Query 018583
Match_columns 353
No_of_seqs 194 out of 408
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 10:13:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018583.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018583hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14379 Myb_CC_LHEQLE: MYB-CC 99.9 1.3E-24 2.9E-29 161.9 6.8 51 266-316 1-51 (51)
2 PLN03162 golden-2 like transcr 99.9 3.6E-24 7.9E-29 211.3 7.7 64 178-242 230-293 (526)
3 TIGR01557 myb_SHAQKYF myb-like 99.9 7.9E-22 1.7E-26 148.9 6.9 56 183-238 1-56 (57)
4 PF00249 Myb_DNA-binding: Myb- 97.3 0.00055 1.2E-08 48.9 5.5 48 185-236 1-48 (48)
5 smart00426 TEA TEA domain. 89.8 0.33 7.2E-06 39.0 3.0 46 187-234 5-67 (68)
6 PF14379 Myb_CC_LHEQLE: MYB-CC 89.2 0.34 7.5E-06 36.9 2.6 39 281-320 6-44 (51)
7 PF15235 GRIN_C: G protein-reg 76.0 2 4.2E-05 38.7 2.2 21 287-307 70-90 (137)
8 PF12776 Myb_DNA-bind_3: Myb/S 66.8 9.3 0.0002 30.0 4.0 50 187-236 1-62 (96)
9 PF01285 TEA: TEA/ATTS domain 62.8 9.1 0.0002 39.8 4.1 54 181-235 45-112 (431)
10 cd00167 SANT 'SWI3, ADA2, N-Co 62.6 36 0.00079 22.1 5.7 44 187-235 1-44 (45)
11 smart00717 SANT SANT SWI3, AD 62.3 40 0.00087 22.1 5.9 44 186-234 2-45 (49)
12 smart00501 BRIGHT BRIGHT, ARID 59.7 10 0.00022 30.4 3.1 46 190-236 32-84 (93)
13 PF01519 DUF16: Protein of unk 51.5 69 0.0015 27.8 6.9 30 286-315 65-94 (102)
14 PF07384 DUF1497: Protein of u 33.7 36 0.00078 26.5 2.3 22 186-207 36-57 (59)
15 KOG3841 TEF-1 and related tran 29.2 70 0.0015 33.6 4.1 52 185-238 76-144 (455)
16 TIGR02894 DNA_bind_RsfA transc 26.3 40 0.00086 31.3 1.6 50 182-237 45-94 (161)
17 PF09535 Gmx_para_CXXCG: Prote 21.2 44 0.00094 32.7 0.9 16 193-209 214-229 (237)
18 PF00690 Cation_ATPase_N: Cati 21.0 1.3E+02 0.0028 22.7 3.2 31 210-240 5-38 (69)
No 1
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=99.91 E-value=1.3e-24 Score=161.92 Aligned_cols=51 Identities=63% Similarity=0.883 Sum_probs=48.8
Q ss_pred ccCHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 018583 266 TLQIKEALQLQLDVQRRLHEQLEIQRKLQLRIEEQGKHLQMLFDQQQKASK 316 (353)
Q Consensus 266 ~~qi~EALrlQmEVQrrLHEQLEVQR~LQLRIEAQGKYLQsmLekaqk~~~ 316 (353)
|++|+|||++||||||||||||||||+||+|||||||||++|||+|+++++
T Consensus 1 g~~i~EALr~QmEvQrrLhEQLEvQr~Lqlrieaqgkyl~~ilek~~~~~s 51 (51)
T PF14379_consen 1 GMQITEALRMQMEVQRRLHEQLEVQRHLQLRIEAQGKYLQSILEKAQKALS 51 (51)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence 578999999999999999999999999999999999999999999999863
No 2
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.90 E-value=3.6e-24 Score=211.27 Aligned_cols=64 Identities=41% Similarity=0.660 Sum_probs=59.4
Q ss_pred CCCCCCCCcccChHHHHHHHHHHHHhCCCCCCChHHHHhhhCCCCccHHHHHHHHhhhHhccCCC
Q 018583 178 PVITNKTRIRWTQDLHEKFVECVNRLGGADKATPKAILKLMDSEGLTIFHVKSHLQKYRMAKYVP 242 (353)
Q Consensus 178 ~~~~~K~RlrWT~eLH~rFV~AV~qLGG~dkAtPK~IL~lM~v~GLT~~hVkSHLQKYRl~~~~p 242 (353)
....+|+||+||+|||+|||+||++|| .++||||+||++|+|+|||++||||||||||+.++..
