Query psy15899
Match_columns 104
No_of_seqs 166 out of 1020
Neff 7.8
Searched_HMMs 46136
Date Sat Aug 17 00:27:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15899.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15899hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0328 RnhA Ribonuclease HI [ 99.9 2.8E-26 6E-31 154.1 8.0 95 3-98 40-146 (154)
2 PRK06548 ribonuclease H; Provi 99.9 9.5E-25 2.1E-29 148.1 9.8 92 3-97 39-142 (161)
3 PRK08719 ribonuclease H; Revie 99.9 5.9E-24 1.3E-28 142.3 9.5 88 3-96 47-146 (147)
4 PRK00203 rnhA ribonuclease H; 99.9 8.5E-24 1.8E-28 141.6 8.4 95 3-101 40-146 (150)
5 PF00075 RNase_H: RNase H; In 99.9 9.4E-24 2E-28 136.9 7.3 85 3-95 37-131 (132)
6 cd06222 RnaseH RNase H (RNase 99.8 1.3E-19 2.7E-24 113.9 11.0 92 3-95 38-130 (130)
7 PRK13907 rnhA ribonuclease H; 99.8 3.4E-18 7.3E-23 111.3 8.5 89 3-96 38-126 (128)
8 KOG3752|consensus 99.7 1E-17 2.2E-22 124.9 8.0 94 3-96 253-364 (371)
9 PRK07708 hypothetical protein; 99.7 1E-16 2.2E-21 113.5 10.1 97 3-103 115-214 (219)
10 PF13456 RVT_3: Reverse transc 99.7 1.4E-16 3E-21 96.2 8.4 85 6-95 1-85 (87)
11 PRK07238 bifunctional RNase H/ 99.6 6.2E-15 1.3E-19 110.8 10.1 91 2-97 41-132 (372)
12 KOG1812|consensus 92.4 0.67 1.5E-05 35.6 6.8 90 4-97 47-138 (384)
13 COG0296 GlgB 1,4-alpha-glucan 89.9 0.49 1.1E-05 38.7 4.1 72 13-87 166-247 (628)
14 smart00642 Aamy Alpha-amylase 75.9 13 0.00029 25.0 5.9 70 11-81 18-97 (166)
15 PRK10933 trehalose-6-phosphate 73.3 11 0.00024 30.3 5.6 73 8-81 29-108 (551)
16 TIGR02403 trehalose_treC alpha 70.0 14 0.00031 29.5 5.6 73 9-82 24-103 (543)
17 TIGR02402 trehalose_TreZ malto 69.7 15 0.00032 29.5 5.6 71 11-84 110-190 (542)
18 COG3341 Predicted double-stran 67.1 5.8 0.00013 28.4 2.5 87 5-96 107-200 (225)
19 PRK12568 glycogen branching en 60.3 13 0.00028 31.2 3.7 64 18-84 276-349 (730)
20 TIGR01515 branching_enzym alph 60.0 28 0.0006 28.4 5.5 72 11-85 155-237 (613)
21 PLN03244 alpha-amylase; Provis 58.2 19 0.0004 30.8 4.3 32 51-83 439-470 (872)
22 PRK05402 glycogen branching en 58.1 33 0.00072 28.5 5.8 73 11-84 264-345 (726)
23 PRK12313 glycogen branching en 57.2 36 0.00078 27.8 5.7 71 11-84 169-250 (633)
24 PRK02228 V-type ATP synthase s 57.2 44 0.00095 20.6 6.7 74 16-96 13-95 (100)
25 PRK14705 glycogen branching en 54.1 18 0.0004 32.1 3.8 65 17-84 771-845 (1224)
26 PRK14706 glycogen branching en 52.8 21 0.00046 29.3 3.8 33 51-84 215-247 (639)
27 PRK10785 maltodextrin glucosid 51.8 47 0.001 27.0 5.6 70 8-82 175-254 (598)
28 TIGR02456 treS_nterm trehalose 49.7 53 0.0012 26.2 5.6 73 9-82 25-104 (539)
29 PRK11657 dsbG disulfide isomer 45.9 51 0.0011 23.7 4.5 37 26-76 118-154 (251)
30 PF00336 DNA_pol_viral_C: DNA 42.2 16 0.00035 26.2 1.4 59 5-77 124-182 (245)
31 PF09345 DUF1987: Domain of un 41.1 49 0.0011 20.6 3.4 25 51-76 61-85 (99)
32 PF14437 MafB19-deam: MafB19-l 40.2 43 0.00094 22.5 3.2 38 4-43 78-115 (146)
33 PF01990 ATP-synt_F: ATP synth 37.5 78 0.0017 19.0 3.9 74 15-92 10-94 (95)
34 PLN02960 alpha-amylase 37.4 47 0.001 28.7 3.6 70 12-82 416-494 (897)
35 PF10580 Neuromodulin_N: Gap j 37.1 38 0.00083 16.7 1.9 23 75-97 5-27 (32)
36 PRK09505 malS alpha-amylase; R 36.7 1.1E+02 0.0024 25.6 5.6 72 9-81 227-319 (683)
37 PF00128 Alpha-amylase: Alpha 35.8 47 0.001 23.3 3.1 74 11-85 3-83 (316)
38 COG4566 TtrR Response regulato 34.9 81 0.0018 22.4 4.0 67 13-83 15-90 (202)
39 PF10298 WhiA_N: WhiA N-termin 33.9 46 0.00099 19.7 2.4 35 7-41 4-39 (86)
40 COG0590 CumB Cytosine/adenosin 32.8 57 0.0012 21.7 2.9 31 7-37 57-87 (152)
41 PLN02447 1,4-alpha-glucan-bran 32.0 65 0.0014 27.3 3.6 65 16-81 255-327 (758)
42 KOG3243|consensus 31.8 60 0.0013 21.7 2.8 16 67-82 50-65 (158)
43 PRK00061 ribH 6,7-dimethyl-8-r 30.7 1E+02 0.0022 20.8 3.8 22 60-82 36-60 (154)
44 PF00885 DMRL_synthase: 6,7-di 30.5 1.2E+02 0.0027 20.0 4.2 32 59-93 26-60 (144)
45 TIGR02104 pulA_typeI pullulana 30.5 85 0.0018 25.5 4.0 28 53-81 229-256 (605)
46 COG1519 KdtA 3-deoxy-D-manno-o 30.4 63 0.0014 25.4 3.1 38 55-94 247-284 (419)
47 PF12163 HobA: DNA replication 30.0 1.3E+02 0.0028 21.0 4.2 36 10-47 28-70 (180)
48 cd01285 nucleoside_deaminase N 29.2 97 0.0021 19.0 3.4 32 5-36 44-75 (109)
49 PF08806 Sep15_SelM: Sep15/Sel 28.9 41 0.0009 20.0 1.5 14 67-80 30-43 (78)
50 COG1212 KdsB CMP-2-keto-3-deox 28.8 92 0.002 22.8 3.5 30 16-45 33-62 (247)
51 PRK10860 tRNA-specific adenosi 28.4 71 0.0015 21.8 2.8 30 7-36 61-90 (172)
52 PLN02404 6,7-dimethyl-8-ribity 28.3 1.2E+02 0.0027 20.1 3.8 30 60-92 31-63 (141)
53 PRK12419 riboflavin synthase s 27.2 1.2E+02 0.0027 20.6 3.7 23 59-82 33-58 (158)
54 PF15216 TSLP: Thymic stromal 26.3 21 0.00045 23.2 -0.1 12 73-84 80-91 (124)
55 COG3981 Predicted acetyltransf 25.5 1.1E+02 0.0025 21.1 3.3 25 12-36 117-141 (174)
56 TIGR03628 arch_S11P archaeal r 24.8 2E+02 0.0043 18.5 4.9 32 2-34 41-72 (114)
57 COG0295 Cdd Cytidine deaminase 24.7 2.1E+02 0.0047 18.9 4.8 40 7-54 54-93 (134)
58 PF05830 NodZ: Nodulation prot 24.2 2E+02 0.0044 21.9 4.7 33 13-45 198-233 (321)
59 PF00289 CPSase_L_chain: Carba 23.4 1.3E+02 0.0028 18.8 3.2 30 7-38 9-38 (110)
60 TIGR01506 ribC_arch riboflavin 22.8 94 0.002 21.0 2.5 31 59-92 19-51 (151)
61 TIGR02401 trehalose_TreY malto 22.6 4.1E+02 0.0089 23.0 6.7 71 12-83 16-94 (825)
62 PRK14507 putative bifunctional 22.1 2.6E+02 0.0055 26.3 5.6 79 11-90 757-845 (1693)
63 KOG1123|consensus 22.1 1.1E+02 0.0023 25.4 3.0 26 16-41 530-558 (776)
64 COG0054 RibH Riboflavin syntha 21.5 2.7E+02 0.0059 18.8 4.5 24 69-94 47-70 (152)
65 TIGR00114 lumazine-synth 6,7-d 21.5 1.9E+02 0.0042 19.0 3.8 23 69-93 35-57 (138)
66 PRK11396 hypothetical protein; 21.0 65 0.0014 22.6 1.5 13 68-80 175-187 (191)
67 PRK14511 maltooligosyl trehalo 21.0 5.1E+02 0.011 22.6 7.0 76 11-87 19-104 (879)
68 cd00384 ALAD_PBGS Porphobilino 20.9 1E+02 0.0022 23.4 2.6 22 13-34 52-73 (314)
69 PRK11835 hypothetical protein; 20.9 54 0.0012 21.1 1.0 13 69-81 13-25 (114)
70 PLN00196 alpha-amylase; Provis 20.9 1.5E+02 0.0033 23.2 3.6 66 11-81 43-119 (428)
71 TIGR01676 GLDHase galactonolac 20.6 1.7E+02 0.0037 23.9 3.9 27 52-80 240-266 (541)
72 COG0400 Predicted esterase [Ge 20.6 1.4E+02 0.003 21.0 3.1 18 61-79 171-189 (207)
73 TIGR00854 pts-sorbose PTS syst 20.5 1.3E+02 0.0028 20.0 2.9 25 53-78 123-147 (151)
74 PF02887 PK_C: Pyruvate kinase 20.5 2.2E+02 0.0048 17.5 3.8 20 25-44 38-57 (117)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.93 E-value=2.8e-26 Score=154.14 Aligned_cols=95 Identities=24% Similarity=0.268 Sum_probs=83.1
Q ss_pred cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC---CC--------Ch-HHHHHHHHHHHHHHhCCcce
Q psy15899 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPY---LS--------CP-IISQIYSAWCDLKTVGQYYV 70 (104)
Q Consensus 3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~---~~--------~~-~~~~i~~~~~~l~~~~~~~v 70 (104)
.+||++||++|++.||+.+.+.+.+.|.|+|||+|++++|+.|. .. .| ..+++++.+.++..+ ...|
T Consensus 40 ~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~-~~~v 118 (154)
T COG0328 40 RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKR-HELV 118 (154)
T ss_pred cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhh-CCeE
Confidence 58999999999999999999889999999999999999999541 11 12 346888888888887 6799
Q ss_pred EEEeecCCCCCchhHHHHHHHccccCCC
Q psy15899 71 KLMWCPSHCGIRGNEAVDQAAKDPLLSP 98 (104)
Q Consensus 71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~~ 98 (104)
.++|||||+|.++||+||+||+.+++.+
T Consensus 119 ~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 119 FWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred EEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 9999999999999999999999998765
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.92 E-value=9.5e-25 Score=148.08 Aligned_cols=92 Identities=23% Similarity=0.253 Sum_probs=76.1
Q ss_pred cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC---------CCCCCh--H-HHHHHHHHHHHHHhCCcce
Q psy15899 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIAN---------PYLSCP--I-ISQIYSAWCDLKTVGQYYV 70 (104)
Q Consensus 3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~---------~~~~~~--~-~~~i~~~~~~l~~~~~~~v 70 (104)
..||++|||+|++.||+.+.. +...|.|+|||+|++++++. |...++ + .+++++.+.++.++ ..|
T Consensus 39 ~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~--~~v 115 (161)
T PRK06548 39 IATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN--RNI 115 (161)
T ss_pred CCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc--Cce
Confidence 479999999999999986643 45689999999999999994 323333 3 47888888788764 479
Q ss_pred EEEeecCCCCCchhHHHHHHHccccCC
Q psy15899 71 KLMWCPSHCGIRGNEAVDQAAKDPLLS 97 (104)
Q Consensus 71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~ 97 (104)
.|.|||||+|++|||.||+||++|+..
