Query psy13847
Match_columns 91
No_of_seqs 97 out of 99
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 21:58:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13847.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13847hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3701|consensus 100.0 2.3E-32 5E-37 223.3 6.3 86 1-86 1-89 (411)
2 cd00049 MH1 MH1 is a small DNA 100.0 1.9E-29 4.2E-34 178.0 6.8 76 10-86 1-78 (121)
3 smart00523 DWA Domain A in dwa 99.9 1.2E-25 2.6E-30 156.4 6.2 63 23-86 1-64 (109)
4 PF03165 MH1: MH1 domain; Int 99.9 1.9E-24 4.1E-29 148.5 2.2 58 28-85 1-60 (103)
5 PF07624 PSD2: Protein of unkn 84.3 2.8 6.2E-05 26.7 4.5 49 7-55 23-72 (76)
6 cd00860 ThrRS_anticodon ThrRS 73.8 1.6 3.5E-05 26.6 0.8 25 64-88 36-60 (91)
7 KOG2884|consensus 66.0 19 0.00042 28.9 5.5 58 10-67 92-176 (259)
8 cd00861 ProRS_anticodon_short 66.0 6 0.00013 24.4 2.2 25 65-89 40-64 (94)
9 PF09260 DUF1966: Domain of un 65.5 4.1 8.8E-05 27.3 1.5 28 60-87 55-82 (91)
10 COG4054 McrB Methyl coenzyme M 53.6 16 0.00035 31.0 3.3 40 30-69 36-78 (447)
11 PF02783 MCR_beta_N: Methyl-co 47.3 22 0.00047 27.4 2.9 40 30-69 28-70 (182)
12 COG4001 Predicted metal-bindin 46.1 29 0.00062 24.4 3.1 32 12-43 36-68 (102)
13 TIGR02930 vnfG_nitrog V-contai 40.2 17 0.00036 25.9 1.3 31 43-76 78-108 (109)
14 COG3682 Predicted transcriptio 38.2 29 0.00064 24.9 2.3 23 23-45 32-54 (123)
15 TIGR03257 met_CoM_red_bet meth 37.6 41 0.00089 28.8 3.4 40 30-69 29-71 (433)
16 TIGR03031 cas_csx12 CRISPR-ass 36.6 67 0.0015 29.4 4.7 52 7-67 277-329 (802)
17 KOG1466|consensus 36.2 74 0.0016 26.3 4.5 44 10-53 12-57 (313)
18 PF11269 DUF3069: Protein of u 35.3 25 0.00055 25.5 1.6 16 27-42 91-106 (121)
19 smart00542 FYRC "FY-rich" doma 34.8 22 0.00047 23.2 1.1 17 4-20 52-68 (86)
20 TIGR02929 anfG_nitrog Fe-only 32.9 26 0.00057 25.0 1.3 31 43-76 78-108 (109)
21 smart00546 CUE Domain that may 32.3 93 0.002 17.3 3.3 29 3-36 11-40 (43)
22 PF05965 FYRC: F/Y rich C-term 32.1 17 0.00036 23.2 0.2 15 4-18 56-70 (86)
23 cd01452 VWA_26S_proteasome_sub 31.2 97 0.0021 23.0 4.2 38 29-66 122-174 (187)
24 PF07499 RuvA_C: RuvA, C-termi 29.3 83 0.0018 18.1 2.9 22 28-51 20-41 (47)
25 PRK13749 transcriptional regul 29.1 1.5E+02 0.0033 20.7 4.7 49 5-54 59-108 (121)
26 cd01269 PLX Pollux (PLX) Phosp 28.7 12 0.00026 27.3 -1.0 16 69-84 9-24 (129)
27 cd00858 GlyRS_anticodon GlyRS 28.7 35 0.00076 22.7 1.3 23 66-88 64-86 (121)
28 PF03139 AnfG_VnfG: Vanadium/a 28.4 32 0.0007 24.6 1.1 61 11-76 37-111 (112)
29 PRK05302 30S ribosomal protein 27.9 2.1E+02 0.0046 20.6 5.4 52 7-58 18-72 (156)
30 PF11291 DUF3091: Protein of u 26.7 1.5E+02 0.0032 20.6 4.1 39 26-68 14-52 (100)
31 PF06838 Met_gamma_lyase: Meth 25.9 45 0.00098 28.4 1.8 22 44-68 143-164 (403)
32 smart00806 AIP3 Actin interact 25.6 48 0.001 28.3 1.9 21 32-52 399-421 (426)
33 cd00859 HisRS_anticodon HisRS 25.5 35 0.00076 19.9 0.8 22 66-87 38-59 (91)
34 PF02845 CUE: CUE domain; Int 25.3 1.2E+02 0.0027 16.8 3.0 29 3-36 10-39 (42)
35 PF11267 DUF3067: Protein of u 25.2 77 0.0017 22.1 2.5 42 31-72 51-95 (99)
36 PF11815 DUF3336: Domain of un 24.9 1.1E+02 0.0025 21.6 3.5 44 12-55 36-85 (145)
37 cd01816 Raf_RBD Ubiquitin doma 24.1 73 0.0016 21.2 2.2 25 46-70 24-48 (74)
38 PRK14142 heat shock protein Gr 23.9 94 0.002 24.3 3.1 32 23-56 73-104 (223)
39 PF00607 Gag_p24: gag gene pro 23.7 1.8E+02 0.0038 21.8 4.4 31 28-58 169-199 (206)
40 COG1753 Predicted antotoxin, c 22.8 2.4E+02 0.0052 18.9 4.4 43 7-54 8-50 (74)
41 cd00738 HGTP_anticodon HGTP an 22.8 49 0.0011 19.9 1.1 23 66-88 41-63 (94)
42 PF05205 COMPASS-Shg1: COMPASS 22.5 71 0.0015 21.6 1.9 24 33-56 1-24 (106)
43 TIGR03237 dnd_assoc_2 dnd syst 21.7 34 0.00074 32.9 0.3 16 76-91 574-589 (1256)
44 PF14383 VARLMGL: DUF761-assoc 21.2 57 0.0012 18.9 1.1 13 7-19 13-25 (34)
45 PF03915 AIP3: Actin interacti 20.5 34 0.00073 28.9 0.0 20 32-51 397-418 (424)
46 PF00745 GlutR_dimer: Glutamyl 20.3 50 0.0011 20.8 0.8 19 21-39 52-70 (101)
47 PF03965 Penicillinase_R: Peni 20.1 84 0.0018 20.8 1.9 23 23-45 29-51 (115)
No 1
>KOG3701|consensus
Probab=99.97 E-value=2.3e-32 Score=223.27 Aligned_cols=86 Identities=44% Similarity=0.611 Sum_probs=82.7
Q ss_pred CCCCCCCCHHHHHHHhhhcc-CCCcchhHHHHHHHHHHHhhhc-CcHHHHHHHHhcCCC-CCcceeecccccccccccCc
Q psy13847 1 MTSLFPFTPPIVKKLLGWKK-GDGEDKYSEKAVKSLVKKLKKS-NGLDELEKAITTQDP-NTKCVTIPRLQFEDLQQSGV 77 (91)
Q Consensus 1 ~~~~~~~~~~~Vk~LL~wkq-g~eeek~aeKAIkSLVKKLKk~-~~le~Le~Altt~~~-~tkCVTIpRslDGRLQVs~r 77 (91)
++++++|+.|+|+.||+|+| |++||+|++||++|||||||++ +.||+|++||++++. +++||||||+|||||||+||
T Consensus 1 ~~~~~~~~~p~v~~~~~~r~~~~~~e~~~~ka~~slvkklk~~~~~le~l~~av~s~g~~~~~CvtiprslD~Rlq~~~r 80 (411)
T KOG3701|consen 1 TSSLLPFTGPAVKDLLGPRQLGGEDEKFAEKAVESLVKKLKDKKGELENLIKAVESPGTKPTGCVTIPRSLDGRLQVAHR 80 (411)
T ss_pred CCcccCCCCcchhhccCccccCchhHHHHHHHHHHHHHHhhcccchHHHHHHHhcCCCCCCCceEECCCCCCccccccCC
Confidence 57899999999999999999 9999999999999999999998 899999999999995 69999999999999999999
Q ss_pred CCCceEEee
Q psy13847 78 CSSPVALSW 86 (91)
Q Consensus 78 KglPhviy~ 86 (91)
||||||||-
T Consensus 81 kg~Phviy~ 89 (411)
T KOG3701|consen 81 KGFPHVIYC 89 (411)
T ss_pred CCCCceEEE
Confidence 999999994
No 2
>cd00049 MH1 MH1 is a small DNA binding domain, binding in an unusal way involving a beta hairpin structure binding to the major groove. MH1 is present in Smad proteins, an important family of proteins involved in TGF-beta signalling and frequent targets of tumorigenic mutations. Also known as Domain A in dwarfin family proteins.
