Query psy13859
Match_columns 108
No_of_seqs 103 out of 360
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 22:13:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13859.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13859hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0948|consensus 100.0 5.9E-35 1.3E-39 256.7 7.9 93 1-94 937-1041(1041)
2 PF08148 DSHCT: DSHCT (NUC185) 100.0 9E-33 1.9E-37 205.9 5.4 91 1-94 78-180 (180)
3 KOG0947|consensus 99.9 2.7E-28 5.9E-33 218.2 7.1 94 1-94 1143-1248(1248)
4 COG4581 Superfamily II RNA hel 99.8 4.8E-20 1E-24 166.6 7.4 90 2-94 940-1041(1041)
5 KOG3337|consensus 81.4 2.9 6.3E-05 32.5 4.3 59 20-81 126-185 (201)
6 PF06411 HdeA: HdeA/HdeB famil 58.7 32 0.0007 22.9 4.9 53 20-74 37-94 (94)
7 PF02609 Exonuc_VII_S: Exonucl 50.5 31 0.00068 20.7 3.5 31 48-83 4-37 (53)
8 PRK14067 exodeoxyribonuclease 50.2 37 0.00079 22.7 4.1 35 44-83 8-45 (80)
9 PRK14068 exodeoxyribonuclease 46.4 47 0.001 21.9 4.1 34 45-83 8-44 (76)
10 PRK14064 exodeoxyribonuclease 46.4 38 0.00082 22.3 3.6 36 44-84 7-45 (75)
11 PRK14069 exodeoxyribonuclease 44.9 47 0.001 23.0 4.1 35 44-83 9-46 (95)
12 PHA02537 M terminase endonucle 44.5 1.1E+02 0.0024 24.2 6.6 49 2-52 102-157 (230)
13 TIGR01280 xseB exodeoxyribonuc 44.3 54 0.0012 20.9 4.1 32 47-83 5-39 (67)
14 PRK14070 exodeoxyribonuclease 43.3 38 0.00083 22.1 3.3 13 49-61 1-13 (69)
15 PRK00977 exodeoxyribonuclease 42.8 56 0.0012 21.6 4.1 34 45-83 12-48 (80)
16 PF08546 ApbA_C: Ketopantoate 42.7 91 0.002 20.9 5.3 50 52-103 40-91 (125)
17 COG3079 Uncharacterized protei 42.2 67 0.0015 24.9 4.9 55 27-83 95-163 (186)
18 PF00512 HisKA: His Kinase A ( 39.3 54 0.0012 19.4 3.3 23 43-65 43-65 (68)
19 COG3845 ABC-type uncharacteriz 38.2 76 0.0017 28.1 5.2 78 2-81 118-206 (501)
20 PF11407 RestrictionMunI: Type 37.4 30 0.00065 27.1 2.4 32 24-55 124-166 (202)
21 TIGR01592 holin_SPP1 holin, SP 37.4 78 0.0017 21.0 4.1 46 42-93 3-51 (75)
22 PRK14063 exodeoxyribonuclease 35.6 86 0.0019 20.6 4.1 35 44-83 6-43 (76)
23 PRK14066 exodeoxyribonuclease 34.9 1.2E+02 0.0025 20.0 4.6 35 44-83 5-42 (75)
24 PRK13505 formate--tetrahydrofo 34.5 1.7E+02 0.0038 26.2 6.9 76 4-90 363-466 (557)
25 PRK10208 acid-resistance prote 33.9 12 0.00025 27.0 -0.3 62 20-82 47-113 (114)
26 PF01627 Hpt: Hpt domain; Int 33.4 1.1E+02 0.0024 18.4 4.4 39 48-86 28-66 (90)
27 PF09058 L27_1: L27_1; InterP 32.4 44 0.00095 21.8 2.2 34 46-83 9-42 (64)
28 cd03569 VHS_Hrs_Vps27p VHS dom 32.3 1.2E+02 0.0026 21.7 4.7 43 44-88 97-139 (142)
29 KOG2145|consensus 31.5 35 0.00076 28.9 2.0 39 68-106 43-89 (397)
30 COG0707 MurG UDP-N-acetylgluco 31.0 2.7E+02 0.0059 23.0 7.2 42 42-83 311-355 (357)
31 PF08279 HTH_11: HTH domain; 29.1 8.1 0.00018 22.6 -1.6 41 51-91 1-41 (55)
32 PF08828 DSX_dimer: Doublesex 28.6 97 0.0021 20.1 3.3 37 25-61 18-54 (62)
33 cd00088 HPT Histidine Phosphot 28.3 1E+02 0.0022 19.5 3.5 44 48-91 31-77 (94)
34 PF05944 Phage_term_smal: Phag 28.2 1.3E+02 0.0029 21.7 4.4 37 2-40 67-103 (132)
35 COG4877 Uncharacterized protei 27.9 46 0.00099 21.6 1.7 17 24-40 11-27 (63)
36 TIGR03569 NeuB_NnaB N-acetylne 27.7 67 0.0015 26.5 3.1 81 4-89 185-283 (329)
37 PF02084 Bindin: Bindin; Inte 26.9 1.4E+02 0.0029 24.1 4.5 55 3-80 107-161 (238)
38 PF01288 HPPK: 7,8-dihydro-6-h 26.2 42 0.0009 23.7 1.4 38 69-106 9-52 (127)
39 PF14223 UBN2: gag-polypeptide 25.4 74 0.0016 21.2 2.5 38 41-78 39-76 (119)
40 PF11027 DUF2615: Protein of u 24.5 58 0.0013 22.9 1.8 17 47-63 16-32 (103)
41 PRK00304 hypothetical protein; 23.5 1E+02 0.0023 20.5 2.9 20 68-87 31-50 (75)
42 COG2759 MIS1 Formyltetrahydrof 23.0 3.1E+02 0.0068 24.6 6.4 48 34-89 404-462 (554)
43 KOG4175|consensus 22.9 2.5E+02 0.0054 22.7 5.3 87 2-95 137-240 (268)
44 PTZ00332 paraflagellar rod pro 22.8 1.8E+02 0.004 26.1 4.9 59 2-60 75-147 (589)
45 smart00709 Zpr1 Duplicated dom 22.8 60 0.0013 24.1 1.8 39 41-83 98-136 (160)
46 PF14922 FWWh: Protein of unkn 22.2 55 0.0012 24.3 1.4 20 21-40 130-149 (161)
47 PRK00254 ski2-like helicase; P 22.1 3.1E+02 0.0067 24.4 6.3 61 28-88 569-642 (720)
48 cd03565 VHS_Tom1 VHS domain fa 21.8 1.8E+02 0.004 20.8 4.1 38 48-88 102-140 (141)
49 PF03800 Nuf2: Nuf2 family; I 21.6 85 0.0018 22.2 2.3 37 2-40 14-50 (146)
50 PF06457 Ectatomin: Ectatomin; 21.6 1.4E+02 0.0031 17.0 2.8 24 28-51 7-30 (34)
51 PRK14151 heat shock protein Gr 21.5 15 0.00032 27.8 -1.7 46 3-50 109-156 (176)
52 smart00073 HPT Histidine Phosp 20.4 2.1E+02 0.0047 17.4 3.8 21 53-73 31-51 (87)
53 KOG4484|consensus 20.3 1.1E+02 0.0025 23.8 2.9 34 44-80 90-123 (199)
54 COG1701 Uncharacterized protei 20.2 90 0.002 25.2 2.4 23 42-64 197-219 (256)
55 PF08158 NUC130_3NT: NUC130/3N 20.1 1.3E+02 0.0028 18.5 2.6 21 67-87 31-52 (52)
56 PF14518 Haem_oxygenas_2: Iron 20.1 1.6E+02 0.0034 19.2 3.2 53 6-59 23-91 (106)
57 PF06971 Put_DNA-bind_N: Putat 20.1 38 0.00082 20.7 0.2 39 48-86 7-49 (50)
No 1
>KOG0948|consensus
Probab=100.00 E-value=5.9e-35 Score=256.74 Aligned_cols=93 Identities=39% Similarity=0.633 Sum_probs=91.5
Q ss_pred ChHHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc------------CCchhHHHHHHHHHHHHHHHHHhhhhCC
Q psy13859 1 MNIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ------------KEGIIVRCIQQLSELLRSIKDGAKIFGE 68 (108)
Q Consensus 1 ~a~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G------------~EGsIVR~irRL~ELlrql~~Aa~~iG~ 68 (108)
.|++||+|+.+|+++++++ +|+++|+|+||+|||+||+| ||||||||+||||||||||.+||++|||
T Consensus 937 ~ArrIAkVs~ecKlEide~-~Yv~sFkp~LMdvVy~W~~GatF~eIckmTdvfEGSiIR~~RRLeElLrQl~~AAk~iGn 1015 (1041)
T KOG0948|consen 937 SARRIAKVSKECKLEIDEE-DYVESFKPELMDVVYAWAKGATFAEICKMTDVFEGSIIRTFRRLEELLRQLIDAAKVIGN 1015 (1041)
T ss_pred HHHHHHHHHHhhccccCHH-HHHHhcChHHHHHHHHHHccccHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4899999999999999998 99999999999999999999 9999999999999999999999999999
Q ss_pred CcHHHHHHHHHHhhcCCccccchhhh
Q psy13859 69 RDLPLKMDQAIQVIKRDIVFAPSLWT 94 (108)
Q Consensus 69 ~~L~~k~~~a~~~ikRdIVf~~SLYl 94 (108)
.+|++||+.++.+|||||||++||||
T Consensus 1016 teLe~Kf~~~~~~ikRDIVFAaSLYL 1041 (1041)
T KOG0948|consen 1016 TELENKFEEAIKKIKRDIVFAASLYL 1041 (1041)
T ss_pred hHHHHHHHHHHHHHhhceeehhhccC
Confidence 99999999999999999999999997
No 2
>PF08148 DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961 This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [].; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 4A4Z_A 2XGJ_B 3L9O_A.