T Consensus 116 ~~~wVkgHsg~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 116 RMSWVNAHTGHPLNEAADSLARQAANN 142 (161)
T ss_pred EEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 999999999999999999999998853
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.91 E-value=5.9e-24 Score=142.35 Aligned_cols=88 Identities=24% Similarity=0.306 Sum_probs=72.0
Q ss_pred cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhc--------CCCC-CCh--H-HHHHHHHHHHHHHhCCcce
Q psy15899 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIA--------NPYL-SCP--I-ISQIYSAWCDLKTVGQYYV 70 (104)
Q Consensus 3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~--------~~~~-~~~--~-~~~i~~~~~~l~~~~~~~v 70 (104)
..||++|||.|++.||+.+.+. .+|+|||+|++++++ +.+. ..+ + ..++++.+.++.. ...|
T Consensus 47 ~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~--~~~i 120 (147)
T PRK08719 47 YTDNAELELLALIEALEYARDG----DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA--RKYV 120 (147)
T ss_pred CccHHHHHHHHHHHHHHHcCCC----CEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC--CCcE
Confidence 4799999999999999999653 389999999999984 3333 222 2 3677777766765 5679
Q ss_pred EEEeecCCCCCchhHHHHHHHccccC
Q psy15899 71 KLMWCPSHCGIRGNEAVDQAAKDPLL 96 (104)
Q Consensus 71 ~~~WVpgH~g~~gNe~AD~lAk~a~~ 96 (104)
.|.|||||+|++|||.||+||++|++
T Consensus 121 ~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 121 EVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred EEEEecCCCCChhHHHHHHHHHHHhh
Confidence 99999999999999999999999875
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.90 E-value=8.5e-24 Score=141.60 Aligned_cols=95 Identities=21% Similarity=0.277 Sum_probs=76.7
Q ss_pred cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCC--------C-CCC--hH-HHHHHHHHHHHHHhCCcce
Q psy15899 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANP--------Y-LSC--PI-ISQIYSAWCDLKTVGQYYV 70 (104)
Q Consensus 3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~--------~-~~~--~~-~~~i~~~~~~l~~~~~~~v 70 (104)
..|+++|||.|++.||+.+.+ ...|.|+|||++++++|+.| + ..+ ++ ..++++.+.++.. ...|
T Consensus 40 ~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~--~~~v 115 (150)
T PRK00203 40 LTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK--RHQI 115 (150)
T ss_pred CCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc--cCce
Confidence 468999999999999998864 46899999999999999862 1 122 22 2556666666664 5789
Q ss_pred EEEeecCCCCCchhHHHHHHHccccCCCccc
Q psy15899 71 KLMWCPSHCGIRGNEAVDQAAKDPLLSPVIE 101 (104)
Q Consensus 71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~~~~~ 101 (104)
.|.|||||+|++||+.||+||++|+..+..+
T Consensus 116 ~~~wV~~H~~~~~N~~AD~lA~~a~~~~~~~ 146 (150)
T PRK00203 116 KWHWVKGHAGHPENERCDELARAGAEEATLE 146 (150)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHhhhc
Confidence 9999999999999999999999998766544
No 5
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.90 E-value=9.4e-24 Score=136.88 Aligned_cols=85 Identities=32% Similarity=0.495 Sum_probs=68.1
Q ss_pred cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC-----CCCCC----hHHHHHHHHHHHHHHhCCcceEEE
Q psy15899 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIAN-----PYLSC----PIISQIYSAWCDLKTVGQYYVKLM 73 (104)
Q Consensus 3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~-----~~~~~----~~~~~i~~~~~~l~~~~~~~v~~~ 73 (104)
..|+++|||.|+..||+ +.. .+.++|||||+++++.+.. .+... ++..+|+ ++..+ +..|.|.
T Consensus 37 ~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~----~~~~~-~~~v~~~ 108 (132)
T PF00075_consen 37 GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIW----ELLSR-GIKVRFR 108 (132)
T ss_dssp SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHH----HHHHH-SSEEEEE
T ss_pred ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHHHHhccccccccccccccchhhee----ecccc-ceEEeee
Confidence 46899999999999999 543 3999999999999998877 33222 2445555 44455 8899999
Q ss_pred eecCCCCC-chhHHHHHHHcccc
Q psy15899 74 WCPSHCGI-RGNEAVDQAAKDPL 95 (104)
Q Consensus 74 WVpgH~g~-~gNe~AD~lAk~a~ 95 (104)
|||||+|+ .||+.||+|||+|+
T Consensus 109 ~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 109 WVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp ESSSSSSSHHHHHHHHHHHHHHH
T ss_pred eccCcCCCchhHHHHHHHHHHhc
Confidence 99999999 69999999999986
No 6
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=99.83 E-value=1.3e-19 Score=113.91 Aligned_cols=92 Identities=25% Similarity=0.324 Sum_probs=77.2
Q ss_pred cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC-CChHHHHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL-SCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGI 81 (104)
Q Consensus 3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~ 81 (104)
..|++.+|+.|++.||+++...+..++.|+|||+.+++.++++.. .......++..+.++..+ +..+.|.|||+|+|.
T Consensus 38 ~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~i~~v~~h~~~ 116 (130)
T cd06222 38 NTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKR-FHKVRFEWVPGHSGI 116 (130)
T ss_pred CCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhC-CCeEEEEEcCCCCCC
Confidence 578999999999999999998899999999999999999998764 222334444444455555 889999999999999
Q ss_pred chhHHHHHHHcccc
Q psy15899 82 RGNEAVDQAAKDPL 95 (104)
Q Consensus 82 ~gNe~AD~lAk~a~ 95 (104)
++|+.||.|||++.
T Consensus 117 ~~n~~ad~la~~~~ 130 (130)
T cd06222 117 EGNERADALAKEAA 130 (130)
T ss_pred cchHHHHHHHHhhC
Confidence 99999999999874
No 7
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.76 E-value=3.4e-18 Score=111.27 Aligned_cols=89 Identities=21% Similarity=0.230 Sum_probs=76.5
Q ss_pred cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeecCCCCCc
Q psy15899 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIR 82 (104)
Q Consensus 3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~ 82 (104)
.+|++.||+.|++.||+.+.+.+..+|.|+|||+++++.+++.+..++-...+++.+..+..+ +..+.|.|||+ +
T Consensus 38 ~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~-f~~~~~~~v~r----~ 112 (128)
T PRK13907 38 TMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKS-FDLFFIKWIPS----S 112 (128)
T ss_pred ccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhc-CCceEEEEcCc----h
Confidence 479999999999999999999888999999999999999998765544456666666677776 77888999995 7
Q ss_pred hhHHHHHHHccccC
Q psy15899 83 GNEAVDQAAKDPLL 96 (104)
Q Consensus 83 gNe~AD~lAk~a~~ 96 (104)
+|+.||.||+.|..
T Consensus 113 ~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 113 QNKVADELARKAIL 126 (128)
T ss_pred hchhHHHHHHHHHh
Confidence 99999999999875
No 8
>KOG3752|consensus
Probab=99.73 E-value=1e-17 Score=124.91 Aligned_cols=94 Identities=20% Similarity=0.227 Sum_probs=74.4
Q ss_pred cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC---CC--------h----H--HHHHHHHHHHHHHh
Q psy15899 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL---SC--------P----I--ISQIYSAWCDLKTV 65 (104)
Q Consensus 3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~---~~--------~----~--~~~i~~~~~~l~~~ 65 (104)
-.|+|+|||.|+..||+.+.+.+..+|+|.|||+++++.|+.|.. +. + + ..+....+.+|.+.
T Consensus 253 ~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~ 332 (371)
T KOG3752|consen 253 RQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQE 332 (371)
T ss_pred cccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhh
Confidence 468999999999999999998888899999999999999986421 11 1 1 12333344455543
Q ss_pred -CCcceEEEeecCCCCCchhHHHHHHHccccC
Q psy15899 66 -GQYYVKLMWCPSHCGIRGNEAVDQAAKDPLL 96 (104)
Q Consensus 66 -~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~ 96 (104)
....|.+.|||||.|+.||++||.||++++.
T Consensus 333 ~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~ 364 (371)
T KOG3752|consen 333 ISNKKVQQEYVGGHSGILGNEMADALARKGST 364 (371)
T ss_pred hccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence 1589999999999999999999999999854
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.71 E-value=1e-16 Score=113.52 Aligned_cols=97 Identities=16% Similarity=0.089 Sum_probs=79.9
Q ss_pred cchhhHHHHHHHHHHHHHhhhCCCCe--EEEEeccHHHHHHhcCCCC-CChHHHHHHHHHHHHHHhCCcceEEEeecCCC
Q psy15899 3 HCSNGIAELIAILLCLRSIKNHPAMR--FLLVSDSMGSLSAIANPYL-SCPIISQIYSAWCDLKTVGQYYVKLMWCPSHC 79 (104)
Q Consensus 3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~--v~I~tDS~~~l~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~ 79 (104)
.+|++.||+.|++.||+.+.+.+.++ |.|++||+++++.+++.+. .++....+.+.+.++.+++...+.|.|||
T Consensus 115 ~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp--- 191 (219)
T PRK07708 115 IYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS--- 191 (219)
T ss_pred cccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC---
Confidence 47999999999999999999887655 8999999999999997654 45555566666666666645568889998
Q ss_pred CCchhHHHHHHHccccCCCccccc
Q psy15899 80 GIRGNEAVDQAAKDPLLSPVIEKK 103 (104)
Q Consensus 80 g~~gNe~AD~lAk~a~~~~~~~~~ 103 (104)
++.|+.||+||++|++....+++
T Consensus 192 -R~~N~~AD~LAk~Al~~~~~~~~ 214 (219)
T PRK07708 192 -RKQNKEADQLATQALEGTVIESH 214 (219)
T ss_pred -chhhhHHHHHHHHHHhcCCCCch
Confidence 68999999999999988777665
No 10
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.70 E-value=1.4e-16 Score=96.17 Aligned_cols=85 Identities=22% Similarity=0.130 Sum_probs=66.5
Q ss_pred hhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeecCCCCCchhH
Q psy15899 6 NGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNE 85 (104)
Q Consensus 6 ~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~gNe 85 (104)
|..||+.|+..||+++.+.+.++|.|+|||+.+++.+++..........+.+.+..+.+. +..+.|.||| +++|.
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~i~----r~~N~ 75 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDR-FWNVSVSHIP----REQNK 75 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCC-CSCEEEEE------GGGSH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhcc-ccceEEEEEC----hHHhH
Confidence 578999999999999999999999999999999999998743322334444445467776 8899999999 79999
Q ss_pred HHHHHHcccc
Q psy15899 86 AVDQAAKDPL 95 (104)
Q Consensus 86 ~AD~lAk~a~ 95 (104)
.||.|||.|.
T Consensus 76 ~A~~LA~~a~ 85 (87)
T PF13456_consen 76 VADALAKFAL 85 (87)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHh
Confidence 9999999875
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.61 E-value=6.2e-15 Score=110.78 Aligned_cols=91 Identities=16% Similarity=0.194 Sum_probs=76.8
Q ss_pred CcchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC-CChHHHHHHHHHHHHHHhCCcceEEEeecCCCC
Q psy15899 2 FHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL-SCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCG 80 (104)
Q Consensus 2 ~~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g 80 (104)
..+||+.||+.|++.||+.+.+.+.++|.|++||+++++.+++.+. +++-...+.+.+.++.++ +..+.|.|||+
T Consensus 41 ~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~-f~~~~i~~v~r--- 116 (372)
T PRK07238 41 GRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQ-FGRVTYTWIPR--- 116 (372)
T ss_pred CCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhc-CCceEEEECCc---
Confidence 3589999999999999999999899999999999999999997654 455445555556677776 78999999994
Q ss_pred CchhHHHHHHHccccCC
Q psy15899 81 IRGNEAVDQAAKDPLLS 97 (104)
Q Consensus 81 ~~gNe~AD~lAk~a~~~ 97 (104)
++|+.||.||+.|...
T Consensus 117 -~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 117 -ARNAHADRLANEAMDA 132 (372)
T ss_pred -hhhhHHHHHHHHHHHh
Confidence 8999999999998643
No 12
>KOG1812|consensus
Probab=92.39 E-value=0.67 Score=35.63 Aligned_cols=90 Identities=12% Similarity=0.024 Sum_probs=54.8
Q ss_pred chhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCCh--HHHHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899 4 CSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCP--IISQIYSAWCDLKTVGQYYVKLMWCPSHCGI 81 (104)
Q Consensus 4 ~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~~--~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~ 81 (104)
.+...+|++|+..+|..+.+.+...+++++|+....+.+.....+.. .+..+.+.+..++.+ .....-.-+|. .
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~~~~~~~~~~l~~~v~~~r~~-l~~~~~i~~~~---~ 122 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREKPEQHRKIVLLVELVQRIREQ-LTSSEPILVPK---N 122 (384)
T ss_pred cchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH-hhcccceeccc---c
Confidence 46788999999999999999999999999997766665544332221 233344444444443 22122222221 1
Q ss_pred chhHHHHHHHccccCC
Q psy15899 82 RGNEAVDQAAKDPLLS 97 (104)
Q Consensus 82 ~gNe~AD~lAk~a~~~ 97 (104)
.....|=.||+++..+
T Consensus 123 ~d~~~~~~lA~e~i~s 138 (384)
T KOG1812|consen 123 ADIKFAYKLAREAIVS 138 (384)
T ss_pred hhhHHHHHHHHHhhcc
Confidence 1223466788877654
No 13
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=89.92 E-value=0.49 Score=38.65 Aligned_cols=72 Identities=14% Similarity=0.009 Sum_probs=45.2
Q ss_pred HHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC--------CCC--hHHHHHHHHHHHHHHhCCcceEEEeecCCCCCc
Q psy15899 13 AILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPY--------LSC--PIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIR 82 (104)
Q Consensus 13 Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~--------~~~--~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~ 82 (104)
++..=|.++++.|.+.|.+.-=++..-. .+|. +.+ |--.++...++++.+. |..|-+-|||+|.+..
