Query psy1866
Match_columns 235
No_of_seqs 53 out of 55
Neff 2.7
Searched_HMMs 46136
Date Fri Aug 16 18:19:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1866.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1866hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3835|consensus 100.0 1.3E-69 2.9E-74 506.4 14.8 220 5-228 3-271 (495)
2 PF04904 NCD1: NAB conserved r 100.0 2E-52 4.4E-57 319.6 9.3 81 6-86 2-82 (82)
3 PF04905 NCD2: NAB conserved r 99.9 1.5E-22 3.3E-27 171.5 3.5 80 155-234 29-113 (164)
4 PF00536 SAM_1: SAM domain (St 97.3 0.0013 2.7E-08 45.5 6.6 59 13-77 5-63 (64)
5 cd00166 SAM Sterile alpha moti 96.3 0.024 5.2E-07 37.8 6.7 57 15-77 6-62 (63)
6 smart00454 SAM Sterile alpha m 95.4 0.12 2.5E-06 34.6 7.1 61 14-79 7-67 (68)
7 PF07647 SAM_2: SAM domain (St 94.7 0.13 2.9E-06 35.5 6.0 58 15-77 8-65 (66)
8 KOG4384|consensus 94.4 0.13 2.9E-06 49.3 7.2 67 17-88 219-285 (361)
9 PRK10880 adenine DNA glycosyla 90.5 0.32 6.9E-06 45.7 4.0 56 21-80 44-99 (350)
10 PRK13910 DNA glycosylase MutY; 89.3 0.46 1E-05 43.6 4.0 49 27-79 13-61 (289)
11 TIGR01084 mutY A/G-specific ad 86.6 1.2 2.7E-05 40.3 4.9 55 22-80 41-95 (275)
12 KOG3037|consensus 80.5 4.7 0.0001 38.6 6.2 37 151-187 219-258 (330)
13 PF07766 LETM1: LETM1-like pro 75.1 11 0.00024 33.9 6.7 63 12-79 191-253 (268)
14 cd00814 MetRS_core catalytic c 70.9 8.6 0.00019 34.6 5.1 83 2-84 3-115 (319)
15 cd00056 ENDO3c endonuclease II 65.2 24 0.00053 27.9 6.1 56 23-81 16-71 (158)
16 PRK13913 3-methyladenine DNA g 62.9 18 0.00038 32.2 5.4 54 23-76 46-106 (218)
17 PF14520 HHH_5: Helix-hairpin- 62.1 8 0.00017 26.9 2.5 42 30-76 19-60 (60)
18 PF00730 HhH-GPD: HhH-GPD supe 58.8 9.5 0.00021 28.4 2.6 50 26-78 15-66 (108)
19 KOG2507|consensus 57.5 19 0.00041 36.2 5.0 58 34-91 60-131 (506)
20 TIGR01083 nth endonuclease III 57.3 24 0.00053 29.7 5.0 53 23-79 42-95 (191)
21 smart00478 ENDO3c endonuclease 55.6 35 0.00075 26.9 5.4 49 25-76 10-58 (149)
22 KOG0427|consensus 55.2 8.3 0.00018 33.5 1.9 16 67-82 17-32 (161)
23 PF07462 MSP1_C: Merozoite sur 54.7 66 0.0014 33.1 8.3 64 13-78 187-255 (574)
24 cd03569 VHS_Hrs_Vps27p VHS dom 53.9 41 0.00088 27.6 5.7 50 28-79 64-114 (142)
25 KOG0199|consensus 52.0 41 0.00088 36.4 6.6 68 9-85 5-76 (1039)
26 TIGR00398 metG methionyl-tRNA 47.5 23 0.0005 33.9 3.8 84 1-84 1-114 (530)
27 cd03035 ArsC_Yffb Arsenate Red 46.8 31 0.00068 26.7 3.8 50 15-90 40-94 (105)
28 TIGR01954 nusA_Cterm_rpt trans 46.5 53 0.0011 21.3 4.4 42 30-76 7-48 (50)
29 PF06222 Phage_TAC: Phage tail 45.6 9.9 0.00021 32.2 0.9 47 20-75 70-116 (127)
30 KOG0260|consensus 44.5 77 0.0017 35.9 7.4 17 39-55 1366-1382(1605)
31 PF00790 VHS: VHS domain; Int 42.5 42 0.00091 26.9 4.0 51 27-79 64-118 (140)
32 PRK00133 metG methionyl-tRNA s 42.0 41 0.0009 33.7 4.7 84 2-85 5-118 (673)
33 cd03032 ArsC_Spx Arsenate Redu 41.9 41 0.00089 26.0 3.8 54 13-90 39-96 (115)
34 TIGR01493 HAD-SF-IA-v2 Haloaci 40.0 33 0.00071 26.9 3.0 43 15-60 112-154 (175)
35 PF12156 ATPase-cat_bd: Putati 36.5 37 0.00081 26.0 2.8 40 14-53 33-79 (88)
36 KOG3263|consensus 36.2 48 0.001 29.9 3.7 55 34-89 127-194 (196)
37 PF13543 KSR1-SAM: SAM like do 33.1 83 0.0018 26.5 4.5 39 36-76 89-127 (129)
38 cd03567 VHS_GGA VHS domain fam 33.0 1.7E+02 0.0038 24.2 6.3 49 29-79 62-116 (139)
39 KOG4154|consensus 32.7 20 0.00044 31.4 0.9 25 55-79 127-151 (178)
40 KOG2499|consensus 31.9 30 0.00066 35.2 2.0 76 15-90 309-392 (542)
41 PTZ00484 GTP cyclohydrolase I; 31.8 1.6E+02 0.0034 27.4 6.4 63 157-219 64-129 (259)
42 PRK15344 type III secretion sy 31.5 76 0.0016 24.5 3.7 32 47-79 17-48 (71)
43 TIGR02289 M3_not_pepF oligoend 30.3 1.7E+02 0.0037 28.6 6.7 57 13-79 486-546 (549)
44 COG4565 CitB Response regulato 28.6 35 0.00075 31.3 1.7 28 57-84 97-124 (224)
45 PF11904 GPCR_chapero_1: GPCR- 28.2 51 0.0011 30.6 2.7 40 49-91 215-258 (307)
46 PF09921 DUF2153: Uncharacteri 27.9 49 0.0011 28.1 2.3 18 66-83 41-58 (126)
47 PF12987 DUF3871: Domain of un 27.6 43 0.00093 32.2 2.1 27 10-36 273-299 (323)
48 smart00540 LEM in nuclear memb 27.3 1.1E+02 0.0023 21.5 3.5 35 38-75 1-42 (44)
49 PRK10702 endonuclease III; Pro 26.9 1.4E+02 0.003 26.2 5.0 52 23-78 45-97 (211)
50 cd03568 VHS_STAM VHS domain fa 26.4 1.3E+02 0.0028 24.9 4.5 48 28-79 60-110 (144)
51 cd03561 VHS VHS domain family; 26.2 2.5E+02 0.0054 22.3 6.0 48 28-79 60-112 (133)
52 PF13618 Gluconate_2-dh3: Gluc 25.8 1.2E+02 0.0026 23.5 4.0 67 162-233 1-67 (131)
53 smart00288 VHS Domain present 25.3 3E+02 0.0065 22.1 6.3 50 26-79 58-111 (133)
54 PF11569 Homez: Homeodomain le 25.0 58 0.0013 24.0 2.0 23 25-47 13-35 (56)
55 COG0177 Nth Predicted EndoIII- 24.7 84 0.0018 28.2 3.3 42 39-80 60-102 (211)
56 COG0637 Predicted phosphatase/ 24.2 52 0.0011 28.1 1.8 42 15-59 115-156 (221)
57 PF11130 TraC_F_IV: F pilus as 23.9 1.5E+02 0.0032 25.1 4.5 43 40-84 140-182 (235)
58 smart00389 HOX Homeodomain. DN 23.3 1.1E+02 0.0023 20.0 2.9 25 47-80 26-50 (56)
59 COG4755 Uncharacterized protei 23.1 66 0.0014 28.0 2.2 18 66-83 59-76 (151)
60 cd08538 SAM_PNT-ESE-2-like Ste 22.9 48 0.001 25.7 1.3 19 41-59 43-61 (78)
61 cd08757 SAM_PNT_ESE Sterile al 22.9 38 0.00082 25.0 0.7 20 40-59 37-56 (68)
62 KOG2814|consensus 22.7 50 0.0011 32.1 1.6 30 36-67 189-218 (345)
63 PF05155 Phage_X: Phage X fami 22.6 1.3E+02 0.0028 23.4 3.6 31 19-52 10-40 (92)
64 PRK11409 antitoxin YefM; Provi 22.4 1.2E+02 0.0027 22.9 3.4 56 22-80 10-74 (83)
65 TIGR02253 CTE7 HAD superfamily 22.2 40 0.00087 27.3 0.8 44 16-81 124-167 (221)
66 PF03374 ANT: Phage antirepres 21.9 1.3E+02 0.0027 22.8 3.4 15 23-37 9-23 (111)
67 PF12793 SgrR_N: Sugar transpo 21.8 1.2E+02 0.0027 24.3 3.5 46 24-77 1-46 (115)
68 PF05396 Phage_T7_Capsid: Phag 21.8 2.8E+02 0.006 23.5 5.6 59 15-74 6-71 (123)
69 PF11663 Toxin_YhaV: Toxin wit 21.5 1.5E+02 0.0033 25.5 4.1 50 163-213 9-58 (140)
70 PF08006 DUF1700: Protein of u 21.3 1.8E+02 0.0039 24.1 4.5 40 21-60 21-66 (181)
71 cd06562 GH20_HexA_HexB-like Be 21.0 78 0.0017 29.3 2.5 60 30-89 150-213 (348)
No 1
>KOG3835|consensus
Probab=100.00 E-value=1.3e-69 Score=506.40 Aligned_cols=220 Identities=36% Similarity=0.536 Sum_probs=168.3
Q ss_pred ccCCCChhhHHHHHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcCCCCc
Q psy1866 5 TSTPNNEAELQLYRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTNPAMF 84 (235)
Q Consensus 5 ~~~p~~~~elqly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~p~~F 84 (235)
-++|+|+|||||||||||||||+|||+||+||||||||||+||||||||||+||||++||||||||||||+||++||++|
T Consensus 3 malPrTLgElQLyrVLqkANLlsYyd~FIqQGGDDvqQlceagEeEFLEIMaLVGMa~KPLHVRRlQkALrew~tnpglF 82 (495)
T KOG3835|consen 3 MALPRTLGELQLYRVLQKANLLSYYDVFIQQGGDDVQQLCEAGEEEFLEIMALVGMAPKPLHVRRLQKALREWSTNPGLF 82 (495)
T ss_pred CCCccchHHHHHHHHHHHhhHHHHHHHHHHhcchHHHHHHHhhHHHHHHHHHHhccCCcchhHHHHHHHHHHHhcCcchh
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCC------------------CCCcccccCCCCCCCCCCCCCCC------cccCC------CCCCCCCCCCCCCCC
Q psy1866 85 QTPLVSP------------------GLPSTNFLTRSLPSFLGTTPPLV------TSLSS------PSVSSNVPLPSSPPP 134 (235)
Q Consensus 85 q~PL~s~------------------~~pc~~~~~~~~~~~~s~~p~~~------~s~s~------p~~s~~~~lP~~s~~ 134 (235)
++||..+ |+||....+.+. .|+++.. +.+++ ++.+++..+++...+
T Consensus 83 nqpl~~ipvssip~yk~~et~pt~lgl~~~s~~~s~~----~p~~~~~s~~s~~~~~v~tlge~~s~~~gs~s~~~~g~s 158 (495)
T KOG3835|consen 83 NQPLQQIPVSSIPNYKPAETDPTALGLPGISAATSPK----FPSLRFLSQLSSVAEKVSTLGEAASTSSGSPSNLNTGSS 158 (495)
T ss_pred cCcccccCCCCCccccCCCCCcccccCccchhccCCC----CCchhhccccccccccccccccccCCCCCCcccCCCCCC
Confidence 9999865 455544333322 1222221 11111 112222224433322
Q ss_pred C-----C--CCCCCCCCCCCCCC-CCCC-----CCCCCCCCHHHHHH--HHHHHHHHHhhCCCCCchhh----hhhhhhH
Q psy1866 135 V-----E--STSQNFSPGQSPAE-VSSP-----LQLTPVLDDSQIAK--LADIAQQLVRALPHLEPKAQ----NSKKKIC 195 (235)
Q Consensus 135 ~-----~--sts~S~S~~~~~gs-~sSp-----~q~tp~L~~~qi~~--v~ecaeRL~~tLPq~dp~~~----~~nKKla 195 (235)
+ . .+..+.|-.++.|| ++|| ++.+..++.++.-. |.||||||++++|+.|.+++ |+|||++
T Consensus 159 r~wpg~~~~es~~~~s~~~d~gS~p~Sp~~~~~pets~a~~~aa~~ag~v~etverv~~a~P~~d~~ev~~llk~nkkLa 238 (495)
T KOG3835|consen 159 RSWPGAFKFESPLLESLASDQGSSPTSPVRSVLPETSSATSHAALPAGIVPETVERVSAAVPPPDSREVAVLLKNNKKLA 238 (495)
