  Identities=17%  Similarity=0.072  Sum_probs=22.1

Q ss_pred             CCEEECCCCCCEEEEEEEECCCCCCCCEEE
Q ss_conf             837887899782440464257786768796
Q gi|254780361|r   25 PAYVEDKKSGELRRPHHVDMKTGLYRGRQV   54 (61)
Q Consensus        25 p~l~~c~~cG~~~~~H~vc~~cG~YkGr~V   54 (61)
                      ++-..||.||........||.||+--.|.+
T Consensus       307 ~tS~~C~~cg~~~~r~~~C~~cg~~~~rD~  336 (364)
T COG0675         307 YTSKTCPCCGHLSGRLFKCPRCGFVHDRDV  336 (364)
T ss_pred             CCCCCCCCCCCCCCCEEECCCCCCEECCHH
T ss_conf             877778877874785488899897406538


No 35 
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=77.36  E-value=1.7  Score=23.36  Aligned_cols=22  Identities=32%  Similarity=0.218  Sum_probs=14.4

Q ss_pred             EEECCCCCCEEEEE-------EEECCCCC
Q ss_conf             78878997824404-------64257786
Q gi|254780361|r   27 YVEDKKSGELRRPH-------HVDMKTGL   48 (61)
Q Consensus        27 l~~c~~cG~~~~~H-------~vc~~cG~   48 (61)
                      +..||.||.+..|-       .+|++|||
T Consensus         2 m~FCp~Cgsll~p~~~~~~~~l~C~~Cgy   30 (113)
T COG1594           2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGY   30 (113)
T ss_pred             CCCCCCCCCEEEEEECCCCCEEECCCCCC
T ss_conf             52268766856785748884788888786


No 36 
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=76.72  E-value=1  Score=24.45  Aligned_cols=26  Identities=12%  Similarity=-0.064  Sum_probs=20.1

Q ss_pred             CCCCEEECCCCCCE-EEEEEEECCCCC
Q ss_conf             68837887899782-440464257786
Q gi|254780361|r   23 TPPAYVEDKKSGEL-RRPHHVDMKTGL   48 (61)
Q Consensus        23 ~~p~l~~c~~cG~~-~~~H~vc~~cG~   48 (61)
                      ....+..|++||-. ..-|..||.||-
T Consensus       514 ~ntp~~~C~~CG~~~~~~~~~CP~CG~  540 (555)
T cd01675         514 INTPIDICNDCGYIGEGEGFKCPKCGS  540 (555)
T ss_pred             EECCCEECCCCCCCCCCCCCCCCCCCC
T ss_conf             822884778999827567876909839


No 37 
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=76.40  E-value=1  Score=24.47  Aligned_cols=20  Identities=20%  Similarity=0.127  Sum_probs=14.8

Q ss_pred             ECCCCCC-EEEEEE----EECCCCC
Q ss_conf             8789978-244046----4257786
Q gi|254780361|r   29 EDKKSGE-LRRPHH----VDMKTGL   48 (61)
Q Consensus        29 ~c~~cG~-~~~~H~----vc~~cG~   48 (61)
                      .||+||. ..+.+|    .|..|||
T Consensus        21 ~CPrCG~gvfmA~H~dR~~CGkCgy   45 (51)
T COG1998          21 FCPRCGPGVFMADHKDRWACGKCGY   45 (51)
T ss_pred             CCCCCCCCCHHHHCCCEEEECCCCC
T ss_conf             2888888434341576067435452


No 38 
>PRK04023 DNA polymerase II large subunit; Validated
Probab=76.21  E-value=1  Score=24.48  Aligned_cols=25  Identities=16%  Similarity=0.093  Sum_probs=14.9

Q ss_pred             EEECCCCCCEEEEEEEECCCCCCCC
Q ss_conf             7887899782440464257786768
Q gi|254780361|r   27 YVEDKKSGELRRPHHVDMKTGLYRG   51 (61)
Q Consensus        27 l~~c~~cG~~~~~H~vc~~cG~YkG   51 (61)
                      ...|+.||..+.++..|+.||.-.+
T Consensus       645 ~~~C~~CG~~T~~~~~c~~C~~~~~  669 (1128)
T PRK04023        645 YRRCPFCGTHTEPVYRCPRCGIEVD  669 (1128)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             5578777996654324776666556


No 39 
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=76.21  E-value=1  Score=24.54  Aligned_cols=28  Identities=18%  Similarity=-0.059  Sum_probs=17.2

Q ss_pred             HCCCCCCEEECCCCCC---EEEE--EEEECCCC
Q ss_conf             1026883788789978---2440--46425778
Q gi|254780361|r   20 DALTPPAYVEDKKSGE---LRRP--HHVDMKTG   47 (61)
Q Consensus        20 ~~l~~p~l~~c~~cG~---~~~~--H~vc~~cG   47 (61)
                      +.-..+.+..|+.||-   ....  +-.||.||
T Consensus       634 Y~~~n~~~d~C~~CGy~Ge~~~~~~g~~CP~CG  666 (711)
T PRK09263        634 YLGTNTPIDECYECGFTGEFECTEKGFTCPKCG  666 (711)
T ss_pred             EEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             387587866566789766235777898093999


No 40 
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=75.84  E-value=1.5  Score=23.56  Aligned_cols=33  Identities=9%  Similarity=-0.022  Sum_probs=22.9

Q ss_pred             CCEEECCCCCCEEE------EEEEECCCCCCCCEEEEEE
Q ss_conf             83788789978244------0464257786768796434
Q gi|254780361|r   25 PAYVEDKKSGELRR------PHHVDMKTGLYRGRQVFVL   57 (61)
Q Consensus        25 p~l~~c~~cG~~~~------~H~vc~~cG~YkGr~Vi~~   57 (61)
                      -.-..||+||...+      --.||..||+-=+-.+|+.
T Consensus         9 ~~~~kCp~Cg~~~ii~D~~~G~~vC~~CG~Vi~e~~ID~   47 (310)
T PRK00423          9 EEELRCPECGSDKLIYDYERGEIVCADCGYVIEENLIDQ   47 (310)
T ss_pred             CCEEECCCCCCCCEEEECCCCCEECCCCCCEEECCCCCC
T ss_conf             873589898698535678998775302887611320236


No 41 
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=74.94  E-value=1.7  Score=23.29  Aligned_cols=23  Identities=13%  Similarity=0.105  Sum_probs=18.0

Q ss_pred             ECCCCCCEEEEEE----EECCCCCCCC
Q ss_conf             8789978244046----4257786768
Q gi|254780361|r   29 EDKKSGELRRPHH----VDMKTGLYRG   51 (61)
Q Consensus        29 ~c~~cG~~~~~H~----vc~~cG~YkG   51 (61)
                      .||+||...+-+.    +|.+||+=-|
T Consensus      1149 ~CpeCGs~tmvrnG~C~~C~~CG~tsG 1175 (1177)
T PRK07562       1149 SCSECGNFTLVRNGTCLKCDTCGATTG 1175 (1177)
T ss_pred             CCCCCCCCCEEECCCCCCCCCCCCCCC
T ss_conf             788889964073586031013899878


No 42 
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=73.99  E-value=2.3  Score=22.59  Aligned_cols=20  Identities=30%  Similarity=0.288  Sum_probs=16.8

Q ss_pred             ECCCCCCEEEE-------EEEECCCCC
Q ss_conf             87899782440-------464257786
Q gi|254780361|r   29 EDKKSGELRRP-------HHVDMKTGL   48 (61)
Q Consensus        29 ~c~~cG~~~~~-------H~vc~~cG~   48 (61)
                      .||.||....|       -.+|.+|||
T Consensus         2 FCp~C~n~l~p~~~~~~~~~~C~~C~y   28 (52)
T smart00661        2 FCPKCGNMLIPKEGKEKRRFVCRKCGY   28 (52)
T ss_pred             CCCCCCCEEEEEECCCCEEEECCCCCC
T ss_conf             786528887685369953897489998


No 43 
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=73.76  E-value=3.4  Score=21.77  Aligned_cols=30  Identities=7%  Similarity=-0.298  Sum_probs=21.2

Q ss_pred             CCCCEEECCCCCCE-EE--EEE-EECCCCCCCCE
Q ss_conf             68837887899782-44--046-42577867687
Q gi|254780361|r   23 TPPAYVEDKKSGEL-RR--PHH-VDMKTGLYRGR   52 (61)
Q Consensus        23 ~~p~l~~c~~cG~~-~~--~H~-vc~~cG~YkGr   52 (61)
                      ..|....|.+||+. .+  .+. .||.||-+.-+
T Consensus        66 ~vp~~~~C~~C~~~~~~~~~~~~~CP~Cgs~~~~   99 (114)
T PRK03681         66 EQEAECWCETCQQYVTLLTQRVRRCPQCHGDMLR   99 (114)
T ss_pred             ECCCEEECCCCCCEEEECCCCCCCCCCCCCCCCE
T ss_conf             5285899655998554067767739088399758


No 44 
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=73.63  E-value=1.6  Score=23.54  Aligned_cols=27  Identities=11%  Similarity=0.138  Sum_probs=22.1

Q ss_pred             CCCEEECCCCCC--EEEEEEEECCCCCCC
Q ss_conf             883788789978--244046425778676
Q gi|254780361|r   24 PPAYVEDKKSGE--LRRPHHVDMKTGLYR   50 (61)
Q Consensus        24 ~p~l~~c~~cG~--~~~~H~vc~~cG~Yk   50 (61)
                      ..+.+.|.-||.  ++.....|.+|||=.
T Consensus        14 ~ktHi~CRRCGr~Syh~qk~~CasCGfg~   42 (62)
T PRK04179         14 GKTHIRCRRCGRHSYNVRKKYCAACGFGR   42 (62)
T ss_pred             CCCCCCCCCCCCHHHHHCCCEECCCCCCC
T ss_conf             96551305667222211354305778874


No 45 
>TIGR01374 soxD sarcosine oxidase, delta subunit family; InterPro: IPR006279   These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate .    Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process.
Probab=72.95  E-value=1.1  Score=24.27  Aligned_cols=11  Identities=27%  Similarity=0.286  Sum_probs=8.1

Q ss_pred             EEECCCCCCEE
Q ss_conf             78878997824
Q gi|254780361|r   27 YVEDKKSGELR   37 (61)
Q Consensus        27 l~~c~~cG~~~   37 (61)
                      |+.||+|||+.
T Consensus         1 LI~CP~CGE~R   11 (85)
T TIGR01374         1 LIPCPYCGEPR   11 (85)
T ss_pred             CCCCCCCCCCC
T ss_conf             96488998978


No 46 
>PRK10220 hypothetical protein; Provisional
Probab=72.25  E-value=1.7  Score=23.32  Aligned_cols=23  Identities=4%  Similarity=-0.190  Sum_probs=14.9

Q ss_pred             CEEECCCCCCEEE----EEEEECCCCC
Q ss_conf             3788789978244----0464257786
Q gi|254780361|r   26 AYVEDKKSGELRR----PHHVDMKTGL   48 (61)
Q Consensus        26 ~l~~c~~cG~~~~----~H~vc~~cG~   48 (61)
                      +|-.||+|+..-.    .-.+||.||+
T Consensus         2 tlP~CP~C~seytYedg~~~vCpeC~h   28 (111)
T PRK10220          2 SLPHCPKCNSEYTYEDNGMYICPECAH   28 (111)
T ss_pred             CCCCCCCCCCCCEECCCCEEECCCCCC
T ss_conf             888699898924382799789977647


No 47 
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=71.78  E-value=3.4  Score=21.78  Aligned_cols=29  Identities=17%  Similarity=-0.028  Sum_probs=19.3

Q ss_pred             CCCCEEECCCCCCEEEE---------------E---------EEECCCCCCCC
Q ss_conf             68837887899782440---------------4---------64257786768
Q gi|254780361|r   23 TPPAYVEDKKSGELRRP---------------H---------HVDMKTGLYRG   51 (61)
Q Consensus        23 ~~p~l~~c~~cG~~~~~---------------H---------~vc~~cG~YkG   51 (61)
                      ..|....|.+||.---+               |         -.||.||-+.-
T Consensus        66 ~vp~~~~C~~Cg~ef~~~~~~~~~~~~~~~~~h~~pe~~~~~~~CP~Cgs~~~  118 (135)
T PRK03824         66 EEEAVLKCRNCGYEWSLKEVKDKLDEEIREAIHFIPEVVHAFLKCPKCGSRDF  118 (135)
T ss_pred             ECCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             61756892338987244433321000001111234212355662909989886


No 48 
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=70.74  E-value=1.4  Score=23.79  Aligned_cols=24  Identities=21%  Similarity=0.257  Sum_probs=15.5

Q ss_pred             EEECCCCCCEEEEEE-----------EECCCCCCC
Q ss_conf             788789978244046-----------425778676
Q gi|254780361|r   27 YVEDKKSGELRRPHH-----------VDMKTGLYR   50 (61)
Q Consensus        27 l~~c~~cG~~~~~H~-----------vc~~cG~Yk   50 (61)
                      ...||+||.--.+|.           =|++||+..
T Consensus         6 y~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~   40 (201)
T COG1326           6 YIECPSCGSEEVSHEVIKERGREPLVRCEECGTVH   40 (201)
T ss_pred             EEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCEE
T ss_conf             88899987403467888734975279845787484


No 49 
>pfam01155 HypA Hydrogenase expression/synthesis hypA family. Four conserved cysteines lie either side of the least conserved region.
Probab=69.88  E-value=4.3  Score=21.20  Aligned_cols=28  Identities=14%  Similarity=0.081  Sum_probs=22.0

Q ss_pred             CCCCEEECCCCCCEE---EEEEEECCCCCCC
Q ss_conf             688378878997824---4046425778676
Q gi|254780361|r   23 TPPAYVEDKKSGELR---RPHHVDMKTGLYR   50 (61)
Q Consensus        23 ~~p~l~~c~~cG~~~---~~H~vc~~cG~Yk   50 (61)
                      ..|....|.+||...   ..+..||.||-+.
T Consensus        65 ~vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~   95 (112)
T pfam01155        65 EVPGVARCRDCGQEFELEERFFRCPKCGSLD   95 (112)
T ss_pred             ECCCEEECCCCCCEECCCCCCCCCCCCCCCC
T ss_conf             5187489989997142577767990897998


No 50 
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=69.77  E-value=3.8  Score=21.49  Aligned_cols=29  Identities=7%  Similarity=-0.165  Sum_probs=21.8

Q ss_pred             EEECCCCCCEEEEE---EEECCCCCCCCEEEE
Q ss_conf             78878997824404---642577867687964
Q gi|254780361|r   27 YVEDKKSGELRRPH---HVDMKTGLYRGRQVF   55 (61)
Q Consensus        27 l~~c~~cG~~~~~H---~vc~~cG~YkGr~Vi   55 (61)
                      ...|+.||.+..+-   -.||.||+---|+|-
T Consensus       150 ~A~C~~cg~~m~~~~~~~~Cp~cg~~e~RKva  181 (187)
T PRK09521        150 KALCSRCRTPLVKKGNTLKCPNCGNVETRKLS  181 (187)
T ss_pred             EEECCCCCCCEEEECCEEECCCCCCEEEEEEE
T ss_conf             99577678858673999999999998967010


No 51 
>TIGR00340 zpr1_rel zinc finger protein ZPR1 homolog; InterPro: IPR004470   Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, however they are now recognised to bind DNA, RNA, protein and/or lipid substrates , , , , . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.    (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries).   This entry represents ZPR1-type zinc finger domains. ZPR1 was shown experimentally to bind approximately two moles of zinc, and has two copies of a domain homologous to this protein, each containing a putative zinc finger of the form CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of epidermal growth factor receptor but is displaced by receptor activation and autophosphorylation after which it redistributes in part to the nucleus. The proteins described by this family by analogy may be suggested to play a role in signal transduction as proven for other Z-finger binding proteins.   Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) . ZPR1 interacts with complexes formed by SMN , and may act as a modifier that effects the severity of SMA.   More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0008270 zinc ion binding.
Probab=68.56  E-value=5  Score=20.86  Aligned_cols=40  Identities=28%  Similarity=0.319  Sum_probs=30.4

Q ss_pred             CCCCCC-EEECCCCCCEEEEEEEECCCCCCCCEEEEEEECCC
Q ss_conf             026883-78878997824404642577867687964342369
Q gi|254780361|r   21 ALTPPA-YVEDKKSGELRRPHHVDMKTGLYRGRQVFVLKTKE   61 (61)
Q Consensus        21 ~l~~p~-l~~c~~cG~~~~~H~vc~~cG~YkGr~Vi~~~~~e   61 (61)
                      -|.+.+ +..=|-.|+..++--.|-+|| ||-..|+-.+++|
T Consensus         9 ~L~Av~~~~~iPy~G~~~~s~~~Ce~Cg-YR~~Dv~~lEeke   49 (168)
T TIGR00340         9 TLKAVTYVYDIPYFGKVMLSTLICEKCG-YRSADVVVLEEKE   49 (168)
T ss_pred             EEEEEEEECCCCCCCEEEEEEEEECCCC-CCEEEEEEECCCC
T ss_conf             1576655405881026989776632689-7000016622669