Probab=99.96 E-value=1.9e-29 Score=178.01 Aligned_cols=76 Identities=46% Similarity=0.632 Sum_probs=71.9
Q ss_pred HHHHHHhhhcc-CCCcchhHHHHHHHHHHHhhhcCcHHHHHHHHhcCC-CCCcceeecccccccccccCcCCCceEEee
Q psy13847 10 PIVKKLLGWKK-GDGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQD-PNTKCVTIPRLQFEDLQQSGVCSSPVALSW 86 (91)
Q Consensus 10 ~~Vk~LL~wkq-g~eeek~aeKAIkSLVKKLKk~~~le~Le~Altt~~-~~tkCVTIpRslDGRLQVs~rKglPhviy~ 86 (91)
++|++||+|+| |+++|+|++||++|||||||++.++|+|++||+++| .+|+||||||+ |||||++||+++|||+|-
T Consensus 1 ~~~~~ll~~~~~~~~~e~~~~k~~~sLlKkLKk~~~le~L~~AV~s~g~~~t~CV~i~r~-D~rl~~~~r~~~phv~~c 78 (121)
T cd00049 1 ALVKRLLGEKKIGGEEEKWKKKAAESLLKKLKKKIQLEELEDAVESRGGPPTRCVLIPRS-DGRLQVSHRKGLPHVIYC 78 (121)
T ss_pred ChhHHhhcccccCcchHHHHHHHHHHHHHHHhcccCHHHHHHHHHcCCCCCCCeEEeccc-cccccccccCCCcceEEE
Confidence 47999999999 899999999999999999999779999999999998 56999999999 999999999999999993
No 3
>smart00523 DWA Domain A in dwarfin family proteins.
Probab=99.92 E-value=1.2e-25 Score=156.44 Aligned_cols=63 Identities=41% Similarity=0.543 Sum_probs=60.0
Q ss_pred CcchhHHHHHHHHHHHhhhcCcHHHHHHHHhcCC-CCCcceeecccccccccccCcCCCceEEee
Q psy13847 23 GEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQD-PNTKCVTIPRLQFEDLQQSGVCSSPVALSW 86 (91)
Q Consensus 23 eeek~aeKAIkSLVKKLKk~~~le~Le~Altt~~-~~tkCVTIpRslDGRLQVs~rKglPhviy~ 86 (91)
.+|+|++||++|||||||++ ++|+|++||+++| .+|+||||||++|||||||+|+++|||||-
T Consensus 1 ~~ek~~~k~~~sL~KklK~k-~le~L~~AV~s~g~~~t~CV~i~~~~dgrl~~~~~~~~phvi~c 64 (109)
T smart00523 1 VEEKWAKKATESLLKKLKKK-QLEELLQAVESKGGPPTRCVLIPRSLDGRLQVAHRKGLPHVLYC 64 (109)
T ss_pred CcHHHHHHHHHHHHHHHHHH-HHHHHHHHHHcCCCCCCCeEEeCcccCcccccccCCCCCcEEEE
Confidence 47899999999999999997 9999999999999 689999999999999999999999999983
No 4
>PF03165 MH1: MH1 domain; InterPro: IPR003619 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3QSV_A 1MHD_A 1OZJ_A 3KMP_B.
Probab=99.89 E-value=1.9e-24 Score=148.48 Aligned_cols=58 Identities=53% Similarity=0.662 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHhhhc-CcHHHHHHHHhcCC-CCCcceeecccccccccccCcCCCceEEe
Q psy13847 28 SEKAVKSLVKKLKKS-NGLDELEKAITTQD-PNTKCVTIPRLQFEDLQQSGVCSSPVALS 85 (91)
Q Consensus 28 aeKAIkSLVKKLKk~-~~le~Le~Altt~~-~~tkCVTIpRslDGRLQVs~rKglPhviy 85 (91)
.+|||+|||||||++ +++|+|++||+++| .+|+||||||++||||||++++++|||||
T Consensus 1 ~~k~~~sLlkkLK~~~~~le~L~~Av~s~g~~~t~CV~i~r~~dgrl~v~~~k~~phvl~ 60 (103)
T PF03165_consen 1 CEKAIKSLLKKLKKKIGQLEELLKAVESRGDPPTKCVTIPRSLDGRLQVSGRKGLPHVLY 60 (103)
T ss_dssp HHHHHHHHHHHHTTTCTHHHHHHHHHHCTTTSTS---EEE--TTS-EEETTEEE-HHHHH
T ss_pred ChHHHHHHHHHHccccchHHHHHHHHhcCCCCCCCcEEecCccCccccccccccCceEEE
Confidence 489999999999998 89999999999886 89999999999999999999999999998
No 5
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=84.32 E-value=2.8 Score=26.69 Aligned_cols=49 Identities=24% Similarity=0.297 Sum_probs=41.8
Q ss_pred CCHHHHHHHhhhccCCCcchhHHHHHHHHHHHhhhc-CcHHHHHHHHhcC
Q psy13847 7 FTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKS-NGLDELEKAITTQ 55 (91)
Q Consensus 7 ~~~~~Vk~LL~wkqg~eeek~aeKAIkSLVKKLKk~-~~le~Le~Altt~ 55 (91)
|....+++||.|--|.+.+---+.+|+.++.+++.. ..+.+|..+|.+.
T Consensus 23 ~~~~~~~kl~~YAlGR~~~~~D~~~i~~i~~~~~~~~y~~~~Li~~iv~S 72 (76)
T PF07624_consen 23 FARCFAEKLLTYALGRPLEFSDRCEIDRIVEAFKANGYRLRDLILAIVTS 72 (76)
T ss_pred HHHHHHHHHHHHHcCCCCCcchHHHHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 455678999999999888777888999999999998 6799999988664
No 6
>cd00860 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=73.83 E-value=1.6 Score=26.59 Aligned_cols=25 Identities=12% Similarity=0.084 Sum_probs=21.9
Q ss_pred ecccccccccccCcCCCceEEeecc
Q psy13847 64 IPRLQFEDLQQSGVCSSPVALSWGA 88 (91)
Q Consensus 64 IpRslDGRLQVs~rKglPhviy~~~ 88 (91)
-.++++-+++-|.++|+|++|+-|.
