Query 013045
Match_columns 450
No_of_seqs 245 out of 1064
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 23:51:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013045.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013045hhsearch_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 4.6E-33 9.9E-38 270.8 18.3 209 171-424 26-249 (334)
2 KOG0773 Transcription factor M 99.9 1.1E-28 2.4E-33 246.0 0.4 252 170-429 46-305 (342)
3 PF03791 KNOX2: KNOX2 domain ; 99.9 5.3E-23 1.1E-27 157.8 7.2 50 231-284 3-52 (52)
4 PF03790 KNOX1: KNOX1 domain ; 99.8 8.1E-20 1.8E-24 136.4 3.4 44 174-217 1-44 (45)
5 PF05920 Homeobox_KN: Homeobox 99.6 1.5E-15 3.2E-20 110.8 4.2 40 381-420 1-40 (40)
6 PF03792 PBC: PBC domain; Int 99.5 2.2E-13 4.7E-18 128.6 13.1 150 171-362 24-190 (191)
7 cd00086 homeodomain Homeodomai 99.4 2.7E-13 5.8E-18 101.8 6.9 58 364-424 1-58 (59)
8 smart00389 HOX Homeodomain. DN 99.4 6.7E-13 1.5E-17 99.3 6.7 55 365-422 2-56 (56)
9 PF00046 Homeobox: Homeobox do 99.4 6.8E-13 1.5E-17 100.4 5.3 57 364-423 1-57 (57)
10 KOG0775 Transcription factor S 99.1 2.8E-11 6E-16 119.8 4.6 48 372-422 185-232 (304)
11 KOG0487 Transcription factor A 98.7 6.5E-09 1.4E-13 104.9 3.3 59 364-425 236-294 (308)
12 TIGR01565 homeo_ZF_HD homeobox 98.7 2E-08 4.3E-13 79.1 5.1 53 363-418 1-57 (58)
13 KOG3802 Transcription factor O 98.6 3.6E-08 7.8E-13 102.0 5.9 68 356-426 287-354 (398)
14 KOG0843 Transcription factor E 98.6 3E-08 6.5E-13 93.7 4.2 63 362-427 101-163 (197)
15 KOG0489 Transcription factor z 98.6 2.6E-08 5.6E-13 98.1 3.7 66 363-431 159-224 (261)
16 KOG0493 Transcription factor E 98.5 6.4E-08 1.4E-12 96.0 4.7 60 363-425 246-305 (342)
17 KOG0485 Transcription factor N 98.5 1.9E-07 4.1E-12 90.7 6.3 60 362-424 103-162 (268)
18 KOG0850 Transcription factor D 98.5 8.1E-08 1.8E-12 93.6 3.7 59 364-425 123-181 (245)
19 KOG0842 Transcription factor t 98.5 7.8E-08 1.7E-12 97.2 3.0 59 362-423 152-210 (307)
20 KOG0483 Transcription factor H 98.5 1.5E-07 3.2E-12 90.1 4.4 58 363-423 50-107 (198)
21 COG5576 Homeodomain-containing 98.4 1.7E-07 3.7E-12 86.7 4.3 62 362-426 50-111 (156)
22 KOG0488 Transcription factor B 98.4 3.5E-07 7.7E-12 92.5 4.6 61 362-425 171-231 (309)
23 KOG0491 Transcription factor B 98.3 3.8E-07 8.2E-12 85.5 2.8 60 362-424 99-158 (194)
24 KOG0484 Transcription factor P 98.3 3.9E-07 8.5E-12 80.0 2.6 65 357-424 11-75 (125)
25 KOG2251 Homeobox transcription 98.2 1.2E-06 2.6E-11 85.1 5.3 58 364-424 38-95 (228)
26 KOG0492 Transcription factor M 98.2 8.8E-07 1.9E-11 85.6 2.9 66 355-423 136-201 (246)
27 KOG0494 Transcription factor C 98.0 3.7E-06 8E-11 83.7 4.2 54 367-423 145-198 (332)
28 KOG4577 Transcription factor L 98.0 2.4E-06 5.1E-11 86.0 2.3 72 356-430 160-231 (383)
29 KOG0486 Transcription factor P 98.0 3E-06 6.6E-11 85.9 2.5 58 364-424 113-170 (351)
30 KOG0848 Transcription factor C 98.0 2.3E-06 5E-11 85.3 0.8 55 368-425 204-258 (317)
31 KOG1168 Transcription factor A 97.7 8E-06 1.7E-10 82.4 0.5 73 357-432 303-375 (385)
32 KOG0490 Transcription factor, 97.6 2.3E-05 5.1E-10 73.1 2.0 62 360-424 57-118 (235)
33 KOG0849 Transcription factor P 97.5 6.3E-05 1.4E-09 77.5 3.9 59 364-425 177-235 (354)
34 KOG2252 CCAAT displacement pro 97.5 0.00011 2.3E-09 79.3 5.6 55 364-421 421-475 (558)
35 KOG0844 Transcription factor E 97.3 7.6E-05 1.7E-09 75.9 1.5 55 367-424 185-239 (408)
36 KOG0773 Transcription factor M 97.3 0.00011 2.5E-09 74.1 2.3 64 363-427 95-158 (342)
37 KOG0847 Transcription factor, 97.3 0.00018 3.8E-09 70.6 2.9 60 362-424 166-225 (288)
38 PF03789 ELK: ELK domain ; In 96.8 0.001 2.2E-08 43.6 2.3 22 341-362 1-22 (22)
39 PF11569 Homez: Homeodomain le 96.6 0.0019 4.2E-08 51.0 3.0 43 375-420 10-52 (56)
40 KOG0490 Transcription factor, 94.4 0.03 6.5E-07 52.4 2.8 60 364-426 154-213 (235)
41 KOG1146 Homeobox protein [Gene 89.8 0.26 5.6E-06 58.6 3.4 61 362-425 902-962 (1406)
42 PF04218 CENP-B_N: CENP-B N-te 81.7 2.9 6.4E-05 32.1 4.5 47 364-418 1-47 (53)
43 KOG3623 Homeobox transcription 76.3 6.1 0.00013 45.4 6.6 51 375-428 568-618 (1007)
44 PF01527 HTH_Tnp_1: Transposas 69.9 8.3 0.00018 30.2 4.3 46 365-418 2-48 (76)
45 cd06171 Sigma70_r4 Sigma70, re 62.3 12 0.00027 25.9 3.6 46 369-422 10-55 (55)
46 cd00569 HTH_Hin_like Helix-tur 60.7 16 0.00034 22.6 3.6 40 367-414 3-42 (42)
47 PF08281 Sigma70_r4_2: Sigma-7 53.3 24 0.00052 26.1 4.0 44 369-420 10-53 (54)
48 PF04545 Sigma70_r4: Sigma-70, 47.8 21 0.00045 26.3 2.9 46 369-422 4-49 (50)
49 KOG4445 Uncharacterized conser 44.9 41 0.0009 35.3 5.4 47 237-285 134-180 (368)
50 KOG2070 Guanine nucleotide exc 42.8 69 0.0015 35.8 6.9 25 235-259 183-214 (661)
51 PRK06759 RNA polymerase factor 38.9 35 0.00077 29.7 3.4 48 368-423 105-152 (154)
52 PF05190 MutS_IV: MutS family 38.6 52 0.0011 26.3 4.1 25 234-258 1-25 (92)
53 PF12022 DUF3510: Domain of un 36.5 1.6E+02 0.0035 26.3 7.2 21 265-285 79-99 (125)