T ss_pred cccccccccCCcccccchhhcCCCCCCCccccCCCCccccccccccccccHHHHHhhhccCCCCchhHHHHHHhhhHHhh
Confidence 2 1 11222221234443 5666 56677777777777 99999999999999999975 6999999
Q ss_pred HhHHHHhcCCcccchhhhhhccccchhhhhhhh
Q psy1866 196 KDLEAVFQMSDEAVILKVKDNVHDSNLERITNK 228 (235)
Q Consensus 196 K~lehIf~Mse~DP~re~e~~~~~~~~~~~~~~ 228 (235)
++++|||+|.++||++|||||||+--.-|...|
T Consensus 239 ~s~ghifem~d~dp~keeeIrkyS~iyGRfdSk 271 (495)
T KOG3835|consen 239 FSGGHIFEMHDVDPPKEEEIRKYSTIYGRFDSK 271 (495)
T ss_pred hcccceeeecCCCCchhhhhhcchhhhcccccc
Confidence 999999999999999999999999876665544
No 2
>PF04904 NCD1: NAB conserved region 1 (NCD1); InterPro: IPR006988 Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors []. This entry represents the N-terminal NAB domain, which interacts with the EGR1 inhibitory domain (R1) []. It may also mediate multimerisation.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=100.00 E-value=2e-52 Score=319.59 Aligned_cols=81 Identities=81% Similarity=1.240 Sum_probs=79.7
Q ss_pred cCCCChhhHHHHHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcCCCCcc
Q psy1866 6 STPNNEAELQLYRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTNPAMFQ 85 (235)
Q Consensus 6 ~~p~~~~elqly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~p~~Fq 85 (235)
+.|+|+||||||+||||||||+|||+||++|||||||||+++|+||+|||+||||++||||||||||||+||++||++||
T Consensus 2 ~~p~~l~elqly~vLqrAnLl~Yyd~fi~~GgDDvqQL~~~~e~eF~eim~lvGM~sKPLHVrRlqKAL~ew~~~p~~Fq 81 (82)
T PF04904_consen 2 STPQTLGELQLYRVLQRANLLQYYDTFIAQGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWSTNPHAFQ 81 (82)
T ss_pred CCCCcHHHHHHHHHHHHhhHHHHHHHHHHHcChhHHHHHhcChHHHHHHHHHhCccCccHHHHHHHHHHHHHhcChhhhc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred c
Q psy1866 86 T 86 (235)
Q Consensus 86 ~ 86 (235)
.
T Consensus 82 ~ 82 (82)
T PF04904_consen 82 D 82 (82)
T ss_pred C
Confidence 4
No 3
>PF04905 NCD2: NAB conserved region 2 (NCD2); InterPro: IPR006989 Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors []. This entry represents a NAB domain near the C terminus of the protein. It is necessary for transcriptional repression by the Nab proteins []. It is also required for transcription activation by Nab proteins at Nab-activated promoters [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2YUF_A.
Probab=99.86 E-value=1.5e-22 Score=171.48 Aligned_cols=80 Identities=35% Similarity=0.555 Sum_probs=53.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHhhCCCCC----chhhhhhhhhHHhHHHHhcCCcccchhhhhhccccchhhhhhhhh-
Q psy1866 155 LQLTPVLDDSQIAKLADIAQQLVRALPHLE----PKAQNSKKKICKDLEAVFQMSDEAVILKVKDNVHDSNLERITNKK- 229 (235)
Q Consensus 155 ~q~tp~L~~~qi~~v~ecaeRL~~tLPq~d----p~~~~~nKKlaK~lehIf~Mse~DP~re~e~~~~~~~~~~~~~~~- 229 (235)
.+.+|+||++||++|++|||||+++||++| ++.+++|||++|+|+|||+|+++||+|++|||||+.-.-|..-|+
T Consensus 29 s~~~~~L~~~~v~~l~e~~erl~k~lP~~~~~e~~~~~~~kKK~~k~l~~v~~M~~~dp~r~eEiRkySaIygrfDskRr 108 (164)
T PF04905_consen 29 SSPTPVLDEEQVQKLAECVERLIKTLPRFDLSEVPKLLNTKKKLAKELEHVLEMSEDDPRREEEIRKYSAIYGRFDSKRR 108 (164)
T ss_dssp ------S-HHHHHHHHHHHHHHHHHS----HHHHHHHHHH-SHHHHHHTHHHHS-SS-HHHHHHHHHH--SSS-S---TT
T ss_pred ccccccCCHHHHHHHHHHHHHHHHhCCCCchhhhHHHHHhhhHHHHHHHHHHcCCCCChHHHHHHHHHHHHhCccccCCC
Confidence 344599999999999999999999999999 889999999999999999999999999999999998777654443
Q ss_pred hhccc
Q psy1866 230 YGRQL 234 (235)
Q Consensus 230 ~~~~~ 234 (235)
-|++|
T Consensus 109 ~~k~L 113 (164)
T PF04905_consen 109 PGKPL 113 (164)
T ss_dssp ---S-
T ss_pred CCCCc
Confidence 35544
No 4
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=97.28 E-value=0.0013 Score=45.51 Aligned_cols=59 Identities=22% Similarity=0.293 Sum_probs=51.8
Q ss_pred hHHHHHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Q psy1866 13 ELQLYRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEW 77 (235)
Q Consensus 13 elqly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w 77 (235)
.-++...|+.-+|-+|.+.| ..|-.|.+.|+...++++.+ +|+ .++-|-+||.++++++
T Consensus 5 ~~~V~~WL~~~~l~~y~~~F-~~~~i~g~~L~~lt~~dL~~----lgi-~~~ghr~ki~~~i~~L 63 (64)
T PF00536_consen 5 VEDVSEWLKSLGLEQYAENF-EKNYIDGEDLLSLTEEDLEE----LGI-TKLGHRKKILRAIQKL 63 (64)
T ss_dssp HHHHHHHHHHTTGGGGHHHH-HHTTSSHHHHTTSCHHHHHH----TT--SSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHH-HcCCchHHHHHhcCHHHHHH----cCC-CCHHHHHHHHHHHHHh
Confidence 45788899999999999999 99999999999999999776 455 4679999999999986
No 5
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=96.31 E-value=0.024 Score=37.76 Aligned_cols=57 Identities=26% Similarity=0.330 Sum_probs=48.6
Q ss_pred HHHHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Q psy1866 15 QLYRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEW 77 (235)
Q Consensus 15 qly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w 77 (235)
++...|++.++-.|.+.|.+.|= |.+.|+...++++. -+|+ .+|-|.+|+.+++.+.
T Consensus 6 ~V~~wL~~~~~~~y~~~f~~~~i-~g~~L~~l~~~dL~----~lgi-~~~g~r~~i~~~i~~l 62 (63)
T cd00166 6 DVAEWLESLGLGQYADNFRENGI-DGDLLLLLTEEDLK----ELGI-TLPGHRKKILKAIQKL 62 (63)
T ss_pred HHHHHHHHcChHHHHHHHHHcCC-CHHHHhHCCHHHHH----HcCC-CCHHHHHHHHHHHHHc
Confidence 56678999999999999999988 89999999988865 4576 4589999999999864
No 6
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=95.43 E-value=0.12 Score=34.58 Aligned_cols=61 Identities=23% Similarity=0.291 Sum_probs=45.3
Q ss_pred HHHHHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhc
Q psy1866 14 LQLYRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTT 79 (235)
Q Consensus 14 lqly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~ 79 (235)
-++...|+.-++-+|-+.|.+.|=|-...+....++++ +-+|+ .+|.|-+||.+++.+...
T Consensus 7 ~~v~~wL~~~g~~~y~~~f~~~~i~g~~ll~~~~~~~l----~~lgi-~~~~~r~~ll~~i~~l~~ 67 (68)
T smart00454 7 ESVADWLESIGLEQYADNFRKNGIDGALLLLLTSEEDL----KELGI-TKLGHRKKILKAIQKLKD 67 (68)
T ss_pred HHHHHHHHHCChHHHHHHHHHCCCCHHHHHhcChHHHH----HHcCC-CcHHHHHHHHHHHHHHHh
Confidence 35667899999999999999987655554443334443 33787 569999999999998754
No 7
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=94.73 E-value=0.13 Score=35.46 Aligned_cols=58 Identities=28% Similarity=0.375 Sum_probs=48.5
Q ss_pred HHHHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Q psy1866 15 QLYRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEW 77 (235)
Q Consensus 15 qly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w 77 (235)
++-..|.+.+|-+|.+.|.++|=|.+..|....++++. -.|+. ++-|.+||.+++++-
T Consensus 8 ~v~~WL~~~gl~~y~~~f~~~~i~g~~~L~~l~~~~L~----~lGI~-~~~~r~kll~~i~~L 65 (66)
T PF07647_consen 8 DVAEWLKSLGLEQYADNFRENGIDGLEDLLQLTEEDLK----ELGIT-NLGHRRKLLSAIQEL 65 (66)
T ss_dssp HHHHHHHHTTCGGGHHHHHHTTCSHHHHHTTSCHHHHH----HTTTT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCcHHHHHHHHHcCCcHHHHHhhCCHHHHH----HcCCC-CHHHHHHHHHHHHHc
Confidence 45567889999999999999999999999999888773 45663 577999999999863
No 8
>KOG4384|consensus
Probab=94.45 E-value=0.13 Score=49.26 Aligned_cols=67 Identities=27% Similarity=0.354 Sum_probs=58.4
Q ss_pred HHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcCCCCccccC
Q psy1866 17 YRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTNPAMFQTPL 88 (235)
Q Consensus 17 y~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~p~~Fq~PL 88 (235)
-..|++-||-.|..+|+++|=||++-+-+..|+++.|| |+ .+|=|-++|-.|++-|+.-+..|-++.
T Consensus 219 ~ewL~~i~le~y~~~~L~nGYd~le~~k~i~e~dL~~l----gI-~nP~Hr~kLL~av~~~~e~d~~~~~~~ 285 (361)
T KOG4384|consen 219 EEWLRRIGLEEYIETLLENGYDTLEDLKDITEEDLEEL----GI-DNPDHRKKLLSAVELLKEIDSGSEQVG 285 (361)
T ss_pred HHHHHHhhHHHHHHHHHHcchHHHHHHHhccHHHHHHh----CC-CCHHHHHHHHHHHHHHHhccccccccC
Confidence 34599999999999999999999999999999998875 54 589999999999999998777765443
No 9
>PRK10880 adenine DNA glycosylase; Provisional
Probab=90.53 E-value=0.32 Score=45.73 Aligned_cols=56 Identities=27% Similarity=0.388 Sum_probs=47.9
Q ss_pred HhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcC
Q psy1866 21 QRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTN 80 (235)
Q Consensus 21 qrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~ 80 (235)
+-++...||+.|++. .-|++.|++++++|.+++..=+|..+| .|+|+++.+.++..
