Query 014791
Match_columns 418
No_of_seqs 196 out of 403
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 08:33:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014791.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014791hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0773 Transcription factor M 100.0 3.2E-32 7E-37 264.9 0.5 242 170-417 46-303 (342)
2 PF03791 KNOX2: KNOX2 domain ; 99.9 8.4E-25 1.8E-29 166.7 7.0 50 231-284 3-52 (52)
3 PF03790 KNOX1: KNOX1 domain ; 99.8 4.7E-22 1E-26 147.7 3.2 44 174-217 1-44 (45)
4 KOG0774 Transcription factor P 99.7 3.8E-16 8.2E-21 152.1 16.7 194 171-416 26-251 (334)
5 PF05920 Homeobox_KN: Homeobox 99.2 2.3E-12 5.1E-17 93.3 1.8 30 381-410 1-40 (40)
6 PF03789 ELK: ELK domain ; In 98.5 3.4E-08 7.4E-13 64.2 1.5 22 341-362 1-22 (22)
7 cd00086 homeodomain Homeodomai 98.3 4.6E-07 1E-11 66.6 3.5 47 364-413 1-57 (59)
8 smart00389 HOX Homeodomain. DN 98.2 2.1E-06 4.5E-11 63.0 3.8 45 364-411 1-55 (56)
9 KOG0775 Transcription factor S 97.7 3E-05 6.5E-10 77.0 3.6 34 374-410 187-230 (304)
10 PF00046 Homeobox: Homeobox do 97.6 4.7E-05 1E-09 56.5 2.7 44 364-410 1-54 (57)
11 KOG0773 Transcription factor M 97.3 4.7E-05 1E-09 75.1 -0.2 76 339-415 58-156 (342)
12 PF03792 PBC: PBC domain; Int 94.9 0.32 6.9E-06 46.6 11.0 43 172-214 25-78 (191)
13 KOG2252 CCAAT displacement pro 88.4 0.37 8E-06 52.3 3.1 45 364-411 421-475 (558)
14 TIGR01565 homeo_ZF_HD homeobox 72.3 5.9 0.00013 31.3 3.8 43 363-408 1-57 (58)
15 KOG3802 Transcription factor O 66.5 3.4 7.3E-05 43.6 1.8 45 362-410 293-348 (398)
16 COG1103 Archaea-specific pyrid 53.9 6.5 0.00014 40.6 1.3 44 347-390 3-49 (382)
17 COG5576 Homeodomain-containing 49.7 15 0.00032 34.1 2.8 44 365-411 53-106 (156)
18 PF12022 DUF3510: Domain of un 48.7 86 0.0019 27.7 7.3 35 251-285 65-99 (125)
19 KOG4445 Uncharacterized conser 44.8 42 0.00091 35.1 5.3 47 237-285 134-180 (368)
20 PHA02510 X gene X product; Rev 44.5 22 0.00047 32.0 2.9 61 339-412 6-66 (116)
21 PF11288 DUF3089: Protein of u 39.5 13 0.00028 36.0 0.8 46 155-205 93-138 (207)
22 PF12323 HTH_OrfB_IS605: Helix 39.4 13 0.00027 27.1 0.6 26 388-413 8-42 (46)
23 PF05190 MutS_IV: MutS family 35.7 63 0.0014 25.4 4.1 24 234-257 1-24 (92)
24 PF13097 CENP-U: CENP-A nucleo 34.1 1.1E+02 0.0023 29.5 5.9 45 236-283 103-148 (175)
25 KOG0486 Transcription factor P 33.4 27 0.00059 36.4 2.0 42 365-409 114-165 (351)
26 KOG4511 Uncharacterized conser 33.3 2.4E+02 0.0052 29.3 8.6 27 179-205 50-78 (335)
27 PF07425 Pardaxin: Pardaxin; 28.6 37 0.0008 24.2 1.4 18 177-194 6-23 (33)
28 KOG4460 Nuclear pore complex, 27.8 1E+02 0.0022 34.7 5.3 38 239-283 568-605 (741)
29 KOG0490 Transcription factor, 24.4 51 0.0011 30.2 2.0 46 363-411 60-115 (235)
30 PHA03397 vlf-1 very late expre 21.6 83 0.0018 33.0 3.1 31 174-205 13-43 (363)
