Query 034230
Match_columns 100
No_of_seqs 102 out of 588
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 11:12:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034230.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034230hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00151 SWIB SWI complex, B 100.0 4.1E-29 8.8E-34 159.2 7.5 77 20-97 1-77 (77)
2 PF02201 SWIB: SWIB/MDM2 domai 100.0 3.6E-30 7.7E-35 163.8 2.5 75 20-95 1-75 (76)
3 KOG1946 RNA polymerase I trans 99.9 3.2E-27 7E-32 177.9 8.1 81 18-99 98-178 (240)
4 COG5531 SWIB-domain-containing 99.9 3.7E-24 8.1E-29 160.9 6.4 84 15-99 116-199 (237)
5 PRK14724 DNA topoisomerase III 99.9 3.1E-23 6.6E-28 179.6 7.6 80 16-96 908-987 (987)
6 KOG2570 SWI/SNF transcription 99.8 3.6E-20 7.8E-25 147.6 5.7 78 21-99 206-283 (420)
7 PRK06319 DNA topoisomerase I/S 99.6 1.2E-15 2.6E-20 131.1 5.7 77 20-97 784-860 (860)
8 KOG2522 Filamentous baseplate 95.2 0.055 1.2E-06 45.0 5.7 57 20-76 357-419 (560)
9 PRK05350 acyl carrier protein; 87.9 0.38 8.2E-06 30.1 1.8 53 39-95 2-54 (82)
10 PRK05828 acyl carrier protein; 83.5 1.5 3.3E-05 28.0 3.0 53 39-95 1-53 (84)
11 CHL00124 acpP acyl carrier pro 82.1 0.94 2E-05 28.0 1.6 53 39-95 1-53 (82)
12 PRK12449 acyl carrier protein; 80.2 2.5 5.4E-05 25.9 3.0 53 39-95 1-53 (80)
13 PTZ00171 acyl carrier protein; 76.7 2.5 5.4E-05 29.9 2.5 58 34-95 61-118 (148)
14 cd04762 HTH_MerR-trunc Helix-T 56.6 26 0.00056 18.3 3.5 24 28-58 4-27 (49)
15 PRK07117 acyl carrier protein; 55.3 10 0.00022 23.8 1.9 50 39-93 1-51 (79)
16 PF01047 MarR: MarR family; I 52.3 4.4 9.6E-05 23.1 -0.1 37 29-65 22-58 (59)
17 COG1654 BirA Biotin operon rep 51.7 13 0.00028 23.7 2.0 23 25-54 20-42 (79)
18 smart00667 LisH Lissencephaly 51.4 12 0.00026 18.4 1.5 21 40-60 2-22 (34)
19 PF08463 EcoEI_R_C: EcoEI R pr 50.1 9.7 0.00021 26.3 1.3 70 24-95 87-163 (164)
20 PF13545 HTH_Crp_2: Crp-like h 48.4 15 0.00031 21.8 1.8 44 23-70 26-70 (76)
21 PRK00071 nadD nicotinic acid m 48.0 14 0.00029 26.6 1.8 17 42-58 185-201 (203)
22 PLN02945 nicotinamide-nucleoti 47.5 15 0.00033 27.3 2.1 17 42-58 219-235 (236)
23 TIGR01764 excise DNA binding d 46.8 21 0.00046 18.8 2.2 25 28-59 5-29 (49)
24 PRK05883 acyl carrier protein; 46.4 20 0.00044 22.9 2.3 54 38-95 9-62 (91)
25 PRK07639 acyl carrier protein; 45.7 20 0.00044 22.6 2.2 54 39-95 1-54 (86)
26 TIGR00482 nicotinate (nicotina 45.5 17 0.00036 26.0 2.0 17 42-58 177-193 (193)
27 PF12728 HTH_17: Helix-turn-he 44.7 29 0.00062 19.2 2.5 26 28-60 5-30 (51)
28 PRK06973 nicotinic acid mononu 43.2 18 0.00039 27.3 2.0 19 40-58 223-241 (243)
29 PF13950 Epimerase_Csub: UDP-g 42.7 57 0.0012 19.4 3.8 45 12-56 14-59 (62)
30 KOG2076 RNA polymerase III tra 38.9 55 0.0012 29.6 4.4 86 7-99 116-206 (895)
31 cd01104 HTH_MlrA-CarA Helix-Tu 38.3 79 0.0017 18.1 4.0 26 28-60 4-29 (68)
32 PF07587 PSD1: Protein of unkn 37.7 45 0.00098 25.3 3.4 55 29-96 5-63 (266)
33 PF13333 rve_2: Integrase core 37.6 34 0.00075 19.4 2.2 21 36-56 15-35 (52)
34 PF07037 DUF1323: Putative tra 37.5 49 0.0011 22.9 3.2 43 27-76 3-52 (122)