T Consensus 44 ~v~~v~~~~~rl~~~-fPt~~~La~a~~eel~~~~~glGyy~R---Ar~L~~~A~~i~~~ 99 (350)
T PRK10880 44 QVATVIPYFERFMAR-FPTVTDLANAPLDEVLHLWTGLGYYAR---ARNLHKAAQQVATL 99 (350)
T ss_pred cHHHHHHHHHHHHHH-CcCHHHHHCcCHHHHHHHHHcCChHHH---HHHHHHHHHHHHHH
Confidence 346778899999996 568999999999999999999999865 88888888877654
No 10
>PRK13910 DNA glycosylase MutY; Provisional
Probab=89.35 E-value=0.46 Score=43.61 Aligned_cols=49 Identities=24% Similarity=0.332 Sum_probs=42.6
Q ss_pred HHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhc
Q psy1866 27 AYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTT 79 (235)
Q Consensus 27 ~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~ 79 (235)
.||+.|++.-. |++.|++++++|++++..=+|.-+| .|+|+++.+..+.
T Consensus 13 ~yy~rf~~~fP-t~e~La~a~~~el~~~~~glGyy~R---Ar~L~~~A~~i~~ 61 (289)
T PRK13910 13 RFYSPFLEAFP-TLKDLANAPLEEVLLLWRGLGYYSR---AKNLKKSAEICVK 61 (289)
T ss_pred HHHHHHHHHCC-CHHHHHCCCHHHHHHHHHcCCcHHH---HHHHHHHHHHHHH
Confidence 49999999877 5999999999999999999999876 7888887776654
No 11
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=86.56 E-value=1.2 Score=40.34 Aligned_cols=55 Identities=31% Similarity=0.462 Sum_probs=46.4
Q ss_pred hhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcC
Q psy1866 22 RASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTN 80 (235)
Q Consensus 22 rAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~ 80 (235)
-++...||+.|++. --+++.|++++++|+++++.=+|+.+| .|+|+++.+....+
T Consensus 41 v~~v~~~~~rl~~~-fpt~~~La~a~~eeL~~~~~~lG~y~R---Ar~L~~~A~~i~~~ 95 (275)
T TIGR01084 41 VATVIPYFERFLER-FPTVQALANAPQDEVLKLWEGLGYYAR---ARNLHKAAQEVVEE 95 (275)
T ss_pred HHHHHHHHHHHHHh-CCCHHHHHCcCHHHHHHHHHHCCcHHH---HHHHHHHHHHHHHH
Confidence 35667899999986 578999999999999999999999876 78888887766553
No 12
>KOG3037|consensus
Probab=80.53 E-value=4.7 Score=38.62 Aligned_cols=37 Identities=24% Similarity=0.328 Sum_probs=32.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHH---HHHHHhhCCCCCchh
Q psy1866 151 VSSPLQLTPVLDDSQIAKLADI---AQQLVRALPHLEPKA 187 (235)
Q Consensus 151 ~sSp~q~tp~L~~~qi~~v~ec---aeRL~~tLPq~dp~~ 187 (235)
+.+...+..+|.++.|..|..| .|||+.+||..+++.
T Consensus 219 g~~~vdLa~vL~~e~v~~vl~~~~v~erL~phlP~d~~~~ 258 (330)
T KOG3037|consen 219 GASTVDLATVLKPEAVAPVLANPGVQERLMPHLPSDHDRA 258 (330)
T ss_pred CccceehhhhcChHHHHHHhhCcchhhhhcccCCCCCcch
Confidence 3446789999999999999998 899999999988874
No 13
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=75.06 E-value=11 Score=33.88 Aligned_cols=63 Identities=25% Similarity=0.335 Sum_probs=48.8
Q ss_pred hhHHHHHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhc
Q psy1866 12 AELQLYRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTT 79 (235)
Q Consensus 12 ~elqly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~ 79 (235)
..+--+++..+++.+..=|.+|...|- + ...++|+.+....=||..--+...+|.+.|++|+.
T Consensus 191 ~~~lr~rL~~~~~~l~~dD~~i~~eGv--~---~Ls~~EL~~Ac~~RGl~~~~~s~~~lr~~L~~WL~ 253 (268)
T PF07766_consen 191 SSLLRRRLRKRLRYLKQDDRLIKREGV--D---SLSEEELQDACYERGLRSTGLSEEELREWLKQWLQ 253 (268)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH-G--G---GS-HHHHHHHHHHTT---TT--HHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhcc--c---cCCHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHH
Confidence 556678899999999999999998863 2 34689999999999999999999999999999974
No 14
>cd00814 MetRS_core catalytic core domain of methioninyl-tRNA synthetases. Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function.
Probab=70.95 E-value=8.6 Score=34.56 Aligned_cols=83 Identities=24% Similarity=0.396 Sum_probs=62.9
Q ss_pred ceeccCCCChhhH--------HHHHHHHhhhhHHHHHHHHHcCCchH---------------HHHHhhChHHHHHHHHHh
Q psy1866 2 MVLTSTPNNEAEL--------QLYRVMQRASLLAYYDTLLEMGGDDV---------------QQLCEAGEEEFLEIMALV 58 (235)
Q Consensus 2 ~v~~~~p~~~~el--------qly~vlqrAnLl~Yyd~~i~~GgDdv---------------qql~~~~e~efleim~lv 58 (235)
+|+|+.|.--|.+ =+.+|+.|..-+.-|+.+.-.|=||. +++|+.-.++|.+.++.+
T Consensus 3 ~it~~~Py~ng~~HlGH~~~~~~~Dv~~R~~r~~G~~V~~~~g~Dd~g~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~L 82 (319)
T cd00814 3 LITTALPYVNGVPHLGHLYGTVLADVFARYQRLRGYDVLFVTGTDEHGTKIEQKAEEEGVTPQELCDKYHEIFKDLFKWL 82 (319)
T ss_pred EEEeCCCCCCCCcchhhHHHHHHHHHHHHHHHhCCCcccccCccCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHc
Confidence 5788888754443 44577777766667777777777765 678888899999999999
Q ss_pred cCC-------CCchHHHHHHHHHHHHhcCCCCc
Q psy1866 59 GMA-------SKPLHVRRLQKALQEWTTNPAMF 84 (235)
Q Consensus 59 GM~-------~KPlHVrRlqkal~~w~~~p~~F 84 (235)
|+. +-|-|....++.+++...+-.++
T Consensus 83 gI~~D~~~~tt~~~~~~~v~~i~~~L~ekG~iY 115 (319)
T cd00814 83 NISFDYFIRTTSPRHKEIVQEFFKKLYENGYIY 115 (319)
T ss_pred CCcCCCCeeCCCHHHHHHHHHHHHHHHHCCCEE
Confidence 974 45779998899988887765554
No 15
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=65.19 E-value=24 Score=27.94 Aligned_cols=56 Identities=21% Similarity=0.274 Sum_probs=44.9
Q ss_pred hhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcCC
Q psy1866 23 ASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTNP 81 (235)
Q Consensus 23 AnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~p 81 (235)
++-...|..|.+..|.|.+.|.+++++|+.++..-+| ..--.++|+++.+.+...-
T Consensus 16 ~~a~~~~~~l~~~~gpt~~~l~~~~~~~l~~~~~~~G---~~~kA~~i~~~a~~~~~~~ 71 (158)
T cd00056 16 KAVNKAYERLFERYGPTPEALAAADEEELRELIRSLG---YRRKAKYLKELARAIVEGF 71 (158)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHCCCHHHHHHHHHhcC---hHHHHHHHHHHHHHHHHHc
Confidence 4455678899999889999999999999999999999 3455677777777766543
No 16
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=62.94 E-value=18 Score=32.24 Aligned_cols=54 Identities=11% Similarity=0.144 Sum_probs=40.8
Q ss_pred hhhHHHHHHHHHcC---Cc---hHHHHHhhChHHHHHHHHHhcCCC-CchHHHHHHHHHHH
Q psy1866 23 ASLLAYYDTLLEMG---GD---DVQQLCEAGEEEFLEIMALVGMAS-KPLHVRRLQKALQE 76 (235)
Q Consensus 23 AnLl~Yyd~~i~~G---gD---dvqql~~~~e~efleim~lvGM~~-KPlHVrRlqkal~~ 76 (235)
+|....|+.|.+.| || |.+.|++++++|+.+++.=+|+.. |--+++.+-+++.+
T Consensus 46 ~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~ 106 (218)
T PRK13913 46 EAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILK 106 (218)
T ss_pred HHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence 45667778887764 33 999999999999999999999954 76555555555543
No 17
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=62.12 E-value=8 Score=26.87 Aligned_cols=42 Identities=26% Similarity=0.467 Sum_probs=32.4
Q ss_pred HHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHH
Q psy1866 30 DTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQE 76 (235)
Q Consensus 30 d~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~ 76 (235)
..|++.|=..+++|..++.++ ++++-|+..| .+++|..++++
T Consensus 19 ~~L~~~G~~t~~~l~~a~~~~---L~~i~Gig~~--~a~~i~~~~~~ 60 (60)
T PF14520_consen 19 EKLYEAGIKTLEDLANADPEE---LAEIPGIGEK--TAEKIIEAARE 60 (60)
T ss_dssp HHHHHTTCSSHHHHHTSHHHH---HHTSTTSSHH--HHHHHHHHHHH
T ss_pred HHHHhcCCCcHHHHHcCCHHH---HhcCCCCCHH--HHHHHHHHHhC
Confidence 567778888999999997765 5667788544 78888888875
No 18
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=58.78 E-value=9.5 Score=28.36 Aligned_cols=50 Identities=26% Similarity=0.356 Sum_probs=39.0
Q ss_pred HHHHHHHHHc-CCchHHHHHhhChHHHHHHHHHhcCC-CCchHHHHHHHHHHHHh
Q psy1866 26 LAYYDTLLEM-GGDDVQQLCEAGEEEFLEIMALVGMA-SKPLHVRRLQKALQEWT 78 (235)
Q Consensus 26 l~Yyd~~i~~-GgDdvqql~~~~e~efleim~lvGM~-~KPlHVrRlqkal~~w~ 78 (235)
...|..|++. |.-+.++|.+++++|+.+++.-+|+. .|- ++|+.+.+.|.
T Consensus 15 ~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka---~~i~~~a~~~~ 66 (108)
T PF00730_consen 15 RKIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKA---KYIIELARAIL 66 (108)
T ss_dssp HHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHH---HHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHH---HHHHHHHHHhh
Confidence 4567777777 56999999999999999999999998 665 45555555555
No 19
>KOG2507|consensus
Probab=57.47 E-value=19 Score=36.22 Aligned_cols=58 Identities=19% Similarity=0.279 Sum_probs=33.9
Q ss_pred HcCCchHHHHHhhChHHHHHHHHHhcCCCCchHH-----------HHHHHHHH---HHhcCCCCccccCCCC
Q psy1866 34 EMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHV-----------RRLQKALQ---EWTTNPAMFQTPLVSP 91 (235)
Q Consensus 34 ~~GgDdvqql~~~~e~efleim~lvGM~~KPlHV-----------rRlqkal~---~w~~~p~~Fq~PL~s~ 91 (235)
+.|--+-+|+++.=.---.--+.++|..++||.| -|+.|++. =+-+.-+.|..+++..
T Consensus 60 qags~aa~qFs~IYp~v~vPs~ffIg~sGtpLevitg~v~adeL~~~i~Kv~~~~h~~~t~~s~f~~a~a~s 131 (506)
T KOG2507|consen 60 QAGSVAATQFSAIYPYVSVPSIFFIGFSGTPLEVITGFVTADELASSIEKVWLGLHIQETTASIFSAALASS 131 (506)
T ss_pred ccCchhhhhhhhhcccccccceeeecCCCceeEEeeccccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhh
Confidence 3444555555543222222223467999999964 57777653 4456667788887653
No 20
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=57.26 E-value=24 Score=29.68 Aligned_cols=53 Identities=23% Similarity=0.241 Sum_probs=37.5
Q ss_pred hhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCC-CchHHHHHHHHHHHHhc
Q psy1866 23 ASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMAS-KPLHVRRLQKALQEWTT 79 (235)
Q Consensus 23 AnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~-KPlHVrRlqkal~~w~~ 79 (235)
++-...|+.|.+. .-|.++|++++++|+.+++.=+|+.. |- ++|++..+.+..