No 52 
>pfam08274 PhnA_Zn_Ribbon PhnA Zinc-Ribbon.
Probab=68.17  E-value=2.3  Score=22.64  Aligned_cols=22  Identities=5%  Similarity=-0.306  Sum_probs=14.3

Q ss_pred             EEECCCCCCEEEE----EEEECCCCC
Q ss_conf             7887899782440----464257786
Q gi|254780361|r   27 YVEDKKSGELRRP----HHVDMKTGL   48 (61)
Q Consensus        27 l~~c~~cG~~~~~----H~vc~~cG~   48 (61)
                      |..||.|+.----    --|||.||+
T Consensus         2 lP~Cp~C~seytY~d~~~~vCpeC~h   27 (30)
T pfam08274         2 LPKCPLCNSEYTYEDGALLVCPECAH   27 (30)
T ss_pred             CCCCCCCCCCCEECCCCEEECCCCCC
T ss_conf             78788789812474799979975456


No 53 
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=67.98  E-value=3.8  Score=21.50  Aligned_cols=29  Identities=17%  Similarity=0.002  Sum_probs=18.6

Q ss_pred             CCCCEEECCCCCC------EEEEEE----EECCCCCCCCE
Q ss_conf             6883788789978------244046----42577867687
Q gi|254780361|r   23 TPPAYVEDKKSGE------LRRPHH----VDMKTGLYRGR   52 (61)
Q Consensus        23 ~~p~l~~c~~cG~------~~~~H~----vc~~cG~YkGr   52 (61)
                      ..|....| +||.      ....|.    .||.||-+...
T Consensus        66 ~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~  104 (124)
T PRK00762         66 MIPPELEC-ECGYKGVVDEDEIDHYAAVMECPVCGNKHAH  104 (124)
T ss_pred             ECCCEEEE-ECCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
T ss_conf             71725996-2899555332100025677719188797778


No 54 
>pfam04135 Nop10p Nucleolar RNA-binding protein, Nop10p family. Nop10p is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10p is probably necessary for the stability of these RNPs.
Probab=66.45  E-value=2.3  Score=22.61  Aligned_cols=21  Identities=5%  Similarity=-0.243  Sum_probs=16.3

Q ss_pred             EEECCCCCCEEEEEEEECCCCC
Q ss_conf             7887899782440464257786
Q gi|254780361|r   27 YVEDKKSGELRRPHHVDMKTGL   48 (61)
Q Consensus        27 l~~c~~cG~~~~~H~vc~~cG~   48 (61)
                      |..|+.|+.+.|.. .||.||-
T Consensus         5 ~r~c~~c~~YTLk~-~cp~cG~   25 (53)
T pfam04135         5 LRKCPGCRVYTLKD-KCPECGG   25 (53)
T ss_pred             HHHCCCCCCEECCC-CCCCCCC
T ss_conf             54088999676778-4688988


No 55 
>pfam03833 PolC_DP2 DNA polymerase II large subunit DP2.
Probab=66.32  E-value=3.2  Score=21.89  Aligned_cols=22  Identities=18%  Similarity=0.223  Sum_probs=18.1

Q ss_pred             CEEECCCCCCEEEEEEEECCCCC
Q ss_conf             37887899782440464257786
Q gi|254780361|r   26 AYVEDKKSGELRRPHHVDMKTGL   48 (61)
Q Consensus        26 ~l~~c~~cG~~~~~H~vc~~cG~   48 (61)
                      .+-.||.||... +...|+.||.
T Consensus       628 g~R~C~~Cg~~t-~~~~C~~CG~  649 (852)
T pfam03833       628 GFRRCPSCGKES-PESTCPKCGS  649 (852)
T ss_pred             EEEECCCCCCCC-CCCCCCCCCC
T ss_conf             003888999977-8714999998


No 56 
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=65.93  E-value=6.4  Score=20.33  Aligned_cols=26  Identities=19%  Similarity=0.154  Sum_probs=20.8

Q ss_pred             CCCEEECCCCCCEEEE-----------EEEECCCCCC
Q ss_conf             8837887899782440-----------4642577867
Q gi|254780361|r   24 PPAYVEDKKSGELRRP-----------HHVDMKTGLY   49 (61)
Q Consensus        24 ~p~l~~c~~cG~~~~~-----------H~vc~~cG~Y   49 (61)
                      .+..-.||-||..+..           --+|.+||.|
T Consensus        19 L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls   55 (104)
T COG4888          19 LPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLS   55 (104)
T ss_pred             CCCEEECCCCCCEEEEEEEEEECCCEEEEECCCCCCE
T ss_conf             8835716855872355788974274568971457553


No 57 
>pfam09297 zf-NADH-PPase NADH pyrophosphatase zinc ribbon domain. This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.
Probab=65.82  E-value=2.6  Score=22.40  Aligned_cols=21  Identities=19%  Similarity=0.107  Sum_probs=16.8

Q ss_pred             EECCCCCCEEEEE-----EEECCCCC
Q ss_conf             8878997824404-----64257786
Q gi|254780361|r   28 VEDKKSGELRRPH-----HVDMKTGL   48 (61)
Q Consensus        28 ~~c~~cG~~~~~H-----~vc~~cG~   48 (61)
                      ..|+.||.+..+.     ++||+||.
T Consensus         4 rfC~~CG~~t~~~~~g~~r~C~~Cg~   29 (32)
T pfam09297         4 RFCGRCGAPTEPAEGGWARVCPSCGH   29 (32)
T ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCC
T ss_conf             44244688475077851766887676


No 58 
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300; InterPro: IPR012644   Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown..
Probab=65.04  E-value=3.1  Score=21.99  Aligned_cols=22  Identities=27%  Similarity=0.166  Sum_probs=15.6

Q ss_pred             EEECCCCCC----EEEEEEEECCCCC
Q ss_conf             788789978----2440464257786
Q gi|254780361|r   27 YVEDKKSGE----LRRPHHVDMKTGL   48 (61)
Q Consensus        27 l~~c~~cG~----~~~~H~vc~~cG~   48 (61)
                      =.+||+||.    +-+.=-|||.||-
T Consensus         9 KrIcP~tg~KFYDLNr~P~vsPytGe   34 (157)
T TIGR02300         9 KRICPETGKKFYDLNRDPVVSPYTGE   34 (157)
T ss_pred             CCCCCCCCCCCCCCCCCCEECCCCCC
T ss_conf             22068777722000789534177887


No 59 
>pfam12172 DUF35_N Rubredoxin-like zinc ribbon domain (DUF35_N). This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in a hypothetical protein from Mycobacterium tuberculosis. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment.
Probab=64.94  E-value=2.9  Score=22.11  Aligned_cols=22  Identities=23%  Similarity=0.252  Sum_probs=17.5

Q ss_pred             CEEECCCCCCEEE-EEEEECCCC
Q ss_conf             3788789978244-046425778
Q gi|254780361|r   26 AYVEDKKSGELRR-PHHVDMKTG   47 (61)
Q Consensus        26 ~l~~c~~cG~~~~-~H~vc~~cG   47 (61)
                      .+..|+.||.... |-.+|++||
T Consensus        10 ~~~rC~~Cg~~~fPpr~~C~~C~   32 (37)
T pfam12172        10 VGQRCRDCGTVRFPPRPVCPHCG   32 (37)
T ss_pred             EECCCCCCCCEEECCCCCCCCCC
T ss_conf             85546789985848977786637


No 60 
>pfam09332 Mcm10 Mcm10 replication factor. Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha.
Probab=62.82  E-value=4.5  Score=21.09  Aligned_cols=26  Identities=19%  Similarity=0.372  Sum_probs=21.1

Q ss_pred             CCEEECCCCCC-----EEEEEEEECCCCCCC
Q ss_conf             83788789978-----244046425778676
Q gi|254780361|r   25 PAYVEDKKSGE-----LRRPHHVDMKTGLYR   50 (61)
Q Consensus        25 p~l~~c~~cG~-----~~~~H~vc~~cG~Yk   50 (61)
                      .-+-.|++||.     ..+|...|.+||-++
T Consensus       285 KRFFkC~dC~~Rtisl~r~P~~~C~~Cg~~k  315 (346)
T pfam09332       285 KRFFKCPDCGNRTISLDRLPKKHCKNCGLFK  315 (346)
T ss_pred             EEEEECCCCCCCEEEEECCCCCCCCCCCCCC
T ss_conf             3224568878744562107622232367751


No 61 
>PRK05978 hypothetical protein; Provisional
Probab=62.52  E-value=2.8  Score=22.18  Aligned_cols=29  Identities=17%  Similarity=-0.056  Sum_probs=19.0

Q ss_pred             CCCCCCEEECCCCCCEEE------EEEEECCCCCC
Q ss_conf             026883788789978244------04642577867
Q gi|254780361|r   21 ALTPPAYVEDKKSGELRR------PHHVDMKTGLY   49 (61)
Q Consensus        21 ~l~~p~l~~c~~cG~~~~------~H~vc~~cG~Y   49 (61)
                      ++.---.-.||+||+-++      .--.|..||.-
T Consensus        28 al~RGlr~rCP~CG~G~LF~gyLkv~~~C~~CG~d   62 (149)
T PRK05978         28 AMWRGFRGRCPHCGEGKLFRAFLKPVDHCSACGED   62 (149)
T ss_pred             HHHHHHCCCCCCCCCCHHHHHHCCCCCCCHHCCCC
T ss_conf             99988737598999941564216676550130852


No 62 
>KOG2879 consensus
Probab=62.23  E-value=3.6  Score=21.65  Aligned_cols=22  Identities=32%  Similarity=0.311  Sum_probs=17.0

Q ss_pred             CEEECCCCCC-EEEEEEEECCCCC
Q ss_conf             3788789978-2440464257786
Q gi|254780361|r   26 AYVEDKKSGE-LRRPHHVDMKTGL   48 (61)
Q Consensus        26 ~l~~c~~cG~-~~~~H~vc~~cG~   48 (61)
                      .-++||-||+ +.+||++ ..||.
T Consensus       238 ~~~~C~~Cg~~PtiP~~~-~~C~H  260 (298)
T KOG2879         238 SDTECPVCGEPPTIPHVI-GKCGH  260 (298)
T ss_pred             CCCEEECCCCCCCCCEEE-CCCCC
T ss_conf             775500669999987310-44564


No 63 
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=62.17  E-value=4.8  Score=20.99  Aligned_cols=24  Identities=8%  Similarity=-0.175  Sum_probs=16.9

Q ss_pred             EEECCCCCCE-----EEEE----EEECCCCCCC
Q ss_conf             7887899782-----4404----6425778676
Q gi|254780361|r   27 YVEDKKSGEL-----RRPH----HVDMKTGLYR   50 (61)
Q Consensus        27 l~~c~~cG~~-----~~~H----~vc~~cG~Yk   50 (61)
                      ...||.|++.     .+-|    .+|+.|||=+
T Consensus      1712 ~~yCPeC~sk~G~~veLv~eEGC~tC~~CGwSK 1744 (1748)
T PRK08332       1712 VAYCPVCYEKDGELVELKMESGCATCPRCGWSK 1744 (1748)
T ss_pred             CCCCCCCCCCCCCCEEEEECCCCEECCCCCCCC
T ss_conf             767998756788740368516963476778871


No 64 
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=61.41  E-value=4.9  Score=20.94  Aligned_cols=22  Identities=18%  Similarity=0.105  Sum_probs=15.6

Q ss_pred             ECCCCCCEEEEEE----EECCCCCCCC
Q ss_conf             8789978244046----4257786768
Q gi|254780361|r   29 EDKKSGELRRPHH----VDMKTGLYRG   51 (61)
Q Consensus        29 ~c~~cG~~~~~H~----vc~~cG~YkG   51 (61)
                      .||+||.. +-+.    +|.+||.=-|
T Consensus       930 ~CpeCGs~-mvRnGgC~kC~~CG~TsG  955 (957)
T PRK06556        930 LCPTCGTI-MVRNGSCYVCEGCGSTSG  955 (957)
T ss_pred             CCCCCCCC-EEECCCCCCCCCCCCCCC
T ss_conf             78755765-378687432356899867


No 65 
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=60.01  E-value=5.2  Score=20.80  Aligned_cols=30  Identities=13%  Similarity=0.157  Sum_probs=21.6

Q ss_pred             CCCEEECCCCCCEEEE--------------------EEEECCCC--CCCCEE
Q ss_conf             8837887899782440--------------------46425778--676879
Q gi|254780361|r   24 PPAYVEDKKSGELRRP--------------------HHVDMKTG--LYRGRQ   53 (61)
Q Consensus        24 ~p~l~~c~~cG~~~~~--------------------H~vc~~cG--~YkGr~   53 (61)
                      .|.++.||.|+..-.+                    --.|++||  |++|.+
T Consensus        94 ~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsH  145 (165)
T COG1656          94 FPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSH  145 (165)
T ss_pred             CCCCCCCCCCCCEECCCCHHHHHHCCCHHHHHCCCCEEECCCCCCCCCCCHH
T ss_conf             6010327434978010767777520652442020014677997623267108


No 66 
>pfam08271 TF_Zn_Ribbon TFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
Probab=58.53  E-value=5  Score=20.88  Aligned_cols=29  Identities=17%  Similarity=0.130  Sum_probs=17.8

Q ss_pred             ECCCCCCEE------EEEEEECCCCCCCCEEEEEE
Q ss_conf             878997824------40464257786768796434
Q gi|254780361|r   29 EDKKSGELR------RPHHVDMKTGLYRGRQVFVL   57 (61)
Q Consensus        29 ~c~~cG~~~------~~H~vc~~cG~YkGr~Vi~~   57 (61)
                      +||+||...      .--.+|+.||+--.-.+++.
T Consensus         2 ~Cp~Cg~~~~~~D~~~Ge~vC~~CG~Vlee~~id~   36 (40)
T pfam08271         2 KCPNCGSTEIVFDYERGEYVCTECGLVLEDNIIDE   36 (40)
T ss_pred             CCCCCCCCCEEEECCCCCEECCCCCEEEECCCCCC
T ss_conf             38879997067727789787057971900023566


No 67 
>pfam03367 zf-ZPR1 ZPR1 zinc-finger domain. The zinc-finger protein ZPR1 is ubiquitous among eukaryotes. It is indeed known to be an essential protein in yeast. In quiescent cells, ZPR1 is localized to the cytoplasm. But in proliferating cells treated with EGF or with other mitogens, ZPR1 accumulates in the nucleolus. ZPR1 interacts with the cytoplasmic domain of the inactive EGF receptor (EGFR) and is thought to inhibit the basal protein tyrosine kinase activity of EGFR. This interaction is disrupted when cells are treated with EGF, though by themselves, inactive EGFRs are not sufficient to sequester ZPR1 to the cytoplasm. Upon stimulation by EGF, ZPR1 directly binds the eukaryotic translation elongation factor-1alpha (eEF-1alpha) to form ZPR1/eEF-1alpha complexes. These move into the nucleus, localising particularly at the nucleolus. Indeed, the interaction between ZPR1 and eEF-1alpha has been shown to be essential for normal cellular proliferation, and ZPR1 is thought to be involved 
Probab=58.25  E-value=11  Score=19.07  Aligned_cols=29  Identities=17%  Similarity=0.079  Sum_probs=17.8

Q ss_pred             EECCCCCCE----------------EEEEEEECCCCCCCCEEEEEE
Q ss_conf             887899782----------------440464257786768796434
Q gi|254780361|r   28 VEDKKSGEL----------------RRPHHVDMKTGLYRGRQVFVL   57 (61)
Q Consensus        28 ~~c~~cG~~----------------~~~H~vc~~cG~YkGr~Vi~~   57 (61)
                      +.||+||+.                .+..-.|++|| |+...|...
T Consensus         2 s~Cp~Cg~~g~t~~~~~~IP~F~evii~sf~C~~CG-yr~~ev~~~   46 (160)
T pfam03367         2 SDCPVCGGEGTTRMKLTDIPYFREVIIMSFICEHCG-YRSNEVQSG   46 (160)
T ss_pred             CCCCCCCCCCEEEEEEECCCCCCEEEEEEEECCCCC-CEEEEEEEC
T ss_conf             979889988779999964898642899999999999-882488897


No 68 
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.46  E-value=3.3  Score=21.79  Aligned_cols=23  Identities=22%  Similarity=0.018  Sum_probs=16.9

Q ss_pred             CEEECCCCCCEEE------EEEEECCCCC
Q ss_conf             3788789978244------0464257786
Q gi|254780361|r   26 AYVEDKKSGELRR------PHHVDMKTGL   48 (61)
Q Consensus        26 ~l~~c~~cG~~~~------~H~vc~~cG~   48 (61)
                      -.-.||+|||=++      +-.+|..||.
T Consensus        20 l~grCP~CGeGrLF~gFLK~~p~C~aCG~   48 (126)
T COG5349          20 LRGRCPRCGEGRLFRGFLKVVPACEACGL   48 (126)
T ss_pred             HCCCCCCCCCCHHHHHHCCCCCHHHHCCC
T ss_conf             46779988983254201453743666064


No 69 
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=57.02  E-value=5.5  Score=20.66  Aligned_cols=29  Identities=14%  Similarity=0.013  Sum_probs=16.6