31 KOG0493 Transcription factor E 20.4 79 0.0017 32.6 2.5 47 364-413 247-303 (342)
32 PF02290 SRP14: Signal recogni 20.2 68 0.0015 27.2 1.8 18 235-252 71-88 (93)
No 1
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.97 E-value=3.2e-32 Score=264.93 Aligned_cols=242 Identities=19% Similarity=0.197 Sum_probs=176.0
Q ss_pred hhhhHHHHHHHhhCCChHHHHHHHHcchhccCCCcchhhHHHHHHhhhhhhhhhhccCCC-C--CCCCCChHHHHHHHHH
Q 014791 170 NWQNARYKAEILSHPLYEQLLSAHVACLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAG-Q--GLVTDDKELDQFMTHY 246 (418)
Q Consensus 170 ~~e~e~iKAkI~sHPlYp~LL~AyIdCqKVGAPpEvl~rLda~l~q~q~~~~k~sa~~~~-~--~~ig~DPELDQFMEaY 246 (418)
.+....+|+.+.+||+|..++.||++|++++.|.+.+.++++.+........++...... . ..-+.+++|+.||..|
T Consensus 46 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k~ 125 (342)
T KOG0773|consen 46 MVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSKL 125 (342)
T ss_pred ccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchHH
Confidence 455667899999999999999999999999999999988777654433332222211110 0 1235889999999999
Q ss_pred HHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHhhhhCCCCCCCCCCCCCCchhhhccCCCccCCCCC-CCCCCCCCCCC
Q 014791 247 VLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFDGSL-EGPDTMGFGPL 325 (418)
Q Consensus 247 C~mL~KYKEELsrP~~~~a~EA~~F~~~IEsQL~sLt~~s~~egtga~~SddEdd~~~Sd~~~~dg~~-e~~D~~gf~pl 325 (418)
+.+|..++..|+..+. -+++++++++|+..+...++..+....+.+...+.++... ...+.. -..+.+|+.+.
T Consensus 126 ~~~ll~~~~~~~~~~~--~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~q~~~~~~~~~~~~~ 199 (342)
T KOG0773|consen 126 EKILLAVITKLTLTQV--STWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEK----AIGGQLSSSEELLGESEQ 199 (342)
T ss_pred HHHHHHHHHHhhhhhH--HHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcc----cccccccccccccccccc
Confidence 9999999999999863 3899999999999999998766554443322221111100 000000 00111122221
Q ss_pred CCchhhhhhh--HHHHHHHHHHHhhhhhhhhhhHHHHHHHhhcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHH--
Q 014791 326 IPTESERSLM--ERVRQELKHELKQGYKEKIVDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLR-- 401 (418)
Q Consensus 326 ~p~e~erslm--er~DqELK~~LlrKYsg~l~~LkqEf~kkKKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~-- 401 (418)
...+.+...+ .+.++.++..|.+.++.++.....+..++|++|+||++++++|+.||+.|+.||||++.+|.+|+.
T Consensus 200 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~T 279 (342)
T KOG0773|consen 200 DDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQT 279 (342)
T ss_pred cccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhc
Confidence 1111121111 344678899999999989888888888999999999999999999999999999999999999998
Q ss_pred --------Hhhccccccccccccc
Q 014791 402 --------FLFKSLPLRHSMMLIH 417 (418)
Q Consensus 402 --------NWFiNaRrR~~~~li~ 417 (418)
|||||||+|+|+++|.
