Query         gi|254781111|ref|YP_003065524.1| geranyltranstransferase protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 237
No_of_seqs    116 out of 4447
Neff          7.4 
Searched_HMMs 39220
Date          Mon May 30 05:02:50 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781111.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10581 geranyltranstransfera 100.0       0       0  412.2  21.0  229    4-237     2-238 (299)
  2 PRK10888 octaprenyl diphosphat 100.0       0       0  375.5  19.4  213    5-236     6-225 (323)
  3 COG0142 IspA Geranylgeranyl py 100.0       0       0  371.0  19.3  217    4-236     2-228 (322)
  4 CHL00151 preA prenyl transfera 100.0       0       0  368.0  19.9  217    2-237     4-230 (288)
  5 pfam00348 polyprenyl_synt Poly 100.0       0       0  370.1  16.3  195   39-237     1-201 (260)
  6 cd00685 Trans_IPPS_HT Trans-Is 100.0       0       0  369.0  16.6  193   36-236     3-203 (298)
  7 TIGR02749 prenyl_cyano solanes 100.0       0       0  350.1  16.4  219    9-236     3-231 (325)
  8 TIGR02748 GerC3_HepT heptapren 100.0       0       0  342.7  14.4  215    4-236     4-226 (325)
  9 KOG0776 consensus              100.0       0       0  330.8  18.1  205   27-233    82-289 (384)
 10 cd00867 Trans_IPPS Trans-Isopr 100.0 2.8E-45       0  285.3  13.1  171   53-234     1-175 (236)
 11 KOG0777 consensus              100.0 1.1E-36 2.9E-41  235.1  11.1  185   31-230    15-204 (322)
 12 KOG0711 consensus              100.0 5.3E-34 1.3E-38  219.4  14.2  209   20-234    20-244 (347)
 13 cd00385 Isoprenoid_Biosyn_C1 I  99.9 1.7E-27 4.4E-32  181.0   8.7  153   73-236    13-171 (243)
 14 pfam07307 HEPPP_synt_1 Heptapr  94.5    0.26 6.6E-06   27.0   7.6   80   66-152    29-108 (212)
 15 TIGR03464 HpnC squalene syntha  94.1    0.42 1.1E-05   25.8  11.9   72  157-235    89-161 (266)
 16 cd00683 Trans_IPPS_HH Trans-Is  94.0    0.25 6.4E-06   27.1   6.6   73  157-235    96-169 (265)
 17 TIGR03465 HpnD squalene syntha  93.9    0.32 8.1E-06   26.5   7.0   71  158-235    89-160 (266)
 18 pfam00494 SQS_PSY Squalene/phy  93.6    0.28 7.1E-06   26.8   6.2   74  157-235    92-166 (262)
 19 PRK13594 consensus              70.4     7.7  0.0002   18.3   7.3   44  191-234   139-183 (278)
 20 KOG0018 consensus               67.7     3.2 8.3E-05   20.5   1.7   13  108-120   516-528 (1141)
 21 pfam06783 UPF0239 Uncharacteri  61.8     9.4 0.00024   17.8   3.2   20  204-223    15-34  (85)
 22 pfam10776 DUF2600 Protein of u  55.3     8.5 0.00022   18.1   2.1   33  201-233   205-238 (330)
 23 PRK13593 consensus              54.1      16  0.0004   16.5   7.7   46  189-234   144-190 (283)
 24 KOG1345 consensus               50.6     7.1 0.00018   18.5   1.1   24   73-97    128-151 (378)
 25 KOG1166 consensus               45.2      16  0.0004   16.5   2.1   36   73-109   801-836 (974)
 26 PRK12887 ubiA tocopherol phyty  42.5      24 0.00061   15.4  10.8  115   79-195   192-307 (309)
 27 cd05105 PTKc_PDGFR_alpha Catal  36.6      10 0.00026   17.7   0.0   22   72-93    243-264 (400)
 28 TIGR01957 nuoB_fam NADH-quinon  35.7      22 0.00057   15.6   1.7   33   69-105    21-55  (146)
 29 cd05061 PTKc_InsR Catalytic Do  32.9      11 0.00029   17.3  -0.2   22   72-93    125-146 (288)
 30 cd05038 PTKc_Jak_rpt2 Catalyti  32.9     9.6 0.00025   17.8  -0.5   22   72-93    115-136 (279)
 31 cd05097 PTKc_DDR_like Catalyti  32.8      10 0.00026   17.6  -0.5   22   72-93    135-156 (295)
 32 cd05049 PTKc_Trk Catalytic Dom  32.7      11 0.00028   17.4  -0.3   22   72-93    128-149 (280)
 33 cd00192 PTKc Catalytic Domain   32.3      13 0.00034   16.9   0.1   22   72-93    110-131 (261)
 34 cd06610 STKc_OSR1_SPAK Serine/  32.2      13 0.00033   17.0  -0.0   21   73-93    109-129 (266)
 35 cd05085 PTKc_Fer Catalytic Dom  32.1      11 0.00029   17.4  -0.3   22   72-93     99-120 (250)
 36 cd05099 PTKc_FGFR4 Catalytic D  32.1      11 0.00029   17.4  -0.3   22   72-93    140-161 (314)
 37 cd05055 PTKc_PDGFR Catalytic D  31.7      13 0.00034   16.9  -0.0   22   72-93    147-168 (302)
 38 cd05096 PTKc_DDR1 Catalytic Do  31.6     8.1 0.00021   18.2  -1.1   22   72-93    144-165 (304)
 39 pfam04703 FaeA FaeA-like prote  31.5      14 0.00037   16.7   0.2   22   89-110    39-60  (61)
 40 cd05053 PTKc_FGFR Catalytic Do  31.0      14 0.00035   16.9  -0.0   22   72-93    139-160 (294)
 41 cd05102 PTKc_VEGFR3 Catalytic   31.0      14 0.00035   16.8   0.0   21   73-93    181-201 (338)
 42 cd05074 PTKc_Tyro3 Catalytic D  30.7      13 0.00034   17.0  -0.1   22   72-93    119-140 (273)
 43 cd05107 PTKc_PDGFR_beta Cataly  30.5      13 0.00033   17.0  -0.2   22   72-93    245-266 (401)
 44 cd05036 PTKc_ALK_LTK Catalytic  30.5      16  0.0004   16.5   0.2   21   73-93    123-143 (277)
 45 TIGR01962 NuoD NADH dehydrogen  30.1      38 0.00097   14.3   3.8  100  119-218    69-180 (408)
 46 TIGR02362 dhaK1b probable dihy  30.1      17 0.00044   16.2   0.4   43   70-113   106-161 (328)
 47 PRK12883 ubiA prenyltransferas  30.0      38 0.00097   14.2   7.8   45  189-234   139-183 (275)
 48 cd05035 PTKc_Axl_like Catalyti  29.9      12 0.00032   17.1  -0.4   22   72-93    119-140 (273)
 49 cd05032 PTKc_InsR_like Catalyt  29.0      17 0.00043   16.3   0.2   22   72-93    125-146 (277)
 50 cd05103 PTKc_VEGFR2 Catalytic   28.4      17 0.00044   16.3   0.1   21   73-93    186-206 (343)
 51 cd05066 PTKc_EphR_A Catalytic   28.4      15 0.00038   16.6  -0.2   22   72-93    112-133 (267)
 52 cd05087 PTKc_Aatyk1_Aatyk3 Cat  28.2      14 0.00036   16.8  -0.3   22   72-93    106-127 (269)
 53 cd05075 PTKc_Axl Catalytic Dom  28.0      14 0.00036   16.8  -0.4   22   72-93    118-139 (272)
 54 TIGR01982 UbiB 2-polyprenylphe  27.9      42  0.0011   14.0   2.3   32   50-81    188-220 (452)
 55 cd05148 PTKc_Srm_Brk Catalytic  27.9      17 0.00042   16.4  -0.0   22   72-93    110-131 (261)
 56 cd05106 PTKc_CSF-1R Catalytic   27.9      15 0.00037   16.7  -0.3   22   72-93    218-239 (374)
 57 KOG0591 consensus               27.4      42  0.0011   14.0   2.1   43   73-127   131-177 (375)
 58 KOG0194 consensus               27.3      14 0.00036   16.8  -0.5   23   71-93    267-289 (474)
 59 cd05063 PTKc_EphR_A2 Catalytic  27.2      14 0.00036   16.8  -0.5   22   72-93    113-134 (268)
 60 cd05101 PTKc_FGFR2 Catalytic D  27.0      13 0.00033   17.0  -0.7   22   72-93    143-164 (304)
 61 cd05056 PTKc_FAK Catalytic Dom  26.9      17 0.00043   16.3  -0.2   22   72-93    113-134 (270)
 62 cd05092 PTKc_TrkA Catalytic Do  26.8      16 0.00041   16.5  -0.3   21   73-93    129-149 (280)
 63 cd05079 PTKc_Jak1_rpt2 Catalyt  26.6     9.7 0.00025   17.7  -1.4   22   72-93    115-136 (284)
 64 cd05058 PTKc_Met_Ron Catalytic  26.4      14 0.00036   16.8  -0.6   22   72-93    104-125 (262)
 65 cd05052 PTKc_Abl Catalytic Dom  25.6      18 0.00046   16.1  -0.2   22   72-93    110-131 (263)
 66 KOG0192 consensus               25.3      11 0.00029   17.4  -1.3   23   71-93    147-170 (362)
 67 cd05109 PTKc_HER2 Catalytic Do  25.2      18 0.00045   16.2  -0.3   22   72-93    115-136 (279)
 68 cd05098 PTKc_FGFR1 Catalytic D  24.9      19 0.00047   16.1  -0.2   22   72-93    146-167 (307)
 69 cd05034 PTKc_Src_like Catalyti  24.9      18 0.00046   16.1  -0.3   22   72-93    109-130 (261)
 70 cd05067 PTKc_Lck_Blk Catalytic  24.4      18 0.00046   16.2  -0.4   22   72-93    108-129 (260)
 71 cd05086 PTKc_Aatyk2 Catalytic   24.2      19 0.00048   16.1  -0.3   22   72-93    105-126 (268)
 72 cd05068 PTKc_Frk_like Catalyti  23.8      20  0.0005   15.9  -0.3   28   72-100   109-136 (261)
 73 cd05077 PTK_Jak1_rpt1 Pseudoki  23.4      23 0.00059   15.5   0.0   22   72-93    111-132 (262)
 74 pfam01040 UbiA UbiA prenyltran  23.3      51  0.0013   13.5   9.7   46  189-234   128-174 (258)
 75 cd05089 PTKc_Tie1 Catalytic Do  23.2      19 0.00048   16.1  -0.5   32  199-230   254-285 (297)
 76 cd05070 PTKc_Fyn_Yrk Catalytic  23.2      21 0.00054   15.8  -0.2   22   72-93    108-129 (260)
 77 cd05054 PTKc_VEGFR Catalytic D  23.1      16  0.0004   16.5  -0.9   21   73-93    180-200 (337)
 78 cd05051 PTKc_DDR Catalytic Dom  22.9      23 0.00058   15.5  -0.1   22   72-93    136-157 (296)
 79 cd05100 PTKc_FGFR3 Catalytic D  22.3      20 0.00052   15.8  -0.4   33  201-233   274-308 (334)
 80 TIGR01437 selA_rel pyridoxal p  22.2      53  0.0014   13.4   2.2   33  159-191   124-157 (391)
 81 cd05042 PTKc_Aatyk Catalytic D  22.2      20 0.00051   15.9  -0.5   22   72-93    106-127 (269)
 82 PRK13852 type IV secretion sys  22.1      54  0.0014   13.4   2.7   41    1-41      1-41  (295)
 83 cd05093 PTKc_TrkB Catalytic Do  22.0      24  0.0006   15.5  -0.2   22   72-93    126-147 (288)
 84 cd05040 PTKc_Ack_like Catalyti  21.9      22 0.00056   15.7  -0.4   22   72-93    103-124 (257)
 85 cd05041 PTKc_Fes_like Catalyti  21.8      21 0.00054   15.8  -0.4   22   72-93     99-120 (251)
 86 cd05057 PTKc_EGFR_like Catalyt  21.5      25 0.00064   15.3  -0.1   22   72-93    115-136 (279)
 87 cd05043 PTK_Ryk Pseudokinase D  21.5      24 0.00061   15.4  -0.2   22   72-93    123-144 (280)
 88 pfam07714 Pkinase_Tyr Protein   21.2      20 0.00052   15.8  -0.6   22   72-93    108-129 (258)
 89 cd05047 PTKc_Tie Catalytic Dom  21.0      21 0.00053   15.8  -0.6   22   72-93    118-139 (270)
 90 cd05104 PTKc_Kit Catalytic Dom  20.7      30 0.00075   14.9   0.1   22   72-93    220-241 (375)
 91 cd05610 STKc_MASTL STKc_MASTL:  20.7      28 0.00072   15.0   0.0   22   72-93    110-131 (669)
 92 cd05090 PTKc_Ror1 Catalytic Do  20.6      25 0.00063   15.4  -0.3   22   72-93    130-151 (283)
 93 cd05614 STKc_MSK2_N STKc_MSK2_  20.5      33 0.00084   14.6   0.3   21   73-93    112-132 (332)
 94 cd05045 PTKc_RET Catalytic Dom  20.5      29 0.00073   15.0  -0.0   21   73-93    129-149 (285)
 95 cd05095 PTKc_DDR2 Catalytic Do  20.4      19 0.00049   16.0  -0.9   22   72-93    136-157 (296)
 96 cd05631 STKc_GRK4 STKc_GRK4: S  20.3      40   0.001   14.1   0.7   21   73-93    109-129 (285)
 97 KOG1024 consensus               20.3      34 0.00085   14.6   0.3   41   53-93    372-423 (563)
 98 cd05626 STKc_LATS2 STKc_LATS2:  20.2      39 0.00099   14.2   0.6   21   73-93    108-128 (381)
 99 cd05091 PTKc_Ror2 Catalytic Do  20.1      31 0.00079   14.8   0.1   22   72-93    130-151 (283)
100 cd05110 PTKc_HER4 Catalytic Do  20.1      30 0.00076   14.9   0.0   22   72-93    115-136 (303)
101 smart00219 TyrKc Tyrosine kina  20.1      26 0.00066   15.2  -0.3   22   72-93    109-130 (258)

No 1  
>PRK10581 geranyltranstransferase; Provisional
Probab=100.00  E-value=0  Score=412.17  Aligned_cols=229  Identities=38%  Similarity=0.618  Sum_probs=202.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC-CCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH
Q ss_conf             48999999999999999999997675302457157999998750-58600799999999996178822224024688889
Q gi|254781111|r    4 GLPSKLQENSKRIDTILDDLLLQTASHMQTQHNDRLLSAIRYAL-LGGKKIRSFLVTECASLFNVNHLTALRVGAAIECI   82 (237)
Q Consensus         4 ~l~~~l~~~~~~id~~l~~~l~~~~~~~~~~~~~~l~~~~~y~l-~gGKr~R~~l~l~~~~~~~~~~~~~~~~AaavEll   82 (237)
                      +|++++++..++|++.|+++++..     ...+..++++|+|.+ .||||+||.||+++++++|++.+.++++|+|||++
T Consensus         2 ~f~~~~~~~~~~~~~~l~~~~~~~-----~~~~~~l~~a~~y~~~~GGKRlRP~L~ll~~~~~g~~~~~~~~~A~AiEli   76 (299)
T PRK10581          2 DFPQQLQACVKQANQALSRFIAPL-----PFQNTPVVEAMQYGALLGGKRLRPFLVYATGQMFGVSTNTLDAPAAAVECI   76 (299)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCC-----CCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             879999999999999999863535-----789726999999898479660879999999998399867789999999999


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999864776544532234455665432434520133222233479999731023-412678888876532223566411
Q gi|254781111|r   83 HCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQ-LKDNIRSQLMLSLTHNIGLQGMLG  161 (237)
Q Consensus        83 H~asLihDDI~~~D~s~~RRG~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~  161 (237)
                      |+||||||||||||+|++|||+||+|++||++.|||+||+|++++|+++++...+ .........+..++.+.+..+++.
T Consensus        77 H~aSLIHDDIp~iD~s~~RRG~pt~h~~~G~~~AIlaGD~L~~~a~~ll~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~~  156 (299)
T PRK10581         77 HAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAPMPEVADRDRISMISELASASGIAGMCG  156 (299)
T ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99898971840125886548987724334852467730289999999997189965326889999999999988988620


Q ss_pred             CCCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---C
Q ss_conf             332221000--000367999999986348999999999975988-8999999999999849999986765344320---6
Q gi|254781111|r  162 GQMLDIQDE--FIDETQVFMIQKMKTGALMCFACESGAIMAHAS-QNEKERLRCFGENLGIIFQLADDLLDCEEDL---P  235 (237)
Q Consensus       162 GQ~~dl~~~--~~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~-~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~---~  235 (237)
                      ||.+|+...  ..+.+.|.+|+++|||+||.+||.+|++++|.+ ++..+.+.+||.++|+||||+||+||++||.   |
T Consensus       157 GQ~lDl~~~~~~~~~~~~~~i~~~KTa~Lf~~a~~~gai~ag~~~~~~~~~l~~~g~~lGiAFQI~DDlLD~~gd~~~~G  236 (299)
T PRK10581        157 GQALDLEAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLG  236 (299)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHC
T ss_conf             18999985237999999999999999999999999999984999899999999999998899998645777038989979


Q ss_pred             CC
Q ss_conf             79
Q gi|254781111|r  236 KK  237 (237)
Q Consensus       236 k~  237 (237)
                      |.
T Consensus       237 K~  238 (299)
T PRK10581        237 KR  238 (299)
T ss_pred             CC
T ss_conf             99