T Consensus 36 ~~~~~~~~~~~a~~~g~~~~iiig~ 60 (91)
T cd00860 36 RNEKLGKKIREAQLQKIPYILVVGD 60 (91)
T ss_pred CCCCHHHHHHHHHHcCCCEEEEECc
Confidence 3577889999999999999999885
No 7
>KOG2884|consensus
Probab=66.01 E-value=19 Score=28.92 Aligned_cols=58 Identities=26% Similarity=0.310 Sum_probs=39.3
Q ss_pred HHHHHHhhhccCC-----------CcchhHHHHHHHHHHHhhhc---------Cc-------HHHHHHHHhcCCCCCcce
Q psy13847 10 PIVKKLLGWKKGD-----------GEDKYSEKAVKSLVKKLKKS---------NG-------LDELEKAITTQDPNTKCV 62 (91)
Q Consensus 10 ~~Vk~LL~wkqg~-----------eeek~aeKAIkSLVKKLKk~---------~~-------le~Le~Altt~~~~tkCV 62 (91)
.|.+--|.++|+. .+-+-.||.+--+.|+|||. |+ |.+++.|+-..+..+.||
T Consensus 92 ~iA~lalkhRqnk~~~~riVvFvGSpi~e~ekeLv~~akrlkk~~Vaidii~FGE~~~~~e~l~~fida~N~~~~gshlv 171 (259)
T KOG2884|consen 92 QIAQLALKHRQNKNQKQRIVVFVGSPIEESEKELVKLAKRLKKNKVAIDIINFGEAENNTEKLFEFIDALNGKGDGSHLV 171 (259)
T ss_pred HHHHHHHHhhcCCCcceEEEEEecCcchhhHHHHHHHHHHHHhcCeeEEEEEeccccccHHHHHHHHHHhcCCCCCceEE
Confidence 4555556667652 33444677888889999983 22 455666666666788999
Q ss_pred eeccc
Q psy13847 63 TIPRL 67 (91)
Q Consensus 63 TIpRs 67 (91)
+||+.
T Consensus 172 ~Vppg 176 (259)
T KOG2884|consen 172 SVPPG 176 (259)
T ss_pred EeCCC
Confidence 99974
No 8
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=65.96 E-value=6 Score=24.39 Aligned_cols=25 Identities=8% Similarity=0.085 Sum_probs=22.0
Q ss_pred cccccccccccCcCCCceEEeeccc
Q psy13847 65 PRLQFEDLQQSGVCSSPVALSWGAE 89 (91)
Q Consensus 65 pRslDGRLQVs~rKglPhviy~~~~ 89 (91)
++++..++.-|.+.|+|.+|+-|.+
T Consensus 40 ~~~l~k~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 40 NERPGVKFADADLIGIPYRIVVGKK 64 (94)
T ss_pred CCCcccchhHHHhcCCCEEEEECCc
Confidence 4689999999999999999998853
No 9
>PF09260 DUF1966: Domain of unknown function (DUF1966); InterPro: IPR015340 Alpha-amylase is classified as family 13 of the glycosyl hydrolases and is present in archaea, bacteria, plants and animals. Alpha-amylase is an essential enzyme in alpha-glucan metabolism, acting to catalyse the hydrolysis of alpha-1,4-glucosidic bonds of glycogen, starch and related polysaccharides. Although all alpha-amylases possess the same catalytic function, they can vary with respect to sequence. In general, they are composed of three domains: a TIM barrel containing the active site residues and chloride ion-binding site (domain A), a long loop region inserted between the third beta strand and the alpha-helix of domain A that contains calcium-binding site(s) (domain B), and a C-terminal beta-sheet domain that appears to show some variability in sequence and length between amylases (domain C) []. Amylases have at least one conserved calcium-binding site, as calcium is essential for the stability of the enzyme. The chloride-binding functions to activate the enzyme, which acts by a two-step mechanism involving a catalytic nucleophile base (usually an Asp) and a catalytic proton donor (usually a Glu) that are responsible for the formation of the beta-linked glycosyl-enzyme intermediate. This domain is found in various fungal alpha-amylase proteins. Its exact function has not, as yet, been defined []. ; GO: 0004556 alpha-amylase activity, 0005509 calcium ion binding, 0016052 carbohydrate catabolic process; PDB: 2AAA_A 2GUY_A 2TAA_B 6TAA_A 2GVY_B 7TAA_A 3KWX_A.
Probab=65.46 E-value=4.1 Score=27.26 Aligned_cols=28 Identities=14% Similarity=0.042 Sum_probs=18.3
Q ss_pred cceeecccccccccccCcCCCceEEeec
Q psy13847 60 KCVTIPRLQFEDLQQSGVCSSPVALSWG 87 (91)
Q Consensus 60 kCVTIpRslDGRLQVs~rKglPhviy~~ 87 (91)
.|.++.-.-+|.|.|.-.+|+|.|+|-.
T Consensus 55 sc~~~tv~~~G~l~v~m~~G~P~Vl~P~ 82 (91)
T PF09260_consen 55 SCTSYTVDSNGTLTVPMSNGEPRVLYPA 82 (91)
T ss_dssp TTEEEE--TTS-EEEEESTT--EEEEEC
T ss_pred cCCEEEECCCCEEEEEEcCCceEEEEEH
Confidence 3555554579999999999999999964
No 10
>COG4054 McrB Methyl coenzyme M reductase, beta subunit [Coenzyme metabolism]
Probab=53.65 E-value=16 Score=30.97 Aligned_cols=40 Identities=33% Similarity=0.405 Sum_probs=31.1
Q ss_pred HHHHHHHHHhhhc--CcHHHHHHHHhcCCCCCcceeec-cccc
Q psy13847 30 KAVKSLVKKLKKS--NGLDELEKAITTQDPNTKCVTIP-RLQF 69 (91)
Q Consensus 30 KAIkSLVKKLKk~--~~le~Le~Altt~~~~tkCVTIp-RslD 69 (91)
-||+++|+..|.+ =+|+-+|.|+.+.....|---|| |-||
T Consensus 36 paI~~iv~diKRsVAvnLaGIenaL~~~~vGGk~~~i~GReld 78 (447)
T COG4054 36 PAIKKIVNDIKRSVAVNLAGIENALKTGKVGGKGCKIPGRELD 78 (447)
T ss_pred HHHHHHHHHhhhHheeeHHhhHhHHhhcccCCCcccccCcccC
Confidence 4899999999998 67999999999987544444455 6554
No 11
>PF02783 MCR_beta_N: Methyl-coenzyme M reductase beta subunit, N-terminal domain; InterPro: IPR022680 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. This entry represents the N-terminal domain from the beta subunit of methyl-conenzyme M reductase (MCR). The N-terminal domain has an alpha/beta ferredoxin-like fold. This entry is found in assocation with PF02241 from PFAM. ; GO: 0050524 coenzyme-B sulfoethylthiotransferase activity; PDB: 3SQG_B 1MRO_E 1HBM_B 3M30_B 3M32_B 1HBU_B 3M2U_E 3M2V_E 3M1V_B 1HBO_B ....