T Consensus 166 ~a~~llpYl~elG~T~IELMPv~e~p~~--~sWGYq~~g~yAp~sryGtPedfk~fVD~aH~~-GIgViLD~V~~HF~~d 242 (628)
T COG0296 166 LAIELLPYLKELGITHIELMPVAEHPGD--RSWGYQGTGYYAPTSRYGTPEDFKALVDAAHQA-GIGVILDWVPNHFPPD 242 (628)
T ss_pred HHHHHhHHHHHhCCCEEEEcccccCCCC--CCCCCCcceeccccccCCCHHHHHHHHHHHHHc-CCEEEEEecCCcCCCC
Confidence 3444566666777777776542221111 0110 011 1335677777778877 9999999999999999
Q ss_pred hhHHH
Q psy15899 83 GNEAV 87 (104)
Q Consensus 83 gNe~A 87 (104)
||-.+
T Consensus 243 ~~~L~ 247 (628)
T COG0296 243 GNYLA 247 (628)
T ss_pred cchhh
Confidence 98765
No 14
>smart00642 Aamy Alpha-amylase domain.
Probab=75.90 E-value=13 Score=24.97 Aligned_cols=70 Identities=13% Similarity=-0.064 Sum_probs=43.3
Q ss_pred HHHHHHHHHHhhhCCCCeEEEEe----------ccHHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeecCCCC
Q psy15899 11 LIAILLCLRSIKNHPAMRFLLVS----------DSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCG 80 (104)
Q Consensus 11 l~Ai~~aL~~~~~~~~~~v~I~t----------DS~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g 80 (104)
+.++..-|.++.+.|.+.|.+-. ++-|...-.......-|...++...+.++.++ |..|-+-.|+.|++
T Consensus 18 ~~gi~~~l~yl~~lG~~~I~l~Pi~~~~~~~~~~~gY~~~d~~~i~~~~Gt~~d~~~lv~~~h~~-Gi~vilD~V~NH~~ 96 (166)
T smart00642 18 LQGIIEKLDYLKDLGVTAIWLSPIFESPQGYPSYHGYDISDYKQIDPRFGTMEDFKELVDAAHAR-GIKVILDVVINHTS 96 (166)
T ss_pred HHHHHHHHHHHHHCCCCEEEECcceeCCCCCCCCCCcCccccCCCCcccCCHHHHHHHHHHHHHC-CCEEEEEECCCCCC
Confidence 66777777778777777665421 11111111111111122346777777788887 99999999999987
Q ss_pred C
Q psy15899 81 I 81 (104)
Q Consensus 81 ~ 81 (104)
.
T Consensus 97 ~ 97 (166)
T smart00642 97 D 97 (166)
T ss_pred C
Confidence 5
No 15
>PRK10933 trehalose-6-phosphate hydrolase; Provisional
Probab=73.30 E-value=11 Score=30.28 Aligned_cols=73 Identities=10% Similarity=0.006 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHHHhhhCCCCeEEEEe-------ccHHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeecCCCC
Q psy15899 8 IAELIAILLCLRSIKNHPAMRFLLVS-------DSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCG 80 (104)
Q Consensus 8 ~aEl~Ai~~aL~~~~~~~~~~v~I~t-------DS~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g 80 (104)
.+.+.+|...|.++.+.|.+.|.+-. |+-|.+.-.......-|...++..++.++.++ |+.|-+-.|+-|++
T Consensus 29 ~Gdl~gi~~~ldyl~~lGv~~i~l~P~~~~~~~~~gY~~~d~~~id~~~Gt~~d~~~lv~~~h~~-gi~vilD~V~NH~s 107 (551)
T PRK10933 29 TGDLRGVTQRLDYLQKLGVDAIWLTPFYVSPQVDNGYDVANYTAIDPTYGTLDDFDELVAQAKSR-GIRIILDMVFNHTS 107 (551)
T ss_pred CcCHHHHHHhhHHHHhCCCCEEEECCCCCCCCCCCCCCcccCCCcCcccCCHHHHHHHHHHHHHC-CCEEEEEECCCCcc
Confidence 46788999999999998888776521 22221111111111112345677777778877 99999999999987
Q ss_pred C
Q psy15899 81 I 81 (104)
Q Consensus 81 ~ 81 (104)
.
T Consensus 108 ~ 108 (551)
T PRK10933 108 T 108 (551)
T ss_pred C
Confidence 6
No 16
>TIGR02403 trehalose_treC alpha,alpha-phosphotrehalase. Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor.
Probab=70.04 E-value=14 Score=29.51 Aligned_cols=73 Identities=14% Similarity=0.010 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHhhhCCCCeEEEEe-------ccHHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899 9 AELIAILLCLRSIKNHPAMRFLLVS-------DSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGI 81 (104)
Q Consensus 9 aEl~Ai~~aL~~~~~~~~~~v~I~t-------DS~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~ 81 (104)
+-+.+|..-|.++.+.|.+.|.+-- |+.|.+.-.....+.-|...++..++.++.++ |..|-+-+|+-|++.
T Consensus 24 G~~~gi~~~l~yl~~lG~~~i~l~Pi~~~~~~~~gY~~~d~~~id~~~Gt~~~~~~lv~~ah~~-gi~vilD~v~NH~~~ 102 (543)
T TIGR02403 24 GDLRGIIEKLDYLKKLGVDYIWLNPFYVSPQKDNGYDVSDYYAINPLFGTMADFEELVSEAKKR-NIKIMLDMVFNHTST 102 (543)
T ss_pred cCHHHHHHhHHHHHHcCCCEEEECCcccCCCCCCCCCccccCccCcccCCHHHHHHHHHHHHHC-CCEEEEEECcccccc
Confidence 4578899999999888877775422 22222221111111223346677777788887 999999999999974
Q ss_pred c
Q psy15899 82 R 82 (104)
Q Consensus 82 ~ 82 (104)
.
T Consensus 103 ~ 103 (543)
T TIGR02403 103 E 103 (543)
T ss_pred c
Confidence 3
No 17
>TIGR02402 trehalose_TreZ malto-oligosyltrehalose trehalohydrolase. Members of this family are the trehalose biosynthetic enzyme malto-oligosyltrehalose trehalohydrolase, formally known as 4-alpha-D-{(1-4)-alpha-D-glucano}trehalose trehalohydrolase (EC 3.2.1.141). It is the TreZ protein of the TreYZ pathway for trehalose biosynthesis, and alternative to the OtsAB system.
Probab=69.72 E-value=15 Score=29.49 Aligned_cols=71 Identities=13% Similarity=-0.073 Sum_probs=46.4
Q ss_pred HHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC-------C---CChHHHHHHHHHHHHHHhCCcceEEEeecCCCC
Q psy15899 11 LIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPY-------L---SCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCG 80 (104)
Q Consensus 11 l~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~-------~---~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g 80 (104)
+.++..-|.++++.|.+.|.+--=..+. .-.+|. . .-|-..++.+.+.++.++ |+.|-+-+|+.|+|
T Consensus 110 ~~gi~~~l~yl~~LGv~~i~L~Pi~~~~--~~~~~GY~~~~~~~~~~~~G~~~e~k~lV~~aH~~-Gi~VilD~V~NH~~ 186 (542)
T TIGR02402 110 FDAAIEKLPYLADLGITAIELMPVAQFP--GTRGWGYDGVLPYAPHNAYGGPDDLKALVDAAHGL-GLGVILDVVYNHFG 186 (542)
T ss_pred HHHHHHhhHHHHHcCCCEEEeCccccCC--CCCCCCCCccCccccccccCCHHHHHHHHHHHHHC-CCEEEEEEccCCCC
Confidence 5678888999988888777542211100 001111 1 112356777888888888 99999999999998
Q ss_pred Cchh
Q psy15899 81 IRGN 84 (104)
Q Consensus 81 ~~gN 84 (104)
..+|
T Consensus 187 ~~~~ 190 (542)
T TIGR02402 187 PEGN 190 (542)
T ss_pred Cccc
Confidence 7654
No 18
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=67.14 E-value=5.8 Score=28.43 Aligned_cols=87 Identities=11% Similarity=0.046 Sum_probs=56.8
Q ss_pred hhhHHHHHHHHHHHHHhhhCCCCeE-EEE----eccHHHHHHhcCCC-CCChHHHHHHHHHHHHHHh-CCcceEEEeecC
Q psy15899 5 SNGIAELIAILLCLRSIKNHPAMRF-LLV----SDSMGSLSAIANPY-LSCPIISQIYSAWCDLKTV-GQYYVKLMWCPS 77 (104)
Q Consensus 5 s~~~aEl~Ai~~aL~~~~~~~~~~v-~I~----tDS~~~l~~l~~~~-~~~~~~~~i~~~~~~l~~~-~~~~v~~~WVpg 77 (104)
++..+|.+|.+.+|+.+...+.++. .+| .||++..+-+.+.. .+..+... .+.... .+....+.|+.-
T Consensus 107 ~n~s~d~la~ly~~~~~~~~~nrk~~i~y~~~~~ds~a~~k~~k~~~~~k~~~~~~-----~e~~~~~~~v~h~~k~i~~ 181 (225)
T COG3341 107 SNDSGDVLAKLYGLRYEVPLDNRKSVINYLTPGNDSWAYFKYVKDKCETKVNLLKD-----REFFSIGKGVFHDEKDINI 181 (225)
T ss_pred cCchHHHHHHhccccccccccCccceeeccCCcchhHHHHHHHhhhhhhHHHHHHh-----HHhhhccchhhhhhhhccc
Confidence 5678999999999999987654444 447 79998888776533 11111110 011111 035566789999
Q ss_pred CCCCchhHHHHHHHccccC
Q psy15899 78 HCGIRGNEAVDQAAKDPLL 96 (104)
Q Consensus 78 H~g~~gNe~AD~lAk~a~~ 96 (104)
|.+..-+...+.++.....
T Consensus 182 ~~~~~~~~~~~s~~~~~~k 200 (225)
T COG3341 182 HIWIFESKKGNSHVYNTSK 200 (225)
T ss_pred ccccchhhhhhhhhhchhh
Confidence 9999888888877765543
No 19
>PRK12568 glycogen branching enzyme; Provisional
Probab=60.29 E-value=13 Score=31.18 Aligned_cols=64 Identities=9% Similarity=-0.002 Sum_probs=40.5
Q ss_pred HHHhhhCCCCeEEEEeccHHHHHHhcCC-------CC---CChHHHHHHHHHHHHHHhCCcceEEEeecCCCCCchh
Q psy15899 18 LRSIKNHPAMRFLLVSDSMGSLSAIANP-------YL---SCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGN 84 (104)
Q Consensus 18 L~~~~~~~~~~v~I~tDS~~~l~~l~~~-------~~---~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~gN 84 (104)
|.++++.|.+.|.+.-=...-.. .+| +. .-|...++...+.++.++ |+.|-+.|||.|++..++
T Consensus 276 l~ylk~LGvt~I~LmPi~e~~~~--~~wGY~~~~~~a~~~~~G~~~dfk~lV~~~H~~-Gi~VIlD~V~nH~~~d~~ 349 (730)
T PRK12568 276 IPYVQQLGFTHIELLPITEHPFG--GSWGYQPLGLYAPTARHGSPDGFAQFVDACHRA-GIGVILDWVSAHFPDDAH 349 (730)
T ss_pred HHHHHHcCCCEEEECccccCCCC--CCCCCCCCcCCccCcccCCHHHHHHHHHHHHHC-CCEEEEEeccccCCcccc
Confidence 57787878777764321111000 011 11 112456778888888888 999999999999987654
No 20
>TIGR01515 branching_enzym alpha-1,4-glucan:alpha-1,4-glucan 6-glycosyltransferase. A sequence from Arabidopsis thaliana, GP|9294564, scores just above trusted, but appears either to contain corrupt sequence or, more likely, to be a pseudogene as some of the conserved catalytic residues common to the alpha amylase family are not conserved here.