35 TIGR02057 PAPS_reductase phosp 37.3 20 0.00043 26.6 1.4 12 47-58 172-183 (226)
36 PF01726 LexA_DNA_bind: LexA D 36.5 36 0.00077 20.6 2.2 17 41-57 8-24 (65)
37 PF08513 LisH: LisH; InterPro 35.8 24 0.00053 17.7 1.2 17 43-59 2-18 (27)
38 PHA03061 putative DNA-binding 35.8 72 0.0016 25.2 4.2 60 20-84 177-246 (311)
39 PF08938 HBS1_N: HBS1 N-termin 35.6 13 0.00029 23.2 0.1 28 24-51 29-56 (79)
40 PF03511 Fanconi_A: Fanconi an 35.2 25 0.00053 21.8 1.3 15 84-98 10-24 (64)
41 PF12368 DUF3650: Protein of u 34.9 20 0.00043 18.7 0.7 10 50-59 9-18 (28)
42 PF13867 SAP30_Sin3_bdg: Sin3 34.2 33 0.00073 19.9 1.7 33 46-97 4-36 (53)
43 PF05643 DUF799: Putative bact 34.1 20 0.00044 27.0 1.0 39 48-88 77-115 (215)
44 TIGR00517 acyl_carrier acyl ca 34.1 29 0.00062 20.9 1.5 50 42-95 2-51 (77)
45 TIGR02055 APS_reductase thiore 32.8 26 0.00057 25.1 1.3 11 47-57 136-146 (191)
46 COG1846 MarR Transcriptional r 32.7 55 0.0012 20.2 2.7 50 25-76 36-90 (126)
47 PF03289 Pox_I1: Poxvirus prot 32.5 91 0.002 24.6 4.3 59 21-84 179-247 (312)
48 COG0021 TktA Transketolase [Ca 32.4 79 0.0017 27.7 4.3 32 38-69 32-66 (663)
49 PRK12563 sulfate adenylyltrans 32.2 26 0.00057 27.7 1.4 24 47-70 203-238 (312)
50 cd09286 NMNAT_Eukarya Nicotina 32.1 36 0.00078 25.2 2.0 17 42-58 209-225 (225)
51 cd02165 NMNAT Nicotinamide/nic 31.4 39 0.00085 23.9 2.0 17 42-58 176-192 (192)
52 PRK13918 CRP/FNR family transc 31.1 61 0.0013 22.4 3.0 45 28-76 153-198 (202)
53 PF00325 Crp: Bacterial regula 30.4 50 0.0011 17.5 1.8 21 28-48 6-26 (32)
54 KOG4144 Arylalkylamine N-acety 30.2 33 0.00072 25.2 1.5 33 44-76 119-151 (190)
55 PRK08887 nicotinic acid mononu 29.4 51 0.0011 23.3 2.4 18 42-59 154-171 (174)
56 PF13401 AAA_22: AAA domain; P 28.7 1.2E+02 0.0026 19.1 3.9 41 27-73 55-98 (131)
57 TIGR03697 NtcA_cyano global ni 28.6 59 0.0013 22.2 2.5 43 24-70 142-185 (193)
58 PF07308 DUF1456: Protein of u 28.3 1.2E+02 0.0025 18.6 3.6 40 28-76 17-58 (68)
59 PRK05253 sulfate adenylyltrans 27.4 36 0.00077 26.6 1.3 12 47-58 193-204 (301)
60 cd04761 HTH_MerR-SF Helix-Turn 27.1 84 0.0018 16.7 2.6 24 28-58 4-27 (49)
61 PF00010 HLH: Helix-loop-helix 27.0 89 0.0019 17.5 2.7 18 37-54 36-53 (55)
62 TIGR00434 cysH phosophoadenyly 26.8 38 0.00083 24.3 1.4 12 47-58 157-168 (212)
63 PRK00982 acpP acyl carrier pro 26.4 40 0.00087 20.1 1.2 49 43-95 3-51 (78)
64 PLN02309 5'-adenylylsulfate re 25.8 39 0.00084 28.1 1.3 12 47-58 262-273 (457)
65 smart00224 GGL G protein gamma 25.8 1.6E+02 0.0034 17.6 3.9 34 28-61 9-42 (63)
66 COG1137 YhbG ABC-type (unclass 25.5 81 0.0018 24.2 2.9 27 62-92 157-183 (243)
67 COG4380 Uncharacterized protei 25.2 40 0.00088 25.0 1.2 35 48-84 76-110 (216)
68 PRK10402 DNA-binding transcrip 25.1 73 0.0016 22.8 2.6 45 28-76 173-218 (226)
69 PRK09391 fixK transcriptional 25.0 1.1E+02 0.0023 22.1 3.4 48 24-75 178-228 (230)
70 cd07212 Pat_PNPLA9 Patatin-lik 24.9 48 0.001 25.7 1.6 12 37-48 290-301 (312)
71 PF10924 DUF2711: Protein of u 24.6 71 0.0015 24.2 2.4 48 37-85 86-136 (217)
72 PTZ00411 transaldolase-like pr 24.4 1.3E+02 0.0028 24.0 4.0 54 40-95 211-266 (333)