T Consensus 42 ~~~~~~~~~l~~~-~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka---~~i~~~a~~i~~ 95 (191)
T TIGR01083 42 KSVNKATKKLFEV-YPTPQALAQAGLEELEEYIKSIGLYRNKA---KNIIALCRILVE 95 (191)
T ss_pred HHHHHHHHHHHHH-CCCHHHHHcCCHHHHHHHHHhcCChHHHH---HHHHHHHHHHHH
Confidence 3445667777764 44899999999999999999999864 54 444444444433
No 21
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=55.63 E-value=35 Score=26.89 Aligned_cols=49 Identities=20% Similarity=0.230 Sum_probs=35.2
Q ss_pred hHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHH
Q psy1866 25 LLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQE 76 (235)
Q Consensus 25 Ll~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~ 76 (235)
-...|..|.+.-| +.++|..++++|+.+++.-+|+... -.++|.+..+.
T Consensus 10 a~~~~~~l~~~~~-~~~~l~~~~~~eL~~~l~~~g~~~~--ka~~i~~~a~~ 58 (149)
T smart00478 10 VNKATERLFEKFP-TPEDLAAADEEELEELIRPLGFYRR--KAKYLIELARI 58 (149)
T ss_pred HHHHHHHHHHHCC-CHHHHHCCCHHHHHHHHHHcCChHH--HHHHHHHHHHH
Confidence 3456667777666 7999999999999999988997542 34555544433
No 22
>KOG0427|consensus
Probab=55.18 E-value=8.3 Score=33.47 Aligned_cols=16 Identities=56% Similarity=1.022 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHhcCCC
Q psy1866 67 VRRLQKALQEWTTNPA 82 (235)
Q Consensus 67 VrRlqkal~~w~~~p~ 82 (235)
-+||||.|-+|.+||-
T Consensus 17 t~RLqKEl~e~q~~pP 32 (161)
T KOG0427|consen 17 TNRLQKELSEWQNNPP 32 (161)
T ss_pred HHHHHHHHHHHhcCCC
Confidence 5899999999999973
No 23
>PF07462 MSP1_C: Merozoite surface protein 1 (MSP1) C-terminus; InterPro: IPR010901 This entry represents the C-terminal region of merozoite surface protein 1 (MSP1), which is found in a number of Plasmodium species. MSP-1 is a 200 kDa protein expressed on the surface of the Plasmodium vivax merozoite. MSP-1 of Plasmodium species is synthesised as a high-molecular-weight precursor and then processed into several fragments. At the time of red cell invasion by the merozoite, only the 19 kDa C-terminal fragment (MSP-119), which contains two epidermal growth factor-like domains, remains on the surface. Antibodies against MSP-119 inhibit merozoite entry into red cells, and immunisation with MSP-119 protects monkeys from challenging infections. Hence, MSP-119 is considered a promising vaccine candidate [].; GO: 0009405 pathogenesis, 0016020 membrane
Probab=54.72 E-value=66 Score=33.11 Aligned_cols=64 Identities=17% Similarity=0.248 Sum_probs=43.4
Q ss_pred hHHHHHHHHhhhhHHHHHHHHHcCCchHHHHHhhC---hHHHHHHHHHhcCCCCchHHHH--HHHHHHHHh
Q psy1866 13 ELQLYRVMQRASLLAYYDTLLEMGGDDVQQLCEAG---EEEFLEIMALVGMASKPLHVRR--LQKALQEWT 78 (235)
Q Consensus 13 elqly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~---e~efleim~lvGM~~KPlHVrR--lqkal~~w~ 78 (235)
-|+=||||.|-- .=.-.=|+.|-..|-+|..-- =.||.||+.=-+.++|.=|.-- ..+||+.|.
T Consensus 187 nlEkFrvlSrlE--grl~~Ni~LeKenIsYlSsgLhHv~tElKeii~nK~YtG~~~~~n~~~Vk~ALq~Yq 255 (574)
T PF07462_consen 187 NLEKFRVLSRLE--GRLGKNINLEKENISYLSSGLHHVFTELKEIIKNKKYTGNDHAKNIAEVKEALQAYQ 255 (574)
T ss_pred hHHHHHHHHHHH--HHhccccccchhhhhhhhhhHHHHHHHHHHHHhcCCCCCCChhhhHHHHHHHHHHHH
Confidence 355667776632 222333566777777777654 4588888888899999876544 889999884
No 24
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=53.94 E-value=41 Score=27.64 Aligned_cols=50 Identities=16% Similarity=0.329 Sum_probs=36.7
Q ss_pred HHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHH-HHHHHHHHHhc
Q psy1866 28 YYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVR-RLQKALQEWTT 79 (235)
Q Consensus 28 Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVr-Rlqkal~~w~~ 79 (235)
--|+++..+|+-+.+... ..+|++-|.-+-...-+..|+ |+-..++.|..
T Consensus 64 LLe~~vkNCG~~fh~eva--s~~fl~~l~~l~~~~~~~~Vk~kil~li~~W~~ 114 (142)
T cd03569 64 LLESCVKNCGTHFHDEVA--SREFMDELKDLIKTTKNEEVRQKILELIQAWAL 114 (142)
T ss_pred HHHHHHHHCCHHHHHHHh--hHHHHHHHHHHHcccCCHHHHHHHHHHHHHHHH
Confidence 347899999999987655 578988654433334566676 88889999984
No 25
>KOG0199|consensus
Probab=52.04 E-value=41 Score=36.35 Aligned_cols=68 Identities=24% Similarity=0.364 Sum_probs=50.0
Q ss_pred CChhhHHHHHHHHhhhhHHHHHHHHHc----CCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcCCCCc
Q psy1866 9 NNEAELQLYRVMQRASLLAYYDTLLEM----GGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTNPAMF 84 (235)
Q Consensus 9 ~~~~elqly~vlqrAnLl~Yyd~~i~~----GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~p~~F 84 (235)
-++|..-|+.+|++|.|-+||-.|... --||.++. .+||+++| ||.- | -.|||.+|+..-..-+..|
T Consensus 5 peagd~wLleLLr~aqL~qf~s~lr~~lnvrr~~hf~yV---k~eDLl~I----GMgR-p-~qRRLrea~kkm~~~~k~k 75 (1039)
T KOG0199|consen 5 PEAGDDWLLELLRKAQLDQFISQLRFLLNVRRFDHFSYV---KDEDLLEI----GMGR-P-QQRRLREAIKKMSREMKNK 75 (1039)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHhccCchhhhhhc---chhhhhhh----ccCc-H-HHHHHHHHHHHhhhhcccc
Confidence 356788899999999999999988763 33444432 46777764 8864 3 5799999998877666655
Q ss_pred c
Q psy1866 85 Q 85 (235)
Q Consensus 85 q 85 (235)
+
T Consensus 76 s 76 (1039)
T KOG0199|consen 76 S 76 (1039)
T ss_pred c
Confidence 3
No 26
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=47.46 E-value=23 Score=33.91 Aligned_cols=84 Identities=23% Similarity=0.324 Sum_probs=61.1
Q ss_pred CceeccCCCChhhH--------HHHHHHHhhhhHHHHHHHHHcCCc---------------hHHHHHhhChHHHHHHHHH
Q psy1866 1 MMVLTSTPNNEAEL--------QLYRVMQRASLLAYYDTLLEMGGD---------------DVQQLCEAGEEEFLEIMAL 57 (235)
Q Consensus 1 ~~v~~~~p~~~~el--------qly~vlqrAnLl~Yyd~~i~~GgD---------------dvqql~~~~e~efleim~l 57 (235)
++|||+.|.--|.+ =..+||.|.--+.-|+++.-.|=| +.+++|+--.++|.+.++.
T Consensus 1 ~~it~~~P~~ng~lHiGH~~~~~~aDvl~R~~r~~G~~V~~v~g~D~~g~~i~~~a~~~g~~~~e~~~~~~~~~~~~l~~ 80 (530)
T TIGR00398 1 ILITTALPYANGKPHLGHAYTTILADVYARYKRLRGYEVLFVCGTDEHGTKIELKAEQEGLTPKELVDKYHEEFKDDWKW 80 (530)
T ss_pred CEEecCCCCCCCCcccchhHHHHHHHHHHHHHHhcCCeEEEecccCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 46888888765543 345677776666666666555544 4678888888999999999
Q ss_pred hcCC-------CCchHHHHHHHHHHHHhcCCCCc
Q psy1866 58 VGMA-------SKPLHVRRLQKALQEWTTNPAMF 84 (235)
Q Consensus 58 vGM~-------~KPlHVrRlqkal~~w~~~p~~F 84 (235)
+|+. .=|.|....++.+.+...+-.++
T Consensus 81 LgI~~D~~~~t~~~~~~~~v~~~~~~L~~kG~iY 114 (530)
T TIGR00398 81 LNISFDRFIRTTDEEHKEIVQKIFQKLKENGYIY 114 (530)
T ss_pred hCCCCCCCccCCCHHHHHHHHHHHHHHHHCCCEE
Confidence 9974 35679988999999988876655
No 27
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=46.84 E-value=31 Score=26.73 Aligned_cols=50 Identities=22% Similarity=0.480 Sum_probs=31.9
Q ss_pred HHHHHHHhhhhHHHHHHHHHcCCchHHHHHhh-----ChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcCCCCccccCC
Q psy1866 15 QLYRVMQRASLLAYYDTLLEMGGDDVQQLCEA-----GEEEFLEIMALVGMASKPLHVRRLQKALQEWTTNPAMFQTPLV 89 (235)
Q Consensus 15 qly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~-----~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~p~~Fq~PL~ 89 (235)
+|..+|++.+ ++.++...|....+|-.. .++|..++| +.||.+++.|++
T Consensus 40 eL~~~l~~~g----~~~li~~~~~~yk~l~l~~~~~~s~~e~~~~l----------------------~~~p~LikRPIi 93 (105)
T cd03035 40 TLERWLAKVG----WETLLNKRGTTWRKLDDAQKAALDAAKAIALM----------------------LEHPSLIKRPVL 93 (105)
T ss_pred HHHHHHHHhC----hHHHHccCchHHHhCChhhhccCCHHHHHHHH----------------------HhCcCeeecceE
Confidence 3455666666 477888887777765322 234444443 589999999886
Q ss_pred C
Q psy1866 90 S 90 (235)
Q Consensus 90 s 90 (235)
=
T Consensus 94 ~ 94 (105)
T cd03035 94 E 94 (105)
T ss_pred E
Confidence 3
No 28
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=46.53 E-value=53 Score=21.35 Aligned_cols=42 Identities=24% Similarity=0.300 Sum_probs=32.2
Q ss_pred HHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHH
Q psy1866 30 DTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQE 76 (235)
Q Consensus 30 d~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~ 76 (235)
+.|.+.|=+.++.|.++..+|+.+| .||. .=.+..++.+.++
T Consensus 7 ~~L~~~G~~s~e~la~~~~~eL~~i---~g~~--~e~a~~ii~~a~~ 48 (50)
T TIGR01954 7 QLLVEEGFTTVEDLAYVPIDELLSI---EGFD--EETAKELINRARN 48 (50)
T ss_pred HHHHHcCCCCHHHHHccCHHHHhcC---CCCC--HHHHHHHHHHHHH
Confidence 5688899999999999999998775 6765 3456666666654
No 29
>PF06222 Phage_TAC: Phage tail assembly chaperone; InterPro: IPR010411 This entry is represented by Bacteriophage HK97, Gp13 and Gp14. These are two overlapping reading frames []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These proteins include several putative tail assembly chaperones encoded by phages of Gram-negative bacteria.; PDB: 2OB9_A.