Probab=60.01 E-value=28 Score=28.39 Aligned_cols=72 Identities=13% Similarity=0.036 Sum_probs=47.4
Q ss_pred HHHHHHHH-HHhhhCCCCeEEEEeccHHHHHHhcCC-------CCCC---hHHHHHHHHHHHHHHhCCcceEEEeecCCC
Q psy15899 11 LIAILLCL-RSIKNHPAMRFLLVSDSMGSLSAIANP-------YLSC---PIISQIYSAWCDLKTVGQYYVKLMWCPSHC 79 (104)
Q Consensus 11 l~Ai~~aL-~~~~~~~~~~v~I~tDS~~~l~~l~~~-------~~~~---~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~ 79 (104)
+.+|..-| .++++.|.+.|.+---.+..-. .+| +... |...++...+.++.++ |+.|-+-+|+.|+
T Consensus 155 ~~~i~~~l~dyl~~LGvt~i~L~Pi~e~~~~--~~wGY~~~~y~~~~~~~Gt~~dlk~lV~~~H~~-Gi~VilD~V~NH~ 231 (613)
T TIGR01515 155 YRELADQLIPYVKELGFTHIELLPVAEHPFD--GSWGYQVTGYYAPTSRFGTPDDFMYFVDACHQA-GIGVILDWVPGHF 231 (613)
T ss_pred HHHHHHHHHHHHHHcCCCEEEECCcccCCCC--CCCCCCcccCcccccccCCHHHHHHHHHHHHHC-CCEEEEEecccCc
Confidence 45566665 8888888888877543332100 011 1111 2346778888888888 9999999999999
Q ss_pred CCchhH
Q psy15899 80 GIRGNE 85 (104)
Q Consensus 80 g~~gNe 85 (104)
+..++.
T Consensus 232 ~~~~~~ 237 (613)
T TIGR01515 232 PKDDHG 237 (613)
T ss_pred CCccch
Confidence 976553
No 21
>PLN03244 alpha-amylase; Provisional
Probab=58.16 E-value=19 Score=30.82 Aligned_cols=32 Identities=9% Similarity=-0.112 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHhCCcceEEEeecCCCCCch
Q psy15899 51 IISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRG 83 (104)
Q Consensus 51 ~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~g 83 (104)
...++...+.++.+. |..|-+-||++|++-.+
T Consensus 439 TPeDLK~LVD~aH~~-GI~VILDvV~NH~~~d~ 470 (872)
T PLN03244 439 TPDDFKRLVDEAHGL-GLLVFLDIVHSYAAADE 470 (872)
T ss_pred CHHHHHHHHHHHHHC-CCEEEEEecCccCCCcc
Confidence 456777888888887 99999999999998654
No 22
>PRK05402 glycogen branching enzyme; Provisional
Probab=58.11 E-value=33 Score=28.54 Aligned_cols=73 Identities=12% Similarity=0.028 Sum_probs=44.2
Q ss_pred HHHHHHHH-HHhhhCCCCeEEEEeccHHHHHH-----hcCCCCCC---hHHHHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899 11 LIAILLCL-RSIKNHPAMRFLLVSDSMGSLSA-----IANPYLSC---PIISQIYSAWCDLKTVGQYYVKLMWCPSHCGI 81 (104)
Q Consensus 11 l~Ai~~aL-~~~~~~~~~~v~I~tDS~~~l~~-----l~~~~~~~---~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~ 81 (104)
+.++..-| .++++.|.+.|.+--=.++.... ........ |-..++...+.++.++ |+.|-+-||+.|++.
T Consensus 264 ~~~i~~~l~~ylk~LGv~~i~L~Pi~e~~~~~~~GY~~~~y~ai~~~~Gt~~dfk~lV~~~H~~-Gi~VilD~V~NH~~~ 342 (726)
T PRK05402 264 YRELADQLIPYVKEMGFTHVELLPIAEHPFDGSWGYQPTGYYAPTSRFGTPDDFRYFVDACHQA-GIGVILDWVPAHFPK 342 (726)
T ss_pred HHHHHHHHHHHHHHcCCCEEEECCcccCCCCCCCCCCcccCCCcCcccCCHHHHHHHHHHHHHC-CCEEEEEECCCCCCC
Confidence 45666664 88888888777643211100000 00001111 2356778888888888 999999999999986
Q ss_pred chh
Q psy15899 82 RGN 84 (104)
Q Consensus 82 ~gN 84 (104)
..+
T Consensus 343 ~~~ 345 (726)
T PRK05402 343 DAH 345 (726)
T ss_pred Ccc
Confidence 543
No 23
>PRK12313 glycogen branching enzyme; Provisional
Probab=57.19 E-value=36 Score=27.80 Aligned_cols=71 Identities=11% Similarity=0.001 Sum_probs=44.1
Q ss_pred HHHHHHH-HHHhhhCCCCeEEEEeccHHHHHHhcCC-------CC---CChHHHHHHHHHHHHHHhCCcceEEEeecCCC
Q psy15899 11 LIAILLC-LRSIKNHPAMRFLLVSDSMGSLSAIANP-------YL---SCPIISQIYSAWCDLKTVGQYYVKLMWCPSHC 79 (104)
Q Consensus 11 l~Ai~~a-L~~~~~~~~~~v~I~tDS~~~l~~l~~~-------~~---~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~ 79 (104)
+.++..- |.++++.|.+.|.+--=.++.. -.+| +. .-|...++...+.++.++ |+.|-+-+|+.|+
T Consensus 169 ~~~~~~~ll~yl~~LGv~~i~L~Pi~~~~~--~~~~GY~~~~y~~i~~~~Gt~~d~k~lv~~~H~~-Gi~VilD~V~nH~ 245 (633)
T PRK12313 169 YRELADELIPYVKEMGYTHVEFMPLMEHPL--DGSWGYQLTGYFAPTSRYGTPEDFMYLVDALHQN-GIGVILDWVPGHF 245 (633)
T ss_pred HHHHHHHHHHHHHHcCCCEEEeCchhcCCC--CCCCCCCCcCcCcCCCCCCCHHHHHHHHHHHHHC-CCEEEEEECCCCC
Confidence 4556655 4888888888776433111000 0111 11 112346777888888888 9999999999999
Q ss_pred CCchh
Q psy15899 80 GIRGN 84 (104)
Q Consensus 80 g~~gN 84 (104)
+..++
T Consensus 246 ~~~~~ 250 (633)
T PRK12313 246 PKDDD 250 (633)
T ss_pred CCCcc
Confidence 86544
No 24
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=57.15 E-value=44 Score=20.62 Aligned_cols=74 Identities=8% Similarity=-0.064 Sum_probs=41.8
Q ss_pred HHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCC--h-------HHHHHHHHHHHHHHhCCcceEEEeecCCCCCchhHH
Q psy15899 16 LCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSC--P-------IISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEA 86 (104)
Q Consensus 16 ~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~--~-------~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~gNe~ 86 (104)
.+++++ |...+...+|...+.+.+.+-.... + +...+-+.+.++..+ ...=.+.-+||+ .|++.
T Consensus 13 ~GFrLa---Gi~~~~~~~~~ee~~~~l~~l~~~~d~gII~Ite~~~~~i~e~i~~~~~~-~~~P~ii~IP~~---~~~~~ 85 (100)
T PRK02228 13 TGFRLA---GIRKVYEVPDDEKLDEAVEEVLEDDDVGILVMHDDDLEKLPRRLRRTLEE-SVEPTVVTLGGG---GGSGG 85 (100)
T ss_pred HHHHHc---CCceEEeeCCHHHHHHHHHHHhhCCCEEEEEEehhHhHhhHHHHHHHHhc-CCCCEEEEECCC---ccchH
Confidence 445554 5666666677566666555432111 2 344455555554444 333344455874 45678
Q ss_pred HHHHHccccC
Q psy15899 87 VDQAAKDPLL 96 (104)
Q Consensus 87 AD~lAk~a~~ 96 (104)
.++++++|..
T Consensus 86 i~~~v~raIG 95 (100)
T PRK02228 86 LREKIKRAIG 95 (100)
T ss_pred HHHHHHHHhC
Confidence 8999998865
No 25
>PRK14705 glycogen branching enzyme; Provisional
Probab=54.15 E-value=18 Score=32.07 Aligned_cols=65 Identities=11% Similarity=0.013 Sum_probs=41.3
Q ss_pred HHHHhhhCCCCeEEEEeccHHHHHHhcCC-------CCCC---hHHHHHHHHHHHHHHhCCcceEEEeecCCCCCchh
Q psy15899 17 CLRSIKNHPAMRFLLVSDSMGSLSAIANP-------YLSC---PIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGN 84 (104)
Q Consensus 17 aL~~~~~~~~~~v~I~tDS~~~l~~l~~~-------~~~~---~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~gN 84 (104)
-|.++++.|.+.|.+.-=++.-.. .+| +..+ |...++...+.++.++ |+.|-+-|||+|.+...+
T Consensus 771 lldYlk~LGvt~IeLmPv~e~p~~--~swGY~~~~y~ap~~ryGt~~dfk~lVd~~H~~-GI~VILD~V~nH~~~d~~ 845 (1224)
T PRK14705 771 LVDYVKWLGFTHVEFMPVAEHPFG--GSWGYQVTSYFAPTSRFGHPDEFRFLVDSLHQA-GIGVLLDWVPAHFPKDSW 845 (1224)
T ss_pred HHHHHHHhCCCEEEECccccCCCC--CCCCCCccccCCcCcccCCHHHHHHHHHHHHHC-CCEEEEEeccccCCcchh
Confidence 367888888887765432111100 111 1111 2456788888888888 999999999999876543
No 26
>PRK14706 glycogen branching enzyme; Provisional
Probab=52.79 E-value=21 Score=29.35 Aligned_cols=33 Identities=18% Similarity=0.170 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHhCCcceEEEeecCCCCCchh
Q psy15899 51 IISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGN 84 (104)
Q Consensus 51 ~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~gN 84 (104)
...++...+.++.+. |+.|-+.||+.|.+...+
T Consensus 215 ~~~~~~~lv~~~H~~-gi~VilD~v~nH~~~~~~ 247 (639)
T PRK14706 215 TPEDFKYLVNHLHGL-GIGVILDWVPGHFPTDES 247 (639)
T ss_pred CHHHHHHHHHHHHHC-CCEEEEEecccccCcchh
Confidence 356788888888888 999999999999987544
No 27
>PRK10785 maltodextrin glucosidase; Provisional
Probab=51.79 E-value=47 Score=26.99 Aligned_cols=70 Identities=11% Similarity=-0.089 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHHhhhCCCCeEEEEe--ccHHHHHHhcCCCC-----CC---hHHHHHHHHHHHHHHhCCcceEEEeecC
Q psy15899 8 IAELIAILLCLRSIKNHPAMRFLLVS--DSMGSLSAIANPYL-----SC---PIISQIYSAWCDLKTVGQYYVKLMWCPS 77 (104)
Q Consensus 8 ~aEl~Ai~~aL~~~~~~~~~~v~I~t--DS~~~l~~l~~~~~-----~~---~~~~~i~~~~~~l~~~~~~~v~~~WVpg 77 (104)
-+-|.+|..-|.++.+.|.+-|.+-- +|.+ -.+... -. |-..++..++.++.++ |++|-+-.|+.
T Consensus 175 GGDl~GI~~kLdYL~~LGv~~I~L~Pif~s~s----~hgYd~~Dy~~iDp~~Gt~~df~~Lv~~aH~r-GikVilD~V~N 249 (598)
T PRK10785 175 GGDLDGISEKLPYLKKLGVTALYLNPIFTAPS----VHKYDTEDYRHVDPQLGGDAALLRLRHATQQR-GMRLVLDGVFN 249 (598)
T ss_pred CcCHHHHHHHHHHHHHcCCCEEEeCCcccCCC----CCCcCcccccccCcccCCHHHHHHHHHHHHHC-CCEEEEEECCC
Confidence 35688999999999998887775421 1210 011011 11 2345677777788888 99999999999
Q ss_pred CCCCc
Q psy15899 78 HCGIR 82 (104)
Q Consensus 78 H~g~~ 82 (104)
|+|..
T Consensus 250 H~~~~ 254 (598)
T PRK10785 250 HTGDS 254 (598)
T ss_pred cCCCC
Confidence 99964
No 28
>TIGR02456 treS_nterm trehalose synthase. Trehalose synthase interconverts maltose and alpha, alpha-trehalose by transglucosylation. This is one of at least three mechanisms for biosynthesis of trehalose, an important and widespread compatible solute. However, it is not driven by phosphate activation of sugars and its physiological role may tend toward trehalose degradation. This view is accentuated by numerous examples of fusion to a probable maltokinase domain. The sequence region described by this model is found both as the whole of a trehalose synthase and as the N-terminal region of a larger fusion protein that includes trehalose synthase activity. Several of these fused trehalose synthases have a domain homologous to proteins with maltokinase activity from Actinoplanes missouriensis and Streptomyces coelicolor (PubMed:15378530).
Probab=49.72 E-value=53 Score=26.22 Aligned_cols=73 Identities=11% Similarity=-0.025 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHhhhCCCCeEEEEe-------ccHHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899 9 AELIAILLCLRSIKNHPAMRFLLVS-------DSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGI 81 (104)
Q Consensus 9 aEl~Ai~~aL~~~~~~~~~~v~I~t-------DS~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~ 81 (104)
+=+.+|..-|.++.+.|.+.|.+-. |..|.+.-.......-|...++..++.++.++ |+.|-+-.|+.|++.