Probab=47.26 E-value=22 Score=27.37 Aligned_cols=40 Identities=25% Similarity=0.303 Sum_probs=25.3
Q ss_pred HHHHHHHHHhhhc--CcHHHHHHHHhcCCCCCc-ceeeccccc
Q psy13847 30 KAVKSLVKKLKKS--NGLDELEKAITTQDPNTK-CVTIPRLQF 69 (91)
Q Consensus 30 KAIkSLVKKLKk~--~~le~Le~Altt~~~~tk-CVTIpRslD 69 (91)
-||+.+|+..|.. =+|+-+|.++.|.....+ |.-.=|.||
T Consensus 28 pai~kii~~tKRTvAVNLaGIE~aLktG~~GGk~~~I~Greld 70 (182)
T PF02783_consen 28 PAIKKIINLTKRTVAVNLAGIENALKTGKVGGKGCQIPGRELD 70 (182)
T ss_dssp HHHHHHHHHHHHEEEEEHHHHHHHHHHT--SSTT---TT----
T ss_pred HHHHHHHHhhhheeEeeHHHHHHHHhccCcCCCcccccCcccC
Confidence 4899999999987 469999999999975544 544446655
No 12
>COG4001 Predicted metal-binding protein [General function prediction only]
Probab=46.12 E-value=29 Score=24.44 Aligned_cols=32 Identities=25% Similarity=0.391 Sum_probs=23.3
Q ss_pred HHHHhhhccCC-CcchhHHHHHHHHHHHhhhcC
Q psy13847 12 VKKLLGWKKGD-GEDKYSEKAVKSLVKKLKKSN 43 (91)
Q Consensus 12 Vk~LL~wkqg~-eeek~aeKAIkSLVKKLKk~~ 43 (91)
|+.-|-+--|+ +|--|-=||.-++|||+-++|
T Consensus 36 ik~Ald~alggR~daCwkCra~a~ivkkive~g 68 (102)
T COG4001 36 IKSALDHALGGRDDACWKCRALASIVKKIVERG 68 (102)
T ss_pred HHHHHHHHHcCchhHHHHHHHHHHHHHHHHHhc
Confidence 33333343333 788999999999999999874
No 13
>TIGR02930 vnfG_nitrog V-containing nitrogenase, delta subunit. Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, VnfG, represents the delta subunit of the V-containing (vanadium) alternative nitrogenase. It is homologous to AnfG, the delta subunit of the Fe-only nitrogenase.
Probab=40.18 E-value=17 Score=25.91 Aligned_cols=31 Identities=23% Similarity=0.188 Sum_probs=20.9
Q ss_pred CcHHHHHHHHhcCCCCCcceeecccccccccccC
Q psy13847 43 NGLDELEKAITTQDPNTKCVTIPRLQFEDLQQSG 76 (91)
Q Consensus 43 ~~le~Le~Altt~~~~tkCVTIpRslDGRLQVs~ 76 (91)
+++.+|++.+...- .-+||.|||++-|.+.|
T Consensus 78 dei~~l~~~lk~rl---~~~tItgSlN~ELt~~~ 108 (109)
T TIGR02930 78 DQILELVESVKKRL---VEITITRSLNGELNHSL 108 (109)
T ss_pred HHHHHHHHHHHHHH---HhhhccccccHhhcccC
Confidence 34555555555543 35789999999987654
No 14
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=38.25 E-value=29 Score=24.88 Aligned_cols=23 Identities=30% Similarity=0.456 Sum_probs=19.1
Q ss_pred CcchhHHHHHHHHHHHhhhcCcH
Q psy13847 23 GEDKYSEKAVKSLVKKLKKSNGL 45 (91)
Q Consensus 23 eeek~aeKAIkSLVKKLKk~~~l 45 (91)
++-.|++..|+.|+..|=|||-+
T Consensus 32 ~~~ews~sTV~TLl~RL~KKg~l 54 (123)
T COG3682 32 ADREWSYSTVKTLLNRLVKKGLL 54 (123)
T ss_pred hcccccHHHHHHHHHHHHhccch
Confidence 34679999999999999888754
No 15
>TIGR03257 met_CoM_red_bet methyl-coenzyme M reductase, beta subunit. Members of this protein family are the beta subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes.
Probab=37.64 E-value=41 Score=28.79 Aligned_cols=40 Identities=20% Similarity=0.283 Sum_probs=30.5
Q ss_pred HHHHHHHHHhhhc--CcHHHHHHHHhcCCCCC-cceeeccccc
Q psy13847 30 KAVKSLVKKLKKS--NGLDELEKAITTQDPNT-KCVTIPRLQF 69 (91)
Q Consensus 30 KAIkSLVKKLKk~--~~le~Le~Altt~~~~t-kCVTIpRslD 69 (91)
-||+.+|+..|.. =+|+-+|+++.+..... .|.-.-|.||
T Consensus 29 ~aI~kii~~~kRTvAVnLaGie~~Lktg~~gGk~~~I~Greld 71 (433)
T TIGR03257 29 AAIQSIIMDIKRTVAVNLAGIEGALASGKMGGKGCQIPGRGLN 71 (433)
T ss_pred HHHHHHHHhhhheeEeeHHHHHHHhhccCcCCCcccccCcccC
Confidence 4899999999887 46999999999998543 4444446655
No 16
>TIGR03031 cas_csx12 CRISPR-associated protein, Csx12 family. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to PFAM model pfam01844, HNH endonuclease.
Probab=36.64 E-value=67 Score=29.44 Aligned_cols=52 Identities=29% Similarity=0.540 Sum_probs=32.0
Q ss_pred CCHHHHHHHhhhccCCCcchhHHHHHHHHHHHhhhc-CcHHHHHHHHhcCCCCCcceeeccc
Q psy13847 7 FTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKS-NGLDELEKAITTQDPNTKCVTIPRL 67 (91)
Q Consensus 7 ~~~~~Vk~LL~wkqg~eeek~aeKAIkSLVKKLKk~-~~le~Le~Altt~~~~tkCVTIpRs 67 (91)
|+..--+-+.+|++.-.+. .+-+++.|+++||.+ +-++-|+. -..|.|||=-
T Consensus 277 f~~~~~r~v~~wrh~K~d~--~~~~~knli~~lKqk~~~i~~L~~-------~~p~~TIPPY 329 (802)
T TIGR03031 277 FGNEFLRMLKNWRHLKGDQ--ESLAVRNLIQQLKQKQDYISILEK-------TPPEITIPPY 329 (802)
T ss_pred HHHHHHHHHHhccCcCCcH--hHHHHHHHHHHHhccchHHHHHHh-------CCCcccCCCc
Confidence 3344455677887532222 456889999999987 44444432 2348899843
No 17
>KOG1466|consensus
Probab=36.19 E-value=74 Score=26.32 Aligned_cols=44 Identities=23% Similarity=0.442 Sum_probs=36.4
Q ss_pred HHHHHHhhhccCCCcchhHHHHHHHHHHHhhhc--CcHHHHHHHHh
Q psy13847 10 PIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKS--NGLDELEKAIT 53 (91)
Q Consensus 10 ~~Vk~LL~wkqg~eeek~aeKAIkSLVKKLKk~--~~le~Le~Alt 53 (91)
.+|...++|.|.|.|-.-+--||+.|+-=|+.+ +.+.+|+.-+.
T Consensus 12 ~iie~f~~~l~eDpd~a~~vAAIraL~~vL~~s~a~Ti~el~~~l~ 57 (313)
T KOG1466|consen 12 SIIEYFLSFLQEDPDLAMAVAAIRALLEVLRRSQATTIAELENELK 57 (313)
T ss_pred hHHHHHHHHHhcCchhhhHHHHHHHHHHHHhhcccchHHHHHHHHH
Confidence 589999999998888888899999999998887 55666666543
No 18
>PF11269 DUF3069: Protein of unknown function (DUF3069); InterPro: IPR021422 This family of proteins with unknown function appear to be restricted to Gammaproteobacteria. ; PDB: 2PV4_A.
Probab=35.33 E-value=25 Score=25.45 Aligned_cols=16 Identities=38% Similarity=0.551 Sum_probs=13.2
Q ss_pred hHHHHHHHHHHHhhhc
Q psy13847 27 YSEKAVKSLVKKLKKS 42 (91)
Q Consensus 27 ~aeKAIkSLVKKLKk~ 42 (91)
-+..+||-+||||||-
T Consensus 91 vl~~~lKd~vKqLKKA 106 (121)
T PF11269_consen 91 VLHNCLKDMVKQLKKA 106 (121)
T ss_dssp HHHTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4566899999999994
No 19
>smart00542 FYRC "FY-rich" domain, C-terminal region. is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.
