Query psy4875
Match_columns 100
No_of_seqs 113 out of 310
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 20:02:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4875.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4875hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3517|consensus 100.0 9.2E-35 2E-39 220.6 4.1 91 3-93 49-139 (334)
2 PF00292 PAX: 'Paired box' dom 100.0 1.3E-34 2.7E-39 200.0 2.1 79 3-81 46-124 (125)
3 KOG3862|consensus 99.9 7.5E-28 1.6E-32 184.0 4.0 87 3-92 54-140 (327)
4 KOG3517|consensus 99.9 2.8E-24 6E-29 163.5 1.2 92 9-100 9-118 (334)
5 PF00292 PAX: 'Paired box' dom 99.9 7.7E-24 1.7E-28 146.3 -1.1 92 9-100 6-115 (125)
6 KOG0849|consensus 99.8 1.5E-20 3.3E-25 148.1 3.7 77 3-79 44-121 (354)
7 KOG3862|consensus 99.7 4.7E-19 1E-23 135.8 0.7 92 9-100 14-123 (327)
8 cd00131 PAX Paired Box domain 99.6 2.2E-15 4.8E-20 103.9 4.6 78 4-81 47-124 (128)
9 smart00351 PAX Paired Box doma 99.5 8E-15 1.7E-19 100.5 5.4 78 4-81 47-124 (125)
10 KOG0849|consensus 99.3 3.9E-13 8.5E-18 106.2 0.5 96 5-100 3-114 (354)
11 PF13565 HTH_32: Homeodomain-l 97.3 0.00032 6.8E-09 43.2 3.8 68 7-79 2-75 (77)
12 cd00131 PAX Paired Box domain 97.2 0.00018 3.9E-09 49.5 2.0 69 32-100 44-115 (128)
13 smart00351 PAX Paired Box doma 97.2 0.00026 5.6E-09 48.4 2.4 69 32-100 44-115 (125)
14 PF13551 HTH_29: Winged helix- 96.2 0.0068 1.5E-07 38.9 3.6 70 7-79 29-106 (112)
15 COG3415 Transposase and inacti 95.3 0.017 3.8E-07 40.6 2.9 57 8-65 39-96 (138)
16 PF01710 HTH_Tnp_IS630: Transp 87.6 0.45 9.7E-06 32.0 2.1 59 7-82 35-93 (119)
17 PF13072 DUF3936: Protein of u 75.5 2.1 4.5E-05 24.0 1.5 10 81-90 16-25 (38)
18 KOG0086|consensus 51.6 6.9 0.00015 28.8 0.8 23 3-26 163-185 (214)
19 PF00325 Crp: Bacterial regula 46.1 15 0.00032 19.6 1.3 14 7-20 19-32 (32)
20 cd01105 HTH_GlnR-like Helix-Tu 37.1 66 0.0014 20.1 3.6 62 3-64 10-72 (88)
21 PF13411 MerR_1: MerR HTH fami 36.9 58 0.0013 18.8 3.2 56 3-60 9-66 (69)
22 PF13011 LZ_Tnp_IS481: leucine 35.5 89 0.0019 20.2 4.0 40 6-46 41-84 (85)
23 cd04762 HTH_MerR-trunc Helix-T 33.8 66 0.0014 16.6 2.9 36 3-39 9-44 (49)
24 cd04761 HTH_MerR-SF Helix-Turn 33.7 61 0.0013 17.3 2.7 39 3-42 9-47 (49)
25 TIGR01529 argR_whole arginine 33.2 18 0.00038 25.3 0.5 39 40-83 6-44 (146)
26 PF13089 PP_kinase_N: Polyphos 31.6 8.5 0.00018 25.6 -1.3 65 1-66 31-106 (109)
27 PF09106 SelB-wing_2: Elongati 26.1 1.2E+02 0.0026 17.4 3.2 45 39-94 3-50 (59)
28 PF13384 HTH_23: Homeodomain-l 24.9 35 0.00076 18.6 0.7 13 6-18 33-45 (50)
29 smart00422 HTH_MERR helix_turn 21.7 1.7E+02 0.0037 16.6 3.7 54 3-58 9-65 (70)
30 PF02082 Rrf2: Transcriptional 21.2 61 0.0013 19.9 1.3 23 7-29 42-66 (83)
31 cd04782 HTH_BltR Helix-Turn-He 20.5 2.4E+02 0.0052 17.8 4.3 57 4-61 10-68 (97)
No 1
>KOG3517|consensus
Probab=100.00 E-value=9.2e-35 Score=220.56 Aligned_cols=91 Identities=47% Similarity=0.719 Sum_probs=85.1
Q ss_pred cccchHHHhhhHhhcccccccccCCCCCCcCcHHHHHHHHHHHhhCCCcchhhhhccccccccccccCCCCCCCcchhHH
Q psy4875 3 FLTLLCPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIPSRECPSIFAW 82 (100)
Q Consensus 3 ~~gcvskiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl~~~~e~psif~~eIR~rL~~~gvc~~~~~ps~ss~~rFaw 82 (100)
-||||||||.||.|||+|.||+||||||+++||.+|..|..+++..|+||+|||||||+.+|||++.|+||++||+|+..