54 TIGR02937 sigma70-ECF RNA poly 35.1 40 0.00087 28.0 3.0 47 369-423 110-156 (158)
55 PF13097 CENP-U: CENP-A nucleo 33.5 1.1E+02 0.0024 29.7 5.9 45 236-283 102-148 (175)
56 PF13443 HTH_26: Cro/C1-type H 32.3 38 0.00083 25.6 2.3 23 395-417 12-34 (63)
57 PRK09644 RNA polymerase sigma 31.2 51 0.0011 29.4 3.2 50 368-425 107-156 (165)
58 PRK09646 RNA polymerase sigma 30.2 45 0.00098 30.7 2.8 49 369-425 142-190 (194)
59 PRK09642 RNA polymerase sigma 30.1 53 0.0012 28.9 3.1 48 369-424 106-153 (160)
60 PRK12514 RNA polymerase sigma 30.0 47 0.001 29.9 2.8 49 368-424 128-176 (179)
61 TIGR02983 SigE-fam_strep RNA p 29.8 55 0.0012 28.8 3.2 52 368-427 109-160 (162)
62 PRK06811 RNA polymerase factor 28.9 59 0.0013 29.8 3.3 49 368-424 130-178 (189)
63 PRK11924 RNA polymerase sigma 28.5 52 0.0011 28.9 2.7 48 369-424 125-172 (179)
64 KOG4511 Uncharacterized conser 28.5 4.2E+02 0.0091 27.8 9.4 27 179-205 50-78 (335)
65 PF06729 CENP-R: Kinetochore c 28.2 5.1E+02 0.011 24.4 9.4 31 237-276 56-86 (139)
66 TIGR02985 Sig70_bacteroi1 RNA 27.5 63 0.0014 27.8 3.1 47 369-423 113-159 (161)
67 PF11288 DUF3089: Protein of u 27.5 26 0.00056 34.4 0.7 45 155-205 93-138 (207)
68 PRK00118 putative DNA-binding 27.2 62 0.0013 28.6 2.9 47 369-423 17-63 (104)
69 PRK03975 tfx putative transcri 26.9 65 0.0014 29.9 3.2 48 367-423 4-51 (141)
70 PRK09652 RNA polymerase sigma 26.5 60 0.0013 28.6 2.8 48 369-424 128-175 (182)
71 TIGR02999 Sig-70_X6 RNA polyme 25.1 72 0.0016 28.7 3.1 48 369-424 134-181 (183)
72 TIGR02989 Sig-70_gvs1 RNA poly 24.8 81 0.0017 27.5 3.3 48 368-423 110-157 (159)
73 PF04859 DUF641: Plant protein 24.4 3.2E+02 0.0069 25.3 7.1 27 233-259 78-105 (131)
74 TIGR02939 RpoE_Sigma70 RNA pol 23.8 56 0.0012 29.4 2.2 49 369-425 138-186 (190)
75 PF13518 HTH_28: Helix-turn-he 23.8 81 0.0018 22.7 2.6 24 396-419 15-38 (52)
76 PRK12541 RNA polymerase sigma 23.1 76 0.0017 28.0 2.8 48 368-423 111-158 (161)
77 PRK12526 RNA polymerase sigma 22.9 75 0.0016 29.8 2.8 49 369-425 153-201 (206)
78 PRK12547 RNA polymerase sigma 22.8 88 0.0019 28.0 3.2 49 368-424 111-159 (164)
79 smart00421 HTH_LUXR helix_turn 22.7 1.9E+02 0.0042 20.2 4.4 47 369-424 3-49 (58)
80 PRK13919 putative RNA polymera 22.6 80 0.0017 28.5 2.9 49 369-425 135-183 (186)
81 PF13551 HTH_29: Winged helix- 22.5 4E+02 0.0086 21.7 6.8 46 370-415 58-109 (112)
82 PF10281 Ish1: Putative stress 22.2 82 0.0018 22.5 2.3 27 373-400 4-31 (38)
83 PF13865 FoP_duplication: C-te 21.8 81 0.0017 26.0 2.5 7 237-243 47-53 (74)
84 KOG4040 NADH:ubiquinone oxidor 21.3 56 0.0012 31.5 1.7 39 371-409 22-61 (186)
85 PRK09648 RNA polymerase sigma 21.1 91 0.002 28.4 3.0 49 368-424 138-186 (189)
86 PF10668 Phage_terminase: Phag 20.9 78 0.0017 25.6 2.1 21 394-414 23-43 (60)
87 PF01381 HTH_3: Helix-turn-hel 20.5 85 0.0018 22.9 2.2 21 397-417 13-33 (55)
88 PRK05602 RNA polymerase sigma 20.3 84 0.0018 28.5 2.6 50 369-426 128-177 (186)
No 1
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=100.00 E-value=4.6e-33 Score=270.75 Aligned_cols=209 Identities=23% Similarity=0.380 Sum_probs=184.8
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHh-----hhhccCCCcchhhHHHHHHHHHHHHhhhhccCCCCCC------C-CCChH
Q 013045 171 WQNARYKAEILSHPLYEQLLSAHVA-----CLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAGQGL------V-TDDKE 238 (450)
Q Consensus 171 ~e~e~lKAkI~sHPlYp~LL~Ayid-----ClKVGAPpevv~~Ld~~l~~~~~~~~k~~~~~~~~~~------~-g~DPE 238 (450)
||+++.|..|.+||+||.|++++|+ .|.|....|.-|. |.++.++++|+..+++.||..+. . |+..+
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 5666999999999999999999999 6667666665555 78888999999999999886421 2 34488
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHhhhCCCCCCCCCCCCCCcchhcccCccccCCCCCCCCC
Q 013045 239 LDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFDGSLEGPD 318 (450)
Q Consensus 239 LDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~fc~~IEsQL~sL~~~s~~e~~~a~~Sdded~~~~sd~~~~d~~~~~~d 318 (450)
+++-+. +|...|++||++ +..+|+++++.+.+|.. +
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 55679999999999996 3
Q ss_pred CCCCCCCCcchhHHHh--HHHHHHHHHHHHHhhhHHHHHHHHHHHhh-cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHH
Q 013045 319 TMGFGPLIPTESERSL--MERVRQELKHELKQGYKEKIVDIREEILR-KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEED 395 (450)
Q Consensus 319 ~~~f~Pi~p~~~e~~l--m~r~~qELK~~Lk~ky~~~i~~lr~e~~k-KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~e 395 (450)
++.||||.|.++|+.+ |.+.|.-++..|++..|+.|..||.++.. +|||++|+|.++.+|..||+.|+.+|||+++.
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 3469999999999864 89999999999999999999999999986 67788999999999999999999999999999
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 396 KARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 396 K~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
|++||++||++..||+|||.|+|.|.||.