Q ss_pred             HCCCCCCE----EECCCCCC--EEEEE---EEECCCCC
Q ss_conf             10268837----88789978--24404---64257786
Q gi|254780361|r   20 DALTPPAY----VEDKKSGE--LRRPH---HVDMKTGL   48 (61)
Q Consensus        20 ~~l~~p~l----~~c~~cG~--~~~~H---~vc~~cG~   48 (61)
                      +.++.-.+    -.||+||.  +.--|   ..|..|||
T Consensus        12 Ykv~~~kv~r~~k~CPrCG~GvfmA~H~dR~~CGKCgy   49 (54)
T PRK00432         12 YEVDGGKVVRKNKFCPRCGPGVFMAEHKDRWACGKCGY   49 (54)
T ss_pred             EEECCCEEEECCCCCCCCCCCEEEEECCCCCCCCCCCC
T ss_conf             89639999886785979999464012588766358667


No 70 
>TIGR00201 comF comF family protein; InterPro: IPR005222   Proteins in this family are found in bacterial species which posses systems for natural transformation with exogenous DNA (eg Bacillus subtilis, Haemophilus influenzae), and also species without these systems (eg Escherichia coli). Competence protein F has been shown to be important for the uptake of exogenous DNA in naturally competent bacteria, though the precise role of this protein is not yet known , . GntX is a periplasmic gluconate binding protein thought to be part of a high-affinity gluconate transport system ..
Probab=56.96  E-value=4.6  Score=21.07  Aligned_cols=19  Identities=11%  Similarity=0.039  Sum_probs=16.1

Q ss_pred             CCCCCCEEEE-EEEECCCCC
Q ss_conf             7899782440-464257786
Q gi|254780361|r   30 DKKSGELRRP-HHVDMKTGL   48 (61)
Q Consensus        30 c~~cG~~~~~-H~vc~~cG~   48 (61)
                      |+-||....+ |-+|+.||.
T Consensus         1 C~~C~k~~~S~~a~C~~C~~   20 (207)
T TIGR00201         1 CSLCGKRIKSSKALCDQCGS   20 (207)
T ss_pred             CCCCCCCCCCCCCCCCCCCC
T ss_conf             98888873007762466662


No 71 
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=56.75  E-value=5.4  Score=20.69  Aligned_cols=22  Identities=9%  Similarity=-0.159  Sum_probs=17.1

Q ss_pred             EEECCCCCCEEEEE-----EEECCCCC
Q ss_conf             78878997824404-----64257786
Q gi|254780361|r   27 YVEDKKSGELRRPH-----HVDMKTGL   48 (61)
Q Consensus        27 l~~c~~cG~~~~~H-----~vc~~cG~   48 (61)
                      -..|+.||++..+.     +.|++||.
T Consensus       100 hrfC~~CG~~t~~~~~g~~~~C~~C~~  126 (257)
T PRK00241        100 HRFCGYCGHPTHPSKTEWAMLCPHCRE  126 (257)
T ss_pred             CCCCCCCCCCCCCCCCCEEEECCCCCC
T ss_conf             984565673663387850698899986


No 72 
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=54.68  E-value=6.2  Score=20.39  Aligned_cols=33  Identities=12%  Similarity=-0.126  Sum_probs=20.7

Q ss_pred             HHHHCCCCCCEEECCCCCCEEE--EEEEECCCCCCC
Q ss_conf             2231026883788789978244--046425778676
Q gi|254780361|r   17 RSADALTPPAYVEDKKSGELRR--PHHVDMKTGLYR   50 (61)
Q Consensus        17 Rsh~~l~~p~l~~c~~cG~~~~--~H~vc~~cG~Yk   50 (61)
                      |-.+.-..+.++.|..||..--  .-. ||.||.=+
T Consensus       631 ri~Y~~~n~~i~~C~~cg~~~~~~~~~-Cp~CG~~d  665 (700)
T COG1328         631 RIGYWGYTTPISVCNRCGYSGEGLRTR-CPKCGSED  665 (700)
T ss_pred             CCCEEECCCCCEEECCCCCCCCCCCCC-CCCCCCCC
T ss_conf             860684488820511479664556465-88878734


No 73 
>PRK10436 hypothetical protein; Provisional
Probab=54.42  E-value=6.4  Score=20.31  Aligned_cols=27  Identities=7%  Similarity=-0.111  Sum_probs=16.1

Q ss_pred             ECCCCCCEEEEE-----------------EEECCCC-CCCCEEEE
Q ss_conf             878997824404-----------------6425778-67687964
Q gi|254780361|r   29 EDKKSGELRRPH-----------------HVDMKTG-LYRGRQVF   55 (61)
Q Consensus        29 ~c~~cG~~~~~H-----------------~vc~~cG-~YkGr~Vi   55 (61)
                      .||+|.+...+.                 .-|+.|. =|+||..|
T Consensus       354 LCp~Ck~~~~~~~~~~~~~~~~~~~~~~~~GC~~C~tGY~GR~~i  398 (461)
T PRK10436        354 LCPHCRQQQSEPVHLPANIWPSPLPHWQAVGCEHCYHGFYGRTAL  398 (461)
T ss_pred             CCHHHCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCEEE
T ss_conf             373327866754210133043433202578873338998860189


No 74 
>PRK06450 threonine synthase; Validated
Probab=52.76  E-value=7.1  Score=20.06  Aligned_cols=20  Identities=20%  Similarity=0.119  Sum_probs=12.4

Q ss_pred             EECCCCCC-EEEEEEEECCCC
Q ss_conf             88789978-244046425778
Q gi|254780361|r   28 VEDKKSGE-LRRPHHVDMKTG   47 (61)
Q Consensus        28 ~~c~~cG~-~~~~H~vc~~cG   47 (61)
                      -.|..||. +.-....||.||
T Consensus         4 l~C~~CG~~~~~~~~~C~~Cg   24 (336)
T PRK06450          4 VRCIRCGKEREGEELRCKKCG   24 (336)
T ss_pred             EECCCCCCCCCCCCEECCCCC
T ss_conf             887855888898875889999


No 75 
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=52.68  E-value=17  Score=18.12  Aligned_cols=23  Identities=22%  Similarity=0.091  Sum_probs=13.5

Q ss_pred             CCEEEEEEEECCCCCCCCEEEEEE
Q ss_conf             782440464257786768796434
Q gi|254780361|r   34 GELRRPHHVDMKTGLYRGRQVFVL   57 (61)
Q Consensus        34 G~~~~~H~vc~~cG~YkGr~Vi~~   57 (61)
                      |+..+..-.|++|| |+...|...
T Consensus        23 ~evii~s~~C~~CG-yr~~ev~~~   45 (160)
T smart00709       23 REVIIMSFECEHCG-YRNNEVKSG   45 (160)
T ss_pred             CEEEEEEEECCCCC-CCCEEEEEC
T ss_conf             43999998999999-852378887


No 76 
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=52.35  E-value=9.4  Score=19.44  Aligned_cols=31  Identities=13%  Similarity=-0.079  Sum_probs=21.0

Q ss_pred             CCCCCCEEECCCCCCEEE--EEEEECCCCCCCC
Q ss_conf             026883788789978244--0464257786768
Q gi|254780361|r   21 ALTPPAYVEDKKSGELRR--PHHVDMKTGLYRG   51 (61)
Q Consensus        21 ~l~~p~l~~c~~cG~~~~--~H~vc~~cG~YkG   51 (61)
                      .+..-.+-+|+.||-...  +--+||.||.=+.
T Consensus       128 ~~~~~~~~vC~vCGy~~~ge~P~~CPiCga~k~  160 (166)
T COG1592         128 RLEEGKVWVCPVCGYTHEGEAPEVCPICGAPKE  160 (166)
T ss_pred             HHHCCCEEECCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             660387787687888126899876999998188


No 77 
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase; InterPro: IPR012833    This entry is found in the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centred radical , a C-terminal zinc binding site , and a set of conserved active site cysteines and asparagines . This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (IPR012837 from INTERPRO). Together the two form an alpha-2/beta-2 heterodimer.; GO: 0008998 ribonucleoside-triphosphate reductase activity, 0016491 oxidoreductase activity.
Probab=51.56  E-value=6.2  Score=20.39  Aligned_cols=31  Identities=13%  Similarity=-0.136  Sum_probs=20.1

Q ss_pred             HHHCCCCCCEEECCCCC-CEEEEE-----EEECCCCC
Q ss_conf             23102688378878997-824404-----64257786
Q gi|254780361|r   18 SADALTPPAYVEDKKSG-ELRRPH-----HVDMKTGL   48 (61)
Q Consensus        18 sh~~l~~p~l~~c~~cG-~~~~~H-----~vc~~cG~   48 (61)
                      -.+.-..+.+..|..|| -...-+     --||.||-
T Consensus       581 i~Y~~in~~~~~C~~Cg~y~~~~~~t~~g~~CP~CGs  617 (655)
T TIGR02487       581 IGYFGINPPVDVCEDCGEYTGEGLNTEKGDKCPKCGS  617 (655)
T ss_pred             CCEEEECCCCCEECCCCCCHHCCCCCCCCCCCCCCCC
T ss_conf             2226767877652576532000000115566889887


No 78 
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=51.52  E-value=7.1  Score=20.06  Aligned_cols=23  Identities=22%  Similarity=0.062  Sum_probs=16.5

Q ss_pred             EEECCCCCCEEEEE-----EEECCCCCC
Q ss_conf             78878997824404-----642577867
Q gi|254780361|r   27 YVEDKKSGELRRPH-----HVDMKTGLY   49 (61)
Q Consensus        27 l~~c~~cG~~~~~H-----~vc~~cG~Y   49 (61)
                      .-.|+.||....+-     ++|++||.+
T Consensus       111 ~RFCg~CG~~~~~~~~g~~~~C~~cg~~  138 (279)
T COG2816         111 HRFCGRCGTKTYPREGGWARVCPKCGHE  138 (279)
T ss_pred             CCCCCCCCCCCCCCCCCEEEECCCCCCC
T ss_conf             7677778980743567324557988870


No 79 
>pfam06906 DUF1272 Protein of unknown function (DUF1272). This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=51.45  E-value=2.3  Score=22.62  Aligned_cols=19  Identities=26%  Similarity=0.137  Sum_probs=13.5

Q ss_pred             EECCCCCCEEEEEEEECCCC
Q ss_conf             88789978244046425778
Q gi|254780361|r   28 VEDKKSGELRRPHHVDMKTG   47 (61)
Q Consensus        28 ~~c~~cG~~~~~H~vc~~cG   47 (61)
                      +.|..|.+-.+ +.+||+||
T Consensus        30 TFC~~C~~~~l-~~~CPNCg   48 (57)
T pfam06906        30 TFCADCAETRL-HGVCPNCG   48 (57)
T ss_pred             EECHHHHHHHH-CCCCCCCC
T ss_conf             12678997886-68484998


No 80 
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=50.80  E-value=12  Score=18.82  Aligned_cols=19  Identities=26%  Similarity=0.123  Sum_probs=14.5

Q ss_pred             CCCCCC-EEEEEEEECCCCC
Q ss_conf             789978-2440464257786
Q gi|254780361|r   30 DKKSGE-LRRPHHVDMKTGL   48 (61)
Q Consensus        30 c~~cG~-~~~~H~vc~~cG~   48 (61)
                      ||.||. .+...-.|++||.
T Consensus         1 CPvCg~~l~Vt~L~C~~C~t   20 (113)
T pfam09862         1 CPVCGEELTVTRLECSKCGT   20 (113)
T ss_pred             CCCCCCCEEEEEEECCCCCC
T ss_conf             99899813899988489986


No 81 
>pfam01907 Ribosomal_L37e Ribosomal protein L37e. This family includes ribosomal protein L37 from eukaryotes and archaebacteria. The family contains many conserved cysteines and histidines suggesting that this protein may bind to zinc.
Probab=50.74  E-value=4.9  Score=20.92  Aligned_cols=27  Identities=11%  Similarity=0.145  Sum_probs=21.9

Q ss_pred             CEEECCCCCC--EEEEEEEECCCCCCCCE
Q ss_conf             3788789978--24404642577867687
Q gi|254780361|r   26 AYVEDKKSGE--LRRPHHVDMKTGLYRGR   52 (61)
Q Consensus        26 ~l~~c~~cG~--~~~~H~vc~~cG~YkGr   52 (61)
                      +-+.|.-||.  +++....|.+|||=..+
T Consensus        14 tH~~CrRCG~~syH~qK~~CasCG~p~~k   42 (54)
T pfam01907        14 THTLCRRCGRRSYHVQKKRCASCGFPRAK   42 (54)
T ss_pred             CCCHHCCCCCHHHHHHCCCCCCCCCCHHH
T ss_conf             50511065834454402205447988311


No 82 
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and  believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=50.67  E-value=9.4  Score=19.43  Aligned_cols=24  Identities=8%  Similarity=-0.117  Sum_probs=17.2

Q ss_pred             EEECCCCCCEEE---EEEEECCCCCCC
Q ss_conf             788789978244---046425778676
Q gi|254780361|r   27 YVEDKKSGELRR---PHHVDMKTGLYR   50 (61)
Q Consensus        27 l~~c~~cG~~~~---~H~vc~~cG~Yk   50 (61)
                      +=.|++||....   +=-+||.||.=+
T Consensus         2 ~w~C~vCGyi~~G~~aP~~CPvC~~~~   28 (34)
T cd00729           2 VWVCPVCGYIHEGEEAPEKCPICGAPK   28 (34)
T ss_pred             EEECCCCCCEEECCCCCCCCCCCCCCH
T ss_conf             688898998868887987586999967


No 83 
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=50.12  E-value=8.5  Score=19.68  Aligned_cols=29  Identities=14%  Similarity=0.061  Sum_probs=19.5

Q ss_pred             EECCCCCCEEE------EEEEECCCCCCCCEEEEE
Q ss_conf             88789978244------046425778676879643
Q gi|254780361|r   28 VEDKKSGELRR------PHHVDMKTGLYRGRQVFV   56 (61)
Q Consensus        28 ~~c~~cG~~~~------~H~vc~~cG~YkGr~Vi~   56 (61)
                      ..||+||....      --.||..||.-=+-+.|+
T Consensus         2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~~~id   36 (285)
T COG1405           2 MSCPECGSTNIITDYERGEIVCADCGLVLEDSLID   36 (285)
T ss_pred             CCCCCCCCCCCEEECCCCEEEECCCCEEECCCCCC
T ss_conf             98999997411130668718833697785553125


No 84 
>TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241    This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. .
Probab=49.35  E-value=3.6  Score=21.65  Aligned_cols=45  Identities=16%  Similarity=0.115  Sum_probs=26.9

Q ss_pred             CCCCCCCHHCCCCHHHHHCCCCCCEEECCCCCCEEEE-------EEEECCCCC
Q ss_conf             8878876100174122310268837887899782440-------464257786
Q gi|254780361|r    3 VPKRKTSPSKRGMRRSADALTPPAYVEDKKSGELRRP-------HHVDMKTGL   48 (61)
Q Consensus         3 VPKrK~S~sr~~~RRsh~~l~~p~l~~c~~cG~~~~~-------H~vc~~cG~   48 (61)
                      |-||+++..=+..|.+=-+=+.--+-.||||. ++.+       --.||.||-
T Consensus        87 v~Krk~~e~~kkLreklEfE~nn~ff~CpN~~-vrftf~eAme~nFtCP~CG~  138 (168)
T TIGR00373        87 VVKRKLEELVKKLREKLEFEKNNMFFVCPNMN-VRFTFDEAMELNFTCPECGA  138 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEEEEECCCE-EEEEHHHHHCCCCCCCCCCC
T ss_conf             98788999999999874231077258713840-57404223116798833132


No 85 
>TIGR02264 gmx_para_CXXCG Myxococcus xanthus double-CXXCG motif paralogous family; InterPro: IPR011750   This entry consists of at least 10 paralogous proteins from Myxococcus xanthus that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment..
Probab=49.09  E-value=6.5  Score=20.27  Aligned_cols=22  Identities=18%  Similarity=0.235  Sum_probs=18.7

Q ss_pred             CCHHHHHCCCCCCEEECCCCCC
Q ss_conf             7412231026883788789978
Q gi|254780361|r   14 GMRRSADALTPPAYVEDKKSGE   35 (61)
Q Consensus        14 ~~RRsh~~l~~p~l~~c~~cG~   35 (61)
                      +.-||.+++..|.|.-||.||+
T Consensus        18 ~L~rAahkW~LPG~~~Cp~CG~   39 (247)
T TIGR02264        18 SLDRAAHKWCLPGVAPCPVCGA   39 (247)
T ss_pred             CHHHCCCCCCCCCCCCCCCCCC
T ss_conf             5311317667888688888787


No 86 
>PRK05580 primosome assembly protein PriA; Validated
Probab=48.96  E-value=13  Score=18.67  Aligned_cols=19  Identities=11%  Similarity=-0.015  Sum_probs=7.7

Q ss_pred             ECCCCCCEEEEEEEECCCC
Q ss_conf             8789978244046425778
Q gi|254780361|r   29 EDKKSGELRRPHHVDMKTG   47 (61)
Q Consensus        29 ~c~~cG~~~~~H~vc~~cG   47 (61)
                      .|..||.-......||+||
T Consensus       433 ~Ch~Cg~~~~~~~~Cp~Cg  451 (699)
T PRK05580        433 RCHHCGYQEPIPRACPECG  451 (699)
T ss_pred             ECCCCCCCCCCCCCCCCCC
T ss_conf             2264688365755465679