No 2  
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=100.00  E-value=0  Score=375.49  Aligned_cols=213  Identities=24%  Similarity=0.399  Sum_probs=181.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC-CCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHH
Q ss_conf             8999999999999999999997675302457157999998750-586007999999999961788222240246888899
Q gi|254781111|r    5 LPSKLQENSKRIDTILDDLLLQTASHMQTQHNDRLLSAIRYAL-LGGKKIRSFLVTECASLFNVNHLTALRVGAAIECIH   83 (237)
Q Consensus         5 l~~~l~~~~~~id~~l~~~l~~~~~~~~~~~~~~l~~~~~y~l-~gGKr~R~~l~l~~~~~~~~~~~~~~~~AaavEllH   83 (237)
                      +.+.+++..++|++.|.+.       +.+ ..+.+.++.+|.+ .||||+||.|++++++++|++.++++++|+++|++|
T Consensus         6 i~~~v~~dl~~v~~~l~~~-------~~~-~~~~i~~~~~~~~~~GGKRlRP~l~ll~~~~~g~~~~~~~~~AaaiEliH   77 (323)
T PRK10888          6 INELTAQDMAGVNAAILEQ-------LNS-DVQLINQLGYYIISGGGKRIRPMIAVLAARAVGYQGNAHVTIAALIEFIH   77 (323)
T ss_pred             HHHHHHHHHHHHHHHHHHH-------HCC-CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             9999999999999999998-------668-81889999999882698608599999999982998388999999999999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99986477654453223445566543243452013322223347999973102341267888887653222356641133
Q gi|254781111|r   84 CYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQ  163 (237)
Q Consensus        84 ~asLihDDI~~~D~s~~RRG~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~GQ  163 (237)
                      +||||||||  ||+|++|||+||+|.+||++.||++||||++.+|++++..+..       +.+..++.+.  ..+++||
T Consensus        78 ~asLiHDDi--iD~s~~RRG~pt~h~~~G~~~AIl~GD~l~~~a~~~l~~~~~~-------~~~~~~~~~~--~~~~eGe  146 (323)
T PRK10888         78 TATLLHDDV--VDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGSL-------KVLEVMSEAV--NVIAEGE  146 (323)
T ss_pred             HHHHHHCCC--CCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHCCCH-------HHHHHHHHHH--HHHHHHH
T ss_conf             999987465--6799888998540133044216762029998888866512766-------8999999999--9999688


Q ss_pred             CCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---CC
Q ss_conf             222100---00003679999999863489999999999759888999999999999849999986765344320---67
Q gi|254781111|r  164 MLDIQD---EFIDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEEDL---PK  236 (237)
Q Consensus       164 ~~dl~~---~~~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~---~k  236 (237)
                      .+|+.+   ...++++|++|+.+|||+||++||++|++++|++++....+.+||+++|+||||+||+||++||.   ||
T Consensus       147 ~~q~~~~~~~~~~~~~yl~~i~~KTa~Lf~~~~~~ga~lag~~~~~~~~l~~fG~~lG~AFQI~DDlLD~~gd~~~~GK  225 (323)
T PRK10888        147 VLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGEQLGK  225 (323)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCC
T ss_conf             9999854278999999999999999999999999999870999999999999999999999999975202478788689


No 3  
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=100.00  E-value=0  Score=371.03  Aligned_cols=217  Identities=42%  Similarity=0.634  Sum_probs=189.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCC-CCCHHHHHHHHHHHHHCCCCCC----CCCCHHHH
Q ss_conf             489999999999999999999976753024571579999987505-8600799999999996178822----22402468
Q gi|254781111|r    4 GLPSKLQENSKRIDTILDDLLLQTASHMQTQHNDRLLSAIRYALL-GGKKIRSFLVTECASLFNVNHL----TALRVGAA   78 (237)
Q Consensus         4 ~l~~~l~~~~~~id~~l~~~l~~~~~~~~~~~~~~l~~~~~y~l~-gGKr~R~~l~l~~~~~~~~~~~----~~~~~Aaa   78 (237)
                      .+...+.+...+|++.|++.+..       ..++.+.+++.|.+. ||||+||.++++++++++.+.+    +++++|++
T Consensus         2 ~~~~~~~~~~~~i~~~L~~~l~~-------~~~~~l~~a~~~~~~aGGKrlRP~l~l~~~~~~~~~~~~~~~~~~~~a~a   74 (322)
T COG0142           2 DLLALLLKRLARIEELLSELLSG-------SDPELLLEAMRYLLLAGGKRLRPLLVLLAAEALGIDLETGGNDALDLAAA   74 (322)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC-------CCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf             17899999999999999987175-------66388999999754068700889999999987698643230789999999


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             88899999864776544532234455665432434520133222233479999731023412678888876532223566
Q gi|254781111|r   79 IECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQG  158 (237)
Q Consensus        79 vEllH~asLihDDI~~~D~s~~RRG~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (237)
                      ||++|++|||||||  ||+|++|||+||+|.+||++.||++||+|++.+|+++++....     ....+..++.  +..+
T Consensus        75 vEliH~~SLiHDDv--mD~s~~RRG~pt~~~~~g~~~AIlaGD~L~~~Af~~l~~~~~~-----~~~~~~~~~~--~~~~  145 (322)
T COG0142          75 IELIHTASLIHDDL--MDDDDLRRGKPTVHAKFGEATAILAGDALLAAAFELLSKLGSE-----ALEAIKALAE--AING  145 (322)
T ss_pred             HHHHHHHHHHHHHH--CCCCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCC-----HHHHHHHHHH--HHHH
T ss_conf             99999999998651--1488643789756667362379999899999999999875852-----2799999999--9999


Q ss_pred             HHCCCCCCCCHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---
Q ss_conf             4113322210000--00367999999986348999999999975988899999999999984999998676534432---
Q gi|254781111|r  159 MLGGQMLDIQDEF--IDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEED---  233 (237)
Q Consensus       159 l~~GQ~~dl~~~~--~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D---  233 (237)
                      +++||.+|+.+..  +|+++|++|+++|||+||++++.+|+++++++++..+.+.+||.++|+||||+|||||++||   
T Consensus       146 ~~~GQ~lDl~~~~~~~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~~~~~~~~l~~~g~~lGlaFQi~DDiLD~~~d~~~  225 (322)
T COG0142         146 LCGGQALDLAFENKPVTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEE  225 (322)
T ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf             97728999866788999999999999989999999999999981998999999999999877888867747750587276


Q ss_pred             HCC
Q ss_conf             067
Q gi|254781111|r  234 LPK  236 (237)
Q Consensus       234 ~~k  236 (237)
                      .||
T Consensus       226 lGK  228 (322)
T COG0142         226 LGK  228 (322)
T ss_pred             HCC
T ss_conf             289


No 4  
>CHL00151 preA prenyl transferase; Reviewed
Probab=100.00  E-value=0  Score=368.03  Aligned_cols=217  Identities=27%  Similarity=0.387  Sum_probs=184.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCC-CCCHHHHHHHHHHHHHCCCCCCCCC---CHHH
Q ss_conf             83489999999999999999999976753024571579999987505-8600799999999996178822224---0246
Q gi|254781111|r    2 NGGLPSKLQENSKRIDTILDDLLLQTASHMQTQHNDRLLSAIRYALL-GGKKIRSFLVTECASLFNVNHLTAL---RVGA   77 (237)
Q Consensus         2 ~~~l~~~l~~~~~~id~~l~~~l~~~~~~~~~~~~~~l~~~~~y~l~-gGKr~R~~l~l~~~~~~~~~~~~~~---~~Aa   77 (237)
                      ++.+.+.+++..++|++.|.+.+.       +. .+.+.++++|.+. ||||+||.|++++++++|++.+...   .+|+
T Consensus         4 ~~~i~~~i~~~l~~ve~~l~~~l~-------s~-~~~l~~a~~y~~~~gGKRlRP~L~ll~~~~~g~~~~~~~~~~~~A~   75 (288)
T CHL00151          4 NFKLLAPVEEDLESVEKNLKKLIG-------TR-HPILSAAARHLFSAGGKRIRPAIVLLVAKATGGNQEIAPPQRRLAE   75 (288)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHC-------CC-CHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             488899999999999999998827-------99-6699999999986599728699999999981998001066899999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             88889999986477654453223445566543243452013322223347999973102341267888887653222356
Q gi|254781111|r   78 AIECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQ  157 (237)
Q Consensus        78 avEllH~asLihDDI~~~D~s~~RRG~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (237)
                      ++|++|+||||||||  ||+|++|||+||+|++||++.||++||+|++.+|+++++.............+         .
T Consensus        76 avEliH~aSLIHDDi--~D~s~~RRG~pt~h~~~G~~~AIL~GD~L~~~a~~~la~~~~~~~~~~~~~~i---------~  144 (288)
T CHL00151         76 ITEMIHTASLVHDDV--VDEDSTRRGVPTVHKRFGTKIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVI---------T  144 (288)
T ss_pred             HHHHHHHHHHHHCCC--CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH---------H
T ss_conf             999999999984677--89986668986532441438999998899999999976046325689999999---------9


Q ss_pred             HHHCCCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             64113322210---000003679999999863489999999999759888999999999999849999986765344320
Q gi|254781111|r  158 GMLGGQMLDIQ---DEFIDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEEDL  234 (237)
Q Consensus       158 ~l~~GQ~~dl~---~~~~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~  234 (237)
                      .++.||..+..   ....++++|++|+.+|||+||++||.+|++++|++++..+.+.+||+++|+||||+||+||++||.
T Consensus       145 ~l~~g~~~~~~~~~~~~~~~~~y~~~~~~KTa~Lf~~a~~~gailaga~~~~~~~l~~~G~~lG~AFQI~DDlLD~~gd~  224 (288)
T CHL00151        145 DLAEGEIRQGLVQFDTTLSTLEYIEKSFYKTASLLAASCKAAALLSDADEELLNDLYLYGKHLGLAFQIIDDILDITGST  224 (288)
T ss_pred             HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCH
T ss_conf             99988898776425888789999999985207999999999999809999999999998641311455349754035898


Q ss_pred             ---CCC
Q ss_conf             ---679
Q gi|254781111|r  235 ---PKK  237 (237)
Q Consensus       235 ---~k~  237 (237)
                         ||.
T Consensus       225 ~~~GK~  230 (288)
T CHL00151        225 ESLGKP  230 (288)
T ss_pred             HHHCCC
T ss_conf             997899


No 5  
>pfam00348 polyprenyl_synt Polyprenyl synthetase.
Probab=100.00  E-value=0  Score=370.06  Aligned_cols=195  Identities=40%  Similarity=0.605  Sum_probs=172.7

Q ss_pred             HHHHHHHHC-CCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             999998750-5860079999999999617882222402468888999998647765445322344556654324345201
Q gi|254781111|r   39 LLSAIRYAL-LGGKKIRSFLVTECASLFNVNHLTALRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAI  117 (237)
Q Consensus        39 l~~~~~y~l-~gGKr~R~~l~l~~~~~~~~~~~~~~~~AaavEllH~asLihDDI~~~D~s~~RRG~pt~h~~~G~~~AI  117 (237)
                      ++++|+|.+ .||||+||.|++++++++|++.+.++++|+++|++|+||||||||  ||+|++|||+||+|.+||++.||
T Consensus         1 l~~am~y~~~~gGKrlRp~L~l~~~~~~g~~~~~~~~~A~avEllH~aSLIHDDI--~D~s~~RRG~pt~h~~~G~~~Ai   78 (260)
T pfam00348         1 LLAAMLYYLLAGGKRIRPLLVVLAARALGVEPETLLYLACAIEMIHTASLVHDDL--MDNSDLRRGKPTCHKKFGEAGAI   78 (260)
T ss_pred             CHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC--CCCCCCCCCCCCCHHHCCHHHHH
T ss_conf             9788998871893408999999999982998889999999999999999995332--46998779998602231117899


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3322223347999973102341267888887653222356641133222100--00003679999999863489999999
Q gi|254781111|r  118 IAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQD--EFIDETQVFMIQKMKTGALMCFACES  195 (237)
Q Consensus       118 l~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~GQ~~dl~~--~~~~~~~y~~i~~~KTa~lf~~~~~~  195 (237)
                      ++||+|++.+|+++++.....+ ......+...+......++. ||.+|+..  ...++++|++|+++|||+||.+||.+
T Consensus        79 l~GD~L~~~a~~~l~~~~~~~~-~~~~~~i~~~~~~~~~~g~~-gQ~~d~~~~~~~~s~~~y~~~~~~KTa~Lf~~~~~~  156 (260)
T pfam00348        79 LAGDALLSRAFQLLALLGHVRP-EPKYILISELANAVGAQGEV-GQLMDLETEGKDITLEEYLRIVSYKTAALFYASVQL  156 (260)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHHHHHHHHH-HHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9758999999999986579983-99999999999999999999-999987567889999999999999759999999999


Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---CCC
Q ss_conf             999759888999999999999849999986765344320---679
Q gi|254781111|r  196 GAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEEDL---PKK  237 (237)
Q Consensus       196 ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~---~k~  237 (237)
                      |++++|++++..+.+.+||.++|++|||+||+||++||.   ||.
T Consensus       157 gailag~~~~~~~~l~~~g~~lGiaFQi~DDiLD~~gd~~~~GK~  201 (260)
T pfam00348       157 GAIVAGADEEDEKDLYDFGRDLGLAFQIQDDILDLTGDTEELGKP  201 (260)
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCCC
T ss_conf             999819999999999999987368999899764144898770999


No 6  
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS), head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesis various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors,  isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX)D) located on opposite walls. These residues mediate binding of pre
Probab=100.00  E-value=0  Score=368.99  Aligned_cols=193  Identities=40%  Similarity=0.594  Sum_probs=173.2

Q ss_pred             CHHHHHHHHHHC-CCCCHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             157999998750-5860079999999999617882-22240246888899999864776544532234455665432434
Q gi|254781111|r   36 NDRLLSAIRYAL-LGGKKIRSFLVTECASLFNVNH-LTALRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDE  113 (237)
Q Consensus        36 ~~~l~~~~~y~l-~gGKr~R~~l~l~~~~~~~~~~-~~~~~~AaavEllH~asLihDDI~~~D~s~~RRG~pt~h~~~G~  113 (237)
                      .+.+.++++|.+ .||||+||.|++++++++++++ +.++++|+++|++|+||||||||  ||+|++|||+||+|.+||+
T Consensus         3 ~~~l~~~~~y~~~~gGKrlRp~l~ll~~~~~~~~~~~~~~~~A~aiEliH~asLiHDDi--iD~s~~RRG~pt~h~~~g~   80 (298)
T cd00685           3 VELLREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDDV--MDNSDLRRGKPTVHKVFGN   80 (298)
T ss_pred             CHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH--HCCCCCCCCCCCHHHHCCC
T ss_conf             38999999988638974387999999999819995688999999999999999998241--0586545899878887299


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHH---HHHHHHHHHHHHHHHHHHHH
Q ss_conf             520133222233479999731023412678888876532223566411332221000---00036799999998634899
Q gi|254781111|r  114 VTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQDE---FIDETQVFMIQKMKTGALMC  190 (237)
Q Consensus       114 ~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~GQ~~dl~~~---~~~~~~y~~i~~~KTa~lf~  190 (237)
                      +.|||+||||++.+|+++++....    ...+++..++++  ...++.||.+|+.+.   .+++++|++|+.+|||+||.
T Consensus        81 ~~AIl~GD~l~~~a~~~l~~~~~~----~~~~~~~~~~~~--~~~~~~Gq~~d~~~~~~~~~~~~~y~~~~~~KTa~l~~  154 (298)
T cd00685          81 ATAILAGDYLLARAFELLARLGNP----YYPRALELFSEA--ILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFA  154 (298)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCC----CHHHHHHHHHHH--HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             644148899999999999867992----209999999999--99998888999863789999999999999999999999


Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---CC
Q ss_conf             99999999759888999999999999849999986765344320---67
Q gi|254781111|r  191 FACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEEDL---PK  236 (237)
Q Consensus       191 ~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~---~k  236 (237)
                      ++|.+|+++++++++..+.+.+||.++|++|||+||++|++||.   ||
T Consensus       155 ~~~~~ga~~~~~~~~~~~~l~~~g~~lG~aFQi~DD~ld~~g~~~~~GK  203 (298)
T cd00685         155 AAPLLGALLAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGK  203 (298)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHCC
T ss_conf             9999999983999999999999988768999999998742289788599


No 7  
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase; InterPro: IPR014120   This entry contains solanesyl diphosphate synthases from cyanobacteria or plastid-containing eukaryotes. A member from Arabidopsis (where both plastoquinone and ubiquinone contain the C(45) prenyl moiety) was characterised by heterologous expression as a solanesyl diphosphate synthase..
Probab=100.00  E-value=0  Score=350.14  Aligned_cols=219  Identities=24%  Similarity=0.301  Sum_probs=192.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC-CCCCHHHHHHHHHHHHHCCCCC------CCCCCHHHHHHH
Q ss_conf             999999999999999997675302457157999998750-5860079999999999617882------222402468888
Q gi|254781111|r    9 LQENSKRIDTILDDLLLQTASHMQTQHNDRLLSAIRYAL-LGGKKIRSFLVTECASLFNVNH------LTALRVGAAIEC   81 (237)
Q Consensus         9 l~~~~~~id~~l~~~l~~~~~~~~~~~~~~l~~~~~y~l-~gGKr~R~~l~l~~~~~~~~~~------~~~~~~AaavEl   81 (237)
                      ..+....|+..|+.+-.+++...-..+| .+..+-.|.. .||||+||.+|++++++.-.+.      ..-=++|-++|+
T Consensus         3 ~~~l~~pVe~dL~~l~~NLk~lvGa~HP-iL~AAAEHLF~AGGKR~RPaiVLLvSrAT~~~~GlkElt~~HRRLAEITEm   81 (325)
T TIGR02749         3 ATSLFAPVEDDLELLTDNLKSLVGARHP-ILYAAAEHLFSAGGKRLRPAIVLLVSRATAEEQGLKELTARHRRLAEITEM   81 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH
T ss_conf             6788899999999999877873145686-789999998715896540689999999988736663576103531336867