T Consensus 221 K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 221 KEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHHHHcCceehhhccccccceeehhhh
Confidence 99999999999999999999999999985
No 2
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.94 E-value=1.1e-28 Score=245.96 Aligned_cols=252 Identities=21% Similarity=0.264 Sum_probs=179.9
Q ss_pred hhhhHHHHHHHhhCCChHHHHHHHHhhhhccCCCcchhhHHHHHHHHHHHHhhhhccCCC-C--CCCCCChHHHHHHHHH
Q 013045 170 NWQNARYKAEILSHPLYEQLLSAHVACLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAG-Q--GLVTDDKELDQFMTHY 246 (450)
Q Consensus 170 ~~e~e~lKAkI~sHPlYp~LL~AyidClKVGAPpevv~~Ld~~l~~~~~~~~k~~~~~~~-~--~~~g~DPELDQFMeaY 246 (450)
......+|..+.+||+|..++.||++|++++++.+.+.+++............++.++.. . ..-+.+.+|+.||..|
T Consensus 46 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k~ 125 (342)
T KOG0773|consen 46 MVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSKL 125 (342)
T ss_pred ccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchHH
Confidence 345556799999999999999999999999999999888765543332222222222211 0 1235779999999999
Q ss_pred HHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHhhhCCCCCCCCCCCCCCcchhccc---CccccCCCCCCCCCCCCCC
Q 013045 247 VLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVD---SDANLFDGSLEGPDTMGFG 323 (450)
Q Consensus 247 C~mL~kYkEEL~kP~~~~~~EA~~fc~~IEsQL~sL~~~s~~e~~~a~~Sdded~~~~---sd~~~~d~~~~~~d~~~f~ 323 (450)
+.+|..++..|+..+. -++|+.++++|+..+..++...+....+.+...+.++... ++.... .+.+++.
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 3899999999999999998766554443322222111100 000000 0111222
Q ss_pred CCCcchhHHHhH--HHHHHHHHHHHHhhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHH
Q 013045 324 PLIPTESERSLM--ERVRQELKHELKQGYKEKIVDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQ 401 (450)
Q Consensus 324 Pi~p~~~e~~lm--~r~~qELK~~Lk~ky~~~i~~lr~e~~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~ 401 (450)
+....+.+...+ .+....++..+.+.+..++.....+..++|+++.||+.++.+|+.||.+|+.||||++.+|..||.
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 234556677777777666677767778889999999999999999999999999999999999999
Q ss_pred HhCCChhhhhhhhhhhhhhccCCCCCCC
Q 013045 402 ETGLQLKQINNWFINQRKRNWHSNPSTS 429 (450)
Q Consensus 402 ~TgLs~kQInNWFiNrRkR~kK~~ps~s 429 (450)
+|||+..||+|||||+|+|.|++....+
T Consensus 278 ~TGLs~~Qv~NWFINaR~R~w~p~~~~~ 305 (342)
T KOG0773|consen 278 QTGLSRPQVSNWFINARVRLWKPMIEEM 305 (342)
T ss_pred hcCCCcccCCchhhhcccccCCchHHHH
Confidence 9999999999999999999999977433
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=99.88 E-value=5.3e-23 Score=157.81 Aligned_cols=50 Identities=50% Similarity=0.712 Sum_probs=47.6
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHhhhC
Q 013045 231 GLVTDDKELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTG 284 (450)
Q Consensus 231 ~~~g~DPELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~fc~~IEsQL~sL~~ 284 (450)
+++|+||||||||++||.||+||||||+||| .||++|||+||+||++||+
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=99.78 E-value=8.1e-20 Score=136.43 Aligned_cols=44 Identities=43% Similarity=0.744 Sum_probs=40.8
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhhhccCCCcchhhHHHHHHHHH
Q 013045 174 ARYKAEILSHPLYEQLLSAHVACLRIATPVDQLPRIDAQLAQSQ 217 (450)
Q Consensus 174 e~lKAkI~sHPlYp~LL~AyidClKVGAPpevv~~Ld~~l~~~~ 217 (450)
+.|||+|++||+||+||+|||+|+|||||||++++||++..+++
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 46999999999999999999999999999999999999886654
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=99.58 E-value=1.5e-15 Score=110.85 Aligned_cols=40 Identities=53% Similarity=1.020 Sum_probs=36.5
Q ss_pred HHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 013045 381 WWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 420 (450)
Q Consensus 381 Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR 420 (450)
||.+|..+|||++++|..||..|||+.+||+|||+|+|+|
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=99.50 E-value=2.2e-13 Score=128.59 Aligned_cols=150 Identities=21% Similarity=0.302 Sum_probs=119.0
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHh-----hhhccCCCcchhhHHHHHHHHHHHHhhhhccCCCCCC------CCC--C-
Q 013045 171 WQNARYKAEILSHPLYEQLLSAHVA-----CLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAGQGL------VTD--D- 236 (450)
Q Consensus 171 ~e~e~lKAkI~sHPlYp~LL~Ayid-----ClKVGAPpevv~~Ld~~l~~~~~~~~k~~~~~~~~~~------~g~--D- 236 (450)
||+.++|..|.+||+||.|++++|+ .+++..+.+..+. |+++.++++|+...++.||+.+. .|. |
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 4779999999999999999999999 5566666554444 78888899999999998886311 111 1
Q ss_pred -hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHhhhCCCCCCCCCCCCCCcchhcccCccccCCCCCC
Q 013045 237 -KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFDGSLE 315 (450)
Q Consensus 237 -PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~fc~~IEsQL~sL~~~s~~e~~~a~~Sdded~~~~sd~~~~d~~~~ 315 (450)
-|-+.|-...-.+...|++||++ +...|+++...+.+|..
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 12334444555888899999987 44579999999999985
Q ss_pred CCCCCCCCCCCcchhHHH--hHHHHHHHHHHHHHhhhHHHHHHHHHHHh
Q 013045 316 GPDTMGFGPLIPTESERS--LMERVRQELKHELKQGYKEKIVDIREEIL 362 (450)
Q Consensus 316 ~~d~~~f~Pi~p~~~e~~--lm~r~~qELK~~Lk~ky~~~i~~lr~e~~ 362 (450)
+++.||||+|.++|+. .|.++|+-+..+||+..|+.|..||..|.