Probab=34.80 E-value=22 Score=23.20 Aligned_cols=17 Identities=29% Similarity=0.479 Sum_probs=13.5
Q ss_pred CCCCCHHHHHHHhhhcc
Q psy13847 4 LFPFTPPIVKKLLGWKK 20 (91)
Q Consensus 4 ~~~~~~~~Vk~LL~wkq 20 (91)
||+|+.|.|.+|+.=-.
T Consensus 52 mFGls~p~V~~lie~Lp 68 (86)
T smart00542 52 MFGLSSPAVVKLIEQLP 68 (86)
T ss_pred HhCCCcHHHHHHHHhCC
Confidence 89999999998875433
No 20
>TIGR02929 anfG_nitrog Fe-only nitrogenase, delta subunit. Nitrogenase, also called dinitrogenase, is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, AnfG, represents the delta subunit of the Fe-only alternative nitrogenase. It is homologous to VnfG, the delta subunit of the V-containing (vanadium) nitrogenase.
Probab=32.94 E-value=26 Score=24.96 Aligned_cols=31 Identities=16% Similarity=0.160 Sum_probs=20.8
Q ss_pred CcHHHHHHHHhcCCCCCcceeecccccccccccC
Q psy13847 43 NGLDELEKAITTQDPNTKCVTIPRLQFEDLQQSG 76 (91)
Q Consensus 43 ~~le~Le~Altt~~~~tkCVTIpRslDGRLQVs~ 76 (91)
+++.+|++++...- .-+||.+||++-|.+.|
T Consensus 78 dei~~l~~~lk~rl---~~ltItgSlN~ELt~~~ 108 (109)
T TIGR02929 78 DEIKTLMQALHEKM---DHLTIKGSLNLELTKEH 108 (109)
T ss_pred HHHHHHHHHHHHHH---HhhhcccccchhhcccC
Confidence 34555666665553 35789999999887654
No 21
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=32.29 E-value=93 Score=17.28 Aligned_cols=29 Identities=24% Similarity=0.611 Sum_probs=18.9
Q ss_pred CCCC-CCHHHHHHHhhhccCCCcchhHHHHHHHHH
Q psy13847 3 SLFP-FTPPIVKKLLGWKKGDGEDKYSEKAVKSLV 36 (91)
Q Consensus 3 ~~~~-~~~~~Vk~LL~wkqg~eeek~aeKAIkSLV 36 (91)
.||| .+...|++.|.-..|+ .+.||.+|.
T Consensus 11 ~mFP~l~~~~I~~~L~~~~g~-----ve~~i~~LL 40 (43)
T smart00546 11 DMFPNLDEEVIKAVLEANNGN-----VEATINNLL 40 (43)
T ss_pred HHCCCCCHHHHHHHHHHcCCC-----HHHHHHHHH
Confidence 3677 6777787777766654 455666664
No 22
>PF05965 FYRC: F/Y rich C-terminus; InterPro: IPR003889 The "FY-rich" domain C-terminal region is sometimes closely juxtaposed with the N-terminal region (IPR003888 from INTERPRO), but sometimes is far distant. It is of unknown function, but occurs frequently in chromatin-associated proteins like trithorax and its homologues.; GO: 0005634 nucleus; PDB: 2WZO_A.
Probab=32.15 E-value=17 Score=23.20 Aligned_cols=15 Identities=27% Similarity=0.620 Sum_probs=12.6
Q ss_pred CCCCCHHHHHHHhhh
Q psy13847 4 LFPFTPPIVKKLLGW 18 (91)
Q Consensus 4 ~~~~~~~~Vk~LL~w 18 (91)
||+|+.|.|.+|+.=
T Consensus 56 ~FGls~p~V~~lie~ 70 (86)
T PF05965_consen 56 MFGLSNPAVQRLIES 70 (86)
T ss_dssp HHSTTSHHHHHHHTT
T ss_pred hcCCCCHHHHHHHHh
Confidence 789999999998853
No 23
>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.
Probab=31.19 E-value=97 Score=23.04 Aligned_cols=38 Identities=29% Similarity=0.466 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhhhc-------------CcHHHHHHHHhcC--CCCCcceeecc
Q psy13847 29 EKAVKSLVKKLKKS-------------NGLDELEKAITTQ--DPNTKCVTIPR 66 (91)
Q Consensus 29 eKAIkSLVKKLKk~-------------~~le~Le~Altt~--~~~tkCVTIpR 66 (91)
++.+..+.|+||+. .+.+-||.-+.+- +..+.+++||=
T Consensus 122 ~~~i~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~~~~~~~~~s~~~~~~~ 174 (187)
T cd01452 122 EKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDAVNGKDGSHLVSVPP 174 (187)
T ss_pred HHHHHHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHHHHhcCCCCceEEEeCC
Confidence 44565666777661 2334444444333 34689999994
No 24
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=29.33 E-value=83 Score=18.14 Aligned_cols=22 Identities=36% Similarity=0.490 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHhhhcCcHHHHHHH
Q psy13847 28 SEKAVKSLVKKLKKSNGLDELEKA 51 (91)
Q Consensus 28 aeKAIkSLVKKLKk~~~le~Le~A 51 (91)
+.+||..+.. ....++|++++.
T Consensus 20 ~~~av~~~~~--~~~~~~e~~ik~ 41 (47)
T PF07499_consen 20 AQKAVSKLLE--KPGMDVEELIKQ 41 (47)
T ss_dssp HHHHHHHHHH--STTS-HHHHHHH
T ss_pred HHHHHHHhhc--CCCCCHHHHHHH
Confidence 5555555555 233457776664
No 25
>PRK13749 transcriptional regulator MerD; Provisional
Probab=29.09 E-value=1.5e+02 Score=20.66 Aligned_cols=49 Identities=14% Similarity=0.161 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHhhhccCCCcchhHHHHHHHHHHHhhhc-CcHHHHHHHHhc
Q psy13847 5 FPFTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKS-NGLDELEKAITT 54 (91)
Q Consensus 5 ~~~~~~~Vk~LL~wkqg~eeek~aeKAIkSLVKKLKk~-~~le~Le~Altt 54 (91)
++|+-.-++.||.....++.+.++. .+..+-..+-.+ ..|..|+.++..
T Consensus 59 ~G~sL~eI~~ll~l~~~~~~~~~~~-~~~~~~~~v~~~i~~L~~l~~~L~~ 108 (121)
T PRK13749 59 AGIGLDALARLCRALDAADGDEAAA-QLAVLRQLVERRREALADLEVQLAT 108 (121)
T ss_pred cCCCHHHHHHHHhhhcCCCcchHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788889999999865443333333 344555555554 566666666643
No 26
>cd01269 PLX Pollux (PLX) Phosphotyrosine-binding (PTB) domain. Pollux (PLX) Phosphotyrosine-binding (PTB) domain. PLX is calmodulin-binding protein containing a TBC domain, which is conserved from yeast to man, but it only has an N-terminal PTB domain in mammals. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=28.74 E-value=12 Score=27.32 Aligned_cols=16 Identities=0% Similarity=-0.070 Sum_probs=14.1
Q ss_pred cccccccCcCCCceEE
Q psy13847 69 FEDLQQSGVCSSPVAL 84 (91)
Q Consensus 69 DGRLQVs~rKglPhvi 84 (91)
=||+.|+|+|+-|.||
T Consensus 9 ~~~~~~~~~~~~~~li 24 (129)
T cd01269 9 CGRVTVTHKKAPSSLI 24 (129)
T ss_pred EeeEEEeeccCChHHH
Confidence 4899999999999876
No 27
>cd00858 GlyRS_anticodon GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=28.70 E-value=35 Score=22.67 Aligned_cols=23 Identities=4% Similarity=-0.039 Sum_probs=20.9
Q ss_pred ccccccccccCcCCCceEEeecc
Q psy13847 66 RLQFEDLQQSGVCSSPVALSWGA 88 (91)
Q Consensus 66 RslDGRLQVs~rKglPhviy~~~ 88 (91)
+++..+++-|.+.|.|.+|+-|.