T Consensus 25 Gdl~gi~~~Ldyl~~LGv~~i~L~Pi~~~~~~~~gY~~~dy~~vd~~~Gt~~df~~Lv~~ah~~-Gi~vilD~V~NH~s~ 103 (539)
T TIGR02456 25 GDFPGLTSKLDYLKWLGVDALWLLPFFQSPLRDDGYDVSDYRAILPEFGTIDDFKDFVDEAHAR-GMRVIIDLVLNHTSD 103 (539)
T ss_pred cCHHHHHHhHHHHHHCCCCEEEECCCcCCCCCCCCCCcccccccChhhCCHHHHHHHHHHHHHC-CCEEEEEeccCcCCC
Confidence 4477888899999888777665321 11111100000000112345677777788887 999999999999875
Q ss_pred c
Q psy15899 82 R 82 (104)
Q Consensus 82 ~ 82 (104)
.
T Consensus 104 ~ 104 (539)
T TIGR02456 104 Q 104 (539)
T ss_pred C
Confidence 3
No 29
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=45.92 E-value=51 Score=23.71 Aligned_cols=37 Identities=16% Similarity=0.159 Sum_probs=25.4
Q ss_pred CCeEEEEeccHHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeec
Q psy15899 26 AMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCP 76 (104)
Q Consensus 26 ~~~v~I~tDS~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVp 76 (104)
...|++|||-. .|+-++++..+..+... + .|+++|+|
T Consensus 118 k~~I~vFtDp~------------CpyC~kl~~~l~~~~~~-g-~V~v~~ip 154 (251)
T PRK11657 118 PRIVYVFADPN------------CPYCKQFWQQARPWVDS-G-KVQLRHIL 154 (251)
T ss_pred CeEEEEEECCC------------ChhHHHHHHHHHHHhhc-C-ceEEEEEe
Confidence 45688999943 56666777666566553 3 58888887
No 30
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=42.17 E-value=16 Score=26.22 Aligned_cols=59 Identities=25% Similarity=0.212 Sum_probs=36.0
Q ss_pred hhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeecC
Q psy15899 5 SNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPS 77 (104)
Q Consensus 5 s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpg 77 (104)
.++.+||.|...|--+.. .++ |.|||-.|+.. .+..-++.-..... .+++ | +.|.+||+
T Consensus 124 ~IhtaELlaaClAr~~~~----~r~-l~tDnt~Vlsr---kyts~PW~lac~A~--wiLr--g--ts~~yVPS 182 (245)
T PF00336_consen 124 PIHTAELLAACLARLMSG----ARC-LGTDNTVVLSR---KYTSFPWLLACAAN--WILR--G--TSFYYVPS 182 (245)
T ss_pred cchHHHHHHHHHHHhccC----CcE-EeecCcEEEec---ccccCcHHHHHHHH--Hhhc--C--ceEEEecc
Confidence 478999999988866652 333 89999877632 33333432222211 2333 4 88889996
No 31
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=41.12 E-value=49 Score=20.58 Aligned_cols=25 Identities=16% Similarity=0.191 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHhCCcceEEEeec
Q psy15899 51 IISQIYSAWCDLKTVGQYYVKLMWCP 76 (104)
Q Consensus 51 ~~~~i~~~~~~l~~~~~~~v~~~WVp 76 (104)
.+..|.+.+.++.++ |..|.+.|.-
T Consensus 61 ~l~~i~~~Le~~~~~-g~~V~v~Wyy 85 (99)
T PF09345_consen 61 ALMDIFDLLEDAAQK-GGKVTVNWYY 85 (99)
T ss_pred HHHHHHHHHHHHHhc-CCcEEEEEEE
Confidence 445667777777666 9999999985
No 32
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=40.24 E-value=43 Score=22.51 Aligned_cols=38 Identities=16% Similarity=-0.004 Sum_probs=30.2
Q ss_pred chhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhc
Q psy15899 4 CSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIA 43 (104)
Q Consensus 4 ~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~ 43 (104)
.+.++||.-+|.+|.+.-.. ..+.++++.| +.+...+.
T Consensus 78 ~~~~HAE~~aiqqA~d~G~~-~g~~~tm~Vd-r~vC~~C~ 115 (146)
T PF14437_consen 78 MAKAHAEAGAIQQAYDAGKT-VGRSMTMYVD-RDVCGYCG 115 (146)
T ss_pred hHHHHHHHHHHHHHHHhcCc-cCCeEEEEEC-cccchHHH
Confidence 45788999999999988543 3789999999 87776665
No 33
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=37.49 E-value=78 Score=19.00 Aligned_cols=74 Identities=14% Similarity=0.124 Sum_probs=40.5
Q ss_pred HHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC--C-------ChHHHHHHHHHHHHHHhCCcceEEEeecCCCC--Cch
Q psy15899 15 LLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL--S-------CPIISQIYSAWCDLKTVGQYYVKLMWCPSHCG--IRG 83 (104)
Q Consensus 15 ~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~--~-------~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g--~~g 83 (104)
..+++++ |...+.+.+|...+...+.+... . ..+...+.+.+.++..+ ...-.+.=||+..| -.+
T Consensus 10 v~gFrLa---Gv~~~~~~~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~~~~~l~~~~~~-~~~P~iv~IP~~~~~~~~~ 85 (95)
T PF01990_consen 10 VLGFRLA---GVEGVYVNTDPEEAEEALKELLKDEDVGIIIITEDLAEKIRDELDEYREE-SSLPLIVEIPSKEGSMGRE 85 (95)
T ss_dssp HHHHHHT---TSEEEEESHSHHHHHHHHHHHHHHTTEEEEEEEHHHHTTHHHHHHHHHHT-SSSSEEEEESTTCCCTSSC
T ss_pred HHHHHHc---CCCCccCCCCHHHHHHHHHHHhcCCCccEEEeeHHHHHHHHHHHHHHHhc-cCCceEEEcCCCCCCCCcc
Confidence 4455555 45555544466666666554331 1 12344555666566555 55566678998876 344
Q ss_pred hHHHHHHHc
Q psy15899 84 NEAVDQAAK 92 (104)
Q Consensus 84 Ne~AD~lAk 92 (104)
-+.-.++.|
T Consensus 86 ~~~i~~~v~ 94 (95)
T PF01990_consen 86 KDSIRELVK 94 (95)
T ss_dssp CHHHHHHHH
T ss_pred hHHHHHHhc
Confidence 455555544
No 34
>PLN02960 alpha-amylase
Probab=37.41 E-value=47 Score=28.69 Aligned_cols=70 Identities=10% Similarity=-0.048 Sum_probs=41.8
Q ss_pred HHHH-HHHHHhhhCCCCeEEEEeccHHHH---HH--hcCCCCCC---hHHHHHHHHHHHHHHhCCcceEEEeecCCCCCc
Q psy15899 12 IAIL-LCLRSIKNHPAMRFLLVSDSMGSL---SA--IANPYLSC---PIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIR 82 (104)
Q Consensus 12 ~Ai~-~aL~~~~~~~~~~v~I~tDS~~~l---~~--l~~~~~~~---~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~ 82 (104)
.++. ..|.++++.|.+.|.+.-=....- .. ....+... |...++...+.++.+. |..|-+.||+.|++..
T Consensus 416 ~~~~e~~LdYLk~LGvt~IeLmPv~e~~~~~swGY~~~~yfa~~~~yGtp~dfk~LVd~aH~~-GI~VILDvV~NH~~~d 494 (897)
T PLN02960 416 KEFTQKVLPHVKKAGYNAIQLIGVQEHKDYSSVGYKVTNFFAVSSRFGTPDDFKRLVDEAHGL-GLLVFLDIVHSYAAAD 494 (897)
T ss_pred HHHHHHHHHHHHHcCCCEEEECCcccCCCCCCCCCCcccCCCcccccCCHHHHHHHHHHHHHC-CCEEEEEecccccCCc
Confidence 3444 458888888888776532111000 00 00111111 1346677777788887 9999999999999875
No 35
>PF10580 Neuromodulin_N: Gap junction protein N-terminal region; InterPro: IPR018947 Neuromodulin is a component of the motile growth cones. It is membrane protein whose expression is widely correlated with successful axon elongation []. It is a crucial component of an effective regeneration response in the nervous system []. Although its function is uncertain, the N-terminal region is well conserved and contains both a calmodulin binding domain, and sites for acylation, membrane attachment and protein kinase C phosphorylation. Structure predictions suggest that the C-terminal region may exist as an extended, negatively-charged rod with some similarity to the side arms of neurofilaments, indicating that the biological role of neuromodulin may depend on its ability to form a dynamic membrane-cytoplasm-calmodulin complex []. This entry represents the neuromodulin N-terminal domain.
Probab=37.10 E-value=38 Score=16.68 Aligned_cols=23 Identities=17% Similarity=0.134 Sum_probs=16.6
Q ss_pred ecCCCCCchhHHHHHHHccccCC
Q psy15899 75 CPSHCGIRGNEAVDQAAKDPLLS 97 (104)
Q Consensus 75 VpgH~g~~gNe~AD~lAk~a~~~ 97 (104)
+..+..++-|+.||+-..+-...
T Consensus 5 ~r~tk~VEKNeeadQkieqDg~K 27 (32)
T PF10580_consen 5 IRRTKPVEKNEEADQKIEQDGIK 27 (32)
T ss_pred eeccccccccchhhhhhhhcCCC
Confidence 44566789999999977665433
No 36
>PRK09505 malS alpha-amylase; Reviewed
Probab=36.66 E-value=1.1e+02 Score=25.58 Aligned_cols=72 Identities=10% Similarity=-0.001 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHhhhCCCCeEEEEeccHHHHH-------------HhcCCCC--------CChHHHHHHHHHHHHHHhCC
Q psy15899 9 AELIAILLCLRSIKNHPAMRFLLVSDSMGSLS-------------AIANPYL--------SCPIISQIYSAWCDLKTVGQ 67 (104)
Q Consensus 9 aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~-------------~l~~~~~--------~~~~~~~i~~~~~~l~~~~~ 67 (104)
+-+.+|..-|.++.+.|.+.|.|-.=.+.+-. .-.+.+. .-|...++..++.++.++ |
T Consensus 227 Gdl~Gi~~kLdyl~~LGv~aIwlsPi~~~~~~~~~~g~~g~~~~~~yhgY~~~D~~~id~~~Gt~~dfk~Lv~~aH~~-G 305 (683)
T PRK09505 227 GDLRGLTEKLDYLQQLGVNALWISSPLEQIHGWVGGGTKGDFPHYAYHGYYTLDWTKLDANMGTEADLRTLVDEAHQR-G 305 (683)
T ss_pred CCHHHHHHhhHHHHHcCCCEEEeCccccccccccccccccCCCcCCCCCCCccccccCCCCCCCHHHHHHHHHHHHHC-C
Confidence 34788999999999998888876421111000 0011111 112346677777788888 9
Q ss_pred cceEEEeecCCCCC
Q psy15899 68 YYVKLMWCPSHCGI 81 (104)
Q Consensus 68 ~~v~~~WVpgH~g~ 81 (104)
+.|-+..|+-|+|.
T Consensus 306 i~VilD~V~NH~~~ 319 (683)
T PRK09505 306 IRILFDVVMNHTGY 319 (683)
T ss_pred CEEEEEECcCCCcc
Confidence 99999999999984
No 37
>PF00128 Alpha-amylase: Alpha amylase, catalytic domain; InterPro: IPR006047 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Enzymes containing this domain, such as alpha-amylase, belong to family 13 (GH13 from CAZY) of the glycosyl hydrolases. The maltogenic alpha-amylase is an enzyme which catalyses hydrolysis of (1-4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains in the conversion of starch to maltose. Other enzymes include neopullulanase, which hydrolyses pullulan to panose, and cyclomaltodextrinase, which hydrolyses cyclodextrins. This entry represents the catalytic domain found in several protein members of this family. It has a structure consisting of an 8 stranded alpha/beta barrel that contains the active site, interrupted by a ~70 amino acid calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain []. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; GO: 0003824 catalytic activity, 0043169 cation binding, 0005975 carbohydrate metabolic process; PDB: 3FAX_A 3FAW_A 2DH3_B 2DH2_A 1CIU_A 1A47_A 3BMW_A 3BMV_A 2FH8_A 2FH6_A ....
Probab=35.82 E-value=47 Score=23.26 Aligned_cols=74 Identities=12% Similarity=-0.082 Sum_probs=43.6
Q ss_pred HHHHHHHHHHhhhCCCCeEEE---Eecc----HHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeecCCCCCch
Q psy15899 11 LIAILLCLRSIKNHPAMRFLL---VSDS----MGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRG 83 (104)
Q Consensus 11 l~Ai~~aL~~~~~~~~~~v~I---~tDS----~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~g 83 (104)
+.+|+.-|.++.+.|.+.|.+ +.-. -|.+.-.......-|-..++.+++.++.++ |+.|-+-.|+.|++...