Probab=99.97 E-value=9e-33 Score=205.89 Aligned_cols=91 Identities=43% Similarity=0.742 Sum_probs=80.7
Q ss_pred ChHHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc------------CCchhHHHHHHHHHHHHHHHHHhhhhCC
Q psy13859 1 MNIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ------------KEGIIVRCIQQLSELLRSIKDGAKIFGE 68 (108)
Q Consensus 1 ~a~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G------------~EGsIVR~irRL~ELlrql~~Aa~~iG~ 68 (108)
++++|.+++.+||+ +.+ +|.++++|+||++||+||+| +||+|||++||++|||||++.||+.+||
T Consensus 78 ~~~~l~~~~~~~~l--~~~-~~~~~~~~~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrql~~aa~~~g~ 154 (180)
T PF08148_consen 78 IAERLAKVEREHGL--DEE-EYVERFDPGLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQLANAAKIIGD 154 (180)
T ss_dssp HHHHHHHHHHHTT---HHH-HHHHCSTTTTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHHHHHHHHCCT-
T ss_pred HHHHHHHHHHHhCC--CCc-ccccCCCccHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 47899999999999 444 89999999999999999999 9999999999999999999999999999
Q ss_pred CcHHHHHHHHHHhhcCCccccchhhh
Q psy13859 69 RDLPLKMDQAIQVIKRDIVFAPSLWT 94 (108)
Q Consensus 69 ~~L~~k~~~a~~~ikRdIVf~~SLYl 94 (108)
++|.+|+++|+++|||||||++||||
T Consensus 155 ~~L~~~~~~a~~~i~R~iV~~~SLYl 180 (180)
T PF08148_consen 155 PELAEKAREAIDLIRRDIVFASSLYL 180 (180)
T ss_dssp HHHHHHHHHHHHHHSHCCCC---TT-
T ss_pred HHHHHHHHHHHHhccCCccccccccC
Confidence 99999999999999999999999997
No 3
>KOG0947|consensus
Probab=99.95 E-value=2.7e-28 Score=218.24 Aligned_cols=94 Identities=44% Similarity=0.685 Sum_probs=90.3
Q ss_pred ChHHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc------------CCchhHHHHHHHHHHHHHHHHHhhhhCC
Q psy13859 1 MNIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ------------KEGIIVRCIQQLSELLRSIKDGAKIFGE 68 (108)
Q Consensus 1 ~a~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G------------~EGsIVR~irRL~ELlrql~~Aa~~iG~ 68 (108)
+|+++.+++..|++..+.+++|...++|+||+|||+||+| .||+|||||+||+|+|||+++|++++||
T Consensus 1143 v~~rl~ev~~~~~~~~~~~e~f~~~lrF~l~evVYeWA~G~sf~eim~~t~~~EG~iVR~I~RLdE~cre~~~aa~ivGd 1222 (1248)
T KOG0947|consen 1143 VAKRLEEVQSSHQLLQTPEEEFPCELRFGLVEVVYEWARGLSFKEIMELTDVLEGLIVRLIQRLDEVCRELRNAARIVGD 1222 (1248)
T ss_pred HHHHHHHHHHhhccccCchhhccccccccHHHHHHHHHcCCCHHHHHhhhCCcchhHHHHHHHHHHHHHhhhccceecCc
Confidence 4789999999999998877688899999999999999999 9999999999999999999999999999
Q ss_pred CcHHHHHHHHHHhhcCCccccchhhh
Q psy13859 69 RDLPLKMDQAIQVIKRDIVFAPSLWT 94 (108)
Q Consensus 69 ~~L~~k~~~a~~~ikRdIVf~~SLYl 94 (108)
|.|..||+.|+++|||||||++|||+
T Consensus 1223 ~~L~~Km~~as~~ikRdIVFaaSLY~ 1248 (1248)
T KOG0947|consen 1223 PVLHEKMEAASALIKRDIVFAASLYL 1248 (1248)
T ss_pred HHHHHHHHHHHHHhccCccchhhccC
Confidence 99999999999999999999999996
No 4
>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]
Probab=99.80 E-value=4.8e-20 Score=166.60 Aligned_cols=90 Identities=37% Similarity=0.598 Sum_probs=87.1
Q ss_pred hHHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc------------CCchhHHHHHHHHHHHHHHHHHhhhhCCC
Q psy13859 2 NIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ------------KEGIIVRCIQQLSELLRSIKDGAKIFGER 69 (108)
Q Consensus 2 a~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G------------~EGsIVR~irRL~ELlrql~~Aa~~iG~~ 69 (108)
+++|.+++.++++++..+ ++.|.++||++||+||+| +|||+||.++|++|+|+|+..|+.++||+
T Consensus 940 ~~kl~~~~~~~~i~~~~~---l~~~~~~lm~vv~~wa~g~s~~~i~~~~~~~eGs~vR~~~r~~ell~ql~~aa~~ig~~ 1016 (1041)
T COG4581 940 ARKLNKDQNSSQIEIYPE---LNDFSVGLMEVVYEWARGLSFADICGLTSLLEGSFVRIFRRLRELLRQLRKAASVIGNP 1016 (1041)
T ss_pred HHHHHHHHHhcCCcCCcc---cccccccHHHHHHHHHhhcchhhhhcCCcccccchhhhhhHHHHHHHHhhhcccccCCH
Confidence 679999999999999865 889999999999999999 99999999999999999999999999999
Q ss_pred cHHHHHHHHHHhhcCCccccchhhh
Q psy13859 70 DLPLKMDQAIQVIKRDIVFAPSLWT 94 (108)
Q Consensus 70 ~L~~k~~~a~~~ikRdIVf~~SLYl 94 (108)
+|..|+..++..|||||||++|||+
T Consensus 1017 ~L~~k~~~~~~~irr~iv~~~sly~ 1041 (1041)
T COG4581 1017 ELEEKAYRAIQEIRRDIVFVDSLYL 1041 (1041)
T ss_pred HHHHHHHHHHHhhhcCeEecccccC
Confidence 9999999999999999999999996
No 5
>KOG3337|consensus
Probab=81.44 E-value=2.9 Score=32.53 Aligned_cols=59 Identities=15% Similarity=0.213 Sum_probs=50.5
Q ss_pred hhhhhhcchhHHHHHHHHhcc-CCchhHHHHHHHHHHHHHHHHHhhhhCCCcHHHHHHHHHHh
Q psy13859 20 SEEADNLNFGLVQVVYEWAMQ-KEGIIVRCIQQLSELLRSIKDGAKIFGERDLPLKMDQAIQV 81 (108)
Q Consensus 20 ~~y~~~~~~~LmevVy~Wa~G-~EGsIVR~irRL~ELlrql~~Aa~~iG~~~L~~k~~~a~~~ 81 (108)
..|+++++||++.-|++|..- |--.|-.+.+=|.+.|.++-+-| .++.+..++-++-..
T Consensus 126 ~kfvss~~~G~~r~Vqe~sl~rFkenv~ktrkGl~yvlqk~fg~a---~~~~~~~~~~~~k~~ 185 (201)
T KOG3337|consen 126 EKFVSSSLFGVSRAVQEFSLARFKENVTKTRKGLEYVLQKLFGEA---NSKTLKMTAIEAKEK 185 (201)
T ss_pred HHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccc---cchHHHHHHHHHHHH
Confidence 488999999999999999976 88899999999999999998766 778887777766543
No 6
>PF06411 HdeA: HdeA/HdeB family; InterPro: IPR010486 HNS (histone-like nucleoid structuring)-dependent expression A (HdeA) protein is a stress response protein found in highly acid resistant bacteria such as Shigella flexneri and Escherichia coli, but which is lacking in mildly acid tolerant bacteria such as Salmonella []. HdeA is one of the most abundant proteins found in the periplasmic space of E. coli, where it is one of a network of proteins that confer an acid resistance phenotype essential for the pathogenesis of enteric bacteria []. HdeA is thought to act as a chaperone, functioning to prevent the aggregation of periplasmic proteins denatured under acidic conditions. The HNS protein, a chromatin-associated protein that influences the gene expression of several environmentally-induced target genes, represses the expression of HdeA. HdeB, which is encoded within the same operon, may form heterodimers with HdeA. HdeA is a single domain protein with an overall fold that is similar to the fold of the N-terminal subdomain of the GluRS anticodon-binding domain. ; PDB: 1BG8_C 1DJ8_C 2XUV_C.
