Query 013698
Match_columns 438
No_of_seqs 243 out of 1076
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 06:29:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013698.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013698hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0774 Transcription factor P 100.0 7.1E-33 1.5E-37 268.7 18.2 209 171-424 26-249 (334)
2 KOG0773 Transcription factor M 99.9 4.6E-29 9.9E-34 248.0 -0.0 250 170-427 46-303 (342)
3 PF03791 KNOX2: KNOX2 domain ; 99.9 3E-23 6.5E-28 158.7 7.2 50 231-284 3-52 (52)
4 PF03790 KNOX1: KNOX1 domain ; 99.8 4.7E-20 1E-24 137.2 3.3 44 174-217 1-44 (45)
5 PF05920 Homeobox_KN: Homeobox 99.6 8.8E-16 1.9E-20 111.7 4.3 40 381-420 1-40 (40)
6 PF03792 PBC: PBC domain; Int 99.5 4.6E-13 9.9E-18 126.0 13.2 150 171-362 24-190 (191)
7 cd00086 homeodomain Homeodomai 99.4 2.7E-13 6E-18 101.4 6.4 57 365-424 2-58 (59)
8 smart00389 HOX Homeodomain. DN 99.4 6.7E-13 1.4E-17 99.0 6.1 55 365-422 2-56 (56)
9 PF00046 Homeobox: Homeobox do 99.4 7E-13 1.5E-17 100.0 5.1 57 364-423 1-57 (57)
10 KOG0775 Transcription factor S 99.2 1.4E-11 3.1E-16 121.4 4.3 47 373-422 186-232 (304)
11 KOG0487 Transcription factor A 98.7 4.4E-09 9.5E-14 105.8 3.0 59 364-425 236-294 (308)
12 KOG0489 Transcription factor z 98.7 1.1E-08 2.3E-13 100.5 3.4 64 363-429 159-222 (261)
13 KOG3802 Transcription factor O 98.7 2E-08 4.3E-13 103.6 5.4 70 354-426 285-354 (398)
14 TIGR01565 homeo_ZF_HD homeobox 98.7 2.3E-08 4.9E-13 78.6 4.5 53 363-418 1-57 (58)
15 KOG0843 Transcription factor E 98.6 2E-08 4.3E-13 94.6 3.8 61 362-425 101-161 (197)
16 KOG0485 Transcription factor N 98.5 1E-07 2.3E-12 92.2 5.9 59 362-423 103-161 (268)
17 KOG0493 Transcription factor E 98.5 7.9E-08 1.7E-12 95.1 4.5 62 363-427 246-307 (342)
18 KOG0850 Transcription factor D 98.5 9E-08 1.9E-12 93.0 3.5 60 364-426 123-182 (245)
19 KOG0842 Transcription factor t 98.5 7.6E-08 1.7E-12 97.0 2.7 59 362-423 152-210 (307)
20 KOG0488 Transcription factor B 98.4 1.9E-07 4E-12 94.2 4.1 58 363-423 172-229 (309)
21 KOG0483 Transcription factor H 98.4 1.8E-07 4E-12 89.2 3.8 58 363-423 50-107 (198)
22 COG5576 Homeodomain-containing 98.4 2.3E-07 5E-12 85.5 4.0 62 362-426 50-111 (156)
23 KOG0491 Transcription factor B 98.4 2.4E-07 5.2E-12 86.5 3.4 59 362-423 99-157 (194)
24 KOG0484 Transcription factor P 98.3 3.6E-07 7.7E-12 80.0 2.4 64 357-423 11-74 (125)
25 KOG0492 Transcription factor M 98.2 8.8E-07 1.9E-11 85.4 2.8 66 355-423 136-201 (246)
26 KOG2251 Homeobox transcription 98.1 1.6E-06 3.4E-11 84.0 3.7 57 364-423 38-94 (228)
27 KOG0494 Transcription factor C 98.1 3E-06 6.6E-11 84.0 3.8 55 367-424 145-199 (332)
28 KOG4577 Transcription factor L 98.0 1.1E-06 2.5E-11 88.0 -0.4 71 356-429 160-230 (383)
29 KOG0486 Transcription factor P 98.0 2.9E-06 6.2E-11 85.9 2.0 56 365-423 114-169 (351)
30 KOG0848 Transcription factor C 98.0 2.3E-06 4.9E-11 85.1 0.9 56 368-426 204-259 (317)
31 KOG1168 Transcription factor A 97.8 6.9E-06 1.5E-10 82.6 1.0 67 360-429 306-372 (385)
32 KOG0490 Transcription factor, 97.6 3.2E-05 6.9E-10 72.0 2.3 63 360-425 57-119 (235)
33 KOG2252 CCAAT displacement pro 97.5 9E-05 2E-09 79.6 5.1 56 363-421 420-475 (558)
34 KOG0844 Transcription factor E 97.5 3.8E-05 8.3E-10 77.8 1.2 54 367-423 185-238 (408)
35 KOG0847 Transcription factor, 97.5 6.3E-05 1.4E-09 73.4 2.5 61 362-425 166-226 (288)
36 KOG0849 Transcription factor P 97.4 0.0001 2.2E-09 75.7 4.0 59 364-425 177-235 (354)
37 KOG0773 Transcription factor M 97.4 7.9E-05 1.7E-09 75.0 2.9 67 363-430 95-161 (342)
38 PF03789 ELK: ELK domain ; In 96.8 0.0011 2.4E-08 43.2 2.3 22 341-362 1-22 (22)
39 PF11569 Homez: Homeodomain le 96.7 0.0015 3.3E-08 51.4 3.2 43 375-420 10-52 (56)
40 KOG0490 Transcription factor, 94.4 0.033 7.2E-07 51.9 3.1 59 364-425 154-212 (235)
41 KOG1146 Homeobox protein [Gene 87.1 0.46 9.9E-06 56.5 3.1 60 363-425 903-962 (1406)
42 PF04218 CENP-B_N: CENP-B N-te 78.1 3.7 8E-05 31.4 4.0 47 364-418 1-47 (53)
43 KOG3623 Homeobox transcription 72.2 7 0.00015 44.7 5.8 48 375-425 568-615 (1007)
44 PF01527 HTH_Tnp_1: Transposas 55.1 14 0.00029 28.9 3.0 47 365-418 2-48 (76)
45 cd00569 HTH_Hin_like Helix-tur 54.2 28 0.00062 21.3 4.0 39 368-414 4-42 (42)
46 cd06171 Sigma70_r4 Sigma70, re 53.7 27 0.00058 24.1 4.1 46 369-422 10-55 (55)
47 KOG2070 Guanine nucleotide exc 45.3 59 0.0013 36.2 6.8 25 235-259 183-214 (661)
48 PF08281 Sigma70_r4_2: Sigma-7 44.9 32 0.0007 25.3 3.5 44 369-420 10-53 (54)
49 PRK06759 RNA polymerase factor 42.2 29 0.00063 30.1 3.4 47 369-423 106-152 (154)
50 PF04545 Sigma70_r4: Sigma-70, 41.3 24 0.00052 25.8 2.3 47 369-423 4-50 (50)
51 KOG4445 Uncharacterized conser 41.2 52 0.0011 34.5 5.4 47 237-285 134-180 (368)
52 PF12022 DUF3510: Domain of un 40.9 1.3E+02 0.0028 26.9 7.3 21 265-285 79-99 (125)
53 PF05190 MutS_IV: MutS family 39.8 49 0.0011 26.4 4.1 25 234-258 1-25 (92)
54 PF13097 CENP-U: CENP-A nucleo 37.3 88 0.0019 30.2 5.9 45 236-283 102-148 (175)
55 PRK09642 RNA polymerase sigma 33.9 44 0.00095 29.3 3.2 48 369-424 106-153 (160)
56 PRK09644 RNA polymerase sigma 33.4 43 0.00093 29.7 3.1 50 368-425 107-156 (165)
57 KOG4511 Uncharacterized conser 33.1 3.2E+02 0.007 28.5 9.4 28 178-205 49-78 (335)
58 PRK09646 RNA polymerase sigma 32.3 44 0.00096 30.7 3.1 49 369-425 142-190 (194)
59 PF13443 HTH_26: Cro/C1-type H 31.9 35 0.00077 25.7 2.0 23 395-417 12-34 (63)
60 TIGR02937 sigma70-ECF RNA poly 31.6 49 0.0011 27.4 3.0 46 370-423 111-156 (158)
61 PRK11924 RNA polymerase sigma 31.3 46 0.00099 29.2 2.9 47 370-424 126-172 (179)
62 PRK09652 RNA polymerase sigma 30.2 51 0.0011 28.9 3.0 48 369-424 128-175 (182)
63 PRK12514 RNA polymerase sigma 29.7 52 0.0011 29.5 3.1 48 369-424 129-176 (179)
64 PRK12541 RNA polymerase sigma 28.2 56 0.0012 28.8 3.0 48 368-423 111-158 (161)
65 PF13518 HTH_28: Helix-turn-he 27.8 63 0.0014 23.2 2.7 24 396-419 15-38 (52)
66 TIGR02985 Sig70_bacteroi1 RNA 27.8 70 0.0015 27.4 3.4 47 369-423 113-159 (161)
67 PRK06811 RNA polymerase factor 27.6 63 0.0014 29.5 3.2 48 369-424 131-178 (189)
68 TIGR02939 RpoE_Sigma70 RNA pol 27.2 50 0.0011 29.6 2.4 49 369-425 138-186 (190)
69 PRK12547 RNA polymerase sigma 26.7 64 0.0014 28.7 3.0 48 369-424 112-159 (164)