No 87 
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=48.93  E-value=15  Score=18.43  Aligned_cols=29  Identities=10%  Similarity=-0.024  Sum_probs=21.3

Q ss_pred             EEECCCCCCEEEE---EEEECCCCCCCCEEEE
Q ss_conf             7887899782440---4642577867687964
Q gi|254780361|r   27 YVEDKKSGELRRP---HHVDMKTGLYRGRQVF   55 (61)
Q Consensus        27 l~~c~~cG~~~~~---H~vc~~cG~YkGr~Vi   55 (61)
                      +..|++|+++...   -..||+||.---|++-
T Consensus       149 ~A~CsrC~~~L~~~~~~l~Cp~Cg~tEkRKia  180 (188)
T COG1096         149 YARCSRCRAPLVKKGNMLKCPNCGNTEKRKIA  180 (188)
T ss_pred             EEECCCCCCCEEECCCEEECCCCCCEEEEEEC
T ss_conf             99836777620884759988877987766422


No 88 
>PRK08620 DNA topoisomerase III; Provisional
Probab=48.92  E-value=12  Score=18.82  Aligned_cols=13  Identities=8%  Similarity=0.015  Sum_probs=6.5

Q ss_pred             CEEECCCCCCEEE
Q ss_conf             3788789978244
Q gi|254780361|r   26 AYVEDKKSGELRR   38 (61)
Q Consensus        26 ~l~~c~~cG~~~~   38 (61)
                      +-..||.||.+.+
T Consensus       608 t~~~Cp~Cg~~m~  620 (726)
T PRK08620        608 TGTKCPDCGKFML  620 (726)
T ss_pred             CCCCCCCCCCCCE
T ss_conf             8985642683211


No 89 
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=48.13  E-value=18  Score=18.00  Aligned_cols=34  Identities=21%  Similarity=0.309  Sum_probs=21.4

Q ss_pred             CEEECCCCCCEEE----------------EEEEECCCCCCCCEEEEEEECC
Q ss_conf             3788789978244----------------0464257786768796434236
Q gi|254780361|r   26 AYVEDKKSGELRR----------------PHHVDMKTGLYRGRQVFVLKTK   60 (61)
Q Consensus        26 ~l~~c~~cG~~~~----------------~H~vc~~cG~YkGr~Vi~~~~~   60 (61)
                      ....||.||..-.                .--+|-+|| ||-..|...++.
T Consensus        13 ~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~Cg-YR~~DV~~~e~~   62 (201)
T COG1779          13 TRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCG-YRSTDVKTLEER   62 (201)
T ss_pred             EEECCCCCCCEEEEEEEEECCCCCCEEEEEEEECCCCC-CCCCCEEECCCC
T ss_conf             35148855102168887413785551899999814468-843221543557


No 90 
>pfam12230 PRP21_like_P Pre-mRNA splicing factor PRP21 like protein. This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with pfam01805. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form.
Probab=48.06  E-value=11  Score=19.09  Aligned_cols=18  Identities=22%  Similarity=0.183  Sum_probs=12.7

Q ss_pred             CCCCCCEEECCCCCCEEE
Q ss_conf             026883788789978244
Q gi|254780361|r   21 ALTPPAYVEDKKSGELRR   38 (61)
Q Consensus        21 ~l~~p~l~~c~~cG~~~~   38 (61)
                      ....+.+.+||+||+...
T Consensus       156 ~~~~~~~~~cPitGq~IP  173 (223)
T pfam12230       156 RKTEAKMIKCPITGELIP  173 (223)
T ss_pred             CCCCCCEEECCCCCCCCC
T ss_conf             567888657787778177


No 91 
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family; InterPro: IPR013429    This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB . Most proteins in this entry have a C-terminal region containing highly degenerate sequence..
Probab=42.29  E-value=11  Score=19.17  Aligned_cols=20  Identities=5%  Similarity=-0.006  Sum_probs=14.9

Q ss_pred             HCCCCC-CEEECCCCCCEEEE
Q ss_conf             102688-37887899782440
Q gi|254780361|r   20 DALTPP-AYVEDKKSGELRRP   39 (61)
Q Consensus        20 ~~l~~p-~l~~c~~cG~~~~~   39 (61)
                      .+++.. .|..||.||+..+.
T Consensus        19 Qk~sD~~pl~~CP~C~~~~~~   39 (43)
T TIGR02605        19 QKISDEEPLTTCPACGGPALR   39 (43)
T ss_pred             ECCCCCCCCCCCCCCCCCCEE
T ss_conf             504775534478767876412


No 92 
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=41.94  E-value=14  Score=18.53  Aligned_cols=30  Identities=10%  Similarity=0.153  Sum_probs=22.7

Q ss_pred             CCCEEECCCCCC--EEEEEEEECCCCCCCCEE
Q ss_conf             883788789978--244046425778676879
Q gi|254780361|r   24 PPAYVEDKKSGE--LRRPHHVDMKTGLYRGRQ   53 (61)
Q Consensus        24 ~p~l~~c~~cG~--~~~~H~vc~~cG~YkGr~   53 (61)
                      ..+-+.|--||.  ++..-..|.+|||=+.+.
T Consensus        13 k~tH~~CRRCGr~syhv~k~~CaaCGfgrs~r   44 (61)
T COG2126          13 KKTHIRCRRCGRRSYHVRKKYCAACGFGRSAR   44 (61)
T ss_pred             CCCEEHHHHCCCHHEEECCCEECCCCCCCCCC
T ss_conf             84320243215401010165313568887610


No 93 
>pfam07754 DUF1610 Domain of unknown function (DUF1610). This zinc ribbon domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=41.82  E-value=8.7  Score=19.62  Aligned_cols=11  Identities=9%  Similarity=-0.020  Sum_probs=6.3

Q ss_pred             EEECCCCCCCC
Q ss_conf             64257786768
Q gi|254780361|r   41 HVDMKTGLYRG   51 (61)
Q Consensus        41 ~vc~~cG~YkG   51 (61)
                      .+||+|||...
T Consensus        11 y~CPnCGf~~~   21 (26)
T pfam07754        11 YPCPNCGFXXX   21 (26)
T ss_pred             CCCCCCCCCCC
T ss_conf             66898663012


No 94 
>KOG2907 consensus
Probab=41.32  E-value=9.7  Score=19.37  Aligned_cols=14  Identities=21%  Similarity=0.140  Sum_probs=9.0

Q ss_pred             EECCCCCCEEEEEE
Q ss_conf             88789978244046
Q gi|254780361|r   28 VEDKKSGELRRPHH   41 (61)
Q Consensus        28 ~~c~~cG~~~~~H~   41 (61)
                      -.||.||...+.-+
T Consensus        75 ~kCpkCghe~m~Y~   88 (116)
T KOG2907          75 HKCPKCGHEEMSYH   88 (116)
T ss_pred             CCCCCCCCCHHHHH
T ss_conf             01755698312155


No 95 
>PRK07219 DNA topoisomerase I; Validated
Probab=40.77  E-value=19  Score=17.85  Aligned_cols=28  Identities=4%  Similarity=-0.209  Sum_probs=17.2

Q ss_pred             CEEECCCCCCEEEE-------EEEEC--CCCCCCCEE
Q ss_conf             37887899782440-------46425--778676879
Q gi|254780361|r   26 AYVEDKKSGELRRP-------HHVDM--KTGLYRGRQ   53 (61)
Q Consensus        26 ~l~~c~~cG~~~~~-------H~vc~--~cG~YkGr~   53 (61)
                      .--.||.||.+.+-       -.+|+  .|+|.+..+
T Consensus       715 ~~e~Cp~Cg~~~~~~~~~~~~~~~C~~~~C~~~~~~~  751 (769)
T PRK07219        715 TGEKCPYCGAPILVLINGRRHWKFCPNIDCEYNKKGK  751 (769)
T ss_pred             CCCCCCCCCCEEEEEECCCCCEEECCCCCCCCCCCCC
T ss_conf             5884777898379997278430068998999853477


No 96 
>pfam09526 DUF2387 Probable metal-binding protein (DUF2387). Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=40.69  E-value=23  Score=17.40  Aligned_cols=27  Identities=11%  Similarity=-0.080  Sum_probs=18.4

Q ss_pred             CEEECCCCCCEE---------EEEEEECCCCCCCCE
Q ss_conf             378878997824---------404642577867687
Q gi|254780361|r   26 AYVEDKKSGELR---------RPHHVDMKTGLYRGR   52 (61)
Q Consensus        26 ~l~~c~~cG~~~---------~~H~vc~~cG~YkGr   52 (61)
                      +-..||.|++.-         ...+-|-+|||-..+
T Consensus         7 AGAvCP~C~~~D~i~~~~~~~~~~~eCV~Cg~~e~~   42 (61)
T pfam09526         7 AGAVCPKCSAMDTIRMWRENGVEYVECVSCGYTDQQ   42 (61)
T ss_pred             CCCCCCCCCCCCEEEEEECCCCEEEEECCCCCCCCC
T ss_conf             654189875653798872399469997789998126


No 97 
>PRK12495 hypothetical protein; Provisional
Probab=39.82  E-value=8.6  Score=19.64  Aligned_cols=28  Identities=11%  Similarity=-0.039  Sum_probs=20.5

Q ss_pred             CCCCCCEE--ECCCCCCEEEEEE---EECCCCC
Q ss_conf             02688378--8789978244046---4257786
Q gi|254780361|r   21 ALTPPAYV--EDKKSGELRRPHH---VDMKTGL   48 (61)
Q Consensus        21 ~l~~p~l~--~c~~cG~~~~~H~---vc~~cG~   48 (61)
                      -|..-++.  -|.+||.|+..|-   .||.|-.
T Consensus        34 LLqGATMTN~HC~~CGdPIFR~dGqeFCPTCQ~   66 (221)
T PRK12495         34 LLQGATMTNAHCDECGSPIFRHDGQEFCPTCQH   66 (221)
T ss_pred             HHCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCC
T ss_conf             973321021200223672340476614864235


No 98 
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=39.57  E-value=20  Score=17.69  Aligned_cols=27  Identities=7%  Similarity=-0.023  Sum_probs=17.5

Q ss_pred             CCEEECCCCCCEEEEE-EEECCCCCCCC
Q ss_conf             8378878997824404-64257786768
Q gi|254780361|r   25 PAYVEDKKSGELRRPH-HVDMKTGLYRG   51 (61)
Q Consensus        25 p~l~~c~~cG~~~~~H-~vc~~cG~YkG   51 (61)
                      .+.-.|.+||...-.- ==||+||-|+-
T Consensus         5 ~t~f~C~~CG~~s~KW~GkCp~Cg~Wns   32 (456)
T COG1066           5 KTAFVCQECGYVSPKWLGKCPACGAWNT   32 (456)
T ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             6278844578878621555988787431


No 99 
>pfam08792 A2L_zn_ribbon A2L zinc ribbon domain. This zinc ribbon domain is found associated with some viral A2L transcription factors.
Probab=39.55  E-value=13  Score=18.75  Aligned_cols=23  Identities=17%  Similarity=-0.021  Sum_probs=16.0

Q ss_pred             CEEECCCCCCEEE-----EEEEECCCCC
Q ss_conf             3788789978244-----0464257786
Q gi|254780361|r   26 AYVEDKKSGELRR-----PHHVDMKTGL   48 (61)
Q Consensus        26 ~l~~c~~cG~~~~-----~H~vc~~cG~   48 (61)
                      ++..|..||...+     .+.+|+.||.
T Consensus         2 ~~~~C~~C~~~~i~~~~~~~~~C~~Cg~   29 (33)
T pfam08792         2 NLKKCKYCGGNGIVNKEDDYEVCIFCGA   29 (33)
T ss_pred             CCCCCEECCCCCEECCCCCEEEEEEECC
T ss_conf             8240415178740115687689999667


No 100
>pfam02150 RNA_POL_M_15KD RNA polymerases M/15 Kd subunit.
Probab=38.98  E-value=9.1  Score=19.52  Aligned_cols=22  Identities=23%  Similarity=0.262  Sum_probs=16.5

Q ss_pred             EEECCCCCCEEEEEE------EECCCCC
Q ss_conf             788789978244046------4257786
Q gi|254780361|r   27 YVEDKKSGELRRPHH------VDMKTGL   48 (61)
Q Consensus        27 l~~c~~cG~~~~~H~------vc~~cG~   48 (61)
                      +..||.||..-+|-.      +|-+|||
T Consensus         1 l~FCp~C~NlL~~~~~k~~~~~Cr~C~y   28 (35)
T pfam02150         1 LIFCPKCGNLLLPKEDKEGRNACRQCGY   28 (35)
T ss_pred             CCCCHHHCCCCCCCCCHHHHHHHHHCCC
T ss_conf             9034000675355512120577860687


No 101
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.93  E-value=14  Score=18.60  Aligned_cols=36  Identities=28%  Similarity=0.258  Sum_probs=24.3

Q ss_pred             CEEECCCCCCEEEEEEEECCC---CCCCCEEEEEEECCC
Q ss_conf             378878997824404642577---867687964342369
Q gi|254780361|r   26 AYVEDKKSGELRRPHHVDMKT---GLYRGRQVFVLKTKE   61 (61)
Q Consensus        26 ~l~~c~~cG~~~~~H~vc~~c---G~YkGr~Vi~~~~~e   61 (61)
                      ....||.||++.-+-.+-.+.   |.|=.-.|++.++.|
T Consensus        48 G~t~CP~Cg~~~e~~fvva~~aLVgl~l~mkVFNaes~E   86 (115)
T COG1885          48 GSTSCPKCGEPFESAFVVANTALVGLILSMKVFNAESDE   86 (115)
T ss_pred             CCCCCCCCCCCCCEEEEEECCEEEEEEEEEEEECCCCHH
T ss_conf             655588779966317898062156889999983379978


No 102
>PRK11032 hypothetical protein; Provisional
Probab=38.53  E-value=19  Score=17.78  Aligned_cols=27  Identities=11%  Similarity=-0.123  Sum_probs=18.1

Q ss_pred             CCCCCEEECCCCCCEEEEEE-----EECCCCC
Q ss_conf             26883788789978244046-----4257786
Q gi|254780361|r   22 LTPPAYVEDKKSGELRRPHH-----VDMKTGL   48 (61)
Q Consensus        22 l~~p~l~~c~~cG~~~~~H~-----vc~~cG~   48 (61)
                      +..|..-.|-+||...--.+     .||.||.
T Consensus       119 ivg~G~LvC~~Cg~~~~~~~~~~ippCp~Cg~  150 (160)
T PRK11032        119 VVGLGNLVCEKCHHHLAFYTPEVLPLCPKCGH  150 (160)
T ss_pred             EEECCEEEHHHCCCEEEEECCCCCCCCCCCCC
T ss_conf             53255665742898778746877988877999


No 103
>pfam07295 DUF1451 Protein of unknown function (DUF1451). This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=38.17  E-value=24  Score=17.33  Aligned_cols=27  Identities=15%  Similarity=0.048  Sum_probs=17.7

Q ss_pred             CCCCCEEECCCCCCEEEEEE-----EECCCCC
Q ss_conf             26883788789978244046-----4257786
Q gi|254780361|r   22 LTPPAYVEDKKSGELRRPHH-----VDMKTGL   48 (61)
Q Consensus        22 l~~p~l~~c~~cG~~~~~H~-----vc~~cG~   48 (61)
                      +..+..-.|-+||...---+     .||.||.
T Consensus       109 vvg~G~LvC~~Cg~~~~~~~p~~ip~Cp~Cg~  140 (148)
T pfam07295       109 IVGLGTLVCENCGHMLTFYHPSVIPPCPKCGH  140 (148)
T ss_pred             EEECCEEEECCCCCEEEEECCCCCCCCCCCCC
T ss_conf             54164577236898788746876889877999


No 104
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308   These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=37.62  E-value=10  Score=19.25  Aligned_cols=12  Identities=25%  Similarity=0.249  Sum_probs=7.8

Q ss_pred             EEEEEEEECCCC
Q ss_conf             244046425778
Q gi|254780361|r   36 LRRPHHVDMKTG   47 (61)
Q Consensus        36 ~~~~H~vc~~cG   47 (61)
                      +=||+.-||.||
T Consensus       738 fDLp~K~CP~Cg  749 (1264)
T TIGR01405       738 FDLPDKDCPKCG  749 (1264)
T ss_pred             CCCCCCCCCCCC
T ss_conf             768578888888


No 105
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=37.52  E-value=18  Score=17.98  Aligned_cols=26  Identities=4%  Similarity=-0.159  Sum_probs=19.7

Q ss_pred             CCCCEEECCCCCC--EEEEEEEECCCCC
Q ss_conf             6883788789978--2440464257786
Q gi|254780361|r   23 TPPAYVEDKKSGE--LRRPHHVDMKTGL   48 (61)
Q Consensus        23 ~~p~l~~c~~cG~--~~~~H~vc~~cG~   48 (61)
                      ....+-.|++|+.  ....+-.|++||.
T Consensus        53 Ad~~i~kC~~c~~~~~y~~~~~C~~cg~   80 (415)
T COG5257          53 ADAKIYKCPECYRPECYTTEPKCPNCGA   80 (415)
T ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf             5574575777788766234787777899