Probab=58.66 E-value=32 Score=22.87 Aligned_cols=53 Identities=19% Similarity=0.136 Sum_probs=41.6
Q ss_pred hhhhhhcchhHHHHHHHHhcc-----CCchhHHHHHHHHHHHHHHHHHhhhhCCCcHHHH
Q psy13859 20 SEEADNLNFGLVQVVYEWAMQ-----KEGIIVRCIQQLSELLRSIKDGAKIFGERDLPLK 74 (108)
Q Consensus 20 ~~y~~~~~~~LmevVy~Wa~G-----~EGsIVR~irRL~ELlrql~~Aa~~iG~~~L~~k 74 (108)
.||+ ..++..+..|--|..| ..|+.| -+..++..--++.+.|+-=++..|.+|
T Consensus 37 ~eFl-~ld~~~~~~v~~w~~g~~~~~k~~d~v-D~~~~~~~tp~v~~~Ckk~P~~~l~~~ 94 (94)
T PF06411_consen 37 KEFL-DLDPDFMPPVVFWMEGWNKGDKGGDYV-DFDGIETVTPKVVEYCKKNPKSSLMDK 94 (94)
T ss_dssp HHHH-TS-HHHHHHHHHHHHHCTSCSSCGCBB--HHHHHHHHHHHHHHHHCTTTSBHHHH
T ss_pred HHHH-cCCHHHHHHHHHHHHhhhccCCCCCee-eHHHHHHhhHHHHHHHHHCccchhhcC
Confidence 4888 5899999999999999 778888 888888888888888876676666543
No 7
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=50.48 E-value=31 Score=20.74 Aligned_cols=31 Identities=23% Similarity=0.521 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHhhhhCCCcHHH---HHHHHHHhhc
Q psy13859 48 CIQQLSELLRSIKDGAKIFGERDLPL---KMDQAIQVIK 83 (108)
Q Consensus 48 ~irRL~ELlrql~~Aa~~iG~~~L~~---k~~~a~~~ik 83 (108)
.+.||++++++|.+ |+..|.+ .+++|..+++
T Consensus 4 ~~~~Le~Iv~~Le~-----~~~sLdes~~lyeeg~~l~~ 37 (53)
T PF02609_consen 4 AMERLEEIVEKLES-----GELSLDESLKLYEEGMELIK 37 (53)
T ss_dssp HHHHHHHHHHHHHT-----T-S-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHc-----CCCCHHHHHHHHHHHHHHHH
Confidence 57888888888876 4555543 5566666554
No 8
>PRK14067 exodeoxyribonuclease VII small subunit; Provisional
Probab=50.22 E-value=37 Score=22.67 Aligned_cols=35 Identities=11% Similarity=0.276 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhCCCcHHH---HHHHHHHhhc
Q psy13859 44 IIVRCIQQLSELLRSIKDGAKIFGERDLPL---KMDQAIQVIK 83 (108)
Q Consensus 44 sIVR~irRL~ELlrql~~Aa~~iG~~~L~~---k~~~a~~~ik 83 (108)
++=-.+.||++++++|-+ |+..|.+ .++++..++|
T Consensus 8 sfEeal~~LEeIV~~LE~-----~~l~Lees~~lyeeG~~L~k 45 (80)
T PRK14067 8 DFEQQLARLQEIVDALEG-----GDLPLEESVALYKEGLGLAR 45 (80)
T ss_pred CHHHHHHHHHHHHHHHHC-----CCCCHHHHHHHHHHHHHHHH
Confidence 344578899999999876 4565544 5566666655
No 9
>PRK14068 exodeoxyribonuclease VII small subunit; Provisional
Probab=46.43 E-value=47 Score=21.94 Aligned_cols=34 Identities=9% Similarity=0.253 Sum_probs=23.7
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhCCCcHHH---HHHHHHHhhc
Q psy13859 45 IVRCIQQLSELLRSIKDGAKIFGERDLPL---KMDQAIQVIK 83 (108)
Q Consensus 45 IVR~irRL~ELlrql~~Aa~~iG~~~L~~---k~~~a~~~ik 83 (108)
+=-.+.||++++.+|-+ |+..|.+ .|++++.++|
T Consensus 8 fEeal~~Le~IV~~LE~-----gdl~Leesl~lyeeG~~L~k 44 (76)
T PRK14068 8 FEEMMQELEQIVQKLDN-----ETVSLEESLDLYQRGMKLSA 44 (76)
T ss_pred HHHHHHHHHHHHHHHHc-----CCCCHHHHHHHHHHHHHHHH
Confidence 34568889999888876 5666654 5666666655
No 10
>PRK14064 exodeoxyribonuclease VII small subunit; Provisional
Probab=46.36 E-value=38 Score=22.26 Aligned_cols=36 Identities=17% Similarity=0.341 Sum_probs=24.6
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhCCCcHHH---HHHHHHHhhcC
Q psy13859 44 IIVRCIQQLSELLRSIKDGAKIFGERDLPL---KMDQAIQVIKR 84 (108)
Q Consensus 44 sIVR~irRL~ELlrql~~Aa~~iG~~~L~~---k~~~a~~~ikR 84 (108)
++=-.+.||++++++|-+ |+-.|.+ .|+++..++|+
T Consensus 7 sfEe~l~~LE~IV~~LE~-----~~l~Leesl~~ye~G~~L~k~ 45 (75)
T PRK14064 7 TFEEAIAELETIVEALEN-----GSASLEDSLDMYQKGIELTKL 45 (75)
T ss_pred CHHHHHHHHHHHHHHHHC-----CCCCHHHHHHHHHHHHHHHHH
Confidence 444578899999988876 4555544 66677776653
No 11
>PRK14069 exodeoxyribonuclease VII small subunit; Provisional
Probab=44.88 E-value=47 Score=23.02 Aligned_cols=35 Identities=9% Similarity=0.250 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhCCCcHHH---HHHHHHHhhc
Q psy13859 44 IIVRCIQQLSELLRSIKDGAKIFGERDLPL---KMDQAIQVIK 83 (108)
Q Consensus 44 sIVR~irRL~ELlrql~~Aa~~iG~~~L~~---k~~~a~~~ik 83 (108)
++=-.+.||++++++|-+ |+..|.+ .++++++++|
T Consensus 9 sFEeal~~LEeIV~~LEs-----gdl~LEesl~lyeeGv~L~k 46 (95)
T PRK14069 9 SFEDALRELEQIAEKLER-----QDFSLEESLKAYERGMELKK 46 (95)
T ss_pred CHHHHHHHHHHHHHHHHC-----CCCCHHHHHHHHHHHHHHHH
Confidence 344578899999999876 5666654 5666666655
No 12
>PHA02537 M terminase endonuclease subunit; Provisional
Probab=44.54 E-value=1.1e+02 Score=24.20 Aligned_cols=49 Identities=18% Similarity=0.215 Sum_probs=38.7
Q ss_pred hHHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc-------CCchhHHHHHHH
Q psy13859 2 NIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ-------KEGIIVRCIQQL 52 (108)
Q Consensus 2 a~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G-------~EGsIVR~irRL 52 (108)
|=+|+....++|++.+. .|-..+-.-++|-|.+||.. +|=.+-+.+..+
T Consensus 102 AL~ia~yAI~~~l~~Pd--~f~R~~~t~vaeev~~~A~~~~~ag~~~e~~~~~~~~~l 157 (230)
T PHA02537 102 ALEIAEYALEHGLTMPD--QFRRTLANFVAEEVANAALKAASAGESVEPYFLRVFLDL 157 (230)
T ss_pred HHHHHHHHHHcCCCCCc--cccCCchHHHHHHHHHHHHHHHHcCCCCChHHHHHHHHH
Confidence 45789999999999874 67778888899999999998 555555555555
No 13
>TIGR01280 xseB exodeoxyribonuclease VII, small subunit. This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides.
Probab=44.28 E-value=54 Score=20.95 Aligned_cols=32 Identities=9% Similarity=0.417 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHhhhhCCCcHHH---HHHHHHHhhc
Q psy13859 47 RCIQQLSELLRSIKDGAKIFGERDLPL---KMDQAIQVIK 83 (108)
Q Consensus 47 R~irRL~ELlrql~~Aa~~iG~~~L~~---k~~~a~~~ik 83 (108)
-++.||++++++|-+ |+-.|.+ .++++.+++|
T Consensus 5 e~l~~Le~Iv~~LE~-----~~l~Leesl~lyeeG~~L~k 39 (67)
T TIGR01280 5 EALSELEQIVQKLES-----GDLALEEALNLFERGMALAR 39 (67)
T ss_pred HHHHHHHHHHHHHHC-----CCCCHHHHHHHHHHHHHHHH
Confidence 367889999988876 4555544 5556666554
No 14
>PRK14070 exodeoxyribonuclease VII small subunit; Provisional
Probab=43.32 E-value=38 Score=22.06 Aligned_cols=13 Identities=15% Similarity=0.626 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHH
Q psy13859 49 IQQLSELLRSIKD 61 (108)
Q Consensus 49 irRL~ELlrql~~ 61 (108)
|.||++++++|-+
T Consensus 1 m~~LEeIV~~LE~ 13 (69)
T PRK14070 1 MKELEEIVNRLEN 13 (69)
T ss_pred CHHHHHHHHHHHC
Confidence 3566666666654
No 15
>PRK00977 exodeoxyribonuclease VII small subunit; Provisional
Probab=42.76 E-value=56 Score=21.60 Aligned_cols=34 Identities=12% Similarity=0.397 Sum_probs=22.7
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhCCCcHHH---HHHHHHHhhc
Q psy13859 45 IVRCIQQLSELLRSIKDGAKIFGERDLPL---KMDQAIQVIK 83 (108)
Q Consensus 45 IVR~irRL~ELlrql~~Aa~~iG~~~L~~---k~~~a~~~ik 83 (108)
+=-++.||++++++|-+ |+-.|.+ .++++..+++
T Consensus 12 fEea~~~LEeIv~~LE~-----~~l~Lees~~lyeeg~~L~k 48 (80)
T PRK00977 12 FEEALAELEEIVTRLES-----GDLPLEESLAAFERGVALAR 48 (80)
T ss_pred HHHHHHHHHHHHHHHHC-----CCCCHHHHHHHHHHHHHHHH
Confidence 34568899999998876 4555544 5566666654
No 16
>PF08546 ApbA_C: Ketopantoate reductase PanE/ApbA C terminal; InterPro: IPR013752 This is the C-terminal domain of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, 1.1.1.169 from EC. The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH. AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway []. ApbA and PanE are allelic []. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway []. ; GO: 0016491 oxidoreductase activity, 0050661 NADP binding, 0055114 oxidation-reduction process; PDB: 1YJQ_A 1KS9_A 2OFP_A 1YON_A 2EW2_B 3EGO_B 3HN2_D 3GHY_B 3G17_E 3HWR_B ....