70 TIGR02989 Sig-70_gvs1 RNA poly 26.5 72 0.0016 27.7 3.3 47 369-423 111-157 (159)
71 TIGR02999 Sig-70_X6 RNA polyme 25.8 75 0.0016 28.5 3.3 48 369-424 134-181 (183)
72 TIGR02983 SigE-fam_strep RNA p 25.3 73 0.0016 28.0 3.1 49 369-425 110-158 (162)
73 smart00421 HTH_LUXR helix_turn 24.9 1.4E+02 0.003 20.9 4.0 47 369-424 3-49 (58)
74 PF04859 DUF641: Plant protein 24.7 3.1E+02 0.0068 25.2 7.1 27 233-259 78-105 (131)
75 PF11288 DUF3089: Protein of u 24.5 28 0.00061 34.0 0.4 46 155-205 93-138 (207)
76 KOG4040 NADH:ubiquinone oxidor 24.5 52 0.0011 31.6 2.1 40 370-409 21-61 (186)
77 PRK03975 tfx putative transcri 23.8 81 0.0018 29.2 3.2 48 367-423 4-51 (141)
78 PRK12526 RNA polymerase sigma 23.7 76 0.0016 29.6 3.1 49 369-425 153-201 (206)
79 PF13730 HTH_36: Helix-turn-he 23.6 2.3E+02 0.0051 20.7 5.1 30 388-420 23-52 (55)
80 PF13865 FoP_duplication: C-te 22.9 74 0.0016 26.1 2.5 7 237-243 47-53 (74)
81 PRK05602 RNA polymerase sigma 22.1 83 0.0018 28.5 2.9 49 370-426 129-177 (186)
82 PRK12523 RNA polymerase sigma 21.8 97 0.0021 27.7 3.3 47 369-423 119-165 (172)
83 PRK12546 RNA polymerase sigma 21.8 83 0.0018 29.2 2.9 49 369-425 113-161 (188)
84 PF10668 Phage_terminase: Phag 21.7 70 0.0015 25.7 2.0 20 395-414 24-43 (60)
85 PRK09648 RNA polymerase sigma 21.6 96 0.0021 28.1 3.2 48 369-424 139-186 (189)
86 PRK00118 putative DNA-binding 21.6 1.3E+02 0.0027 26.6 3.8 47 369-423 17-63 (104)
87 PF12878 SICA_beta: SICA extra 20.8 99 0.0021 29.3 3.2 24 234-259 95-118 (169)
88 PF12362 DUF3646: DNA polymera 20.7 75 0.0016 28.4 2.2 21 173-193 88-108 (117)
89 PRK12516 RNA polymerase sigma 20.2 1E+02 0.0022 28.5 3.0 50 369-426 116-165 (187)
90 KOG4460 Nuclear pore complex, 20.1 1.8E+02 0.0039 33.0 5.3 37 240-283 569-605 (741)
91 PRK09047 RNA polymerase factor 20.1 1.1E+02 0.0025 26.5 3.3 49 368-424 105-153 (161)
92 PRK09649 RNA polymerase sigma 20.0 1.1E+02 0.0024 27.9 3.3 49 369-425 130-178 (185)
No 1
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=100.00 E-value=7.1e-33 Score=268.69 Aligned_cols=209 Identities=23% Similarity=0.380 Sum_probs=184.3
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHh-----hhhccCCCcchhhHHHHHHHHHHHHhhhhccCCCCCC------C-CCChH
Q 013698 171 WQNARYKAEILSHPLYEQLLSAHVA-----CLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAGQGL------V-TDDKE 238 (438)
Q Consensus 171 ~e~e~lKAkI~sHPlYp~LL~Ayid-----ClKVGAPpevv~~Ld~~l~~~~~~~~k~~~~~~~~~~------~-g~DPE 238 (438)
+|+++.|..|.+||+||.|++++|+ .+.|....|.-|. |.++.++++|+..+++.||..+. . |+..+
T Consensus 26 Deaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~-dpqlmRLDnML~AEGVagPekgga~~~~Asgg~hsd 104 (334)
T KOG0774|consen 26 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPP-DPQLMRLDNMLLAEGVAGPEKGGARAAAASGGDHSD 104 (334)
T ss_pred chHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCC-ChHHHHHHHHHHHhcccCccccchhhhhccCCChHH
Confidence 6667999999999999999999999 5666666665554 78888999999999999886421 2 34488
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCCCCcchhcccCCcccCCCCCCCCC
Q 013698 239 LDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFDGSLEGPD 318 (438)
Q Consensus 239 LDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~Fc~~IEsQL~sL~~~s~~e~~g~~~S~ded~~~~s~~~~~~~~~~~~d 318 (438)
+++-+. +|...|++||++ +..+|+++.+.+.+|.. +
T Consensus 105 YR~kL~---qiR~iy~~Elek--------yeqaCneftthV~nlL~---------------------------------e 140 (334)
T KOG0774|consen 105 YRAKLL---QIRQIYHNELEK--------YEQACNEFTTHVMNLLR---------------------------------E 140 (334)
T ss_pred HHHHHH---HHHHHHHHHHHH--------HHHHHHHHHHHHHHHHH---------------------------------H
Confidence 888777 999999999987 45679999999999995 3
Q ss_pred CCCCCCCCcchhhhhh--HHHHHHHHHHHHHHhhHHHHHHHHHHHhh-ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHH
Q 013698 319 TMGFGPLIPTESERSL--MERVRQELKHELKQGYKEKIVDIREEILR-KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEED 395 (438)
Q Consensus 319 ~~~f~Pi~p~~~e~~l--m~r~~qELK~~Lk~~y~~~i~~lr~e~~k-kRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~e 395 (438)
++.||||.+.++|+++ |.+.|.-++..|++..|..|..||.++.. +|||++|+|.++.+|..||+.|+.+|||++++
T Consensus 141 Qsr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~ 220 (334)
T KOG0774|consen 141 QSRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEA 220 (334)
T ss_pred hcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHH
Confidence 3469999999999975 89999999999999999999999999986 67788999999999999999999999999999
Q ss_pred HHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 396 KARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 396 K~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
|++||++||++..||+|||.|+|.|.||.
T Consensus 221 K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 221 KEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHHHHcCceehhhccccccceeehhhh
Confidence 99999999999999999999999999873
No 2
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.94 E-value=4.6e-29 Score=247.97 Aligned_cols=250 Identities=21% Similarity=0.269 Sum_probs=179.4
Q ss_pred hhhhHHHHHHHhhCCChHHHHHHHHhhhhccCCCcchhhHHHHHHHHHHHHhhhhccCCC-C--CCCCCChHHHHHHHHH
Q 013698 170 NWQNARYKAEILSHPLYEQLLSAHVACLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAG-Q--GLVTDDKELDQFMTHY 246 (438)
Q Consensus 170 ~~e~e~lKAkI~sHPlYp~LL~AyidClKVGAPpevv~~Ld~~l~~~~~~~~k~~~~~~~-~--~~~g~DPELDQFMeaY 246 (438)
.....-+|..+.+||+|..++.||++|++++++.+.+.+++............++.++.. . ..-+.+.+|+.||..|
T Consensus 46 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k~ 125 (342)
T KOG0773|consen 46 MVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSKL 125 (342)
T ss_pred ccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchHH
Confidence 345566799999999999999999999999999999888765443332222222222111 0 1235779999999999
Q ss_pred HHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCCCCcchhccc---CCcccCCCCCCCCCCCCCC
Q 013698 247 VLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVD---SDANLFDGSLEGPDTMGFG 323 (438)
Q Consensus 247 C~mL~kYkEEL~kP~~~~~~EA~~Fc~~IEsQL~sL~~~s~~e~~g~~~S~ded~~~~---s~~~~~~~~~~~~d~~~f~ 323 (438)
+.+|..++..|+..+. -++|+.++++|+..+..++..++....+.+...+.++... ++.... .+.+++.