T Consensus 64 ~sl~kqlk~A~k~g~~~~iiiG~ 86 (121)
T cd00858 64 GSIGRRYARQDEIGTPFCVTVDF 86 (121)
T ss_pred CCHHHHHHHhHhcCCCEEEEECc
Confidence 78889999999999999999884
No 28
>PF03139 AnfG_VnfG: Vanadium/alternative nitrogenase delta subunit; InterPro: IPR004349 The nitrogenase complex 1.18.6.1 from EC catalyses the conversion of molecular nitrogen to ammonia (nitrogen fixation). The complex is hexameric, consisting of 2 alpha, 2 beta, and 2 delta subunits. This family represents the delta subunit of a group of nitrogenases that do not utilise molybdenum (Mo) as a cofactor, but instead use either vanadium (V nitrogenases), or iron (alternative nitrogenases). ; GO: 0016163 nitrogenase activity, 0009399 nitrogen fixation, 0055114 oxidation-reduction process
Probab=28.42 E-value=32 Score=24.60 Aligned_cols=61 Identities=18% Similarity=0.215 Sum_probs=35.0
Q ss_pred HHHHHhhhccCC----Ccc-hhHHHHHHHHHHHhhhc---------CcHHHHHHHHhcCCCCCcceeecccccccccccC
Q psy13847 11 IVKKLLGWKKGD----GED-KYSEKAVKSLVKKLKKS---------NGLDELEKAITTQDPNTKCVTIPRLQFEDLQQSG 76 (91)
Q Consensus 11 ~Vk~LL~wkqg~----eee-k~aeKAIkSLVKKLKk~---------~~le~Le~Altt~~~~tkCVTIpRslDGRLQVs~ 76 (91)
.+.+||+..... +|. -|+. | ..|+...|++ .++.+|.+++...- .-+||.+||++-|.+.+
T Consensus 37 kt~qlL~gE~v~~eTp~Drcyw~D-A-v~la~~~k~rfpW~~~~~k~ei~~lm~~lk~rl---d~ltItgSlN~ELt~~~ 111 (112)
T PF03139_consen 37 KTTQLLCGEPVDLETPADRCYWVD-A-VCLAEAFKERFPWINEMSKDEIKSLMQGLKERL---DYLTITGSLNEELTDPL 111 (112)
T ss_pred HHHHHHcCCCCCCCCchhHHHHHH-H-HHHHHHHHHcCcHHHHCCHHHHHHHHHHHHHHH---hHhhhcccccHhhcccC
Confidence 456677765532 121 2333 2 2455555552 34556666665554 35789999999887654
No 29
>PRK05302 30S ribosomal protein S7; Validated
Probab=27.88 E-value=2.1e+02 Score=20.62 Aligned_cols=52 Identities=23% Similarity=0.355 Sum_probs=34.4
Q ss_pred CCHHHHHHHhhhccCCCcchhHHHHHHHHHHHhhh---cCcHHHHHHHHhcCCCC
Q psy13847 7 FTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKK---SNGLDELEKAITTQDPN 58 (91)
Q Consensus 7 ~~~~~Vk~LL~wkqg~eeek~aeKAIkSLVKKLKk---~~~le~Le~Altt~~~~ 58 (91)
|..|+|.+|...---+..-.-|++-+..-+..+++ .+.++-|++||..-.+-
T Consensus 18 ~~~~lv~~lin~lmk~GKK~~A~kI~~~al~~I~~~~~~npl~il~~Ai~nv~P~ 72 (156)
T PRK05302 18 YGSVLVTKFINKLMLDGKKSVAEKIVYGALDIIEEKTGKDPLEVFEKALENVKPV 72 (156)
T ss_pred cCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHhCCCC
Confidence 66899999887633233334455555555544444 37799999999887754
No 30
>PF11291 DUF3091: Protein of unknown function (DUF3091); InterPro: IPR021442 This eukaryotic family of proteins has no known function.
Probab=26.67 E-value=1.5e+02 Score=20.63 Aligned_cols=39 Identities=18% Similarity=0.277 Sum_probs=27.5
Q ss_pred hhHHHHHHHHHHHhhhcCcHHHHHHHHhcCCCCCcceeecccc
Q psy13847 26 KYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNTKCVTIPRLQ 68 (91)
Q Consensus 26 k~aeKAIkSLVKKLKk~~~le~Le~Altt~~~~tkCVTIpRsl 68 (91)
+++++|++-|++-- +.|+.+=..+.+...+..|. .|++.
T Consensus 14 n~s~~v~E~l~~~~---~~Lkq~f~~~qS~~~~mTC~-~PeNI 52 (100)
T PF11291_consen 14 NFSEEVFEKLNRCS---VKLKQYFDKLQSKKENMTCN-RPENI 52 (100)
T ss_pred hchHHHHHHHHHHH---HHHHHHHHHHHhcccCcccC-CCCCC
Confidence 68899999888652 23666666777777777786 67653
No 31
>PF06838 Met_gamma_lyase: Methionine gamma-lyase ; InterPro: IPR009651 This family represents the aluminium resistance protein, which confers resistance to aluminium in bacteria [].; PDB: 3JZL_A 3I16_C 3GWP_A 3FD0_B 3HT4_F.
Probab=25.91 E-value=45 Score=28.41 Aligned_cols=22 Identities=41% Similarity=0.619 Sum_probs=16.8
Q ss_pred cHHHHHHHHhcCCCCCcceeecccc
Q psy13847 44 GLDELEKAITTQDPNTKCVTIPRLQ 68 (91)
Q Consensus 44 ~le~Le~Altt~~~~tkCVTIpRsl 68 (91)
++|.++++|. ..|++|.|+||-
T Consensus 143 D~~~i~~~~~---~~tk~v~IQRSr 164 (403)
T PF06838_consen 143 DWEAIKKALK---PNTKMVLIQRSR 164 (403)
T ss_dssp -HHHHHHHHH---TTEEEEEEE-S-
T ss_pred CHHHHHHhhc---cCceEEEEecCC
Confidence 4788999998 678999999983
No 32
>smart00806 AIP3 Actin interacting protein 3. Aip3p/Bud6p is a regulator of cell and cytoskeletal polarity in Saccharomyces cerevisiae that was previously identified as an actin-interacting protein. Actin-interacting protein 3 (Aip3p) localizes at the cell cortex where cytoskeleton assembly must be achieved to execute polarized cell growth, and deletion of AIP3 causes gross defects in cell and cytoskeletal polarity. Aip3p localization is mediated by the secretory pathway, mutations in early- or late-acting components of the secretory apparatus lead to Aip3p mislocalization PUBMED:10679021.