No 106
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=37.51  E-value=15  Score=18.41  Aligned_cols=34  Identities=18%  Similarity=0.174  Sum_probs=21.8

Q ss_pred             CEEECCCCCCEEEEE--------------------EEECCCCCCCCEEEEEEECCC
Q ss_conf             378878997824404--------------------642577867687964342369
Q gi|254780361|r   26 AYVEDKKSGELRRPH--------------------HVDMKTGLYRGRQVFVLKTKE   61 (61)
Q Consensus        26 ~l~~c~~cG~~~~~H--------------------~vc~~cG~YkGr~Vi~~~~~e   61 (61)
                      ....|.-||..--|-                    .+||.||.  |+++++.-+.|
T Consensus       424 ~~~~c~vc~~~~~~~~~~~~~~~~~~~~~~~~p~~~~cp~c~~--g~~~f~~~~~~  477 (479)
T PRK05452        424 PRMQCSVCQWIYDPALGEPMQDVAPGTPWSEVPDNFLCPECSL--GKDVFDELASE  477 (479)
T ss_pred             CEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CHHHCEECHHC
T ss_conf             4489977204613544787655578872002874436876689--87761432200


No 107
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=37.33  E-value=12  Score=18.93  Aligned_cols=20  Identities=15%  Similarity=-0.047  Sum_probs=14.1

Q ss_pred             ECCCCCC------------EEEEEEEECCCCC
Q ss_conf             8789978------------2440464257786
Q gi|254780361|r   29 EDKKSGE------------LRRPHHVDMKTGL   48 (61)
Q Consensus        29 ~c~~cG~------------~~~~H~vc~~cG~   48 (61)
                      .||+|.-            +-||...||.||.
T Consensus       909 ~Cp~Cky~ef~~~g~~~sGyDLpdk~CP~Cg~  940 (1436)
T PRK00448        909 VCPNCKYSEFFTDGSVGSGYDLPDKDCPKCGT  940 (1436)
T ss_pred             CCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             57655400002466546577786566864343


No 108
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=36.57  E-value=17  Score=18.09  Aligned_cols=20  Identities=10%  Similarity=-0.037  Sum_probs=8.5

Q ss_pred             EECCCCCCEEEEEEEECCCC
Q ss_conf             88789978244046425778
Q gi|254780361|r   28 VEDKKSGELRRPHHVDMKTG   47 (61)
Q Consensus        28 ~~c~~cG~~~~~H~vc~~cG   47 (61)
                      -.|..||.....=..||+||
T Consensus       463 L~CH~Cg~~~~~p~~Cp~Cg  482 (730)
T COG1198         463 LRCHYCGYQEPIPQSCPECG  482 (730)
T ss_pred             EEECCCCCCCCCCCCCCCCC
T ss_conf             67077999899887798999


No 109
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=36.24  E-value=17  Score=18.13  Aligned_cols=23  Identities=9%  Similarity=-0.034  Sum_probs=11.8

Q ss_pred             ECCCCCCEEEE-EEEECCCCCCCC
Q ss_conf             87899782440-464257786768
Q gi|254780361|r   29 EDKKSGELRRP-HHVDMKTGLYRG   51 (61)
Q Consensus        29 ~c~~cG~~~~~-H~vc~~cG~YkG   51 (61)
                      .|.+||..... .==||+||-|+-
T Consensus         2 ~C~~CG~~~~kW~GkCp~Cg~WnT   25 (372)
T cd01121           2 VCSECGYVSPKWLGKCPECGEWNT   25 (372)
T ss_pred             CCCCCCCCCCCCCEECCCCCCCCC
T ss_conf             998899978872426979998643


No 110
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=35.67  E-value=18  Score=17.95  Aligned_cols=22  Identities=14%  Similarity=0.040  Sum_probs=10.6

Q ss_pred             CCCCCEEECCCCCCEEEEEEEE
Q ss_conf             2688378878997824404642
Q gi|254780361|r   22 LTPPAYVEDKKSGELRRPHHVD   43 (61)
Q Consensus        22 l~~p~l~~c~~cG~~~~~H~vc   43 (61)
                      +.....-.||.||...+.++++
T Consensus       148 ~f~~~~~~Cp~CG~~~~~~~~~  169 (177)
T COG1439         148 IFPEPKDFCPICGSPLKRKRVK  169 (177)
T ss_pred             ECCCCCCCCCCCCCCEEEEEEC
T ss_conf             5089888077899911785500


No 111
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=35.46  E-value=13  Score=18.69  Aligned_cols=25  Identities=8%  Similarity=0.038  Sum_probs=20.2

Q ss_pred             CCEEECCCCCC--EEEEEEEECCCCCC
Q ss_conf             83788789978--24404642577867
Q gi|254780361|r   25 PAYVEDKKSGE--LRRPHHVDMKTGLY   49 (61)
Q Consensus        25 p~l~~c~~cG~--~~~~H~vc~~cG~Y   49 (61)
                      .+-..|--||.  +++....|.+|||=
T Consensus        14 KtHtlCrrCG~~syH~QK~~Ca~CGyP   40 (89)
T PTZ00073         14 KTHTLCRRCGRRSFHIQKKRCASCGYP   40 (89)
T ss_pred             CCCCHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf             651476513862022120004203795


No 112
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid    transport and metabolism]
Probab=34.82  E-value=11  Score=19.11  Aligned_cols=21  Identities=10%  Similarity=-0.153  Sum_probs=9.7

Q ss_pred             EEECCCCCCEEEE------EEEECCCC
Q ss_conf             7887899782440------46425778
Q gi|254780361|r   27 YVEDKKSGELRRP------HHVDMKTG   47 (61)
Q Consensus        27 l~~c~~cG~~~~~------H~vc~~cG   47 (61)
                      +..|++||--..+      -.+||+||
T Consensus       315 ~nfc~ncG~~~t~~~~ng~a~fcp~cg  341 (345)
T COG4260         315 LNFCLNCGCGTTADFDNGKAKFCPECG  341 (345)
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHCHHHC
T ss_conf             550334686544687643002076545


No 113
>pfam06677 Auto_anti-p27 Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis.
Probab=33.50  E-value=25  Score=17.19  Aligned_cols=20  Identities=10%  Similarity=-0.200  Sum_probs=14.5

Q ss_pred             EECCCCCCEEEE----EEEECCCC
Q ss_conf             887899782440----46425778
Q gi|254780361|r   28 VEDKKSGELRRP----HHVDMKTG   47 (61)
Q Consensus        28 ~~c~~cG~~~~~----H~vc~~cG   47 (61)
                      ..||.||.+-..    -.+||+|+
T Consensus        18 ~~C~~Cg~pLf~~k~g~~~Cp~C~   41 (41)
T pfam06677        18 EHCPKCGTPLFRLKDGKVFCPSCE   41 (41)
T ss_pred             CCCCCCCCEEEECCCCCEECCCCC
T ss_conf             325456983058489999578779


No 114
>pfam01873 eIF-5_eIF-2B Domain found in IF2B/IF5. This family includes the N terminus of eIF-5, and the C terminus of eIF-2 beta. This region corresponds to the whole of the archaebacterial eIF-2 beta homologue. The region contains a putative zinc binding C4 finger.
Probab=33.00  E-value=37  Score=16.31  Aligned_cols=25  Identities=12%  Similarity=-0.052  Sum_probs=16.6

Q ss_pred             CCCEEECCCCCCEEEE--------EEEECCCCC
Q ss_conf             8837887899782440--------464257786
Q gi|254780361|r   24 PPAYVEDKKSGELRRP--------HHVDMKTGL   48 (61)
Q Consensus        24 ~p~l~~c~~cG~~~~~--------H~vc~~cG~   48 (61)
                      ....+.|++|+.+-..        --.|..||-
T Consensus        90 I~~yVlC~~C~sPdT~l~k~~r~~~l~C~aCGa  122 (125)
T pfam01873        90 IKEYVLCHECKSPDTELIKENRLIFLKCKACGA  122 (125)
T ss_pred             HHHEEECCCCCCCCEEEEEECCEEEEECCCCCC
T ss_conf             876799999999720899938828998456699


No 115
>PRK00418 zinc-binding protein; Reviewed
Probab=32.54  E-value=26  Score=17.09  Aligned_cols=16  Identities=19%  Similarity=0.220  Sum_probs=12.7

Q ss_pred             CCCCEEECCCCCCEEE
Q ss_conf             6883788789978244
Q gi|254780361|r   23 TPPAYVEDKKSGELRR   38 (61)
Q Consensus        23 ~~p~l~~c~~cG~~~~   38 (61)
                      +.|..+.||+||....
T Consensus         2 ~~~~~V~CP~C~~~v~   17 (62)
T PRK00418          2 SEPITVNCPTCGKPVE   17 (62)
T ss_pred             CCCCEEECCCCCCCCC
T ss_conf             9972747989989544


No 116
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer.  Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain.  Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.98  E-value=22  Score=17.46  Aligned_cols=20  Identities=15%  Similarity=-0.052  Sum_probs=13.9

Q ss_pred             ECCCCCCEEE---EEEEECCCCC
Q ss_conf             8789978244---0464257786
Q gi|254780361|r   29 EDKKSGELRR---PHHVDMKTGL   48 (61)
Q Consensus        29 ~c~~cG~~~~---~H~vc~~cG~   48 (61)
                      .|+.||....   +.-+||.||.
T Consensus         3 ~C~vCGyi~~~~~~p~~CP~Cg~   25 (33)
T cd00350           3 VCPVCGYIYDGEEAPWVCPVCGA   25 (33)
T ss_pred             CCCCCCCEEECCCCCCCCCCCCC
T ss_conf             88869988757869872878899


No 117
>pfam09567 RE_MamI MamI restriction endonuclease. This family includes the MamI (recognizes and cleaves GATNN^NNATC) restriction endonuclease.
Probab=31.71  E-value=11  Score=19.17  Aligned_cols=25  Identities=4%  Similarity=-0.193  Sum_probs=18.8

Q ss_pred             CCEEECCCCCCEEE-EEEEECCCCCC
Q ss_conf             83788789978244-04642577867
Q gi|254780361|r   25 PAYVEDKKSGELRR-PHHVDMKTGLY   49 (61)
Q Consensus        25 p~l~~c~~cG~~~~-~H~vc~~cG~Y   49 (61)
                      -++-.|.+||+-.+ ----||+||--
T Consensus        86 DQLg~C~~Cgs~V~~lE~eCPsCgSt  111 (350)
T pfam09567        86 DQLGKCNDCGSEVKALELECPSCAAA  111 (350)
T ss_pred             HHHCCCCCCCHHHHHHHHCCCCCCCC
T ss_conf             44110000013565565228766654


No 118
>PRK11823 DNA repair protein RadA; Provisional
Probab=31.61  E-value=38  Score=16.28  Aligned_cols=28  Identities=7%  Similarity=-0.089  Sum_probs=18.1

Q ss_pred             CCEEECCCCCCEEEEE-EEECCCCCCCCE
Q ss_conf             8378878997824404-642577867687
Q gi|254780361|r   25 PAYVEDKKSGELRRPH-HVDMKTGLYRGR   52 (61)
Q Consensus        25 p~l~~c~~cG~~~~~H-~vc~~cG~YkGr   52 (61)
                      ...-.|.+||.....- ==||+||-|+-=
T Consensus         5 k~~y~C~~CG~~~~kW~GkCp~C~~WnTl   33 (454)
T PRK11823          5 KTAYVCQECGAESPKWLGRCPACGAWNTL   33 (454)
T ss_pred             CCEEECCCCCCCCCCCCEECCCCCCCCCE
T ss_conf             87179988999788714358798986458


No 119
>pfam01927 DUF82 Protein of unknown function DUF82. This prokaryotic protein family has no known function. The protein contains four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=30.64  E-value=29  Score=16.91  Aligned_cols=29  Identities=17%  Similarity=0.235  Sum_probs=19.3

Q ss_pred             CCEEECCCCCCEEE--------------------EEEEECCCC--CCCCEE
Q ss_conf             83788789978244--------------------046425778--676879
Q gi|254780361|r   25 PAYVEDKKSGELRR--------------------PHHVDMKTG--LYRGRQ   53 (61)
Q Consensus        25 p~l~~c~~cG~~~~--------------------~H~vc~~cG--~YkGr~   53 (61)
                      |.++.|+.|+..-.                    .-..|+.||  |+.|-.
T Consensus        88 ~~~sRC~~CN~~L~~v~k~~v~~~vp~~v~~~~~~F~~C~~CgkvYW~GsH  138 (146)
T pfam01927        88 PEFSRCLKCNGPLEPVSKEEVAGRVPPYVYERYDEFWRCPKCGRVYWKGSH  138 (146)
T ss_pred             CCCCCCCCCCCCCEECCHHHHHHHCCCHHHHCCCCEEECCCCCCEECCCCC
T ss_conf             777856567989958187898545672022258814778999998148715


No 120
>TIGR00612 ispG_gcpE 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; InterPro: IPR004588   This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.; GO: 0016114 terpenoid biosynthetic process.
Probab=30.56  E-value=28  Score=16.98  Aligned_cols=15  Identities=13%  Similarity=-0.002  Sum_probs=11.3

Q ss_pred             CCCCCCEEECCCCCC
Q ss_conf             026883788789978
Q gi|254780361|r   21 ALTPPAYVEDKKSGE   35 (61)
Q Consensus        21 ~l~~p~l~~c~~cG~   35 (61)
                      +...+.++.||.||-
T Consensus       525 R~~~v~~vaCP~CGR  539 (633)
T TIGR00612       525 RKRGVEIVACPSCGR  539 (633)
T ss_pred             CCCCCEEEECCCCCC
T ss_conf             756737887888987


No 121
>PRK11788 hypothetical protein; Provisional
Probab=30.43  E-value=35  Score=16.43  Aligned_cols=29  Identities=10%  Similarity=-0.045  Sum_probs=20.4

Q ss_pred             CCCCCCEEECCCCCCEEEEEE-EECCCCCC
Q ss_conf             026883788789978244046-42577867
Q gi|254780361|r   21 ALTPPAYVEDKKSGELRRPHH-VDMKTGLY   49 (61)
Q Consensus        21 ~l~~p~l~~c~~cG~~~~~H~-vc~~cG~Y   49 (61)
                      .+.....-.|.+||-....|+ -||.|..+
T Consensus       348 ~~~~~~~Y~C~~CGF~~~~~~WqCPsC~~W  377 (389)
T PRK11788        348 QLKRKPRYRCRNCGFTARTLYWHCPSCKAW  377 (389)
T ss_pred             HHHCCCCEECCCCCCCCCCEEEECCCCCCC
T ss_conf             971799976999999888314579099986


No 122
>PRK12496 hypothetical protein; Provisional
Probab=30.16  E-value=23  Score=17.38  Aligned_cols=21  Identities=19%  Similarity=0.067  Sum_probs=14.8

Q ss_pred             EECCCCCCEEE---EEEEECCCCC
Q ss_conf             88789978244---0464257786
Q gi|254780361|r   28 VEDKKSGELRR---PHHVDMKTGL   48 (61)
Q Consensus        28 ~~c~~cG~~~~---~H~vc~~cG~   48 (61)
                      -.|+.||...-   +--.||.||.
T Consensus       130 ~~C~gC~~~~~~~~~~~~C~~CGs  153 (166)
T PRK12496        130 YVCKGCKKMYPENYPDEVCDVCGS  153 (166)
T ss_pred             EECCCCCCCCCCCCCCCCCCCCCC
T ss_conf             999987871778899883878898


No 123
>KOG3352 consensus
Probab=30.03  E-value=17  Score=18.15  Aligned_cols=12  Identities=17%  Similarity=0.124  Sum_probs=7.9

Q ss_pred             ECCCCC-CCCEEE
Q ss_conf             257786-768796
Q gi|254780361|r   43 DMKTGL-YRGRQV   54 (61)
Q Consensus        43 c~~cG~-YkGr~V   54 (61)
                      ||.||. |+...|
T Consensus       136 c~eCG~~fkL~~v  148 (153)
T KOG3352         136 CPECGHYFKLVPV  148 (153)
T ss_pred             CCCCCCEEEEEEC
T ss_conf             8766566885445


No 124
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=29.94  E-value=39  Score=16.19  Aligned_cols=25  Identities=16%  Similarity=-0.044  Sum_probs=16.5

Q ss_pred             CCCEEECCCCCCEE--------EEEEEECCCCC
Q ss_conf             88378878997824--------40464257786
Q gi|254780361|r   24 PPAYVEDKKSGELR--------RPHHVDMKTGL   48 (61)
Q Consensus        24 ~p~l~~c~~cG~~~--------~~H~vc~~cG~   48 (61)
                      ....+.|++|+.|-        +-.-.|..||-
T Consensus        77 I~~yVlC~~C~~pdT~l~k~~r~~~l~C~aCGa  109 (110)
T smart00653       77 IKEYVLCPECGSPDTELIKENRLFFLKCEACGA  109 (110)
T ss_pred             HHHEEECCCCCCCCEEEEEECCCEEEECCCCCC
T ss_conf             854899999989722999938908998603389


No 125
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=29.57  E-value=32  Score=16.64  Aligned_cols=25  Identities=20%  Similarity=-0.035  Sum_probs=18.0