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 2346999999999996 48999999999999999999999998775
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=99.44 E-value=2.7e-13 Score=101.81 Aligned_cols=58 Identities=28% Similarity=0.567 Sum_probs=54.2
Q ss_pred cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 364 KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
++++..|++++..+|+.||.. +|||+..++..||..+||+.+||.+||.|+|.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 356789999999999999999 8999999999999999999999999999999998764
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.40 E-value=6.7e-13 Score=99.30 Aligned_cols=55 Identities=27% Similarity=0.531 Sum_probs=51.2
Q ss_pred CCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 013045 365 RRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 422 (450)
Q Consensus 365 RKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~k 422 (450)
+.+..|++++..+|+.||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
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 45677999999999999998 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=6.8e-13 Score=100.38 Aligned_cols=57 Identities=33% Similarity=0.740 Sum_probs=53.9
Q ss_pred cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 364 KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
||+|..|+.++..+|+.+|.. +|||+..++..||..+||+..||.+||.|+|.+.|+
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 577889999999999999998 899999999999999999999999999999998764
No 10
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.15 E-value=2.8e-11 Score=119.81 Aligned_cols=48 Identities=38% Similarity=0.857 Sum_probs=45.7
Q ss_pred hhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 013045 372 GDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 422 (450)
Q Consensus 372 kea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~k 422 (450)
...+..|++||.. +|||++.+|++||+.|||+..||.|||+|+|.|.+
T Consensus 185 ekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 185 EKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred HhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 3589999999996 99999999999999999999999999999999998
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.72 E-value=6.5e-09 Score=104.92 Aligned_cols=59 Identities=22% Similarity=0.342 Sum_probs=54.1
Q ss_pred cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 364 KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
+|||-.++|.++.-|+.-|.-+. |.|++-|.+|++.++|+..||..||+|||+|.||-+
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 45667899999999999888855 999999999999999999999999999999999866
No 12
>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=98.71 E-value=2e-08 Score=79.14 Aligned_cols=53 Identities=19% Similarity=0.437 Sum_probs=50.0
Q ss_pred hcCCCCCCChhHHHHHHHHHHhcCCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 013045 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPY----PTEEDKARLVQETGLQLKQINNWFINQR 418 (450)
Q Consensus 363 kKRKrgkLpkea~~iLk~Wf~~H~~~PY----PSe~eK~~LA~~TgLs~kQInNWFiNrR 418 (450)
+||.|.+|+.+++..|+..|.. .+| |+..++..||..+||+..+|.+||+|-+
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 789 9999999999999999999999999964
No 13
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.63 E-value=3.6e-08 Score=102.02 Aligned_cols=68 Identities=16% Similarity=0.393 Sum_probs=61.7
Q ss_pred HHHHHHhhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCC
Q 013045 356 DIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (450)
Q Consensus 356 ~lr~e~~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~p 426 (450)
.+-..-+|||||..+.-.++..|+..|.+ ||.|+.+|.-.||++.+|.+..|++||+|||.|.|+.++
T Consensus 287 ~i~a~~RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 287 KIGAQSRKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HhhccccccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 34444467777889999999999999998 999999999999999999999999999999999999887
No 14
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.61 E-value=3e-08 Score=93.70 Aligned_cols=63 Identities=19% Similarity=0.293 Sum_probs=57.3
Q ss_pred hhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCCC
Q 013045 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPS 427 (450)
Q Consensus 362 ~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ps 427 (450)
+.||.|+.|+.++...|+..|.. +-|-.-.||..||...+|++.||..||+|+|.|+|+....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 45778899999999999999998 6699999999999999999999999999999999986443
No 15
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.60 E-value=2.6e-08 Score=98.09 Aligned_cols=66 Identities=23% Similarity=0.282 Sum_probs=58.7
Q ss_pred hcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCCCCCcc
Q 013045 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTSTV 431 (450)
Q Consensus 363 kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ps~s~~ 431 (450)
.||.|..|+..++..|+.-|.- |.|.|+..|.+||..+.|++.||.+||+|||++.||.+...+..
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 6788899999999999998877 66999999999999999999999999999999999876544433
No 16
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.55 E-value=6.4e-08 Score=95.98 Aligned_cols=60 Identities=33% Similarity=0.478 Sum_probs=55.9
Q ss_pred hcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 363 kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
.||.|.-|+.++.+-|+.-|.+++ |.|+.-|..||.++||.+.||..||+|+|.+.||..
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enR---YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENR---YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhh---hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 467788999999999999999966 999999999999999999999999999999999863
No 17
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.49 E-value=1.9e-07 Score=90.73 Aligned_cols=60 Identities=20% Similarity=0.304 Sum_probs=55.3
Q ss_pred hhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 362 ~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
.|||.|..|+..++..|+.-|...+ |.+..+|..||.+..|++.||..||+|+|.+.|+.
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~kr---YLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKR---YLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHh---hhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 3567788999999999999999966 99999999999999999999999999999988764
No 18
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.49 E-value=8.1e-08 Score=93.59 Aligned_cols=59 Identities=20% Similarity=0.306 Sum_probs=53.8
Q ss_pred cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 364 KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
+|.|+.++.-+...|..-|++ ..|.--.||.+||..+||++.||..||+|+|-|+||..
T Consensus 123 RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred cCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 345678999999999999998 77999999999999999999999999999999998753
No 19
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.46 E-value=7.8e-08 Score=97.19 Aligned_cols=59 Identities=17% Similarity=0.338 Sum_probs=53.1
Q ss_pred hhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 362 ~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
+|||+|--|++.++-.|+.=|.+.+ |.|-.||+.||..++|+..||+.||+|+|-|-|+
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 3444555799999999999999966 9999999999999999999999999999988886
No 20
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.45 E-value=1.5e-07 Score=90.14 Aligned_cols=58 Identities=29% Similarity=0.447 Sum_probs=53.5
Q ss_pred hcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 363 kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
.++|+.+|+.+++..|+.=|..|. |-.+..|..||+..||.+.||..||+|+|.|-|.
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 456778999999999999999976 8889999999999999999999999999999875
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.44 E-value=1.7e-07 Score=86.66 Aligned_cols=62 Identities=19% Similarity=0.356 Sum_probs=57.1
Q ss_pred hhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCC
Q 013045 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (450)
Q Consensus 362 ~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~p 426 (450)
..+++|.+.+..++.+|+.-|.. +|||+..+|..|+..++++++-|..||+|+|.+.|+...
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 34677889999999999999998 999999999999999999999999999999999987654
No 22
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.35 E-value=3.5e-07 Score=92.50 Aligned_cols=61 Identities=20% Similarity=0.370 Sum_probs=53.6
Q ss_pred hhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 362 ~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
+++|.|..|+..++..|+.-|..-. |.+..||..||...||+-.||..||+|||.|-|+..
T Consensus 171 K~RksRTaFT~~Ql~~LEkrF~~QK---YLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 171 KRRKSRTAFSDHQLFELEKRFEKQK---YLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred ccccchhhhhHHHHHHHHHHHHHhh---cccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 3445567899999999999999855 999999999999999999999999999888776643
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.29 E-value=3.8e-07 Score=85.49 Aligned_cols=60 Identities=18% Similarity=0.372 Sum_probs=53.7
Q ss_pred hhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 362 ~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
.++|.|..|+..+...|+.-|+..+ |.+-.++.+||...+|+++||..||+|+|+++||-
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Qr---YLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQR---YLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhh---hcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 3455677899999999999999755 99999999999999999999999999999999873
No 24
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.28 E-value=3.9e-07 Score=80.01 Aligned_cols=65 Identities=15% Similarity=0.284 Sum_probs=57.0
Q ss_pred HHHHHhhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 357 IREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 357 lr~e~~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
+.+..+.+|-|..|+..+...|+..|.+ .-||..-.|++||.+..|++..|++||+|+|.+++|.
T Consensus 11 l~ekrKQRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 11 LTEKRKQRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred hhHHHHhhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 3344445566789999999999999998 5699999999999999999999999999999999874
No 25
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.25 E-value=1.2e-06 Score=85.08 Aligned_cols=58 Identities=19% Similarity=0.352 Sum_probs=53.1
Q ss_pred cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 364 KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
+|-|..|+..+..+|+.-|.+ .-||+...+++||.+.+|.+.+|.+||.|+|++.++.