Probab=42.67 E-value=91 Score=20.87 Aligned_cols=50 Identities=22% Similarity=0.393 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHhhhhCCCcHHHH-HHHHH-HhhcCCccccchhhhHhhhCCcce
Q psy13859 52 LSELLRSIKDGAKIFGERDLPLK-MDQAI-QVIKRDIVFAPSLWTKLLVGGQPH 103 (108)
Q Consensus 52 L~ELlrql~~Aa~~iG~~~L~~k-~~~a~-~~ikRdIVf~~SLYl~~~~~~~~~ 103 (108)
+..+++++..+++..|-+ +... +.+.. ..++..--..+|.|.+ +..|+|+
T Consensus 40 ~~~l~~E~~~va~a~G~~-l~~~~~~~~~~~~~~~~~~~~~SM~~D-~~~gr~t 91 (125)
T PF08546_consen 40 IRALMREVIAVARALGIP-LDPDDLEEAIERLIRSTPDNRSSMLQD-IEAGRPT 91 (125)
T ss_dssp HHHHHHHHHHHHHHTTSS---HHHHHHHHHHHHHCTTTT--HHHHH-HHTTB--
T ss_pred HHHHHHHHHHHHHHhhcc-CcHHHHHHHHHHHHHhcCCccccHHHH-HHHcccc
Confidence 456788899999999954 5443 33333 3444444458898888 3455553
No 17
>COG3079 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.25 E-value=67 Score=24.91 Aligned_cols=55 Identities=15% Similarity=0.257 Sum_probs=39.2
Q ss_pred chhHHHHHHHHhcc---------CCchhHHHHHHHHHHHHHHHHHhhhhCCC-----cHHHHHHHHHHhhc
Q psy13859 27 NFGLVQVVYEWAMQ---------KEGIIVRCIQQLSELLRSIKDGAKIFGER-----DLPLKMDQAIQVIK 83 (108)
Q Consensus 27 ~~~LmevVy~Wa~G---------~EGsIVR~irRL~ELlrql~~Aa~~iG~~-----~L~~k~~~a~~~ik 83 (108)
=|...+.+.+|||+ .+++-+. --..|.++.|++.|++=+|. ++++-+++.++-+|
T Consensus 95 vf~rADAL~eW~nhFL~GlGL~~~~l~~~~--gE~~EaldDL~~iaQlg~Deded~EE~~~~leEiiEyvR 163 (186)
T COG3079 95 VFDRADALAEWCNHFLLGLGLTQPKLSKLT--GEAGEALDDLANIAQLGYDEDEDQEELEESLEEIIEYVR 163 (186)
T ss_pred HHHHHHHHHHHHHHHHHhhcccccchhhhc--ccHHHHHHHHHHHHHhcCCccccHHHHHHHHHHHHHHHH
Confidence 46778999999999 4444322 23578888888888876665 56677777777665
No 18
>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....
Probab=39.34 E-value=54 Score=19.37 Aligned_cols=23 Identities=26% Similarity=0.374 Sum_probs=19.5
Q ss_pred chhHHHHHHHHHHHHHHHHHhhh
Q psy13859 43 GIIVRCIQQLSELLRSIKDGAKI 65 (108)
Q Consensus 43 GsIVR~irRL~ELlrql~~Aa~~ 65 (108)
..|.++.+|+.+++.++...++.
T Consensus 43 ~~i~~~~~~l~~li~~ll~~sr~ 65 (68)
T PF00512_consen 43 DRIRSAADRLNELINDLLDFSRI 65 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 56888999999999999888764
No 19
>COG3845 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]
Probab=38.20 E-value=76 Score=28.08 Aligned_cols=78 Identities=17% Similarity=0.271 Sum_probs=55.0
Q ss_pred hHHHHHHHHHhCCCCCcchhhhhhcchh---HHHHHHHHhcc------CCchhHHHHHHHHHHHHHHHHHhhhhCCCcH-
Q psy13859 2 NIEVESIEKKHGVERDKSSEEADNLNFG---LVQVVYEWAMQ------KEGIIVRCIQQLSELLRSIKDGAKIFGERDL- 71 (108)
Q Consensus 2 a~~Ia~v~~~~~l~~~~~~~y~~~~~~~---LmevVy~Wa~G------~EGsIVR~irRL~ELlrql~~Aa~~iG~~~L- 71 (108)
.++|.+++.++|++++.+ .++..+..| -+|++-.-.+| .|=+=|=+-.-.++|+.-+++.++ -|..-+
T Consensus 118 ~~~i~~l~~~yGl~vdp~-~~V~dLsVG~qQRVEIlKaLyr~a~iLILDEPTaVLTP~E~~~lf~~l~~l~~-~G~tIi~ 195 (501)
T COG3845 118 RARIKELSERYGLPVDPD-AKVADLSVGEQQRVEILKALYRGARLLILDEPTAVLTPQEADELFEILRRLAA-EGKTIIF 195 (501)
T ss_pred HHHHHHHHHHhCCCCCcc-ceeecCCcchhHHHHHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHHH-CCCEEEE
Confidence 478999999999999998 888777655 47888888888 777777777777776666655432 143322
Q ss_pred -HHHHHHHHHh
Q psy13859 72 -PLKMDQAIQV 81 (108)
Q Consensus 72 -~~k~~~a~~~ 81 (108)
..|+.++.+.
T Consensus 196 ITHKL~Ev~~i 206 (501)
T COG3845 196 ITHKLKEVMAI 206 (501)
T ss_pred EeccHHHHHHh
Confidence 3456665553
No 20
>PF11407 RestrictionMunI: Type II restriction enzyme MunI; InterPro: IPR022725 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Type II restriction enzyme MunI recognises the palindromic sequence C/AATTG. It makes contact with the DNA via the major groove []. ; PDB: 1D02_B.
Probab=37.42 E-value=30 Score=27.05 Aligned_cols=32 Identities=22% Similarity=0.222 Sum_probs=24.5
Q ss_pred hhcchhHHHHHHHHhcc-----------CCchhHHHHHHHHHH
Q psy13859 24 DNLNFGLVQVVYEWAMQ-----------KEGIIVRCIQQLSEL 55 (108)
Q Consensus 24 ~~~~~~LmevVy~Wa~G-----------~EGsIVR~irRL~EL 55 (108)
.-|.||||+++..=.+= ++|+|-|-=.|.-|+
T Consensus 124 k~ftpgl~~~~r~~~~i~~~~~LPFWiV~~GdITRDpkR~REI 166 (202)
T PF11407_consen 124 KFFTPGLLKAYRQISNINDEEILPFWIVFEGDITRDPKRVREI 166 (202)
T ss_dssp GGGSHHHHHHHHHHH----TTS-SEEEEEESGGGG-HHHHHHH
T ss_pred hccCcHHHHHHHHhcCCCCCCccceEEEEecccccCcccceee
Confidence 35899999998876553 999999999888765
No 21
>TIGR01592 holin_SPP1 holin, SPP1 family. This model represents one of more than 30 families of phage proteins, all lacking detectable homology with each other, known or believed to act as holins. Holins act in cell lysis by bacteriophage. Members of this family are found in phage PBSX and phage SPP1, among others.
Probab=37.37 E-value=78 Score=21.04 Aligned_cols=46 Identities=22% Similarity=0.387 Sum_probs=30.5
Q ss_pred CchhHHHHHHHHHHHHHHHHHhhhhCCCcH---HHHHHHHHHhhcCCccccchhh
Q psy13859 42 EGIIVRCIQQLSELLRSIKDGAKIFGERDL---PLKMDQAIQVIKRDIVFAPSLW 93 (108)
Q Consensus 42 EGsIVR~irRL~ELlrql~~Aa~~iG~~~L---~~k~~~a~~~ikRdIVf~~SLY 93 (108)
-|+|+|++-=+.-++.|.-.+. |-+.+ ++-+.+....+ +.+..|||
T Consensus 3 ~gTiiRti~l~lAlvNq~L~~~---G~~pipide~~i~~~v~~v---~t~~~~l~ 51 (75)
T TIGR01592 3 AGTIVRTILLIIALVNQFLAMK---GISPIPVDEEGISTVVDAV---FTIGVSLW 51 (75)
T ss_pred hhHHHHHHHHHHHHHHHHHHHC---CCCCCCccHHHHHHHHHHH---HHHHHHHH
Confidence 5999999999999999988766 64444 34455544443 33444444
No 22
>PRK14063 exodeoxyribonuclease VII small subunit; Provisional
Probab=35.56 E-value=86 Score=20.57 Aligned_cols=35 Identities=20% Similarity=0.356 Sum_probs=22.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhCCCcHHH---HHHHHHHhhc
Q psy13859 44 IIVRCIQQLSELLRSIKDGAKIFGERDLPL---KMDQAIQVIK 83 (108)
Q Consensus 44 sIVR~irRL~ELlrql~~Aa~~iG~~~L~~---k~~~a~~~ik 83 (108)
++=-.+.||++++++|-+ |+-.|.+ .++++..++|
T Consensus 6 sfEeal~~LE~Iv~~LE~-----~~l~Leesl~lyeeG~~L~k 43 (76)
T PRK14063 6 SFEEAISQLEHLVSKLEQ-----GDVPLEEAISYFKEGMELSK 43 (76)
T ss_pred CHHHHHHHHHHHHHHHHC-----CCCCHHHHHHHHHHHHHHHH
Confidence 344578899999988875 5566644 4555555544
No 23
>PRK14066 exodeoxyribonuclease VII small subunit; Provisional
Probab=34.86 E-value=1.2e+02 Score=19.95 Aligned_cols=35 Identities=14% Similarity=0.351 Sum_probs=24.2
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhCCCcHHH---HHHHHHHhhc
Q psy13859 44 IIVRCIQQLSELLRSIKDGAKIFGERDLPL---KMDQAIQVIK 83 (108)
Q Consensus 44 sIVR~irRL~ELlrql~~Aa~~iG~~~L~~---k~~~a~~~ik 83 (108)
++=-.+.||++++++|-+ |+-.|.+ .|+++.+++|
T Consensus 5 ~fEeal~~LE~IV~~LE~-----g~l~Leesl~lyeeG~~L~k 42 (75)
T PRK14066 5 KFETALKKLEEVVKKLEG-----GELSLDDSLKAFEEGVKHAA 42 (75)