Q ss_pred             CCCEEECCCCCCEEEEE---EEECCCCC
Q ss_conf             88378878997824404---64257786
Q gi|254780361|r   24 PPAYVEDKKSGELRRPH---HVDMKTGL   48 (61)
Q Consensus        24 ~p~l~~c~~cG~~~~~H---~vc~~cG~   48 (61)
                      .|....|.+|+.+..+.   ..||.||-
T Consensus        67 ~p~~~~C~~C~~~~~~e~~~~~CP~C~s   94 (115)
T COG0375          67 EPAECWCLDCGQEVELEELDYRCPKCGS   94 (115)
T ss_pred             ECCEEEECCCCCEECCHHHEEECCCCCC
T ss_conf             0447894239976021553108889999


No 126
>pfam04551 GcpE GcpE protein. In a variety of organisms, including plants and several eubacteria, isoprenoids are synthesized by the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Although different enzymes of this pathway have been described, the terminal biosynthetic steps of the MEP pathway have not been fully elucidated. GcpE gene of Escherichia coli is involved in this pathway.
Probab=29.27  E-value=26  Score=17.11  Aligned_cols=14  Identities=7%  Similarity=0.029  Sum_probs=11.1

Q ss_pred             CCCCEEECCCCCCE
Q ss_conf             68837887899782
Q gi|254780361|r   23 TPPAYVEDKKSGEL   36 (61)
Q Consensus        23 ~~p~l~~c~~cG~~   36 (61)
                      ..|.++.||.||-.
T Consensus       252 ~g~~iISCPtCGR~  265 (345)
T pfam04551       252 RGVEIISCPTCGRT  265 (345)
T ss_pred             CCCEEEECCCCCCC
T ss_conf             78648758874661


No 127
>TIGR02443 TIGR02443 conserved hypothetical protein; InterPro: IPR012658   Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria..
Probab=28.71  E-value=31  Score=16.74  Aligned_cols=25  Identities=8%  Similarity=-0.144  Sum_probs=18.5

Q ss_pred             CEEECCCCCC---------EEEEEEEECCCCCCC
Q ss_conf             3788789978---------244046425778676
Q gi|254780361|r   26 AYVEDKKSGE---------LRRPHHVDMKTGLYR   50 (61)
Q Consensus        26 ~l~~c~~cG~---------~~~~H~vc~~cG~Yk   50 (61)
                      +=..||.|++         --..+.=|-.|||-.
T Consensus         8 AGA~CP~C~~~D~l~~W~EN~i~~VECV~Cgy~~   41 (63)
T TIGR02443         8 AGAKCPACSAQDTLAMWKENNIELVECVECGYQE   41 (63)
T ss_pred             CCCCCCCCCCCCCEEEECCCCCCEEEEECCCCCC
T ss_conf             5672888887454000201897726631588512


No 128
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=28.67  E-value=30  Score=16.77  Aligned_cols=31  Identities=16%  Similarity=0.121  Sum_probs=20.3

Q ss_pred             HHHCCCCCCEEECCCCCCE----EEEEE---EECCCCC
Q ss_conf             2310268837887899782----44046---4257786
Q gi|254780361|r   18 SADALTPPAYVEDKKSGEL----RRPHH---VDMKTGL   48 (61)
Q Consensus        18 sh~~l~~p~l~~c~~cG~~----~~~H~---vc~~cG~   48 (61)
                      .+..+....+..||+|+-.    .+.+.   .||-||.
T Consensus         9 ~~~~~~~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~   46 (418)
T COG2995           9 ITEELPPGHLILCPECDMLVSLPRLDSGQSAYCPRCGH   46 (418)
T ss_pred             CCCCCCCCCEECCCCCCCEECCCCCCCCCCCCCCCCCC
T ss_conf             44557961440577778553146678777006998788


No 129
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA; InterPro: IPR004624   This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage . This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA ..
Probab=28.60  E-value=24  Score=17.28  Aligned_cols=23  Identities=13%  Similarity=-0.031  Sum_probs=17.3

Q ss_pred             EEECCCCCCEEEEEE----EECCCCCC
Q ss_conf             788789978244046----42577867
Q gi|254780361|r   27 YVEDKKSGELRRPHH----VDMKTGLY   49 (61)
Q Consensus        27 l~~c~~cG~~~~~H~----vc~~cG~Y   49 (61)
                      +-.||.|...-..|-    +||.|||-
T Consensus         2 ~p~cpkc~~~y~y~d~~~~~cp~c~~e   28 (111)
T TIGR00686         2 LPPCPKCNSEYTYHDGGNLICPDCGYE   28 (111)
T ss_pred             CCCCCCCCCCEEEECCCEEECCCCCCC
T ss_conf             888888775414306850332200122


No 130
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=28.41  E-value=17  Score=18.09  Aligned_cols=18  Identities=17%  Similarity=0.087  Sum_probs=7.3

Q ss_pred             CCCCCCEEEEEE-EECCCC
Q ss_conf             789978244046-425778
Q gi|254780361|r   30 DKKSGELRRPHH-VDMKTG   47 (61)
Q Consensus        30 c~~cG~~~~~H~-vc~~cG   47 (61)
                      |.+|+-..-.-. +||.||
T Consensus         7 C~~Ck~l~~~d~e~CP~Cg   25 (64)
T COG2093           7 CKNCKRLTPEDTEICPVCG   25 (64)
T ss_pred             HHHCCCCCCCCCCCCCCCC
T ss_conf             7634623788774087889


No 131
>pfam06044 DRP Dam-replacing family. Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis.
Probab=28.31  E-value=23  Score=17.39  Aligned_cols=21  Identities=5%  Similarity=-0.263  Sum_probs=14.9

Q ss_pred             EEECCCCCCEEEEEE---------EECCCC
Q ss_conf             788789978244046---------425778
Q gi|254780361|r   27 YVEDKKSGELRRPHH---------VDMKTG   47 (61)
Q Consensus        27 l~~c~~cG~~~~~H~---------vc~~cG   47 (61)
                      -+.||+||...+.+.         .|++|-
T Consensus        31 n~yCP~Cg~~~l~~~~NN~PVaDFyC~~C~   60 (254)
T pfam06044        31 QGYCPNCGSNPLSRFANNQPVADFYCPNCH   60 (254)
T ss_pred             CCCCCCCCCCHHHHCCCCCCCCEEECCCCC
T ss_conf             687998897221223379923303547740


No 132
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=28.16  E-value=28  Score=16.97  Aligned_cols=15  Identities=13%  Similarity=0.173  Sum_probs=11.4

Q ss_pred             CCCCCEEECCCCCCE
Q ss_conf             268837887899782
Q gi|254780361|r   22 LTPPAYVEDKKSGEL   36 (61)
Q Consensus        22 l~~p~l~~c~~cG~~   36 (61)
                      -..+.++.||.||-.
T Consensus       262 ~~g~~iISCPtCGRt  276 (367)
T PRK00366        262 SRGPNVISCPTCGRT  276 (367)
T ss_pred             CCCCEEEECCCCCCC
T ss_conf             368517658875553


No 133
>PRK06260 threonine synthase; Validated
Probab=28.12  E-value=26  Score=17.10  Aligned_cols=20  Identities=10%  Similarity=-0.074  Sum_probs=12.6

Q ss_pred             EECCCCCCEEE---EEEEECCCC
Q ss_conf             88789978244---046425778
Q gi|254780361|r   28 VEDKKSGELRR---PHHVDMKTG   47 (61)
Q Consensus        28 ~~c~~cG~~~~---~H~vc~~cG   47 (61)
                      -.|..||..--   ....||.||
T Consensus         4 L~C~~CG~~~~~~~~~~~Cp~Cg   26 (400)
T PRK06260          4 LKCIECGAEYDPDEIIYTCPECG   26 (400)
T ss_pred             EECCCCCCCCCCCCCCCCCCCCC
T ss_conf             99799989589977675688789


No 134
>TIGR00107 deoD purine nucleoside phosphorylase; InterPro: IPR004402 Purine nucleoside phosphorylase 2.4.2.1 from EC also called inosine phosphorylase (pnp) cleave guanosine or inosine to respective bases and sugar-1-phosphate molecules. These enzymes are involved in the salvage of nucleotides and nucleosides.; GO: 0004731 purine-nucleoside phosphorylase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=27.91  E-value=23  Score=17.36  Aligned_cols=12  Identities=33%  Similarity=0.628  Sum_probs=9.4

Q ss_pred             CCCCCCCCEEEE
Q ss_conf             577867687964
Q gi|254780361|r   44 MKTGLYRGRQVF   55 (61)
Q Consensus        44 ~~cG~YkGr~Vi   55 (61)
                      ...|.||||.|=
T Consensus        44 gFTG~YKGk~Is   55 (234)
T TIGR00107        44 GFTGTYKGKKIS   55 (234)
T ss_pred             CCCCCCCCCEEE
T ss_conf             301110463588


No 135
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=27.27  E-value=33  Score=16.56  Aligned_cols=22  Identities=9%  Similarity=-0.164  Sum_probs=14.7

Q ss_pred             EEECCCCCCEEE-----EEEEECCCCC
Q ss_conf             788789978244-----0464257786
Q gi|254780361|r   27 YVEDKKSGELRR-----PHHVDMKTGL   48 (61)
Q Consensus        27 l~~c~~cG~~~~-----~H~vc~~cG~   48 (61)
                      +=.|..||....     +--.||.||+
T Consensus         6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~   32 (49)
T COG1996           6 EYKCARCGREVELDQETRGIRCPYCGS   32 (49)
T ss_pred             EEEHHHCCCEEEHHHCCCCEECCCCCC
T ss_conf             999345588500010357445798885


No 136
>pfam04035 consensus
Probab=26.90  E-value=30  Score=16.78  Aligned_cols=27  Identities=15%  Similarity=0.146  Sum_probs=13.8

Q ss_pred             CCCCCCEEEEEEEECCCCC------CCCEEEEE
Q ss_conf             7899782440464257786------76879643
Q gi|254780361|r   30 DKKSGELRRPHHVDMKTGL------YRGRQVFV   56 (61)
Q Consensus        30 c~~cG~~~~~H~vc~~cG~------YkGr~Vi~   56 (61)
                      |.+|....-.-.+||.||.      +.|..||.
T Consensus         4 C~~C~~i~~~~~~Cp~Cgs~~~s~dW~G~viI~   36 (60)
T pfam04035         4 CKNCKRLTEEDTTCPVCGSEDLTEEWFGLVIII   36 (60)
T ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEE
T ss_conf             423972789998188983987877613599996


No 137
>TIGR02772 Ku_bact Ku protein; InterPro: IPR009187   This superfamily consists of prokaryotic Ku domain containing proteins. In the eukaryotes it has been shown that the Ku protein is involved in repairing DNA double-strand breaks by non-homologous end-joining , . The Ku protein is a heterodimer of approximately 70 kDa and 80 kDa subunits . Both these subunits have strong sequence similarity and it has been suggested that they may have evolved by gene duplication from a homodimeric ancestor in eukaryotes . The prokaryotic Ku members are homodimers and they have been predicted to be involved in the DNA repair system, which is mechanistically similar to eukaryotic non-homologous end joining , . Recent findings have implicated yeast Ku in telomeric structure maintenance in addition to on-homologous end-joining. Some of the phenotypes of the Ku-knockout mice may indicate a similar role for Ku at mammalian telomeres .   Evolutionary notes: With current available phyletic information it is difficult to determine the correct evolutionary trajectory of the Ku domain. It is possible that the core Ku domain was present in bacteria and archaea even before the presence of the eukaryotes. Eukaryotes might have vertically inherited the Ku-core protein, from a common ancestor shared with a certain archaeal lineage or through horizontal transfer from bacteria. Alternatively, the core Ku domain could have evolved in the eukaryotic lineage and then horizontally transferred to the prokaryotes. Sequencing of additional archaeal genomes and those of early-branching eukaryotes may help resolving the evolutionary history of the Ku domain.   Structure notes: The eukaryotic Ku heterodimer comprises an alpha/beta N-terminal, a central beta-barrel domain and a helical C-terminal arm . Structural analysis of the Ku70/80 heterodimer bound to DNA indicate that subunit contacts lead to the formation of a highly charged channel through which the DNA passes without making any contacts with the DNA bases .  For additional information please see ..
Probab=26.58  E-value=28  Score=16.99  Aligned_cols=20  Identities=30%  Similarity=0.375  Sum_probs=16.6

Q ss_pred             ECCCCCCEEEEEEEECCCCC
Q ss_conf             87899782440464257786
Q gi|254780361|r   29 EDKKSGELRRPHHVDMKTGL   48 (61)
Q Consensus        29 ~c~~cG~~~~~H~vc~~cG~   48 (61)
                      ....||.+...++||+.||=
T Consensus        35 l~~~~~~rv~y~~V~~~tG~   54 (271)
T TIGR02772        35 LHREDGNRVRYRKVDEETGK   54 (271)
T ss_pred             CCHHHCCCCCEEEECCCCCC
T ss_conf             30402895231630652375


No 138
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.56  E-value=41  Score=16.10  Aligned_cols=24  Identities=17%  Similarity=-0.118  Sum_probs=16.8

Q ss_pred             CCEEECCCCCCEEEEEE-----EECCCCC
Q ss_conf             83788789978244046-----4257786
Q gi|254780361|r   25 PAYVEDKKSGELRRPHH-----VDMKTGL   48 (61)
Q Consensus        25 p~l~~c~~cG~~~~~H~-----vc~~cG~   48 (61)
                      -..-.||.||.....--     .|..||+
T Consensus        33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~   61 (89)
T COG1997          33 RAKHVCPFCGRTTVKRIATGIWKCRKCGA   61 (89)
T ss_pred             HCCCCCCCCCCCCEEEECCCEEECCCCCC
T ss_conf             54776997897404552367587178887


No 139
>COG4640 Predicted membrane protein [Function unknown]
Probab=26.53  E-value=27  Score=17.04  Aligned_cols=21  Identities=14%  Similarity=-0.009  Sum_probs=12.6

Q ss_pred             EECCCCCCEEE-EEEEECCCCC
Q ss_conf             88789978244-0464257786
Q gi|254780361|r   28 VEDKKSGELRR-PHHVDMKTGL   48 (61)
Q Consensus        28 ~~c~~cG~~~~-~H~vc~~cG~   48 (61)
                      -.||+||.-.. ----|+.||.
T Consensus         2 ~fC~kcG~qk~Ed~~qC~qCG~   23 (465)
T COG4640           2 KFCPKCGSQKAEDDVQCTQCGH   23 (465)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCC
T ss_conf             7664446532345500111488


No 140
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=26.50  E-value=37  Score=16.31  Aligned_cols=38  Identities=21%  Similarity=0.236  Sum_probs=24.9

Q ss_pred             HCCCCHHHHHCCCCCC-EEECCCCCCEE----EEEEEECCCCC
Q ss_conf             0017412231026883-78878997824----40464257786
Q gi|254780361|r   11 SKRGMRRSADALTPPA-YVEDKKSGELR----RPHHVDMKTGL   48 (61)
Q Consensus        11 sr~~~RRsh~~l~~p~-l~~c~~cG~~~----~~H~vc~~cG~   48 (61)
                      -+++-|++-..++.-. +..|+.||+..    -.-.=||.||.
T Consensus       223 v~rga~~ad~~~e~~g~~~~c~~cg~~~~~~~~~~~~c~~Cg~  265 (380)
T COG1867         223 VRRGARRADKLLENLGYIYHCSRCGEIVGSFREVDEKCPHCGG  265 (380)
T ss_pred             ECCCCHHHHHHHHHCCCEEECCCCCCEECCCCCCCCCCCCCCC
T ss_conf             8147305778997547078826641000355544455776665


No 141
>pfam10005 DUF2248 Uncharacterized protein conserved in bacteria (DUF2248). Members of this family of hypothetical bacterial proteins have no known function.
Probab=26.42  E-value=33  Score=16.58  Aligned_cols=19  Identities=11%  Similarity=-0.012  Sum_probs=8.8

Q ss_pred             CCCCCCEEEE-EEEECCCCC
Q ss_conf             7899782440-464257786
Q gi|254780361|r   30 DKKSGELRRP-HHVDMKTGL   48 (61)
Q Consensus        30 c~~cG~~~~~-H~vc~~cG~   48 (61)
                      |++||...-= -..|.+||.
T Consensus         2 C~~Cg~~vfFeN~~C~~Cg~   21 (340)
T pfam10005         2 CPNCGQPVFFENTACLACGA   21 (340)
T ss_pred             CCCCCCCEEECCCCCCCCCC
T ss_conf             87789902677875366895


No 142
>pfam09889 DUF2116 Uncharacterized protein containing a Zn-ribbon (DUF2116). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=26.39  E-value=21  Score=17.61  Aligned_cols=10  Identities=30%  Similarity=0.487  Sum_probs=5.0

Q ss_pred             EEEEECCCCC
Q ss_conf             0464257786
Q gi|254780361|r   39 PHHVDMKTGL   48 (61)
Q Consensus        39 ~H~vc~~cG~   48 (61)
                      ||+-|++||.
T Consensus         2 pHkHC~vCG~   11 (59)
T pfam09889         2 PHKHCIVCGT   11 (59)
T ss_pred             CCCCCCCCCC
T ss_conf             9853565799