T Consensus 38 RRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 38 RRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 455789999999999999999 5599999999999999999999999999999988754
No 26
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.18 E-value=8.8e-07 Score=85.62 Aligned_cols=66 Identities=15% Similarity=0.275 Sum_probs=60.1
Q ss_pred HHHHHHHhhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 355 VDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 355 ~~lr~e~~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
..||+-...+|.|..|+..+...|++=|.+ ..|.+.+||.+++....|+..||..||+|+|.|.|+
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 467777777788899999999999999999 459999999999999999999999999999999886
No 27
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.04 E-value=3.7e-06 Score=83.67 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=49.9
Q ss_pred CCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 367 rgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
|..|+..+...|+.-|.+ --||..--|+.||.+|+|.+.+|.+||+|+|.+-+|
T Consensus 145 RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk 198 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRK 198 (332)
T ss_pred cchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhh
Confidence 678999999999999998 459999999999999999999999999999987654
No 28
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.02 E-value=2.4e-06 Score=86.03 Aligned_cols=72 Identities=21% Similarity=0.424 Sum_probs=63.0
Q ss_pred HHHHHHhhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCCCCCc
Q 013045 356 DIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTST 430 (450)
Q Consensus 356 ~lr~e~~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ps~s~ 430 (450)
.|..+-..||.|..++.++...|+.-|.. .|.|.+--|++|+.+|||+...|++||+|+|.+.|+.....+.
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 44556778999999999999999998876 8999999999999999999999999999999998876554443
No 29
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=97.99 E-value=3e-06 Score=85.93 Aligned_cols=58 Identities=19% Similarity=0.374 Sum_probs=51.9
Q ss_pred cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 364 KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
+|-|.-|+..+.+.|+.||..++ ||+...|++||--++|++..|++||.|+|.+-+|.
T Consensus 113 rrQrthFtSqqlqele~tF~rNr---ypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 113 RRQRTHFTSQQLQELEATFQRNR---YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhhhHHHHHHHHHHHHhhcc---CCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 34456899999999999999955 99999999999999999999999999999887653
No 30
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=97.95 E-value=2.3e-06 Score=85.32 Aligned_cols=55 Identities=24% Similarity=0.348 Sum_probs=49.3
Q ss_pred CCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
-.++..++-.|+.-|-. .+|.|..-|.+||..+||++.||..||+|||.+.+|-+
T Consensus 204 vVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 204 VVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred EEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 46788899999887765 78999999999999999999999999999999988754
No 31
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.73 E-value=8e-06 Score=82.36 Aligned_cols=73 Identities=21% Similarity=0.389 Sum_probs=61.5
Q ss_pred HHHHHhhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCCCCCccc
Q 013045 357 IREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTSTVL 432 (450)
Q Consensus 357 lr~e~~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ps~s~~~ 432 (450)
|-..-.|||||..+-..-++.|+++|.. -|-|+.+....+|++..|.+..|++||+|+|.+.|+-.-|...++
T Consensus 303 l~~~~ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa~~~m 375 (385)
T KOG1168|consen 303 LLPGGEKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSATAVM 375 (385)
T ss_pred ccCccccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhhceee
Confidence 3334457888888888888999999998 899999999999999999999999999999999988555555444
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.63 E-value=2.3e-05 Score=73.14 Aligned_cols=62 Identities=13% Similarity=0.142 Sum_probs=55.8
Q ss_pred HHhhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 360 EILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 360 e~~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
.++++|.|.+|+..+...|+.-|.. .+||....++.||..+++++..|.+||+|+|++.++.
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 4456677789999999999999998 5899999999999999999999999999999988764
No 33
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.54 E-value=6.3e-05 Score=77.50 Aligned_cols=59 Identities=25% Similarity=0.479 Sum_probs=53.5
Q ss_pred cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 364 KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
+|.|..|+..+...|+.+|.. .|||....|+.||.+++|....|..||.|+|.|.+|..
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 344678999999999999998 78999999999999999999999999999999877654
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.53 E-value=0.00011 Score=79.28 Aligned_cols=55 Identities=22% Similarity=0.371 Sum_probs=52.0
Q ss_pred cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhc
Q 013045 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRN 421 (450)
Q Consensus 364 KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~ 421 (450)
||.|-.|+..+++.|...|.+ +|||+.+.-+.|+.++||...-|.|||-|+|+|.
T Consensus 421 KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 421 KKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 566778999999999999999 8899999999999999999999999999999995
No 35
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.34 E-value=7.6e-05 Score=75.89 Aligned_cols=55 Identities=16% Similarity=0.276 Sum_probs=48.8
Q ss_pred CCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 367 rgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
|.-|+.+++.-|+.-|++ --|-++..|.+||...+|.+.-|.+||+|+|++.|+.
T Consensus 185 RTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred HhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence 367899999999877776 3489999999999999999999999999999999874
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.31 E-value=0.00011 Score=74.08 Aligned_cols=64 Identities=31% Similarity=0.560 Sum_probs=58.9
Q ss_pred hcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCCC
Q 013045 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPS 427 (450)
Q Consensus 363 kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ps 427 (450)
..+++++++.+. .+|+.|...|..+|||++.++..|+..++++.-||.+||+|.|+|.++.+..
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 345678999999 9999999999999999999999999999999999999999999999887654
No 37
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.26 E-value=0.00018 Score=70.56 Aligned_cols=60 Identities=25% Similarity=0.400 Sum_probs=52.7
Q ss_pred hhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 362 ~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
+||..|.+|+..++..|+.-|.+ .-||--.++.+||...|+++.||.+||+|+|.+-+|.
T Consensus 166 ~rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred cccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence 34556678999999999999998 4599999999999999999999999999999877654
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=96.78 E-value=0.001 Score=43.58 Aligned_cols=22 Identities=41% Similarity=0.622 Sum_probs=20.5
Q ss_pred HHHHHHHhhhHHHHHHHHHHHh
Q 013045 341 ELKHELKQGYKEKIVDIREEIL 362 (450)
Q Consensus 341 ELK~~Lk~ky~~~i~~lr~e~~ 362 (450)
|||.+|+++|+++|++||+||+
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 6899999999999999999984
No 39
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.57 E-value=0.0019 Score=51.04 Aligned_cols=43 Identities=21% Similarity=0.502 Sum_probs=31.4
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 013045 375 TSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 420 (450)
Q Consensus 375 ~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR 420 (450)
++.|+++|..|. ++.+.+...|+.+++|+..||..||.-++.+
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 456999999965 8899999999999999999999999877544
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.36 E-value=0.03 Score=52.38 Aligned_cols=60 Identities=27% Similarity=0.518 Sum_probs=51.0
Q ss_pred cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCC
Q 013045 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (450)
Q Consensus 364 KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~p 426 (450)
++.+..+.......|..-|.. .|||....+..|+..+|++...|.+||+|+|.+.++...
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 154 RRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 444567777777888777776 889999999999999999999999999999999987644
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=89.75 E-value=0.26 Score=58.61 Aligned_cols=61 Identities=20% Similarity=0.331 Sum_probs=53.9
Q ss_pred hhcCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 362 ~kKRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
.++++|..+...+..+|+..|..-. ||+.++-+.|.+..+|....|..||+|.|.+.+|..