T ss_pred cHHHHHHHHHHHHHHHHC-----CCCCHHHHHHHHHHHHHHHH
Confidence 445578899999999876 5666654 5666666654
No 24
>PRK13505 formate--tetrahydrofolate ligase; Provisional
Probab=34.54 E-value=1.7e+02 Score=26.22 Aligned_cols=76 Identities=20% Similarity=0.175 Sum_probs=44.9
Q ss_pred HHHHHHHHhCCCCCcchhhhhhcc--hh-HHHHHHHH--------------hccCCchhHHHHHHHHHHHHHHHHHhhh-
Q psy13859 4 EVESIEKKHGVERDKSSEEADNLN--FG-LVQVVYEW--------------AMQKEGIIVRCIQQLSELLRSIKDGAKI- 65 (108)
Q Consensus 4 ~Ia~v~~~~~l~~~~~~~y~~~~~--~~-LmevVy~W--------------a~G~EGsIVR~irRL~ELlrql~~Aa~~- 65 (108)
|..+..+.+|++.-+- +++|. +. -.+.+.+| ++|.||.+ +|-+.+.+|+.-
T Consensus 363 RHIenvr~FGvPvVVA---INKFd~DTe~Ei~~I~~~c~e~Gv~va~~~~~~~Gg~Gai--------~LA~aVveA~~~~ 431 (557)
T PRK13505 363 RHIENIRKFGVPVVVA---INKFVTDTDAEIAALKELCEELGVEVALSEVWAKGGEGGV--------ELAEKVVELIEEG 431 (557)
T ss_pred HHHHHHHHcCCCEEEE---EeCCCCCCHHHHHHHHHHHHHcCCCEEEecccccCCcchH--------HHHHHHHHHHhcC
Confidence 4455666788876544 33432 22 44445554 45577764 555555554431
Q ss_pred --------hCCCcHHHHHHHHHHhhcC--Cccccc
Q psy13859 66 --------FGERDLPLKMDQAIQVIKR--DIVFAP 90 (108)
Q Consensus 66 --------iG~~~L~~k~~~a~~~ikR--dIVf~~ 90 (108)
-.+..+.+|++...+.|.+ +|+|++
T Consensus 432 ~s~f~~lY~~d~sl~eKIe~IAkkIYGA~~V~~s~ 466 (557)
T PRK13505 432 ESNFKPLYDDEDSLEEKIEKIATKIYGAKGVEFSP 466 (557)
T ss_pred CCCCceecCCCCcHHHHHHHHHHHccCCCCeeECH
Confidence 1255788999998888876 777754
No 25
>PRK10208 acid-resistance protein; Provisional
Probab=33.92 E-value=12 Score=27.01 Aligned_cols=62 Identities=11% Similarity=0.032 Sum_probs=41.3
Q ss_pred hhhhhhcchhHHHHHHHHhcc-----CCchhHHHHHHHHHHHHHHHHHhhhhCCCcHHHHHHHHHHhh
Q psy13859 20 SEEADNLNFGLVQVVYEWAMQ-----KEGIIVRCIQQLSELLRSIKDGAKIFGERDLPLKMDQAIQVI 82 (108)
Q Consensus 20 ~~y~~~~~~~LmevVy~Wa~G-----~EGsIVR~irRL~ELlrql~~Aa~~iG~~~L~~k~~~a~~~i 82 (108)
+||+ .+|+.+.++|--|+-| -+|+-+=-+.-++-..-++.++|+-=+...+.+|++....++
T Consensus 47 eEFl-~Ln~s~~Pvvv~wa~~~nkk~K~eD~vvDi~gietvtP~vve~Ckk~Pk~~~~~ki~~~~kk~ 113 (114)
T PRK10208 47 EDFL-AVDESFQPTAVGFAEALNNKDKPEDAVIDVQGIETVTPAIVQACTQDKKASFKDKVKGEWKKI 113 (114)
T ss_pred HHHh-hcCcccCceeehhhhhhcccCCCCCeeEecccchhccHHHHHHHHHChHHHHHHHHHHHHhcc
Confidence 3776 6888999998889966 666644445555555555555665556667777877766554
No 26
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=33.41 E-value=1.1e+02 Score=18.43 Aligned_cols=39 Identities=23% Similarity=0.201 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHhhhhCCCcHHHHHHHHHHhhcCCc
Q psy13859 48 CIQQLSELLRSIKDGAKIFGERDLPLKMDQAIQVIKRDI 86 (108)
Q Consensus 48 ~irRL~ELlrql~~Aa~~iG~~~L~~k~~~a~~~ikRdI 86 (108)
....+..++-.++.++..+|=+.+.+...+..+.++.+-
T Consensus 28 d~~~l~~~~H~lkG~a~~~g~~~l~~~~~~lE~~~~~~~ 66 (90)
T PF01627_consen 28 DWEELRRLAHRLKGSAGNLGAPRLAELAEQLEQALKSGD 66 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTH
T ss_pred hHHHHHHHHHHHhhhHHhcCHHHHHHHHHHHHHHHHcCC
Confidence 344556667788899999999988888877777776653
No 27
>PF09058 L27_1: L27_1; InterPro: IPR015143 The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices []. ; PDB: 3LRA_A 1RSO_A.
Probab=32.45 E-value=44 Score=21.76 Aligned_cols=34 Identities=18% Similarity=0.367 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHhhhhCCCcHHHHHHHHHHhhc
Q psy13859 46 VRCIQQLSELLRSIKDGAKIFGERDLPLKMDQAIQVIK 83 (108)
Q Consensus 46 VR~irRL~ELlrql~~Aa~~iG~~~L~~k~~~a~~~ik 83 (108)
=|++..|++.+.++... +|.+|..-++..++..|
T Consensus 9 ~rALelLe~y~~~L~~~----~D~~lr~~ierli~ifk 42 (64)
T PF09058_consen 9 HRALELLEEYHNKLSRP----EDEELRTAIERLINIFK 42 (64)
T ss_dssp HHHHHHHHHHHHTTSSS----S-CCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcCCc----ccHHHHHHHHHHHHHHH
Confidence 47888888888888877 89999999999888443
No 28
>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=32.34 E-value=1.2e+02 Score=21.73 Aligned_cols=43 Identities=14% Similarity=0.082 Sum_probs=26.7
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhCCCcHHHHHHHHHHhhcCCccc
Q psy13859 44 IIVRCIQQLSELLRSIKDGAKIFGERDLPLKMDQAIQVIKRDIVF 88 (108)
Q Consensus 44 sIVR~irRL~ELlrql~~Aa~~iG~~~L~~k~~~a~~~ikRdIVf 88 (108)
.-.++-.|+-+++.+-..+.+ |+|.|..--+.-.++.++|+.|
T Consensus 97 ~~~~Vk~kil~li~~W~~~f~--~~~~l~~i~~~y~~L~~~G~~F 139 (142)
T cd03569 97 KNEEVRQKILELIQAWALAFR--NKPQLKYVVDTYQILKAEGHKF 139 (142)
T ss_pred CCHHHHHHHHHHHHHHHHHhC--CCcccHHHHHHHHHHHHcCCCC
Confidence 344555688888888877653 4556554444444455668887
No 29
>KOG2145|consensus
Probab=31.49 E-value=35 Score=28.92 Aligned_cols=39 Identities=21% Similarity=0.417 Sum_probs=30.0
Q ss_pred CCcHHHHHHHHHH-----hhcCCccccch---hhhHhhhCCcceeee
Q psy13859 68 ERDLPLKMDQAIQ-----VIKRDIVFAPS---LWTKLLVGGQPHYYH 106 (108)
Q Consensus 68 ~~~L~~k~~~a~~-----~ikRdIVf~~S---LYl~~~~~~~~~~~~ 106 (108)
|++|.++|++..- .+||+|.|+-- +-|+++-.|+|-|+-
T Consensus 43 deeli~R~ek~tg~~~h~flRrg~fFshRDf~~iLd~~eq~kpFyLY 89 (397)
T KOG2145|consen 43 DEELIDRFEKLTGKPPHHFLRRGIFFSHRDFNLILDAYEQGKPFYLY 89 (397)
T ss_pred CHHHHHHHHHhcCCCchHHhhhcceeecccHHHHHHHHHcCCceEEE
Confidence 6778888887654 59999999754 446678899999874
No 30
>COG0707 MurG UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane]
Probab=31.00 E-value=2.7e+02 Score=23.00 Aligned_cols=42 Identities=19% Similarity=0.322 Sum_probs=32.8
Q ss_pred CchhHHHHHHHH---HHHHHHHHHhhhhCCCcHHHHHHHHHHhhc
Q psy13859 42 EGIIVRCIQQLS---ELLRSIKDGAKIFGERDLPLKMDQAIQVIK 83 (108)
Q Consensus 42 EGsIVR~irRL~---ELlrql~~Aa~~iG~~~L~~k~~~a~~~ik 83 (108)
...++..+.++. |-+.+|+++++-+|.++-.+++-+....+.
T Consensus 311 ~~~l~~~i~~l~~~~~~l~~m~~~a~~~~~p~aa~~i~~~~~~~~ 355 (357)
T COG0707 311 PEKLAELILRLLSNPEKLKAMAENAKKLGKPDAAERIADLLLALA 355 (357)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHh
Confidence 346777777777 578899999999999999888877766544
No 31
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=29.07 E-value=8.1 Score=22.63 Aligned_cols=41 Identities=15% Similarity=0.272 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHhhhhCCCcHHHHHHHHHHhhcCCccccch
Q psy13859 51 QLSELLRSIKDGAKIFGERDLPLKMDQAIQVIKRDIVFAPS 91 (108)
Q Consensus 51 RL~ELlrql~~Aa~~iG~~~L~~k~~~a~~~ikRdIVf~~S 91 (108)
|...+++.|...-.-+--.+|++++.-....|+|||=....
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 56677777766654466677888888777788887765443
No 32
>PF08828 DSX_dimer: Doublesex dimerisation domain; InterPro: IPR014932 Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor []. ; PDB: 1ZV1_B 2JZ0_A 2JZ1_B.