T Consensus 49 SHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~DPGIFAWEIRDRLlsdgiCDk~NvPSVSSISRILR 128 (334)
T KOG3517|consen 49 SHGCVSKILARYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQRDPGIFAWEIRDRLLSDGICDKYNVPSVSSISRILR 128 (334)
T ss_pred ccchHHHHHHHhccCCcccccccCCCCCccCChhHHHHHHHhhccCCceeeehhhhhhhhcccccccCCcchHHHHHHHH
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999776
Q ss_pred HHHHHHhhcCC
Q psy4875 83 EIRDRLLQEGV 93 (100)
Q Consensus 83 eir~~l~~~g~ 93 (100)
+.-..|.++|-
T Consensus 129 NKiGsLaqqg~ 139 (334)
T KOG3517|consen 129 NKIGSLAQQGT 139 (334)
T ss_pred hhhcccccCCC
Confidence 66666666654
No 2
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=100.00 E-value=1.3e-34 Score=200.03 Aligned_cols=79 Identities=57% Similarity=0.932 Sum_probs=61.6
Q ss_pred cccchHHHhhhHhhcccccccccCCCCCCcCcHHHHHHHHHHHhhCCCcchhhhhccccccccccccCCCCCCCcchhH
Q psy4875 3 FLTLLCPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIPSRECPSIFA 81 (100)
Q Consensus 3 ~~gcvskiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl~~~~e~psif~~eIR~rL~~~gvc~~~~~ps~ss~~rFa 81 (100)
-||||||||+||+|||+++||++||+||+++||+++.+|.+|++++|+||+||||++|+++|||++.++||+|||||+.
T Consensus 46 s~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~ifawEiR~~L~~~gvc~~~~~PsvssInRil 124 (125)
T PF00292_consen 46 SHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTIFAWEIRDRLIADGVCDRSNVPSVSSINRIL 124 (125)
T ss_dssp -HHHHHHHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS-HHHHHHHHHHTTSS-TTTS--HHHHHHHH
T ss_pred chhHHHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCcchHHHHHHHHHcCCCCCCCCCCHHHHHHhh
Confidence 4899999999999999999999999999999999999999999999999999999999999999999999999999854
No 3
>KOG3862|consensus
Probab=99.94 E-value=7.5e-28 Score=184.00 Aligned_cols=87 Identities=53% Similarity=0.877 Sum_probs=82.2
Q ss_pred cccchHHHhhhHhhcccccccccCCCCCCcCcHHHHHHHHHHHhhCCCcchhhhhccccccccccccCCCCCCCcchhHH
Q psy4875 3 FLTLLCPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIPSRECPSIFAW 82 (100)
Q Consensus 3 ~~gcvskiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl~~~~e~psif~~eIR~rL~~~gvc~~~~~ps~ss~~rFaw 82 (100)
-||||||||+|||||||++||.+||+||+++|+.+|++|..|++++|.+|+||||++|+.++||+..++|+||++++
T Consensus 54 ShGcvSkil~r~yEtgS~~pg~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~~~~ic~~d~vpsVssinr--- 130 (327)
T KOG3862|consen 54 SHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLLAEPICDNDTVPSVSSINR--- 130 (327)
T ss_pred ccCCchhHHHHHHHhcCcccCCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhhcccccCCCCCchHHHHHH---
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHHhhcC
Q psy4875 83 EIRDRLLQEG 92 (100)
Q Consensus 83 eir~~l~~~g 92 (100)
.+|...++.-
T Consensus 131 i~r~~~~~~~ 140 (327)
T KOG3862|consen 131 IIRTKVQQKQ 140 (327)
T ss_pred HHHHhhhhcc
Confidence 6676666543
No 4
>KOG3517|consensus
Probab=99.88 E-value=2.8e-24 Score=163.49 Aligned_cols=92 Identities=34% Similarity=0.477 Sum_probs=87.1
Q ss_pred HHhhhHhhcccccccc---------cCCCCCCcC------cHHHHHHHHHHHhhCCCcchhhh---hccccccccccccC
Q psy4875 9 PLVHRYYETGSIRPRA---------IGGSKPRVA------TAEVVSKISHYKRECPSIFAWEI---RDRLLQEGVCSNDN 70 (100)
Q Consensus 9 kiL~r~~etGsi~Pg~---------iGGskP~~~------s~~~vskIl~~~~e~psif~~eI---R~rL~~~gvc~~~~ 70 (100)
++|+..+-+|++.|-+ -=|.|||++ +|+||+|||.+|.||++|.++.| |+|+.++.|++-+.