Probab=25.62 E-value=48 Score=28.35 Aligned_cols=21 Identities=43% Similarity=0.672 Sum_probs=16.0
Q ss_pred HHHHH--HHhhhcCcHHHHHHHH
Q psy13847 32 VKSLV--KKLKKSNGLDELEKAI 52 (91)
Q Consensus 32 IkSLV--KKLKk~~~le~Le~Al 52 (91)
+.+.| +||||.|++||.|++=
T Consensus 399 Lg~FVe~~kLKksGG~EEvER~R 421 (426)
T smart00806 399 LGNFVENGKLKKSGGIEEVERLR 421 (426)
T ss_pred HHHHhccCCcccCcCHHHHHHHH
Confidence 33444 6799999999999863
No 33
>cd00859 HisRS_anticodon HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=25.51 E-value=35 Score=19.91 Aligned_cols=22 Identities=14% Similarity=0.152 Sum_probs=18.0
Q ss_pred ccccccccccCcCCCceEEeec
Q psy13847 66 RLQFEDLQQSGVCSSPVALSWG 87 (91)
Q Consensus 66 RslDGRLQVs~rKglPhviy~~ 87 (91)
++++-+++-|.+.|.|.+++-|
T Consensus 38 ~~~~~~~~~a~~~~~~~~i~i~ 59 (91)
T cd00859 38 RKLKKQFKYADRSGARFAVILG 59 (91)
T ss_pred CCHHHHHHHHHHcCCCEEEEEc
Confidence 5677788888899999988766
No 34
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=25.30 E-value=1.2e+02 Score=16.77 Aligned_cols=29 Identities=28% Similarity=0.626 Sum_probs=16.8
Q ss_pred CCCC-CCHHHHHHHhhhccCCCcchhHHHHHHHHH
Q psy13847 3 SLFP-FTPPIVKKLLGWKKGDGEDKYSEKAVKSLV 36 (91)
Q Consensus 3 ~~~~-~~~~~Vk~LL~wkqg~eeek~aeKAIkSLV 36 (91)
+||| ++...|+..|.-..|+ .+.||+.|+
T Consensus 10 ~mFP~~~~~~I~~~L~~~~~~-----ve~ai~~LL 39 (42)
T PF02845_consen 10 EMFPDLDREVIEAVLQANNGD-----VEAAIDALL 39 (42)
T ss_dssp HHSSSS-HHHHHHHHHHTTTT-----HHHHHHHHH
T ss_pred HHCCCCCHHHHHHHHHHcCCC-----HHHHHHHHH
Confidence 3566 5667777777544443 455666664
No 35
>PF11267 DUF3067: Protein of unknown function (DUF3067); InterPro: IPR021420 This family of proteins has no known function. ; PDB: 2LJW_A.
Probab=25.16 E-value=77 Score=22.09 Aligned_cols=42 Identities=17% Similarity=0.124 Sum_probs=26.4
Q ss_pred HHHHHHHHhhhcCcHHHHHHHHhcCC---CCCcceeecccccccc
Q psy13847 31 AVKSLVKKLKKSNGLDELEKAITTQD---PNTKCVTIPRLQFEDL 72 (91)
Q Consensus 31 AIkSLVKKLKk~~~le~Le~Altt~~---~~tkCVTIpRslDGRL 72 (91)
=++..+.=|...|..|.....|.+.. .-.+||+||=.+++|.
T Consensus 51 hL~~va~~L~~wG~~~~Vr~~l~~t~~rPRlGkAVsipL~l~~r~ 95 (99)
T PF11267_consen 51 HLDAVAEYLNAWGQADQVRAFLEETRERPRLGKAVSIPLDLGERA 95 (99)
T ss_dssp HHHHHHHHHHHHS-HHHHHHHHHH-----BTTB-EEEEE--HHHH
T ss_pred HHHHHHHHHHHcccHHHHHHHHHhCCCCCCCCeEEEEeecCCchh
Confidence 45666666777788888888876654 2479999998887764
No 36
>PF11815 DUF3336: Domain of unknown function (DUF3336); InterPro: IPR021771 This family of proteins is characterised by an N-terminal domain that is found adjacent to the patatin/phospholipase A2-related domain (see PF01734 from PFAM). The family of proteins, which contain these two domains, have been characterised in Saccharomyces cerevisiae (Baker's yeast) as a bifunctional enzyme with triacylglycerol lipase and lysophosphatidic acid acyltransferase or lysophosphatidylethanolamine acyltransferase activity. They are generally involved in triacylglycerol mobilisation and localized to lipid particles [, ].
Probab=24.86 E-value=1.1e+02 Score=21.61 Aligned_cols=44 Identities=25% Similarity=0.539 Sum_probs=35.3
Q ss_pred HHHHhh---hccCCCcchhHHHHHHHHHHHhhh---cCcHHHHHHHHhcC
Q psy13847 12 VKKLLG---WKKGDGEDKYSEKAVKSLVKKLKK---SNGLDELEKAITTQ 55 (91)
Q Consensus 12 Vk~LL~---wkqg~eeek~aeKAIkSLVKKLKk---~~~le~Le~Altt~ 55 (91)
..++.| ||+.++....--+.|...+..|+. .|+++.|..+|.+.
T Consensus 36 LD~l~G~~~Wk~~~~s~~YD~~lI~~rl~~L~~aR~~~d~~~l~~~Lr~~ 85 (145)
T PF11815_consen 36 LDELEGNDAWKEDDESDYYDYRLIRERLRELREARQSGDIEALMFLLRTG 85 (145)
T ss_pred HHHHcCcchhhcCCCCcccCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 344544 999888889999999999988877 38899998888664
No 37
>cd01816 Raf_RBD Ubiquitin domain of Raf serine/threonine kinases. The Raf serine/threonine kinases are composed of three conserved regions, CR1, CR2 and CR3. CR1 has two Ras binding domains (RBD and CRD), CR2 is a serine/threonine rich domain and CR3 is the catalytic kinase domain. The RBD of Raf is structurally similar to ubiquitin with little of no sequence similarity.The Raf signalling pathway plays an important role in the proliferation and survival of tumor cells.
Probab=24.06 E-value=73 Score=21.22 Aligned_cols=25 Identities=28% Similarity=0.432 Sum_probs=18.7
Q ss_pred HHHHHHHhcCCCCCcceeecccccc
Q psy13847 46 DELEKAITTQDPNTKCVTIPRLQFE 70 (91)
Q Consensus 46 e~Le~Altt~~~~tkCVTIpRslDG 70 (91)
|.|++|++..+-...|-.+-|..||
T Consensus 24 daL~KaLk~R~l~pe~C~V~~~~~~ 48 (74)
T cd01816 24 DALAKALKVRGLQPECCAVFRLGDG 48 (74)
T ss_pred HHHHHHHHHcCCChhHeEEEEcCCC
Confidence 6677777777766677778887777
No 38
>PRK14142 heat shock protein GrpE; Provisional
Probab=23.93 E-value=94 Score=24.35 Aligned_cols=32 Identities=31% Similarity=0.403 Sum_probs=24.1
Q ss_pred CcchhHHHHHHHHHHHhhhcCcHHHHHHHHhcCC
Q psy13847 23 GEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQD 56 (91)
Q Consensus 23 eeek~aeKAIkSLVKKLKk~~~le~Le~Altt~~ 56 (91)
|-+...+.|+++++++|-. .+|.||+|+.+..
T Consensus 73 E~e~~~~~A~e~~~kdLLp--VlDnLERAL~~~~ 104 (223)
T PRK14142 73 DQQAAADRAKASVVSQLLG--VLDDLERARKHGD 104 (223)
T ss_pred HHHHHHHHHHHHHHHHHhc--hHhHHHHHHhccc
Confidence 3445666788888888775 6999999997754
No 39
>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid. This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....