T Consensus 3 ~~gi~~kLdyl~~lGv~~I~l~Pi~~~~~~~~gY~~~d~~~vd~~~Gt~~d~~~Lv~~~h~~-gi~VilD~V~NH~~~~~ 81 (316)
T PF00128_consen 3 FRGIIDKLDYLKDLGVNAIWLSPIFESPNGYHGYDPSDYYAVDPRFGTMEDFKELVDAAHKR-GIKVILDVVPNHTSDDH 81 (316)
T ss_dssp HHHHHHTHHHHHHHTESEEEESS-EESSSSTTTTSESEEEEESTTTBHHHHHHHHHHHHHHT-TCEEEEEEETSEEETTS
T ss_pred HHHHHHhhHHHHHcCCCceecccccccccccccccceeeeccccccchhhhhhhhhhccccc-cceEEEeeecccccccc
Confidence 456677777777776665543 2200 000000000001123456788888888887 99999999999988765
Q ss_pred hH
Q psy15899 84 NE 85 (104)
Q Consensus 84 Ne 85 (104)
..
T Consensus 82 ~~ 83 (316)
T PF00128_consen 82 PW 83 (316)
T ss_dssp HH
T ss_pred cc
Confidence 54
No 38
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=34.92 E-value=81 Score=22.36 Aligned_cols=67 Identities=10% Similarity=0.064 Sum_probs=44.6
Q ss_pred HHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC-------CCh-H-HHHHHHHHHHHHHhCCcceEEEeecCCCCCch
Q psy15899 13 AILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL-------SCP-I-ISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRG 83 (104)
Q Consensus 13 Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~-------~~~-~-~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~g 83 (104)
++..+|.++.+...-.+.-|++.+.-+.......+ .-| . -.++.+ .|..+ +...-+..+-||.+++-
T Consensus 15 ~vr~al~~Ll~s~G~~v~~~~s~~~fL~~~~~~~pGclllDvrMPg~sGlelq~---~L~~~-~~~~PVIfiTGhgDIpm 90 (202)
T COG4566 15 SVRDALAFLLESAGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSGLELQD---RLAER-GIRLPVIFLTGHGDIPM 90 (202)
T ss_pred HHHHHHHHHHHhCCceeeeecCHHHHHhhccCCCCCeEEEecCCCCCchHHHHH---HHHhc-CCCCCEEEEeCCCChHH
Confidence 57788888887777788889999988877322211 001 1 123333 44555 88888889999999874
No 39
>PF10298 WhiA_N: WhiA N-terminal LAGLIDADG-like domain; InterPro: IPR018478 This entry represents the N-terminal domain of sporulation factor WhiA []. This domain is related to the LAGLIDADG homing endonuclease domain while the C-terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain [].; PDB: 3HYI_A 3HYJ_D.
Probab=33.90 E-value=46 Score=19.72 Aligned_cols=35 Identities=17% Similarity=0.198 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHHHHhhh-CCCCeEEEEeccHHHHHH
Q psy15899 7 GIAELIAILLCLRSIKN-HPAMRFLLVSDSMGSLSA 41 (104)
Q Consensus 7 ~~aEl~Ai~~aL~~~~~-~~~~~v~I~tDS~~~l~~ 41 (104)
..|||.|++.---.+.- .+.-.+.+-|||..+.+.
T Consensus 4 ~~AELaAlir~~G~l~~~~~~~~l~~~ten~~vARr 39 (86)
T PF10298_consen 4 RIAELAALIRFSGSLSISNGRISLEISTENAAVARR 39 (86)
T ss_dssp HHHHHHHHHHHHEEECTTTTEEEE--EES-HHHHHH
T ss_pred HHHHHHHHHHhCCEEEEECCEEEEEEEeCCHHHHHH
Confidence 57999999886444432 234466778888765544
No 40
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=32.77 E-value=57 Score=21.71 Aligned_cols=31 Identities=19% Similarity=0.085 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHHHHhhhCCCCeEEEEeccHH
Q psy15899 7 GIAELIAILLCLRSIKNHPAMRFLLVSDSMG 37 (104)
Q Consensus 7 ~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~ 37 (104)
.+||+.||..|-+..........++|+=-.-
T Consensus 57 aHAEi~air~a~~~~~~~~l~~~tlyvT~EP 87 (152)
T COG0590 57 AHAEILAIRAAAETLGNYRLKDCTLYVTLEP 87 (152)
T ss_pred ccHHHHHHHHHHHhhCCCCcCCcEEEEecCC
Confidence 3799999999999987655666677765443
No 41
>PLN02447 1,4-alpha-glucan-branching enzyme
Probab=32.00 E-value=65 Score=27.33 Aligned_cols=65 Identities=12% Similarity=-0.027 Sum_probs=38.8
Q ss_pred HHHHHhhhCCCCeEEEEeccHHHHH-----HhcCCCCC---ChHHHHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899 16 LCLRSIKNHPAMRFLLVSDSMGSLS-----AIANPYLS---CPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGI 81 (104)
Q Consensus 16 ~aL~~~~~~~~~~v~I~tDS~~~l~-----~l~~~~~~---~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~ 81 (104)
..|.++++.|.+.|.+--=....-. ...+.+.. -|...++...+.++.+. |..|-+-||+.|++.
T Consensus 255 ~~L~ylk~LG~t~I~LmPi~e~~~~~~wGY~~~~~fa~~~~~Gtp~dlk~LVd~aH~~-GI~VilDvV~nH~~~ 327 (758)
T PLN02447 255 DVLPRIKALGYNAVQLMAIQEHAYYGSFGYHVTNFFAVSSRSGTPEDLKYLIDKAHSL-GLRVLMDVVHSHASK 327 (758)
T ss_pred HHHHHHHHcCCCEEEECCccccCCCCCCCcCcccCcccccccCCHHHHHHHHHHHHHC-CCEEEEEeccccccc
Confidence 3577777778887765321110000 00011111 12346677777788887 999999999999875
No 42
>KOG3243|consensus
Probab=31.82 E-value=60 Score=21.68 Aligned_cols=16 Identities=13% Similarity=0.522 Sum_probs=12.4
Q ss_pred CcceEEEeecCCCCCc
Q psy15899 67 QYYVKLMWCPSHCGIR 82 (104)
Q Consensus 67 ~~~v~~~WVpgH~g~~ 82 (104)
..++.+.||||---.+
T Consensus 50 eenI~ie~VPGS~Elp 65 (158)
T KOG3243|consen 50 EENIEIEWVPGSFELP 65 (158)
T ss_pred hhceeEEEcCCceecc
Confidence 4679999999975554
No 43
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=30.73 E-value=1e+02 Score=20.76 Aligned_cols=22 Identities=18% Similarity=0.161 Sum_probs=14.4
Q ss_pred HHHHHhCC---cceEEEeecCCCCCc
Q psy15899 60 CDLKTVGQ---YYVKLMWCPSHCGIR 82 (104)
Q Consensus 60 ~~l~~~~~---~~v~~~WVpgH~g~~ 82 (104)
..|... | ..+.+.||||=--+|
T Consensus 36 ~~l~~~-gv~~~~i~v~~VPGa~EiP 60 (154)
T PRK00061 36 DALKRH-GVSEENIDVVRVPGAFEIP 60 (154)
T ss_pred HHHHHc-CCCccceEEEECCCHHHHH
Confidence 344444 6 678999999854444
No 44
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=30.54 E-value=1.2e+02 Score=19.97 Aligned_cols=32 Identities=16% Similarity=0.206 Sum_probs=18.8
Q ss_pred HHHHHHhCCc---ceEEEeecCCCCCchhHHHHHHHcc
Q psy15899 59 WCDLKTVGQY---YVKLMWCPSHCGIRGNEAVDQAAKD 93 (104)
Q Consensus 59 ~~~l~~~~~~---~v~~~WVpgH~g~~gNe~AD~lAk~ 93 (104)
+..|... +. .+...||||=-.+| -.|.+|++.
T Consensus 26 ~~~l~~~-g~~~~~i~~~~VPGa~ElP--~a~~~l~~~ 60 (144)
T PF00885_consen 26 LEELKRH-GVAEENIEVIRVPGAFELP--LAAKRLAES 60 (144)
T ss_dssp HHHHHHT-TTTGGCEEEEEESSGGGHH--HHHHHHHHC
T ss_pred HHHHHHc-CCCccceEEEEcCCHHHHH--HHHHHHhcc
Confidence 3344444 65 89999999854333 234455543
No 45
>TIGR02104 pulA_typeI pullulanase, type I. Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family consists of pullulanases related to the subfamilies described in TIGR02102 and TIGR02103 but having a different domain architecture with shorter sequences. Members are called type I pullulanases.
Probab=30.48 E-value=85 Score=25.54 Aligned_cols=28 Identities=11% Similarity=-0.092 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899 53 SQIYSAWCDLKTVGQYYVKLMWCPSHCGI 81 (104)
Q Consensus 53 ~~i~~~~~~l~~~~~~~v~~~WVpgH~g~ 81 (104)
.++...+.++.++ |+.|-+-+|+.|++-
T Consensus 229 ~efk~lV~~~H~~-Gi~VilDvV~NH~~~ 256 (605)
T TIGR02104 229 RELKQMIQALHEN-GIRVIMDVVYNHTYS 256 (605)
T ss_pred HHHHHHHHHHHHC-CCEEEEEEEcCCccC
Confidence 5788888888888 999999999999863
No 46
>COG1519 KdtA 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]
Probab=30.36 E-value=63 Score=25.45 Aligned_cols=38 Identities=18% Similarity=0.082 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhCCcceEEEeecCCCCCchhHHHHHHHccc
Q psy15899 55 IYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKDP 94 (104)
Q Consensus 55 i~~~~~~l~~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a 94 (104)
+.+....|.++ ..+..+.|||.|..+ .++.++-+.+.+
T Consensus 247 ~l~~~~~l~~~-~~~~llIlVPRHpER-f~~v~~l~~~~g 284 (419)
T COG1519 247 ILDAHQALKKQ-FPNLLLILVPRHPER-FKAVENLLKRKG 284 (419)
T ss_pred HHHHHHHHHhh-CCCceEEEecCChhh-HHHHHHHHHHcC
Confidence 34444566777 778999999999643 445555554443
No 47
>PF12163 HobA: DNA replication regulator; InterPro: IPR021011 This family of proteins is found exclusively in epsilon-proteobacteria. Proteins in this family are approximately 180 amino acids in length. The crystal structure of HobA from Helicobacter pylori has been reported at 1.7A resolution; HobA represents a modified Rossmann fold consisting of a five-stranded parallel beta-sheet (beta1-5) flanked on one side by alpha-2, alpha-3 and alpha-6 helices and alpha-4 and alpha-5 on the other. The alpha-1 helix is extended away from and has minimal interaction with the globular part of the protein. Four monomers interact to form a tetrameric molecule. Four calcium atoms bind to the tetramer and these binding sites may have functional relevance. The closest structural homologue of HobA is a sugar isomerase (SIS) domain containing protein, the phosphoheptose isomerase from Pseudomonas aeruginosa. The SIS proteins share strong sequence homology with DiaA from Escherichia coli; yet, HobA and DiaA share no sequence homology []. HobA is a novel protein essential for initiation of H. pylori chromosome replication. It interacts specifically via DnaA with the oriC-DnaA complex. It is possible that HobA is essential for the correct formation and stabilisation of the orisome by facilitating the spatial positioning of DnaA at oriC [].; PDB: 2UVP_D 2WP0_A.
Probab=29.98 E-value=1.3e+02 Score=21.00 Aligned_cols=36 Identities=33% Similarity=0.325 Sum_probs=24.1
Q ss_pred HHHH-HHHHHHHhhhCCCCeEEEEecc------HHHHHHhcCCCC
Q psy15899 10 ELIA-ILLCLRSIKNHPAMRFLLVSDS------MGSLSAIANPYL 47 (104)
Q Consensus 10 El~A-i~~aL~~~~~~~~~~v~I~tDS------~~~l~~l~~~~~ 47 (104)
|... +..+|+.+.+ ...+.+.||. .|+++.|++...
T Consensus 28 eW~pl~a~~l~~il~--G~s~iliTD~~R~WF~~Yil~~IN~~~~ 70 (180)
T PF12163_consen 28 EWTPLIASALSHILN--GGSFILITDEEREWFEEYILSNINNSHK 70 (180)
T ss_dssp THHHHHHHHHHHHHT--T-EEEEEE-GGGHHHHHHHHHHHS-SST
T ss_pred hhHHHHHHHHHHHhC--CCeEEEEeCchhHHHHHHHHHhcCcccC
Confidence 4444 4477777765 7899999995 589999995443
No 48
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=29.21 E-value=97 Score=19.04 Aligned_cols=32 Identities=19% Similarity=0.094 Sum_probs=23.3
Q ss_pred hhhHHHHHHHHHHHHHhhhCCCCeEEEEeccH
Q psy15899 5 SNGIAELIAILLCLRSIKNHPAMRFLLVSDSM 36 (104)
Q Consensus 5 s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~ 36 (104)
...+||+.||..+.+..........++|+--+
T Consensus 44 ~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~E 75 (109)
T cd01285 44 PTAHAEIVAIRNAARRLGSYLLSGCTLYTTLE 75 (109)
T ss_pred CcccHHHHHHHHHHHHhCCCccCCeEEEEeCC
Confidence 45689999999987775443467788887644
No 49
>PF08806 Sep15_SelM: Sep15/SelM redox domain; InterPro: IPR014912 Sep15 and SelM are eukaryotic selenoproteins that have a thioredoxin-like domain and a surface accessible active site redox motif []. This suggests that they function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum []. ; PDB: 2A4H_A 2A2P_A.