73 PF09626 DHC: Dihaem cytochrom 23.7 1.4E+02 0.0031 20.3 3.6 57 34-94 33-89 (120)
74 TIGR02039 CysD sulfate adenyly 23.6 46 0.001 26.0 1.3 12 47-58 185-196 (294)
75 COG0529 CysC Adenylylsulfate k 23.4 68 0.0015 24.0 2.1 51 7-57 144-194 (197)
76 PRK09392 ftrB transcriptional 23.4 1.2E+02 0.0026 21.6 3.4 44 28-76 177-221 (236)
77 COG4389 Site-specific recombin 23.2 77 0.0017 27.3 2.6 23 35-57 637-659 (677)
78 cd00957 Transaldolase_TalAB Tr 23.1 1.6E+02 0.0034 23.3 4.2 54 41-96 200-255 (313)
79 PF01507 PAPS_reduct: Phosphoa 22.9 44 0.00096 22.4 1.0 12 47-58 143-154 (174)
80 PF14838 INTS5_C: Integrator c 22.8 41 0.00088 29.6 0.9 43 26-71 618-665 (696)
81 KOG4068 Uncharacterized conser 22.3 1E+02 0.0022 22.5 2.8 23 42-64 68-90 (174)
82 PF13758 Prefoldin_3: Prefoldi 22.2 1.6E+02 0.0035 19.6 3.5 36 20-55 42-83 (99)
83 PF08225 Antimicrobial19: Pseu 22.2 53 0.0012 16.1 0.9 19 71-94 4-22 (23)
84 TIGR00424 APS_reduc 5'-adenyly 22.2 50 0.0011 27.5 1.3 11 48-58 268-278 (463)
85 cd04382 RhoGAP_MgcRacGAP RhoGA 22.1 88 0.0019 22.5 2.5 72 28-99 4-84 (193)
86 COG5577 Spore coat protein [Ce 21.4 94 0.002 21.9 2.4 37 26-62 85-121 (145)
87 PF10265 DUF2217: Uncharacteri 20.8 92 0.002 26.5 2.6 64 8-89 425-494 (514)
88 cd00068 GGL G protein gamma su 20.7 1.9E+02 0.0042 16.8 4.0 32 29-60 10-41 (57)
89 COG0175 CysH 3'-phosphoadenosi 20.5 58 0.0012 24.6 1.3 12 47-58 184-195 (261)
No 1
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.96 E-value=4.1e-29 Score=159.23 Aligned_cols=77 Identities=38% Similarity=0.703 Sum_probs=74.4
Q ss_pred ccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCC
Q 034230 20 LIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPK 97 (100)
Q Consensus 20 ~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~ 97 (100)
++++|.+|++|++|+|.+++||++|++++|+|||+||||||+|++.|+||+.|+++| |++++.|++|+++|++||.+
T Consensus 1 ~~~~~~ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~-~~~~v~~~~~~~ll~~Hl~~ 77 (77)
T smart00151 1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIF-GKDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCCcccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHH-CcCeecHHHHHHHHHHHcCC
Confidence 468899999999999999999999999999999999999999999999999999999 99999999999999999975
No 2
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=99.96 E-value=3.6e-30 Score=163.76 Aligned_cols=75 Identities=41% Similarity=0.810 Sum_probs=70.3
Q ss_pred ccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 20 LIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 20 ~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
|.++|+||++|++++|.+++||++|+++||+||++||||||+|++.|+||+.|++|| |++++.+++|+++|++||
T Consensus 1 ~~k~~~ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf-~~~~v~~~~i~~~l~~hl 75 (76)
T PF02201_consen 1 FPKRFKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLF-GKDSVNFFEIPKLLKPHL 75 (76)
T ss_dssp -EEEEHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHH-HTSECSEEETTHHHHHHH
T ss_pred CCCCccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHh-CCCeecHhhHHHHHHHhc