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999864776544532234455665432434520133222233479999731023412678888876532223566411
Q gi|254781111|r   82 IHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLG  161 (237)
Q Consensus        82 lH~asLihDDI~~~D~s~~RRG~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  161 (237)
                      ||+||||||||  +|+|++|||.||+|..||+.+|||+|||||++|-=+|++.++...-++...+|..+++....     
T Consensus        82 IHTASLVHDDV--~DEsd~RRG~~TVhs~F~trvAVLAGDFLFAQaSWYLANLenLEVVKLls~VI~DFAEGEI~-----  154 (325)
T TIGR02749        82 IHTASLVHDDV--IDESDVRRGVETVHSLFGTRVAVLAGDFLFAQASWYLANLENLEVVKLLSKVITDFAEGEIK-----  154 (325)
T ss_pred             HHHHHHHCCCE--ECCCCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHCCCCCCEEHHHHHHHHHHHHHHHH-----
T ss_conf             75232220220--03543448885534568481676204067899999986167721001454787564117888-----


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HCC
Q ss_conf             332221000000367999999986348999999999975988899999999999984999998676534432---067
Q gi|254781111|r  162 GQMLDIQDEFIDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEED---LPK  236 (237)
Q Consensus       162 GQ~~dl~~~~~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D---~~k  236 (237)
                       |.+.-.+-..+.|+|++-..||||||.+.+|+.+|+++..+.+.++.|+.||+++|+||||.|||||++|.   +||
T Consensus       155 -Qg~~~FD~d~~le~YleKSyYKTASL~AaSskaAAvLS~~~~~v~n~LY~yGkhLGLAFQvvDDiLDFTgsTe~LGK  231 (325)
T TIGR02749       155 -QGLNRFDSDLSLEDYLEKSYYKTASLVAASSKAAAVLSDVDSKVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGK  231 (325)
T ss_pred             -HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCC
T ss_conf             -65552578878887665644678999999989988851143899999877656616335445545157788511567


No 8  
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II; InterPro: IPR014119    The proteins in this entry are component II of the heterodimeric heptaprenyl diphosphate synthase. They are found proximate to the gene for component I (IPR009920 from INTERPRO). This enzyme acts in menaquinone-7 isoprenoid side chain biosynthesis..
Probab=100.00  E-value=0  Score=342.75  Aligned_cols=215  Identities=29%  Similarity=0.421  Sum_probs=187.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC-CCCCHHHHHHHHHHHHHC-CCCCCCCCCHHHHHHH
Q ss_conf             48999999999999999999997675302457157999998750-586007999999999961-7882222402468888
Q gi|254781111|r    4 GLPSKLQENSKRIDTILDDLLLQTASHMQTQHNDRLLSAIRYAL-LGGKKIRSFLVTECASLF-NVNHLTALRVGAAIEC   81 (237)
Q Consensus         4 ~l~~~l~~~~~~id~~l~~~l~~~~~~~~~~~~~~l~~~~~y~l-~gGKr~R~~l~l~~~~~~-~~~~~~~~~~AaavEl   81 (237)
                      .+-+.|++....||+.|++.+.       .-..+.+.|+--+.+ .||||+||.+++++++.. +.+-+..-.+|.++||
T Consensus         4 ~~Y~~l~~Di~~iE~EL~~~v~-------Ga~~~~l~eA~l~LL~AGGKRIRPVFVLLag~fGP~Ydl~~~K~vAV~LEL   76 (325)
T TIGR02748         4 DIYSFLQKDIESIEKELEKAVQ-------GAEHPVLSEAALHLLKAGGKRIRPVFVLLAGKFGPDYDLDKIKHVAVALEL   76 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-------HCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             8899988769999999999985-------206873578999999818940017999867630775335546567655767


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999864776544532234455665432434520133222233479999731023412678888876532223566411
Q gi|254781111|r   82 IHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLG  161 (237)
Q Consensus        82 lH~asLihDDI~~~D~s~~RRG~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  161 (237)
                      ||-||||||||  ||++++|||+||+..+||+..|--+|||||+.|++.+.+-..+....+.+..+.+         +|.
T Consensus        77 IHMASLVHDDV--ID~A~LRRG~~Ti~skW~NRiAMYTGDYlfA~slE~~t~i~dp~~H~~LS~tivE---------vc~  145 (325)
T TIGR02748        77 IHMASLVHDDV--IDDADLRRGKPTIKSKWDNRIAMYTGDYLFAKSLETMTEIKDPRAHQILSKTIVE---------VCL  145 (325)
T ss_pred             HHCCCCCCCCC--CCCCCCCCCCHHHCCCCCCEEEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH---------HHH
T ss_conf             73532025652--0587677884201210277322003358999999998516982788999999998---------862


Q ss_pred             CCCCCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HC
Q ss_conf             3322210000---00367999999986348999999999975988899999999999984999998676534432---06
Q gi|254781111|r  162 GQMLDIQDEF---IDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEED---LP  235 (237)
Q Consensus       162 GQ~~dl~~~~---~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D---~~  235 (237)
                      |+.-+|.+++   .+.-.|++-|++|||=|++.+|++||+.||++++..+.|..||+.+||+|||.|||||+.|-   +|
T Consensus       146 GEIEQIkDkYN~dQ~lR~YLRRIKRKTALLIA~SCqLGAia~Ga~~~~~~~LY~FGYYvGMSyQI~DDiLDFvgTee~LG  225 (325)
T TIGR02748       146 GEIEQIKDKYNFDQNLRTYLRRIKRKTALLIAASCQLGAIASGADEAIVKKLYWFGYYVGMSYQIIDDILDFVGTEEELG  225 (325)
T ss_pred             CCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             21010010137888600366566688999999877652000588987877365533542014544432136646631168


Q ss_pred             C
Q ss_conf             7
Q gi|254781111|r  236 K  236 (237)
Q Consensus       236 k  236 (237)
                      |
T Consensus       226 K  226 (325)
T TIGR02748       226 K  226 (325)
T ss_pred             C
T ss_conf             8


No 9  
>KOG0776 consensus
Probab=100.00  E-value=0  Score=330.81  Aligned_cols=205  Identities=30%  Similarity=0.467  Sum_probs=187.8

Q ss_pred             HHHHHCCC-CCHHHHHHHHHHC-CCCCHHHHHHHHHHHHHCC-CCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             67530245-7157999998750-5860079999999999617-8822224024688889999986477654453223445
Q gi|254781111|r   27 TASHMQTQ-HNDRLLSAIRYAL-LGGKKIRSFLVTECASLFN-VNHLTALRVGAAIECIHCYSLIHDDLPSMDNGYIRRG  103 (237)
Q Consensus        27 ~~~~~~~~-~~~~l~~~~~y~l-~gGKr~R~~l~l~~~~~~~-~~~~~~~~~AaavEllH~asLihDDI~~~D~s~~RRG  103 (237)
                      ....++.. .+..+.++++|.+ .+|||+||.+|+..|++.+ +......++|+++|++|++||||||+||||++++|||
T Consensus        82 l~~~~~~~~~~~~i~~a~ry~~la~gKr~rP~l~~~~~e~~~~g~~~~q~~~A~i~EMIHtaSLIHDDv~~mD~~d~RRG  161 (384)
T KOG0776          82 LHYAVPLANEPLLISEAMRYLLLAGGKRVRPLLCLAACELVGSGDESSQRSLAEIVEMIHTASLIHDDVPCMDDADLRRG  161 (384)
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             33312345665025788888887315505745654577760566507788899999999999998437544464311268


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             56654324345201332222334799997310234126788888765322235664113322210000003679999999
Q gi|254781111|r  104 KPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQDEFIDETQVFMIQKM  183 (237)
Q Consensus       104 ~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~GQ~~dl~~~~~~~~~y~~i~~~  183 (237)
                      +||.|++||+.+|||+||+|++.|++.++...++...+.....+.++.+..+.++...||.+|...  ...++|..+..+
T Consensus       162 kpt~h~vfG~k~AvLaGD~LLa~A~~~la~l~n~~v~elm~~aI~dLv~ge~~~~~~~~~~~d~~~--~~~e~~e~~~~~  239 (384)
T KOG0776         162 KPTNHKVFGNKMAVLAGDALLALASEHLASLENPVVVELMASAIADLVRGEFTQGLVAGEGLDLDD--VGLEYLEFKTLL  239 (384)
T ss_pred             CCCCCHHHCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC--CCHHHHHHHHHH
T ss_conf             876311203025544337899999999986168618999999999999766202445554445677--536889999999


Q ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             86348999999999975988899999999999984999998676534432
Q gi|254781111|r  184 KTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEED  233 (237)
Q Consensus       184 KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D  233 (237)
                      |||+|++.+|++|++++|.++++++.+++||+++|++||+.||++|++..
T Consensus       240 KTAsLla~Sc~~~aILgg~s~ev~e~~~~yGR~lGL~fQvvDDildftks  289 (384)
T KOG0776         240 KTASLLAKSCVAAAILGGGSEEVIEAAFEYGRCLGLAFQVVDDILDFTKS  289 (384)
T ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             89989999999999872899999999999988889899986214475433


No 10 
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. The head-to-head (HH) IPPS catalyze t
Probab=100.00  E-value=2.8e-45  Score=285.26  Aligned_cols=171  Identities=35%  Similarity=0.548  Sum_probs=154.5

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHH
Q ss_conf             7999999999961788222240246888899999864776544532234455665432-434520133222233479999
Q gi|254781111|r   53 IRSFLVTECASLFNVNHLTALRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQ-YDEVTAIIAGNGLLTYAFEII  131 (237)
Q Consensus        53 ~R~~l~l~~~~~~~~~~~~~~~~AaavEllH~asLihDDI~~~D~s~~RRG~pt~h~~-~G~~~AIl~Gd~l~~~a~~~l  131 (237)
                      +||.+++++++++|++.+.++++|+++|++|++|||||||  ||+++.|||+||+|.+ ||.+.||++||++++.+|+.+
T Consensus         1 ~Rp~l~~~~~~~~g~~~~~~~~~a~avElih~~slihDDi--~D~~~~RRg~~t~~~~~~g~~~ail~gd~l~~~a~~~l   78 (236)
T cd00867           1 SRPLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDI--VDDSDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLL   78 (236)
T ss_pred             CCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC--CCCCCCCCCCCCHHHHHHCHHHHHHHHHHHHHHHHHHH
T ss_conf             9659999999983988889999999999999999997753--36997778986568886055789997209999999998


Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf             731023412678888876532223566411332221000---00036799999998634899999999997598889999
Q gi|254781111|r  132 SSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQDE---FIDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKE  208 (237)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~GQ~~dl~~~---~~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~  208 (237)
                      ++....       +.+..+.+.  ...++.||.+|+.+.   ..++++|++|+++|||+||.++|.+++++++.+++..+
T Consensus        79 ~~~~~~-------~~~~~~~~~--~~~l~~Gq~~Dl~~~~~~~~t~~~~~~~~~~KTa~l~~~~~~~~a~~~~~~~~~~~  149 (236)
T cd00867          79 ARLGYP-------RALELFAEA--LRELLEGQALDLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAE  149 (236)
T ss_pred             HHCCCH-------HHHHHHHHH--HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf             623878-------999999999--99999988999760478889999999999988699999999999998198999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999849999986765344320
Q gi|254781111|r  209 RLRCFGENLGIIFQLADDLLDCEEDL  234 (237)
Q Consensus       209 ~l~~~g~~lGiafQi~DD~lD~~~D~  234 (237)
                      .+.+||+++|+||||.||++|++||.
T Consensus       150 ~l~~~g~~lG~AfQi~DDllD~~~d~  175 (236)
T cd00867         150 ALKDYGRALGLAFQLTDDLLDVFGDA  175 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCH
T ss_conf             99999999999999999998840896


No 11 
>KOG0777 consensus
Probab=100.00  E-value=1.1e-36  Score=235.08  Aligned_cols=185  Identities=30%  Similarity=0.360  Sum_probs=159.3

Q ss_pred             HCCCCCHHHHHHHHHHC-CCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             02457157999998750-58600799999999996178822224024688889999986477654453223445566543
Q gi|254781111|r   31 MQTQHNDRLLSAIRYAL-LGGKKIRSFLVTECASLFNVNHLTALRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHI  109 (237)
Q Consensus        31 ~~~~~~~~l~~~~~y~l-~gGKr~R~~l~l~~~~~~~~~~~~~~~~AaavEllH~asLihDDI~~~D~s~~RRG~pt~h~  109 (237)
                      ....+.+.+.+|..|.+ .|||.+|..|.+++.+|+..+.++.-.+.-+||++|++||..|||+  |+|++|||.|++|.
T Consensus        15 tq~~~~~ill~Py~yilq~PGKqfR~~L~~afNhwl~~P~dkLaii~~ivemLHNsSLLIDDIE--DNs~LRRG~pvaHs   92 (322)
T KOG0777          15 TQSQNESILLKPYNYILQKPGKQFRLNLIVAFNHWLNLPKDKLAIISQIVEMLHNSSLLIDDIE--DNSPLRRGQPVAHS   92 (322)
T ss_pred             HHHHHHHHHHCHHHHHHHCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCEEECCCC--CCCHHHCCCCCHHH
T ss_conf             3778889985528899847408899999999999982979899999999999822430211123--36422168722112


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHH----HHHHHHHHHHHHHH
Q ss_conf             24345201332222334799997310234126788888765322235664113322210000----00367999999986
Q gi|254781111|r  110 QYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQDEF----IDETQVFMIQKMKT  185 (237)
Q Consensus       110 ~~G~~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~GQ~~dl~~~~----~~~~~y~~i~~~KT  185 (237)
                      .||++..||+++|+|+++.+.+++...+  +.     +..+++.  +.+++.||.+|+.|+.    +|++.|..|+..||
T Consensus        93 IyGvpStINtANY~yFlalekV~qLdhP--~a-----~kifteq--LleLHrGQGldIYWRD~~tcPtee~Yk~Mv~~KT  163 (322)
T KOG0777          93 IYGVPSTINTANYMYFLALEKVSQLDHP--NA-----IKIFTEQ--LLELHRGQGLDIYWRDFLTCPTEEMYKNMVMNKT  163 (322)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHCCCC--HH-----HHHHHHH--HHHHHCCCCCCEEEECCCCCCCHHHHHHHHHHHC
T ss_conf             0167421103579999999999723781--18-----8999999--9998527885056211375887899999988741


Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             348999999999975988899999999999984999998676534
Q gi|254781111|r  186 GALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDC  230 (237)
Q Consensus       186 a~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~  230 (237)
                      |.||+++..+.-..+.    ..+.+..+-..+|+.|||+|||+..
T Consensus       164 GGLF~La~rLMqlfS~----~kedl~pl~n~LGl~fQIRDDY~NL  204 (322)
T KOG0777         164 GGLFRLALRLMQLFSH----HKEDLVPLINLLGLIFQIRDDYLNL  204 (322)
T ss_pred             CCHHHHHHHHHHHHHH----CCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             5679999999999876----3424788999876863004444031


No 12 
>KOG0711 consensus
Probab=100.00  E-value=5.3e-34  Score=219.37  Aligned_cols=209  Identities=22%  Similarity=0.278  Sum_probs=157.5

Q ss_pred             HHHHHHHHHHHHCCCC-CHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCC-------CCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             9999997675302457-1579999987505860079999999999617882-------2224024688889999986477
Q gi|254781111|r   20 LDDLLLQTASHMQTQH-NDRLLSAIRYALLGGKKIRSFLVTECASLFNVNH-------LTALRVGAAIECIHCYSLIHDD   91 (237)
Q Consensus        20 l~~~l~~~~~~~~~~~-~~~l~~~~~y~l~gGKr~R~~l~l~~~~~~~~~~-------~~~~~~AaavEllH~asLihDD   91 (237)
                      +.++.+....+....+ .+.+.+...|.+.|||..|+..++.+.+++.++.       ..+..+++.||++|+.+||-||
T Consensus        20 vr~i~~~~~~~~~~~da~~~~~~~L~yN~~GGK~nRgl~vv~s~~~L~~~~~l~~~~~~~a~~lGw~vElLQaffLiaDD   99 (347)
T KOG0711          20 VRVLTEDLMAHGESGDATEWLKEVLDYNVIGGKLNRGLSVVDSFKALVEPRKLDEEELQLALILGWCVELLQAFFLVADD   99 (347)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999875206897679999999876027675224540489999986577677889999999998999999988987545


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHH
Q ss_conf             65445322344556654324345-20133222233479999731023412678888876532223566411332221000
Q gi|254781111|r   92 LPSMDNGYIRRGKPTVHIQYDEV-TAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQDE  170 (237)
Q Consensus        92 I~~~D~s~~RRG~pt~h~~~G~~-~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~GQ~~dl~~~  170 (237)
                      |  ||+|.+|||+|||+.+.|++ .|||-+-.|-+-...+|.+.....+-  +.+ +.++.+.+.... +.||.++...-
T Consensus       100 I--MDnS~tRRGqpCWy~~~gVG~~AINDA~lLea~Iy~lLkk~fr~~~~--y~~-l~elf~ev~f~T-~lGdllt~~~~  173 (347)
T KOG0711         100 I--MDNSKTRRGQPCWYQKPGVGLDAINDAFLLEAAIYKLLKKHFRNIYC--YVD-LVELFHEVTFQT-ELGDLLTTPEG  173 (347)
T ss_pred             H--HCCCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCH--HHH-HHHHHHHHHHHH-HHHCCCCCCCC
T ss_conf             3--20100237884346668863666508999999999999986268860--788-999887888887-63010147543