T Consensus 280 GLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 280 GLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred CCCcccCCchhhhcccccCCchHH
Confidence 9999999999999873
No 2
>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=99.91 E-value=8.4e-25 Score=166.66 Aligned_cols=50 Identities=50% Similarity=0.712 Sum_probs=47.6
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHhhhhC
Q 014791 231 GLVTDDKELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTG 284 (418)
Q Consensus 231 ~~ig~DPELDQFMEaYC~mL~KYKEELsrP~~~~a~EA~~F~~~IEsQL~sLt~ 284 (418)
+++|+|||||||||+||.||+||||||+||| .||++|||+||+||++|||
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 3
>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=99.84 E-value=4.7e-22 Score=147.73 Aligned_cols=44 Identities=43% Similarity=0.744 Sum_probs=41.0
Q ss_pred HHHHHHHhhCCChHHHHHHHHcchhccCCCcchhhHHHHHHhhh
Q 014791 174 ARYKAEILSHPLYEQLLSAHVACLRIATPVDQLPRIDAQLAQSQ 217 (418)
Q Consensus 174 e~iKAkI~sHPlYp~LL~AyIdCqKVGAPpEvl~rLda~l~q~q 217 (418)
+.|||+|++||+||+||+|||+|+|||||||++++|++++++++
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 47999999999999999999999999999999999999987654
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.70 E-value=3.8e-16 Score=152.07 Aligned_cols=194 Identities=24% Similarity=0.316 Sum_probs=137.0
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHcch-hc---------cCCCc-chhhHHHHHHhhhhhhh---hhhccCCCCCCCCCC
Q 014791 171 WQNARYKAEILSHPLYEQLLSAHVACL-RI---------ATPVD-QLPRIDAQLAQSQHVVS---KYSALGAGQGLVTDD 236 (418)
Q Consensus 171 ~e~e~iKAkI~sHPlYp~LL~AyIdCq-KV---------GAPpE-vl~rLda~l~q~q~~~~---k~sa~~~~~~~ig~D 236 (418)
+|..+.|-.|-+||+||.|.+-.++.. |+ -.||| ++-|||-+|-.. .++ +.-+.+. .-.|.|
T Consensus 26 Deaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~dpqlmRLDnML~AE--GVagPekgga~~~--~Asgg~ 101 (334)
T KOG0774|consen 26 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPPDPQLMRLDNMLLAE--GVAGPEKGGARAA--AASGGD 101 (334)
T ss_pred chHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCCChHHHHHHHHHHHh--cccCccccchhhh--hccCCC
Confidence 445599999999999999998887643 22 25888 899999987431 121 1100000 001222
Q ss_pred -----hHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHhhhhCCCCCCCCCCCCCCchhhhccCCCccCC
Q 014791 237 -----KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFD 311 (418)
Q Consensus 237 -----PELDQFMEaYC~mL~KYKEELsrP~~~~a~EA~~F~~~IEsQL~sLt~~s~~egtga~~SddEdd~~~Sd~~~~d 311 (418)
..|-|.-.-|-..|.||.+. |++.-+-.-+|.. +|
T Consensus 102 hsdYR~kL~qiR~iy~~Elekyeqa---------------CneftthV~nlL~----------------eQ--------- 141 (334)
T KOG0774|consen 102 HSDYRAKLLQIRQIYHNELEKYEQA---------------CNEFTTHVMNLLR----------------EQ--------- 141 (334)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHHH----------------Hh---------
Confidence 33444444444444444322 5555444444442 11
Q ss_pred CCCCCCCCCCCCCCCCchhhh--hhhHHHHHHHHHHHhhhhhhhhhhHHHHHHH-hhcCCCCccchHHHHHHHHHhccCC
Q 014791 312 GSLEGPDTMGFGPLIPTESER--SLMERVRQELKHELKQGYKEKIVDIREEILR-KRRAGKLPGDTTSVLKSWWQSHSKW 388 (418)
Q Consensus 312 g~~e~~D~~gf~pl~p~e~er--slmer~DqELK~~LlrKYsg~l~~LkqEf~k-kKKrGkLPKeAt~iL~~W~~~H~~~ 388 (418)
..+.||.|.+.|| ..|.+--.-+|-+|++--...+..||.+|.. +|||.+|.|.+|.||.+||+.|+.+
T Consensus 142 --------sr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~n 213 (334)
T KOG0774|consen 142 --------SRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSN 213 (334)
T ss_pred --------cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCC
Confidence 1367888998885 4455556778999999999999999999975 7889999999999999999999999
Q ss_pred CCCCHHHHHHHHH----------Hhhcccccccccccc
Q 014791 389 PYPTVSPVTLLLR----------FLFKSLPLRHSMMLI 416 (418)
Q Consensus 389 PYPSE~EK~~La~----------NWFiNaRrR~~~~li 416 (418)
|||||++|+.||. |||.|.|.|+-+.+.