No 143
>TIGR00368 TIGR00368 Mg chelatase homolog; InterPro: IPR004482   This family of bacterial proteins are variously described as 'hypothetical protein yifB', 'competence protein', 'hypothetical protein' or 'Mg chelatase-related protein'. These proteins are a subset of the magnesium chelatase, ChlI subunit family and either belong to or show significant homology to the non-peptidase homologs of the MEROPS peptidase family S16 (lon protease family, clan SF), IPR001984 from INTERPRO. .
Probab=26.11  E-value=25  Score=17.22  Aligned_cols=22  Identities=32%  Similarity=0.457  Sum_probs=8.5

Q ss_pred             HHCCCCCCEE---ECCCCCCEEEEE
Q ss_conf             3102688378---878997824404
Q gi|254780361|r   19 ADALTPPAYV---EDKKSGELRRPH   40 (61)
Q Consensus        19 h~~l~~p~l~---~c~~cG~~~~~H   40 (61)
                      ||.++.+.|+   .-|.=||..|.|
T Consensus       274 HHsAS~~~lvGGG~~P~PGEiSLAh  298 (505)
T TIGR00368       274 HHSASKPALVGGGSIPKPGEISLAH  298 (505)
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEHHC
T ss_conf             5002566640587522285120200


No 144
>cd00789 KU_like Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku homologs are predicted to form homodimers. It is proposed that the Ku homologs are functionally associated with ATP-dependent DNA ligase and the eukaryotic-type primase, probably as components of a double-strand break repair system.
Probab=26.04  E-value=55  Score=15.43  Aligned_cols=19  Identities=37%  Similarity=0.317  Sum_probs=16.2

Q ss_pred             ECCCCCCEEEEEEEECCCC
Q ss_conf             8789978244046425778
Q gi|254780361|r   29 EDKKSGELRRPHHVDMKTG   47 (61)
Q Consensus        29 ~c~~cG~~~~~H~vc~~cG   47 (61)
                      ....||...+..+||+.||
T Consensus        33 lh~~~~~rIry~~vc~~~g   51 (256)
T cd00789          33 LHKKDGARIRYQRVCPETG   51 (256)
T ss_pred             EECCCCCCEEEEEECCCCC
T ss_conf             4457798110588778779


No 145
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=25.49  E-value=30  Score=16.81  Aligned_cols=10  Identities=20%  Similarity=0.195  Sum_probs=7.9

Q ss_pred             CEEECCCCCC
Q ss_conf             3788789978
Q gi|254780361|r   26 AYVEDKKSGE   35 (61)
Q Consensus        26 ~l~~c~~cG~   35 (61)
                      .|+.||.||+
T Consensus         2 lLI~CP~Cg~   11 (97)
T COG4311           2 LLIPCPYCGE   11 (97)
T ss_pred             CEECCCCCCC
T ss_conf             5001898887


No 146
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.40  E-value=29  Score=16.84  Aligned_cols=21  Identities=10%  Similarity=-0.042  Sum_probs=16.1

Q ss_pred             EECCCCCCEE----------EEEEEECCCCC
Q ss_conf             8878997824----------40464257786
Q gi|254780361|r   28 VEDKKSGELR----------RPHHVDMKTGL   48 (61)
Q Consensus        28 ~~c~~cG~~~----------~~H~vc~~cG~   48 (61)
                      ..||-|+...          ...-.|++||+
T Consensus        31 ~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~   61 (129)
T COG3677          31 VNCPRCKSSNVVKIGGIRRGHQRYKCKSCGS   61 (129)
T ss_pred             CCCCCCCCCCEEEECCCCCCCCCCCCCCCCC
T ss_conf             7689888511023777426652535687586


No 147
>KOG0506 consensus
Probab=25.15  E-value=15  Score=18.43  Aligned_cols=31  Identities=19%  Similarity=0.003  Sum_probs=25.1

Q ss_pred             HCCCCCCEEECCCCCCEEEEEEEEC-------CCCCCC
Q ss_conf             1026883788789978244046425-------778676
Q gi|254780361|r   20 DALTPPAYVEDKKSGELRRPHHVDM-------KTGLYR   50 (61)
Q Consensus        20 ~~l~~p~l~~c~~cG~~~~~H~vc~-------~cG~Yk   50 (61)
                      .+.+..+-.+||-+||-.+.-+.|-       +||+|.
T Consensus       382 MAaTLANGGvcPit~E~~l~~~~cRdtLSLMySCGMYD  419 (622)
T KOG0506         382 MAATLANGGVCPITGERCLSPRACRDTLSLMYSCGMYD  419 (622)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCC
T ss_conf             99997538837787770368377778999987526622


No 148
>KOG1705 consensus
Probab=25.05  E-value=38  Score=16.25  Aligned_cols=29  Identities=21%  Similarity=0.225  Sum_probs=21.5

Q ss_pred             EECCCCCCEEEEE---EEECCCC--CCCCEEEEE
Q ss_conf             8878997824404---6425778--676879643
Q gi|254780361|r   28 VEDKKSGELRRPH---HVDMKTG--LYRGRQVFV   56 (61)
Q Consensus        28 ~~c~~cG~~~~~H---~vc~~cG--~YkGr~Vi~   56 (61)
                      ..||.|-.+.+|-   |+|.+|.  -|-++-||-
T Consensus        28 gkC~ICDS~VRP~tlVRiC~eC~~Gs~q~~ciic   61 (110)
T KOG1705          28 GKCVICDSYVRPCTLVRICDECNYGSYQGRCVIC   61 (110)
T ss_pred             CCCCCCCCCCCCCCEEEEEHHCCCCCCCCCEEEE
T ss_conf             9775334654653023330112764325643674


No 149
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF; InterPro: IPR004421   The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . Members of the HypF family are accessory proteins involved in hydrogenase maturation. They contain the following domains: acylphosphatase, zinc fingers (2 repeats), a YrdC-like domain, and a C-terminal domain with a putative O-carbamoyltransferase motif.   The presence of CO and CN- ligands of the active site iron atoms is essential for [NiFe]-hydrogenase enzyme activity . Both ligands have been suggested to originate from carbamoylphosphate , which is required for maturation of [NiFe]-hydrogenases . Escherichia coli HypF interacts with carbamoylphosphate as a substrate and releases inorganic phosphate . In addition, HypF also cleaves ATP into AMP and pyrophosphate in the presence of carbamoylphosphate. This, and the fact that HypF catalyzes a carbamoylphosphate-dependent pyrophosphate ATP exchange reaction, suggest that the protein catalyzes the activation of carbamoylphosphate .   The mechanism of action of HypF, as well as of its individual domains, is not yet clear. Mutations in any of the three major signature motifs, the acylphosphatase, the zinc fingers, and the O-carbamoyltransferase motif, can block carbamoylphosphate phosphatase activity. This indicates an integrated cooperativity between these domains in the cleavage reaction .   The N-terminal acylphosphatase (ACP) domain is thought to support the conversion of carbamoylphosphate into CO and CN- , . Biochemical results demonstrating its ACP activity are not available , . ACPs are small enzymes that specifically catalyze the hydrolysis of carboxylphosphate bonds in acylphosphates, including carbamoylphosphate . Zinc fingers have been implicated in bivalent cation binding or as part of a chaperone domain interacting with the large subunit precursor, but experimental studies on such a function are lacking thus far. The YrdC-like domain is present in protein families with regulatory functions (IPR012200 from INTERPRO, IPR010923 from INTERPRO) and has been implicated in RNA binding . It is not clear what function it may have in members of the HypF family. A C-terminal domain is distantly related to peptidase M22, but contains a conserved O-carbamoyltransferase motif required for the carbamoylphosphate phosphatase activity . The function of this domain is not clear.   Nomenclature note: the following names are used as synonyms of HypF: HupY in Azotobacter chroococcum, HupN in Rhizobium leguminosarum, HydA in Escherichia coli. In other organisms, these names are used to designate various "hydrogenase cluster" proteins unrelated to the members of this family. ; GO: 0030528 transcription regulator activity.
Probab=25.01  E-value=32  Score=16.66  Aligned_cols=19  Identities=26%  Similarity=0.315  Sum_probs=13.3

Q ss_pred             EEECCCC-----CCCCEEEEEEEC
Q ss_conf             6425778-----676879643423
Q gi|254780361|r   41 HVDMKTG-----LYRGRQVFVLKT   59 (61)
Q Consensus        41 ~vc~~cG-----~YkGr~Vi~~~~   59 (61)
                      ..||.||     .++|.+||..++
T Consensus       175 ~aCP~CGP~L~f~~~~~~vIae~~  198 (799)
T TIGR00143       175 IACPRCGPKLEFVSRGGEVIAEKD  198 (799)
T ss_pred             CCCCCCCCCCCEECCCCEEEECCC
T ss_conf             277335786530216871675277


No 150
>COG1273 Ku-homolog [Replication, recombination, and repair]
Probab=24.99  E-value=37  Score=16.32  Aligned_cols=16  Identities=44%  Similarity=0.461  Sum_probs=14.7

Q ss_pred             CCCCEEEEEEEECCCC
Q ss_conf             9978244046425778
Q gi|254780361|r   32 KSGELRRPHHVDMKTG   47 (61)
Q Consensus        32 ~cG~~~~~H~vc~~cG   47 (61)
                      .||.....|.||+.||
T Consensus        39 ~t~nrV~~~~Vd~~tG   54 (278)
T COG1273          39 KTGNRVRYKYVDSVTG   54 (278)
T ss_pred             HHCCCEEEEEECCCCC
T ss_conf             3199325687253227


No 151
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.99  E-value=25  Score=17.23  Aligned_cols=27  Identities=15%  Similarity=0.023  Sum_probs=17.2

Q ss_pred             ECCCCCCEEEE----EEEECCCCC-CCCEEEE
Q ss_conf             87899782440----464257786-7687964
Q gi|254780361|r   29 EDKKSGELRRP----HHVDMKTGL-YRGRQVF   55 (61)
Q Consensus        29 ~c~~cG~~~~~----H~vc~~cG~-YkGr~Vi   55 (61)
                      .||.||.-..+    -.=|+.||+ |+..+..
T Consensus       352 ~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~  383 (421)
T COG1571         352 VCPRCGGRMKSAGRNGFRCKKCGTRARETLIK  383 (421)
T ss_pred             CCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf             89766771311678985266426617755323


No 152
>pfam00798 Arena_glycoprot Arenavirus glycoprotein.
Probab=24.98  E-value=26  Score=17.14  Aligned_cols=13  Identities=38%  Similarity=0.935  Sum_probs=7.6

Q ss_pred             EEEE-----EECCCCCCCC
Q ss_conf             4046-----4257786768
Q gi|254780361|r   38 RPHH-----VDMKTGLYRG   51 (61)
Q Consensus        38 ~~H~-----vc~~cG~YkG   51 (61)
                      +|||     +| +||+|+-
T Consensus       453 kPHRL~~~g~C-sCG~yk~  470 (473)
T pfam00798       453 KPHRLNSNGIC-SCGLYKQ  470 (473)
T ss_pred             CCCCCCCCCCC-CCCCCCC
T ss_conf             96203889713-5765688


No 153
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724    Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.   Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate.  DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately.    This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=24.89  E-value=64  Score=15.06  Aligned_cols=32  Identities=13%  Similarity=0.048  Sum_probs=14.8

Q ss_pred             EEECCCCCCE-EEEEEEECCC---CCCCCEEEEEEE
Q ss_conf             7887899782-4404642577---867687964342
Q gi|254780361|r   27 YVEDKKSGEL-RRPHHVDMKT---GLYRGRQVFVLK   58 (61)
Q Consensus        27 l~~c~~cG~~-~~~H~vc~~c---G~YkGr~Vi~~~   58 (61)
                      -+.||+|+-- +....=|..|   |+++-+.-|.++
T Consensus       214 ~~tC~~C~G~G~ii~~~C~~C~G~G~~~~~~~~~v~  249 (386)
T TIGR02349       214 QQTCPTCGGEGKIIKEPCSTCKGKGRVKERKTISVK  249 (386)
T ss_pred             EEECCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEE
T ss_conf             587788584238963368998874069888899996


No 154
>PRK10996 thioredoxin 2; Provisional
Probab=24.86  E-value=30  Score=16.77  Aligned_cols=10  Identities=0%  Similarity=-0.127  Sum_probs=6.9

Q ss_pred             EEECCCCCCE
Q ss_conf             7887899782
Q gi|254780361|r   27 YVEDKKSGEL   36 (61)
Q Consensus        27 l~~c~~cG~~   36 (61)
                      .+.||+||..
T Consensus         2 ~~vC~~C~~~   11 (139)
T PRK10996          2 NTVCTHCQAI   11 (139)
T ss_pred             EEECCCCCCC
T ss_conf             7989775764


No 155
>pfam09723 CxxC_CxxC_SSSS Zinc ribbon domain. This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=24.67  E-value=45  Score=15.90  Aligned_cols=16  Identities=19%  Similarity=0.106  Sum_probs=8.2

Q ss_pred             EEEECCCCCCCCEEEE
Q ss_conf             4642577867687964
Q gi|254780361|r   40 HHVDMKTGLYRGRQVF   55 (61)
Q Consensus        40 H~vc~~cG~YkGr~Vi   55 (61)
                      ...||.||--.-+++|
T Consensus        26 ~~~CP~C~~~~~~r~~   41 (42)
T pfam09723        26 LATCPECGSTKVRRVI   41 (42)
T ss_pred             CCCCCCCCCCCEEEEC
T ss_conf             8769799998358814


No 156
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=24.26  E-value=42  Score=16.04  Aligned_cols=26  Identities=15%  Similarity=0.203  Sum_probs=12.3

Q ss_pred             ECCCCCC-EE-------EEEEEECCCCCCCCEEEE
Q ss_conf             8789978-24-------404642577867687964
Q gi|254780361|r   29 EDKKSGE-LR-------RPHHVDMKTGLYRGRQVF   55 (61)
Q Consensus        29 ~c~~cG~-~~-------~~H~vc~~cG~YkGr~Vi   55 (61)
                      .|..||. +-       .+--.||.||- .-++||
T Consensus         7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~-~~~r~i   40 (41)
T smart00834        7 RCEDCGHTFEVLQKISDDPLATCPECGG-DVRRLI   40 (41)
T ss_pred             EECCCCCEEEEEEECCCCCCCCCCCCCC-CCEECC
T ss_conf             9689999799998657887885868999-227732


No 157
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.25  E-value=29  Score=16.87  Aligned_cols=23  Identities=30%  Similarity=0.289  Sum_probs=16.3

Q ss_pred             CEEECCCCCC----EEEEEEEECCCCC
Q ss_conf             3788789978----2440464257786
Q gi|254780361|r   26 AYVEDKKSGE----LRRPHHVDMKTGL   48 (61)
Q Consensus        26 ~l~~c~~cG~----~~~~H~vc~~cG~   48 (61)
                      +-.+||+||.    ..+.-.|||.||-
T Consensus         8 tKridPetg~KFYDLNrdPiVsPytG~   34 (129)
T COG4530           8 TKRIDPETGKKFYDLNRDPIVSPYTGK   34 (129)
T ss_pred             CCCCCCCCCCHHHCCCCCCCCCCCCCC
T ss_conf             532183424321203778623676555


No 158
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=24.09  E-value=30  Score=16.78  Aligned_cols=20  Identities=15%  Similarity=0.066  Sum_probs=14.0

Q ss_pred             EECCCCCCEEE------EEEEECCCCC
Q ss_conf             88789978244------0464257786
Q gi|254780361|r   28 VEDKKSGELRR------PHHVDMKTGL   48 (61)
Q Consensus        28 ~~c~~cG~~~~------~H~vc~~cG~   48 (61)
                      -+| .||.++.      ...+|..||-
T Consensus        67 ~eC-~CGKYK~i~~~k~~g~vCerCGV   92 (668)
T CHL00018         67 GIC-ACGNYRVIGDEKEDPKFCEQCGV   92 (668)
T ss_pred             CEE-ECCCCCCCCCCCCCCCCCCCCCC
T ss_conf             667-58775224655657624687783


No 159
>pfam04475 DUF555 Protein of unknown function (DUF555). Family of uncharacterized, hypothetical archaeal proteins.
Probab=23.91  E-value=38  Score=16.23  Aligned_cols=36  Identities=22%  Similarity=0.122  Sum_probs=22.7

Q ss_pred             CCEEECCCCCCEEEEEEEECCCC---CCCCEEEEEEECC
Q ss_conf             83788789978244046425778---6768796434236
Q gi|254780361|r   25 PAYVEDKKSGELRRPHHVDMKTG---LYRGRQVFVLKTK   60 (61)
Q Consensus        25 p~l~~c~~cG~~~~~H~vc~~cG---~YkGr~Vi~~~~~   60 (61)
                      ...+.||.||++.-+--+-.+.+   .+=--+|++.+++
T Consensus        45 vG~~~cP~Cge~~~~afvvA~taLVgl~l~mkVFnAes~   83 (102)
T pfam04475        45 VGSTACPKCGEELESVFVVAGTALVGLILEMKVFNAESE   83 (102)
T ss_pred             CCCCCCCCCCCCCCCEEEEECCCEEEEEEEEEEEECCCH
T ss_conf             575108876786674789825424788999998405998