T Consensus 9 NQLGGVFVNGRPLPna~RlrIVELarlGiRPCDISRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR 88 (334)
T KOG3517|consen 9 NQLGGVFVNGRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPKVVKYIR 88 (334)
T ss_pred hhccceeEcCccCcchhhhhHHHHHHcCCCccchhhhhhhccchHHHHHHHhccCCcccccccCCCCCccCChhHHHHHH
Confidence 6899999999999976 358999976 69999999999999999999999 89999999999999
Q ss_pred CCCCCCcchhHHHHHHHHhhcCCCCCCCCC
Q psy4875 71 IPSRECPSIFAWEIRDRLLQEGVCSNDNIP 100 (100)
Q Consensus 71 ~ps~ss~~rFaweir~~l~~~g~c~~~~~p 100 (100)
.++..+|.+|||||||||+.+|+||+.|||
T Consensus 89 ~~Kq~DPGIFAWEIRDRLlsdgiCDk~NvP 118 (334)
T KOG3517|consen 89 SLKQRDPGIFAWEIRDRLLSDGICDKYNVP 118 (334)
T ss_pred HhhccCCceeeehhhhhhhhcccccccCCc
Confidence 999999999999999999999999999998
No 5
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=99.87 E-value=7.7e-24 Score=146.35 Aligned_cols=92 Identities=37% Similarity=0.538 Sum_probs=69.9
Q ss_pred HHhhhHhhccccccc---------ccCCCCCCc------CcHHHHHHHHHHHhhCCCcchhhh---hccccccccccccC
Q psy4875 9 PLVHRYYETGSIRPR---------AIGGSKPRV------ATAEVVSKISHYKRECPSIFAWEI---RDRLLQEGVCSNDN 70 (100)
Q Consensus 9 kiL~r~~etGsi~Pg---------~iGGskP~~------~s~~~vskIl~~~~e~psif~~eI---R~rL~~~gvc~~~~ 70 (100)
++|++-|.+|++.|. +..|.+||. ++|+||+||+.+|+||+++.|+.| ++|++++.+..++.
T Consensus 6 NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~ 85 (125)
T PF00292_consen 6 NQLGGVFINGRPLPNELRQRIVELAKEGVRPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIE 85 (125)
T ss_dssp -TTS-EEETTSSS-HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCHHHHHH
T ss_pred cccCceeeCCccCcHHHHHHHHHHhhhcCCHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHH
Confidence 579999999999994 678999986 479999999999999999999998 79999999999999
Q ss_pred CCCCCCcchhHHHHHHHHhhcCCCCCCCCC
Q psy4875 71 IPSRECPSIFAWEIRDRLLQEGVCSNDNIP 100 (100)
Q Consensus 71 ~ps~ss~~rFaweir~~l~~~g~c~~~~~p 100 (100)
.++.++|++|+||||++|+++|+|+++++|
T Consensus 86 ~~k~enP~ifawEiR~~L~~~gvc~~~~~P 115 (125)
T PF00292_consen 86 QYKRENPTIFAWEIRDRLIADGVCDRSNVP 115 (125)
T ss_dssp HHHHH-TTS-HHHHHHHHHHTTSS-TTTS-
T ss_pred HHHhcCCCcchHHHHHHHHHcCCCCCCCCC
Confidence 999999999999999999999999999998
No 6
>KOG0849|consensus
Probab=99.80 E-value=1.5e-20 Score=148.10 Aligned_cols=77 Identities=55% Similarity=0.946 Sum_probs=74.7
Q ss_pred cccchHHHhhhHhhcccccccccCCCCCC-cCcHHHHHHHHHHHhhCCCcchhhhhccccccccccccCCCCCCCcch
Q psy4875 3 FLTLLCPLVHRYYETGSIRPRAIGGSKPR-VATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIPSRECPSI 79 (100)
Q Consensus 3 ~~gcvskiL~r~~etGsi~Pg~iGGskP~-~~s~~~vskIl~~~~e~psif~~eIR~rL~~~gvc~~~~~ps~ss~~r 79 (100)
-||||||||+||++||+|+|+.+||++|+ +.+++++.+|++|++++|++|+||||++|+.+++|+..++|+++++++
T Consensus 44 s~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~~~i~~~k~~~P~~~~~~ir~~l~~~~~~~~~t~Ps~ssi~r 121 (354)
T KOG0849|consen 44 SHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVEAKIEQYKRENPAMFAWEIRDQLLHEGLCTQATLPSVSSINR 121 (354)
T ss_pred hhHHHHhhhcccccccccccccccccccCCCCCchhHHHHHHHHhcCCcccchhhhhcccCcccccCCCCCChhhhhH
Confidence 48999999999999999999999999998 899999999999999999999999999999999999999999888887
No 7
>KOG3862|consensus
Probab=99.73 E-value=4.7e-19 Score=135.85 Aligned_cols=92 Identities=34% Similarity=0.492 Sum_probs=86.8
Q ss_pred HHhhhHhhccccccc---------ccCCCCCCcC------cHHHHHHHHHHHhhCCCcchhhh---hccccccccccccC
Q psy4875 9 PLVHRYYETGSIRPR---------AIGGSKPRVA------TAEVVSKISHYKRECPSIFAWEI---RDRLLQEGVCSNDN 70 (100)
Q Consensus 9 kiL~r~~etGsi~Pg---------~iGGskP~~~------s~~~vskIl~~~~e~psif~~eI---R~rL~~~gvc~~~~ 70 (100)
++|+..+-+|+++|- +.-|.+||.+ +|+||+|||-+|.|++||.++.| +++++++.|++++.