Q ss_pred             -----HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             -----000367999999986348-9999999999759-888999999999999849999986765344320
Q gi|254781111|r  171 -----FIDETQVFMIQKMKTGAL-MCFACESGAIMAH-ASQNEKERLRCFGENLGIIFQLADDLLDCEEDL  234 (237)
Q Consensus       171 -----~~~~~~y~~i~~~KTa~l-f~~~~~~ga~lag-~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~  234 (237)
                           ..|++.|..|+++|||.| |.+|..++-++|| .+.+.......+...+|..||++||||||+||-
T Consensus       174 ~~~ls~fsl~~y~~Iv~~KTa~YsFYLPialAl~~ag~~~~k~~~~~k~v~~~lg~~FQvQDDYLd~fgDp  244 (347)
T KOG0711         174 NKDLSKFSLEKYVFIVEYKTAYYSFYLPVALALLLAGIANLKEHACEKKVLLLLGEYFQVQDDYLDCFGDP  244 (347)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCH
T ss_conf             30376641777778863131202330189999998423058877568899999988983106777742882


No 13 
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoter
Probab=99.94  E-value=1.7e-27  Score=181.04  Aligned_cols=153  Identities=35%  Similarity=0.496  Sum_probs=132.6

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC---CCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             40246888899999864776544532234455665432---434520133222233479999731023412678888876
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQ---YDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLS  149 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~~~D~s~~RRG~pt~h~~---~G~~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~  149 (237)
                      ...++++|++|++++|||||  +|++.+|||+|++|..   ||.+.+++.|+++++.+++.+.....   .    .....
T Consensus        13 ~~~~~~~~~~~~~~~i~DDi--~D~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~----~~~~~   83 (243)
T cd00385          13 SRLRAAVEKLHAASLVHDDI--VDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAREGS---P----EALEI   83 (243)
T ss_pred             HHHHHHHHHHHHHHHHHHCC--CCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC---H----HHHHH
T ss_conf             99999999999999999715--669999886385999987048399999999999999999986478---9----99999


Q ss_pred             HHHHHHHHHHHCCCCCCCCHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             532223566411332221000---00036799999998634899999999997598889999999999998499999867
Q gi|254781111|r  150 LTHNIGLQGMLGGQMLDIQDE---FIDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADD  226 (237)
Q Consensus       150 ~~~~~~~~~l~~GQ~~dl~~~---~~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD  226 (237)
                      +.++  ...++.||.+|+.+.   .++.++|.++++.|||.++...+..++..++.+.+....+.++|..+|++||+.||
T Consensus        84 ~~~~--~~~~~~g~~~d~~~~~~~~~s~~~y~~~~~~kta~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~a~ql~nD  161 (243)
T cd00385          84 LAEA--LLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTND  161 (243)
T ss_pred             HHHH--HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999--99999999999986579999999999974228999999999999998099999999999999999999999995


Q ss_pred             HHHHHHHHCC
Q ss_conf             6534432067
Q gi|254781111|r  227 LLDCEEDLPK  236 (237)
Q Consensus       227 ~lD~~~D~~k  236 (237)
                      ++|+++|..+
T Consensus       162 l~d~~~d~~~  171 (243)
T cd00385         162 LLDYEGDAER  171 (243)
T ss_pred             CCCCCCCCCC
T ss_conf             6246848024


No 14 
>pfam07307 HEPPP_synt_1 Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1. This family contains subunit 1 of bacterial heptaprenyl diphosphate synthase (HEPPP synthase) (EC:2.5.1.30) (approximately 230 residues long). The enzyme consists of two subunits, both of which are required for catalysis of heptaprenyl diphosphate synthesis.
Probab=94.54  E-value=0.26  Score=27.00  Aligned_cols=80  Identities=10%  Similarity=0.070  Sum_probs=53.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf             78822224024688889999986477654453223445566543243452013322223347999973102341267888
Q gi|254781111|r   66 NVNHLTALRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQ  145 (237)
Q Consensus        66 ~~~~~~~~~~AaavEllH~asLihDDI~~~D~s~~RRG~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~  145 (237)
                      ..+++.+.....++=|+|.|-..||-|   |+....+.  ..+  =...-.|++|||.-++-+.+|+..+...--+..+.
T Consensus        29 ~~~~~~~~~~i~t~mLvq~aLDTHd~V---~~~~~~~~--~~~--k~RQLtVLAGDyyS~lYY~lLa~~~~i~lIr~la~  101 (212)
T pfam07307        29 ELTPEQAERYILTAMLVQIALDTHDKV---SNANAETQ--ETK--KNRQLTVLAGDYYSGLYYYLLSESGDIALIRLLAE  101 (212)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHH---CCCCCCCC--HHH--HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             999899999999999999998778764---54231210--355--63103201102331899999983798699999999


Q ss_pred             HHHHHHH
Q ss_conf             8876532
Q gi|254781111|r  146 LMLSLTH  152 (237)
Q Consensus       146 ~~~~~~~  152 (237)
                      .+..+++
T Consensus       102 ~I~eiNe  108 (212)
T pfam07307       102 AIKEINE  108 (212)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 15 
>TIGR03464 HpnC squalene synthase HpnC. This family of genes are members of a superfamily (pfam00494) of phytoene and squalene synthases which catalyze the head-t0-head condensation of polyisoprene pyrophosphates. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnD gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.
Probab=94.08  E-value=0.42  Score=25.76  Aligned_cols=72  Identities=10%  Similarity=0.082  Sum_probs=47.6

Q ss_pred             HHHHCCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             664113322210000-0036799999998634899999999997598889999999999998499999867653443206
Q gi|254781111|r  157 QGMLGGQMLDIQDEF-IDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEEDLP  235 (237)
Q Consensus       157 ~~l~~GQ~~dl~~~~-~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~~  235 (237)
                      ..++.|+..|+.... .|.+++..-+..--|+...+.+.   +++..+++    ...++..+|+|+|+.|=+-|+-.|..
T Consensus        89 ~~li~g~~~Dl~~~~~~t~~dL~~Yc~~vAg~VG~~~~~---i~g~~~~~----~~~~a~~lG~AlQltNilRDi~eD~~  161 (266)
T TIGR03464        89 LDLLDAFRQDVVVTRYATWAELLDYCRRSANPVGRLVLD---LYGASDPE----NVALSDAICTALQLINFWQDVGKDLR  161 (266)
T ss_pred             HHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH---HHCCCCHH----HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999884146799999999999999963899999999---82789888----99999999799999999998587998


No 16 
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS), head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosp
Probab=94.03  E-value=0.25  Score=27.09  Aligned_cols=73  Identities=19%  Similarity=0.188  Sum_probs=48.1

Q ss_pred             HHHHCCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             664113322210000-0036799999998634899999999997598889999999999998499999867653443206
Q gi|254781111|r  157 QGMLGGQMLDIQDEF-IDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEEDLP  235 (237)
Q Consensus       157 ~~l~~GQ~~dl~~~~-~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~~  235 (237)
                      ..++.|+..|+.... .|++++..-+.+-.|+.-.+.+.+   ++..+   .+....++..+|+|+|+.|=+-|+-.|..
T Consensus        96 ~~li~g~~~Dl~~~~~~t~~eL~~Yc~~vAg~VG~l~~~i---~g~~~---~~~~~~~A~~lG~AlQltNilRDi~eD~~  169 (265)
T cd00683          96 RDLLAGMAMDLDKRRYETLDELDEYCYYVAGVVGLMLLRV---FGASS---DEAALERARALGLALQLTNILRDVGEDAR  169 (265)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH---HCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999987567899999999999997117999999999---58788---18899999998899999989987999995


No 17 
>TIGR03465 HpnD squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.
Probab=93.93  E-value=0.32  Score=26.48  Aligned_cols=71  Identities=20%  Similarity=0.262  Sum_probs=47.6

Q ss_pred             HHHCCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             64113322210000-0036799999998634899999999997598889999999999998499999867653443206
Q gi|254781111|r  158 GMLGGQMLDIQDEF-IDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEEDLP  235 (237)
Q Consensus       158 ~l~~GQ~~dl~~~~-~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~~  235 (237)
                      .++.|+..|+.... .|.+++..-+..--|+...+++.   +++..+++    ...++..+|+|+|+.+=+-|+-.|..
T Consensus        89 ~li~g~~~Dl~~~~~~t~~~L~~Y~~~vA~~vg~m~~~---ilg~~~~~----~~~~A~~lG~A~QltNilRDv~eD~~  160 (266)
T TIGR03465        89 EVIDGMEMDLEQTRYPDFAELDLYCDRVAGAVGRLSAR---IFGATDAR----TLEYAHHLGRALQLTNILRDVGEDAR  160 (266)
T ss_pred             HHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH---HCCCCCHH----HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999985578999999999999999863699999998---80899757----89999999999999999997188997


No 18 
>pfam00494 SQS_PSY Squalene/phytoene synthase.
Probab=93.61  E-value=0.28  Score=26.83  Aligned_cols=74  Identities=16%  Similarity=0.214  Sum_probs=49.2

Q ss_pred             HHHHCCCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             66411332221000-00036799999998634899999999997598889999999999998499999867653443206
Q gi|254781111|r  157 QGMLGGQMLDIQDE-FIDETQVFMIQKMKTGALMCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEEDLP  235 (237)
Q Consensus       157 ~~l~~GQ~~dl~~~-~~~~~~y~~i~~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~~  235 (237)
                      ..++.|+..|+... ..|.+++..-+.+--|+...+.+.+   ++..+  .......++..+|+|+|+.+=+-|+-.|..
T Consensus        92 ~~li~g~~~Dl~~~~~~t~~dL~~Y~~~vAg~Vg~l~~~i---~g~~~--~~~~~~~~A~~lG~AlQltNilRDi~eD~~  166 (262)
T pfam00494        92 LELIDGMEMDLEKDRYETLAELEEYCYRVAGVVGLLLLRL---LGVRD--DAEAADEAARHLGLALQLTNILRDVGEDAR  166 (262)
T ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH---HCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9999999987367999999999999988168999999999---57789--458899999999999999999974699983


No 19 
>PRK13594 consensus
Probab=70.41  E-value=7.7  Score=18.31  Aligned_cols=44  Identities=16%  Similarity=-0.031  Sum_probs=24.4

Q ss_pred             HHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999975988-8999999999999849999986765344320
Q gi|254781111|r  191 FACESGAIMAHAS-QNEKERLRCFGENLGIIFQLADDLLDCEEDL  234 (237)
Q Consensus       191 ~~~~~ga~lag~~-~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~  234 (237)
                      .+.-.|+...+.. ....-.+.-+.-.+.++=.|.-|+.|.+||.
T Consensus       139 ~~~~fg~~~~~~~~~~~~~~l~~~aFl~~l~REIvKDieDieGD~  183 (278)
T PRK13594        139 SIFLFGGAIAGTEGLLSMLPIAAITFLAMLARELLKDAEDIEGDR  183 (278)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             999999999745641899999999999999999994553012388


No 20 
>KOG0018 consensus
Probab=67.66  E-value=3.2  Score=20.55  Aligned_cols=13  Identities=15%  Similarity=0.531  Sum_probs=4.7

Q ss_pred             CCCCCCCCCHHHH
Q ss_conf             4324345201332
Q gi|254781111|r  108 HIQYDEVTAIIAG  120 (237)
Q Consensus       108 h~~~G~~~AIl~G  120 (237)
                      |.+|+.+.++..|
T Consensus       516 ~kkYeiAvt~~Lg  528 (1141)
T KOG0018         516 QKKYEIAVTVVLG  528 (1141)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             8888999999975


No 21 
>pfam06783 UPF0239 Uncharacterized protein family (UPF0239).
Probab=61.83  E-value=9.4  Score=17.81  Aligned_cols=20  Identities=40%  Similarity=0.481  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999998499999
Q gi|254781111|r  204 QNEKERLRCFGENLGIIFQL  223 (237)
Q Consensus       204 ~~~~~~l~~~g~~lGiafQi  223 (237)
                      ++..+.+-+||..+|-.||+
T Consensus        15 ED~~~~~~rygl~~gaifq~   34 (85)
T pfam06783        15 EDFFELLIRYGLFLGAIFQF   34 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999999999999999


No 22 
>pfam10776 DUF2600 Protein of unknown function (DUF2600). This is a bacterial family of proteins. Some members in the family are annotated as YtpB however currently no function is known.
Probab=55.32  E-value=8.5  Score=18.07  Aligned_cols=33  Identities=21%  Similarity=0.371  Sum_probs=16.9

Q ss_pred             CCCHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98889999999-9999984999998676534432
Q gi|254781111|r  201 HASQNEKERLR-CFGENLGIIFQLADDLLDCEED  233 (237)
Q Consensus       201 g~~~~~~~~l~-~~g~~lGiafQi~DD~lD~~~D  233 (237)
                      +.+++....+. .|--.+.-.-=+.|=++|...|
T Consensus       205 ~~t~~~a~~i~~aYFPwi~gLHiLLDyfIDqeED  238 (330)
T pfam10776       205 DLTEEDADKIRDAYFPWIQGLHILLDYFIDQEED  238 (330)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHH
T ss_conf             9999999999983318997999999987356766


No 23 
>PRK13593 consensus
Probab=54.07  E-value=16  Score=16.52  Aligned_cols=46  Identities=13%  Similarity=-0.054  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999975988-8999999999999849999986765344320
Q gi|254781111|r  189 MCFACESGAIMAHAS-QNEKERLRCFGENLGIIFQLADDLLDCEEDL  234 (237)
Q Consensus       189 f~~~~~~ga~lag~~-~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~  234 (237)
                      ...+...|+...+.. ....--+.-+.--.....-+.-|+.|.+||.
T Consensus       144 ~g~~~l~G~~av~~~~~~~~~~l~~~~fl~t~~reiikdi~DieGD~  190 (283)
T PRK13593        144 TGSTFLFGAAAVGRILAFGVVVLFALAALATAAREIIKDVEDLDGDR  190 (283)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999758887389999999999999999999998642198


No 24 
>KOG1345 consensus
Probab=50.64  E-value=7.1  Score=18.54  Aligned_cols=24  Identities=38%  Similarity=0.585  Sum_probs=19.8

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             4024688889999986477654453
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLPSMDN   97 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~~~D~   97 (237)
                      -+++.|+|++|.--|||.||. +||
T Consensus       128 ~ql~SAi~fMHsknlVHRdlK-~eN  151 (378)
T KOG1345         128 AQLLSAIEFMHSKNLVHRDLK-AEN  151 (378)
T ss_pred             HHHHHHHHHHHCCCHHHCCCC-CCE
T ss_conf             999989877630012202123-110


No 25 
>KOG1166 consensus
Probab=45.18  E-value=16  Score=16.49  Aligned_cols=36  Identities=25%  Similarity=0.291  Sum_probs=29.7

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             4024688889999986477654453223445566543
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLPSMDNGYIRRGKPTVHI  109 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~~~D~s~~RRG~pt~h~  109 (237)
                      ..+.-+||-+|..-.||-||- -||--+||+.+.-|-
T Consensus       801 ~qml~ive~lH~~~IIHgDiK-PDNfll~~~~~~~~~  836 (974)
T KOG1166         801 CQMLRIVEHLHAMGIIHGDIK-PDNFLLRREICADSD  836 (974)
T ss_pred             HHHHHHHHHHHHCCEECCCCC-CCEEEEECCCCCCCC
T ss_conf             999999999875163104678-651475146678886


No 26 
>PRK12887 ubiA tocopherol phytyltransferase; Reviewed
Probab=42.46  E-value=24  Score=15.44  Aligned_cols=115  Identities=14%  Similarity=0.063  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             88899999864776544532234455665432434520133222233479999731023412678888876532223566
Q gi|254781111|r   79 IECIHCYSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYAFEIISSPKTQLKDNIRSQLMLSLTHNIGLQG  158 (237)
Q Consensus        79 vEllH~asLihDDI~~~D~s~~RRG~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (237)
                      +-+.-.+-=+..|+|++++| .+.|-.|.-.++|...+-..+-+++..++-...-.+.. .............++....-
T Consensus       192 ~~~fa~~Iai~KDipDIEGD-r~~GI~Tl~V~LG~k~v~~l~~~ll~~~Y~~~i~~g~~-~~~~~~~~~~~~~H~~l~~~  269 (309)
T PRK12887        192 VLVFTFAIAIFKDIPDMEGD-RQYNITTFTLRLGKQRVFKLSCWVLTACYLGMIAVGLL-FLPSINSAFLIVSHLLLLAL  269 (309)
T ss_pred             HHHHHHHHHHHCCCCCCCCC-HHCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999998157423432-75197654347538999999999999999999999997-24668889999999999999


Q ss_pred             -HHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             -4113322210000003679999999863489999999
Q gi|254781111|r  159 -MLGGQMLDIQDEFIDETQVFMIQKMKTGALMCFACES  195 (237)
Q Consensus       159 -l~~GQ~~dl~~~~~~~~~y~~i~~~KTa~lf~~~~~~  195 (237)
                       .-..|..|++++.--.+-|.-|.+.=-+.||-.|..|
T Consensus       270 l~~~~~~vdl~~k~~i~sfY~fIWkLFy~EY~l~P~~~  307 (309)
T PRK12887        270 LWWRSQRVDLEDKSAIAQFYQFIWKLFFLEYLLFPIAC  307 (309)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99997307853468999999999999999999999998


No 27 
>cd05105 PTKc_PDGFR_alpha Catalytic Domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor alpha. Protein Tyrosine Kinase (PTK) family; Platelet Derived Growth Factor Receptor (PDGFR) alpha; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. PDGFR alpha is a receptor tyr kinase (RTK) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding to its ligands, the PDGFs, leads to receptor dimerization, trans phosphorylation and activation, and intracellular signaling. PDGFR alpha forms homodimers or heterodimers with PDGFR beta, depending on the nature of the PDGF ligand. PDGF-AA, PDGF-
Probab=36.57  E-value=10  Score=17.65  Aligned_cols=22  Identities=23%  Similarity=0.431  Sum_probs=19.5