Probab=28.57 E-value=97 Score=20.11 Aligned_cols=37 Identities=5% Similarity=0.195 Sum_probs=23.5
Q ss_pred hcchhHHHHHHHHhccCCchhHHHHHHHHHHHHHHHH
Q psy13859 25 NLNFGLVQVVYEWAMQKEGIIVRCIQQLSELLRSIKD 61 (108)
Q Consensus 25 ~~~~~LmevVy~Wa~G~EGsIVR~irRL~ELlrql~~ 61 (108)
.+.+.+|+.||-=-++.-|++=-+-||++|--+.+.+
T Consensus 18 ~YpWEmmpLmyVILK~A~~D~eeA~rrI~E~~~~v~~ 54 (62)
T PF08828_consen 18 RYPWEMMPLMYVILKYADADVEEASRRIDEAKNVVNE 54 (62)
T ss_dssp T--GGGHHHHHHHHHHTTT-HHHHHHHHHH-------
T ss_pred CCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHH
Confidence 3578999999998888888988888888886555444
No 33
>cd00088 HPT Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is modulated by phosphorylation and dephosphorylation of a conserved aspartic acid residue; two-component proteins are abundant in most eubacteria; In E. coli there are 62 two-component proteins involved in a variety of processes such as chemotaxis, osmoregulation, metabolism and transport 1; also present in both Gram positive and Gram negative pathogenic bacteria where they regulate basic housekeeping functions and control expression of toxins and other proteins important for pathogenesis; in archaea and eukaryotes, two-component pathways constitute a very small number of all signaling systems; in fungi they mediate environmental stress responses and, in pathogenic yeast, hyphal development. In Dictyostelium and in plants, they are i
Probab=28.32 E-value=1e+02 Score=19.48 Aligned_cols=44 Identities=11% Similarity=0.262 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHhhhhCCCcHHHHHH---HHHHhhcCCccccch
Q psy13859 48 CIQQLSELLRSIKDGAKIFGERDLPLKMD---QAIQVIKRDIVFAPS 91 (108)
Q Consensus 48 ~irRL~ELlrql~~Aa~~iG~~~L~~k~~---~a~~~ikRdIVf~~S 91 (108)
-+..+...+..++.+|..+|-+.|..... .+...-+++..+.++
T Consensus 31 d~~~l~~~~H~LkGsa~~~G~~~l~~~~~~lE~~~~~~~~~~~~~~~ 77 (94)
T cd00088 31 DLNEIFRAAHTLKGSAASLGLQRLAQLAHQLEDLLDALRDGLEVTPE 77 (94)
T ss_pred HHHHHHHHHHhhhhHHhcCChHHHHHHHHHHHHHHHHHHcCCCCCHH
Confidence 34566777888888888888887766444 444445555555544
No 34
>PF05944 Phage_term_smal: Phage small terminase subunit; InterPro: IPR010270 This entry is represented by Bacteriophage P2, GpM. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage small terminase subunit proteins as well as some related bacterial sequences []. M protein is probably an endonuclease which directs cos cleavage. The Q, P and M proteins are needed to package DNA into proheads and for the conversion of proheads to capsids.; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0019069 viral capsid assembly
Probab=28.17 E-value=1.3e+02 Score=21.66 Aligned_cols=37 Identities=16% Similarity=0.338 Sum_probs=31.7
Q ss_pred hHHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc
Q psy13859 2 NIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ 40 (108)
Q Consensus 2 a~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G 40 (108)
|=+++....++|++.+. .|-..+-.-+.|-|.+||..
T Consensus 67 AL~~a~yAi~~~l~~P~--~f~R~~~t~vaeev~~~a~~ 103 (132)
T PF05944_consen 67 ALDIAEYAIEHGLPMPD--RFKRTLPTFVAEEVADWALR 103 (132)
T ss_pred HHHHHHHHHHcCCCccc--cccCcchHHHHHHHHHHHHH
Confidence 45789999999999874 67788888899999999986
No 35
>COG4877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.89 E-value=46 Score=21.57 Aligned_cols=17 Identities=18% Similarity=0.347 Sum_probs=15.0
Q ss_pred hhcchhHHHHHHHHhcc
Q psy13859 24 DNLNFGLVQVVYEWAMQ 40 (108)
Q Consensus 24 ~~~~~~LmevVy~Wa~G 40 (108)
-++.|.+...+-+||.|
T Consensus 11 LRl~paiy~Aia~wA~d 27 (63)
T COG4877 11 LRLEPAIYAAIAQWAED 27 (63)
T ss_pred eecCHHHHHHHHHHHHH
Confidence 36889999999999987
No 36
>TIGR03569 NeuB_NnaB N-acetylneuraminate synthase. This family is a subset of the Pfam model pfam03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine.
Probab=27.74 E-value=67 Score=26.48 Aligned_cols=81 Identities=14% Similarity=0.220 Sum_probs=47.5
Q ss_pred HHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc-------------CCc---hhHHHHHHHHHHHHHHHHHhhhhC
Q psy13859 4 EVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ-------------KEG---IIVRCIQQLSELLRSIKDGAKIFG 67 (108)
Q Consensus 4 ~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G-------------~EG---sIVR~irRL~ELlrql~~Aa~~iG 67 (108)
.|..+.+.+++++-. +....|..-.+.+=|.| ..| ..--.-..+.+|+++++.+..++|
T Consensus 185 ~I~~Lk~~f~~pVG~-----SdHt~G~~~~~aAvalGA~iIEkH~tldk~~~G~D~~~Sl~p~el~~lv~~ir~~~~~lG 259 (329)
T TIGR03569 185 AMDTLKEAFDLPVGY-----SDHTLGIEAPIAAVALGATVIEKHFTLDKNLPGPDHKASLEPDELKEMVQGIRNVEKALG 259 (329)
T ss_pred HHHHHHHHhCCCEEE-----CCCCccHHHHHHHHHcCCCEEEeCCChhhcCCCCChhhcCCHHHHHHHHHHHHHHHHHcC
Confidence 456666777765432 23444555556667777 222 233335677888889999999999
Q ss_pred CCcH--HHHHHHHHHhhcCCcccc
Q psy13859 68 ERDL--PLKMDQAIQVIKRDIVFA 89 (108)
Q Consensus 68 ~~~L--~~k~~~a~~~ikRdIVf~ 89 (108)
+..- .+.=.......||.|+.+
T Consensus 260 ~~~k~~~~~E~~~~~~~rrsl~a~ 283 (329)
T TIGR03569 260 DGVKRPTPSEQKNRDVARKSLVAA 283 (329)
T ss_pred CCCCCcCHHHHHHHHhcceEEEEc
Confidence 8742 222222333456766664
No 37
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=26.85 E-value=1.4e+02 Score=24.13 Aligned_cols=55 Identities=16% Similarity=0.288 Sum_probs=32.5
Q ss_pred HHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHhhhhCCCcHHHHHHHHHH
Q psy13859 3 IEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQKEGIIVRCIQQLSELLRSIKDGAKIFGERDLPLKMDQAIQ 80 (108)
Q Consensus 3 ~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G~EGsIVR~irRL~ELlrql~~Aa~~iG~~~L~~k~~~a~~ 80 (108)
++|-.|--.-||++.+ |.-+.++.+| +.|- ||.=++.-.-||||+..+....|++
T Consensus 107 ~~ikavLgaTKiDLPV--DINDPYDlGL--------------LLRh-------LRHHSNLLAnIgdP~VreqVLsAMq 161 (238)
T PF02084_consen 107 EDIKAVLGATKIDLPV--DINDPYDLGL--------------LLRH-------LRHHSNLLANIGDPEVREQVLSAMQ 161 (238)
T ss_pred HHHHHHhccccccccc--ccCChhhHHH--------------HHHH-------HHHHHHHHhhcCCHHHHHHHHHHHh
Confidence 3455555556666655 3345677776 2333 2333444556899999887766553
No 38
>PF01288 HPPK: 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK); InterPro: IPR000550 All organisms require reduced folate cofactors for the synthesis of a variety of metabolites. Most microorganisms must synthesise folate de novo because they lack the active transport system of higher vertebrate cells which allows these organisms to use dietary folates. Enzymes involved in folate biosynthesis are therefore targets for a variety of antimicrobial agents such as trimethoprim or sulphonamides. 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (2.7.6.3 from EC) (HPPK) catalyses the attachment of pyrophosphate to 6-hydroxymethyl-7,8-dihydropterin to form 6-hydroxymethyl-7,8-dihydropteridine pyrophosphate. This is the first step in a three-step pathway leading to 7,8 dihydrofolate. Bacterial HPPK (gene folK or sulD) [] is a protein of 160 to 270 amino acids. In the lower eukaryote Pneumocystis carinii, HPPK is the central domain of a multifunctional folate synthesis enzyme (gene fas) [].; GO: 0003848 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity, 0009396 folic acid-containing compound biosynthetic process; PDB: 2QX0_B 1RU1_B 2F65_A 1RU2_A 1EQ0_A 3ILJ_A 3HSJ_A 3HD1_A 1TMM_B 1RB0_A ....
Probab=26.24 E-value=42 Score=23.66 Aligned_cols=38 Identities=18% Similarity=0.317 Sum_probs=28.7
Q ss_pred CcHHHHHHHHHHhhcCC----ccccchhhhH--hhhCCcceeee
Q psy13859 69 RDLPLKMDQAIQVIKRD----IVFAPSLWTK--LLVGGQPHYYH 106 (108)
Q Consensus 69 ~~L~~k~~~a~~~ikRd----IVf~~SLYl~--~~~~~~~~~~~ 106 (108)
.+-.+-+.+|...++.. ++..+++|-+ ...++||.|+-
T Consensus 9 ~~~~~~l~~A~~~L~~~~~~~~~~~S~~y~t~p~g~~~~~~F~N 52 (127)
T PF01288_consen 9 GDREQNLRQALQALSALPGFGVIRFSSIYETEPVGFESQPDFLN 52 (127)
T ss_dssp SSHHHHHHHHHHHHHCSTTEEEEEEEEEEEE--SSSSSS-CEEE
T ss_pred HhHHHHHHHHHHHHhcCCCCCcEEECCCEEECCccCCCCcCeee
Confidence 45567888999988875 7888999977 56778888874
No 39
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=25.44 E-value=74 Score=21.19 Aligned_cols=38 Identities=18% Similarity=0.269 Sum_probs=31.4
Q ss_pred CCchhHHHHHHHHHHHHHHHHHhhhhCCCcHHHHHHHH
Q psy13859 41 KEGIIVRCIQQLSELLRSIKDGAKIFGERDLPLKMDQA 78 (108)
Q Consensus 41 ~EGsIVR~irRL~ELlrql~~Aa~~iG~~~L~~k~~~a 78 (108)
...+|---+.|+.+++.+|+.+..-+.|.++-.++-.+
T Consensus 39 ~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~v~~iL~~ 76 (119)
T PF14223_consen 39 DGESVDEYISRLKEIVDELRAIGKPISDEDLVSKILRS 76 (119)
T ss_pred ccccHHHHHHHHHHhhhhhhhcCCcccchhHHHHHHhc
Confidence 56778888999999999999998888888887765543
No 40
>PF11027 DUF2615: Protein of unknown function (DUF2615); InterPro: IPR020309 This entry represents a group of uncharacterised protein from the Metazoa, including CD034 (or C4orf34) and YQF4 (or C34C12.4).