T Consensus 14 NQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisrQl~vShGcvSkil~r~yEtgS~~pg~iggsk~KvAtp~Vvk~i~ 93 (327)
T KOG3862|consen 14 NQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVKKIA 93 (327)
T ss_pred hhccceeecCccCchHHHHHHHHHHHcCCcchhHHHHHhhccCCchhHHHHHHHhcCcccCCCCCCccccccchHHHHHH
Confidence 689999999999984 5789999965 79999999999999999999998 79999999999999
Q ss_pred CCCCCCcchhHHHHHHHHhhcCCCCCCCCC
Q psy4875 71 IPSRECPSIFAWEIRDRLLQEGVCSNDNIP 100 (100)
Q Consensus 71 ~ps~ss~~rFaweir~~l~~~g~c~~~~~p 100 (100)
.++..++.||+||||++|+++++|+.+++|
T Consensus 94 ~~k~~n~~mfaweiR~~l~~~~ic~~d~vp 123 (327)
T KOG3862|consen 94 LYKRQNPTMFAWEIRDRLLAEPICDNDTVP 123 (327)
T ss_pred HHhhcCcchhhhhhhhhhhcccccCCCCCc
Confidence 999999999999999999999999999987
No 8
>cd00131 PAX Paired Box domain
Probab=99.57 E-value=2.2e-15 Score=103.95 Aligned_cols=78 Identities=62% Similarity=0.995 Sum_probs=74.0
Q ss_pred ccchHHHhhhHhhcccccccccCCCCCCcCcHHHHHHHHHHHhhCCCcchhhhhccccccccccccCCCCCCCcchhH
Q psy4875 4 LTLLCPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIPSRECPSIFA 81 (100)
Q Consensus 4 ~gcvskiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl~~~~e~psif~~eIR~rL~~~gvc~~~~~ps~ss~~rFa 81 (100)
.++|.+++.||.|||++.|+..||.+|+..++..+..|+.+..++|+++++||++.|.+.|+|...+.||++++++|+
T Consensus 47 ~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L 124 (128)
T cd00131 47 HGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRIL 124 (128)
T ss_pred HHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHH
Confidence 468999999999999999999999999999999999999999999999999999999999999999999999999985
No 9
>smart00351 PAX Paired Box domain.
Probab=99.54 E-value=8e-15 Score=100.54 Aligned_cols=78 Identities=60% Similarity=0.994 Sum_probs=74.5
Q ss_pred ccchHHHhhhHhhcccccccccCCCCCCcCcHHHHHHHHHHHhhCCCcchhhhhccccccccccccCCCCCCCcchhH
Q psy4875 4 LTLLCPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIPSRECPSIFA 81 (100)
Q Consensus 4 ~gcvskiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl~~~~e~psif~~eIR~rL~~~gvc~~~~~ps~ss~~rFa 81 (100)
..+|+|++.||.+||++.|++.||.+|+..++.++..|+.+..++|+++++||++.|.+.||+...++|+.+++++|+
T Consensus 47 ~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 47 HGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred HHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence 468999999999999999999999999999999999999999999999999999999999999999999999999864
No 10
>KOG0849|consensus
Probab=99.30 E-value=3.9e-13 Score=106.19 Aligned_cols=96 Identities=31% Similarity=0.360 Sum_probs=78.2
Q ss_pred cchHHHhhhHhhcccccc------cccCCCCCCcC------cHHHHHHHHHHHhhCCCcchhhh---hcc-ccccccccc
Q psy4875 5 TLLCPLVHRYYETGSIRP------RAIGGSKPRVA------TAEVVSKISHYKRECPSIFAWEI---RDR-LLQEGVCSN 68 (100)
Q Consensus 5 gcvskiL~r~~etGsi~P------g~iGGskP~~~------s~~~vskIl~~~~e~psif~~eI---R~r-L~~~gvc~~ 68 (100)
||.+.++..+.|.....+ ++.-|.+|+++ +++||++||++|+++++|.+..| +++ ++++.+..+
T Consensus 3 ~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~~~~~l~vs~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~~~ 82 (354)
T KOG0849|consen 3 VNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCVISRQLKVSHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVEAK 82 (354)
T ss_pred cccCCcccccCCCCCCchhhccccccccccCcccchhhhhhhhHHHHhhhcccccccccccccccccccCCCCCchhHHH
Confidence 344444444444444333 34566777764 69999999999999999999999 455 889999999
Q ss_pred cCCCCCCCcchhHHHHHHHHhhcCCCCCCCCC
Q psy4875 69 DNIPSRECPSIFAWEIRDRLLQEGVCSNDNIP 100 (100)
Q Consensus 69 ~~~ps~ss~~rFaweir~~l~~~g~c~~~~~p 100 (100)
+..++.++|.+|+||||++|+.+++|++.++|
T Consensus 83 i~~~k~~~P~~~~~~ir~~l~~~~~~~~~t~P 114 (354)
T KOG0849|consen 83 IEQYKRENPAMFAWEIRDQLLHEGLCTQATLP 114 (354)
T ss_pred HHHHHhcCCcccchhhhhcccCcccccCCCCC
Confidence 99999999999999999999999999999887
No 11
>PF13565 HTH_32: Homeodomain-like domain
Probab=97.34 E-value=0.00032 Score=43.18 Aligned_cols=68 Identities=28% Similarity=0.347 Sum_probs=51.4
Q ss_pred hHHHhhhHhhcc-----cccccccCCCCCCcCcHHHHHHHHHHHhhCCCcchhhhhcccccc-ccccccCCCCCCCcch
Q psy4875 7 LCPLVHRYYETG-----SIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQE-GVCSNDNIPSRECPSI 79 (100)
Q Consensus 7 vskiL~r~~etG-----si~Pg~iGGskP~~~s~~~vskIl~~~~e~psif~~eIR~rL~~~-gvc~~~~~ps~ss~~r 79 (100)
|++.+.||.++| ...++.-.| +|+. +++....|+....++|...+.+|.+.|.+. |+-. .+|.+++.+
T Consensus 2 v~rw~~ry~~~G~~gL~~~~~~~~~G-rp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~---~~S~~tv~R 75 (77)
T PF13565_consen 2 VYRWLKRYREEGLEGLKDRKRRPRPG-RPRK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV---RVSRSTVYR 75 (77)
T ss_pred HHHHHHHHHhhCchhhhcccccCCCC-CCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC---CccHhHHHH
Confidence 688999999999 755566666 4444 788889999999999999999999988876 4321 235555554
No 12
>cd00131 PAX Paired Box domain
Probab=97.24 E-value=0.00018 Score=49.53 Aligned_cols=69 Identities=43% Similarity=0.622 Sum_probs=50.4
Q ss_pred cCcHHHHHHHHHHHhhCCCcchhhh---hccccccccccccCCCCCCCcchhHHHHHHHHhhcCCCCCCCCC
Q psy4875 32 VATAEVVSKISHYKRECPSIFAWEI---RDRLLQEGVCSNDNIPSRECPSIFAWEIRDRLLQEGVCSNDNIP 100 (100)
Q Consensus 32 ~~s~~~vskIl~~~~e~psif~~eI---R~rL~~~gvc~~~~~ps~ss~~rFaweir~~l~~~g~c~~~~~p 100 (100)
.++...|.+++++|++++++.+.-. +++..++.....+...-.+++..++|||++.|.++|+|.+++.|
T Consensus 44 ~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~ 115 (128)
T cd00131 44 RVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVP 115 (128)
T ss_pred CcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCC
Confidence 3578999999999999999887654 35544433222222224588999999999999999999766554
No 13
>smart00351 PAX Paired Box domain.