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +.++|.++|++|.-..||-|+.
T Consensus       243 a~qIA~GM~YL~s~~iIHRDLa  264 (400)
T cd05105         243 TYQVARGMEFLASKNCVHRDLA  264 (400)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999987784646577


No 28 
>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit; InterPro: IPR006138   Respiratory-chain NADH dehydrogenase (1.6.5.3 from EC) (also known as complex I or NADH-ubiquinone oxidoreductase) is an oligomeric enzymatic complex located in the inner mitochondrial membrane which also seems to exist in the chloroplast and in cyanobacteria (as a NADH-plastoquinone oxidoreductase).    Among the 25 to 30 polypeptide subunits of this bioenergetic enzyme complex there is one with a molecular weight of 20 kDa (in mammals) , which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 4Fe-4S iron-sulphur cluster. The 20 kDa subunit has been found to be nuclear encoded, as a precursor form with a transit peptide in mammals, and in Neurospora crassa. It is mitochondrial encoded in Paramecium (gene psbG) and chloroplast encoded in various higher plants (gene ndhK or psbG).; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0006120 mitochondrial electron transport NADH to ubiquinone.
Probab=35.65  E-value=22  Score=15.62  Aligned_cols=33  Identities=27%  Similarity=0.209  Sum_probs=22.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCCCC--CCCCCCCCC
Q ss_conf             2222402468888999998647765445--322344556
Q gi|254781111|r   69 HLTALRVGAAIECIHCYSLIHDDLPSMD--NGYIRRGKP  105 (237)
Q Consensus        69 ~~~~~~~AaavEllH~asLihDDI~~~D--~s~~RRG~p  105 (237)
                      +..-=-++||||++|+++=-||    +|  ++..+|.-|
T Consensus        21 P~tFGlACCaIEMm~t~~s~yD----ldRFG~~~fR~SP   55 (146)
T TIGR01957        21 PLTFGLACCAIEMMATGASRYD----LDRFGSVVFRASP   55 (146)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCC----HHHCCCCCCCCCC
T ss_conf             1122365589999997554126----3133721587787


No 29 
>cd05061 PTKc_InsR Catalytic Domain of the Protein Tyrosine Kinase, Insulin Receptor. Protein Tyrosine Kinase (PTK) family; Insulin Receptor (InsR); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. InsR is a receptor tyr kinase (RTK) that is composed of two alphabeta heterodimers. Binding of the insulin ligand to the extracellular alpha subunit activates the intracellular tyr kinase domain of the transmembrane beta subunit. Receptor activation leads to autophosphorylation, stimulating downstream kinase activities, which initiate signaling cascades and biological function. InsR signaling plays an important role in many cellular processes including glucose homeostasis, glycogen synthesis, lipid and protein meta
Probab=32.93  E-value=11  Score=17.31  Aligned_cols=22  Identities=18%  Similarity=0.451  Sum_probs=18.5

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|....||-||-
T Consensus       125 ~~qia~gl~yLH~~~IiHRDLK  146 (288)
T cd05061         125 AAEIADGMAYLNAKKFVHRDLA  146 (288)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999861995547668


No 30 
>cd05038 PTKc_Jak_rpt2 Catalytic (Repeat 2) Domain of the Protein Tyrosine Kinases, Janus kinases. Protein Tyrosine Kinase (PTK) family; Janus kinase (Jak) subfamily; catalytic (c) domain (repeat 2). The Jak subfamily is composed of Jak1, Jak2, Jak3, TYK2, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Jak subfamily proteins are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase catalytic domain. Most Jaks are expressed in a wide variety of tissues, except for Jak3, which is expressed only in hematopoietic cells. Jaks are crucial for cytokine receptor signaling. They are activated by aut
Probab=32.88  E-value=9.6  Score=17.76  Aligned_cols=22  Identities=32%  Similarity=0.579  Sum_probs=19.3

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|....||-||.
T Consensus       115 ~~qia~gL~yLH~~~iiHrDlK  136 (279)
T cd05038         115 ALQIAKGMDYLGSKRLIHRDLA  136 (279)
T ss_pred             HHHHHHHHHHHHHCCEEECCCC
T ss_conf             9999999998875897655256


No 31 
>cd05097 PTKc_DDR_like Catalytic Domain of Discoidin Domain Receptor-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Discoidin domain receptor (DDR)-like proteins; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR-like proteins are members of the DDR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDRs regulate cell adhesion, proliferation, and extracellular matrix remodeling. They have been linked to a variety of human cancers including 
Probab=32.78  E-value=10  Score=17.65  Aligned_cols=22  Identities=18%  Similarity=0.560  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-..||-||.
T Consensus       135 a~qia~gl~yLh~~~iiHrDLK  156 (295)
T cd05097         135 AVQIASGMKYLASLNFVHRDLA  156 (295)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999999854985526667


No 32 
>cd05049 PTKc_Trk Catalytic Domain of the Protein Tyrosine Kinases, Tropomyosin Related Kinases. Protein Tyrosine Kinase (PTK) family; Tropomyosin related kinase (Trk) subfamily; catalytic (c) domain. The Trk subfamily consists of TrkA, TrkB, TrkC, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Trk subfamily members are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, the nerve growth factor (NGF) family of neutrotrophins, leads to Trk receptor oligomerization and activation of the catalyt
Probab=32.70  E-value=11  Score=17.45  Aligned_cols=22  Identities=18%  Similarity=0.471  Sum_probs=19.3

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|....||-||.
T Consensus       128 ~~qia~gl~yLH~~~ivHrDlK  149 (280)
T cd05049         128 AVQIASGMVYLASQHFVHRDLA  149 (280)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999998866893426657


No 33 
>cd00192 PTKc Catalytic Domain of Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family, catalytic domain. This PTKc family is part of a larger superfamily that includes the catalytic domains of protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. They can be classified into receptor and non-receptor tyr kinases. PTKs play important roles in many cellular processes including, lymphocyte activation, epithelium growth and maintenance, metabolism control, organogenesis regulation, survival, proliferation, differentiation, migration, adhesion, motility, and morphogenesis. Receptor tyr kinases (RTKs) are integral membrane proteins which contain an extracellular ligand-binding region, a transmembrane segment, and an intracellular tyr kinase domain. RTKs are usually activated through ligan
Probab=32.30  E-value=13  Score=16.94  Aligned_cols=22  Identities=23%  Similarity=0.537  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|...+||-||.
T Consensus       110 ~~qia~gl~yLH~~~iiHrDiK  131 (261)
T cd00192         110 AYQIASGMEYLASKNFVHRDLA  131 (261)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999976995578776


No 34 
>cd06610 STKc_OSR1_SPAK Serine/threonine kinases (STKs), oxidative stress response kinase (OSR1) and Ste20-related proline alanine-rich kinase (SPAK) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The OSR1 and SPAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. SPAK is also referred to as STK39 or PASK (proline-alanine-rich STE20-related kinase). OSR1 and SPAK regulate the activity of cation-chloride cotransporters through direct interaction and phosphorylation. They are also implicated in cytoskeletal rearrangement, cell differentiation, transformation and proliferation. OSR1 and SPAK contain a conserved C-terminal (CCT) domain, which recognizes a unique motif ([RK]FX[VI]) present in their activating kinases (WN
Probab=32.23  E-value=13  Score=17.04  Aligned_cols=21  Identities=29%  Similarity=0.371  Sum_probs=18.3

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC
Q ss_conf             402468888999998647765
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~   93 (237)
                      .+++.|++.+|.--.||-||.
T Consensus       109 ~qi~~al~ylH~~~iiHRDiK  129 (266)
T cd06610         109 KEVLKGLEYLHKNGQIHRDIK  129 (266)
T ss_pred             HHHHHHHHHHHHCCCCCCCCC
T ss_conf             999999999997893226666


No 35 
>cd05085 PTKc_Fer Catalytic Domain of the Protein Tyrosine Kinase, Fer. Protein Tyrosine Kinase (PTK) family; Fer kinase; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Fer kinase is a member of the Fes subfamily of proteins which are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal region with FCH (Fes/Fer/CIP4 homology) and coiled-coil domains, followed by a SH2 domain, and a C-terminal catalytic domain. Fer kinase is expressed in a wide variety of tissues, and is found to reside in both the cytoplasm and the nucleus. It plays important roles in neuronal polarization and neurite development, cytoskeletal reorganization, cell migration, growth factor signaling, and the regulation of cell-c
Probab=32.09  E-value=11  Score=17.36  Aligned_cols=22  Identities=32%  Similarity=0.469  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-..||-||.
T Consensus        99 ~~~ia~gl~yLH~~~iiHrDlK  120 (250)
T cd05085          99 ALDAAAGMAYLESKNCIHRDLA  120 (250)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999842996447537


No 36 
>cd05099 PTKc_FGFR4 Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 4. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 4 (FGFR4); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR4 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to
Probab=32.06  E-value=11  Score=17.36  Aligned_cols=22  Identities=32%  Similarity=0.483  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-.+||-||.
T Consensus       140 a~qia~gl~yLH~~~iiHRDLK  161 (314)
T cd05099         140 AYQVARGMEYLESRRCIHRDLA  161 (314)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999984899688767


No 37 
>cd05055 PTKc_PDGFR Catalytic Domain of the Protein Tyrosine Kinases, Platelet Derived Growth Factor Receptors. Protein Tyrosine Kinase (PTK) family; Platelet Derived Growth Factor Receptor (PDGFR) subfamily; catalytic (c) domain. The PDGFR subfamily consists of PDGFR alpha, PDGFR beta, KIT, CSF-1R, the mammalian FLT3, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. PDGFR subfamily members are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. PDGFR kinase domains are autoinhibited by their juxtamembrane regions containing tyr residues. The binding to their ligands leads to recept
Probab=31.67  E-value=13  Score=16.95  Aligned_cols=22  Identities=23%  Similarity=0.401  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +.++|.+++.+|.-.+||-||-
T Consensus       147 ~~qia~gl~yLH~~~iiHRDLK  168 (302)
T cd05055         147 SYQVAKGMAFLASKNCIHRDLA  168 (302)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999976894777465


No 38 
>cd05096 PTKc_DDR1 Catalytic Domain of the Protein Tyrosine Kinase, Discoidin Domain Receptor 1. Protein Tyrosine Kinase (PTK) family; mammalian Discoidin domain receptor 1 (DDR1) and homologs; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR1 is a member of the DDR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDR1 binds to all collagens tested to date (types I-IV). It is widely expressed in many tissues. It is abundant in the brain and is also found in k
Probab=31.61  E-value=8.1  Score=18.19  Aligned_cols=22  Identities=23%  Similarity=0.602  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-..||-||.
T Consensus       144 a~qia~gl~yLh~~~iiHrDLK  165 (304)
T cd05096         144 ALQIASGMKYLSSLNFVHRDLA  165 (304)
T ss_pred             HHHHHHHHHHHHCCCEEECCCC
T ss_conf             9999998789872998827566


No 39 
>pfam04703 FaeA FaeA-like protein. This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase.
Probab=31.51  E-value=14  Score=16.73  Aligned_cols=22  Identities=23%  Similarity=0.385  Sum_probs=16.1

Q ss_pred             HCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             4776544532234455665432
Q gi|254781111|r   89 HDDLPSMDNGYIRRGKPTVHIQ  110 (237)
Q Consensus        89 hDDI~~~D~s~~RRG~pt~h~~  110 (237)
                      .+|--.+..++.|||.|+.|..
T Consensus        39 Lek~g~i~rsp~rrG~~tlW~l   60 (61)
T pfam04703        39 LEKEGKIERSPLRRGAPTLWRL   60 (61)
T ss_pred             HHHCCCEECCCCCCCCHHHHHC
T ss_conf             9870752305534672146650


No 40 
>cd05053 PTKc_FGFR Catalytic Domain of the Protein Tyrosine Kinases, Fibroblast Growth Factor Receptors. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor (FGFR) subfamily; catalytic (c) domain. The FGFR subfamily consists of FGFR1, FGFR2, FGFR3, FGFR4, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K).PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR subfamily members are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, and to heparin/heparan sulfate (HS) results in the formation of a ternary complex, which leads to receptor dimerization and activation, 
Probab=31.05  E-value=14  Score=16.86  Aligned_cols=22  Identities=32%  Similarity=0.465  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|...+||-||-
T Consensus       139 ~~qia~gl~yLH~~~IvHRDlK  160 (294)
T cd05053         139 AYQVARGMEYLASKKCIHRDLA  160 (294)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999984899677677


No 41 
>cd05102 PTKc_VEGFR3 Catalytic Domain of the Protein Tyrosine Kinase, Vascular Endothelial Growth Factor Receptor 3. Protein Tyrosine Kinase (PTK) family; Vascular Endothelial Growth Factor Receptor 3 (VEGFR3); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. VEGFR3 (or Flt4) is a member of the VEGFR subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and an intracellular catalytic domain. In VEGFR3, the fifth Ig-like domain is replaced by a disulfide bridge. The binding of VEGFRs to their ligands, the VEGFs, leads to receptor dimerization, activation, and intracellular signaling. V
Probab=31.05  E-value=14  Score=16.82  Aligned_cols=21  Identities=29%  Similarity=0.480  Sum_probs=18.8

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC
Q ss_conf             402468888999998647765
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~   93 (237)
                      .++|.+++.+|..-.||-||.
T Consensus       181 ~qia~gm~yLh~~~iiHRDLK  201 (338)
T cd05102         181 FQVARGMEFLASRKCIHRDLA  201 (338)
T ss_pred             HHHHHHHHHHHHCCCCCCCCC
T ss_conf             999999999985892346688


No 42 
>cd05074 PTKc_Tyro3 Catalytic Domain of the Protein Tyrosine Kinase, Tyro3. Protein Tyrosine Kinase (PTK) family; Tyro3; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Tyro3 (or Sky) is a member of the Axl subfamily, which is composed of receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with two immunoglobulin-like domains followed by two fibronectin type III repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, Gas6 and protein S, leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. Tyro3 is predominantly expressed in the central nervous system and the brain, and functions as a neurotrophic fac
Probab=30.75  E-value=13  Score=16.95  Aligned_cols=22  Identities=23%  Similarity=0.528  Sum_probs=18.9

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-..||-||-
T Consensus       119 ~~qia~gl~yLH~~~iiHRDlK  140 (273)
T cd05074         119 MIDIASGMEYLSSKNFIHRDLA  140 (273)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999985893625565


No 43 
>cd05107 PTKc_PDGFR_beta Catalytic Domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta. Protein Tyrosine Kinase (PTK) family; Platelet Derived Growth Factor Receptor (PDGFR) beta; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. PDGFR beta is a receptor tyr kinase (RTK) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding to its ligands, the PDGFs, leads to receptor dimerization, trans phosphorylation and activation, and intracellular signaling. PDGFR beta forms homodimers or heterodimers with PDGFR alpha, depending on the nature of the PDGF ligand. PDGF-BB and PDGF-D
Probab=30.55  E-value=13  Score=17.00  Aligned_cols=22  Identities=23%  Similarity=0.443  Sum_probs=19.5

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +.++|..+|++|.--.||-|+.
T Consensus       245 a~qIA~GM~yL~s~~iiHRDLa  266 (401)
T cd05107         245 SYQVANGMEFLASKNCVHRDLA  266 (401)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999989988976787254466


No 44 
>cd05036 PTKc_ALK_LTK Catalytic Domain of the Protein Tyrosine Kinases, Anaplastic Lymphoma Kinase and Leukocyte Tyrosine Kinase. Protein Tyrosine Kinase (PTK) family; Anaplastic lymphoma kinase (ALK) and Leukocyte tyrosine (tyr) kinase (LTK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyr residues in protein substrates. ALK and LTK are orphan receptor tyr kinases (RTKs) whose ligands are not yet well-defined. RTKs contain an extracellular ligand-binding domain, a transmembrane region, and an intracellular tyr kinase domain. They are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. ALK appears to play an important role in mammalian neural development as well
Probab=30.50  E-value=16  Score=16.54  Aligned_cols=21  Identities=19%  Similarity=0.306  Sum_probs=18.1

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC
Q ss_conf             402468888999998647765
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~   93 (237)
                      ..+|.+++.+|....||-||.
T Consensus       123 ~~ia~gl~yLH~~~ivHrDlK  143 (277)
T cd05036         123 RDVAKGCKYLEENHFIHRDIA  143 (277)
T ss_pred             HHHHHHHHHHHHCCCCCCCCC
T ss_conf             999999999987991568775


No 45 
>TIGR01962 NuoD NADH dehydrogenase I, D subunit; InterPro: IPR010219   This entry recognises specifically the D subunit of NADH dehydrogenase I complex. It excludes the related chain of NAD(P)H-quinone oxidoreductases from chloroplast and Synechocystis, where the quinone may be plastoquinone rather than ubiquinone. This subunit often appears as a subunit C/D fusion.; GO: 0016651 oxidoreductase activity acting on NADH or NADPH, 0006118 electron transport.
Probab=30.13  E-value=38  Score=14.25  Aligned_cols=100  Identities=16%  Similarity=0.179  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHHHHHH--HHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHH------HHHHHHHHHHHHHHHH-HH
Q ss_conf             322223347999973--10234126788888765322235664113322210000------0036799999998634-89
Q gi|254781111|r  119 AGNGLLTYAFEIISS--PKTQLKDNIRSQLMLSLTHNIGLQGMLGGQMLDIQDEF------IDETQVFMIQKMKTGA-LM  189 (237)
Q Consensus       119 ~Gd~l~~~a~~~l~~--~~~~~~~~~~~~~~~~~~~~~~~~~l~~GQ~~dl~~~~------~~~~~y~~i~~~KTa~-lf  189 (237)
                      +=++-|++|.|-|+.  ..-+.-....=.++.+++|-..+.-.+.-+.+|+..-+      .+.|..++..+.=||+ +-
T Consensus        69 ~ne~AY~LAVEKLlGit~evP~RA~vIRV~l~EL~RI~sHLl~igt~~lD~GAmTp~lyaFr~RE~~~DL~E~~~G~RM~  148 (408)
T TIGR01962        69 SNELAYALAVEKLLGITIEVPRRAQVIRVILLELNRISSHLLFIGTHALDLGAMTPFLYAFREREKILDLFEAITGARMH  148 (408)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             10048888878770761246731589999999988998899999998777877769999888799999999876300246