T Consensus 214 PYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 214 PYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred CCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 9999999999998 899999999887654
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=99.24 E-value=2.3e-12 Score=93.28 Aligned_cols=30 Identities=27% Similarity=0.432 Sum_probs=27.3
Q ss_pred HHHhccCCCCCCHHHHHHHHH----------Hhhcccccc
Q 014791 381 WWQSHSKWPYPTVSPVTLLLR----------FLFKSLPLR 410 (418)
Q Consensus 381 W~~~H~~~PYPSE~EK~~La~----------NWFiNaRrR 410 (418)
||..|+.+||||++||..|+. |||+|+|||
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 999999999999999999998 899999998
No 6
>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=98.53 E-value=3.4e-08 Score=64.23 Aligned_cols=22 Identities=41% Similarity=0.622 Sum_probs=21.0
Q ss_pred HHHHHHhhhhhhhhhhHHHHHH
Q 014791 341 ELKHELKQGYKEKIVDIREEIL 362 (418)
Q Consensus 341 ELK~~LlrKYsg~l~~LkqEf~ 362 (418)
|||++|+|||+|||++||+||+
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 7999999999999999999995
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=98.33 E-value=4.6e-07 Score=66.57 Aligned_cols=47 Identities=15% Similarity=0.296 Sum_probs=42.8
Q ss_pred hhcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHH----------Hhhccccccccc
Q 014791 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLR----------FLFKSLPLRHSM 413 (418)
Q Consensus 364 kKKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~----------NWFiNaRrR~~~ 413 (418)
++++..++++...+|..|+.. +|||+.+++..||. +||.|.|.|...
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 467889999999999999998 89999999999998 799999998654
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.16 E-value=2.1e-06 Score=62.95 Aligned_cols=45 Identities=18% Similarity=0.322 Sum_probs=40.0
Q ss_pred hhcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHH----------Hhhccccccc
Q 014791 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLR----------FLFKSLPLRH 411 (418)
Q Consensus 364 kKKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~----------NWFiNaRrR~ 411 (418)
+|.|+.++++...+|..|+..+ |||+.+++..||. +||.|.|+|.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~---~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKN---PYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 4667889999999999999755 4999999999998 8999999885
No 9
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=97.68 E-value=3e-05 Score=77.00 Aligned_cols=34 Identities=29% Similarity=0.536 Sum_probs=31.9
Q ss_pred hHHHHHHHHHhccCCCCCCHHHHHHHHH----------Hhhcccccc
Q 014791 374 TTSVLKSWWQSHSKWPYPTVSPVTLLLR----------FLFKSLPLR 410 (418)
Q Consensus 374 At~iL~~W~~~H~~~PYPSE~EK~~La~----------NWFiNaRrR 410 (418)
+|.+||+|+. ..||||-+||+.||+ |||.|.|-|
T Consensus 187 SR~~LrewY~---~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQR 230 (304)
T KOG0775|consen 187 SRSLLREWYL---QNPYPSPREKRELAEATGLTITQVSNWFKNRRQR 230 (304)
T ss_pred hHHHHHHHHh---cCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhh
Confidence 7899999987 789999999999999 999999977
No 10
>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=97.59 E-value=4.7e-05 Score=56.49 Aligned_cols=44 Identities=23% Similarity=0.425 Sum_probs=40.4
Q ss_pred hhcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHH----------Hhhcccccc
Q 014791 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLR----------FLFKSLPLR 410 (418)
Q Consensus 364 kKKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~----------NWFiNaRrR 410 (418)
||+|-.+.++...+|..++.. .|||+.+++..||. +||-|.|++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k 54 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRK 54 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHH
Confidence 578899999999999999985 89999999999998 899998876
No 11
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.32 E-value=4.7e-05 Score=75.13 Aligned_cols=76 Identities=24% Similarity=0.299 Sum_probs=61.4
Q ss_pred HHHHHHHHhhhhhhhhh-------------hHHHHHHHhhcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHH----
Q 014791 339 RQELKHELKQGYKEKIV-------------DIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLR---- 401 (418)
Q Consensus 339 DqELK~~LlrKYsg~l~-------------~LkqEf~kkKKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~---- 401 (418)
-++|.+.++.-|.+++. .++.-....+++|+++.++ .+|++|+..|...|||++-+|..|+.
T Consensus 58 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~ 136 (342)
T KOG0773|consen 58 AQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKL 136 (342)
T ss_pred chhHHhHHhhccccccccccCcCccccccccccCccccccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHh
Confidence 36788888877777631 1122224678899999999 99999999999999999999999998
Q ss_pred ------Hhhccccccccccc
Q 014791 402 ------FLFKSLPLRHSMML 415 (418)
Q Consensus 402 ------NWFiNaRrR~~~~l 415 (418)
+||+|+|||+-+-+
T Consensus 137 ~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 137 TLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred hhhhHHHHHHHHHHHHHhcc
Confidence 79999999986543
No 12
>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=94.93 E-value=0.32 Score=46.63 Aligned_cols=43 Identities=26% Similarity=0.312 Sum_probs=34.5
Q ss_pred hhHHHHHHHhhCCChHHHHHHHHcch-hcc---------CCCc-chhhHHHHHH
Q 014791 172 QNARYKAEILSHPLYEQLLSAHVACL-RIA---------TPVD-QLPRIDAQLA 214 (418)
Q Consensus 172 e~e~iKAkI~sHPlYp~LL~AyIdCq-KVG---------APpE-vl~rLda~l~ 214 (418)
|....|-.|-+||+||.|-+..++-. |++ .||| ++.|||-+|.