T Consensus 230 ~~g~KKpRLrWTpELH~rFVeAV~qLG-~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l 293 (526)
T PLN03162 230 APGKKKAKVDWTPELHRRFVHAVEQLG-VEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHL 293 (526)
T ss_pred CCCCCCCcccCCHHHHHHHHHHHHHhC-cCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccc
Confidence 344689999999999999999999998 7999999999999999999999999999999997643
No 3
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=99.86 E-value=7.9e-22 Score=148.95 Aligned_cols=56 Identities=57% Similarity=0.945 Sum_probs=54.4
Q ss_pred CCCcccChHHHHHHHHHHHHhCCCCCCChHHHHhhhCCCCccHHHHHHHHhhhHhc
Q 018583 183 KTRIRWTQDLHEKFVECVNRLGGADKATPKAILKLMDSEGLTIFHVKSHLQKYRMA 238 (353)
Q Consensus 183 K~RlrWT~eLH~rFV~AV~qLGG~dkAtPK~IL~lM~v~GLT~~hVkSHLQKYRl~ 238 (353)
|+|++||+|+|++|++||+.||+.+.||||.|+++|++++||+.+|+|||||||+.
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 78999999999999999999998899999999999999999999999999999985
No 4
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=97.34 E-value=0.00055 Score=48.87 Aligned_cols=48 Identities=35% Similarity=0.456 Sum_probs=41.7
Q ss_pred CcccChHHHHHHHHHHHHhCCCCCCChHHHHhhhCCCCccHHHHHHHHhhhH
Q 018583 185 RIRWTQDLHEKFVECVNRLGGADKATPKAILKLMDSEGLTIFHVKSHLQKYR 236 (353)
Q Consensus 185 RlrWT~eLH~rFV~AV~qLGG~dkAtPK~IL~lM~v~GLT~~hVkSHLQKYR 236 (353)
|-.||+|=++.|++||.++|. + .-+.|.+.|+ .|-|..++++|.++|+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~-~--~W~~Ia~~~~-~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGK-D--NWKKIAKRMP-GGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTT-T--HHHHHHHHHS-SSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCC-c--HHHHHHHHcC-CCCCHHHHHHHHHhhC
Confidence 568999999999999999982 2 7899999999 8999999999999985
No 5
>smart00426 TEA TEA domain.
Probab=89.80 E-value=0.33 Score=38.95 Aligned_cols=46 Identities=24% Similarity=0.291 Sum_probs=30.5
Q ss_pred ccChHHHHHHHHHHHHhCCCCCCChH-HHHhh---h-----------CCCCc--cHHHHHHHHhh
Q 018583 187 RWTQDLHEKFVECVNRLGGADKATPK-AILKL---M-----------DSEGL--TIFHVKSHLQK 234 (353)
Q Consensus 187 rWT~eLH~rFV~AV~qLGG~dkAtPK-~IL~l---M-----------~v~GL--T~~hVkSHLQK 234 (353)
.|.++|-..|++|+...- ...+=| .++.. . ...|. |..+|.||||.
T Consensus 5 vWp~~lE~Af~~aL~~~~--~~g~~kik~~~r~k~~gRNelIs~YI~~~tGk~Rt~KQVsShIQv 67 (68)
T smart00426 5 VWSPDIEQAFQEALAIYP--PCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQV 67 (68)
T ss_pred cCcHHHHHHHHHHHHHcC--ccCcccchhhhcCcccchhHHHHHHHHHHhCCccchhhhcchhee
Confidence 699999999999999885 222222 22211 1 12454 77889999985
No 6
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=89.20 E-value=0.34 Score=36.92 Aligned_cols=39 Identities=33% Similarity=0.469 Sum_probs=29.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCC
Q 018583 281 RRLHEQLEIQRKLQLRIEEQGKHLQMLFDQQQKASKDHSK 320 (353)
Q Consensus 281 rrLHEQLEVQR~LQLRIEAQGKYLQsmLekaqk~~~s~~~ 320 (353)
.-|..|+||||+|.=.+|.| |-||.-+|.+.+-+.+.+.