T Consensus 126 ~~~ll~~~~~~~~~~~--~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~------~~~~~~~ 197 (342)
T KOG0773|consen 126 EKILLAVITKLTLTQV--STWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSS------EELLGES 197 (342)
T ss_pred HHHHHHHHHHhhhhhH--HHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccc------ccccccc
Confidence 9999999999999763 3899999999999999998876655444333322221100 000000 0111222
Q ss_pred CCCcchhhhhhH--HHHHHHHHHHHHHhhHHHHHHHHHHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHH
Q 013698 324 PLIPTESERSLM--ERVRQELKHELKQGYKEKIVDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQ 401 (438)
Q Consensus 324 Pi~p~~~e~~lm--~r~~qELK~~Lk~~y~~~i~~lr~e~~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~ 401 (438)
+....+.+...+ .+....++..+.+.+..++.....+..++|+++.||+.++.+|+.||.+|+.||||++.+|..||.
T Consensus 198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~ 277 (342)
T KOG0773|consen 198 EQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAK 277 (342)
T ss_pred cccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccch
Confidence 211111111111 234556666777777666666667777889999999999999999999999999999999999999
Q ss_pred HhCCChhhhhhhhhhHHhhcccCCCC
Q 013698 402 ETGLQLKQINNWFINQRKRNWHSNPS 427 (438)
Q Consensus 402 ~TGLs~kQVnNWFiNrRkR~kK~~~s 427 (438)
+|||+..||+|||||+|+|.|++...
T Consensus 278 ~TGLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 278 QTGLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred hcCCCcccCCchhhhcccccCCchHH
Confidence 99999999999999999999998763
No 3
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.89 E-value=3e-23 Score=158.66 Aligned_cols=50 Identities=50% Similarity=0.712 Sum_probs=47.6
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhhC
Q 013698 231 GLVTDDKELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTG 284 (438)
Q Consensus 231 ~~~g~DPELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~Fc~~IEsQL~sL~~ 284 (438)
+++|+||||||||++||.||+||||||+||| .||++|||+||+||++||+
T Consensus 3 ~~~~~dpELDqFMeaYc~~L~kykeeL~~p~----~EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 3 SSIGADPELDQFMEAYCDMLVKYKEELQRPF----QEAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCCccHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhC
Confidence 4689999999999999999999999999998 5999999999999999995
No 4
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.79 E-value=4.7e-20 Score=137.25 Aligned_cols=44 Identities=43% Similarity=0.744 Sum_probs=40.8
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhhhccCCCcchhhHHHHHHHHH
Q 013698 174 ARYKAEILSHPLYEQLLSAHVACLRIATPVDQLPRIDAQLAQSQ 217 (438)
Q Consensus 174 e~lKAkI~sHPlYp~LL~AyidClKVGAPpevv~~Ld~~l~~~~ 217 (438)
+.|||+|++||+||+||+|||+|+|||||||++++||++..+++
T Consensus 1 e~iKA~I~~HP~Y~~Ll~Ayi~C~KVGAP~e~~~~L~e~~~~~~ 44 (45)
T PF03790_consen 1 EAIKAKIASHPLYPRLLAAYIDCQKVGAPPEVVARLDEILAESQ 44 (45)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhc
Confidence 46999999999999999999999999999999999999886653
No 5
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.59 E-value=8.8e-16 Score=111.68 Aligned_cols=40 Identities=53% Similarity=1.020 Sum_probs=36.5
Q ss_pred HHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 013698 381 WWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 420 (438)
Q Consensus 381 Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR 420 (438)
||.+|..+|||+++||..||..|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 9999999999999999999999999999999999999998
No 6
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=99.48 E-value=4.6e-13 Score=126.02 Aligned_cols=150 Identities=21% Similarity=0.300 Sum_probs=118.4
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHh-----hhhccCCCcchhhHHHHHHHHHHHHhhhhccCCCCCC------CCC--C-
Q 013698 171 WQNARYKAEILSHPLYEQLLSAHVA-----CLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAGQGL------VTD--D- 236 (438)
Q Consensus 171 ~e~e~lKAkI~sHPlYp~LL~Ayid-----ClKVGAPpevv~~Ld~~l~~~~~~~~k~~~~~~~~~~------~g~--D- 236 (438)
+|+.++|..|.+||+||.|.+++|+ .+++..+.+..+. |+++.++++|+...++.||+.+. .|. |
T Consensus 24 Deaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~-dpQl~RLDNML~AEGV~gPe~~~~~~~~~~~~~~~~ 102 (191)
T PF03792_consen 24 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPP-DPQLMRLDNMLLAEGVAGPEKGGRAAAAAAGTAADN 102 (191)
T ss_pred hHHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCC-chhhhhhhcchhhhcCcCCCCcccchhhhhccCccc
Confidence 5779999999999999999999999 5556666554444 78888899999999998886311 111 1
Q ss_pred -hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCCCCcchhcccCCcccCCCCCC
Q 013698 237 -KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFDGSLE 315 (438)
Q Consensus 237 -PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~Fc~~IEsQL~sL~~~s~~e~~g~~~S~ded~~~~s~~~~~~~~~~ 315 (438)
-|-+.|-...-.+...|++||++ +...|+++...+.+|..
T Consensus 103 ~~d~~dYr~kL~~ir~~y~~el~k--------ye~ac~eF~~hV~~lLr------------------------------- 143 (191)
T PF03792_consen 103 SIDHSDYRAKLSQIRQIYHSELEK--------YEQACNEFTEHVMNLLR------------------------------- 143 (191)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHH--------HHHHhhhhHHHHHHHHH-------------------------------
Confidence 12334444455888899999987 44569999999999985
Q ss_pred CCCCCCCCCCCcchhhhhh--HHHHHHHHHHHHHHhhHHHHHHHHHHHh
Q 013698 316 GPDTMGFGPLIPTESERSL--MERVRQELKHELKQGYKEKIVDIREEIL 362 (438)
Q Consensus 316 ~~d~~~f~Pi~p~~~e~~l--m~r~~qELK~~Lk~~y~~~i~~lr~e~~ 362 (438)
+++.||||+|.++|+++ |.+.|+-+..+||+..|+.|..||..|.