Probab=45.57 E-value=9.9 Score=32.18 Aligned_cols=47 Identities=30% Similarity=0.543 Sum_probs=31.0
Q ss_pred HHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHH
Q psy1866 20 MQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQ 75 (235)
Q Consensus 20 lqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~ 75 (235)
=.+|+..-|.|.|++..|. =--+++|..+++++.| |.|.|=|.+||.
T Consensus 70 n~~Adv~LFidVL~dE~~~-----rVFsd~D~~~V~~~YG----PVHaRLl~qALe 116 (127)
T PF06222_consen 70 NLRADVVLFIDVLLDEDGQ-----RVFSDDDAEQVAAIYG----PVHARLLRQALE 116 (127)
T ss_dssp HHHHHHHHHHHHEE-TTS------BSS-GGGHHHHHCC------HHHHHHHHHHHT
T ss_pred hhhcchhhhhHHHhcCCCC-----cccCcchHHHHHHHhc----hHHHHHHHHHHH
Confidence 3456666667777666665 2235778888888888 999999999985
No 30
>KOG0260|consensus
Probab=44.51 E-value=77 Score=35.86 Aligned_cols=17 Identities=29% Similarity=0.399 Sum_probs=11.0
Q ss_pred hHHHHHhhChHHHHHHH
Q psy1866 39 DVQQLCEAGEEEFLEIM 55 (235)
Q Consensus 39 dvqql~~~~e~efleim 55 (235)
|+-+|+-+.=||--+|+
T Consensus 1366 ~tgaLmrcSfEetv~il 1382 (1605)
T KOG0260|consen 1366 DTGALMRCSFEETVDIL 1382 (1605)
T ss_pred hccccccccHHHHHHHH
Confidence 56677777666655554
No 31
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=42.55 E-value=42 Score=26.90 Aligned_cols=51 Identities=24% Similarity=0.408 Sum_probs=37.8
Q ss_pred HHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchH---HH-HHHHHHHHHhc
Q psy1866 27 AYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLH---VR-RLQKALQEWTT 79 (235)
Q Consensus 27 ~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlH---Vr-Rlqkal~~w~~ 79 (235)
.--|.++..+|+.+..-+.. .+|++-|.-+-..++.-. || |+.+-|++|..
T Consensus 64 ~lld~lvkNcg~~f~~ev~~--~~fl~~l~~l~~~~~~~~~~~Vk~k~l~ll~~W~~ 118 (140)
T PF00790_consen 64 TLLDALVKNCGPRFHREVAS--KEFLDELVKLIKSKKTDPETPVKEKILELLQEWAE 118 (140)
T ss_dssp HHHHHHHHHSHHHHHHHHTS--HHHHHHHHHHHHHTTTHHHSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHHhH--HHHHHHHHHHHccCCCCchhHHHHHHHHHHHHHHH
Confidence 34588999999999765543 479987776666666554 66 78888899975
No 32
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=41.96 E-value=41 Score=33.75 Aligned_cols=84 Identities=14% Similarity=0.117 Sum_probs=65.7
Q ss_pred ceeccCCCChh--------hHHHHHHHHhhhhHHHHHHHHHcCCch---------------HHHHHhhChHHHHHHHHHh
Q psy1866 2 MVLTSTPNNEA--------ELQLYRVMQRASLLAYYDTLLEMGGDD---------------VQQLCEAGEEEFLEIMALV 58 (235)
Q Consensus 2 ~v~~~~p~~~~--------elqly~vlqrAnLl~Yyd~~i~~GgDd---------------vqql~~~~e~efleim~lv 58 (235)
+|||+.|..-| ..=+.+|+.|..-+.-|+++.-.|-|| .+++|+--.++|.+.++.+
T Consensus 5 ~itt~~py~ng~~HiGH~~~~l~aDv~aR~~r~~G~~V~~~~g~D~hG~~i~~~A~~~g~~p~e~~~~~~~~~~~~~~~l 84 (673)
T PRK00133 5 LVTCALPYANGPIHLGHLVEYIQADIWVRYQRMRGHEVLFVCADDAHGTPIMLKAEKEGITPEELIARYHAEHKRDFAGF 84 (673)
T ss_pred EEeCCCCCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEeCccCCCChHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence 68888885443 344567788877777788888788774 5778888899999999999
Q ss_pred cC-------CCCchHHHHHHHHHHHHhcCCCCcc
Q psy1866 59 GM-------ASKPLHVRRLQKALQEWTTNPAMFQ 85 (235)
Q Consensus 59 GM-------~~KPlHVrRlqkal~~w~~~p~~Fq 85 (235)
|. +.-|-|++..|+.++.-..+=.++.
T Consensus 85 ~i~~d~f~rtt~~~h~~~v~~~~~~L~~~G~iy~ 118 (673)
T PRK00133 85 GISFDNYGSTHSEENRELAQEIYLKLKENGYIYE 118 (673)
T ss_pred CCCCCCCccCCcHHHHHHHHHHHHHHHHCCCEEE
Confidence 96 2467899999999999888776664
No 33
>cd03032 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif.
Probab=41.86 E-value=41 Score=26.01 Aligned_cols=54 Identities=11% Similarity=0.308 Sum_probs=30.3
Q ss_pred hHHHHHHHHhhhhHHHHHHHHHcCCchHHHHH----hhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcCCCCccccC
Q psy1866 13 ELQLYRVMQRASLLAYYDTLLEMGGDDVQQLC----EAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTNPAMFQTPL 88 (235)
Q Consensus 13 elqly~vlqrAnLl~Yyd~~i~~GgDdvqql~----~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~p~~Fq~PL 88 (235)
.-+|.++|+..++- ++.++.-.|....+|- +..++|..++ -+.||.+++.|+
T Consensus 39 ~~el~~~~~~~~~~--~~~l~n~~~~~~k~l~~~~~~ls~~e~i~~----------------------l~~~p~LikRPi 94 (115)
T cd03032 39 KEELKEILSLTENG--VEDIISTRSKAFKNLNIDIDELSLSELIRL----------------------ISEHPSLLRRPI 94 (115)
T ss_pred HHHHHHHHHHhcCC--HHHHHhcCcHHHHHcCCCcccCCHHHHHHH----------------------HHhChhheeCCE
Confidence 33455566555432 5555555555555543 1223444333 358999999998
Q ss_pred CC
Q psy1866 89 VS 90 (235)
Q Consensus 89 ~s 90 (235)
+-
T Consensus 95 i~ 96 (115)
T cd03032 95 II 96 (115)
T ss_pred EE
Confidence 74
No 34
>TIGR01493 HAD-SF-IA-v2 Haloacid dehalogenase superfamily, subfamily IA, variant 2 with 3rd motif like haloacid dehalogenase. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that modelling it with a single alignment is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms : (1) hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only o
Probab=40.04 E-value=33 Score=26.87 Aligned_cols=43 Identities=21% Similarity=0.326 Sum_probs=29.9
Q ss_pred HHHHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcC
Q psy1866 15 QLYRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGM 60 (235)
Q Consensus 15 qly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM 60 (235)
.+-.+|++.+|..|||..+ ++||+.. ..-..+=|+.+++.+|+
T Consensus 112 ~~~~~l~~~~l~~~fd~v~--~~~~~~~-~KP~p~~f~~~~~~~~~ 154 (175)
T TIGR01493 112 AFDQFAQQAGLPWYFDRAF--SVDTVRA-YKPDPVVYELVFDTVGL 154 (175)
T ss_pred HHHHHHHHCCCHHHHhhhc--cHhhcCC-CCCCHHHHHHHHHHHCC
Confidence 4456789999999998754 6776643 23346667888888776
No 35
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=36.48 E-value=37 Score=25.96 Aligned_cols=40 Identities=18% Similarity=0.374 Sum_probs=29.1
Q ss_pred HHHHHHHHhhhhHHHHHHHHHcCCc-------hHHHHHhhChHHHHH
Q psy1866 14 LQLYRVMQRASLLAYYDTLLEMGGD-------DVQQLCEAGEEEFLE 53 (235)
Q Consensus 14 lqly~vlqrAnLl~Yyd~~i~~GgD-------dvqql~~~~e~efle 53 (235)
..+|.+|+.++|-+||+---+.|.- +.+++...+.++|.+
T Consensus 33 ~~V~~~i~~~gL~~yY~~r~~~~~~p~~~~~~~~~~~~~~D~~~v~~ 79 (88)
T PF12156_consen 33 QAVYQLIHENGLESYYQKRTDPGLSPDPLVPDQLEDLAYYDDPEVQQ 79 (88)
T ss_pred HHHHHHHHHcchHHHHhccCccCCCCcccccccHHHHHHcCCHHHHH
Confidence 5689999999999999977665432 345566666666654
No 36
>KOG3263|consensus
Probab=36.18 E-value=48 Score=29.91 Aligned_cols=55 Identities=25% Similarity=0.459 Sum_probs=34.8
Q ss_pred HcCCchHHHHHhhChHHHHHHHHHhcCC------CCchH------H-HHHHHHHHHHhcCCCCccccCC
Q psy1866 34 EMGGDDVQQLCEAGEEEFLEIMALVGMA------SKPLH------V-RRLQKALQEWTTNPAMFQTPLV 89 (235)
Q Consensus 34 ~~GgDdvqql~~~~e~efleim~lvGM~------~KPlH------V-rRlqkal~~w~~~p~~Fq~PL~ 89 (235)
+-|-|+.-.|--+.| |-.|.|++.|+. .|+.- | -=+|.--++|.+-++-||-||-
T Consensus 127 ~~~K~~~ad~eg~ee-EeiEMmk~MGf~gFDtTkgkkv~g~dV~~v~~v~KrkyRQYMNR~GGFNRPLd 194 (196)
T KOG3263|consen 127 EVGKDAMADLEGKEE-EEIEMMKIMGFSGFDTTKGKKVGGSDVGGVYKVKKRKYRQYMNRKGGFNRPLD 194 (196)
T ss_pred cccchhhhhccCCCH-HHHHHHHHhCcCcccCCCCccccCcccchhhhhhhhhHHHHhccCCCCCCCCC
Confidence 334444444444434 447777777764 36654 1 2245667899999999999984
No 37
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=33.14 E-value=83 Score=26.47 Aligned_cols=39 Identities=31% Similarity=0.360 Sum_probs=32.3
Q ss_pred CCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHH
Q psy1866 36 GGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQE 76 (235)
Q Consensus 36 GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~ 76 (235)
..-=+++|.+..|+|..+||.-+|-. -=-+|||.+||+-
T Consensus 89 ~~~tLe~Llemsd~el~~~l~~~g~~--~EE~rRL~~Al~~ 127 (129)
T PF13543_consen 89 KVLTLEALLEMSDEELKEILNRCGAR--EEECRRLCRALSN 127 (129)
T ss_pred hhcCHHHHHhCCHHHHHHHHHHhCCC--HHHHHHHHHHHHh
Confidence 55667888888999999999998876 4578999999863
No 38
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=32.98 E-value=1.7e+02 Score=24.18 Aligned_cols=49 Identities=20% Similarity=0.395 Sum_probs=34.6
Q ss_pred HHHHHHcCCchHHHHHhhChHHHH-HHHHHhcC----CCCchHHH-HHHHHHHHHhc
Q psy1866 29 YDTLLEMGGDDVQQLCEAGEEEFL-EIMALVGM----ASKPLHVR-RLQKALQEWTT 79 (235)
Q Consensus 29 yd~~i~~GgDdvqql~~~~e~efl-eim~lvGM----~~KPlHVr-Rlqkal~~w~~ 79 (235)
-|++++-+|+.+++... ..+|+ |+++++-= ..-|.+|+ |+-.-|+.|..
T Consensus 62 Le~~vkNCG~~fh~eva--s~~Fl~el~kl~~~k~~~~~~~~~Vk~kil~li~~W~~ 116 (139)
T cd03567 62 LEACMKNCGERFHSEVG--KFRFLNELIKLVSPKYLGSRTSEKVKTKIIELLYSWTL 116 (139)
T ss_pred HHHHHHHcCHHHHHHHH--hHHHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHH
Confidence 47889999999986654 56887 67777720 11255665 67778899985
No 39
>KOG4154|consensus
Probab=32.70 E-value=20 Score=31.41 Aligned_cols=25 Identities=32% Similarity=0.616 Sum_probs=20.4
Q ss_pred HHHhcCCCCchHHHHHHHHHHHHhc
Q psy1866 55 MALVGMASKPLHVRRLQKALQEWTT 79 (235)
Q Consensus 55 m~lvGM~~KPlHVrRlqkal~~w~~ 79 (235)
+.|-...=|-|.|+-|+|-|.||-.