T Consensus 6 EALr~QmEvQrrLhEQLEvQ-r~Lqlrieaqgkyl~~ile 44 (51)
T PF14379_consen 6 EALRMQMEVQRRLHEQLEVQ-RHLQLRIEAQGKYLQSILE 44 (51)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhHHHHHHHH
Confidence 45778899999998888888 5677777777776655443
No 7
>PF15235 GRIN_C: G protein-regulated inducer of neurite outgrowth C-terminus
Probab=75.97 E-value=2 Score=38.70 Aligned_cols=21 Identities=29% Similarity=0.428 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 018583 287 LEIQRKLQLRIEEQGKHLQML 307 (353)
Q Consensus 287 LEVQR~LQLRIEAQGKYLQsm 307 (353)
+-||+||+++||+|+|.+..-
T Consensus 70 ~AIQkHLE~qi~e~~~q~~~~ 90 (137)
T PF15235_consen 70 MAIQKHLERQIEEHERQRAPQ 90 (137)
T ss_pred HHHHHHHHHHHHHhhhccccc
Confidence 368999999999999886653
No 8
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=66.80 E-value=9.3 Score=29.95 Aligned_cols=50 Identities=12% Similarity=0.238 Sum_probs=34.0
Q ss_pred ccChHHHHHHHHHHHH---hCCC-CCCCh-----HHHHhhhCC---CCccHHHHHHHHhhhH
Q 018583 187 RWTQDLHEKFVECVNR---LGGA-DKATP-----KAILKLMDS---EGLTIFHVKSHLQKYR 236 (353)
Q Consensus 187 rWT~eLH~rFV~AV~q---LGG~-dkAtP-----K~IL~lM~v---~GLT~~hVkSHLQKYR 236 (353)
+||++..+.||+++-. .|.- ..... ..|.+.|+- -.+|..+|++|+...|
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk 62 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLK 62 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHH
Confidence 5999999999998833 3433 23333 445666652 4468899999987644
No 9
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=62.85 E-value=9.1 Score=39.76 Aligned_cols=54 Identities=20% Similarity=0.258 Sum_probs=29.8
Q ss_pred CCCCCcccChHHHHHHHHHHHHhCCCCCCChHHHH-hhhC-----------CCC--ccHHHHHHHHhhh
Q 018583 181 TNKTRIRWTQDLHEKFVECVNRLGGADKATPKAIL-KLMD-----------SEG--LTIFHVKSHLQKY 235 (353)
Q Consensus 181 ~~K~RlrWT~eLH~rFV~AV~qLGG~dkAtPK~IL-~lM~-----------v~G--LT~~hVkSHLQKY 235 (353)
..+..-+|.+++...|++|+...--..+++ -.+. +..| ..| =|+.+|.||+|..
T Consensus 45 ~~~~~~vw~~~~e~af~~al~~~~~~g~~k-~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 45 DGDGEGVWPPDIEQAFQEALAIYPPCGRRK-LSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp -GGGS--S-HHHHHHHHHHHHHS-SSS----HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCCcc-cccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 356788999999999999998874222333 1111 1111 123 4788999999998
No 10
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=62.62 E-value=36 Score=22.09 Aligned_cols=44 Identities=23% Similarity=0.367 Sum_probs=33.9
Q ss_pred ccChHHHHHHHHHHHHhCCCCCCChHHHHhhhCCCCccHHHHHHHHhhh
Q 018583 187 RWTQDLHEKFVECVNRLGGADKATPKAILKLMDSEGLTIFHVKSHLQKY 235 (353)
Q Consensus 187 rWT~eLH~rFV~AV~qLGG~dkAtPK~IL~lM~v~GLT~~hVkSHLQKY 235 (353)
.||++=+..|+.++.++|- ..-+.|-+.|+ +=|...|+.|..++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~---~~w~~Ia~~~~--~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK---NNWEKIAKELP--GRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc---CCHHHHHhHcC--CCCHHHHHHHHHHh
Confidence 4999999999999999982 33567777764 46888888776543
No 11
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=62.27 E-value=40 Score=22.14 Aligned_cols=44 Identities=23% Similarity=0.345 Sum_probs=33.8
Q ss_pred cccChHHHHHHHHHHHHhCCCCCCChHHHHhhhCCCCccHHHHHHHHhh
Q 018583 186 IRWTQDLHEKFVECVNRLGGADKATPKAILKLMDSEGLTIFHVKSHLQK 234 (353)
Q Consensus 186 lrWT~eLH~rFV~AV~qLGG~dkAtPK~IL~lM~v~GLT~~hVkSHLQK 234 (353)
-.||++=...|+.+|.++| . ..-+.|-+.|+ +=|...|+.+...