Probab=97.18 E-value=0.00026 Score=48.37 Aligned_cols=69 Identities=42% Similarity=0.580 Sum_probs=52.4
Q ss_pred cCcHHHHHHHHHHHhhCCCcchhhh---hccccccccccccCCCCCCCcchhHHHHHHHHhhcCCCCCCCCC
Q psy4875 32 VATAEVVSKISHYKRECPSIFAWEI---RDRLLQEGVCSNDNIPSRECPSIFAWEIRDRLLQEGVCSNDNIP 100 (100)
Q Consensus 32 ~~s~~~vskIl~~~~e~psif~~eI---R~rL~~~gvc~~~~~ps~ss~~rFaweir~~l~~~g~c~~~~~p 100 (100)
.+++..|.+++.+|+++++..+.-. +++.+++.....+.....+++..++|||++.|.++|+|...++|
T Consensus 44 gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~P 115 (125)
T smart00351 44 CVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVP 115 (125)
T ss_pred CcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCC
Confidence 3578999999999999998877422 34444443333333335688999999999999999999998887
No 14
>PF13551 HTH_29: Winged helix-turn helix
Probab=96.22 E-value=0.0068 Score=38.95 Aligned_cols=70 Identities=21% Similarity=0.262 Sum_probs=48.0
Q ss_pred hHHHhhhHhhcc--cccc-cccCCCCCCcCcHHHHHHHHHHHhhCC-----CcchhhhhccccccccccccCCCCCCCcc
Q psy4875 7 LCPLVHRYYETG--SIRP-RAIGGSKPRVATAEVVSKISHYKRECP-----SIFAWEIRDRLLQEGVCSNDNIPSRECPS 78 (100)
Q Consensus 7 vskiL~r~~etG--si~P-g~iGGskP~~~s~~~vskIl~~~~e~p-----sif~~eIR~rL~~~gvc~~~~~ps~ss~~ 78 (100)
|.+.+.+|.++| .+.+ +.-+|..+...++++...|.++..++| ..++.+|.+.|++...-. .+|.+++.
T Consensus 29 v~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~---~~s~~ti~ 105 (112)
T PF13551_consen 29 VYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGI---DVSPSTIR 105 (112)
T ss_pred HHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCc---cCCHHHHH
Confidence 688999999999 7777 455554333489999999999999988 355566777764433211 12555555
Q ss_pred h
Q psy4875 79 I 79 (100)
Q Consensus 79 r 79 (100)
+
T Consensus 106 r 106 (112)
T PF13551_consen 106 R 106 (112)
T ss_pred H
Confidence 4
No 15
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=95.32 E-value=0.017 Score=40.59 Aligned_cols=57 Identities=28% Similarity=0.253 Sum_probs=44.1
Q ss_pred HHHhhhHhhcccccccccCCCCCCcCcHHHHHHHHHHHhhCCCcchhhhhcccc-cccc
Q psy4875 8 CPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLL-QEGV 65 (100)
Q Consensus 8 skiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl~~~~e~psif~~eIR~rL~-~~gv 65 (100)
=+-++||.+||+..|...||.+|+..++..+.-++..-++.. .+..+++..|. +.||
T Consensus 39 y~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~-wTl~~~~~~l~~e~gv 96 (138)
T COG3415 39 YRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD-WTLKELVEELGLEFGV 96 (138)
T ss_pred HHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc-chHHHHHHHHhhhcCe
Confidence 356899999999999999999999999998888888766644 55555566644 4565
No 16
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=87.56 E-value=0.45 Score=31.96 Aligned_cols=59 Identities=22% Similarity=0.278 Sum_probs=41.8
Q ss_pred hHHHhhhHhhcccccccccCCCCCCcCcHHHHHHHHHHHhhCCCcchhhhhccccccccccccCCCCCCCcchhHH
Q psy4875 7 LCPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIPSRECPSIFAW 82 (100)
Q Consensus 7 vskiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl~~~~e~psif~~eIR~rL~~~gvc~~~~~ps~ss~~rFaw 82 (100)
|-+-+. ..+||+..|++-|+. +. ..+.+..+-.++|+++..||-.+| || +.+++++|..