Probab=28.87 E-value=41 Score=19.96 Aligned_cols=14 Identities=14% Similarity=0.104 Sum_probs=9.9
Q ss_pred CcceEEEeecCCCC
Q psy15899 67 QYYVKLMWCPSHCG 80 (104)
Q Consensus 67 ~~~v~~~WVpgH~g 80 (104)
...|.+.|||||.-
T Consensus 30 y~~v~vk~i~G~~P 43 (78)
T PF08806_consen 30 YPNVEVKYIPGAPP 43 (78)
T ss_dssp BTTEEEEEESS---
T ss_pred cCceEEEEeCCCCC
Confidence 56899999999863
No 50
>COG1212 KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell envelope biogenesis, outer membrane]
Probab=28.77 E-value=92 Score=22.76 Aligned_cols=30 Identities=13% Similarity=0.035 Sum_probs=23.9
Q ss_pred HHHHHhhhCCCCeEEEEeccHHHHHHhcCC
Q psy15899 16 LCLRSIKNHPAMRFLLVSDSMGSLSAIANP 45 (104)
Q Consensus 16 ~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~ 45 (104)
+-.+.+.+.+..+|.+-||++.+.+.+.+.
T Consensus 33 rV~e~a~~s~~~rvvVATDde~I~~av~~~ 62 (247)
T COG1212 33 RVAERALKSGADRVVVATDDERIAEAVQAF 62 (247)
T ss_pred HHHHHHHHcCCCeEEEEcCCHHHHHHHHHh
Confidence 344555566899999999999999988864
No 51
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=28.39 E-value=71 Score=21.80 Aligned_cols=30 Identities=17% Similarity=0.024 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHHhhhCCCCeEEEEeccH
Q psy15899 7 GIAELIAILLCLRSIKNHPAMRFLLVSDSM 36 (104)
Q Consensus 7 ~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~ 36 (104)
.+||+.||..|.+..........++|+--.
T Consensus 61 ~HAEi~Ai~~a~~~~~~~~l~g~tlY~TlE 90 (172)
T PRK10860 61 AHAEIMALRQGGLVLQNYRLLDATLYVTLE 90 (172)
T ss_pred cCHHHHHHHHHHHhcCCCCcCCcEEEeeCC
Confidence 479999999987765433445566666533
No 52
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=28.29 E-value=1.2e+02 Score=20.11 Aligned_cols=30 Identities=20% Similarity=0.381 Sum_probs=17.9
Q ss_pred HHHHHhCCc---ceEEEeecCCCCCchhHHHHHHHc
Q psy15899 60 CDLKTVGQY---YVKLMWCPSHCGIRGNEAVDQAAK 92 (104)
Q Consensus 60 ~~l~~~~~~---~v~~~WVpgH~g~~gNe~AD~lAk 92 (104)
..|... |. .+.+.||||---+| -.+.+|++
T Consensus 31 ~~l~~~-gv~~~~i~v~~VPGa~EiP--~a~~~l~~ 63 (141)
T PLN02404 31 ETFKRY-SVKEENIDVVWVPGSFEIP--VVAQRLAK 63 (141)
T ss_pred HHHHHc-CCCccceEEEEcCcHHHHH--HHHHHHHh
Confidence 344444 64 48999999854444 34455554
No 53
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=27.15 E-value=1.2e+02 Score=20.56 Aligned_cols=23 Identities=13% Similarity=0.130 Sum_probs=14.5
Q ss_pred HHHHHHhCC---cceEEEeecCCCCCc
Q psy15899 59 WCDLKTVGQ---YYVKLMWCPSHCGIR 82 (104)
Q Consensus 59 ~~~l~~~~~---~~v~~~WVpgH~g~~ 82 (104)
+..|.+. | ..+.+.||||---+|
T Consensus 33 ~~~l~~~-G~~~~~i~v~~VPGA~EiP 58 (158)
T PRK12419 33 VAEIAAR-GGAASQVDIFDVPGAFEIP 58 (158)
T ss_pred HHHHHHc-CCCccceEEEECCcHHHHH
Confidence 3344444 6 568999999854433
No 54
>PF15216 TSLP: Thymic stromal lymphopoietin
Probab=26.31 E-value=21 Score=23.25 Aligned_cols=12 Identities=25% Similarity=0.520 Sum_probs=10.5
Q ss_pred EeecCCCCCchh
Q psy15899 73 MWCPSHCGIRGN 84 (104)
Q Consensus 73 ~WVpgH~g~~gN 84 (104)
.|+||+++..-|
T Consensus 80 ~~CPGyse~QiN 91 (124)
T PF15216_consen 80 NYCPGYSETQIN 91 (124)
T ss_pred HhCCCcchhhcc
Confidence 399999998877
No 55
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=25.51 E-value=1.1e+02 Score=21.15 Aligned_cols=25 Identities=16% Similarity=0.187 Sum_probs=21.2
Q ss_pred HHHHHHHHHhhhCCCCeEEEEeccH
Q psy15899 12 IAILLCLRSIKNHPAMRFLLVSDSM 36 (104)
Q Consensus 12 ~Ai~~aL~~~~~~~~~~v~I~tDS~ 36 (104)
..+..||+.+...+.++|.|.+|..
T Consensus 117 emLkl~L~~ar~lgi~~Vlvtcd~d 141 (174)
T COG3981 117 EMLKLALEKARELGIKKVLVTCDKD 141 (174)
T ss_pred HHHHHHHHHHHHcCCCeEEEEeCCC
Confidence 3567889999999999999999954
No 56
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=24.83 E-value=2e+02 Score=18.45 Aligned_cols=32 Identities=13% Similarity=-0.145 Sum_probs=22.8
Q ss_pred CcchhhHHHHHHHHHHHHHhhhCCCCeEEEEec
Q psy15899 2 FHCSNGIAELIAILLCLRSIKNHPAMRFLLVSD 34 (104)
Q Consensus 2 ~~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tD 34 (104)
+..|+|-|++.|- .+.+.+.+.+.+.|.|+.-
T Consensus 41 kk~TpyAAq~aa~-~~~~~~~~~Gi~~v~v~ik 72 (114)
T TIGR03628 41 DESSPYAAMQAAG-RAAEKAKERGITGLHIKVR 72 (114)
T ss_pred ccCCHHHHHHHHH-HHHHHHHHcCCcEEEEEEE
Confidence 3467887776665 5666667788998888764
No 57
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=24.71 E-value=2.1e+02 Score=18.85 Aligned_cols=40 Identities=23% Similarity=0.268 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHHHH
Q psy15899 7 GIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQ 54 (104)
Q Consensus 7 ~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~~~~~~ 54 (104)
.-||-.||..|+.. -......|.+++|+ ..+..+.|.-++
T Consensus 54 ~CAErsAI~~ais~-G~~~~~~v~v~~~~-------~~~~sPCG~CRQ 93 (134)
T COG0295 54 VCAERSAIFKAISE-GKRKFDAVVVVADT-------GKPVSPCGACRQ 93 (134)
T ss_pred hhHHHHHHHHHHHc-CCCcEEEEEEEcCC-------CCCcCCcHHHHH
Confidence 46999999999887 34467888999998 334445554444
No 58
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=24.16 E-value=2e+02 Score=21.87 Aligned_cols=33 Identities=15% Similarity=0.265 Sum_probs=21.2
Q ss_pred HHHHHHHHhhhC---CCCeEEEEeccHHHHHHhcCC
Q psy15899 13 AILLCLRSIKNH---PAMRFLLVSDSMGSLSAIANP 45 (104)
Q Consensus 13 Ai~~aL~~~~~~---~~~~v~I~tDS~~~l~~l~~~ 45 (104)
-+..+++.++.. ...+|-+.|||+.++..+.+.
T Consensus 198 ~V~~ai~~ak~~~~~k~~~IFLATDSaeVid~fr~~ 233 (321)
T PF05830_consen 198 QVCTAIDKAKALAPPKPVRIFLATDSAEVIDQFRKK 233 (321)
T ss_dssp HHHHHHHHHHTS--SS-EEEEEEES-HHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCCCeeEEEecCcHHHHHHHHHH
Confidence 344566555533 345678889999999988753
No 59
>PF00289 CPSase_L_chain: Carbamoyl-phosphate synthase L chain, N-terminal domain; InterPro: IPR005481 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the N-terminal domain of the large subunit of carbamoyl phosphate synthase. This domain can also be found in certain other related proteins. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VA7_A 3OUU_A 3OUZ_B 1W96_B 1W93_A 1ULZ_A 3HB9_C 3HO8_A 3BG5_C 3HBL_A ....
Probab=23.36 E-value=1.3e+02 Score=18.80 Aligned_cols=30 Identities=10% Similarity=0.106 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHHHHhhhCCCCeEEEEeccHHH
Q psy15899 7 GIAELIAILLCLRSIKNHPAMRFLLVSDSMGS 38 (104)
Q Consensus 7 ~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~ 38 (104)
+++|. ..++++.+.+.+.+.|.|+|+....
T Consensus 9 nrGei--a~r~~ra~r~~Gi~tv~v~s~~d~~ 38 (110)
T PF00289_consen 9 NRGEI--AVRIIRALRELGIETVAVNSNPDTV 38 (110)
T ss_dssp S-HHH--HHHHHHHHHHTTSEEEEEEEGGGTT
T ss_pred CCCHH--HHHHHHHHHHhCCcceeccCchhcc
Confidence 35565 5677788888899999999987653
No 60
>TIGR01506 ribC_arch riboflavin synthase. This archaeal protein catalyzes the same reaction, the final step in riboflavin biosynthesis, as bacterial riboflavin biosynthesis alpha chain. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain.
Probab=22.76 E-value=94 Score=20.98 Aligned_cols=31 Identities=10% Similarity=-0.004 Sum_probs=18.7
Q ss_pred HHHHHH--hCCcceEEEeecCCCCCchhHHHHHHHc
Q psy15899 59 WCDLKT--VGQYYVKLMWCPSHCGIRGNEAVDQAAK 92 (104)
Q Consensus 59 ~~~l~~--~~~~~v~~~WVpgH~g~~gNe~AD~lAk 92 (104)
+..|.+ . +..+.+.||||=-.+|. .|.+|++
T Consensus 19 ~~~L~~~g~-g~~i~v~~VPGa~EiP~--aak~l~~ 51 (151)
T TIGR01506 19 IDELRKHTA-GIKIIRRTVPGIKDLPV--AAKKLLE 51 (151)
T ss_pred HHHHHhcCC-CCeEEEEECCcHhHHHH--HHHHHHh
Confidence 334444 4 77899999998544442 3445543
No 61
>TIGR02401 trehalose_TreY malto-oligosyltrehalose synthase. This enzyme, formally named (1-4)-alpha-D-glucan 1-alpha-D-glucosylmutase, is the TreY enzyme of the TreYZ pathway of trehalose biosynthesis, an alternative to the OtsAB pathway. Trehalose may be incorporated into more complex compounds but is best known as compatible solute. It is one of the most effective osmoprotectants, and unlike the various betaines does not require nitrogen for its synthesis.
Probab=22.55 E-value=4.1e+02 Score=22.97 Aligned_cols=71 Identities=7% Similarity=-0.125 Sum_probs=41.7
Q ss_pred HHHHHHHHHhhhCCCCeEEEEeccHHHHHHhc-----CCCCCC---hHHHHHHHHHHHHHHhCCcceEEEeecCCCCCch
Q psy15899 12 IAILLCLRSIKNHPAMRFLLVSDSMGSLSAIA-----NPYLSC---PIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRG 83 (104)
Q Consensus 12 ~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~-----~~~~~~---~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~g 83 (104)
.++..-|.++.+.|.+.|.+--=.++.-..-. .+..-+ |-..++...+.++.++ |+.|-+-.||-|.+..+
T Consensus 16 ~~~~~~L~YL~~LGv~~V~lsPi~~a~~gs~hGYdv~D~~~idp~lGt~edf~~Lv~aah~~-Gm~vIlDiVpNH~a~~~ 94 (825)
T TIGR02401 16 DDAAALLPYLKSLGVSHLYLSPILTAVPGSTHGYDVVDHSEINPELGGEEGLRRLSEAARAR-GLGLIVDIVPNHMAVHL 94 (825)
T ss_pred HHHHHhhHHHHHcCCCEEEeCcCccCCCCCCCCCCCCCCCCcCCCCCCHHHHHHHHHHHHHC-CCEEEEEeccccccccc
Confidence 45666677777778777754321000000000 011111 2345666677677777 99999999999999874
No 62
>PRK14507 putative bifunctional 4-alpha-glucanotransferase/malto-oligosyltrehalose synthase; Provisional
Probab=22.06 E-value=2.6e+02 Score=26.29 Aligned_cols=79 Identities=11% Similarity=-0.081 Sum_probs=45.3
Q ss_pred HHHHHHHHHHhhhCCCCeEEEEeccHHHHHH-----hcCCCCCC---hHHHHHHHHHHHHHHhCCcceEEEeecCCCCCc
Q psy15899 11 LIAILLCLRSIKNHPAMRFLLVSDSMGSLSA-----IANPYLSC---PIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIR 82 (104)
Q Consensus 11 l~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~-----l~~~~~~~---~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~ 82 (104)
+.++..-|.++.+.|.+.|.+-.=.++.-.. +.++..-+ |-..++...+.++.++ |+.|-+-+||.|.|..