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g-~--~~w~~Ia~~~~--~rt~~~~~~~~~~ 45 (49)
T smart00717 2 GEWTEEEDELLIELVKKYG-K--NNWEKIAKELP--GRTAEQCRERWNN 45 (49)
T ss_pred CCCCHHHHHHHHHHHHHHC-c--CCHHHHHHHcC--CCCHHHHHHHHHH
Confidence 4699999999999999998 1 23566777765 7788888777554
No 12
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=59.65 E-value=10 Score=30.41 Aligned_cols=46 Identities=24% Similarity=0.325 Sum_probs=34.6
Q ss_pred hHHHHHHHHHHHHhCCCCCCC----hHHHHhhhCCCCc---cHHHHHHHHhhhH
Q 018583 190 QDLHEKFVECVNRLGGADKAT----PKAILKLMDSEGL---TIFHVKSHLQKYR 236 (353)
Q Consensus 190 ~eLH~rFV~AV~qLGG~dkAt----PK~IL~lM~v~GL---T~~hVkSHLQKYR 236 (353)
-+|++.|+ +|..+||.+..+ =+.|.+.||++.- ...++|+|-.||=
T Consensus 32 vdL~~Ly~-~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L 84 (93)
T smart00501 32 LDLYRLYR-LVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYL 84 (93)
T ss_pred CcHHHHHH-HHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHh
Confidence 47999998 599999987544 3678899998752 3566788887773
No 13
>PF01519 DUF16: Protein of unknown function DUF16; InterPro: IPR002862 Proteins that contain this domain are of unknown function. It appears to be confined to proteins from Mycoplasma pneumoniae [].; PDB: 2BA2_C.
Probab=51.50 E-value=69 Score=27.77 Aligned_cols=30 Identities=33% Similarity=0.429 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 018583 286 QLEIQRKLQLRIEEQGKHLQMLFDQQQKAS 315 (353)
Q Consensus 286 QLEVQR~LQLRIEAQGKYLQsmLekaqk~~ 315 (353)
|=|.-+.||.+|++||+-|++|++.-+...
T Consensus 65 QGEqIkel~~e~k~qgktL~~I~~~L~~in 94 (102)
T PF01519_consen 65 QGEQIKELQVEQKAQGKTLQLILKTLQSIN 94 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455668899999999999999998776654
No 14
>PF07384 DUF1497: Protein of unknown function (DUF1497); InterPro: IPR009972 This entry is represented by Bacteriophage r1t, Orf17. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown.
Probab=33.70 E-value=36 Score=26.50 Aligned_cols=22 Identities=27% Similarity=0.706 Sum_probs=19.4
Q ss_pred cccChHHHHHHHHHHHHhCCCC
Q 018583 186 IRWTQDLHEKFVECVNRLGGAD 207 (353)
Q Consensus 186 lrWT~eLH~rFV~AV~qLGG~d 207 (353)
-++..|+|..|-+-|.+|||-+
T Consensus 36 ~kfnqem~aefheri~klggk~ 57 (59)
T PF07384_consen 36 NKFNQEMQAEFHERIKKLGGKN 57 (59)
T ss_pred hHhhHHHHHHHHHHHHHhcccc
Confidence 4688999999999999999854
No 15
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=29.18 E-value=70 Score=33.65 Aligned_cols=52 Identities=23% Similarity=0.303 Sum_probs=34.7
Q ss_pred CcccChHHHHHHHHHHHHhCCCCCCChHHHH--------------hhhC---CCCccHHHHHHHHhhhHhc
Q 018583 185 RIRWTQDLHEKFVECVNRLGGADKATPKAIL--------------KLMD---SEGLTIFHVKSHLQKYRMA 238 (353)
Q Consensus 185 RlrWT~eLH~rFV~AV~qLGG~dkAtPK~IL--------------~lM~---v~GLT~~hVkSHLQKYRl~ 238 (353)
-=+|+++.-+.|.||+...- .--+-|-|| +... =+-=|+.+|.||.|..-..