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~---~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQR---TPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhcc---CChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 3455667788889999999999855 999999999999999999999999999999999863
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=81.67 E-value=2.9 Score=32.10 Aligned_cols=47 Identities=15% Similarity=0.186 Sum_probs=31.9
Q ss_pred cCCCCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 013045 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQR 418 (450)
Q Consensus 364 KRKrgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrR 418 (450)
||+|..|+-+.+..+-.-+.. .+ -...||+.+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 467778888876555555554 22 578999999999999999999964
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=76.33 E-value=6.1 Score=45.36 Aligned_cols=51 Identities=25% Similarity=0.533 Sum_probs=44.9
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCCCC
Q 013045 375 TSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPST 428 (450)
Q Consensus 375 ~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ps~ 428 (450)
..+|+.+|.. ++.|++++...+|...||...-|..||.+.+........++
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsp 618 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSP 618 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCc
Confidence 6788888887 88999999999999999999999999999998887654333
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=69.93 E-value=8.3 Score=30.22 Aligned_cols=46 Identities=17% Similarity=0.340 Sum_probs=30.6
Q ss_pred CCCCCCChhHHHHH-HHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 013045 365 RRAGKLPGDTTSVL-KSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQR 418 (450)
Q Consensus 365 RKrgkLpkea~~iL-k~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrR 418 (450)
++++.||.+.+..+ ...+.. ......+|...|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 45678998885555 443333 57788999999999999999987776
No 45
>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=62.31 E-value=12 Score=25.91 Aligned_cols=46 Identities=13% Similarity=0.154 Sum_probs=35.1
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 422 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~k 422 (450)
.|+...+.++...+... -.-..+|+.+|++...|..|....+.+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 47777888887776432 23457899999999999999988877653
No 46
>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=60.75 E-value=16 Score=22.57 Aligned_cols=40 Identities=10% Similarity=0.174 Sum_probs=27.9
Q ss_pred CCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 013045 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWF 414 (450)
Q Consensus 367 rgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWF 414 (450)
+..++.+.+..+...+.. .+ ....+|+.+|++...|.+|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 445676666666665543 22 34578889999999999984
No 47
>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=53.33 E-value=24 Score=26.06 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=32.5
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 420 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR 420 (450)
.||...+.++...|.. .-.-.++|+.+|++.+-|.+|....|++
T Consensus 10 ~L~~~~r~i~~l~~~~--------g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQ--------GMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH--------CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 5888888888766554 3445689999999999999999988876
No 48
>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=47.78 E-value=21 Score=26.25 Aligned_cols=46 Identities=11% Similarity=0.182 Sum_probs=35.6
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 422 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~k 422 (450)
.||+..+.+|..-|.. ...-.++|+..|++...|..+.....++.+
T Consensus 4 ~L~~~er~vi~~~y~~--------~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE--------GLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS--------T-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC--------CCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 5888888999877743 233568999999999999999988887765
No 49
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=44.95 E-value=41 Score=35.31 Aligned_cols=47 Identities=13% Similarity=0.217 Sum_probs=37.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHhhhCC
Q 013045 237 KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGV 285 (450)
Q Consensus 237 PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~fc~~IEsQL~sL~~~ 285 (450)
-+-|.||.-||. .+|-.+|.+=+|-++++|..-+..+-.|+..||.+
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 50
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=42.80 E-value=69 Score=35.80 Aligned_cols=25 Identities=12% Similarity=0.290 Sum_probs=14.7
Q ss_pred CChHHHHHHHHHH-------HHHHHHHHHHhH
Q 013045 235 DDKELDQFMTHYV-------LLLCSFKEQLQQ 259 (450)
Q Consensus 235 ~DPELDQFMeaYC-------~mL~kYkEEL~k 259 (450)
.-|++....-+|| .||.||++||++
T Consensus 183 ~ap~mkt~~~aYcanHP~AV~VL~k~~dELek 214 (661)
T KOG2070|consen 183 LAPQMKTLYLAYCANHPSAVNVLTKHSDELEK 214 (661)
T ss_pred hhHHHHHHHHHHHhcCchhhhHHHHhHHHHHH
Confidence 3366666555666 466666666654
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=38.88 E-value=35 Score=29.70 Aligned_cols=48 Identities=8% Similarity=0.068 Sum_probs=37.9
Q ss_pred CCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
..||+..+.++..-|.... .-.++|+.+|++...|.+|....|++.++
T Consensus 105 ~~L~~~~r~ii~l~~~~~~--------s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 105 SVLDEKEKYIIFERFFVGK--------TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred HhCCHHHHHHHHHHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 3688888888865544422 24589999999999999999999998865
No 52
>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=38.56 E-value=52 Score=26.34 Aligned_cols=25 Identities=28% Similarity=0.349 Sum_probs=20.4
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHh
Q 013045 234 TDDKELDQFMTHYVLLLCSFKEQLQ 258 (450)
Q Consensus 234 g~DPELDQFMeaYC~mL~kYkEEL~ 258 (450)
|-|+|||...+.|..+.....+.+.
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 53
>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=36.45 E-value=1.6e+02 Score=26.32 Aligned_cols=21 Identities=29% Similarity=0.316 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHhhhCC
Q 013045 265 AMEAVMACWEIEQSLQSLTGV 285 (450)
Q Consensus 265 ~~EA~~fc~~IEsQL~sL~~~ 285 (450)
+.|...-++++|..|+-|-..
T Consensus 79 ~~evL~sv~KtEeSL~rlkk~ 99 (125)
T PF12022_consen 79 ASEVLTSVRKTEESLKRLKKR 99 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 346677788999999999653
No 54
>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=35.05 E-value=40 Score=28.00 Aligned_cols=47 Identities=17% Similarity=0.250 Sum_probs=35.4
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
.||+..+.++..-+.. .| .-..+|+.+|++...|.+|....+++.++
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4677777777544332 12 34489999999999999999999988765
No 55
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=33.52 E-value=1.1e+02 Score=29.68 Aligned_cols=45 Identities=16% Similarity=0.258 Sum_probs=36.7
Q ss_pred C-hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHH-HHHHHHHHHHHHhhh
Q 013045 236 D-KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEA-VMACWEIEQSLQSLT 283 (450)
Q Consensus 236 D-PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA-~~fc~~IEsQL~sL~ 283 (450)
| -|||-.+.++-.++..|++.++-.+= .+| ..||..|..||-.+.
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 89999999999999999999976552 233 358889999987766
No 56
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=32.31 E-value=38 Score=25.58 Aligned_cols=23 Identities=13% Similarity=0.304 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCChhhhhhhhhhh
Q 013045 395 DKARLVQETGLQLKQINNWFINQ 417 (450)
Q Consensus 395 eK~~LA~~TgLs~kQInNWFiNr 417 (450)
....||+.+|++...|+.|+.+.
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 57
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=31.16 E-value=51 Score=29.35 Aligned_cols=50 Identities=14% Similarity=0.005 Sum_probs=40.5
Q ss_pred CCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
..||...+.++.-++..++ .-.++|..+|++...|.+|..-.|++.++-.
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 4588889999987665533 3458999999999999999999999987643
No 58
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=30.24 E-value=45 Score=30.71 Aligned_cols=49 Identities=6% Similarity=-0.001 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
.||...+.+|..-+... -.-.++|+.+|++...|.+++...|++.++..
T Consensus 142 ~L~~~~r~vl~l~~~~~--------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 48888989887655442 23457899999999999999999999988754
No 59
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=30.07 E-value=53 Score=28.93 Aligned_cols=48 Identities=13% Similarity=0.205 Sum_probs=38.2
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
+||...+.++...+...+ .-.++|+.+|++...|.+.+.-.|++.++.
T Consensus 106 ~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEK--------SYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 489998888866555422 234799999999999999999999988764
No 60
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=29.99 E-value=47 Score=29.91 Aligned_cols=49 Identities=10% Similarity=0.217 Sum_probs=38.8
Q ss_pred CCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
..||...+.++...|...+ .-.++|+.+|++...|.+++.-.|++.++-
T Consensus 128 ~~L~~~~r~i~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 128 EELEKDRAAAVRRAYLEGL--------SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 3488888888877765422 245799999999999999999999988764
No 61
>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=29.83 E-value=55 Score=28.81 Aligned_cols=52 Identities=12% Similarity=0.190 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCCC
Q 013045 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPS 427 (450)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ps 427 (450)
..||...+.++..-+...+ .-.++|+.+|++...|.++....|++.++....