Q ss_pred             HHHHHHHHHHCCCC---HHHHHHHHHHHHHHH
Q ss_conf             99999999975988---899999999999984
Q gi|254781111|r  190 CFACESGAIMAHAS---QNEKERLRCFGENLG  218 (237)
Q Consensus       190 ~~~~~~ga~lag~~---~~~~~~l~~~g~~lG  218 (237)
                      ...++.|++.-+-+   +...+.+++|-..+=
T Consensus       149 ~~y~R~GGV~~DLPdf~~n~l~~i~~Fl~~~p  180 (408)
T TIGR01962       149 SAYFRIGGVAEDLPDFMENWLEEIREFLEQFP  180 (408)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             67634587132103454338999999998614


No 46 
>TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit; InterPro: IPR012735    Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated 2.7.1.29 from EC. By contract, Escherichia coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex..
Probab=30.08  E-value=17  Score=16.24  Aligned_cols=43  Identities=33%  Similarity=0.434  Sum_probs=22.0

Q ss_pred             CCCCCHHHHHHHHH------HHHHHHCCCCCCCCCC----CCCCCC-C--CCCCCCC
Q ss_conf             22240246888899------9998647765445322----344556-6--5432434
Q gi|254781111|r   70 LTALRVGAAIECIH------CYSLIHDDLPSMDNGY----IRRGKP-T--VHIQYDE  113 (237)
Q Consensus        70 ~~~~~~AaavEllH------~asLihDDI~~~D~s~----~RRG~p-t--~h~~~G~  113 (237)
                      .++-....|.+...      .+-.+|||| ++|.+.    .|||-- |  +|+..|-
T Consensus       106 AD~~~F~~A~~qar~EG~~~~~~iv~DDi-SVe~~~~f~~R~RGvAGtvLvHKIlGa  161 (328)
T TIGR02362       106 ADLSEFSQAIEQARQEGRDIKYIIVHDDI-SVESESSFKKRRRGVAGTVLVHKILGA  161 (328)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEECCCC-CCCCHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             77899999999998638950379972753-317645563303563257799899999


No 47 
>PRK12883 ubiA prenyltransferase UbiA-like protein; Reviewed
Probab=29.96  E-value=38  Score=14.23  Aligned_cols=45  Identities=16%  Similarity=0.063  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999759888999999999999849999986765344320
Q gi|254781111|r  189 MCFACESGAIMAHASQNEKERLRCFGENLGIIFQLADDLLDCEEDL  234 (237)
Q Consensus       189 f~~~~~~ga~lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~  234 (237)
                      ...+...|+...+. ....-.+.-++-.+.+++-|.-|+.|.+||.
T Consensus       139 ~g~~~l~g~~a~g~-~~~~~~l~~~afl~~l~reivkdieD~egD~  183 (275)
T PRK12883        139 TAATPIYGAVGVGR-IGLAGYLAICAFLVNVSREIMKDIEDIEGDM  183 (275)
T ss_pred             HHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999575-4099999999999999999999999861098


No 48 
>cd05035 PTKc_Axl_like Catalytic Domain of Axl-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Axl subfamily; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). The Axl subfamily consists of Axl, Tyro3 (or Sky), Mer (or Mertk), and similar proteins. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Axl subfamily members are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with two immunoglobulin-like domains followed by two fibronectin type III repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, Gas6 and protein S, leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. Axl subfamily members are implicated in a variety of cellu
Probab=29.88  E-value=12  Score=17.12  Aligned_cols=22  Identities=23%  Similarity=0.454  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-.+||-||.
T Consensus       119 ~~~ia~gl~yLH~~~ivHrDlK  140 (273)
T cd05035         119 MVDIALGMEYLSNRNFIHRDLA  140 (273)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999998820992767676


No 49 
>cd05032 PTKc_InsR_like Catalytic Domain of Insulin Receptor-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Insulin Receptor (InsR) subfamily; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). The InsR subfamily is composed of InsR, Insulin-like Growth Factor-1 Receptor (IGF-1R), and similar proteins. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. InsR and IGF-1R are receptor tyr kinases (RTKs) composed of two alphabeta heterodimers. Binding of the ligand (insulin, IGF-1, or IGF-2) to the extracellular alpha subunit activates the intracellular tyr kinase domain of the transmembrane beta subunit. Receptor activation leads to autophosphorylation, stimulating downstream kinase activities, which initiate signaling cascades and biological 
Probab=29.00  E-value=17  Score=16.33  Aligned_cols=22  Identities=18%  Similarity=0.421  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-..||-||.
T Consensus       125 ~~qia~gl~yLH~~~IiHrDlK  146 (277)
T cd05032         125 AAEIADGMAYLAAKKFVHRDLA  146 (277)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999986895447788


No 50 
>cd05103 PTKc_VEGFR2 Catalytic Domain of the Protein Tyrosine Kinase, Vascular Endothelial Growth Factor Receptor 2. Protein Tyrosine Kinase (PTK) family; Vascular Endothelial Growth Factor Receptor 2 (VEGFR2); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. VEGFR2 (or Flk1) is a member of the VEGFR subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of VEGFRs to their ligands, the VEGFs, leads to receptor dimerization, activation, and intracellular signaling. The carboxyl terminus of VEGFR2 plays an important role in its autophosp
Probab=28.42  E-value=17  Score=16.26  Aligned_cols=21  Identities=29%  Similarity=0.483  Sum_probs=18.6

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC
Q ss_conf             402468888999998647765
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~   93 (237)
                      .++|.+++++|..-.||-||.
T Consensus       186 ~qia~gl~yLh~~~ivHRDLK  206 (343)
T cd05103         186 FQVAKGMEFLASRKCIHRDLA  206 (343)
T ss_pred             HHHHHHHHHHHHCCCCCCCCC
T ss_conf             999999999987886667478


No 51 
>cd05066 PTKc_EphR_A Catalytic Domain of the Protein Tyrosine Kinases, Class EphA Ephrin Receptors. Protein Tyrosine Kinase (PTK) family; Ephrin Receptor (EphR) subfamily; most class EphA receptors including EphA3, EphA4, EphA5, and EphA7, but excluding EphA1, EphA2 and EphA10; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EphRs comprise the largest subfamily of receptor tyr kinases (RTKs). In general, class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. One exception is EphA4, which also binds ephrins-B2/B3. EphRs contain an ephrin-binding domain and two fibronectin repeats extracellul
Probab=28.40  E-value=15  Score=16.65  Aligned_cols=22  Identities=14%  Similarity=0.326  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|....||-||.
T Consensus       112 ~~~ia~gl~yLh~~~iiHRDlK  133 (267)
T cd05066         112 LRGIASGMKYLSDMGYVHRDLA  133 (267)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999999966985546676


No 52 
>cd05087 PTKc_Aatyk1_Aatyk3 Catalytic Domain of the Protein Tyrosine Kinases, Apoptosis-associated tyrosine kinases 1 and 3. Protein Tyrosine Kinase (PTK) family; Apoptosis-associated tyrosine kinase 1 (Aatyk1) and Aatyk3; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Aatyk1 and Aatyk3 are members of the Aatyk subfamily of proteins. Aatyk3 is a receptor kinase containing a transmembrane segment and a long C-terminal cytoplasmic tail with a catalytic domain. Aatyk1 has a similar domain arrangement but without the transmembrane segment and is thus, a cytoplasmic (or nonreceptor) kinase. The expression of Aatyk1 (also referred simply as Aatyk) is upregulated during growth arrest and apoptosis in myeloid cells
Probab=28.21  E-value=14  Score=16.77  Aligned_cols=22  Identities=23%  Similarity=0.433  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.--.||-||.
T Consensus       106 ~~qia~gl~yLH~~~iiHrDLK  127 (269)
T cd05087         106 ACEIASGLLHLHKHNYVHSDLA  127 (269)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999952995646455


No 53 
>cd05075 PTKc_Axl Catalytic Domain of the Protein Tyrosine Kinase, Axl. Protein Tyrosine Kinase (PTK) family; Axl; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Axl is a member of the Axl subfamily, which is composed of receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with two immunoglobulin-like domains followed by two fibronectin type III repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, Gas6 and protein S, leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. Axl is widely expressed in a variety of organs and cells including epithelial, mesenchymal, hematopoietic, as well as non-transfor
Probab=28.02  E-value=14  Score=16.81  Aligned_cols=22  Identities=27%  Similarity=0.486  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-.+||-||-
T Consensus       118 ~~~ia~gL~yLH~~~ivHrDLK  139 (272)
T cd05075         118 MTDIASGMEYLSSKSFIHRDLA  139 (272)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999998710983647676


No 54 
>TIGR01982 UbiB 2-polyprenylphenol 6-hydroxylase; InterPro: IPR010232   This entry represents the enzyme (UbiB) which catalyses the first hydroxylation step in the ubiquinone biosynthetic pathway in bacteria , . The gene is also known as AarF in certain species. It is believed that the reaction converts 2-polyprenylphenol to 6-hydroxy-2-polyprenylphenol. Members are mainly proteobacteria.; GO: 0006744 ubiquinone biosynthetic process.
Probab=27.94  E-value=42  Score=14.02  Aligned_cols=32  Identities=13%  Similarity=0.015  Sum_probs=12.0

Q ss_pred             CCHHHHHHHHHHH-HHCCCCCCCCCCHHHHHHH
Q ss_conf             6007999999999-9617882222402468888
Q gi|254781111|r   50 GKKIRSFLVTECA-SLFNVNHLTALRVGAAIEC   81 (237)
Q Consensus        50 GKr~R~~l~l~~~-~~~~~~~~~~~~~AaavEl   81 (237)
                      +||+||.-++... +.+...-+=....|.|-||
T Consensus       188 ~~RlrP~evV~~f~~~l~~ELDl~~Eaa~A~~L  220 (452)
T TIGR01982       188 SRRLRPTEVVKEFEKTLRNELDLRREAANASEL  220 (452)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             255460367889999999876499999999999


No 55 
>cd05148 PTKc_Srm_Brk Catalytic Domain of the Protein Tyrosine Kinases, Srm and Brk. Protein Tyrosine Kinase (PTK) family; Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites (Srm) and breast tumor kinase (Brk, also called protein tyrosine kinase 6); catalytic (c) domains. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Srm and Brk are a member of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) tyr kinases. Src kinases in general contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr; they are activated by autophosphorylation at the tyr kinase dom
Probab=27.88  E-value=17  Score=16.38  Aligned_cols=22  Identities=27%  Similarity=0.377  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|..-.||-||.
T Consensus       110 ~~qia~gl~yLH~~~iiHrDLK  131 (261)
T cd05148         110 ACQVAEGMAYLEEQNSIHRDLA  131 (261)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999986996667566


No 56 
>cd05106 PTKc_CSF-1R Catalytic Domain of the Protein Tyrosine Kinase, Colony-Stimulating Factor-1 Receptor. Protein Tyrosine Kinase (PTK) family; Colony-stimulating factor-1 receptor (CSF-1R); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. CSF-1R, also called c-Fms, is a member of the Platelet Derived Growth Factor Receptor (PDGFR) subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of CSF-1R to its ligand, CSF-1, leads to receptor dimerization, trans phosphorylation and activation, and intracellular signaling. CSF-1R signaling is criti
Probab=27.85  E-value=15  Score=16.69  Aligned_cols=22  Identities=18%  Similarity=0.380  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +.++|.++|++|.--.||-||.
T Consensus       218 a~qIA~GM~YL~s~~iIHRDLa  239 (374)
T cd05106         218 SSQVAQGMDFLASKNCIHRDVA  239 (374)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999999987892327677


No 57 
>KOG0591 consensus
Probab=27.38  E-value=42  Score=13.96  Aligned_cols=43  Identities=21%  Similarity=0.252  Sum_probs=25.1

Q ss_pred             CCHHHHHHHHHH----HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             402468888999----9986477654453223445566543243452013322223347
Q gi|254781111|r   73 LRVGAAIECIHC----YSLIHDDLPSMDNGYIRRGKPTVHIQYDEVTAIIAGNGLLTYA  127 (237)
Q Consensus        73 ~~~AaavEllH~----asLihDDI~~~D~s~~RRG~pt~h~~~G~~~AIl~Gd~l~~~a  127 (237)
                      .+++.|++-.|+    .+.+|-||           ||+ +.-...+..+-.||+-++..
T Consensus       131 ~QL~~AL~~cH~~~~r~~VmHRDI-----------KPa-NIFl~~~gvvKLGDfGL~r~  177 (375)
T KOG0591         131 VQLCRALYHCHSKIPRGTVMHRDI-----------KPA-NIFLTANGVVKLGDFGLGRF  177 (375)
T ss_pred             HHHHHHHHHHHCCCCCCCEEECCC-----------CCH-HEEECCCCCEEECCCHHHHH
T ss_conf             999999999841166555234357-----------601-06871788566434115767


No 58 
>KOG0194 consensus
Probab=27.29  E-value=14  Score=16.77  Aligned_cols=23  Identities=22%  Similarity=0.408  Sum_probs=20.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             22402468888999998647765
Q gi|254781111|r   71 TALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        71 ~~~~~AaavEllH~asLihDDI~   93 (237)
                      -.+.+|+.+|.||.-.+||-||.
T Consensus       267 ~~~~AA~Gl~YLh~k~~IHRDIA  289 (474)
T KOG0194         267 FCYDAARGLEYLHSKNCIHRDIA  289 (474)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             99999867999987798536576


No 59 
>cd05063 PTKc_EphR_A2 Catalytic Domain of the Protein Tyrosine Kinase, Ephrin Receptor A2. Protein Tyrosine Kinase (PTK) family; Ephrin Receptor (EphR) subfamily; EphA2 receptor; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EphRs comprise the largest subfamily of receptor tyr kinases (RTKs). In general, class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphRs contain an ephrin binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyr kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored 
Probab=27.18  E-value=14  Score=16.81  Aligned_cols=22  Identities=18%  Similarity=0.353  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|....||-||.
T Consensus       113 ~~~ia~gL~yLH~~~iiHrDlK  134 (268)
T cd05063         113 LRGIAAGMKYLSDMNYVHRDLA  134 (268)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999999832998755347


No 60 
>cd05101 PTKc_FGFR2 Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 2. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 2 (FGFR2); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR2 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to
Probab=27.00  E-value=13  Score=17.02  Aligned_cols=22  Identities=27%  Similarity=0.443  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.--.||-||.
T Consensus       143 ~~qia~gl~yLH~~~iiHRDLK  164 (304)
T cd05101         143 TYQVARGMEYLASQKCIHRDLA  164 (304)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999974886578777


No 61 
>cd05056 PTKc_FAK Catalytic Domain of the Protein Tyrosine Kinase, Focal Adhesion Kinase. Protein Tyrosine Kinase (PTK) family; Focal Adhesion kinase (FAK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FAK is a cytoplasmic (or nonreceptor) tyr kinase that contains an autophosphorylation site and a FERM domain at the N-terminus, a central tyr kinase domain, proline-rich regions, and a C-terminal FAT (focal adhesion targeting) domain. FAK activity is dependent on integrin-mediated cell adhesion, which facilitates N-terminal autophosphorylation. Full activation is achieved by the phosphorylation of its two adjacent A-loop tyrosines. FAK is important in mediating signaling initiated at sites of cell adhesions
Probab=26.90  E-value=17  Score=16.34  Aligned_cols=22  Identities=14%  Similarity=0.451  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.--.||-||.
T Consensus       113 ~~qia~gl~ylH~~~iiHrDlK  134 (270)
T cd05056         113 SYQLSTALAYLESKRFVHRDIA  134 (270)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999974996357578


No 62 
>cd05092 PTKc_TrkA Catalytic Domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase A. Protein Tyrosine Kinase (PTK) family; Tropomyosin related kinase A (TrkA); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkA is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkA to its ligand, nerve growth factor (NGF), results in receptor oligomerization and activation of the catalytic domain. TrkA is expressed mainly in neural-crest-derived sensory
Probab=26.77  E-value=16  Score=16.47  Aligned_cols=21  Identities=14%  Similarity=0.434  Sum_probs=18.5

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC
Q ss_conf             402468888999998647765
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~   93 (237)
                      .++|.+++.+|....||-||.
T Consensus       129 ~qia~gl~yLHs~~iiHRDlK  149 (280)
T cd05092         129 AQIASGMVYLASLHFVHRDLA  149 (280)
T ss_pred             HHHHHHHHHHHHCCCCCCCCC
T ss_conf             999999999840997368667


No 63 
>cd05079 PTKc_Jak1_rpt2 Catalytic (Repeat 2) Domain of the Protein Tyrosine Kinase, Janus kinase 1. Protein Tyrosine Kinase (PTK) family; Janus kinase 1 (Jak1); catalytic (c) domain (repeat 2). The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Jak1 is a member of the Janus kinase (Jak) subfamily of proteins, which are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase domain. Jaks are crucial for cytokine receptor signaling. They are activated by autophosphorylation upon cytokine-induced receptor aggregation, and subsequently trigger downstream signaling events such as the phosphorylation of signal transducers a
Probab=26.59  E-value=9.7  Score=17.74  Aligned_cols=22  Identities=18%  Similarity=0.445  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +.++|.+++.+|.-..||-||.
T Consensus       115 ~~qia~gl~yLH~~~ivHrDlK  136 (284)
T cd05079         115 AVQICKGMDYLGSRQYVHRDLA  136 (284)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999998703983647776