T Consensus 35 v~~W~k-~~~~G~~~~k~r~~~--Ki----d~~~L~~~v~~~pd~tl~Ela~~l---~V-------s~~ti~~~Lk 93 (119)
T PF01710_consen 35 VYRWLK-RKETGDLEPKPRGRK--KI----DRDELKALVEENPDATLRELAERL---GV-------SPSTIWRALK 93 (119)
T ss_pred HHHHHH-hcccccccccccccc--cc----cHHHHHHHHHHCCCcCHHHHHHHc---CC-------CHHHHHHHHH
Confidence 344566 678999999987765 22 245678888999999999997765 33 5566666543
No 17
>PF13072 DUF3936: Protein of unknown function (DUF3936)
Probab=75.51 E-value=2.1 Score=23.96 Aligned_cols=10 Identities=60% Similarity=1.162 Sum_probs=8.1
Q ss_pred HHHHHHHHhh
Q psy4875 81 AWEIRDRLLQ 90 (100)
Q Consensus 81 aweir~~l~~ 90 (100)
|||||..|-+
T Consensus 16 AWeIr~~Lke 25 (38)
T PF13072_consen 16 AWEIRAKLKE 25 (38)
T ss_pred HHHHHHHHHH
Confidence 8999888865
No 18
>KOG0086|consensus
Probab=51.59 E-value=6.9 Score=28.85 Aligned_cols=23 Identities=26% Similarity=0.652 Sum_probs=19.6
Q ss_pred cccchHHHhhhHhhcccccccccC
Q psy4875 3 FLTLLCPLVHRYYETGSIRPRAIG 26 (100)
Q Consensus 3 ~~gcvskiL~r~~etGsi~Pg~iG 26 (100)
|+-|+++||++. |+|.+-|..+|
T Consensus 163 Fl~c~~tIl~kI-E~GElDPer~g 185 (214)
T KOG0086|consen 163 FLKCARTILNKI-ESGELDPERMG 185 (214)
T ss_pred HHHHHHHHHHHH-hhcCCCHHHcc
Confidence 788999999985 89999997654
No 19
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=46.06 E-value=15 Score=19.59 Aligned_cols=14 Identities=14% Similarity=0.361 Sum_probs=11.9
Q ss_pred hHHHhhhHhhcccc
Q psy4875 7 LCPLVHRYYETGSI 20 (100)
Q Consensus 7 vskiL~r~~etGsi 20 (100)
||.+|.++.+.|-|
T Consensus 19 VSR~l~~l~~~glI 32 (32)
T PF00325_consen 19 VSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHcCCC
Confidence 89999999998854
No 20
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.09 E-value=66 Score=20.14 Aligned_cols=62 Identities=13% Similarity=0.051 Sum_probs=40.0
Q ss_pred cccchHHHhhhHhhcccccccccCCCCCCcCcHHHHHHHHHHH-hhCCCcchhhhhccccccc
Q psy4875 3 FLTLLCPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYK-RECPSIFAWEIRDRLLQEG 64 (100)
Q Consensus 3 ~~gcvskiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl~~~-~e~psif~~eIR~rL~~~g 64 (100)
..|.-..-|..|.+.|-+.|....+.--+.-++..+..+...+ -..-++...+|+.-+....
T Consensus 10 ~~gvs~~tLR~ye~~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~~~ 72 (88)
T cd01105 10 LTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRR 72 (88)
T ss_pred HHCcCHHHHHHHHHCCCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcc
Confidence 3566777888899999998865432223456677666555432 1225688889987765443
No 21
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=36.90 E-value=58 Score=18.78 Aligned_cols=56 Identities=20% Similarity=0.202 Sum_probs=38.2
Q ss_pred cccchHHHhhhHhhcccccccccCCCCCCcCcHHHHHHHHHH--HhhCCCcchhhhhccc
Q psy4875 3 FLTLLCPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHY--KRECPSIFAWEIRDRL 60 (100)
Q Consensus 3 ~~gcvskiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl~~--~~e~psif~~eIR~rL 60 (100)
..|.-...|..|.+.|-+.|....+ ..+.-++..+..+... ..+ -++...+|+.-|
T Consensus 9 ~~gvs~~tlr~y~~~gll~~~~~~~-g~r~y~~~dv~~l~~i~~l~~-~G~sl~~I~~~l 66 (69)
T PF13411_consen 9 LLGVSPSTLRYYEREGLLPPPRDEN-GYRYYSEEDVERLREIKELRK-QGMSLEEIKKLL 66 (69)
T ss_dssp HTTTTHHHHHHHHHTTSSTTBESTT-SSEEE-HHHHHHHHHHHHHHH-TTTHHHHHHHHH
T ss_pred HHCcCHHHHHHHHHhcCcccccccC-ceeeccHHHHHHHHHHHHHHH-CcCCHHHHHHHH
Confidence 3567778899999999999988333 3377778777766653 222 467777777654
No 22
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=35.52 E-value=89 Score=20.20 Aligned_cols=40 Identities=23% Similarity=0.295 Sum_probs=26.3
Q ss_pred chHHHhhhHhhcccccccccCCCCCC----cCcHHHHHHHHHHHh
Q psy4875 6 LLCPLVHRYYETGSIRPRAIGGSKPR----VATAEVVSKISHYKR 46 (100)
Q Consensus 6 cvskiL~r~~etGsi~Pg~iGGskP~----~~s~~~vskIl~~~~ 46 (100)
|+.|-+.||.+.|.-- ..=--|+|. .+.++.+..|+...+
T Consensus 41 Ta~kW~~Ryra~G~~G-L~DRSSRP~~sP~~t~~~~~~~I~~lRr 84 (85)
T PF13011_consen 41 TAYKWLARYRAEGEAG-LQDRSSRPHRSPRRTPPEVERRIIELRR 84 (85)
T ss_pred HHHHHHHHHHHcCccc-ccccCCCCCCCCccCCHHHHHHHHHHhc
Confidence 6789999999988421 111234553 456788888887654
No 23
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=33.83 E-value=66 Score=16.60 Aligned_cols=36 Identities=17% Similarity=0.249 Sum_probs=23.2
Q ss_pred cccchHHHhhhHhhcccccccccCCCCCCcCcHHHHH
Q psy4875 3 FLTLLCPLVHRYYETGSIRPRAIGGSKPRVATAEVVS 39 (100)
Q Consensus 3 ~~gcvskiL~r~~etGsi~Pg~iGGskP~~~s~~~vs 39 (100)
.+|+-..-+.++.++|.+.+...+| +....+...+.