T Consensus 25 eaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~dpQl~RLDNML~ 78 (191)
T PF03792_consen 25 EAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPPDPQLMRLDNMLL 78 (191)
T ss_pred HHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCCchhhhhhhcchh
Confidence 56899999999999999999998854 221 2555 7899999885
No 13
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=88.39 E-value=0.37 Score=52.30 Aligned_cols=45 Identities=11% Similarity=0.080 Sum_probs=34.1
Q ss_pred hhcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHH----------Hhhccccccc
Q 014791 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLR----------FLFKSLPLRH 411 (418)
Q Consensus 364 kKKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~----------NWFiNaRrR~ 411 (418)
||-|=.|...-+..|+.-|.+ .+||+.+.-+.|++ |||-|||||-
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 344555555666777655543 69999999999998 9999999994
No 14
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=72.26 E-value=5.9 Score=31.31 Aligned_cols=43 Identities=12% Similarity=0.214 Sum_probs=35.6
Q ss_pred HhhcCCCCccchHHHHHHHHHhccCCCC----CCHHHHHHHHH----------Hhhcccc
Q 014791 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPY----PTVSPVTLLLR----------FLFKSLP 408 (418)
Q Consensus 363 kkKKrGkLPKeAt~iL~~W~~~H~~~PY----PSE~EK~~La~----------NWFiNaR 408 (418)
|||+|-++..+....|..-+.. .+| |+..+...||. -||-|.+
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 4788999999999999866543 566 99999999999 4998864
No 15
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=66.53 E-value=3.4 Score=43.65 Aligned_cols=45 Identities=18% Similarity=0.300 Sum_probs=35.5
Q ss_pred HHhhcCCCCccchHHHHHHHHHhc-cCCCCCCHHHHHHHHH----------Hhhcccccc
Q 014791 362 LRKRRAGKLPGDTTSVLKSWWQSH-SKWPYPTVSPVTLLLR----------FLFKSLPLR 410 (418)
Q Consensus 362 ~kkKKrGkLPKeAt~iL~~W~~~H-~~~PYPSE~EK~~La~----------NWFiNaRrR 410 (418)
.|||||-.+---++..| ..| .++|.||-+|--.||+ =||-|.|-+
T Consensus 293 RkRKKRTSie~~vr~aL----E~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQk 348 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGAL----EKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQK 348 (398)
T ss_pred cccccccceeHHHHHHH----HHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccc
Confidence 56677777776677777 555 5799999999999999 399997754
No 16
>COG1103 Archaea-specific pyridoxal phosphate-dependent enzymes [General function prediction only]
Probab=53.90 E-value=6.5 Score=40.63 Aligned_cols=44 Identities=16% Similarity=0.277 Sum_probs=32.3
Q ss_pred hhhhhhhhhhHHHHHH---HhhcCCCCccchHHHHHHHHHhccCCCC
Q 014791 347 KQGYKEKIVDIREEIL---RKRRAGKLPGDTTSVLKSWWQSHSKWPY 390 (418)
Q Consensus 347 lrKYsg~l~~LkqEf~---kkKKrGkLPKeAt~iL~~W~~~H~~~PY 390 (418)
|.||+..+..+...|. --.+.|+||++|++.|.+|+---+.+-|
T Consensus 3 l~ky~nl~r~~~r~~iNv~PiQrGGiLt~eArkal~E~gDGYSvCD~ 49 (382)
T COG1103 3 LDKYGNLTRRLTRGFINVNPIQRGGILTEEARKALLEWGDGYSVCDF 49 (382)
T ss_pred hhhhhhhhhHhhcCccccChhhccCcCCHHHHHHHHHhcCCcchhhh
Confidence 5677777666665554 3478999999999999999965444444
No 17
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=49.67 E-value=15 Score=34.11 Aligned_cols=44 Identities=16% Similarity=0.230 Sum_probs=30.3
Q ss_pred hcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHH----------Hhhccccccc
Q 014791 365 RRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLR----------FLFKSLPLRH 411 (418)
Q Consensus 365 KKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~----------NWFiNaRrR~ 411 (418)
++|-.+......+|..=| -..|||+-.+|..|+. =||=|.|-+.