T Consensus 144 --eQs~~RPIs~keiE~m~~~i~~Kf~~iq~qLKQstCEaVm~LRsRfl 190 (191)
T PF03792_consen 144 --EQSEFRPISPKEIERMVNIIHRKFSKIQMQLKQSTCEAVMILRSRFL 190 (191)
T ss_pred --HhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 23469999999999964 8999999999999999999999998774
No 7
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.43 E-value=2.7e-13 Score=101.45 Aligned_cols=57 Identities=28% Similarity=0.561 Sum_probs=53.5
Q ss_pred cCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 365 RRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 365 RkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
+++..+++++..+|+.||.. +|||+..++..||..+||+.+||.+||.|+|.|.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 56678999999999999999 8899999999999999999999999999999998764
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.39 E-value=6.7e-13 Score=99.01 Aligned_cols=55 Identities=27% Similarity=0.531 Sum_probs=50.9
Q ss_pred cCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcc
Q 013698 365 RRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 422 (438)
Q Consensus 365 RkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~k 422 (438)
+.+..|++++..+|+.||.. +|||+.+++..||..+||+..||.+||+|+|.|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 45567999999999999998 77999999999999999999999999999999864
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.37 E-value=7e-13 Score=99.99 Aligned_cols=57 Identities=33% Similarity=0.740 Sum_probs=53.7
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 364 kRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
||++..|+.++..+|+.+|.. +|||+.+++..||..+||+..||.+||.|+|.|.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 467789999999999999998 889999999999999999999999999999999764
No 10
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.18 E-value=1.4e-11 Score=121.42 Aligned_cols=47 Identities=38% Similarity=0.881 Sum_probs=45.1
Q ss_pred chHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcc
Q 013698 373 DTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 422 (438)
Q Consensus 373 ea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~k 422 (438)
..+..|++||.. +|||++.+|++||+.|||+..||.|||+|+|.|.+
T Consensus 186 kSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 186 KSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 589999999996 99999999999999999999999999999999987
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.74 E-value=4.4e-09 Score=105.81 Aligned_cols=59 Identities=22% Similarity=0.342 Sum_probs=54.1
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 364 kRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
+|||-.++|.++..|+.-|.-+. |.|++-|.+|++.++|+..||+.||+|||+|.||-+
T Consensus 236 RKKRcPYTK~QtlELEkEFlfN~---YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFLFNM---YITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred ccccCCchHHHHHHHHHHHHHHH---HHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 45567899999999999888866 999999999999999999999999999999999866
No 12
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.68 E-value=1.1e-08 Score=100.45 Aligned_cols=64 Identities=23% Similarity=0.290 Sum_probs=57.4
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCCCC
Q 013698 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTS 429 (438)
Q Consensus 363 kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~s~~ 429 (438)
.||.|..|+..++..|+.-|.- +.|-|+..|.+||..+.|++.||.+||+|||+|.||.+.-.+
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 5778889999999999998876 559999999999999999999999999999999997665443
No 13
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.67 E-value=2e-08 Score=103.60 Aligned_cols=70 Identities=17% Similarity=0.391 Sum_probs=62.3
Q ss_pred HHHHHHHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013698 354 IVDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (438)
Q Consensus 354 i~~lr~e~~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~ 426 (438)
+..+-...+|||||..+...++..|+..|.. +|.|+-+|.-.||+.++|.+..|++||+|||.|.|+.++
T Consensus 285 ~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 285 IEKIGAQSRKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HHHhhccccccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3344444466777789999999999999998 999999999999999999999999999999999999888
No 14
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=98.67 E-value=2.3e-08 Score=78.57 Aligned_cols=53 Identities=19% Similarity=0.437 Sum_probs=49.6
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhHH
Q 013698 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPY----PTEEDKARLVQETGLQLKQINNWFINQR 418 (438)
Q Consensus 363 kkRkrgkLpkea~~iLk~Wf~~H~~~PY----PSe~eK~~LA~~TGLs~kQVnNWFiNrR 418 (438)
+||.|.+|+.+++..|+..|.. .+| |+..++..||..+||+..+|.+||+|-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4788899999999999999998 779 9999999999999999999999999954
No 15
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.64 E-value=2e-08 Score=94.59 Aligned_cols=61 Identities=20% Similarity=0.303 Sum_probs=55.7
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 362 ~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
+.||.|..|+.++...|+..|.. +-|-.-.||..||..++|+..||..||+|+|.|+|+..
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~ 161 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQ 161 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHH
Confidence 45777889999999999999998 45999999999999999999999999999999998743
No 16
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.54 E-value=1e-07 Score=92.17 Aligned_cols=59 Identities=20% Similarity=0.308 Sum_probs=54.5
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 362 ~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
.|||.|..|+..++..|+.-|.... |.+-+||..||.++.|++.||..||+|+|.|.|+
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~kr---YLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKR 161 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKR---YLSSAERAGLAASLQLTETQVKIWFQNRRNKWKR 161 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHh---hhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHH
Confidence 4567788999999999999999977 9999999999999999999999999999998665
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.52 E-value=7.9e-08 Score=95.06 Aligned_cols=62 Identities=34% Similarity=0.466 Sum_probs=56.9
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCC
Q 013698 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPS 427 (438)
Q Consensus 363 kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~s 427 (438)
.||.|..|+.++.+-|+.-|.+++ |.|+.-|..||.++||.+.||..||+|+|.+.||..-+
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enR---YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs 307 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENR---YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS 307 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhh---hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence 367788999999999999999966 99999999999999999999999999999999986543
No 18
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.47 E-value=9e-08 Score=93.01 Aligned_cols=60 Identities=20% Similarity=0.297 Sum_probs=53.7
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013698 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (438)
Q Consensus 364 kRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~ 426 (438)
+|.|..++.-+.+.|.+=|++ .-|..-.||.+||..+||++.||..||+|||-|+||...
T Consensus 123 RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 455678999999999999998 669999999999999999999999999999999987443
No 19
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.46 E-value=7.6e-08 Score=96.96 Aligned_cols=59 Identities=17% Similarity=0.338 Sum_probs=53.3
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 362 ~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
+|||+|--|++.++-.|++=|.+.+ |-|-.||+.||...+||..||+.||+|+|-|-|+
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQR---YLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR 210 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQR---YLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKR 210 (307)
T ss_pred cccccccccchhHHHHHHHHHHhhh---ccccHhHHHHHHhcCCCchheeeeeecchhhhhh
Confidence 3455556899999999999999966 9999999999999999999999999999988775
No 20
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.41 E-value=1.9e-07 Score=94.22 Aligned_cols=58 Identities=21% Similarity=0.397 Sum_probs=51.8
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 363 kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
++|.|..|+..++..|+.=|+.-. |-+..||..||...||+-.||..||+|||.|-|+
T Consensus 172 ~RksRTaFT~~Ql~~LEkrF~~QK---YLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKr 229 (309)
T KOG0488|consen 172 RRKSRTAFSDHQLFELEKRFEKQK---YLSVADRIELAASLGLTDAQVKTWFQNRRTKWKR 229 (309)
T ss_pred cccchhhhhHHHHHHHHHHHHHhh---cccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHH
Confidence 345567899999999999999855 9999999999999999999999999999988544
No 21
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.41 E-value=1.8e-07 Score=89.19 Aligned_cols=58 Identities=29% Similarity=0.447 Sum_probs=52.3
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 363 kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
.++|+.+|+.++...|+.-|..|. |-.+..|..||.+.||++.||..||+|||.|-|.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~---~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~ 107 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEK---KLEPERKKKLAKELGLQPRQVAVWFQNRRARWKT 107 (198)
T ss_pred cccccccccHHHHHHhHHhhcccc---ccChHHHHHHHHhhCCChhHHHHHHhhccccccc
Confidence 345667899999999999999976 8899999999999999999999999999999553
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.39 E-value=2.3e-07 Score=85.51 Aligned_cols=62 Identities=19% Similarity=0.356 Sum_probs=56.3
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013698 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (438)
Q Consensus 362 ~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~ 426 (438)
..+++|.+.+..++.+|+..|.. +|||+..+|..|+..++|+++-|..||+|+|.+.|+...
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 34667788999999999999997 999999999999999999999999999999999987554
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.37 E-value=2.4e-07 Score=86.55 Aligned_cols=59 Identities=19% Similarity=0.377 Sum_probs=52.8
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 362 ~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
.++|.|..|+..+...|+.-|+... |-+-.|+.+||...+|+++||..||+|+|+++||
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Qr---YLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQR---YLSTPERQELANALSLSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhh---hcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 3445567899999999999999755 9999999999999999999999999999999986
No 24
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.29 E-value=3.6e-07 Score=79.98 Aligned_cols=64 Identities=16% Similarity=0.287 Sum_probs=56.1
Q ss_pred HHHHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 357 IREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 357 lr~e~~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
+-+..+.+|-|..|+..+...|+..|.+ .-||..-.|++||.+..|++..|.+||+|+|.+++|
T Consensus 11 l~ekrKQRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRK 74 (125)
T KOG0484|consen 11 LTEKRKQRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRK 74 (125)
T ss_pred hhHHHHhhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHH
Confidence 3344445566789999999999999999 559999999999999999999999999999999876
No 25
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.18 E-value=8.8e-07 Score=85.37 Aligned_cols=66 Identities=15% Similarity=0.298 Sum_probs=59.6
Q ss_pred HHHHHHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 355 VDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 355 ~~lr~e~~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
..||+....+|.|..|+..+...|++=|.+.. |-+.+||.+++..+.|+..||..||+|+|.|-|+
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfrekq---YLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFREKQ---YLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhHhh---hhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 45676667778888999999999999999955 9999999999999999999999999999999875
No 26
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.14 E-value=1.6e-06 Score=83.98 Aligned_cols=57 Identities=19% Similarity=0.357 Sum_probs=52.0
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 364 kRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
+|-|..|+..+..+|+.-|.+ .-||+...+++||.+.+|.+.+|.+||.|+|.+.++
T Consensus 38 RRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~ 94 (228)
T KOG2251|consen 38 RRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRR 94 (228)
T ss_pred ccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhH
Confidence 455789999999999999999 559999999999999999999999999999988754
No 27
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.06 E-value=3e-06 Score=83.98 Aligned_cols=55 Identities=20% Similarity=0.319 Sum_probs=50.1
Q ss_pred CCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 367 rgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
|..|+..+...|+.-|.+-. ||..--|+.||.+|+|.+..|.+||+|+|.+-+|.