T Consensus 76 egvWSpdIEqsFqEALaiyp--pcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarr 144 (455)
T KOG3841|consen 76 EGVWSPDIEQSFQEALAIYP--PCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARR 144 (455)
T ss_pred ccccChhHHHHHHHHHhhcC--CCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHH
Confidence 34899999999999998874 222333333 1111 1445889999999976443
No 16
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=26.27 E-value=40 Score=31.25 Aligned_cols=50 Identities=20% Similarity=0.323 Sum_probs=37.2
Q ss_pred CCCCcccChHHHHHHHHHHHHhCCCCCCChHHHHhhhCCCCccHHHHHHHHhhhHh
Q 018583 182 NKTRIRWTQDLHEKFVECVNRLGGADKATPKAILKLMDSEGLTIFHVKSHLQKYRM 237 (353)
Q Consensus 182 ~K~RlrWT~eLH~rFV~AV~qLGG~dkAtPK~IL~lM~v~GLT~~hVkSHLQKYRl 237 (353)
....+||...+-..+.+||...- -.+-.++.. ...||+..|=+-||.|..
T Consensus 45 AACGFRWNs~VRkqY~~~i~~AK-kqRk~~~~~-----~~~ltl~~vI~fLq~l~~ 94 (161)
T TIGR02894 45 AACGFRWNAYVRKQYEEAIELAK-KQRKELKRE-----AGSLTLQDVISFLQNLKT 94 (161)
T ss_pred HHhcchHHHHHHHHHHHHHHHHH-HHHhccccC-----cccCCHHHHHHHHHHHHh
Confidence 46789999999999999998653 122222211 367999999999999974
No 17
>PF09535 Gmx_para_CXXCG: Protein of unknown function (Gmx_para_CXXCG); InterPro: IPR011750 This entry consists of at least 10 paralogous proteins from Myxococcus xanthus that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment.
Probab=21.24 E-value=44 Score=32.73 Aligned_cols=16 Identities=56% Similarity=0.883 Sum_probs=12.6
Q ss_pred HHHHHHHHHHhCCCCCC
Q 018583 193 HEKFVECVNRLGGADKA 209 (353)
Q Consensus 193 H~rFV~AV~qLGG~dkA 209 (353)
-+|||+||++|| ++.-
T Consensus 214 TERFVeAv~rL~-l~Gv 229 (237)
T PF09535_consen 214 TERFVEAVQRLG-LDGV 229 (237)
T ss_pred eHHHHHHHHhcC-CCcc
Confidence 379999999998 5443
No 18
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=20.96 E-value=1.3e+02 Score=22.66 Aligned_cols=31 Identities=26% Similarity=0.409 Sum_probs=25.4
Q ss_pred ChHHHHhhhC---CCCccHHHHHHHHhhhHhccC
Q 018583 210 TPKAILKLMD---SEGLTIFHVKSHLQKYRMAKY 240 (353)
Q Consensus 210 tPK~IL~lM~---v~GLT~~hVkSHLQKYRl~~~ 240 (353)
+...|++.++ ..|||.++|+..+++|-.+..
T Consensus 5 ~~~~v~~~l~t~~~~GLs~~ev~~r~~~~G~N~l 38 (69)
T PF00690_consen 5 SVEEVLKRLNTSSSQGLSSEEVEERRKKYGPNEL 38 (69)
T ss_dssp SHHHHHHHHTTBTSSBBTHHHHHHHHHHHSSSST
T ss_pred CHHHHHHHHCcCCCCCCCHHHHHHHHHhcccccc
Confidence 4567888887 599999999999999966643
Done!