No 160
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=23.74  E-value=66  Score=15.02  Aligned_cols=26  Identities=19%  Similarity=0.009  Sum_probs=18.3

Q ss_pred             CCCEEECCCCCCE--------EEEEEEECCCCCC
Q ss_conf             8837887899782--------4404642577867
Q gi|254780361|r   24 PPAYVEDKKSGEL--------RRPHHVDMKTGLY   49 (61)
Q Consensus        24 ~p~l~~c~~cG~~--------~~~H~vc~~cG~Y   49 (61)
                      .-..+.|+.||.|        .+.--.|..||--
T Consensus        95 i~eYV~C~~C~sPDT~L~ke~r~~~L~C~ACGA~  128 (201)
T PRK12336         95 VDEYVICSECGRPDTRLVKSDRVLMLKCDACGAH  128 (201)
T ss_pred             HHHCEECCCCCCCCCEEEEECCEEEEEECCCCCC
T ss_conf             9861897899998868999798599996378999


No 161
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=23.66  E-value=16  Score=18.26  Aligned_cols=11  Identities=27%  Similarity=0.359  Sum_probs=8.1

Q ss_pred             EEEEECCCCCC
Q ss_conf             04642577867
Q gi|254780361|r   39 PHHVDMKTGLY   49 (61)
Q Consensus        39 ~H~vc~~cG~Y   49 (61)
                      +..+|..||.|
T Consensus        20 ~~~LCNaCgly   30 (54)
T cd00202          20 GSTLCNACGLY   30 (54)
T ss_pred             CCEEEHHHHHH
T ss_conf             87422888999


No 162
>pfam06676 DUF1178 Protein of unknown function (DUF1178). This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=23.43  E-value=27  Score=17.07  Aligned_cols=24  Identities=13%  Similarity=0.033  Sum_probs=16.7

Q ss_pred             HHHCCCCCCEEECCCCCCEEEEEE
Q ss_conf             231026883788789978244046
Q gi|254780361|r   18 SADALTPPAYVEDKKSGELRRPHH   41 (61)
Q Consensus        18 sh~~l~~p~l~~c~~cG~~~~~H~   41 (61)
                      +.+......|+.||.||.....-.
T Consensus        23 ~fe~Q~~~gli~CP~Cgs~~V~Ka   46 (145)
T pfam06676        23 DFDKQQARGLVSCPVCGSTEVEKA   46 (145)
T ss_pred             HHHHHHHCCCCCCCCCCCCEEEEE
T ss_conf             999999869917999999836561


No 163
>PRK07591 threonine synthase; Validated
Probab=23.16  E-value=48  Score=15.74  Aligned_cols=25  Identities=28%  Similarity=0.272  Sum_probs=16.1

Q ss_pred             CCCC-EEECCCCCCEE--EEEEEECCCC
Q ss_conf             6883-78878997824--4046425778
Q gi|254780361|r   23 TPPA-YVEDKKSGELR--RPHHVDMKTG   47 (61)
Q Consensus        23 ~~p~-l~~c~~cG~~~--~~H~vc~~cG   47 (61)
                      +.|+ --.|+.||..-  -+-+.|+.||
T Consensus        14 ~~~~t~L~C~~CG~~y~~~~~~~C~~Cg   41 (422)
T PRK07591         14 TGPATALKCRECGAEYPLEPLHVCEECF   41 (422)
T ss_pred             CCCCCEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             7896465876647916986546677799


No 164
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.97  E-value=25  Score=17.17  Aligned_cols=27  Identities=15%  Similarity=-0.012  Sum_probs=17.3

Q ss_pred             CCCCCEEECCCCCCEEE-----------EEEEECCCCC
Q ss_conf             26883788789978244-----------0464257786
Q gi|254780361|r   22 LTPPAYVEDKKSGELRR-----------PHHVDMKTGL   48 (61)
Q Consensus        22 l~~p~l~~c~~cG~~~~-----------~H~vc~~cG~   48 (61)
                      -.....-.||+|+.---           ..-.||.||-
T Consensus        94 e~~~~~Y~C~~C~~ryt~~eA~~l~~~~~~F~Cp~Cg~  131 (147)
T smart00531       94 ETNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGE  131 (147)
T ss_pred             CCCCCEEECCCCCCEECHHHHHHHCCCCCCEECCCCCC
T ss_conf             74898788999997862999988418998378899999


No 165
>PHA00732 hypothetical protein
Probab=22.79  E-value=24  Score=17.32  Aligned_cols=11  Identities=0%  Similarity=-0.146  Sum_probs=7.3

Q ss_pred             CEEECCCCCCE
Q ss_conf             37887899782
Q gi|254780361|r   26 AYVEDKKSGEL   36 (61)
Q Consensus        26 ~l~~c~~cG~~   36 (61)
                      .|.+||-||..
T Consensus        26 ~l~kCPVC~~~   36 (79)
T PHA00732         26 VLTKCPVCNNS   36 (79)
T ss_pred             CCCCCCCCCHH
T ss_conf             65227750478


No 166
>PRK03922 hypothetical protein; Provisional
Probab=22.44  E-value=42  Score=16.04  Aligned_cols=36  Identities=22%  Similarity=0.128  Sum_probs=22.9

Q ss_pred             CCEEECCCCCCEEEEEEEECCCC---CCCCEEEEEEECC
Q ss_conf             83788789978244046425778---6768796434236
Q gi|254780361|r   25 PAYVEDKKSGELRRPHHVDMKTG---LYRGRQVFVLKTK   60 (61)
Q Consensus        25 p~l~~c~~cG~~~~~H~vc~~cG---~YkGr~Vi~~~~~   60 (61)
                      .....||.||++.-+--+-.+.+   .+=--+|++.+++
T Consensus        47 vG~~~cP~Cge~~~~afvvA~taLVgl~lemkVFnAes~   85 (113)
T PRK03922         47 VGSTSCPKCGEPFDSAFVVADTALVGLLLEMKVFNAESP   85 (113)
T ss_pred             CCCCCCCCCCCCCCCEEEEECCCEEEEEEEEEEEECCCH
T ss_conf             575218877786674789835424788999999515998


No 167
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=22.03  E-value=64  Score=15.09  Aligned_cols=31  Identities=16%  Similarity=0.103  Sum_probs=18.9

Q ss_pred             EEECCCCCCEE--EEE----EEECCCCCC-----CCEEEEEE
Q ss_conf             78878997824--404----642577867-----68796434
Q gi|254780361|r   27 YVEDKKSGELR--RPH----HVDMKTGLY-----RGRQVFVL   57 (61)
Q Consensus        27 l~~c~~cG~~~--~~H----~vc~~cG~Y-----kGr~Vi~~   57 (61)
                      .+.||.||...  -.|    -.|+.||--     .|+..|..
T Consensus        19 ~VkCpdC~N~q~vFshast~V~C~~CG~~l~~PTGGka~i~~   60 (67)
T COG2051          19 RVKCPDCGNEQVVFSHASTVVTCLICGTTLAEPTGGKAKISG   60 (67)
T ss_pred             EEECCCCCCEEEEECCCCEEEEEECCCCEEEECCCCEEEEEE
T ss_conf             988899997789952576089930156589844897076611


No 168
>KOG1729 consensus
Probab=22.00  E-value=19  Score=17.80  Aligned_cols=27  Identities=26%  Similarity=0.139  Sum_probs=19.5

Q ss_pred             CCCCCCEEECCCCCC-----EEEEEEEECCCCC
Q ss_conf             026883788789978-----2440464257786
Q gi|254780361|r   21 ALTPPAYVEDKKSGE-----LRRPHHVDMKTGL   48 (61)
Q Consensus        21 ~l~~p~l~~c~~cG~-----~~~~H~vc~~cG~   48 (61)
                      .+.....+.|..|+.     .-+.|| |-+||.
T Consensus       162 W~PD~ea~~C~~C~~~~Ftl~~RRHH-CR~CG~  193 (288)
T KOG1729         162 WLPDSEATECMVCGCTEFTLSERRHH-CRNCGD  193 (288)
T ss_pred             CCCCCCCEECCCCCCCCCCHHHHHHH-HHHCCH
T ss_conf             16752030345578754548887778-876124


No 169
>COG0492 TrxB Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]
Probab=21.72  E-value=56  Score=15.37  Aligned_cols=20  Identities=20%  Similarity=0.434  Sum_probs=13.0

Q ss_pred             EEEEECCC-CCCCCEEEEEEE
Q ss_conf             04642577-867687964342
Q gi|254780361|r   39 PHHVDMKT-GLYRGRQVFVLK   58 (61)
Q Consensus        39 ~H~vc~~c-G~YkGr~Vi~~~   58 (61)
                      .-+.|+.| |+|+|+.|+.+-
T Consensus       130 gv~yc~~cdg~~~~k~v~ViG  150 (305)
T COG0492         130 GVSYCATCDGFFKGKDVVVIG  150 (305)
T ss_pred             CEEEEEECCCCCCCCEEEEEC
T ss_conf             759977347635798499999


No 170
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase; InterPro: IPR014192   Members of this entry belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are paired with genes for an activating protein that creates a glycine radical. Members of this entry are related to IPR012833 from INTERPRO, a functionally equivalent protein set; no genome has members in both entries. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons ..
Probab=21.34  E-value=48  Score=15.71  Aligned_cols=28  Identities=7%  Similarity=-0.149  Sum_probs=17.6

Q ss_pred             CCCCCCEEECCCCCC-EEEEEEEECCCCC
Q ss_conf             026883788789978-2440464257786
Q gi|254780361|r   21 ALTPPAYVEDKKSGE-LRRPHHVDMKTGL   48 (61)
Q Consensus        21 ~l~~p~l~~c~~cG~-~~~~H~vc~~cG~   48 (61)
                      ..-+..+++|-.|+. .++.=+-||.||-
T Consensus       577 F~~N~kitvCn~c~~idkR~L~~C~~Cgs  605 (638)
T TIGR02827       577 FCVNIKITVCNECHHIDKRTLERCPECGS  605 (638)
T ss_pred             EEEECCEEEECCCCCCCCCCCCCCCCCCC
T ss_conf             99715402324787646763000788764


No 171
>TIGR00269 TIGR00269 conserved hypothetical protein TIGR00269; InterPro: IPR000541 The following uncharacterised proteins have been shown to share regions of similarities, yeast chromosome VII hypothetical protein YGL211w; Dictyostelium discoideum (Slime mold) protein veg136; and Methanococcus jannaschii hypothetical proteins MJ1157 and MJ1478..
Probab=21.27  E-value=18  Score=17.90  Aligned_cols=23  Identities=13%  Similarity=0.170  Sum_probs=19.9

Q ss_pred             CEEECCCCCCEEEEEEEECCCCC
Q ss_conf             37887899782440464257786
Q gi|254780361|r   26 AYVEDKKSGELRRPHHVDMKTGL   48 (61)
Q Consensus        26 ~l~~c~~cG~~~~~H~vc~~cG~   48 (61)
                      .+..|-.||+|.=|-.+|-.|-|
T Consensus        80 ~~~~C~~CGeP~SPG~~CkaC~f  102 (106)
T TIGR00269        80 ELRRCERCGEPASPGKICKACKF  102 (106)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             56500014788887544366688


No 172
>PRK05778 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated
Probab=21.14  E-value=27  Score=17.00  Aligned_cols=13  Identities=15%  Similarity=0.071  Sum_probs=7.6

Q ss_pred             EEEEEEECCCCCC
Q ss_conf             4404642577867
Q gi|254780361|r   37 RRPHHVDMKTGLY   49 (61)
Q Consensus        37 ~~~H~vc~~cG~Y   49 (61)
                      .+||.-||-||.+
T Consensus        15 ~~p~~wCpGCG~~   27 (306)
T PRK05778         15 GLPTTWCPGCGNF   27 (306)
T ss_pred             CCCCCCCCCCCCH
T ss_conf             9977658999858


No 173
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=20.88  E-value=16  Score=18.18  Aligned_cols=11  Identities=9%  Similarity=-0.019  Sum_probs=5.3

Q ss_pred             CEEECCCCCCE
Q ss_conf             37887899782
Q gi|254780361|r   26 AYVEDKKSGEL   36 (61)
Q Consensus        26 ~l~~c~~cG~~   36 (61)
                      ++..||-||..
T Consensus       184 ~~~~CPvCGS~  194 (308)
T COG3058         184 SRQYCPVCGSM  194 (308)
T ss_pred             CCCCCCCCCCC
T ss_conf             64107776887


No 174
>pfam02591 DUF164 Putative zinc ribbon domain.
Probab=20.72  E-value=49  Score=15.70  Aligned_cols=11  Identities=18%  Similarity=0.193  Sum_probs=7.6

Q ss_pred             CCEEECCCCCC
Q ss_conf             83788789978
Q gi|254780361|r   25 PAYVEDKKSGE   35 (61)
Q Consensus        25 p~l~~c~~cG~   35 (61)
                      ..++.||+||-
T Consensus        44 ~~i~~Cp~CgR   54 (56)
T pfam02591        44 DEIVRCPHCGR   54 (56)
T ss_pred             CCEEECCCCCC
T ss_conf             98579979886


No 175
>KOG3134 consensus
Probab=20.66  E-value=35  Score=16.47  Aligned_cols=14  Identities=7%  Similarity=-0.078  Sum_probs=10.4

Q ss_pred             CCCEEECCCCCCEE
Q ss_conf             88378878997824
Q gi|254780361|r   24 PPAYVEDKKSGELR   37 (61)
Q Consensus        24 ~p~l~~c~~cG~~~   37 (61)
                      +..++.||||+|+.
T Consensus        21 ~irlt~C~nC~e~v   34 (225)
T KOG3134          21 NIRLTKCPNCQEVV   34 (225)
T ss_pred             CEEEEECCCHHHHH
T ss_conf             47885388440577


No 176
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=20.49  E-value=48  Score=15.73  Aligned_cols=27  Identities=4%  Similarity=-0.016  Sum_probs=14.2

Q ss_pred             ECCCCCCEEEEEEEECCCCC------CCCEEEEE
Q ss_conf             87899782440464257786------76879643
Q gi|254780361|r   29 EDKKSGELRRPHHVDMKTGL------YRGRQVFV   56 (61)
Q Consensus        29 ~c~~cG~~~~~H~vc~~cG~------YkGr~Vi~   56 (61)
                      .|.+|.-..- .-.||.||.      +.|-.||.
T Consensus         5 ACr~C~~i~~-~~~CP~Cgs~~~s~dW~G~viI~   37 (61)
T PRK08351          5 ACRHCHYITT-EDRCPVCGSRDLSEEWFDLVIII   37 (61)
T ss_pred             HHHHCCCCCC-CCCCCCCCCCCCCCCCCEEEEEE
T ss_conf             4655776268-99589997986887734599996


No 177
>pfam09535 Gmx_para_CXXCG Protein of unknown function (Gmx_para_CXXCG). This entry consists of at least 10 paralogous proteins from Myxococcus xanthus and that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment.
Probab=20.42  E-value=41  Score=16.10  Aligned_cols=24  Identities=17%  Similarity=0.073  Sum_probs=19.4

Q ss_pred             CCCCHHHHHCCCCCCEEECCCCCC
Q ss_conf             017412231026883788789978
Q gi|254780361|r   12 KRGMRRSADALTPPAYVEDKKSGE   35 (61)
Q Consensus        12 r~~~RRsh~~l~~p~l~~c~~cG~   35 (61)
                      -+++=++.+++..|.+.-|+.||+
T Consensus        13 ~tG~l~A~h~W~LPGv~~C~~Cg~   36 (237)
T pfam09535        13 FTGNLNAAHKWGLPGVSPCPVCGA   36 (237)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             455524525667898877886667


No 178
>pfam09884 DUF2111 Uncharacterized protein conserved in archaea (DUF2111). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=20.41  E-value=66  Score=15.01  Aligned_cols=17  Identities=41%  Similarity=0.528  Sum_probs=14.1

Q ss_pred             EEECCCCCCCCEEEEEE
Q ss_conf             64257786768796434
Q gi|254780361|r   41 HVDMKTGLYRGRQVFVL   57 (61)
Q Consensus        41 ~vc~~cG~YkGr~Vi~~   57 (61)
                      ++-|.+|-|+|.-|+..
T Consensus        48 k~~p~~G~Y~G~pVvVa   64 (84)
T pfam09884        48 RVTPITGPYKGVPVVVA   64 (84)
T ss_pred             EECCCCCCCCCCEEEEE
T ss_conf             84568755279338996


No 179
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.36  E-value=32  Score=16.63  Aligned_cols=22  Identities=9%  Similarity=0.012  Sum_probs=15.0

Q ss_pred             EECCCCCCEE-EEEEEECCCCCC
Q ss_conf             8878997824-404642577867
Q gi|254780361|r   28 VEDKKSGELR-RPHHVDMKTGLY   49 (61)
Q Consensus        28 ~~c~~cG~~~-~~H~vc~~cG~Y   49 (61)
                      -.|++||+.. .--..|..||.-
T Consensus         4 FhC~~CgQ~v~FeN~~C~~Cg~~   26 (349)
T COG4307           4 FHCPNCGQRVAFENSACLSCGSA   26 (349)
T ss_pred             CCCCCCCCEEEECCHHHHHHHHH
T ss_conf             55787788324432388751367


Done!