Probab=23.71 E-value=1.8e+02 Score=21.79 Aligned_cols=31 Identities=16% Similarity=0.278 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHhhhcCcHHHHHHHHhcCCCC
Q psy13847 28 SEKAVKSLVKKLKKSNGLDELEKAITTQDPN 58 (91)
Q Consensus 28 aeKAIkSLVKKLKk~~~le~Le~Altt~~~~ 58 (91)
|-...+..++-|++...|||..+|+...|.+
T Consensus 169 AN~~C~~~~~~l~~~~~lee~~~~C~~vg~~ 199 (206)
T PF00607_consen 169 ANPDCRRIIRPLGKDAPLEEMIRACQGVGGP 199 (206)
T ss_dssp S-HHHHHHHHHH-TTSTHHHHHHHTTTTSST
T ss_pred chHHHHHHHHccCCCCCHHHHHHHhhccCCH
Confidence 3334555556666667899999998877744
No 40
>COG1753 Predicted antotoxin, copG family [Signal transduction mechanisms]
Probab=22.82 E-value=2.4e+02 Score=18.87 Aligned_cols=43 Identities=28% Similarity=0.570 Sum_probs=28.6
Q ss_pred CCHHHHHHHhhhccCCCcchhHHHHHHHHHHHhhhcCcHHHHHHHHhc
Q psy13847 7 FTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNGLDELEKAITT 54 (91)
Q Consensus 7 ~~~~~Vk~LL~wkqg~eeek~aeKAIkSLVKKLKk~~~le~Le~Altt 54 (91)
-+-.+-.+|+.-|. +.+.|++ .|.-|+. ||++++|-|..|.-+
T Consensus 8 I~ddvYe~L~kmK~--g~~SFSd-vI~~l~~--kKr~~levl~~~~g~ 50 (74)
T COG1753 8 ISDDVYEKLVKMKR--GKESFSD-VIRELIE--KKRGNLEVLMRAFGT 50 (74)
T ss_pred ecHHHHHHHHHHHc--ccccHHH-HHHHHHH--HhhhhHHHHHHHhCC
Confidence 34556677887777 5566777 7777777 455677777666543
No 41
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=22.78 E-value=49 Score=19.92 Aligned_cols=23 Identities=17% Similarity=0.255 Sum_probs=20.2
Q ss_pred ccccccccccCcCCCceEEeecc
Q psy13847 66 RLQFEDLQQSGVCSSPVALSWGA 88 (91)
Q Consensus 66 RslDGRLQVs~rKglPhviy~~~ 88 (91)
+++.-++.-|.+.|.|.+++-|.
T Consensus 41 ~~~~k~~~~a~~~g~~~~iiig~ 63 (94)
T cd00738 41 RKIGKKFREADLRGVPFAVVVGE 63 (94)
T ss_pred cCHhHHHHHHHhCCCCEEEEECC
Confidence 67888999999999999999884
No 42
>PF05205 COMPASS-Shg1: COMPASS (Complex proteins associated with Set1p) component shg1
Probab=22.47 E-value=71 Score=21.60 Aligned_cols=24 Identities=33% Similarity=0.430 Sum_probs=18.8
Q ss_pred HHHHHHhhhcCcHHHHHHHHhcCC
Q psy13847 33 KSLVKKLKKSNGLDELEKAITTQD 56 (91)
Q Consensus 33 kSLVKKLKk~~~le~Le~Altt~~ 56 (91)
|+||-.+|++|.+|.|-+-|-.+-
T Consensus 1 ~~Lv~~fKk~G~FD~lRk~~l~~~ 24 (106)
T PF05205_consen 1 KQLVEEFKKQGHFDKLRKECLADF 24 (106)
T ss_pred ChHHHHHHhCCChHHHHHHHHHhc
Confidence 478889999999999988665443
No 43
>TIGR03237 dnd_assoc_2 dnd system-associated protein 2. cereus E33L, Hahella chejuensis KCTC 2396, and Pseudoalteromonas haloplanktis TAC12.
Probab=21.66 E-value=34 Score=32.89 Aligned_cols=16 Identities=25% Similarity=0.393 Sum_probs=14.2
Q ss_pred CcCCCceEEeeccccC
Q psy13847 76 GVCSSPVALSWGAEYR 91 (91)
Q Consensus 76 ~rKglPhviy~~~~~~ 91 (91)
+++.+|.+.||+.|||
T Consensus 574 ~~ktlPSL~~w~~el~ 589 (1256)
T TIGR03237 574 HKKGLPSLCGWGDELV 589 (1256)
T ss_pred hcCCCceeeeeCHHHH
Confidence 6889999999999885
No 44
>PF14383 VARLMGL: DUF761-associated sequence motif
Probab=21.22 E-value=57 Score=18.92 Aligned_cols=13 Identities=31% Similarity=0.652 Sum_probs=10.6
Q ss_pred CCHHHHHHHhhhc
Q psy13847 7 FTPPIVKKLLGWK 19 (91)
Q Consensus 7 ~~~~~Vk~LL~wk 19 (91)
-+|.+|.||||..
T Consensus 13 r~P~vvarLMGld 25 (34)
T PF14383_consen 13 RAPGVVARLMGLD 25 (34)
T ss_pred cChhHHHHHhccc
Confidence 3688999999975
No 45
>PF03915 AIP3: Actin interacting protein 3; InterPro: IPR022782 This entry represents a domain found in yeast actin interacting protein 3 and bud site selection protein 6. In these proteins it is typically found towards the C terminus. It is also found in metazoan proteins, such as the mouse enhancer trap locus 4 protein. ; PDB: 3ONX_B 3OKQ_A.
Probab=20.48 E-value=34 Score=28.92 Aligned_cols=20 Identities=50% Similarity=0.816 Sum_probs=0.0
Q ss_pred HHHHH--HHhhhcCcHHHHHHH
Q psy13847 32 VKSLV--KKLKKSNGLDELEKA 51 (91)
Q Consensus 32 IkSLV--KKLKk~~~le~Le~A 51 (91)
+.+.| +||||.|+.||.|+.
T Consensus 397 L~~FV~~~kLKksGG~eEvER~ 418 (424)
T PF03915_consen 397 LGNFVEEKKLKKSGGIEEVERL 418 (424)
T ss_dssp ----------------------
T ss_pred HHHHhccCcccccCCHHHHHHH
Confidence 33444 789999999999985
No 46
>PF00745 GlutR_dimer: Glutamyl-tRNAGlu reductase, dimerisation domain; InterPro: IPR015896 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents the helical dimerisation domain of glutamyl-tRNA reductase (1.2.1.70 from EC) []. This enzyme reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway [, ]. The enzyme requires NADPH as a cofactor.; GO: 0008883 glutamyl-tRNA reductase activity, 0050661 NADP binding, 0033014 tetrapyrrole biosynthetic process, 0055114 oxidation-reduction process; PDB: 1GPJ_A.
Probab=20.28 E-value=50 Score=20.84 Aligned_cols=19 Identities=37% Similarity=0.571 Sum_probs=9.7
Q ss_pred CCCcchhHHHHHHHHHHHh
Q psy13847 21 GDGEDKYSEKAVKSLVKKL 39 (91)
Q Consensus 21 g~eeek~aeKAIkSLVKKL 39 (91)
++++++-.++.+.|+++||
T Consensus 52 ~~~~~~~i~~~~~~~~~Kl 70 (101)
T PF00745_consen 52 DEDDEEVIEKLTRSLVNKL 70 (101)
T ss_dssp --------TTHHHHHHHHH
T ss_pred CccHHHHHHHHHHHHHHHH
Confidence 4577788889999999884
No 47
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=20.13 E-value=84 Score=20.76 Aligned_cols=23 Identities=22% Similarity=0.354 Sum_probs=17.2
Q ss_pred CcchhHHHHHHHHHHHhhhcCcH
Q psy13847 23 GEDKYSEKAVKSLVKKLKKSNGL 45 (91)
Q Consensus 23 eeek~aeKAIkSLVKKLKk~~~l 45 (91)
++..|+.-.|.++++.|-+||-+
T Consensus 29 ~~~~~~~sTv~t~L~rL~~Kg~l 51 (115)
T PF03965_consen 29 EERSWAYSTVQTLLNRLVEKGFL 51 (115)
T ss_dssp TTSS--HHHHHHHHHHHHHTTSE
T ss_pred hccccchhHHHHHHHHHHhCCce
Confidence 34579999999999999998754
Done!