T Consensus 757 f~~~~~~l~Yl~~LGv~~i~lsPi~~a~~gs~hGYdv~D~~~idp~lG~~edf~~Lv~~ah~~-Gi~vilDiV~NH~~~~ 835 (1693)
T PRK14507 757 FADAEAILPYLAALGISHVYASPILKARPGSTHGYDIVDHSQINPEIGGEEGFERFCAALKAH-GLGQLLDIVPNHMGVG 835 (1693)
T ss_pred HHHHHHHhHHHHHcCCCEEEECCCcCCCCCCCCCCCCCCCCccCcccCCHHHHHHHHHHHHHC-CCEEEEEecccccCCC
Confidence 3456677778877788777542111100000 00111111 1234566666677777 9999999999999974
Q ss_pred --hhHHHHHH
Q psy15899 83 --GNEAVDQA 90 (104)
Q Consensus 83 --gNe~AD~l 90 (104)
.|..=...
T Consensus 836 ~~~n~w~~dv 845 (1693)
T PRK14507 836 GADNPWWLDV 845 (1693)
T ss_pred ccCCHHHHHH
Confidence 56554433
No 63
>KOG1123|consensus
Probab=22.06 E-value=1.1e+02 Score=25.40 Aligned_cols=26 Identities=12% Similarity=0.157 Sum_probs=19.2
Q ss_pred HHHHHhh---hCCCCeEEEEeccHHHHHH
Q psy15899 16 LCLRSIK---NHPAMRFLLVSDSMGSLSA 41 (104)
Q Consensus 16 ~aL~~~~---~~~~~~v~I~tDS~~~l~~ 41 (104)
+|.+.+. +....++.+|+||-++++.
T Consensus 530 raCqfLI~~HE~RgDKiIVFsDnvfALk~ 558 (776)
T KOG1123|consen 530 RACQFLIKFHERRGDKIIVFSDNVFALKE 558 (776)
T ss_pred HHHHHHHHHHHhcCCeEEEEeccHHHHHH
Confidence 4445554 2367899999999999975
No 64
>COG0054 RibH Riboflavin synthase beta-chain [Coenzyme metabolism]
Probab=21.52 E-value=2.7e+02 Score=18.84 Aligned_cols=24 Identities=17% Similarity=0.234 Sum_probs=19.7
Q ss_pred ceEEEeecCCCCCchhHHHHHHHccc
Q psy15899 69 YVKLMWCPSHCGIRGNEAVDQAAKDP 94 (104)
Q Consensus 69 ~v~~~WVpgH~g~~gNe~AD~lAk~a 94 (104)
+|.+.||||--.+| -.|.+||+.+
T Consensus 47 ~i~vv~VPGa~EiP--l~a~~La~~~ 70 (152)
T COG0054 47 NIDVVRVPGAFEIP--LAAKKLARTG 70 (152)
T ss_pred cceEEEeCCcchhH--HHHHHHHhcC
Confidence 46799999998888 7788888765
No 65
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=21.49 E-value=1.9e+02 Score=19.02 Aligned_cols=23 Identities=22% Similarity=0.494 Sum_probs=13.7
Q ss_pred ceEEEeecCCCCCchhHHHHHHHcc
Q psy15899 69 YVKLMWCPSHCGIRGNEAVDQAAKD 93 (104)
Q Consensus 69 ~v~~~WVpgH~g~~gNe~AD~lAk~ 93 (104)
++...||||=--+|. .|.+|++.
T Consensus 35 ~i~v~~VPGa~EiP~--a~~~l~~~ 57 (138)
T TIGR00114 35 NIDVIWVPGAFELPL--AVKKLAET 57 (138)
T ss_pred ceEEEECCcHHHHHH--HHHHHHhc
Confidence 478999998544442 34455543
No 66
>PRK11396 hypothetical protein; Provisional
Probab=21.02 E-value=65 Score=22.59 Aligned_cols=13 Identities=15% Similarity=0.611 Sum_probs=10.6
Q ss_pred cceEEEeecCCCC
Q psy15899 68 YYVKLMWCPSHCG 80 (104)
Q Consensus 68 ~~v~~~WVpgH~g 80 (104)
.-+.+.|.|||+-
T Consensus 175 l~~~i~~~~~~~~ 187 (191)
T PRK11396 175 LFSEINWLAGHSP 187 (191)
T ss_pred EEEEEEECCCCCc
Confidence 4588999999974
No 67
>PRK14511 maltooligosyl trehalose synthase; Provisional
Probab=21.02 E-value=5.1e+02 Score=22.62 Aligned_cols=76 Identities=8% Similarity=-0.091 Sum_probs=43.7
Q ss_pred HHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhc-----CCCCCC---hHHHHHHHHHHHHHHhCCcceEEEeecCCCCCc
Q psy15899 11 LIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIA-----NPYLSC---PIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIR 82 (104)
Q Consensus 11 l~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~-----~~~~~~---~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~ 82 (104)
+.++..-|.++.+.|.+.|.+-.=.++.-..-. .+..-+ |-..++...+.++.++ |+.|-+-.||-|.+..
T Consensus 19 f~~~~~~l~YL~~LGis~IyLsPi~~a~~gs~hGYdv~D~~~idp~lGt~e~f~~Lv~aah~~-Gi~VIlDiV~NH~~~~ 97 (879)
T PRK14511 19 FDDAAELVPYFADLGVSHLYLSPILAARPGSTHGYDVVDHTRINPELGGEEGLRRLAAALRAH-GMGLILDIVPNHMAVG 97 (879)
T ss_pred HHHHHHHhHHHHHcCCCEEEECcCccCCCCCCCCCCcCCCCCcCCCCCCHHHHHHHHHHHHHC-CCEEEEEeccccccCc
Confidence 345666777777777777754321000000000 011111 2335666666677777 9999999999999875
Q ss_pred --hhHHH
Q psy15899 83 --GNEAV 87 (104)
Q Consensus 83 --gNe~A 87 (104)
.|..-
T Consensus 98 ~~~n~ww 104 (879)
T PRK14511 98 GPDNPWW 104 (879)
T ss_pred CccCHHH
Confidence 46543
No 68
>cd00384 ALAD_PBGS Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. They either contain a cysteine-rich zinc binding site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an aspartate-rich magnesium binding site (consensus DXALDX(Y/F)X3G(H/Q)DG). The cyste
Probab=20.94 E-value=1e+02 Score=23.36 Aligned_cols=22 Identities=5% Similarity=0.016 Sum_probs=15.6
Q ss_pred HHHHHHHHhhhCCCCeEEEEec
Q psy15899 13 AILLCLRSIKNHPAMRFLLVSD 34 (104)
Q Consensus 13 Ai~~aL~~~~~~~~~~v~I~tD 34 (104)
-+...++.+.+.|.+.|.+|-=
T Consensus 52 ~l~~~~~~~~~~Gi~~v~LFgv 73 (314)
T cd00384 52 SLVEEAEELADLGIRAVILFGI 73 (314)
T ss_pred HHHHHHHHHHHCCCCEEEEECC
Confidence 3455566666779999998864
No 69
>PRK11835 hypothetical protein; Provisional
Probab=20.90 E-value=54 Score=21.08 Aligned_cols=13 Identities=15% Similarity=0.360 Sum_probs=10.9
Q ss_pred ceEEEeecCCCCC
Q psy15899 69 YVKLMWCPSHCGI 81 (104)
Q Consensus 69 ~v~~~WVpgH~g~ 81 (104)
.-+++|..||.|.
T Consensus 13 PQsYRW~sG~~G~ 25 (114)
T PRK11835 13 PQSYRWSAGFAGS 25 (114)
T ss_pred CcceeeccCccCc
Confidence 4578999999995
No 70
>PLN00196 alpha-amylase; Provisional
Probab=20.88 E-value=1.5e+02 Score=23.21 Aligned_cols=66 Identities=12% Similarity=-0.053 Sum_probs=40.8
Q ss_pred HHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhc-CCC-C-----C----ChHHHHHHHHHHHHHHhCCcceEEEeecCCC
Q psy15899 11 LIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIA-NPY-L-----S----CPIISQIYSAWCDLKTVGQYYVKLMWCPSHC 79 (104)
Q Consensus 11 l~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~-~~~-~-----~----~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~ 79 (104)
+..|..-|..+.+.|.+.|-|--=+++ .. .++ . - -|-..++..++.++.++ |++|-+-.|+-|+
T Consensus 43 ~~~i~~kldyL~~LGvtaIWL~P~~~s----~s~hGY~~~D~y~ld~~~fGt~~elk~Lv~~aH~~-GIkVilDvV~NH~ 117 (428)
T PLN00196 43 YNFLMGKVDDIAAAGITHVWLPPPSHS----VSEQGYMPGRLYDLDASKYGNEAQLKSLIEAFHGK-GVQVIADIVINHR 117 (428)
T ss_pred HHHHHHHHHHHHHcCCCEEEeCCCCCC----CCCCCCCccccCCCCcccCCCHHHHHHHHHHHHHC-CCEEEEEECccCc
Confidence 345666777777777666654321111 11 011 0 1 12345677778788888 9999999999999
Q ss_pred CC
Q psy15899 80 GI 81 (104)
Q Consensus 80 g~ 81 (104)
+.
T Consensus 118 ~~ 119 (428)
T PLN00196 118 TA 119 (428)
T ss_pred cc
Confidence 84
No 71
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=20.61 E-value=1.7e+02 Score=23.85 Aligned_cols=27 Identities=15% Similarity=0.108 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHhCCcceEEEeecCCCC
Q psy15899 52 ISQIYSAWCDLKTVGQYYVKLMWCPSHCG 80 (104)
Q Consensus 52 ~~~i~~~~~~l~~~~~~~v~~~WVpgH~g 80 (104)
..++.+.+.++... ...++|.|.| |++
T Consensus 240 ~~e~l~~~~~~~~~-~~h~~f~wfP-~t~ 266 (541)
T TIGR01676 240 MKDIKKNHKKFLAD-NKHVKYLHIP-YTD 266 (541)
T ss_pred HHHHHHHHHHHHhc-CCcEEEEEEc-CCC
Confidence 35666666677776 8899999999 654
No 72
>COG0400 Predicted esterase [General function prediction only]
Probab=20.57 E-value=1.4e+02 Score=21.00 Aligned_cols=18 Identities=22% Similarity=0.287 Sum_probs=13.5
Q ss_pred HHHHhCCcceEEEeec-CCC
Q psy15899 61 DLKTVGQYYVKLMWCP-SHC 79 (104)
Q Consensus 61 ~l~~~~~~~v~~~WVp-gH~ 79 (104)
.|... |..|.++|++ ||+
T Consensus 171 ~l~~~-g~~v~~~~~~~GH~ 189 (207)
T COG0400 171 YLTAS-GADVEVRWHEGGHE 189 (207)
T ss_pred HHHHc-CCCEEEEEecCCCc
Confidence 34444 9999999998 663
No 73
>TIGR00854 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters.
Probab=20.48 E-value=1.3e+02 Score=19.99 Aligned_cols=25 Identities=28% Similarity=0.086 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHhCCcceEEEeecCC
Q psy15899 53 SQIYSAWCDLKTVGQYYVKLMWCPSH 78 (104)
Q Consensus 53 ~~i~~~~~~l~~~~~~~v~~~WVpgH 78 (104)
.+=.+.+.+|..+ |..|.++.+|+-
T Consensus 123 ~~e~~~l~~l~~~-Gv~v~~q~vP~d 147 (151)
T TIGR00854 123 DQDITAFRFLKQR-GVKLFLRDVPSD 147 (151)
T ss_pred HHHHHHHHHHHHc-CCEEEEEECcCC
Confidence 3334556688887 999999999964
No 74
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=20.45 E-value=2.2e+02 Score=17.52 Aligned_cols=20 Identities=10% Similarity=0.207 Sum_probs=13.0
Q ss_pred CCCeEEEEeccHHHHHHhcC
Q psy15899 25 PAMRFLLVSDSMGSLSAIAN 44 (104)
Q Consensus 25 ~~~~v~I~tDS~~~l~~l~~ 44 (104)
+...|..+|+++.+.+.|.=
T Consensus 38 P~~pIiavt~~~~~~r~l~l 57 (117)
T PF02887_consen 38 PKVPIIAVTPNESVARQLSL 57 (117)
T ss_dssp TSSEEEEEESSHHHHHHGGG
T ss_pred CCCeEEEEcCcHHHHhhhhc
Confidence 55666677777776666663
Done!