T Consensus 127 idlnsvdlkklkvkdlkkilddw~e 151 (178)
T KOG4154|consen 127 IDLNSVDLKKLKVKDLKKILDDWDE 151 (178)
T ss_pred cCcchhhHHHHhHHHHHHHHhhhhh
Confidence 4455566789999999999999954
No 40
>KOG2499|consensus
Probab=31.87 E-value=30 Score=35.20 Aligned_cols=76 Identities=21% Similarity=0.418 Sum_probs=56.9
Q ss_pred HHHHHHHhh--h-hHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCc-----hHHHHHHHHHHHHhcCCCCccc
Q psy1866 15 QLYRVMQRA--S-LLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKP-----LHVRRLQKALQEWTTNPAMFQT 86 (235)
Q Consensus 15 qly~vlqrA--n-Ll~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KP-----lHVrRlqkal~~w~~~p~~Fq~ 86 (235)
..|.||..- . --+|=|.|+-+|||+|.-=|=-...+..+-|.-=|...+= +-++++++.+..|-..+-.+|.
T Consensus 309 ~tydvls~i~~dv~evFp~~~~HlGGDEV~~~CW~s~~~Iq~fM~~kGfg~~~~~~~~~~~~~~~~i~~s~~~~~I~Wqe 388 (542)
T KOG2499|consen 309 HTYDVLSEIFEDVSEVFPDEFFHLGGDEVSTPCWKSNPEIQDFMRKKGFGLDTKSLERLYIQFLLDILNSWNKTVIVWQE 388 (542)
T ss_pred hHHHHHHHHHHHHHHhCcHHHeecCCceeecccccCChHHHHHHHhCCCCchHHHHHHHHHHHHHHHHHhcCceEEEeeh
Confidence 467776531 0 0133467788999999966666788999999998888876 6789999999999888777666
Q ss_pred cCCC
Q psy1866 87 PLVS 90 (235)
Q Consensus 87 PL~s 90 (235)
-+..
T Consensus 389 vf~n 392 (542)
T KOG2499|consen 389 VFDN 392 (542)
T ss_pred hccc
Confidence 5554
No 41
>PTZ00484 GTP cyclohydrolase I; Provisional
Probab=31.77 E-value=1.6e+02 Score=27.40 Aligned_cols=63 Identities=14% Similarity=0.240 Sum_probs=47.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhhCCCCCch---hhhhhhhhHHhHHHHhcCCcccchhhhhhcccc
Q psy1866 157 LTPVLDDSQIAKLADIAQQLVRALPHLEPK---AQNSKKKICKDLEAVFQMSDEAVILKVKDNVHD 219 (235)
Q Consensus 157 ~tp~L~~~qi~~v~ecaeRL~~tLPq~dp~---~~~~nKKlaK~lehIf~Mse~DP~re~e~~~~~ 219 (235)
....|.++.+.++.+++..|.+.|-..||. ..++=||.+|+...+|.=-..||........|.
T Consensus 64 ~~~~~~~~~~~~ie~avr~iL~al~GeDp~RegL~~TP~RVak~~~e~~~Gy~~~~~~~l~~~~~~ 129 (259)
T PTZ00484 64 TCATLMEEKKGAIESARRKILKSLEGEDPDRDGLKKTPKRVAKALEFLTKGYHMSVEEVIKKALFK 129 (259)
T ss_pred cccccchhhHHHHHHHHHHHHHHhcCCCCCCcchhhhHHHHHHHHHHHHhcccCCHHHHhcccccc
Confidence 344578899999999999999999444443 467899999999999976667776655434443
No 42
>PRK15344 type III secretion system needle protein SsaG; Provisional
Probab=31.52 E-value=76 Score=24.54 Aligned_cols=32 Identities=22% Similarity=0.246 Sum_probs=23.9
Q ss_pred ChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhc
Q psy1866 47 GEEEFLEIMALVGMASKPLHVRRLQKALQEWTT 79 (235)
Q Consensus 47 ~e~efleim~lvGM~~KPlHVrRlqkal~~w~~ 79 (235)
.-+|+..-|+-.+-. -|-|.-+||-++++|..
T Consensus 17 ~~q~vq~~m~a~~~~-nP~~ml~lQf~i~QyS~ 48 (71)
T PRK15344 17 AGQAINDKMNGNDLL-NPESMIKAQFALQQYST 48 (71)
T ss_pred HHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHH
Confidence 345666666654444 59999999999999964
No 43
>TIGR02289 M3_not_pepF oligoendopeptidase, M3 family. This family consists of probable oligoendopeptidases in the M3 family, related to lactococcal PepF and group B streptococcal PepB (TIGR00181) but in a distinct clade with considerable sequence differences. The likely substrate is small peptides and not whole proteins, as with PepF, but members are not characterized and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family.
Probab=30.26 E-value=1.7e+02 Score=28.60 Aligned_cols=57 Identities=21% Similarity=0.454 Sum_probs=39.9
Q ss_pred hHHHHHHHHh--hhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCC--chHHHHHHHHHHHHhc
Q psy1866 13 ELQLYRVMQR--ASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASK--PLHVRRLQKALQEWTT 79 (235)
Q Consensus 13 elqly~vlqr--AnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~K--PlHVrRlqkal~~w~~ 79 (235)
-+|||...++ +.-++.|..|+..||-. .+.|+++..|...- +=.++..-+.+.+|+.
T Consensus 486 a~~l~~~~~~~~~~~~~~Y~~~L~~Ggs~----------~~~ell~~aGid~~f~~~~~~~~~~~~~~~l~ 546 (549)
T TIGR02289 486 ALQIYKIYKEDPEKALKDYKKLCSAGGSQ----------SFLELYETAGLTFPFSEERIKEIVSFVEKLLE 546 (549)
T ss_pred HHHHHHHHHhCHHHHHHHHHHHHhccCCc----------CHHHHHHHhCCCCCCCcccHHHHHHHHHHHHh
Confidence 4566655533 35677888888888854 78899999996543 4447777778888864
No 44
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=28.63 E-value=35 Score=31.32 Aligned_cols=28 Identities=29% Similarity=0.466 Sum_probs=22.9
Q ss_pred HhcCCCCchHHHHHHHHHHHHhcCCCCc
Q psy1866 57 LVGMASKPLHVRRLQKALQEWTTNPAMF 84 (235)
Q Consensus 57 lvGM~~KPlHVrRlqkal~~w~~~p~~F 84 (235)
.|+--=||++-.||+.||..|..--+.+
T Consensus 97 v~DYLiKPf~~eRl~~aL~~y~~~r~~l 124 (224)
T COG4565 97 VVDYLIKPFTFERLQQALTRYRQKRHAL 124 (224)
T ss_pred chhheecceeHHHHHHHHHHHHHHHHHH
Confidence 3556679999999999999999765554
No 45
>PF11904 GPCR_chapero_1: GPCR-chaperone; InterPro: IPR021832 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 409 to 630 amino acids in length. This protein is found associated with PF00023 from PFAM. This protein has a conserved FPVK sequence motif.
Probab=28.24 E-value=51 Score=30.57 Aligned_cols=40 Identities=25% Similarity=0.465 Sum_probs=29.0
Q ss_pred HHHHHHHHHhcCCCCchHHHHHHHHHHHHhcCCCCc----cccCCCC
Q psy1866 49 EEFLEIMALVGMASKPLHVRRLQKALQEWTTNPAMF----QTPLVSP 91 (235)
Q Consensus 49 ~efleim~lvGM~~KPlHVrRlqkal~~w~~~p~~F----q~PL~s~ 91 (235)
++|+-|++++.+..| |++||+.-|+-= -.|+-| .+||.+.
T Consensus 215 eqllPILdvlA~~~k--h~~kLrefit~k-LP~~GFPVKieIPl~~t 258 (307)
T PF11904_consen 215 EQLLPILDVLANTNK--HFAKLREFITLK-LPPGGFPVKIEIPLFPT 258 (307)
T ss_pred HHHHHHHHHHccccH--HHHHHHHHHHHh-CCCCCCceEEEEeeeeE
Confidence 899999999887777 899998877662 222244 6677664
No 46
>PF09921 DUF2153: Uncharacterized protein conserved in archaea (DUF2153); InterPro: IPR014450 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.86 E-value=49 Score=28.08 Aligned_cols=18 Identities=33% Similarity=0.785 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHhcCCCC
Q psy1866 66 HVRRLQKALQEWTTNPAM 83 (235)
Q Consensus 66 HVrRlqkal~~w~~~p~~ 83 (235)
|+-|-.||...|.+||-+
T Consensus 41 hm~RTlKaFd~WLqdP~I 58 (126)
T PF09921_consen 41 HMMRTLKAFDQWLQDPMI 58 (126)
T ss_pred HHHHHHHHHHHHHcCchh
Confidence 888999999999999854
No 47
>PF12987 DUF3871: Domain of unknown function, B. Theta Gene description (DUF3871); InterPro: IPR024353 This entry represents proteins of unknown function found primarily in Bacteroides species. The B. thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture [, ].
Probab=27.56 E-value=43 Score=32.23 Aligned_cols=27 Identities=19% Similarity=0.395 Sum_probs=24.0
Q ss_pred ChhhHHHHHHHHhhhhHHHHHHHHHcC
Q psy1866 10 NEAELQLYRVMQRASLLAYYDTLLEMG 36 (235)
Q Consensus 10 ~~~elqly~vlqrAnLl~Yyd~~i~~G 36 (235)
.+.=|++|-+|-.||=.+|.|+|++-.
T Consensus 273 ~Is~W~~ynLlT~AnKsSYID~fLdR~ 299 (323)
T PF12987_consen 273 EISMWNFYNLLTGANKSSYIDSFLDRS 299 (323)
T ss_pred cccHHHHHHHHhcccchhhHHHHHhhc
Confidence 456799999999999999999999864
No 48
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=27.28 E-value=1.1e+02 Score=21.47 Aligned_cols=35 Identities=29% Similarity=0.469 Sum_probs=26.7
Q ss_pred chHHHHHhhChHHHHHHHHHhcCCC-------CchHHHHHHHHHH
Q psy1866 38 DDVQQLCEAGEEEFLEIMALVGMAS-------KPLHVRRLQKALQ 75 (235)
Q Consensus 38 Ddvqql~~~~e~efleim~lvGM~~-------KPlHVrRlqkal~ 75 (235)
||+++|.+. |+.+-+.-.|... +.+..+||++++.
T Consensus 1 ~d~~~LSd~---eL~~~L~~~G~~~gPIt~sTR~vy~kkL~~~~~ 42 (44)
T smart00540 1 DDVDRLSDA---ELRAELKQYGLPPGPITDTTRKLYEKKLRKLRR 42 (44)
T ss_pred CchhHcCHH---HHHHHHHHcCCCCCCcCcchHHHHHHHHHHHHc
Confidence 567776654 8888888888864 5578999999874
No 49
>PRK10702 endonuclease III; Provisional
Probab=26.91 E-value=1.4e+02 Score=26.16 Aligned_cols=52 Identities=17% Similarity=0.154 Sum_probs=37.5
Q ss_pred hhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCC-CCchHHHHHHHHHHHHh
Q psy1866 23 ASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMA-SKPLHVRRLQKALQEWT 78 (235)
Q Consensus 23 AnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~-~KPlHVrRlqkal~~w~ 78 (235)
.+....|+.|.+. .-+.+.|..++++|+.+++.=+|+. .|-- +|+++.+.+.