T Consensus 109 ~~L~~~~r~i~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 109 RRLPARQRAVVVLRYYEDL--------SEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred HhCCHHHHHHhhhHHHhcC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 3588888888866554422 234789999999999999999999998876543
No 62
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=28.90 E-value=59 Score=29.83 Aligned_cols=49 Identities=16% Similarity=0.198 Sum_probs=39.5
Q ss_pred CCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
.+||+..+.++.-.|... -.-.++|+.+|++...|.+...-.|++.++.
T Consensus 130 ~~L~~~~r~i~~l~~~~g--------~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG--------EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred HhCCHHHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 368999999987655442 2235799999999999999999999998875
No 63
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=28.52 E-value=52 Score=28.94 Aligned_cols=48 Identities=10% Similarity=0.121 Sum_probs=37.4
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
.||+..+.++..-+... -.-..+|+..|++...|.+|..-.|++.++.
T Consensus 125 ~L~~~~r~i~~l~~~~~--------~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 125 ALPVKQREVFLLRYVEG--------LSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred hCCHHHHHHhhHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888886654432 2336899999999999999999999998764
No 64
>KOG4511 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.47 E-value=4.2e+02 Score=27.84 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=22.8
Q ss_pred HHhhCCChHHHHHHHHh--hhhccCCCcc
Q 013045 179 EILSHPLYEQLLSAHVA--CLRIATPVDQ 205 (450)
Q Consensus 179 kI~sHPlYp~LL~Ayid--ClKVGAPpev 205 (450)
=|+.|-=|..|+.-.++ |--||.-|++
T Consensus 50 y~~IH~EYk~LVd~lle~f~eevgi~p~q 78 (335)
T KOG4511|consen 50 YIMIHKEYKQLVDTLLECFCEEVGITPTQ 78 (335)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCHHH
Confidence 47889999999999999 5678988764
No 65
>PF06729 CENP-R: Kinetochore component, CENP-R; InterPro: IPR009601 This family consists of mammalian nuclear receptor co-activator NRIF3 proteins. NRIF3 exhibits a distinct receptor specificity in interacting with and potentiating the activity of only TRs and RXRs but not other examined nuclear receptors. NRIF3 as a coregulator that possesses both transactivation and transrepression domains and/or functions. Collectively, the NRIF3 family of coregulators may play dual roles in mediating both positive and negative regulatory effects on gene expression [].
Probab=28.25 E-value=5.1e+02 Score=24.38 Aligned_cols=31 Identities=29% Similarity=0.416 Sum_probs=19.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHH
Q 013045 237 KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIE 276 (450)
Q Consensus 237 PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~fc~~IE 276 (450)
.+.|.||. +|-+-+.-|.+ |||++.-|..|-
T Consensus 56 t~dD~fm~----L~SkvekS~ee-----ime~~qnL~slQ 86 (139)
T PF06729_consen 56 TEDDEFMV----LLSKVEKSLEE-----IMEIRQNLSSLQ 86 (139)
T ss_pred cchhHHHH----HHHHHHHHHHH-----HHHHHHHHHHHH
Confidence 45599996 56666666654 577776555443
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=27.52 E-value=63 Score=27.77 Aligned_cols=47 Identities=15% Similarity=0.167 Sum_probs=36.3
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
.||...+.+|...+... + .-.++|..+|++...|.++..-.|++.++
T Consensus 113 ~L~~~~r~il~l~~~~~----~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG----K----SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 57888888887654431 2 23468999999999999999999988875
No 67
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=27.47 E-value=26 Score=34.39 Aligned_cols=45 Identities=22% Similarity=0.319 Sum_probs=33.8
Q ss_pred CCCCceeccCC-CccchhhhHHHHHHHhhCCChHHHHHHHHhhhhccCCCcc
Q 013045 155 KSEGVVVESGA-DGVVNWQNARYKAEILSHPLYEQLLSAHVACLRIATPVDQ 205 (450)
Q Consensus 155 ~~~~~~~~~~~-~~~~~~e~e~lKAkI~sHPlYp~LL~AyidClKVGAPpev 205 (450)
+|-.+|..|-. |++ -=...||.+|..+|++.+||.||+ ||.|.-+
T Consensus 93 ~GRPfILaGHSQGs~--~l~~LL~e~~~~~pl~~rLVAAYl----iG~~v~~ 138 (207)
T PF11288_consen 93 NGRPFILAGHSQGSM--HLLRLLKEEIAGDPLRKRLVAAYL----IGYPVTV 138 (207)
T ss_pred CCCCEEEEEeChHHH--HHHHHHHHHhcCchHHhhhheeee----cCccccH
Confidence 56677777733 333 234679999999999999999998 8887543
No 68
>PRK00118 putative DNA-binding protein; Validated
Probab=27.20 E-value=62 Score=28.59 Aligned_cols=47 Identities=6% Similarity=0.065 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
.||...+.++..++... -.-..+|+.+|++..-|..|+...|++.++
T Consensus 17 ~L~ekqRevl~L~y~eg--------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD--------YSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57888889987776652 234569999999999999999998888765
No 69
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=26.87 E-value=65 Score=29.89 Aligned_cols=48 Identities=10% Similarity=0.040 Sum_probs=38.1
Q ss_pred CCCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 367 rgkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
...|++.++.+|.. +.+. -.-.++|+.+|++...|..|....|++.++
T Consensus 4 ~~~Lt~rqreVL~l-r~~G--------lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRL-RERG--------LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHH-HHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999977 3331 224589999999999999999999888765
No 70
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=26.53 E-value=60 Score=28.62 Aligned_cols=48 Identities=8% Similarity=0.120 Sum_probs=36.9
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
.||+..+.+|...|... + .-..+|+.+|++...|.+|....|++.++.
T Consensus 128 ~L~~~~r~vl~l~~~~~----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG----L----SYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888886644431 2 234789999999999999999999988763
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=25.13 E-value=72 Score=28.66 Aligned_cols=48 Identities=6% Similarity=0.064 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
.||+..+.++.-.+...+ .-.++|+.+|++..-|.+.+...|++.++.
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 489999999877765522 235799999999999999999999988753
No 72
>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=24.82 E-value=81 Score=27.52 Aligned_cols=48 Identities=19% Similarity=0.228 Sum_probs=37.2
Q ss_pred CCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
..||...+.++..-+... -.-.++|+.+|++...|.++..-.|++.++
T Consensus 110 ~~L~~~~r~v~~l~~~~g--------~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG--------VSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 458888888887744432 223578999999999999999999888764
No 73
>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=24.38 E-value=3.2e+02 Score=25.25 Aligned_cols=27 Identities=11% Similarity=0.415 Sum_probs=23.2
Q ss_pred CCCC-hHHHHHHHHHHHHHHHHHHHHhH
Q 013045 233 VTDD-KELDQFMTHYVLLLCSFKEQLQQ 259 (450)
Q Consensus 233 ~g~D-PELDQFMeaYC~mL~kYkEEL~k 259 (450)
+++. .|+..-|.+|--++.+++.|+..