No 64 
>cd05058 PTKc_Met_Ron Catalytic Domain of the Protein Tyrosine Kinases, Met and Ron. Protein Tyrosine Kinase (PTK) family; Met and Ron; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Met and Ron are receptor tyr kinases (RTKs) composed of an alpha-beta heterodimer. The extracellular alpha chain is disulfide linked to the beta chain, which contains an extracellular ligand-binding region with a sema domain, a PSI domain and four IPT repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. Met binds to the ligand, hepatocyte growth factor/scatter factor (HGF/SF), and is also ca
Probab=26.40  E-value=14  Score=16.79  Aligned_cols=22  Identities=27%  Similarity=0.539  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|..-.||-||-
T Consensus       104 ~~qia~gl~yLH~~~ivHrDlK  125 (262)
T cd05058         104 GLQVAKGMEYLASKKFVHRDLA  125 (262)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCC
T ss_conf             9999999999801994757578


No 65 
>cd05052 PTKc_Abl Catalytic Domain of the Protein Tyrosine Kinase, Abelson kinase. Protein Tyrosine Kinase (PTK) family; Abelson (Abl) kinase; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Abl (or c-Abl) is a ubiquitously-expressed cytoplasmic (or nonreceptor) tyr kinase that contains SH3, SH2, and tyr kinase domains in its N-terminal region, as well as nuclear localization motifs, a putative DNA-binding domain, and F- and G-actin binding domains in its C-terminal tail. It also contains a short autoinhibitory cap region in its N-terminus. Abl is normally inactive and requires phosphorylation and myristoylation for activation. Abl function depends on its subcellular localization. In the cytoplasm, Abl plays
Probab=25.61  E-value=18  Score=16.15  Aligned_cols=22  Identities=32%  Similarity=0.533  Sum_probs=19.3

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-..||-||.
T Consensus       110 a~qia~gl~yLH~~~iiHrDLK  131 (263)
T cd05052         110 ATQISSAMEYLEKKNFIHRDLA  131 (263)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999965895357566


No 66 
>KOG0192 consensus
Probab=25.26  E-value=11  Score=17.37  Aligned_cols=23  Identities=35%  Similarity=0.606  Sum_probs=20.2

Q ss_pred             CCCCHHHHHHHHHHHH-HHHCCCC
Q ss_conf             2240246888899999-8647765
Q gi|254781111|r   71 TALRVGAAIECIHCYS-LIHDDLP   93 (237)
Q Consensus        71 ~~~~~AaavEllH~as-LihDDI~   93 (237)
                      -++++|.++|++|.-. +||-|+-
T Consensus       147 ~aldiArGm~YLH~~~~iIHrDLK  170 (362)
T KOG0192         147 IALDIARGMEYLHSEGPIIHRDLK  170 (362)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEECC
T ss_conf             999999888765058977874358


No 67 
>cd05109 PTKc_HER2 Catalytic Domain of the Protein Tyrosine Kinase, HER2. Protein Tyrosine Kinase (PTK) family; HER2 (ErbB2, HER2/neu); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. HER2 is a member of the EGFR (HER, ErbB) subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. Unlike other tyr kinases, phosphorylation of the activation loop of EGFR proteins is not critical to their activation. Instead, they are activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve
Probab=25.22  E-value=18  Score=16.21  Aligned_cols=22  Identities=18%  Similarity=0.462  Sum_probs=19.4

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|....||-||.
T Consensus       115 ~~qia~gl~yLH~~~IiHrDlK  136 (279)
T cd05109         115 CVQIAKGMSYLEEVRLVHRDLA  136 (279)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999999985990137657


No 68 
>cd05098 PTKc_FGFR1 Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 1. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 1 (FGFR1); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR1 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to
Probab=24.93  E-value=19  Score=16.08  Aligned_cols=22  Identities=32%  Similarity=0.465  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.--.||-||.
T Consensus       146 ~~qia~gl~yLH~~~iiHRDLK  167 (307)
T cd05098         146 AYQVARGMEYLASKKCIHRDLA  167 (307)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999984899678667


No 69 
>cd05034 PTKc_Src_like Catalytic Domain of Src kinase-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Src kinase subfamily; catalytic (c) domain. Src subfamily members include Src, Lck, Hck, Blk, Lyn, Fgr, Fyn, Yrk, and Yes. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Src (or c-Src) proteins are cytoplasmic (or non-receptor) tyr kinases which are anchored to the plasma membrane. They contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-t
Probab=24.92  E-value=18  Score=16.13  Aligned_cols=22  Identities=23%  Similarity=0.454  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.--.||-||.
T Consensus       109 ~~qia~gl~yLH~~~iiHrDlK  130 (261)
T cd05034         109 AAQIAEGMAYLESRNYIHRDLA  130 (261)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999986995754327


No 70 
>cd05067 PTKc_Lck_Blk Catalytic Domain of the Protein Tyrosine Kinases, Lymphocyte-specific kinase and Blk. Protein Tyrosine Kinase (PTK) family; Lck and Blk kinases; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Lck (lymphocyte-specific kinase) and Blk are members of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) tyr kinases. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). Sr
Probab=24.38  E-value=18  Score=16.16  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=19.5

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-..||-||.
T Consensus       108 ~~qia~gl~yLH~~~ivHrDlK  129 (260)
T cd05067         108 AAQIAEGMAYIERKNYIHRDLR  129 (260)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999999974897605466


No 71 
>cd05086 PTKc_Aatyk2 Catalytic Domain of the Protein Tyrosine Kinase, Apoptosis-associated tyrosine kinase 2. Protein Tyrosine Kinase (PTK) family; Apoptosis-associated tyrosine kinase 2 (Aatyk2); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Aatyk2 is a member of the Aatyk subfamily of proteins, which are receptor kinases containing a transmembrane segment and a long C-terminal cytoplasmic tail with a catalytic domain. Aatyk2 is also called lemur tyrosine kinase 2 (Lmtk2) or brain-enriched kinase (Brek). It is expressed at high levels in early postnatal brain, and has been shown to play a role in nerve growth factor (NGF) signaling. Studies with knockout mice reveal that Aatyk2 is essential for late stage
Probab=24.19  E-value=19  Score=16.07  Aligned_cols=22  Identities=27%  Similarity=0.519  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.--.||-||.
T Consensus       105 ~~qia~gl~yLH~~~ivHrDLK  126 (268)
T cd05086         105 ACEIAAGVTHMHKHNFLHSDLA  126 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999986897167777


No 72 
>cd05068 PTKc_Frk_like Catalytic Domain of Fyn-related kinase-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Human Fyn-related kinase (Frk) and similar proteins; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Frk and Srk are members of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) tyr kinases. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). Src proteins a
Probab=23.82  E-value=20  Score=15.95  Aligned_cols=28  Identities=25%  Similarity=0.411  Sum_probs=21.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             24024688889999986477654453223
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLPSMDNGYI  100 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~~~D~s~~  100 (237)
                      +.++|.+++.+|.--.||-||- -+|=-+
T Consensus       109 ~~qia~gl~yLH~~~iiHrDLK-p~NILl  136 (261)
T cd05068         109 AAQVASGMAYLEAQNYIHRDLA-ARNVLV  136 (261)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC-CCEEEE
T ss_conf             9999999999986797206566-155898


No 73 
>cd05077 PTK_Jak1_rpt1 Pseudokinase (Repeat 1) Domain of the Protein Tyrosine Kinase, Janus kinase 1. Protein Tyrosine Kinase (PTK) family; Janus kinase 1 (Jak1); pseudokinase domain (repeat 1). The PTKc (catalytic domain) family to which this subfamily belongs, is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Jak1 is a member of the Janus kinase (Jak) subfamily of proteins, which are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase domain. The pseudokinase domain shows similarity to tyr kinases but lacks crucial residues for catalytic activity and ATP binding. It modulates the kinase activity of the C-terminal catalytic dom
Probab=23.41  E-value=23  Score=15.52  Aligned_cols=22  Identities=18%  Similarity=0.344  Sum_probs=19.4

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.--+||-||.
T Consensus       111 a~~ia~gl~yLH~~~iiHrDlk  132 (262)
T cd05077         111 AKQLASALSYLEDKDLVHGNVC  132 (262)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999983994377434


No 74 
>pfam01040 UbiA UbiA prenyltransferase family.
Probab=23.26  E-value=51  Score=13.50  Aligned_cols=46  Identities=24%  Similarity=0.129  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999975988-8999999999999849999986765344320
Q gi|254781111|r  189 MCFACESGAIMAHAS-QNEKERLRCFGENLGIIFQLADDLLDCEEDL  234 (237)
Q Consensus       189 f~~~~~~ga~lag~~-~~~~~~l~~~g~~lGiafQi~DD~lD~~~D~  234 (237)
                      +..+...|+...+.+ +...-.+.-...-++..+.+.+|+.|.++|.
T Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~e~D~  174 (258)
T pfam01040       128 FGLLILLGAYAVGGDIPSPLLLLALPLFLLGLAILLANDIRDVEGDR  174 (258)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             88999999999808886999999999999999999999703578799


No 75 
>cd05089 PTKc_Tie1 Catalytic Domain of the Protein Tyrosine Kinase, Tie1. Protein Tyrosine Kinase (PTK) family; Tie1; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Tie1 is a receptor tyr kinase (RTK) containing an extracellular region, a transmembrane segment, and an intracellular catalytic domain. The extracellular region contains an immunoglobulin (Ig)-like domain, three epidermal growth factor (EGF)-like domains, a second Ig-like domain, and three fibronectin type III repeats. Tie receptors are specifically expressed in endothelial cells and hematopoietic stem cells. No specific ligand has been identified for Tie1, although the angiopoietin, Ang-1, binds to Tie1 through integrins at high concentrations.
Probab=23.24  E-value=19  Score=16.06  Aligned_cols=32  Identities=6%  Similarity=0.083  Sum_probs=26.7

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             75988899999999999984999998676534
Q gi|254781111|r  199 MAHASQNEKERLRCFGENLGIIFQLADDLLDC  230 (237)
Q Consensus       199 lag~~~~~~~~l~~~g~~lGiafQi~DD~lD~  230 (237)
                      +=..+|+....+.+....|.-..|-+-+|.+.
T Consensus       254 Cw~~~P~~RPtf~eI~~~L~~il~~~k~~~~~  285 (297)
T cd05089         254 CWRDRPYERPPFAQISVQLSRMLEARKAYVNM  285 (297)
T ss_pred             HCCCCHHHCCCHHHHHHHHHHHHHHHHHHCCC
T ss_conf             81899668909899999999999731423431


No 76 
>cd05070 PTKc_Fyn_Yrk Catalytic Domain of the Protein Tyrosine Kinases, Fyn and Yrk. Protein Tyrosine Kinase (PTK) family; Fyn and Yrk kinases; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Fyn and Yrk are members of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) tyr kinases. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). Src proteins are involved in signaling pathways that r
Probab=23.21  E-value=21  Score=15.75  Aligned_cols=22  Identities=36%  Similarity=0.484  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.++..+|..-.||-||.
T Consensus       108 ~~qia~gL~yLH~~~iiHrDlK  129 (260)
T cd05070         108 AAQVAAGMAYIERMNYIHRDLR  129 (260)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999855892345046


No 77 
>cd05054 PTKc_VEGFR Catalytic Domain of the Protein Tyrosine Kinases, Vascular Endothelial Growth Factor Receptors. Protein Tyrosine Kinase (PTK) family; Vascular Endothelial Growth Factor Receptor (VEGFR) subfamily; catalytic (c) domain. The VEGFR subfamily consists of VEGFR1 (Flt1), VEGFR2 (Flk1), VEGFR3 (Flt4), and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. VEGFR subfamily members are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and an intracellular catalytic domain. In VEGFR3, the fifth Ig-like domain is replaced by a disulfide bridge. The binding of VEGFRs to their ligands, the VEGFs, leads to recepto
Probab=23.13  E-value=16  Score=16.52  Aligned_cols=21  Identities=29%  Similarity=0.480  Sum_probs=18.7

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC
Q ss_conf             402468888999998647765
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~   93 (237)
                      +++|.+++.+|.--.||-||.
T Consensus       180 ~qia~gl~yLH~~~iiHRDLK  200 (337)
T cd05054         180 FQVARGMEFLASRKCIHRDLA  200 (337)
T ss_pred             HHHHHHHHHHHHCCEECCCCC
T ss_conf             999999998976891346365


No 78 
>cd05051 PTKc_DDR Catalytic Domain of the Protein Tyrosine Kinases, Discoidin Domain Receptors. Protein Tyrosine Kinase (PTK) family; Discoidin domain receptor (DDR) subfamily; catalytic (c) domain. The DDR subfamily consists of homologs of mammalian DDR1, DDR2, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR subfamily members are receptor tyr kinases (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDRs regulate cell adhesion, proliferation, and extracellular matrix remodeling. They have been linke
Probab=22.88  E-value=23  Score=15.55  Aligned_cols=22  Identities=18%  Similarity=0.531  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-.+||-||-
T Consensus       136 ~~qia~gl~yLh~~~iiHrDlK  157 (296)
T cd05051         136 ATQIASGMKYLESLNFVHRDLA  157 (296)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999999977993447567


No 79 
>cd05100 PTKc_FGFR3 Catalytic Domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 3. Protein Tyrosine Kinase (PTK) family; Fibroblast Growth Factor Receptor 3 (FGFR3); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FGFR3 is part of the FGFR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to
Probab=22.31  E-value=20  Score=15.83  Aligned_cols=33  Identities=21%  Similarity=0.366  Sum_probs=25.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHH
Q ss_conf             9888999999999999849999--98676534432
Q gi|254781111|r  201 HASQNEKERLRCFGENLGIIFQ--LADDLLDCEED  233 (237)
Q Consensus       201 g~~~~~~~~l~~~g~~lGiafQ--i~DD~lD~~~D  233 (237)
                      ..+|+....+.++-+.|.-+.+  ..|.|||+.-+
T Consensus       274 ~~~P~~RPtf~eiv~~L~~il~~~~~~~~~~~~~~  308 (334)
T cd05100         274 HAVPSQRPTFKQLVEDLDRVLTVTSTDEYLDLSVP  308 (334)
T ss_pred             CCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             78854690989999999999874265663557880


No 80 
>TIGR01437 selA_rel pyridoxal phosphate-dependent enzyme, putative; InterPro: IPR006337    Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .   PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic .   This entry represents a group of proteins that are related to a number of pyridoxal phosphate-dependent enzymes, and in particular to selenocysteine synthase (SelA), which converts Ser to selenocysteine on its tRNA. While resembling SelA, this protein is found only in species that have a better candidate SelA or else lack the other genes (selB, selC, and selD) required for selenocysteine incorporation. .
Probab=22.20  E-value=53  Score=13.38  Aligned_cols=33  Identities=27%  Similarity=0.436  Sum_probs=26.2

Q ss_pred             HHCCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHH
Q ss_conf             4113322210000-00367999999986348999
Q gi|254781111|r  159 MLGGQMLDIQDEF-IDETQVFMIQKMKTGALMCF  191 (237)
Q Consensus       159 l~~GQ~~dl~~~~-~~~~~y~~i~~~KTa~lf~~  191 (237)
                      +..||..+..... .|+++...++..||+.++..
T Consensus       124 ~gGg~ivE~G~~n~~s~~~lE~~I~~kt~aiLyv  157 (391)
T TIGR01437       124 LGGGRIVEVGDENLVSEESLEETIKEKTAAILYV  157 (391)
T ss_pred             CCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             1899489977888756789999997734675556


No 81 
>cd05042 PTKc_Aatyk Catalytic Domain of the Protein Tyrosine Kinases, Apoptosis-associated tyrosine kinases. Protein Tyrosine Kinase (PTK) family; Apoptosis-associated tyrosine kinase (Aatyk) subfamily; catalytic (c) domain. The Aatyk subfamily is also referred to as the lemur tyrosine kinase (Lmtk) subfamily. It consists of Aatyk1 (Lmtk1), Aatyk2 (Lmtk2, Brek), Aatyk3 (Lmtk3), and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Aatyk proteins are mostly receptor tyr kinases (RTKs) containing a transmembrane segment and a long C-terminal cytoplasmic tail with a catalytic domain. Aatyk1 does not contain a transmembrane segment and is a cytoplasmic (or nonreceptor) kinase. Aatyk proteins are classified as tyr kina
Probab=22.19  E-value=20  Score=15.89  Aligned_cols=22  Identities=32%  Similarity=0.486  Sum_probs=18.9

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|....||-||.
T Consensus       106 a~~ia~gl~yLH~~~ivHrDlK  127 (269)
T cd05042         106 ACEVASGLLWLHQADFIHSDLA  127 (269)
T ss_pred             HHHHHHHHHHHHHCCEEECCCC
T ss_conf             9999999999975895426765


No 82 
>PRK13852 type IV secretion system protein VirB6; Provisional
Probab=22.09  E-value=54  Score=13.36  Aligned_cols=41  Identities=20%  Similarity=0.233  Sum_probs=31.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf             98348999999999999999999997675302457157999
Q gi|254781111|r    1 MNGGLPSKLQENSKRIDTILDDLLLQTASHMQTQHNDRLLS   41 (237)
Q Consensus         1 m~~~l~~~l~~~~~~id~~l~~~l~~~~~~~~~~~~~~l~~   41 (237)
                      ||.++|+.+.....++|+.++.++.+..+...+...+.+.-
T Consensus         1 m~f~~~~~Ft~I~~~~d~~l~~~v~~~~s~I~s~vs~pL~a   41 (295)
T PRK13852          1 MNFSIPAPFTAIHTIFDTAFTTSLDSDLGSIQSAVSAPLVA   41 (295)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98787886599999999999999985389999986199999