T Consensus 53 ~~r~R~t~~Q~~vL~~~F---~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~ 106 (156)
T COG5576 53 SKRRRTTDEQLMVLEREF---EINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKE 106 (156)
T ss_pred ccceechHHHHHHHHHHh---ccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHH
Confidence 334444555555664222 3589999999999999 2999988653
No 18
>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=48.68 E-value=86 Score=27.70 Aligned_cols=35 Identities=17% Similarity=0.137 Sum_probs=21.8
Q ss_pred HHHHHHHhhhhhhhHHHHHHHHHHHHHHHhhhhCC
Q 014791 251 CSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGV 285 (418)
Q Consensus 251 ~KYKEELsrP~~~~a~EA~~F~~~IEsQL~sLt~~ 285 (418)
.+.-++++.-|...+.|...-.+++|.+|+-|-..
T Consensus 65 ~~v~~~v~~~y~~~~~evL~sv~KtEeSL~rlkk~ 99 (125)
T PF12022_consen 65 QKVITEVTERYYEIASEVLTSVRKTEESLKRLKKR 99 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33333333333333457677788999999999643
No 19
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=44.84 E-value=42 Score=35.06 Aligned_cols=47 Identities=13% Similarity=0.217 Sum_probs=36.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHhhhhCC
Q 014791 237 KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGV 285 (418)
Q Consensus 237 PELDQFMEaYC~mL~KYKEELsrP~~~~a~EA~~F~~~IEsQL~sLt~~ 285 (418)
-+-|.||-.|| |.+|-.++.+-+|.++++|-.-+..+-.|...+|.+
T Consensus 134 T~C~Hy~H~~C--laRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpV 180 (368)
T KOG4445|consen 134 TACDHYMHFAC--LARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPV 180 (368)
T ss_pred ehhHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhH
Confidence 36799999999 456666666666666678887788899999999864
No 20
>PHA02510 X gene X product; Reviewed
Probab=44.46 E-value=22 Score=31.98 Aligned_cols=61 Identities=8% Similarity=0.066 Sum_probs=49.3
Q ss_pred HHHHHHHHhhhhhhhhhhHHHHHHHhhcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHHHhhcccccccc
Q 014791 339 RQELKHELKQGYKEKIVDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLRFLFKSLPLRHS 412 (418)
Q Consensus 339 DqELK~~LlrKYsg~l~~LkqEf~kkKKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~NWFiNaRrR~~ 412 (418)
|.+++..|+.||..+- |+|++|..-...|..|...+-..=| ++-|..|.+..|-..|+++.
T Consensus 6 d~~v~~~l~~~~~t~t-----------~~G~~s~aka~~~f~~y~~l~~~g~--~~vk~~l~k~tFyrhr~~L~ 66 (116)
T PHA02510 6 DSQVIDAIINKFFSIT-----------KSGNLSSAKAMRYFGFYRRLVNEGY--DNVADTMSRATFWRHRKVLK 66 (116)
T ss_pred HHHHHHHHHhhheeeC-----------CCCCcCHHHHHHHHHHHHhhhhhhH--HHHHHHccHHHHHHHHHHHH
Confidence 6789999999999885 7999999988899999988765555 56788888877777666654
No 21
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=39.52 E-value=13 Score=36.03 Aligned_cols=46 Identities=24% Similarity=0.356 Sum_probs=35.1
Q ss_pred CCCCceeccCCCcchhhhhHHHHHHHhhCCChHHHHHHHHcchhccCCCcc
Q 014791 155 KSEGVVVESGADGVVNWQNARYKAEILSHPLYEQLLSAHVACLRIATPVDQ 205 (418)
Q Consensus 155 ~~~~~~~~~~~~~~~~~e~e~iKAkI~sHPlYp~LL~AyIdCqKVGAPpEv 205 (418)
++-.+|..|-.+|.. -=...||.+|..+|++.+||+||+ ||.|+-+
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 566778777554432 225689999999999999999999 8887543
No 22
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=39.42 E-value=13 Score=27.10 Aligned_cols=26 Identities=19% Similarity=-0.029 Sum_probs=21.3
Q ss_pred CCCCCHHHHHHHHH---------Hhhccccccccc
Q 014791 388 WPYPTVSPVTLLLR---------FLFKSLPLRHSM 413 (418)
Q Consensus 388 ~PYPSE~EK~~La~---------NWFiNaRrR~~~ 413 (418)
--|||.+++..|.+ ||.+..|.+.|.