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 89999999999999999999976
No 74
>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=23.82 E-value=56 Score=29.39 Aligned_cols=49 Identities=8% Similarity=0.014 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
.||...+.++.--|.. .-.-.++|+.+|++...|.++.-..|++.++..
T Consensus 138 ~L~~~~r~v~~l~~~~--------~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELE--------GLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4677787887654433 233458999999999999999999999987654
No 75
>PF13518 HTH_28: Helix-turn-helix domain
Probab=23.75 E-value=81 Score=22.69 Aligned_cols=24 Identities=17% Similarity=0.432 Sum_probs=20.8
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhh
Q 013045 396 KARLVQETGLQLKQINNWFINQRK 419 (450)
Q Consensus 396 K~~LA~~TgLs~kQInNWFiNrRk 419 (450)
...+|..+|++..+|..|...-+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456999999999999999987765
No 76
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=23.06 E-value=76 Score=28.04 Aligned_cols=48 Identities=21% Similarity=0.140 Sum_probs=38.4
Q ss_pred CCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccC
Q 013045 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (450)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK 423 (450)
..||..++.++.-.+.... .-.++|..+|++...|..+..-.|++.++
T Consensus 111 ~~L~~~~r~v~~l~~~~~~--------s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYGF--------SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4689989888877655422 23478999999999999999999998875
No 77
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=22.86 E-value=75 Score=29.77 Aligned_cols=49 Identities=16% Similarity=0.176 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
.||...+.+|..-+... -.-.++|+.+|++...|.+++...|++.++-.
T Consensus 153 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE--------LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888888887655442 23458999999999999999999998887543
No 78
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.78 E-value=88 Score=27.95 Aligned_cols=49 Identities=14% Similarity=0.024 Sum_probs=39.3
Q ss_pred CCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
..||...+.++.-.+...+ .-.++|+.+|++...|.++..-.|++.++-
T Consensus 111 ~~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 111 NLLSADQREAIILIGASGF--------SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4588989998877665533 245799999999999999999999988753
No 79
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.75 E-value=1.9e+02 Score=20.25 Aligned_cols=47 Identities=13% Similarity=0.176 Sum_probs=34.2
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
.|+.....++..+ .. . + ....+|+.+|++...|..|....+.+..-.
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 5777777777543 22 1 1 346889999999999999999887776543
No 80
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=22.61 E-value=80 Score=28.52 Aligned_cols=49 Identities=14% Similarity=0.079 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~ 425 (450)
.||...+.+|.-.+...+ .-.++|+.+|++...|.++..-.|++.++..
T Consensus 135 ~L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQGY--------THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 488889899876554422 2357899999999999999999999887643
No 81
>PF13551 HTH_29: Winged helix-turn helix
Probab=22.46 E-value=4e+02 Score=21.73 Aligned_cols=46 Identities=17% Similarity=0.081 Sum_probs=28.3
Q ss_pred CChhHHHHHHHHHHhcCCCC--CCCHHHHHH-H-HHHh--CCChhhhhhhhh
Q 013045 370 LPGDTTSVLKSWWQSHSKWP--YPTEEDKAR-L-VQET--GLQLKQINNWFI 415 (450)
Q Consensus 370 Lpkea~~iLk~Wf~~H~~~P--YPSe~eK~~-L-A~~T--gLs~kQInNWFi 415 (450)
++.+....|.+++.++...- ..+...-.. | .+.+ .++...|..|+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 89999999999999843211 223333333 3 2333 367777777764
No 82
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=22.18 E-value=82 Score=22.51 Aligned_cols=27 Identities=37% Similarity=0.615 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHhcCCCCCCCHH-HHHHHH
Q 013045 373 DTTSVLKSWWQSHSKWPYPTEE-DKARLV 400 (450)
Q Consensus 373 ea~~iLk~Wf~~H~~~PYPSe~-eK~~LA 400 (450)
.....|+.|+..|. .|+|... .|..|.
T Consensus 4 Ws~~~L~~wL~~~g-i~~~~~~~~rd~Ll 31 (38)
T PF10281_consen 4 WSDSDLKSWLKSHG-IPVPKSAKTRDELL 31 (38)
T ss_pred CCHHHHHHHHHHcC-CCCCCCCCCHHHHH
Confidence 34678999999987 7777544 555553
No 83
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=21.78 E-value=81 Score=26.00 Aligned_cols=7 Identities=57% Similarity=1.004 Sum_probs=3.1
Q ss_pred hHHHHHH
Q 013045 237 KELDQFM 243 (450)
Q Consensus 237 PELDQFM 243 (450)
.|||+||
T Consensus 47 aELD~Ym 53 (74)
T PF13865_consen 47 AELDAYM 53 (74)
T ss_pred HHHHHHH
Confidence 4444444
No 84
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=21.30 E-value=56 Score=31.47 Aligned_cols=39 Identities=26% Similarity=0.579 Sum_probs=30.4
Q ss_pred ChhHHHHHHHHHHhcCCCCCCC-HHHHHHHHHHhCCChhh
Q 013045 371 PGDTTSVLKSWWQSHSKWPYPT-EEDKARLVQETGLQLKQ 409 (450)
Q Consensus 371 pkea~~iLk~Wf~~H~~~PYPS-e~eK~~LA~~TgLs~kQ 409 (450)
.....+..-.|...|.-.|||+ ++||..-|++.||-+..
T Consensus 22 ~~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 22 MPRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred cccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 3444566778998899999995 68888899999987654
No 85
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=21.10 E-value=91 Score=28.38 Aligned_cols=49 Identities=10% Similarity=-0.030 Sum_probs=38.5
Q ss_pred CCCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCC
Q 013045 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (450)
Q Consensus 368 gkLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~ 424 (450)
..||...+.++..-|... -.-.++|+.+|++..-|..+....|++.++.
T Consensus 138 ~~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 138 DTLPEKQREILILRVVVG--------LSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 358888888887655442 2356899999999999999999999988753
No 86
>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=20.86 E-value=78 Score=25.58 Aligned_cols=21 Identities=14% Similarity=0.341 Sum_probs=18.0
Q ss_pred HHHHHHHHHhCCChhhhhhhh
Q 013045 394 EDKARLVQETGLQLKQINNWF 414 (450)
Q Consensus 394 ~eK~~LA~~TgLs~kQInNWF 414 (450)
-.-..||++.|++..+|..|=
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHh
Confidence 345689999999999999994
No 87
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=20.54 E-value=85 Score=22.92 Aligned_cols=21 Identities=14% Similarity=0.189 Sum_probs=18.4
Q ss_pred HHHHHHhCCChhhhhhhhhhh
Q 013045 397 ARLVQETGLQLKQINNWFINQ 417 (450)
Q Consensus 397 ~~LA~~TgLs~kQInNWFiNr 417 (450)
..||+.+|+++..|..|..+.
T Consensus 13 ~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTS
T ss_pred HHHHHHhCCCcchhHHHhcCC
Confidence 689999999999999999883
No 88
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=20.28 E-value=84 Score=28.54 Aligned_cols=50 Identities=6% Similarity=0.077 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccCCCC
Q 013045 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (450)
Q Consensus 369 kLpkea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQInNWFiNrRkR~kK~~p 426 (450)
.||+..+.++..-|.... .-.++|+.+|++...|.++....|++.++...
T Consensus 128 ~L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 128 ALPERQREAIVLQYYQGL--------SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred hCCHHHHHHhhHHHhcCC--------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 467888888865444322 23578999999999999999999999887543
Done!