Confidence 568899999999999999999999999999999999999999999999999999999 889999999999999997
No 3
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.94 E-value=3.2e-27 Score=177.95 Aligned_cols=81 Identities=43% Similarity=0.749 Sum_probs=78.2
Q ss_pred CCccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCC
Q 034230 18 ANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPK 97 (100)
Q Consensus 18 ~~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~ 97 (100)
+|+++.+.+|+.|+.|+|.+++||.+|++.||+|||+||||||.|++.|+||++|+.|| |..+|++++|.++|.+||.+
T Consensus 98 ~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF-~~k~v~~fem~KLL~~H~~~ 176 (240)
T KOG1946|consen 98 WGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIF-GKKRVGMFEMLKLLTKHFLK 176 (240)
T ss_pred cCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHh-ccCccceeeHHHHHHHhccC
Confidence 68999999999999999999999999999999999999999999999999999999999 88889999999999999987
Q ss_pred CC
Q 034230 98 DP 99 (100)
Q Consensus 98 ~p 99 (100)
..
T Consensus 177 ~~ 178 (240)
T KOG1946|consen 177 NQ 178 (240)
T ss_pred cc
Confidence 54
No 4
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.90 E-value=3.7e-24 Score=160.88 Aligned_cols=84 Identities=33% Similarity=0.558 Sum_probs=79.7
Q ss_pred CCCCCccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhcc
Q 034230 15 KKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLH 94 (100)
Q Consensus 15 ~~~~~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~H 94 (100)
.+++...+.|.+|+.||.|||..++||+|||+.||+|||.||||||+||+.|.||++|+.|| |.+.+.||+|.+.|.+|
T Consensus 116 ~~~~~~~~~~~lS~~La~ilG~~~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~-g~~p~~mf~~~k~l~~h 194 (237)
T COG5531 116 SKNSPSGEKVKLSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVL-GSDPIDMFELTKPLSPH 194 (237)
T ss_pred ccccCCCCceecCHHHHHHhCCCCCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHh-CCCchhhhhhhcccccc
Confidence 45677899999999999999999999999999999999999999999999999999999999 78999999999999999
Q ss_pred CCCCC
Q 034230 95 FPKDP 99 (100)
Q Consensus 95 l~~~p 99 (100)
+.+-|
T Consensus 195 l~~~~ 199 (237)
T COG5531 195 LIKYT 199 (237)
T ss_pred eecCc
Confidence 98854
No 5
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.88 E-value=3.1e-23 Score=179.60 Aligned_cols=80 Identities=34% Similarity=0.613 Sum_probs=75.6
Q ss_pred CCCCccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 16 KLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 16 ~~~~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
+...+...+.+|++|++|+|..++||++|++.||+|||+||||||.|++.|+||++|+.|| |++++.|++|+++|++||
T Consensus 908 ~~~~~~~~~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vf-g~~~~~~~~~~~~l~~hl 986 (987)
T PRK14724 908 KAAPPAAGLKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVF-GKDQVTMFELAGIVGKHL 986 (987)
T ss_pred hccccccccCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHh-CCCcccHHHHHHHHHHhc
Confidence 3334677999999999999999999999999999999999999999999999999999999 999999999999999998
Q ss_pred C
Q 034230 96 P 96 (100)
Q Consensus 96 ~ 96 (100)
.