T Consensus 45 ~~v~~~~~~L~~~-~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~---~l~~~a~~i~ 97 (211)
T PRK10702 45 VSVNKATAKLYPV-ANTPAAMLELGVEGVKTYIKTIGLYNSKAE---NVIKTCRILL 97 (211)
T ss_pred HHHHHHHHHHHHH-cCCHHHHHCCCHHHHHHHHHHcCCHHHHHH---HHHHHHHHHH
Confidence 4555677777754 5679999999999999999999984 3544 4444444443
No 50
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=26.42 E-value=1.3e+02 Score=24.94 Aligned_cols=48 Identities=21% Similarity=0.436 Sum_probs=34.5
Q ss_pred HHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchH--H-HHHHHHHHHHhc
Q psy1866 28 YYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLH--V-RRLQKALQEWTT 79 (235)
Q Consensus 28 Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlH--V-rRlqkal~~w~~ 79 (235)
--|+++..+|+.+.+-.. ..+|++. |+.|.+++.| | +|+-.-|++|..
T Consensus 60 LLe~~vkNCG~~fh~eva--sk~Fl~e--L~kl~~~~~~~~Vk~kil~li~~W~~ 110 (144)
T cd03568 60 LLDACAENCGKRFHQEVA--SRDFTQE--LKKLINDRVHPTVKEKLREVVKQWAD 110 (144)
T ss_pred HHHHHHHHCCHHHHHHHh--hHHHHHH--HHHHhcccCCHHHHHHHHHHHHHHHH
Confidence 347888899999986553 4689887 5566666454 4 366777899974
No 51
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=26.23 E-value=2.5e+02 Score=22.34 Aligned_cols=48 Identities=23% Similarity=0.351 Sum_probs=33.6
Q ss_pred HHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCC----CchHHH-HHHHHHHHHhc
Q psy1866 28 YYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMAS----KPLHVR-RLQKALQEWTT 79 (235)
Q Consensus 28 Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~----KPlHVr-Rlqkal~~w~~ 79 (235)
--|.++..+|+-+.+.... .+|+.- |+++.+ .+..|+ |+..-|+.|..
T Consensus 60 lLd~~vkNcg~~f~~~i~s--~~fl~~--l~~l~~~~~~~~~~Vk~kil~ll~~W~~ 112 (133)
T cd03561 60 LLELLVKNCGKPFHLQVAD--KEFLLE--LVKIAKNSPKYDPKVREKALELILAWSE 112 (133)
T ss_pred HHHHHHHhCChHHHHHHhh--HHHHHH--HHHHhCCCCCCCHHHHHHHHHHHHHHHH
Confidence 3588999999998766654 677765 444443 466675 67778899976
No 52
>PF13618 Gluconate_2-dh3: Gluconate 2-dehydrogenase subunit 3
Probab=25.85 E-value=1.2e+02 Score=23.45 Aligned_cols=67 Identities=18% Similarity=0.118 Sum_probs=38.6
Q ss_pred CHHHHHHHHHHHHHHHhhCCCCCchhhhhhhhhHHhHHHHhcCCcccchhhhhhccccchhhhhhhhhhhcc
Q psy1866 162 DDSQIAKLADIAQQLVRALPHLEPKAQNSKKKICKDLEAVFQMSDEAVILKVKDNVHDSNLERITNKKYGRQ 233 (235)
Q Consensus 162 ~~~qi~~v~ecaeRL~~tLPq~dp~~~~~nKKlaK~lehIf~Mse~DP~re~e~~~~~~~~~~~~~~~~~~~ 233 (235)
|+.|..-|.+.+++|++.=-.-..++...-.-|-++|.+ ..+|.....++..=..|+....++||+-
T Consensus 1 t~~e~~~L~ai~~~iiP~~~~pgA~~~~v~~fId~~l~~-----~~~~~~~~~~~~gl~~ld~~a~~~~g~~ 67 (131)
T PF13618_consen 1 TAEEAATLAAIADTIIPADDTPGASDAGVPEFIDRMLAD-----CYMPEDRRAFRAGLAALDAYAQKRYGKS 67 (131)
T ss_pred CHHHHHHHHHHHHHhcCCCCCCChhhcChHHHHHHHHhc-----CCCHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 568889999999999865322122233444555555555 2223334455555555666666777753
No 53
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=25.30 E-value=3e+02 Score=22.07 Aligned_cols=50 Identities=24% Similarity=0.438 Sum_probs=34.6
Q ss_pred HHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchH----HHHHHHHHHHHhc
Q psy1866 26 LAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLH----VRRLQKALQEWTT 79 (235)
Q Consensus 26 l~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlH----VrRlqkal~~w~~ 79 (235)
|..-|.++..+|+.+.+-+. ..+|++ .|+.+.+++-+ ..|+-.-+++|..
T Consensus 58 L~lLe~~vkNcg~~f~~ev~--s~~fl~--~L~~l~~~~~~~~~Vk~kil~li~~W~~ 111 (133)
T smart00288 58 LTLLDACVKNCGSKFHLEVA--SKEFLN--ELVKLIKPKYPLPLVKKRILELIQEWAD 111 (133)
T ss_pred HHHHHHHHHHCCHHHHHHHH--hHHHHH--HHHHHHcCCCCcHHHHHHHHHHHHHHHH
Confidence 44568899999999976553 678988 44455554443 3466677888975
No 54
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=24.96 E-value=58 Score=24.04 Aligned_cols=23 Identities=26% Similarity=0.599 Sum_probs=15.1
Q ss_pred hHHHHHHHHHcCCchHHHHHhhC
Q psy1866 25 LLAYYDTLLEMGGDDVQQLCEAG 47 (235)
Q Consensus 25 Ll~Yyd~~i~~GgDdvqql~~~~ 47 (235)
|..||...-..--.|++.||+..
T Consensus 13 L~~Yy~~h~~L~E~DL~~L~~kS 35 (56)
T PF11569_consen 13 LEDYYLKHKQLQEEDLDELCDKS 35 (56)
T ss_dssp HHHHHHHT----TTHHHHHHHHT
T ss_pred HHHHHHHcCCccHhhHHHHHHHH
Confidence 67899887666668888888774
No 55
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=24.75 E-value=84 Score=28.20 Aligned_cols=42 Identities=26% Similarity=0.385 Sum_probs=36.9
Q ss_pred hHHHHHhhChHHHHHHHHHhcCC-CCchHHHHHHHHHHHHhcC
Q psy1866 39 DVQQLCEAGEEEFLEIMALVGMA-SKPLHVRRLQKALQEWTTN 80 (235)
Q Consensus 39 dvqql~~~~e~efleim~lvGM~-~KPlHVrRlqkal~~w~~~ 80 (235)
+.|.|..++++|..+.+.-+|+- .|-=++.++-+.|.|+..-
T Consensus 60 t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g 102 (211)
T COG0177 60 TPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG 102 (211)
T ss_pred CHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCC
Confidence 89999999999999999999985 6888888888888888544
No 56
>COG0637 Predicted phosphatase/phosphohexomutase [General function prediction only]
Probab=24.19 E-value=52 Score=28.07 Aligned_cols=42 Identities=29% Similarity=0.493 Sum_probs=30.7
Q ss_pred HHHHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhc
Q psy1866 15 QLYRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVG 59 (235)
Q Consensus 15 qly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvG 59 (235)
-.-++|.+++|+.||+.++ .||||.+- .=.++=|+.-.+.+|
T Consensus 115 ~~~~~L~~~gl~~~f~~~v--~~~dv~~~-KP~Pd~yL~Aa~~Lg 156 (221)
T COG0637 115 AAERVLARLGLLDYFDVIV--TADDVARG-KPAPDIYLLAAERLG 156 (221)
T ss_pred HHHHHHHHccChhhcchhc--cHHHHhcC-CCCCHHHHHHHHHcC
Confidence 3557899999999999976 56777665 334566777766666
No 57
>PF11130 TraC_F_IV: F pilus assembly Type-IV secretion system for plasmid transfer
Probab=23.88 E-value=1.5e+02 Score=25.08 Aligned_cols=43 Identities=21% Similarity=0.252 Sum_probs=34.2
Q ss_pred HHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcCCCCc
Q psy1866 40 VQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTNPAMF 84 (235)
Q Consensus 40 vqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~p~~F 84 (235)
+++|.+. -+.|.+.+.-.|+..+++-...|..-|.+|. ||..-
T Consensus 140 ~~~l~~~-~~~~~~~L~~~gi~~~~~~~~~l~~~l~~~~-Np~~~ 182 (235)
T PF11130_consen 140 IEELNEL-RERLESSLRSAGIPPRRLDPEDLISWLRRIF-NPNPD 182 (235)
T ss_pred HHHHHHH-HHHHHHHHHHCCCccEEcCHHHHHHHHHHHc-CCCcc
Confidence 4444444 4578889999999999999999999999997 56543
No 58
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=23.28 E-value=1.1e+02 Score=20.01 Aligned_cols=25 Identities=28% Similarity=0.557 Sum_probs=20.9
Q ss_pred ChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcC
Q psy1866 47 GEEEFLEIMALVGMASKPLHVRRLQKALQEWTTN 80 (235)
Q Consensus 47 ~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~ 80 (235)
+.++..+|.+.+||. .+.++.|..|
T Consensus 26 ~~~~~~~la~~~~l~---------~~qV~~WF~n 50 (56)
T smart00389 26 SREEREELAAKLGLS---------ERQVKVWFQN 50 (56)
T ss_pred CHHHHHHHHHHHCcC---------HHHHHHhHHH
Confidence 578899999999998 6778888765
No 59
>COG4755 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.08 E-value=66 Score=27.98 Aligned_cols=18 Identities=33% Similarity=0.776 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHhcCCCC
Q psy1866 66 HVRRLQKALQEWTTNPAM 83 (235)
Q Consensus 66 HVrRlqkal~~w~~~p~~ 83 (235)
|.-|--||..+|.+||-.
T Consensus 59 hm~rtLKaFd~WLqdP~v 76 (151)
T COG4755 59 HMARTLKAFDSWLQDPVV 76 (151)
T ss_pred HHHHHHHHHHHHHhCchH
Confidence 888999999999999843
No 60
>cd08538 SAM_PNT-ESE-2-like Sterile alpha motif (SAM)/Pointed domain of ESE-2 like ETS transcriptional regulators. SAM Pointed domain of ESE-2-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It can act as a major transactivator by providing a potential docking site for co-activators. ESE-2 factors are involved in regulation of gene expression in a variety of epithelial (glandular and secretory) cells. ESE-2 mRNA was found in skin keratinocytes, salivary gland, mammary gland, stomach, prostate, and kidneys. The DNA binding consensus motif for ESE-2 consists of a GGA core and AT-rich flanks. The expression profiles of these factors are altered in epithelial cancers. Members of this subfamily are potential targets for cancer therapy.
Probab=22.93 E-value=48 Score=25.68 Aligned_cols=19 Identities=42% Similarity=0.802 Sum_probs=15.7
Q ss_pred HHHHhhChHHHHHHHHHhc
Q psy1866 41 QQLCEAGEEEFLEIMALVG 59 (235)
Q Consensus 41 qql~~~~e~efleim~lvG 59 (235)
++||..+.|||+++.-..|
T Consensus 43 k~LC~ms~eeF~~~~p~~G 61 (78)
T cd08538 43 LQLCSMTQEEFIEAAGICG 61 (78)
T ss_pred HHHHcCCHHHHHHHcccch
Confidence 6899999999998765544
No 61
>cd08757 SAM_PNT_ESE Sterile alpha motif (SAM)/Pointed domain of ESE-like ETS transcriptional regulators. SAM Pointed domain of ESE-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It can act as a major transactivator by providing a potential docking site for co-activators. ETS factors are important for cell differentiation. They can be involved in regulation of gene expression in different types of epithelial cells. They are expressed in salivary gland, intestine, stomach, pancreas, lungs, kidneys, colon, mammary gland, and prostate. Members of this group are proto-oncogenes. Expression profiles of these factors are altered in epithelial cancers, which makes them potential targets for cancer therapy.