T Consensus 9 ~lgvs~~tl~~~~~~g~~~~~~~~~-~~~~~~~~ei~ 44 (49)
T cd04762 9 LLGVSPSTLRRWVKEGKLKAIRTPG-GHRRFPEEDLE 44 (49)
T ss_pred HHCcCHHHHHHHHHcCCCCceeCCC-CceecCHHHHH
Confidence 4677778889999999987655444 33344444333
No 24
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.67 E-value=61 Score=17.26 Aligned_cols=39 Identities=13% Similarity=0.217 Sum_probs=26.5
Q ss_pred cccchHHHhhhHhhcccccccccCCCCCCcCcHHHHHHHH
Q psy4875 3 FLTLLCPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKIS 42 (100)
Q Consensus 3 ~~gcvskiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl 42 (100)
.+|.-..-+..|.+.|-+.|...+| ..+..++..+..+.
T Consensus 9 ~~gv~~~tlr~~~~~g~l~~~~~~~-~~~~y~~~~v~~l~ 47 (49)
T cd04761 9 LTGVSPSTLRYYERIGLLSPARTEG-GYRLYSDADLERLR 47 (49)
T ss_pred HHCcCHHHHHHHHHCCCCCCCcCCC-CCEEeCHHHHHHhh
Confidence 3566667788999999988755444 34566777666553
No 25
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=33.24 E-value=18 Score=25.28 Aligned_cols=39 Identities=21% Similarity=0.033 Sum_probs=27.7
Q ss_pred HHHHHHhhCCCcchhhhhccccccccccccCCCCCCCcchhHHH
Q psy4875 40 KISHYKRECPSIFAWEIRDRLLQEGVCSNDNIPSRECPSIFAWE 83 (100)
Q Consensus 40 kIl~~~~e~psif~~eIR~rL~~~gvc~~~~~ps~ss~~rFawe 83 (100)
.|....++++-....||..+|.+.|+.. +.+.++|...|
T Consensus 6 ~i~~Li~~~~i~tqeeL~~~L~~~G~~v-----sqaTIsRdL~e 44 (146)
T TIGR01529 6 RIKEIITEEKISTQEELVALLKAEGIEV-----TQATVSRDLRE 44 (146)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHhCCCc-----CHHHHHHHHHH
Confidence 4555666777778888888888888765 66777775554
No 26
>PF13089 PP_kinase_N: Polyphosphate kinase N-terminal domain; PDB: 2O8R_A 1XDP_A 1XDO_B.
Probab=31.61 E-value=8.5 Score=25.60 Aligned_cols=65 Identities=20% Similarity=0.381 Sum_probs=38.1
Q ss_pred CccccchHHHhhhHhh-----------cccccccccCCCCCCcCcHHHHHHHHHHHhhCCCcchhhhhccccccccc
Q psy4875 1 LKFLTLLCPLVHRYYE-----------TGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVC 66 (100)
Q Consensus 1 ~~~~gcvskiL~r~~e-----------tGsi~Pg~iGGskP~~~s~~~vskIl~~~~e~psif~~eIR~rL~~~gvc 66 (100)
|||++-+|.=|--|+. .|.-.+. ..|..|...-..+-..+....++.-.++-.+|.+.|++.||.