T Consensus 987 ~ 987 (987)
T PRK14724 987 S 987 (987)
T ss_pred C
Confidence 5
No 6
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.80 E-value=3.6e-20 Score=147.65 Aligned_cols=78 Identities=32% Similarity=0.617 Sum_probs=75.2
Q ss_pred cccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCCCC
Q 034230 21 IDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPKDP 99 (100)
Q Consensus 21 ~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~~p 99 (100)
...|++||.||.+||+...||++|+.+||+|||.|+|||++++.+|+||..|+++| |++++.|.+|+.+|++||.+.|
T Consensus 206 P~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif-~~~rl~F~elp~~l~~lL~P~d 283 (420)
T KOG2570|consen 206 PEEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIF-GVDRLKFPELPQLLNPLLSPPD 283 (420)
T ss_pred CcccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhh-cccccccccchhhhhhccCCCC
Confidence 34589999999999999999999999999999999999999999999999999999 9999999999999999999876
No 7
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.59 E-value=1.2e-15 Score=131.09 Aligned_cols=77 Identities=27% Similarity=0.498 Sum_probs=73.0
Q ss_pred ccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCC
Q 034230 20 LIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPK 97 (100)
Q Consensus 20 ~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~ 97 (100)
.+..|.+|++|+.++|..+++|.++++.+|+||++|+||||++++.|.||++|+++| |++++.+++|+++++.|+.+
T Consensus 784 ~~~~~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf-~~~~~~~~~~~k~l~~hl~~ 860 (860)
T PRK06319 784 AGPLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVI-GPDPIDMFQLSKKLSQHLIK 860 (860)
T ss_pred cccccccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhh-CcCccchhhhHHHHHhhhcC
Confidence 445688999999999999999999999999999999999999999999999999999 89999999999999999865
No 8
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=95.15 E-value=0.055 Score=45.01 Aligned_cols=57 Identities=25% Similarity=0.293 Sum_probs=46.1
Q ss_pred ccccccCCHHHHHhh---CC---CcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhh
Q 034230 20 LIDLVNLPSTLREFV---GQ---SRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSIL 76 (100)
Q Consensus 20 ~~~~~~lS~~La~~l---G~---~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf 76 (100)
+...|+.+.....++ |. ...|-+||...+.+||+.|||-|+.||..|+.|.-|....
T Consensus 357 i~~lYk~~~~~~~Lf~evg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~ 419 (560)
T KOG2522|consen 357 ILTLYKPFNLAKDLFKEVGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMV 419 (560)
T ss_pred eeeeeccchHHHHHHHhcCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHH
Confidence 445566666555555 43 4677899999999999999999999999999999998865
No 9
>PRK05350 acyl carrier protein; Provisional
Probab=87.92 E-value=0.38 Score=30.09 Aligned_cols=53 Identities=9% Similarity=0.118 Sum_probs=43.4
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 39 ISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 39 ~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
|||.+|...+.++|.+. +. .+...|.+|..|..-+ |-+++.+-+|.-.|..+|
T Consensus 2 m~~~~i~~~v~~ii~~~-~~--~~~~~i~~d~~l~~dl-g~DSld~veli~~lE~~f 54 (82)
T PRK05350 2 MTREEILERLRAILVEL-FE--IDPEDITPEANLYEDL-DLDSIDAVDLVVHLQKLT 54 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hC--CCHHHCCCCccchhhc-CCCHHHHHHHHHHHHHHH
Confidence 78999999999999987 42 1224699999997777 999999988888887776
No 10
>PRK05828 acyl carrier protein; Validated
Probab=83.48 E-value=1.5 Score=28.02 Aligned_cols=53 Identities=11% Similarity=0.246 Sum_probs=41.4
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 39 ISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 39 ~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
|||.+|...|-+.|.+.++.- +-..|.+|..|.. + |-|++.+-++.-.|...|
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~--~~d~i~~~~~~~d-L-g~DSLd~velv~~lE~~f 53 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAV--TLDESNINKPYRE-L-KIDSLDMFSIIVSLESEF 53 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCC--CcccccCCCCHHh-c-CCCHHHHHHHHHHHHHHH
Confidence 689999999999998865422 2235688899988 6 999998888888777665
No 11
>CHL00124 acpP acyl carrier protein; Validated
Probab=82.07 E-value=0.94 Score=27.98 Aligned_cols=53 Identities=21% Similarity=0.278 Sum_probs=41.7