Probab=22.89 E-value=38 Score=24.96 Aligned_cols=20 Identities=45% Similarity=0.582 Sum_probs=16.0
Q ss_pred HHHHHhhChHHHHHHHHHhc
Q psy1866 40 VQQLCEAGEEEFLEIMALVG 59 (235)
Q Consensus 40 vqql~~~~e~efleim~lvG 59 (235)
=++||...+|||.++..-.|
T Consensus 37 Gk~LC~ms~edF~~~~p~~G 56 (68)
T cd08757 37 GQTLCSMTEEEFREAAGSYG 56 (68)
T ss_pred HHHHHcCCHHHHHHHcCCcH
Confidence 37899999999998765443
No 62
>KOG2814|consensus
Probab=22.71 E-value=50 Score=32.05 Aligned_cols=30 Identities=47% Similarity=0.572 Sum_probs=25.4
Q ss_pred CCchHHHHHhhChHHHHHHHHHhcCCCCchHH
Q psy1866 36 GGDDVQQLCEAGEEEFLEIMALVGMASKPLHV 67 (235)
Q Consensus 36 GgDdvqql~~~~e~efleim~lvGM~~KPlHV 67 (235)
-+||||+.|+.-|.-|.||+..+| +||+-+
T Consensus 189 ~dd~vq~a~e~les~~~e~~~~~~--~kp~~i 218 (345)
T KOG2814|consen 189 NDDDVQKALEILESTFQEIRIDVG--EKPLFI 218 (345)
T ss_pred ChHHHHHHHHHHHHHHHHHHhccC--CCceee
Confidence 489999999999999999999987 555543
No 63
>PF05155 Phage_X: Phage X family ; InterPro: IPR022688 The sequences matched by this entry represent a family of phage and plasmid replication proteins. In bacteriophage IKe and related phage, the full-length protein is designated gene II protein. A much shorter protein of unknown function, translated from a conserved in-frame alternative initiator, is designated gene X protein. Members of this family also include plasmid replication proteins. ; GO: 0006260 DNA replication
Probab=22.55 E-value=1.3e+02 Score=23.44 Aligned_cols=31 Identities=23% Similarity=0.476 Sum_probs=23.6
Q ss_pred HHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHH
Q psy1866 19 VMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFL 52 (235)
Q Consensus 19 vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efl 52 (235)
..+-||+.++|..+..+| +|+.+.+ ...-|-
T Consensus 10 ~~ka~~~~~~y~~lw~~G-~~lk~~~--~kstfy 40 (92)
T PF05155_consen 10 TTKAANAFRFYALLWQHG-DDLKSTL--SKSTFY 40 (92)
T ss_pred HHHhHHHHHHHHHHHHCC-hHHhhhc--cHHHHH
Confidence 457799999999999999 9996644 334444
No 64
>PRK11409 antitoxin YefM; Provisional
Probab=22.45 E-value=1.2e+02 Score=22.89 Aligned_cols=56 Identities=20% Similarity=0.269 Sum_probs=44.1
Q ss_pred hhhhHHHHHHHHH---------cCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcC
Q psy1866 22 RASLLAYYDTLLE---------MGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTN 80 (235)
Q Consensus 22 rAnLl~Yyd~~i~---------~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~ 80 (235)
|+||-.|.|...+ .||.++ .-...+||..+++.+-..+-|=...||.+++.+|.+.
T Consensus 10 R~~l~~~l~~v~~~~epv~ITr~g~~~~---Vl~S~~~yesl~Etl~ll~~p~~~~~l~~~i~~~~~G 74 (83)
T PRK11409 10 RQNLSATMMKAVEDHAPILITRQNGEAC---VLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSG 74 (83)
T ss_pred HHHHHHHHHHHhccCCcEEEEeCCCCCE---EEEeHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHcC
Confidence 6788888877664 254443 3446789999999999899999999999999999763
No 65
>TIGR02253 CTE7 HAD superfamily (subfamily IA) hydrolase, TIGR02253. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549).
Probab=22.21 E-value=40 Score=27.34 Aligned_cols=44 Identities=18% Similarity=0.465 Sum_probs=28.1
Q ss_pred HHHHHHhhhhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHHhcCC
Q psy1866 16 LYRVMQRASLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWTTNP 81 (235)
Q Consensus 16 ly~vlqrAnLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w~~~p 81 (235)
+...|++.+|..|||..+ +++|+. ..|| |.+-++++++++--+|
T Consensus 124 ~~~~l~~~~l~~~f~~i~--~~~~~~-------------------~~KP-~~~~~~~~~~~~~~~~ 167 (221)
T TIGR02253 124 QWEKLERLGVRDFFDAVI--TSEEEG-------------------VEKP-HPKIFYAALKRLGVKP 167 (221)
T ss_pred HHHHHHhCChHHhccEEE--EeccCC-------------------CCCC-CHHHHHHHHHHcCCCh
Confidence 446678888888887643 444332 2577 6666777887765444
No 66
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=21.86 E-value=1.3e+02 Score=22.80 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=11.6
Q ss_pred hhhHHHHHHHHHcCC
Q psy1866 23 ASLLAYYDTLLEMGG 37 (235)
Q Consensus 23 AnLl~Yyd~~i~~Gg 37 (235)
|=...|||+|++..|
T Consensus 9 ~PKa~~~d~~~~~~~ 23 (111)
T PF03374_consen 9 APKAEFYDAFVDSDG 23 (111)
T ss_pred ChhhHHHHHHHcCCC
Confidence 345689999999775
No 67
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=21.82 E-value=1.2e+02 Score=24.30 Aligned_cols=46 Identities=28% Similarity=0.294 Sum_probs=29.4
Q ss_pred hhHHHHHHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Q psy1866 24 SLLAYYDTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEW 77 (235)
Q Consensus 24 nLl~Yyd~~i~~GgDdvqql~~~~e~efleim~lvGM~~KPlHVrRlqkal~~w 77 (235)
+|+.||..|....++. -... -..||-++..-+ +=|||++-|.++++
T Consensus 1 rl~~~y~~L~~~~~~~---~~~v---tl~elA~~l~cS--~Rn~r~lLkkm~~~ 46 (115)
T PF12793_consen 1 RLLEQYQRLWQHYGGQ---PVEV---TLDELAELLFCS--RRNARTLLKKMQEE 46 (115)
T ss_pred CHHHHHHHHHHHcCCC---Ccce---eHHHHHHHhCCC--HHHHHHHHHHHHHC
Confidence 4789999999987722 1122 233344444444 44999999998873
No 68
>PF05396 Phage_T7_Capsid: Phage T7 capsid assembly protein; InterPro: IPR008768 This family contains the capsid assembly protein (scaffolding protein) of bacteriophage T7.; GO: 0019069 viral capsid assembly
Probab=21.79 E-value=2.8e+02 Score=23.55 Aligned_cols=59 Identities=22% Similarity=0.403 Sum_probs=33.7
Q ss_pred HHHHHHHhhhhH-HHHHHHHH----cCCchHHHHHhh--ChHHHHHHHHHhcCCCCchHHHHHHHHH
Q psy1866 15 QLYRVMQRASLL-AYYDTLLE----MGGDDVQQLCEA--GEEEFLEIMALVGMASKPLHVRRLQKAL 74 (235)
Q Consensus 15 qly~vlqrAnLl-~Yyd~~i~----~GgDdvqql~~~--~e~efleim~lvGM~~KPlHVrRlqkal 74 (235)
+-|.-|.+|++. ++-|.+|+ +=.-.|+++.+. |+|.|..||.-+ =+.-|=-+.-|-+|+
T Consensus 6 eSY~~L~~AGysr~~VDsYI~GqeAL~~~yV~~V~~~AGG~e~f~~i~~~~-~~~~~~~~ea~~~Ai 71 (123)
T PF05396_consen 6 ESYEKLAKAGYSRSFVDSYIQGQEALAEQYVNSVKGYAGGEEGFAAIMSHA-EANSPAAAEAFNEAI 71 (123)
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH-HhCCHHHHHHHHHHH
Confidence 569999999985 45566664 223344444444 577777777655 222344444343333
No 69
>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV; InterPro: IPR021679 YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF. The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity [].
Probab=21.51 E-value=1.5e+02 Score=25.53 Aligned_cols=50 Identities=12% Similarity=0.070 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCchhhhhhhhhHHhHHHHhcCCcccchhhh
Q psy1866 163 DSQIAKLADIAQQLVRALPHLEPKAQNSKKKICKDLEAVFQMSDEAVILKV 213 (235)
Q Consensus 163 ~~qi~~v~ecaeRL~~tLPq~dp~~~~~nKKlaK~lehIf~Mse~DP~re~ 213 (235)
.+|++.+++.||++-+.=|+.= ...+.-|.++.-..-||+-=..||.+.+
T Consensus 9 ~~ql~~L~~~Ve~l~~~dP~~y-~~~~~~KlLaai~~li~e~IP~DP~~~~ 58 (140)
T PF11663_consen 9 LEQLEALIAAVERLRAKDPEGY-RKKPNTKLLAAISKLIFEVIPADPTRPE 58 (140)
T ss_pred HHHHHHHHHHHHHHHhcChHhh-hhchHHHHHHHHHHHHHhhccCCCCchH
Confidence 4799999999999988844311 1233567788888888899999998876
No 70
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=21.32 E-value=1.8e+02 Score=24.05 Aligned_cols=40 Identities=23% Similarity=0.518 Sum_probs=26.4
Q ss_pred HhhhhHHHHHHHHHcCCc---hHHHHHhh--ChHHH-HHHHHHhcC
Q psy1866 21 QRASLLAYYDTLLEMGGD---DVQQLCEA--GEEEF-LEIMALVGM 60 (235)
Q Consensus 21 qrAnLl~Yyd~~i~~GgD---dvqql~~~--~e~ef-leim~lvGM 60 (235)
.|.+.++||+..++-||+ +-+|.++. +++|+ .||++-.++
T Consensus 21 e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~~~i 66 (181)
T PF08006_consen 21 EREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAEYSI 66 (181)
T ss_pred HHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHhhhh
Confidence 378899999999997665 35676665 34444 355554443
No 71
>cd06562 GH20_HexA_HexB-like Beta-N-acetylhexosaminidases catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. The hexA and hexB genes encode the alpha- and beta-subunits of the two major beta-N-acetylhexosaminidase isoenzymes, N-acetyl-beta-D-hexosaminidase A (HexA) and beta-N-acetylhexosaminidase B (HexB). Both the alpha and the beta catalytic subunits have a TIM-barrel fold and belong to the glycosyl hydrolase family 20 (GH20). The HexA enzyme is a heterodimer containing one alpha and one beta subunit while the HexB enzyme is a homodimer containing two beta-subunits. Hexosaminidase mutations cause an inability to properly hydrolyze certain sphingolipids which accumulate in lysosomes within the brain, resulting in the lipid storage disorders Tay-Sachs and Sandhoff. Mutations in the alpha subunit cause in a deficiency in the HexA enzyme and result in
Probab=21.01 E-value=78 Score=29.26 Aligned_cols=60 Identities=17% Similarity=0.319 Sum_probs=44.2
Q ss_pred HHHHHcCCchHHHHHhhChHHHHHHHHHhcCCCCc----hHHHHHHHHHHHHhcCCCCccccCC
Q psy1866 30 DTLLEMGGDDVQQLCEAGEEEFLEIMALVGMASKP----LHVRRLQKALQEWTTNPAMFQTPLV 89 (235)
Q Consensus 30 d~~i~~GgDdvqql~~~~e~efleim~lvGM~~KP----lHVrRlqkal~~w~~~p~~Fq~PL~ 89 (235)
..+|-.|||++..-|-...+++.+.|+-.|+.+-. -+++|+.+.|++--..|-.++..+.
T Consensus 150 ~~~iHiGgDE~~~~~w~~~p~~~~~m~~~g~~~~~~l~~~f~~~~~~~l~~~Gk~~i~W~d~~~ 213 (348)
T cd06562 150 DKYFHLGGDEVNFNCWNSNPEIQKFMKKNNGTDYSDLESYFIQRALDIVRSLGKTPIVWEEVFD 213 (348)
T ss_pred CcceEeecCCCCCCcccCCHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHcCCeEEEeeeccc
Confidence 44577899999988877788999999999965422 2678888888877666666655443
Done!