T Consensus 145 RTiFT~~Qle~LEkaFkeaH---YPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEAH---YPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred cchhhHHHHHHHHHHHhhcc---CccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 67899999999999999944 99999999999999999999999999999885543
No 28
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.00 E-value=1.1e-06 Score=88.00 Aligned_cols=71 Identities=21% Similarity=0.431 Sum_probs=61.8
Q ss_pred HHHHHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCCCC
Q 013698 356 DIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTS 429 (438)
Q Consensus 356 ~lr~e~~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~s~~ 429 (438)
.|..+-..||.|..++..+...|+.-|.. .|.|.+-.|++|+.+|||+...|.+||+|+|.+.|+...-++
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 34456678999999999999999998876 899999999999999999999999999999998876555443
No 29
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=97.97 E-value=2.9e-06 Score=85.85 Aligned_cols=56 Identities=20% Similarity=0.373 Sum_probs=50.6
Q ss_pred cCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 365 RRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 365 RkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
|-|.-|+..+.+.|+.||..+. ||+.+.|++||.-++|++..|++||.|+|.+-+|
T Consensus 114 rQrthFtSqqlqele~tF~rNr---ypdMstrEEIavwtNlTE~rvrvwfknrrakwrk 169 (351)
T KOG0486|consen 114 RQRTHFTSQQLQELEATFQRNR---YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 169 (351)
T ss_pred hhhhhhHHHHHHHHHHHHhhcc---CCccchhhHHHhhccccchhhhhhcccchhhhhh
Confidence 3456799999999999999955 9999999999999999999999999999988654
No 30
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=97.95 E-value=2.3e-06 Score=85.09 Aligned_cols=56 Identities=23% Similarity=0.338 Sum_probs=49.1
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013698 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (438)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~ 426 (438)
-.++..+|-.|+.-|-- .+|.|..-|.+||..+||++.||..||+|||.|.+|-++
T Consensus 204 vVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 204 VVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred EEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 45788899999876654 789999999999999999999999999999999887554
No 31
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.79 E-value=6.9e-06 Score=82.58 Aligned_cols=67 Identities=21% Similarity=0.389 Sum_probs=58.0
Q ss_pred HHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCCCC
Q 013698 360 EILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTS 429 (438)
Q Consensus 360 e~~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~s~~ 429 (438)
.--|||||..+-..-++.|+++|.. -|-|+-+....+|++++|.+..|++||+|+|.+.|+-.-|.+
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa~ 372 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSAT 372 (385)
T ss_pred ccccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhhc
Confidence 3347788888887888999999997 899999999999999999999999999999999987655544
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.59 E-value=3.2e-05 Score=72.03 Aligned_cols=63 Identities=13% Similarity=0.145 Sum_probs=55.8
Q ss_pred HHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 360 EILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 360 e~~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
.++++|.|.+|+..+...|+.-|.. .+||+...++.||..+++++..|.+||+|+|.+.++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 3455677788999999999999988 48999999999999999999999999999999887643
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.54 E-value=9e-05 Score=79.60 Aligned_cols=56 Identities=21% Similarity=0.363 Sum_probs=52.2
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhc
Q 013698 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRN 421 (438)
Q Consensus 363 kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~ 421 (438)
-||.|-.|+..+++.|...|.+ +|||+.+.-+.|+.++||...-|.|||-|+|+|.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3566778999999999999999 8899999999999999999999999999999994
No 34
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.47 E-value=3.8e-05 Score=77.76 Aligned_cols=54 Identities=17% Similarity=0.308 Sum_probs=47.7
Q ss_pred CCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 367 rgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
|..|+++++.-|+.-|+.. -|-++-.|.+||..++|.+.-|++||+|+|+|.|+
T Consensus 185 RTAFTReQIaRLEKEFyrE---NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKR 238 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYRE---NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKR 238 (408)
T ss_pred HhhhhHHHHHHHHHHHHHh---ccccCchhhhHHHhhCCCcceeehhhhhchhhhhh
Confidence 3678899999998777763 38999999999999999999999999999999885
No 35
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.46 E-value=6.3e-05 Score=73.41 Aligned_cols=61 Identities=25% Similarity=0.400 Sum_probs=52.5
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 362 ~kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
+||..|.+|+..++..|+.-|.+ .-||--.++.+||...|+++.||.+||+|+|.+-+|..
T Consensus 166 ~rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred cccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 34555667999999999999998 44999999999999999999999999999998865543
No 36
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.44 E-value=0.0001 Score=75.71 Aligned_cols=59 Identities=25% Similarity=0.479 Sum_probs=53.3
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 364 kRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
+|.|..|+..+...|+.+|.. .|||....|+.||.++||....|..||.|+|.|.+|-.
T Consensus 177 rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 344678999999999999997 77999999999999999999999999999999876654
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.43 E-value=7.9e-05 Score=74.95 Aligned_cols=67 Identities=31% Similarity=0.525 Sum_probs=60.8
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCCCCc
Q 013698 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTST 430 (438)
Q Consensus 363 kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~s~~~ 430 (438)
..+++++++.+. .+|+.|...|..+|||++.++..|+..++++.-||.+||+|.|+|.++....+..
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~ 161 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWG 161 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCC
Confidence 345678999999 9999999999999999999999999999999999999999999999987776543
No 38
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=96.75 E-value=0.0011 Score=43.22 Aligned_cols=22 Identities=41% Similarity=0.622 Sum_probs=20.5
Q ss_pred HHHHHHHHhhHHHHHHHHHHHh
Q 013698 341 ELKHELKQGYKEKIVDIREEIL 362 (438)
Q Consensus 341 ELK~~Lk~~y~~~i~~lr~e~~ 362 (438)
|||.+|+++|+++|++||+||+
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 6899999999999999999974
No 39
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.69 E-value=0.0015 Score=51.40 Aligned_cols=43 Identities=21% Similarity=0.502 Sum_probs=31.5
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 013698 375 TSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 420 (438)
Q Consensus 375 ~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR 420 (438)
++.|+++|..|. ++.+.+-..|+.+++|+..||..||.-++.+
T Consensus 10 ~~pL~~Yy~~h~---~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKHK---QLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT-------TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHcC---CccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 456999999966 8999999999999999999999999877544
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.39 E-value=0.033 Score=51.93 Aligned_cols=59 Identities=27% Similarity=0.532 Sum_probs=49.7
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 364 kRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
++.+..+.......|..-|.. .|||....+..|+..+|++...|.+||+|+|.+.++..
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 154 RRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred CCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 344556777777777777666 88999999999999999999999999999999997643
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=87.05 E-value=0.46 Score=56.46 Aligned_cols=60 Identities=20% Similarity=0.361 Sum_probs=52.1
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 363 kkRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
+++.|..+...+..+|+..|..-. ||++++-+.|....+|....|..||+|.|.+.+|..
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~---~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQR---TPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhcc---CChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 344556777788999999998855 999999999999999999999999999999988743
No 42
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=78.06 E-value=3.7 Score=31.43 Aligned_cols=47 Identities=15% Similarity=0.186 Sum_probs=30.5
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHH
Q 013698 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQR 418 (438)
Q Consensus 364 kRkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrR 418 (438)
||+|..|+-+..-.+-.-+.. . + -+..||..+|+...+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~---g--~---s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE---G--E---SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC---T--T----HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc---C--C---CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 456677877765544444443 2 2 578999999999999999999964
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=72.16 E-value=7 Score=44.75 Aligned_cols=48 Identities=25% Similarity=0.556 Sum_probs=43.1
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 375 TSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 375 ~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
...|+.+|.. ++.|++++-..+|.+-||...-|..||.+.+.......