Probab=24.49 E-value=58 Score=22.92 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHh
Q psy13859 47 RCIQQLSELLRSIKDGA 63 (108)
Q Consensus 47 R~irRL~ELlrql~~Aa 63 (108)
-++|||..+|||=.+.+
T Consensus 16 ~AMrRLl~~LRqsQ~~C 32 (103)
T PF11027_consen 16 MAMRRLLNLLRQSQNYC 32 (103)
T ss_pred HHHHHHHHHHHHhhCcc
Confidence 37999999999987766
No 41
>PRK00304 hypothetical protein; Provisional
Probab=23.53 E-value=1e+02 Score=20.53 Aligned_cols=20 Identities=15% Similarity=0.187 Sum_probs=17.0
Q ss_pred CCcHHHHHHHHHHhhcCCcc
Q psy13859 68 ERDLPLKMDQAIQVIKRDIV 87 (108)
Q Consensus 68 ~~~L~~k~~~a~~~ikRdIV 87 (108)
+..|++|.+++...+|+|.+
T Consensus 31 E~sL~~kv~qv~~qL~~G~~ 50 (75)
T PRK00304 31 ETPLETRVLRVRQALTKGQA 50 (75)
T ss_pred cccHHHHHHHHHHHHHcCCE
Confidence 44799999999999999854
No 42
>COG2759 MIS1 Formyltetrahydrofolate synthetase [Nucleotide transport and metabolism]
Probab=23.03 E-value=3.1e+02 Score=24.60 Aligned_cols=48 Identities=23% Similarity=0.293 Sum_probs=32.4
Q ss_pred HHHHhccCCchhHHHHHHHHHHHHHHHHHhhh---------hCCCcHHHHHHHHHHhhcC--Ccccc
Q psy13859 34 VYEWAMQKEGIIVRCIQQLSELLRSIKDGAKI---------FGERDLPLKMDQAIQVIKR--DIVFA 89 (108)
Q Consensus 34 Vy~Wa~G~EGsIVR~irRL~ELlrql~~Aa~~---------iG~~~L~~k~~~a~~~ikR--dIVf~ 89 (108)
.+-|++|.||.+ ||-+.+..++.- --+..+++|++.....+-+ ++.|+
T Consensus 404 s~vwakGg~Gg~--------eLA~kVv~~~~~~~~~f~~lYd~~~~i~~Ki~~I~~~iYga~~v~~s 462 (554)
T COG2759 404 SEVWAKGGEGGI--------ELAKKVVEAIEQNDSEFKRLYDVEDPIEEKIEKIAKEIYGADGVEFS 462 (554)
T ss_pred hhhhhccCccHH--------HHHHHHHHHHhCCcccceeecccCCcHHHHHHHHHHHhcCCcceeeC
Confidence 457999999975 566666665543 1145678899988887766 45553
No 43
>KOG4175|consensus
Probab=22.92 E-value=2.5e+02 Score=22.73 Aligned_cols=87 Identities=22% Similarity=0.213 Sum_probs=53.3
Q ss_pred hHHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc---------CCchhHHHHHHHHHHHHHHHHHhhhhCCCcH-
Q psy13859 2 NIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ---------KEGIIVRCIQQLSELLRSIKDGAKIFGERDL- 71 (108)
Q Consensus 2 a~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G---------~EGsIVR~irRL~ELlrql~~Aa~~iG~~~L- 71 (108)
|..+.+-++++|+..-.- -..+-...=|+..-+-|.+ .-|+=--.-..|++||.+++.++ ||..|
T Consensus 137 a~~~Rne~~k~gislvpL--vaPsTtdeRmell~~~adsFiYvVSrmG~TG~~~svn~~l~~L~qrvrk~t---~dtPlA 211 (268)
T KOG4175|consen 137 AETLRNEARKHGISLVPL--VAPSTTDERMELLVEAADSFIYVVSRMGVTGTRESVNEKLQSLLQRVRKAT---GDTPLA 211 (268)
T ss_pred HHHHHHHHHhcCceEEEe--eCCCChHHHHHHHHHhhcceEEEEEeccccccHHHHHHHHHHHHHHHHHhc---CCCcee
Confidence 345566777888753210 0122334567888888888 55555556678999999999998 77776
Q ss_pred -------HHHHHHHHHhhcCCccccchhhhH
Q psy13859 72 -------PLKMDQAIQVIKRDIVFAPSLWTK 95 (108)
Q Consensus 72 -------~~k~~~a~~~ikRdIVf~~SLYl~ 95 (108)
.+-|.+.-+- -|=|-..|--.+
T Consensus 212 VGFGvst~EHf~qVgsv--aDGVvvGSkiv~ 240 (268)
T KOG4175|consen 212 VGFGVSTPEHFKQVGSV--ADGVVVGSKIVK 240 (268)
T ss_pred EeeccCCHHHHHhhhhh--ccceEecHHHHH
Confidence 3556665444 333333453433
No 44
>PTZ00332 paraflagellar rod protein; Provisional
Probab=22.79 E-value=1.8e+02 Score=26.14 Aligned_cols=59 Identities=7% Similarity=0.109 Sum_probs=41.6
Q ss_pred hHHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc--------------CCchhHHHHHHHHHHHHHHH
Q psy13859 2 NIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ--------------KEGIIVRCIQQLSELLRSIK 60 (108)
Q Consensus 2 a~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G--------------~EGsIVR~irRL~ELlrql~ 60 (108)
|-.++++++-|||+.++.+=|...=+|.+|+||-.=..= |-|.|=..++.+++.=-+|+
T Consensus 75 ~~~~~~lm~~C~L~ms~r~l~~~e~~~~~~~ii~l~~~Lq~lk~~~~~t~~~~~~~~~~~~~~~~E~~E~elr 147 (589)
T PTZ00332 75 AYDLAKLMRVCGLEMSQRELYRPEDKPQFMDIIALKKVLQDLKQNRNKTRVVSFTQMIDNAIAKMEKVEEELR 147 (589)
T ss_pred hhhHHHHHHHccchhhHHHhcCccccccHHHHHHHHHHHHHHHhCCCcCcccccccchHHHHHHHHHHHHHHH
Confidence 456899999999999876445556789999998653321 77777666666665544443
No 45
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=22.79 E-value=60 Score=24.10 Aligned_cols=39 Identities=23% Similarity=0.456 Sum_probs=26.7
Q ss_pred CCchhHHHHHHHHHHHHHHHHHhhhhCCCcHHHHHHHHHHhhc
Q psy13859 41 KEGIIVRCIQQLSELLRSIKDGAKIFGERDLPLKMDQAIQVIK 83 (108)
Q Consensus 41 ~EGsIVR~irRL~ELlrql~~Aa~~iG~~~L~~k~~~a~~~ik 83 (108)
-||-|-|....|+.++...+..+ +++..+|+++-.+.|+
T Consensus 98 VEGlL~~i~~~L~~~~~~~~~~~----~~e~~~k~~~~~~~L~ 136 (160)
T smart00709 98 VEGLLSRVREVLSQAIQETRDDS----DPETKEKIDEFLEKLK 136 (160)
T ss_pred hHHHHHHHHHHHHhhhhhhcccC----CHHHHHHHHHHHHHHH
Confidence 78888888888887765444332 5677777777766543
No 46
>PF14922 FWWh: Protein of unknown function
Probab=22.21 E-value=55 Score=24.35 Aligned_cols=20 Identities=15% Similarity=0.223 Sum_probs=17.8
Q ss_pred hhhhhcchhHHHHHHHHhcc
Q psy13859 21 EEADNLNFGLVQVVYEWAMQ 40 (108)
Q Consensus 21 ~y~~~~~~~LmevVy~Wa~G 40 (108)
.|.+.|+..+...++.|..|
T Consensus 130 ~F~~~FK~~l~~~~~~w~sG 149 (161)
T PF14922_consen 130 LFNEEFKSNLYNTCSEWISG 149 (161)
T ss_pred HHhHHHHHHHHHHHHHHHcC
Confidence 46677999999999999999
No 47
>PRK00254 ski2-like helicase; Provisional
Probab=22.11 E-value=3.1e+02 Score=24.43 Aligned_cols=61 Identities=16% Similarity=0.269 Sum_probs=46.5
Q ss_pred hhHHHHHHHHhcc------------CCchhHHHHHHHHHHHHHHHHHhhhhCC-CcHHHHHHHHHHhhcCCccc
Q psy13859 28 FGLVQVVYEWAMQ------------KEGIIVRCIQQLSELLRSIKDGAKIFGE-RDLPLKMDQAIQVIKRDIVF 88 (108)
Q Consensus 28 ~~LmevVy~Wa~G------------~EGsIVR~irRL~ELlrql~~Aa~~iG~-~~L~~k~~~a~~~ikRdIVf 88 (108)
+--.-+..+|.+| ..|++=+.+.+..-|+.-+.+.++.+|. +++...+.+....++-++-.
T Consensus 569 ~k~~~ll~~~~~~~~~~~~~~~~~~~~gd~~~~~~~~~~l~~a~~~i~~~~~~~~~~~~~l~~l~~rl~~g~~~ 642 (720)
T PRK00254 569 FKTAKVLLDWINEVPEGEIVETYNIDPGDLYRILELADWLMYSLIELYKLFEPKQEVLDYLETLHLRVKHGVRE 642 (720)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHhCcchhHHHHHHHHHHHHHcCCCH
Confidence 3445688999999 3688888888999999999998888994 56666666666666666544
No 48
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=21.84 E-value=1.8e+02 Score=20.76 Aligned_cols=38 Identities=21% Similarity=0.395 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHhhhhCCCcHHHHHHHHHHhh-cCCccc
Q psy13859 48 CIQQLSELLRSIKDGAKIFGERDLPLKMDQAIQVI-KRDIVF 88 (108)
Q Consensus 48 ~irRL~ELlrql~~Aa~~iG~~~L~~k~~~a~~~i-kRdIVf 88 (108)
+-.|+-+|+++.+.+.+ |+|.|. .+..+.+.| ++|+.|
T Consensus 102 Vk~kil~li~~W~~~f~--~~~~l~-~i~~~y~~L~~~G~~F 140 (141)
T cd03565 102 VQEKVLALIQAWADAFR--GSPDLT-GVVEVYEELKKKGIEF 140 (141)
T ss_pred HHHHHHHHHHHHHHHhC--CCccch-HHHHHHHHHHHcCCCC
Confidence 44788888888887753 455544 455555544 457766
No 49
>PF03800 Nuf2: Nuf2 family; InterPro: IPR005549 Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex []. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein has been included in this family that has previously not been identified as a member of this family, Q9C953 from SWISSPROT. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region.; GO: 0007067 mitosis, 0000775 chromosome, centromeric region; PDB: 2VE7_D 3IZ0_D.