T Consensus 31 l~Fl~I~ssNlDEFFmVRVA~Lk~~~~~g~~~~~-~~g~tP~eqL~~I~~~v~~l~~~q~~~~~~~Llp~L~~~GI~ 106 (109)
T PF13089_consen 31 LKFLAIFSSNLDEFFMVRVAGLKRQIEAGVKKRD-PDGLTPQEQLDAIRKRVHELVEEQYEIYNEELLPELAEEGIH 106 (109)
T ss_dssp HHHHHHHHHHHHHHHHCCCHHHHHHCCHHHCC----S---HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHCTTEE
T ss_pred HHHHhhhhcchhHHHHHHHHHHHHHHHhccCCCC-cCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCE
Confidence 3566767666665553 2222222 334444444455666666667777778888899999999985
No 27
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=26.06 E-value=1.2e+02 Score=17.43 Aligned_cols=45 Identities=24% Similarity=0.369 Sum_probs=24.2
Q ss_pred HHHHHHHhhCC---CcchhhhhccccccccccccCCCCCCCcchhHHHHHHHHhhcCCC
Q psy4875 39 SKISHYKRECP---SIFAWEIRDRLLQEGVCSNDNIPSRECPSIFAWEIRDRLLQEGVC 94 (100)
Q Consensus 39 skIl~~~~e~p---sif~~eIR~rL~~~gvc~~~~~ps~ss~~rFaweir~~l~~~g~c 94 (100)
+.+.+|-+++| ++--.|+|.|+..+++-. .++-.+=+.|+++|..
T Consensus 3 ~~L~~yH~~~Plr~G~~keeLrsrl~~~~l~~-----------k~~~~ll~~l~~~g~l 50 (59)
T PF09106_consen 3 EILAEYHRENPLRPGMPKEELRSRLFKPRLPP-----------KLFNALLEALVAEGRL 50 (59)
T ss_dssp HHHHHHHHH-TTSS-EEHHHHHHHCST-TS-H-----------CCHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHCcCccCcCHHHHHHHHhhccCCH-----------HHHHHHHHHHHHCCCe
Confidence 44555666665 566667777765544432 3444566667766654
No 28
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.89 E-value=35 Score=18.61 Aligned_cols=13 Identities=31% Similarity=0.588 Sum_probs=5.5
Q ss_pred chHHHhhhHhhcc
Q psy4875 6 LLCPLVHRYYETG 18 (100)
Q Consensus 6 cvskiL~r~~etG 18 (100)
-|++++.+|.++|
T Consensus 33 Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 33 TVYRWIKRYREEG 45 (50)
T ss_dssp HHHHHHT------
T ss_pred HHHHHHHHccccc
Confidence 3788889998888
No 29
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=21.70 E-value=1.7e+02 Score=16.63 Aligned_cols=54 Identities=20% Similarity=0.271 Sum_probs=31.9
Q ss_pred cccchHHHhhhHhhccccccc--ccCCCCCCcCcHHHHHHHHHHHhh-CCCcchhhhhc
Q psy4875 3 FLTLLCPLVHRYYETGSIRPR--AIGGSKPRVATAEVVSKISHYKRE-CPSIFAWEIRD 58 (100)
Q Consensus 3 ~~gcvskiL~r~~etGsi~Pg--~iGGskP~~~s~~~vskIl~~~~e-~psif~~eIR~ 58 (100)
..|+-..-|..|.+.|-+.|. .-+|. +.-+...+..+.....- .-++...+|+.
T Consensus 9 ~~gvs~~tlr~~~~~gli~~~~~~~~g~--r~y~~~dl~~l~~i~~lr~~g~~~~~i~~ 65 (70)
T smart00422 9 LAGVSVRTLRYYERIGLLPPPIRTEGGY--RLYSDEDLERLRFIKRLKELGFSLEEIKE 65 (70)
T ss_pred HHCcCHHHHHHHHHCCCCCCCccCCCCC--EecCHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 356777888999999999986 33443 34555555554443211 13455555543
No 30
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=21.23 E-value=61 Score=19.86 Aligned_cols=23 Identities=22% Similarity=0.368 Sum_probs=19.6
Q ss_pred hHHHhhhHhhccccc--ccccCCCC
Q psy4875 7 LCPLVHRYYETGSIR--PRAIGGSK 29 (100)
Q Consensus 7 vskiL~r~~etGsi~--Pg~iGGsk 29 (100)
+.||+....+.|-+. +|.-||..
T Consensus 42 l~kil~~L~~~Gli~s~~G~~GGy~ 66 (83)
T PF02082_consen 42 LRKILQKLKKAGLIESSRGRGGGYR 66 (83)
T ss_dssp HHHHHHHHHHTTSEEEETSTTSEEE
T ss_pred HHHHHHHHhhCCeeEecCCCCCcee
Confidence 689999999999988 67888864
No 31
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.47 E-value=2.4e+02 Score=17.81 Aligned_cols=57 Identities=21% Similarity=0.201 Sum_probs=34.5
Q ss_pred ccchHHHhhhHhhcccccccccCCCCCCcCcHHHHHHHHHH--HhhCCCcchhhhhcccc
Q psy4875 4 LTLLCPLVHRYYETGSIRPRAIGGSKPRVATAEVVSKISHY--KRECPSIFAWEIRDRLL 61 (100)
Q Consensus 4 ~gcvskiL~r~~etGsi~Pg~iGGskP~~~s~~~vskIl~~--~~e~psif~~eIR~rL~ 61 (100)
.|.-..-|.-|.+.|-+.|...+...-+.-++..+..+... .++ -++...||+.-+.
T Consensus 10 ~gvs~~tlR~ye~~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~-~G~~l~eI~~~l~ 68 (97)
T cd04782 10 CGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKE-LGISLKEIKDYLD 68 (97)
T ss_pred HCcCHHHHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 45555667778889999886543233345566555544332 233 3588899987543
Done!