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 6788888887 88999999999999999999999999999998876554
No 44
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=55.13 E-value=14 Score=28.89 Aligned_cols=47 Identities=15% Similarity=0.246 Sum_probs=29.6
Q ss_pred cCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHH
Q 013698 365 RRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQR 418 (438)
Q Consensus 365 RkrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrR 418 (438)
++++.||.+.+..+-.-+.. .......+|...|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~-------~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE-------SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH-------HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH-------CCCceEeeecccccccccccHHHHHHh
Confidence 34567888875554333322 246778999999999999999987776
No 45
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=54.18 E-value=28 Score=21.26 Aligned_cols=39 Identities=10% Similarity=0.176 Sum_probs=26.6
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 013698 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWF 414 (438)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWF 414 (438)
..++.+.+..+...+.. .+ ....+|+.+|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 44666666666555543 22 34578899999999999984
No 46
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=53.68 E-value=27 Score=24.07 Aligned_cols=46 Identities=13% Similarity=0.159 Sum_probs=34.3
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcc
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 422 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~k 422 (438)
.++...+.++...+.... .-..+|..+|++...|..|....+.+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~~--------~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEGL--------SYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 367777777777664422 3457899999999999999988877653
No 47
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=45.32 E-value=59 Score=36.19 Aligned_cols=25 Identities=12% Similarity=0.290 Sum_probs=15.4
Q ss_pred CChHHHHHHHHHH-------HHHHHHHHHHhH
Q 013698 235 DDKELDQFMTHYV-------LLLCSFKEQLQQ 259 (438)
Q Consensus 235 ~DPELDQFMeaYC-------~mL~kYkEEL~k 259 (438)
.-|++....-+|| .||.||++||++
T Consensus 183 ~ap~mkt~~~aYcanHP~AV~VL~k~~dELek 214 (661)
T KOG2070|consen 183 LAPQMKTLYLAYCANHPSAVNVLTKHSDELEK 214 (661)
T ss_pred hhHHHHHHHHHHHhcCchhhhHHHHhHHHHHH
Confidence 3466666666666 466666666655
No 48
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=44.89 E-value=32 Score=25.28 Aligned_cols=44 Identities=14% Similarity=0.238 Sum_probs=32.0
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 420 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR 420 (438)
.||...+.++...|... -.-.++|+.+|++...|.+|....|++
T Consensus 10 ~L~~~~r~i~~l~~~~g--------~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG--------MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC--------cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 47888888887655542 345689999999999999999988876
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=42.20 E-value=29 Score=30.11 Aligned_cols=47 Identities=9% Similarity=0.067 Sum_probs=37.1
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
.||+..+.++..-|.... .-.++|..+|++...|.+|....|++.++
T Consensus 106 ~L~~~~r~ii~l~~~~~~--------s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGK--------TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 488888888865544422 24589999999999999999999998865
No 50
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=41.25 E-value=24 Score=25.84 Aligned_cols=47 Identities=11% Similarity=0.179 Sum_probs=35.4
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
.||...+.+|..-|... -.-.++|+..|++...|..+.....++.++
T Consensus 4 ~L~~~er~vi~~~y~~~--------~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG--------LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTST---------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC--------CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 47788888887776432 234579999999999999999988887653
No 51
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=41.20 E-value=52 Score=34.51 Aligned_cols=47 Identities=13% Similarity=0.217 Sum_probs=37.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhhCC
Q 013698 237 KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGV 285 (438)
Q Consensus 237 PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~Fc~~IEsQL~sL~~~ 285 (438)
-+-|.||.-||. .+|-.+|.+=+|-++++|..-+..+-.|+..||.+
T Consensus 134 T~C~Hy~H~~Cl--aRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpV 180 (368)
T KOG4445|consen 134 TACDHYMHFACL--ARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPV 180 (368)
T ss_pred ehhHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhH
Confidence 478999999994 46666666666666778888888999999999864
No 52
>PF12022 DUF3510: Domain of unknown function (DUF3510); InterPro: IPR024603 The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function []. This uncharacterised domain is found in the C-terminal of COG complex subunit 2 proteins.
Probab=40.94 E-value=1.3e+02 Score=26.86 Aligned_cols=21 Identities=29% Similarity=0.316 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHhhCC
Q 013698 265 AMEAVMACWEIEQSLQSLTGV 285 (438)
Q Consensus 265 ~~EA~~Fc~~IEsQL~sL~~~ 285 (438)
+.|...-.+++|..|+-|-..
T Consensus 79 ~~evL~sv~KtEeSL~rlkk~ 99 (125)
T PF12022_consen 79 ASEVLTSVRKTEESLKRLKKR 99 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 346667788999999999653
No 53
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=39.77 E-value=49 Score=26.41 Aligned_cols=25 Identities=28% Similarity=0.349 Sum_probs=20.4
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHh
Q 013698 234 TDDKELDQFMTHYVLLLCSFKEQLQ 258 (438)
Q Consensus 234 g~DPELDQFMeaYC~mL~kYkEEL~ 258 (438)
|-|+|||...+.|..+.....+.+.
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~~ 25 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELLE 25 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 5799999999999988777666654
No 54
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=37.27 E-value=88 Score=30.18 Aligned_cols=45 Identities=16% Similarity=0.258 Sum_probs=37.0
Q ss_pred C-hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHH-HHHHHHHHHHHHHhh
Q 013698 236 D-KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEA-VMACWEIEQSLQSLT 283 (438)
Q Consensus 236 D-PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA-~~Fc~~IEsQL~sL~ 283 (438)
| -|||-.+.++-.++..|++.++-.+= .+| ..||..|..||-.+.
T Consensus 102 DItELDVvL~~FEk~~~eYkq~ieS~~c---r~AI~~F~~~~keqL~~~i 148 (175)
T PF13097_consen 102 DITELDVVLSAFEKTALEYKQSIESKIC---RKAINKFYSNFKEQLIEMI 148 (175)
T ss_pred cchHHHHHHHHHHHHHHHHHHhhccHHH---HHHHHHHHHHHHHHHHHHH
Confidence 6 89999999999999999999977652 233 358999999998776
No 55
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=33.92 E-value=44 Score=29.34 Aligned_cols=48 Identities=13% Similarity=0.204 Sum_probs=37.8
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
+||...+.++...+.+.. + -.++|+.+|++...|.+.+.-.|++.++.
T Consensus 106 ~Lp~~~r~v~~l~~~~g~----s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEK----S----YQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHhCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 388888888876555433 1 24799999999999999999999988764
No 56
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=33.39 E-value=43 Score=29.71 Aligned_cols=50 Identities=14% Similarity=0.005 Sum_probs=40.0
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
..||...+.++..++..++ .-.++|..+|++...|.+|..-.|++.++..
T Consensus 107 ~~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHEL--------TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhcC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3478888888887665533 2458999999999999999999999987643
No 57
>KOG4511 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.15 E-value=3.2e+02 Score=28.52 Aligned_cols=28 Identities=25% Similarity=0.437 Sum_probs=23.2
Q ss_pred HHHhhCCChHHHHHHHHh--hhhccCCCcc
Q 013698 178 AEILSHPLYEQLLSAHVA--CLRIATPVDQ 205 (438)
Q Consensus 178 AkI~sHPlYp~LL~Ayid--ClKVGAPpev 205 (438)
.=|+.|-=|..|+.-.++ |--||.-|++
T Consensus 49 ~y~~IH~EYk~LVd~lle~f~eevgi~p~q 78 (335)
T KOG4511|consen 49 VYIMIHKEYKQLVDTLLECFCEEVGITPTQ 78 (335)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCCHHH
Confidence 347889999999999999 6678988764
No 58
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=32.32 E-value=44 Score=30.68 Aligned_cols=49 Identities=6% Similarity=0.004 Sum_probs=39.0
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
.||...+.+|..-+...+ .-.++|+.+|++...|.+++...|++.++..
T Consensus 142 ~L~~~~r~vl~l~~~~~~--------s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGGL--------TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 388888888876555432 2357999999999999999999999987654
No 59
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=31.86 E-value=35 Score=25.67 Aligned_cols=23 Identities=13% Similarity=0.304 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCChhhhhhhhhhH
Q 013698 395 DKARLVQETGLQLKQINNWFINQ 417 (438)
Q Consensus 395 eK~~LA~~TGLs~kQVnNWFiNr 417 (438)
....||+.+|++...|+.|+.+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcc
Confidence 45689999999999999999976
No 60
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=31.64 E-value=49 Score=27.37 Aligned_cols=46 Identities=15% Similarity=0.232 Sum_probs=34.3
Q ss_pred CCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 370 LPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 370 Lpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
||+..+.++..-+.. .| .-..+|..+|+++..|.+|....+++.++
T Consensus 111 L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 666677776544332 12 33489999999999999999999988765
No 61
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.35 E-value=46 Score=29.16 Aligned_cols=47 Identities=11% Similarity=0.131 Sum_probs=36.4
Q ss_pred CCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 370 LPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 370 Lpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
||+..+.++...+...+ .-..+|+..|++...|.+|+.-.|++.++.