No 83 
>cd05093 PTKc_TrkB Catalytic Domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase B. Protein Tyrosine Kinase (PTK) family; Tropomyosin related kinase B (TrkB); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkB is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkB to its ligands, brain-derived neurotrophic factor (BDNF) or neurotrophin 4 (NT4), results in receptor oligomerization and activation of the catalytic domain. TrkB is broadly 
Probab=21.96  E-value=24  Score=15.46  Aligned_cols=22  Identities=23%  Similarity=0.439  Sum_probs=18.9

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.--.||-||.
T Consensus       126 ~~qia~gl~yLH~~~iiHRDLK  147 (288)
T cd05093         126 AQQIAAGMVYLASQHFVHRDLA  147 (288)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999844894678777


No 84 
>cd05040 PTKc_Ack_like Catalytic Domain of the Protein Tyrosine Kinase, Activated Cdc42-associated kinase. Protein Tyrosine Kinase (PTK) family; Activated Cdc42-associated kinase (Ack) subfamily; catalytic (c) domain. Ack subfamily members include Ack1, thirty-eight-negative kinase 1 (Tnk1), and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ack subfamily members are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal catalytic domain, an SH3 domain, a Cdc42-binding CRIB domain, and a proline-rich region. They are mainly expressed in brain and skeletal tissues and are involved in the regulation of cell adhesion and growth, receptor degradation, and axonal guidance. Ack1 is also associated with and
Probab=21.85  E-value=22  Score=15.66  Aligned_cols=22  Identities=23%  Similarity=0.510  Sum_probs=19.4

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.++..+|.--.||-||.
T Consensus       103 ~~qia~aL~yLH~~~ivHrDlK  124 (257)
T cd05040         103 AVQIANGMRYLESKRFIHRDLA  124 (257)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999852896457457


No 85 
>cd05041 PTKc_Fes_like Catalytic Domain of Fes-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Fes subfamily; catalytic (c) domain. Fes subfamily members include Fes (or Fps), Fer, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Fes subfamily proteins are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal region with FCH (Fes/Fer/CIP4 homology) and coiled-coil domains, followed by a SH2 domain, and a C-terminal catalytic domain. The genes for Fes (feline sarcoma) and Fps (Fujinami poultry sarcoma) were first isolated from tumor-causing retroviruses. The viral oncogenes encode chimeric Fes proteins consisting of Gag sequences at the N-termini, resulting in unregulated tyr k
Probab=21.85  E-value=21  Score=15.76  Aligned_cols=22  Identities=32%  Similarity=0.504  Sum_probs=18.9

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-..||-||.
T Consensus        99 ~~~ia~gl~yLH~~~ivHrDlK  120 (251)
T cd05041          99 SLDAAAGMEYLESKNCIHRDLA  120 (251)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999998832895278615


No 86 
>cd05057 PTKc_EGFR_like Catalytic Domain of Epidermal Growth Factor Receptor-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Epidermal Growth Factor Receptor (EGFR) subfamily; catalytic (c) domain. EGFR (HER, ErbB) subfamily members include EGFR (HER1, ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4 (ErbB4), and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The EGFR proteins are receptor tyr kinases (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. Unlike other tyr kinases, phosphorylation of the activation loop of EGFR proteins is not critical to their activation. Instea
Probab=21.53  E-value=25  Score=15.32  Aligned_cols=22  Identities=18%  Similarity=0.451  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.--.||-||.
T Consensus       115 ~~qia~gl~yLH~~~iiHRDlK  136 (279)
T cd05057         115 CVQIAKGMSYLEERRLVHRDLA  136 (279)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999976896346576


No 87 
>cd05043 PTK_Ryk Pseudokinase Domain of the Receptor related to tyrosine kinase. Protein Tyrosine Kinase (PTK) family; Receptor related to tyrosine kinase (Ryk); pseudokinase domain. The PTKc (catalytic domain) family to which this subfamily belongs, is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ryk is a receptor tyr kinase (RTK) containing an extracellular region with two leucine-rich motifs, a transmembrane segment, and an intracellular inactive pseudokinase domain. The extracellular region of Ryk shows homology to the N-terminal domain of Wnt inhibitory factor-1 (WIF) and serves as the ligand (Wnt) binding domain of Ryk. Ryk is expressed in many different tissues both during development and in adults, suggesting a widespread function. It ac
Probab=21.51  E-value=24  Score=15.45  Aligned_cols=22  Identities=23%  Similarity=0.579  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-.+||-||.
T Consensus       123 ~~qia~gl~yLH~~~ivHRDLK  144 (280)
T cd05043         123 AIQIACGMSYLHKRGVIHKDIA  144 (280)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999999975993545125


No 88 
>pfam07714 Pkinase_Tyr Protein tyrosine kinase.
Probab=21.20  E-value=20  Score=15.85  Aligned_cols=22  Identities=27%  Similarity=0.593  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..++.+++.+|..-.||-||-
T Consensus       108 ~~qi~~gl~yLH~~~iiHrDiK  129 (258)
T pfam07714       108 ALQIAKGMEYLESKNFVHRDLA  129 (258)
T ss_pred             HHHHHHHHHHHHHCCEEECCCC
T ss_conf             9999999999985997516676


No 89 
>cd05047 PTKc_Tie Catalytic Domain of Tie Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Tie subfamily; catalytic (c) domain. The Tie subfamily consists of Tie1 and Tie2. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Tie proteins are receptor tyr kinases (RTKs) containing an extracellular region, a transmembrane segment, and an intracellular catalytic domain. The extracellular region contains an immunoglobulin (Ig)-like domain, three epidermal growth factor (EGF)-like domains, a second Ig-like domain, and three fibronectin type III repeats. Tie receptors are specifically expressed in endothelial cells and hematopoietic stem cells. The angiopoietins (Ang-1 to Ang-4) serve as ligands for Tie2, while no specific l
Probab=20.97  E-value=21  Score=15.80  Aligned_cols=22  Identities=27%  Similarity=0.431  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-.+||-||.
T Consensus       118 ~~~ia~gl~yLH~~~iiHRDlK  139 (270)
T cd05047         118 AADVARGMDYLSQKQFIHRDLA  139 (270)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCC
T ss_conf             9999999998710992537677


No 90 
>cd05104 PTKc_Kit Catalytic Domain of the Protein Tyrosine Kinase, Kit. Protein Tyrosine Kinase (PTK) family; Kit (or c-Kit); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Kit is a member of the Platelet Derived Growth Factor Receptor (PDGFR) subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of Kit to its ligand, the stem-cell factor (SCF), leads to receptor dimerization, trans phosphorylation and activation, and intracellular signaling. Kit is important in the development of melanocytes, germ cells, mast cells, hematopoietic stem ce
Probab=20.71  E-value=30  Score=14.89  Aligned_cols=22  Identities=23%  Similarity=0.404  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +.++|.+++++|.--.||-|+.
T Consensus       220 a~qIA~Gm~yL~~~~~iHrDLa  241 (375)
T cd05104         220 SYQVAKGMSFLASKNCIHRDLA  241 (375)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999998986890436157


No 91 
>cd05610 STKc_MASTL STKc_MASTL: Serine/Threonine Kinases (STKs), Microtubule-associated serine/threonine (MAST) kinase subfamily, MAST-like (MASTL) kinases, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAST kinase subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MAST kinases contain an N-terminal domain of unknown function, a central catalytic domain, and a C-terminal PDZ domain that mediates protein-protein interactions. The MASTL kinases in this group carry only a catalytic domain, which contains a long insertion relative to MAST kinases. The human MASTL gene has also been labelled FLJ14813. A missense mutation in FLJ14813 is associated with autosomal dominant thrombocytopenia. To date, the function of MASTL is unknow
Probab=20.70  E-value=28  Score=15.02  Aligned_cols=22  Identities=32%  Similarity=0.501  Sum_probs=18.8

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      ...++.|++.+|..-.||-||-
T Consensus       110 ~~qi~~aL~~lH~~gIiHRDiK  131 (669)
T cd05610         110 ISEVALALDYLHRHGIIHRDLK  131 (669)
T ss_pred             HHHHHHHHHHHHHCCCEECCCC
T ss_conf             9999999999997887622578


No 92 
>cd05090 PTKc_Ror1 Catalytic Domain of the Protein Tyrosine Kinase, Receptor tyrosine kinase-like Orphan Receptor 1. Protein Tyrosine Kinase (PTK) family; Receptor tyrosine kinase-like orphan receptor 1 (Ror1); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ror proteins are orphan receptor tyr kinases (RTKs) containing an extracellular region with immunoglobulin-like, cysteine-rich, and kringle domains, a transmembrane segment, and an intracellular catalytic domain. Ror RTKs are unrelated to the nuclear receptor subfamily called retinoid-related orphan receptors (RORs). RTKs are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase cataly
Probab=20.56  E-value=25  Score=15.37  Aligned_cols=22  Identities=27%  Similarity=0.563  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|....||-||.
T Consensus       130 ~~qia~gl~yLH~~~iiHrDlK  151 (283)
T cd05090         130 AIQIAAGMEYLSSHFFVHKDLA  151 (283)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999999844985645048


No 93 
>cd05614 STKc_MSK2_N STKc_MSK2_N: Serine/Threonine Kinases (STKs), Mitogen and stress-activated kinase (MSK) subfamily, MSK2, N-terminal catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MSK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family, similar to 90 kDa ribosomal protein S6 kinases (RSKs). MSKs are activated by two major signaling cascades, the Ras-MAPK and p38 stress kinase pathways, which trigger phosphorylation in the activation loop (A-loop) of the CTD of MSK. The active CTD phosphorylates the hydrophobic motif (HM) of NTD, which facilitates the phosphorylation of the A-loop and activates the 
Probab=20.47  E-value=33  Score=14.61  Aligned_cols=21  Identities=19%  Similarity=0.281  Sum_probs=18.1

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC
Q ss_conf             402468888999998647765
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~   93 (237)
                      ..++.|++.+|..-.||-||-
T Consensus       112 ~qi~~aL~yLH~~gIiHRDlK  132 (332)
T cd05614         112 GEIILALEHLHKLGIVYRDIK  132 (332)
T ss_pred             HHHHHHHHHHHHCCCEECCCC
T ss_conf             999999999987886525676


No 94 
>cd05045 PTKc_RET Catalytic Domain of the Protein Tyrosine Kinase, REarranged during Transfection protein. Protein Tyrosine Kinase (PTK) family; RET (rearranged during transfection) protein; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. RET is a receptor tyr kinase (RTK) containing an extracellular region with four cadherin-like repeats, a calcium-binding site, and a cysteine-rich domain, a transmembrane segment, and an intracellular catalytic domain. It is part of a multisubunit complex that binds glial-derived neurotropic factor (GDNF) family ligands (GFLs) including GDNF, neurturin, artemin, and persephin. GFLs bind RET along with four GPI-anchored coreceptors, bringing two RET molecules together, leadi
Probab=20.45  E-value=29  Score=14.98  Aligned_cols=21  Identities=19%  Similarity=0.455  Sum_probs=18.3

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC
Q ss_conf             402468888999998647765
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~   93 (237)
                      ..+|.+++.+|..-+||-||-
T Consensus       129 ~qia~gl~yLH~~~iiHRDlK  149 (285)
T cd05045         129 WQISRGMQYLAEMKLVHRDLA  149 (285)
T ss_pred             HHHHHHHHHHHHCCCEECCCC
T ss_conf             999999999874890605677


No 95 
>cd05095 PTKc_DDR2 Catalytic Domain of the Protein Tyrosine Kinase, Discoidin Domain Receptor 2. Protein Tyrosine Kinase (PTK) family; mammalian Discoidin domain receptor 2 (DDR2) and homologs; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR2 is a member of the DDR subfamily, which are receptor tyr kinases (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDR2 binds mostly to fibrillar collagens. More recently, it has been reported to also bind collagen X. DDR2 is widely expressed in many tissues wit
Probab=20.35  E-value=19  Score=16.00  Aligned_cols=22  Identities=18%  Similarity=0.510  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-..||-||.
T Consensus       136 ~~qia~gl~yLh~~~ivHrDlK  157 (296)
T cd05095         136 ASQIASGMKYLSSLNFVHRDLA  157 (296)
T ss_pred             HHHHHHHHHHHHCCCEECCCCC
T ss_conf             9999999998711987757566


No 96 
>cd05631 STKc_GRK4 STKc_GRK4: Serine/Threonine Kinases (STKs), G protein-coupled Receptor Kinase (GRK) subfamily, GRK4 isoform, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The GRK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. There are seven types of GRKs, named GRK1 to GRK7. GRK4 has a limited tissue distribution. It is mainly found in the testis, but is also present in the cerebellum and kidney. It is expressed as 
Probab=20.30  E-value=40  Score=14.12  Aligned_cols=21  Identities=14%  Similarity=0.218  Sum_probs=18.4

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC
Q ss_conf             402468888999998647765
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~   93 (237)
                      .+++.|++.+|.--.||-||-
T Consensus       109 ~qi~~al~ylH~~~IiHRDlK  129 (285)
T cd05631         109 AELCCGLEDLQRERIVYRDLK  129 (285)
T ss_pred             HHHHHHHHHHHHCCCCCCCCC
T ss_conf             999999999997797577668


No 97 
>KOG1024 consensus
Probab=20.29  E-value=34  Score=14.57  Aligned_cols=41  Identities=17%  Similarity=0.178  Sum_probs=27.9

Q ss_pred             HHH-HHHHHHHHHCCCCCC----------CCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             799-999999996178822----------22402468888999998647765
Q gi|254781111|r   53 IRS-FLVTECASLFNVNHL----------TALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        53 ~R~-~l~l~~~~~~~~~~~----------~~~~~AaavEllH~asLihDDI~   93 (237)
                      +|- ...+..|+.-..+..          .+.++|.|+|-+|+.-.||.||.
T Consensus       372 ~gNLK~FL~~Cr~~~~~~aqtvtt~qlV~masQla~am~hlh~~~ViHkDiA  423 (563)
T KOG1024         372 VGNLKSFLQICRGDDPSYAQTVTTIQLVLMASQLAMAMEHLHNHGVIHKDIA  423 (563)
T ss_pred             CCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             3339999998606887655210488999999999999999986473000024


No 98 
>cd05626 STKc_LATS2 STKc_LATS2: Serine/Threonine Kinases (STKs), Large Tumor Suppressor (LATS) subfamily, LATS2 isoform, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The LATS subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. LATS functions as a tumor suppressor and is implicated in cell cycle regulation. LATS2 is an essential mitotic regulator responsible for coordinating accurate cytokinesis completion and governing the stabilization of other mitotic regulators. It is also critical in the maintenance of proper chromosome number, genomic stability, mitotic fidelity, and the integrity of centrosome duplication. Downregulation of LATS2 is associated with poor prognosis in acute lymphoblastic leukemia and breast cancer.
Probab=20.22  E-value=39  Score=14.19  Aligned_cols=21  Identities=33%  Similarity=0.539  Sum_probs=18.1

Q ss_pred             CCHHHHHHHHHHHHHHHCCCC
Q ss_conf             402468888999998647765
Q gi|254781111|r   73 LRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        73 ~~~AaavEllH~asLihDDI~   93 (237)
                      ..++.|++.+|..-.||-||-
T Consensus       108 ~qi~~aL~ylH~~gIiHRDLK  128 (381)
T cd05626         108 AELTLAIESVHKMGFIHRDIK  128 (381)
T ss_pred             HHHHHHHHHHHHCCCCCCCCC
T ss_conf             999999999986667302154


No 99 
>cd05091 PTKc_Ror2 Catalytic Domain of the Protein Tyrosine Kinase, Receptor tyrosine kinase-like Orphan Receptor 2. Protein Tyrosine Kinase (PTK) family; Receptor tyrosine kinase-like orphan receptor 2 (Ror2); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ror proteins are orphan receptor tyr kinases (RTKs) containing an extracellular region with immunoglobulin-like, cysteine-rich, and kringle domains, a transmembrane segment, and an intracellular catalytic domain. Ror RTKs are unrelated to the nuclear receptor subfamily called retinoid-related orphan receptors (RORs). RTKs are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase cataly
Probab=20.15  E-value=31  Score=14.78  Aligned_cols=22  Identities=23%  Similarity=0.498  Sum_probs=19.4

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.-.+||-||-
T Consensus       130 ~~qia~gl~yLH~~~ivHrDlK  151 (283)
T cd05091         130 VTQIAAGMEFLSSHHVVHKDLA  151 (283)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999976992678676


No 100
>cd05110 PTKc_HER4 Catalytic Domain of the Protein Tyrosine Kinase, HER4. Protein Tyrosine Kinase (PTK) family; HER4 (ErbB4); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. HER4 is a member of the EGFR (HER, ErbB) subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. Unlike other tyr kinases, phosphorylation of the activation loop of EGFR proteins is not critical to their activation. Instead, they are activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as bindin
Probab=20.13  E-value=30  Score=14.86  Aligned_cols=22  Identities=18%  Similarity=0.418  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +..+|.+++.+|.--.||-||.
T Consensus       115 ~~qia~gl~yLH~~~IiHRDLK  136 (303)
T cd05110         115 CVQIAKGMMYLEERRLVHRDLA  136 (303)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999966895346653


No 101
>smart00219 TyrKc Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily.
Probab=20.11  E-value=26  Score=15.21  Aligned_cols=22  Identities=32%  Similarity=0.603  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             2402468888999998647765
Q gi|254781111|r   72 ALRVGAAIECIHCYSLIHDDLP   93 (237)
Q Consensus        72 ~~~~AaavEllH~asLihDDI~   93 (237)
                      +.++|.+++.+|..-.||-||-
T Consensus       109 ~~qi~~gl~yLH~~~ivHrDiK  130 (258)
T smart00219      109 ALQIARGMEYLESKNFIHRDLA  130 (258)
T ss_pred             HHHHHHHHHHHHHCCEECCCCC
T ss_conf             9999999999986998506175


Done!