T Consensus 8 rl~Pt~~Q~~~L~~~~~~~R~vyN~~L~~~~~~y~ 42 (46)
T PF12323_consen 8 RLYPTKEQEEKLERWFGACRFVYNWALAERKEAYK 42 (46)
T ss_pred EEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35899999999998 888888876654
No 23
>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=35.73 E-value=63 Score=25.40 Aligned_cols=24 Identities=29% Similarity=0.340 Sum_probs=19.7
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHH
Q 014791 234 TDDKELDQFMTHYVLLLCSFKEQL 257 (418)
Q Consensus 234 g~DPELDQFMEaYC~mL~KYKEEL 257 (418)
|-|++||+..+.|.++.....+.+
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~ 24 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELL 24 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999998877766655
No 24
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=34.12 E-value=1.1e+02 Score=29.51 Aligned_cols=45 Identities=13% Similarity=0.234 Sum_probs=36.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHH-HHHHHHHHHHhhhh
Q 014791 236 DKELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAV-MACWEIEQSLQSLT 283 (418)
Q Consensus 236 DPELDQFMEaYC~mL~KYKEELsrP~~~~a~EA~-~F~~~IEsQL~sLt 283 (418)
=-|||-...++-.++..||+.+.-.+= .+|+ .|+..+..||-.+-
T Consensus 103 ItELDVvL~~FEk~~~eYkq~ieS~~c---r~AI~~F~~~~keqL~~~i 148 (175)
T PF13097_consen 103 ITELDVVLSAFEKTALEYKQSIESKIC---RKAINKFYSNFKEQLIEMI 148 (175)
T ss_pred chHHHHHHHHHHHHHHHHHHhhccHHH---HHHHHHHHHHHHHHHHHHH
Confidence 379999999999999999999987663 3444 57889999987654
No 25
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=33.41 E-value=27 Score=36.43 Aligned_cols=42 Identities=19% Similarity=0.241 Sum_probs=32.9
Q ss_pred hcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHH----------Hhhccccc
Q 014791 365 RRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLR----------FLFKSLPL 409 (418)
Q Consensus 365 KKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~----------NWFiNaRr 409 (418)
|.|-.|...--+-|+.||.. .=||+-+.+..+|- +||.|-|-
T Consensus 114 rQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrra 165 (351)
T KOG0486|consen 114 RQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRA 165 (351)
T ss_pred hhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchh
Confidence 33566777777889999987 45999999999886 79998664
No 26
>KOG4511 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.32 E-value=2.4e+02 Score=29.34 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=22.2
Q ss_pred HHhhCCChHHHHHHHHcc--hhccCCCcc
Q 014791 179 EILSHPLYEQLLSAHVAC--LRIATPVDQ 205 (418)
Q Consensus 179 kI~sHPlYp~LL~AyIdC--qKVGAPpEv 205 (418)
=|+-|--|.+||.-.+.| -.||.-|++
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 477899999999999986 468987764
No 27
>PF07425 Pardaxin: Pardaxin; InterPro: IPR009990 This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin []. Pardaxin has also been found to have a shark repellent action [].; GO: 0005576 extracellular region; PDB: 1XC0_A 2KNS_A.
Probab=28.59 E-value=37 Score=24.22 Aligned_cols=18 Identities=44% Similarity=0.619 Sum_probs=15.3
Q ss_pred HHHHhhCCChHHHHHHHH
Q 014791 177 KAEILSHPLYEQLLSAHV 194 (418)
Q Consensus 177 KAkI~sHPlYp~LL~AyI 194 (418)
--||++-|+|.-||+|--
T Consensus 6 ipkiissplfktllsavg 23 (33)
T PF07425_consen 6 IPKIISSPLFKTLLSAVG 23 (33)
T ss_dssp HHHHCCTTTCHHHHHHHH
T ss_pred hhHHHccHHHHHHHHHHH
Confidence 358999999999998843
No 28
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.79 E-value=1e+02 Score=34.69 Aligned_cols=38 Identities=32% Similarity=0.499 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHhhhh
Q 014791 239 LDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLT 283 (418)
Q Consensus 239 LDQFMEaYC~mL~KYKEELsrP~~~~a~EA~~F~~~IEsQL~sLt 283 (418)
..-|-|.|..-=.+-|+|++||+ -..|..+++||+.|.