T Consensus 126 L~~~~r~i~~l~~~~~~--------~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 126 LPVKQREVFLLRYVEGL--------SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCHHHHHHhhHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 77777777766544422 235899999999999999999999998753
No 62
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=30.24 E-value=51 Score=28.94 Aligned_cols=48 Identities=8% Similarity=0.105 Sum_probs=36.4
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
.||+..+.+|...|...+ + -..+|..+|++...|.+|....|++.++.
T Consensus 128 ~L~~~~r~vl~l~~~~~~----s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEGL----S----YEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 377778888866544322 2 24789999999999999999999988763
No 63
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=29.72 E-value=52 Score=29.50 Aligned_cols=48 Identities=10% Similarity=0.227 Sum_probs=38.0
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
.||...+.++...|.+.+ + -.++|..+|++...|.+++.-.|++.++.
T Consensus 129 ~L~~~~r~i~~l~~~~g~----s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEGL----S----YKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHcCC----C----HHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 377778888877765522 2 45799999999999999999999998764
No 64
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=28.23 E-value=56 Score=28.77 Aligned_cols=48 Identities=21% Similarity=0.140 Sum_probs=38.2
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
..||..++.++.-.+.... + -.++|..+|++...|..+..-.|++.++
T Consensus 111 ~~L~~~~r~v~~l~~~~~~----s----~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYGF----S----YKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3588888888877655433 2 3478999999999999999999999875
No 65
>PF13518 HTH_28: Helix-turn-helix domain
Probab=27.81 E-value=63 Score=23.18 Aligned_cols=24 Identities=17% Similarity=0.432 Sum_probs=20.8
Q ss_pred HHHHHHHhCCChhhhhhhhhhHHh
Q 013698 396 KARLVQETGLQLKQINNWFINQRK 419 (438)
Q Consensus 396 K~~LA~~TGLs~kQVnNWFiNrRk 419 (438)
...+|..+|++..+|..|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 446999999999999999987765
No 66
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=27.79 E-value=70 Score=27.41 Aligned_cols=47 Identities=15% Similarity=0.167 Sum_probs=35.8
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
.||...+.+|...+... ++ -.++|..+|++...|.++..-.|++.++
T Consensus 113 ~L~~~~r~il~l~~~~~----~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG----KS----YKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46777788887644431 22 3468999999999999999999988875
No 67
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=27.65 E-value=63 Score=29.55 Aligned_cols=48 Identities=15% Similarity=0.176 Sum_probs=38.3
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
+||+..+.++...|.+.. .-.++|+.+|++...|.+...-.|++.++.
T Consensus 131 ~L~~~~r~i~~l~~~~g~--------s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 131 DLEKLDREIFIRRYLLGE--------KIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred hCCHHHHHHHHHHHHccC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 588889899876555422 235799999999999999999999988764
No 68
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=27.17 E-value=50 Score=29.64 Aligned_cols=49 Identities=8% Similarity=0.010 Sum_probs=37.0
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
.||...+.++..-|... -.-.++|+.+|++...|.++.-..|++.++..
T Consensus 138 ~L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG--------LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 36777777776544332 23458999999999999999999999987654
No 69
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=26.66 E-value=64 Score=28.72 Aligned_cols=48 Identities=15% Similarity=0.021 Sum_probs=38.6
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
.||...+.++.-.+.+.. .-.++|+.+|++...|.++..-.|++.++.
T Consensus 112 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGASGF--------SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 488888888877665533 234899999999999999999999988753
No 70
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=26.48 E-value=72 Score=27.73 Aligned_cols=47 Identities=19% Similarity=0.244 Sum_probs=36.5
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
.||...+.++..-+...+ .-.++|+.+|++...|.++..-.|++.++
T Consensus 111 ~L~~~~r~v~~l~~~~g~--------~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQRGV--------SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHhcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 478888888877444422 23478999999999999999999988765
No 71
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=25.80 E-value=75 Score=28.46 Aligned_cols=48 Identities=6% Similarity=0.064 Sum_probs=38.6
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
.||...+.++...+.+.+ .-.++|+.+|++..-|.+.+...|++.++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAGL--------TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 488888888877765533 235799999999999999999999988753
No 72
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=25.32 E-value=73 Score=27.95 Aligned_cols=49 Identities=12% Similarity=0.210 Sum_probs=38.0
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
.||...+.++..-+...+ .-.++|..+|++...|.++....|++.++..
T Consensus 110 ~L~~~~r~i~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYEDL--------SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHhcC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 478888888866554422 2347899999999999999999999987654
No 73
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=24.95 E-value=1.4e+02 Score=20.92 Aligned_cols=47 Identities=13% Similarity=0.176 Sum_probs=33.6
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
.|+.....++..+ .. . + ....+|+.+|++...|..|....+.+..-.
T Consensus 3 ~l~~~e~~i~~~~-~~-g---~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRLL-AE-G---L----TNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHHH-Hc-C---C----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 4666677776543 22 1 1 346889999999999999999888776543
No 74
>PF04859 DUF641: Plant protein of unknown function (DUF641); InterPro: IPR006943 This conserved region is found in a number of plant proteins of unknown function.
Probab=24.70 E-value=3.1e+02 Score=25.23 Aligned_cols=27 Identities=11% Similarity=0.415 Sum_probs=23.2
Q ss_pred CCCC-hHHHHHHHHHHHHHHHHHHHHhH
Q 013698 233 VTDD-KELDQFMTHYVLLLCSFKEQLQQ 259 (438)
Q Consensus 233 ~g~D-PELDQFMeaYC~mL~kYkEEL~k 259 (438)
+++. .|+..-|.+|--++.+++.|+..
T Consensus 78 l~a~~~e~qsli~~yE~~~~kLe~e~~~ 105 (131)
T PF04859_consen 78 LAAEIQEQQSLIKTYEIVVKKLEAELRA 105 (131)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444 89999999999999999999975
No 75
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=24.49 E-value=28 Score=34.01 Aligned_cols=46 Identities=24% Similarity=0.328 Sum_probs=32.7
Q ss_pred CCCCcccccCCCccchhhhHHHHHHHhhCCChHHHHHHHHhhhhccCCCcc
Q 013698 155 KSEGVVVESGADGVVNWQNARYKAEILSHPLYEQLLSAHVACLRIATPVDQ 205 (438)
Q Consensus 155 ~~~~~~~~~~~~~~~~~e~e~lKAkI~sHPlYp~LL~AyidClKVGAPpev 205 (438)
+|-.+|-.|-.+|- .-=...||.+|..+|++.+||.||+ ||.|.-+
T Consensus 93 ~GRPfILaGHSQGs-~~l~~LL~e~~~~~pl~~rLVAAYl----iG~~v~~ 138 (207)
T PF11288_consen 93 NGRPFILAGHSQGS-MHLLRLLKEEIAGDPLRKRLVAAYL----IGYPVTV 138 (207)
T ss_pred CCCCEEEEEeChHH-HHHHHHHHHHhcCchHHhhhheeee----cCccccH
Confidence 45555555533332 2335679999999999999999998 8888543
No 76
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=24.46 E-value=52 Score=31.56 Aligned_cols=40 Identities=25% Similarity=0.580 Sum_probs=30.8
Q ss_pred CCcchHHHHHHHHHhcCCCCCCC-HHHHHHHHHHhCCChhh
Q 013698 370 LPGDTTSVLKSWWQSHSKWPYPT-EEDKARLVQETGLQLKQ 409 (438)
Q Consensus 370 Lpkea~~iLk~Wf~~H~~~PYPS-e~eK~~LA~~TGLs~kQ 409 (438)
......+..-.|...|.-.|||+ ++||..-|++.||-+..
T Consensus 21 v~~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 21 VMPRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred ccccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 33445566778998999999995 67888889999987654
No 77
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=23.76 E-value=81 Score=29.17 Aligned_cols=48 Identities=10% Similarity=0.045 Sum_probs=37.3
Q ss_pred CCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 367 rgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
...|++..+.+|.. +.+.+ .-.++|+.+|++...|.+|....|++.++
T Consensus 4 ~~~Lt~rqreVL~l-r~~Gl--------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRL-RERGL--------TQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHH-HHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35688888899876 33322 24589999999999999999998888764
No 78
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=23.72 E-value=76 Score=29.62 Aligned_cols=49 Identities=16% Similarity=0.180 Sum_probs=37.9
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
.||...+.+|..-+...+ .-.++|+.+|++...|.+++...|++.++-.