Probab=21.62 E-value=85 Score=22.16 Aligned_cols=37 Identities=19% Similarity=0.246 Sum_probs=25.1
Q ss_pred hHHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc
Q psy13859 2 NIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ 40 (108)
Q Consensus 2 a~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G 40 (108)
..+|...-.++|++.+. +-..+++|..+.-+|+|.--
T Consensus 14 ~~eIv~~L~~~~~~~t~--~dl~kPt~e~v~~ly~~~L~ 50 (146)
T PF03800_consen 14 PDEIVNCLQECGIPVTE--EDLKKPTPEFVQKLYERFLE 50 (146)
T ss_dssp HHHHHHHHHHHT--HHH--HC--G--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCcCH--HHHcCCCHHHHHHHHHHHHH
Confidence 35788888999998554 45678999999999999874
No 50
>PF06457 Ectatomin: Ectatomin; InterPro: IPR009458 Ectatomin is a toxin from the venom of the ant Ectatomma tuberculatum. Ectatomin can efficiently insert into the plasma membrane, where it can form channels. Ectatomin was shown to inhibit L-type calcium currents in isolated rat cardiac myocytes []. In these cells, ectatomin induces a gradual, irreversible increase in ion leakage across the membrane, which can lead to cell death. Ectatomin is comprised of two subunits, A and B, which are homologous. The structure of ectatomin reveals that each subunit consists of two alpha helices with a connecting hinge region, which form a hairpin structure that is stabilised by disulphide bridges. A disulphide bridge between the hinge regions of the two subunits links the heterodimer together, forming a closed bundle of four helices with a left-handed twist [].; GO: 0005216 ion channel activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1ECI_A.
Probab=21.60 E-value=1.4e+02 Score=17.00 Aligned_cols=24 Identities=25% Similarity=0.380 Sum_probs=20.5
Q ss_pred hhHHHHHHHHhccCCchhHHHHHH
Q psy13859 28 FGLVQVVYEWAMQKEGIIVRCIQQ 51 (108)
Q Consensus 28 ~~LmevVy~Wa~G~EGsIVR~irR 51 (108)
....+-+..||+--||+|--.|+|
T Consensus 7 ~ticpt~~~~akkc~g~iat~ik~ 30 (34)
T PF06457_consen 7 ETICPTVKPWAKKCSGSIATMIKR 30 (34)
T ss_dssp HHHHHHHHHHHCTBSCCHHHHHHH
T ss_pred hhcCcccHHHHHHccccHHHHHHH
Confidence 356678899999999999998887
No 51
>PRK14151 heat shock protein GrpE; Provisional
Probab=21.45 E-value=15 Score=27.78 Aligned_cols=46 Identities=11% Similarity=0.045 Sum_probs=30.7
Q ss_pred HHHHHHHHHhCCCCCcchhhhhhcchhHHHHHHHHhcc--CCchhHHHHH
Q psy13859 3 IEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWAMQ--KEGIIVRCIQ 50 (108)
Q Consensus 3 ~~Ia~v~~~~~l~~~~~~~y~~~~~~~LmevVy~Wa~G--~EGsIVR~ir 50 (108)
+.+.++-.++|+..-. .--+.|+|.+.++|..=... .+|+|+.+++
T Consensus 109 k~l~~~L~k~Gv~~i~--~~G~~FDP~~HEAv~~~~~~~~~~gtI~~v~q 156 (176)
T PRK14151 109 KMFQDTLKRYQLEAVD--PHGEPFNPEHHQAMAMQESADVEPNSVLKVFQ 156 (176)
T ss_pred HHHHHHHHHCCCEEeC--CCCCCCCHHHhhcceeeCCCCCCcCeEEEEee
Confidence 4567788899995221 11258999999998654433 6788876554
No 52
>smart00073 HPT Histidine Phosphotransfer domain. Contains an active histidine residue that mediates phosphotransfer reactions. Domain detected only in eubacteria. This alignment is an extension to that shown in the Cell structure paper.
Probab=20.44 E-value=2.1e+02 Score=17.41 Aligned_cols=21 Identities=19% Similarity=0.227 Sum_probs=11.4
Q ss_pred HHHHHHHHHHhhhhCCCcHHH
Q psy13859 53 SELLRSIKDGAKIFGERDLPL 73 (108)
Q Consensus 53 ~ELlrql~~Aa~~iG~~~L~~ 73 (108)
...+-.++.+|..+|=+.|.+
T Consensus 31 ~~~~H~LKG~a~~~g~~~l~~ 51 (87)
T smart00073 31 FRAAHTLKGSAGSLGLQQLAQ 51 (87)
T ss_pred HHHHHhhhhhHHhcCHHHHHH
Confidence 344555666666666554444
No 53
>KOG4484|consensus
Probab=20.30 E-value=1.1e+02 Score=23.75 Aligned_cols=34 Identities=12% Similarity=0.251 Sum_probs=24.7
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhCCCcHHHHHHHHHH
Q psy13859 44 IIVRCIQQLSELLRSIKDGAKIFGERDLPLKMDQAIQ 80 (108)
Q Consensus 44 sIVR~irRL~ELlrql~~Aa~~iG~~~L~~k~~~a~~ 80 (108)
-+-|.|+||+-++++ ...-.+|.++++++..+-.
T Consensus 90 KaeR~irrLeK~~ke---S~ad~kd~~i~~qlrk~ki 123 (199)
T KOG4484|consen 90 KAERSIRRLEKLIKE---SGADVKDKQIQQQLRKLKI 123 (199)
T ss_pred HHHHHHHHHHHHHHh---hccchhhHHHHHHHHHHHH
Confidence 577999999999983 3334477778887776644
No 54
>COG1701 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.22 E-value=90 Score=25.23 Aligned_cols=23 Identities=26% Similarity=0.527 Sum_probs=19.3
Q ss_pred CchhHHHHHHHHHHHHHHHHHhh
Q psy13859 42 EGIIVRCIQQLSELLRSIKDGAK 64 (108)
Q Consensus 42 EGsIVR~irRL~ELlrql~~Aa~ 64 (108)
--.|||++.++.+..++|+++.+
T Consensus 197 VDnivRA~p~li~~~~em~~~~r 219 (256)
T COG1701 197 VDNIVRAVPNLIEFVKEMKNASR 219 (256)
T ss_pred eHHHHHHHHHHHHHHHHHhccCH
Confidence 44689999999999999987653
No 55
>PF08158 NUC130_3NT: NUC130/3NT domain; InterPro: IPR012977 This N-terminal domain is found in a novel nucleolar protein family defined by NUC130/133 [].
Probab=20.12 E-value=1.3e+02 Score=18.46 Aligned_cols=21 Identities=24% Similarity=0.542 Sum_probs=16.3
Q ss_pred CCCcHHHHHHHHHHhhcC-Ccc
Q psy13859 67 GERDLPLKMDQAIQVIKR-DIV 87 (108)
Q Consensus 67 G~~~L~~k~~~a~~~ikR-dIV 87 (108)
=+|+|..++-+|.-++|+ |+|
T Consensus 31 L~p~lR~~lv~aLiLLRnK~~I 52 (52)
T PF08158_consen 31 LDPDLRMKLVKALILLRNKDLI 52 (52)
T ss_pred CCHHHHHHHHHHHHHHHccCCC
Confidence 479999999999887764 553
No 56
>PF14518 Haem_oxygenas_2: Iron-containing redox enzyme; PDB: 3BJD_B.
Probab=20.07 E-value=1.6e+02 Score=19.17 Aligned_cols=53 Identities=13% Similarity=0.238 Sum_probs=27.2
Q ss_pred HHHHHHhCCCCCcchhhhhhcchh---HHHHHHHHhc--c-----------CCchhHHHHHHHHHHHHHH
Q psy13859 6 ESIEKKHGVERDKSSEEADNLNFG---LVQVVYEWAM--Q-----------KEGIIVRCIQQLSELLRSI 59 (108)
Q Consensus 6 a~v~~~~~l~~~~~~~y~~~~~~~---LmevVy~Wa~--G-----------~EGsIVR~irRL~ELlrql 59 (108)
.+..+++|++.+.. .+.+.+.+. +......+|. . .|+++....+++.+.||++
T Consensus 23 ~~~L~~~Gi~~~~~-~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~lG~~~~~E~~~~~~~~~~~~~l~r~ 91 (106)
T PF14518_consen 23 RRFLRALGIDDEPG-AYRDPYPPETLALINLFLALCLHRSHYPEALGALLATESSVPQIYRRLIKGLRRL 91 (106)
T ss_dssp HHHHHHTT-----T-T-----HHHHHHHHHHHHHH--H-SSTHHHHHHHHHHHTHHHHHHHHHHHHHHHT
T ss_pred HHHHHHcCCCCccc-cccccCCHHHHHHHHHHHHhcccchhHHHHHHHHHHHhhcChHHHHHHHHHHHHc
Confidence 46778889876533 333333333 3444444442 1 8888888888888888874
No 57
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=20.06 E-value=38 Score=20.68 Aligned_cols=39 Identities=15% Similarity=0.285 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHh----hhhCCCcHHHHHHHHHHhhcCCc
Q psy13859 48 CIQQLSELLRSIKDGA----KIFGERDLPLKMDQAIQVIKRDI 86 (108)
Q Consensus 48 ~irRL~ELlrql~~Aa----~~iG~~~L~~k~~~a~~~ikRdI 86 (108)
+++||---+|-|.+.- ..|-..+|++.+.--...+|||.
T Consensus 7 ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 7 TIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 6778777777666544 35666777777776667777764
Done!