T Consensus 568 ~~vfrEqYi~~~dlV~~e~qrH~-------~~l~~~k~~QlQ~l~ 605 (741)
T KOG4460|consen 568 TQVFREQYILKQDLVKEEIQRHV-------KLLCDQKKKQLQDLS 605 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHH
Confidence 34588899988888999999997 356889999999996
No 29
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=24.37 E-value=51 Score=30.15 Aligned_cols=46 Identities=11% Similarity=0.090 Sum_probs=33.3
Q ss_pred HhhcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHH----------Hhhccccccc
Q 014791 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLR----------FLFKSLPLRH 411 (418)
Q Consensus 363 kkKKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~----------NWFiNaRrR~ 411 (418)
+++.|-++.....+.|..=+... +||.-.-+..|+. .||-|-|...
T Consensus 60 ~rr~rt~~~~~ql~~ler~f~~~---h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~ 115 (235)
T KOG0490|consen 60 KRCARCKFTISQLDELERAFEKV---HLPCFACRECLALLLTGDEFRVQVWFQNRRAKD 115 (235)
T ss_pred ccccCCCCCcCHHHHHHHhhcCC---CcCccchHHHHhhcCCCCeeeeehhhhhhcHhh
Confidence 34445556666777776444433 9999999999997 7999988644
No 30
>PHA03397 vlf-1 very late expression factor 1; Provisional
Probab=21.64 E-value=83 Score=33.02 Aligned_cols=31 Identities=23% Similarity=0.426 Sum_probs=27.0
Q ss_pred HHHHHHHhhCCChHHHHHHHHcchhccCCCcc
Q 014791 174 ARYKAEILSHPLYEQLLSAHVACLRIATPVDQ 205 (418)
Q Consensus 174 e~iKAkI~sHPlYp~LL~AyIdCqKVGAPpEv 205 (418)
...|.+|-+||+|+..+..=++=|| ++|++|
T Consensus 13 ~~w~~~i~~~~~f~~~~~~~~~rq~-~~~~~~ 43 (363)
T PHA03397 13 NIWKLVIQNHPRFEEVFDLAIDRQK-CTPDEV 43 (363)
T ss_pred HHHHHHHhccchHHHHHHHHHHhhc-CCCccc
Confidence 4789999999999999999999999 566644
No 31
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=20.38 E-value=79 Score=32.60 Aligned_cols=47 Identities=19% Similarity=0.202 Sum_probs=36.3
Q ss_pred hhcCCCCccchHHHHHHHHHhccCCCCCCHHHHHHHHH----------Hhhccccccccc
Q 014791 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTVSPVTLLLR----------FLFKSLPLRHSM 413 (418)
Q Consensus 364 kKKrGkLPKeAt~iL~~W~~~H~~~PYPSE~EK~~La~----------NWFiNaRrR~~~ 413 (418)
||-|--|..|--+.|+.=|..++ |=||.-++.|++ -||-|.|..|-|
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enR---YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKK 303 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENR---YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKK 303 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhh---hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhh
Confidence 34455566677788887776665 789999999998 399999998765
No 32
>PF02290 SRP14: Signal recognition particle 14kD protein; InterPro: IPR003210 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the 14 kDa SRP14 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0030942 endoplasmic reticulum signal peptide binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0005786 signal recognition particle, endoplasmic reticulum targeting; PDB: 1914_A 1RY1_D 1E8O_B 2W9J_B.
Probab=20.16 E-value=68 Score=27.25 Aligned_cols=18 Identities=33% Similarity=0.597 Sum_probs=15.2
Q ss_pred CChHHHHHHHHHHHHHHH
Q 014791 235 DDKELDQFMTHYVLLLCS 252 (418)
Q Consensus 235 ~DPELDQFMEaYC~mL~K 252 (418)
.-.+|+.|...|+.+|..
T Consensus 71 ~~~~l~~F~~~Y~~v~K~ 88 (93)
T PF02290_consen 71 DPDDLDKFWQSYANVLKA 88 (93)
T ss_dssp ETTCHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHh
Confidence 457899999999999853
Done!