T Consensus 153 ~L~~~~r~vl~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQEL--------SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888876554432 2458999999999999999999999886543
No 79
>PF13730 HTH_36: Helix-turn-helix domain
Probab=23.65 E-value=2.3e+02 Score=20.70 Aligned_cols=30 Identities=10% Similarity=0.307 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 013698 388 WPYPTEEDKARLVQETGLQLKQINNWFINQRKR 420 (438)
Q Consensus 388 ~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR 420 (438)
..||+ ...||+.+|++...|..++..-+.+
T Consensus 23 ~~~pS---~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 23 GCFPS---QETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CCCcC---HHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 48897 5679999999999998887655443
No 80
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=22.92 E-value=74 Score=26.10 Aligned_cols=7 Identities=57% Similarity=1.004 Sum_probs=3.0
Q ss_pred hHHHHHH
Q 013698 237 KELDQFM 243 (438)
Q Consensus 237 PELDQFM 243 (438)
.|||+||
T Consensus 47 aELD~Ym 53 (74)
T PF13865_consen 47 AELDAYM 53 (74)
T ss_pred HHHHHHH
Confidence 4444444
No 81
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=22.05 E-value=83 Score=28.47 Aligned_cols=49 Identities=6% Similarity=0.081 Sum_probs=37.1
Q ss_pred CCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013698 370 LPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (438)
Q Consensus 370 Lpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~ 426 (438)
||+..+.++..-|.... .-.++|+.+|++...|.++....|++.++...
T Consensus 129 L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 129 LPERQREAIVLQYYQGL--------SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CCHHHHHHhhHHHhcCC--------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 67777787765444322 23479999999999999999999999877443
No 82
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=21.82 E-value=97 Score=27.71 Aligned_cols=47 Identities=9% Similarity=0.198 Sum_probs=36.8
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
.||...+.++.-.+.+.+ + -.++|+.+|++..-|.++....|+|.+.
T Consensus 119 ~Lp~~~r~v~~L~~~~g~--s------~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRLDGM--G------HAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHHcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888888876555432 2 3479999999999999999999998764
No 83
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=21.76 E-value=83 Score=29.16 Aligned_cols=49 Identities=14% Similarity=0.061 Sum_probs=38.7
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
.||...+.++.-.+.+.+ + -.++|..+|++...|.+++.-.|++.++..
T Consensus 113 ~Lp~~~r~v~~L~~~~g~----s----~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGASGF----S----YEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 488888888877655422 2 347899999999999999999999987643
No 84
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=21.74 E-value=70 Score=25.73 Aligned_cols=20 Identities=15% Similarity=0.403 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCChhhhhhhh
Q 013698 395 DKARLVQETGLQLKQINNWF 414 (438)
Q Consensus 395 eK~~LA~~TGLs~kQVnNWF 414 (438)
.-..||+++|++..+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45689999999999999994
No 85
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=21.63 E-value=96 Score=28.12 Aligned_cols=48 Identities=10% Similarity=-0.026 Sum_probs=37.6
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
.||...+.++..-|.... .-.++|..+|++..-|..+....|++.++.
T Consensus 139 ~L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVVGL--------SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478888888876544422 245899999999999999999999988763
No 86
>PRK00118 putative DNA-binding protein; Validated
Probab=21.61 E-value=1.3e+02 Score=26.56 Aligned_cols=47 Identities=6% Similarity=0.070 Sum_probs=37.4
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK 423 (438)
.||...+.++..++.... .-..+|+.+|++..-|..|+...|++.++
T Consensus 17 ~L~ekqRevl~L~y~eg~--------S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY--------SLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 477888888877766533 23469999999999999999998888765
No 87
>PF12878 SICA_beta: SICA extracellular beta domain; InterPro: IPR024285 The schizont-infected cell agglutination (SICA) proteins of Plasmodium knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. SICA proteins comprise multiple domains, with the extracellular cysteine-rich domains (CRDs) occurring at different frequencies. They contain a five-cysteine CRD (SICA-alpha) at the N terminus, which occurs once or twice, then between 1 and 10 SICA-beta CRDs with 7-10 cysteine residues, a transmembrane domain, and a conserved C-terminal domain []. This entry represents the extracellular SICA-beta domain.
Probab=20.76 E-value=99 Score=29.34 Aligned_cols=24 Identities=21% Similarity=0.492 Sum_probs=21.8
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHhH
Q 013698 234 TDDKELDQFMTHYVLLLCSFKEQLQQ 259 (438)
Q Consensus 234 g~DPELDQFMeaYC~mL~kYkEEL~k 259 (438)
..+|.++|.|- |.+|..|...|..
T Consensus 95 ~~~~~f~qtm~--C~lLnaYAkkmke 118 (169)
T PF12878_consen 95 DDNPSFKQTMG--CFLLNAYAKKMKE 118 (169)
T ss_pred cCCccHHHHHH--HHHHHHHHHHHHH
Confidence 46799999999 9999999999975
No 88
>PF12362 DUF3646: DNA polymerase III gamma and tau subunits C terminal; InterPro: IPR022107 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00004 from PFAM. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Probab=20.69 E-value=75 Score=28.44 Aligned_cols=21 Identities=29% Similarity=0.450 Sum_probs=18.2
Q ss_pred hHHHHHHHhhCCChHHHHHHH
Q 013698 173 NARYKAEILSHPLYEQLLSAH 193 (438)
Q Consensus 173 ~e~lKAkI~sHPlYp~LL~Ay 193 (438)
.+..++.+..||++...|.+|
T Consensus 88 ~~~~~~~a~~~P~V~avL~~F 108 (117)
T PF12362_consen 88 KEARRAAARAHPLVKAVLAAF 108 (117)
T ss_pred HHHHHHHHHhCcHHHHHHHHC
Confidence 346889999999999999886
No 89
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=20.15 E-value=1e+02 Score=28.50 Aligned_cols=50 Identities=16% Similarity=0.079 Sum_probs=38.3
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~~ 426 (438)
.||...+.++...+.+.+ + -.++|+.+|++..-|.++....|++.++...
T Consensus 116 ~Lp~~~r~i~~L~~~~g~----s----~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGASGF----A----YEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 378888888876555432 2 2478999999999999999999999876443
No 90
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.14 E-value=1.8e+02 Score=32.98 Aligned_cols=37 Identities=32% Similarity=0.524 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhh
Q 013698 240 DQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLT 283 (438)
Q Consensus 240 DQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~Fc~~IEsQL~sL~ 283 (438)
.-|.|.|..--.+-++|+++|+ ...|..++.||+.|.
T Consensus 569 ~vfrEqYi~~~dlV~~e~qrH~-------~~l~~~k~~QlQ~l~ 605 (741)
T KOG4460|consen 569 QVFREQYILKQDLVKEEIQRHV-------KLLCDQKKKQLQDLS 605 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHH
Confidence 3477778777778889999975 457899999999996
No 91
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=20.10 E-value=1.1e+02 Score=26.53 Aligned_cols=49 Identities=10% Similarity=0.049 Sum_probs=38.0
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013698 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (438)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~ 424 (438)
.+||+..+.++.--+.+.+ + -.++|..+|++...|.+...-.|++.++.
T Consensus 105 ~~Lp~~~r~v~~l~~~~g~----s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 105 QKLPARQREAFLLRYWEDM----D----VAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred HhCCHHHHHHHHHHHHhcC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3488888888876554422 2 35799999999999999999999888754
No 92
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.02 E-value=1.1e+02 Score=27.93 Aligned_cols=49 Identities=14% Similarity=0.005 Sum_probs=38.7
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013698 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (438)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TGLs~kQVnNWFiNrRkR~kK~~ 425 (438)
.||...+.++.-.+...+ .-.++|+.+|+++.-|.++..-.|++.++-+
T Consensus 130 ~Lp~~~r~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~ 178 (185)
T PRK09649 130 DLTTDQREALLLTQLLGL--------SYADAAAVCGCPVGTIRSRVARARDALLADA 178 (185)
T ss_pred hCCHHHhHHhhhHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 488888888876555433 2347999999999999999999999988743
Done!