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 39 ISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 39 ~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
|+|.+|...+-++|.+.-=.++. .|.+|..|..-+ |-+++.+-+|...|...|
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~~---~i~~d~~l~~dl-g~DSl~~~eli~~le~~f 53 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEKS---EVTLDANFTRDL-GADSLDVVELVMAIEEKF 53 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCHH---HCCCCcchhhhc-CCcHHHHHHHHHHHHHHH
Confidence 67899999999999887423333 599999999977 999998888887776655
No 12
>PRK12449 acyl carrier protein; Provisional
Probab=80.19 E-value=2.5 Score=25.92 Aligned_cols=53 Identities=19% Similarity=0.236 Sum_probs=40.6
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 39 ISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 39 ~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
|+|.+|...+-+++.+.-=.++. .|.+|..|..-+ |-+++.+.+|.-.|...|
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~~---~i~~~~~l~~dl-g~DSl~~~~li~~lE~~f 53 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLSL---AITEQTHLKDDL-AVDSIELVEFIINVEDEF 53 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCcc---ccCCCCcHHHHc-CCcHHHHHHHHHHHHHHh
Confidence 57889999999998874323332 589999998887 999998888877776554
No 13
>PTZ00171 acyl carrier protein; Provisional
Probab=76.68 E-value=2.5 Score=29.90 Aligned_cols=58 Identities=21% Similarity=0.251 Sum_probs=46.2
Q ss_pred hCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 34 VGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 34 lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
-|...+++.+|...|+++|.+.--.++ ..|.+|..+..-+ |-|++.+-+|.-.|..+|
T Consensus 61 ~~~~~~~~~~v~~~l~eiiae~l~vd~---~~I~~ds~~~~dL-g~DSLd~veLv~~LEdeF 118 (148)
T PTZ00171 61 SKQYLLSKEDVLTRVKKVVKNFEKVDA---SKITPESNFVKDL-GADSLDVVELLIAIEQEF 118 (148)
T ss_pred ccccccCHHHHHHHHHHHHHHHhCCCH---hhCCCCcchhhhc-CCCHHHHHHHHHHHHHHH
Confidence 355688899999999999998753333 3588899998887 999998888887777665
No 14
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=56.58 E-value=26 Score=18.31 Aligned_cols=24 Identities=21% Similarity=0.376 Sum_probs=18.1
Q ss_pred HHHHHhhCCCcccHHHHHHHHHHHHhhcCCC
Q 034230 28 STLREFVGQSRISRLGCFMRVWSYIKTNNLQ 58 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lq 58 (100)
.++|+.+|++.- .||.|++...+.
T Consensus 4 ~e~a~~lgvs~~-------tl~~~~~~g~~~ 27 (49)
T cd04762 4 KEAAELLGVSPS-------TLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCC
Confidence 477888887654 689999987663
No 15
>PRK07117 acyl carrier protein; Validated
Probab=55.32 E-value=10 Score=23.84 Aligned_cols=50 Identities=14% Similarity=0.135 Sum_probs=37.2
Q ss_pred ccHHHHHHHHHHHHhhcC-CCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhc
Q 034230 39 ISRLGCFMRVWSYIKTNN-LQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKL 93 (100)
Q Consensus 39 ~sr~~v~~~lW~YIK~~~-Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~ 93 (100)
||+.+|...+-+-|++.- =. +...|..|..|+. | |.+++.+-++--.+..
T Consensus 1 M~~~ei~~~v~~ii~e~~p~i---~~~~I~~~~~l~D-L-g~DSlD~veiv~~led 51 (79)
T PRK07117 1 MDKQRIFDILVRHIREVLPDL---DQHQFQPEDSLVD-L-GANSMDRAEIVIMTLE 51 (79)
T ss_pred CCHHHHHHHHHHHHHHHcCCC---CHHHCCCCCChhh-c-CCChHHHHHHHHHHHH
Confidence 577888888888887764 12 3347899999998 7 9999988777665544
No 16
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=52.25 E-value=4.4 Score=23.07 Aligned_cols=37 Identities=22% Similarity=0.200 Sum_probs=17.5
Q ss_pred HHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCce
Q 034230 29 TLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNV 65 (100)
Q Consensus 29 ~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~ 65 (100)
+||+.+|.+..+-+.+++.|-+.==-..-+||+|+|.
T Consensus 22 ~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~R~ 58 (59)
T PF01047_consen 22 ELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDRRQ 58 (59)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTETTS
T ss_pred HHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCCc
Confidence 7888888754444444444433100012245566554
No 17
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=51.74 E-value=13 Score=23.66 Aligned_cols=23 Identities=35% Similarity=0.446 Sum_probs=16.2
Q ss_pred cCCHHHHHhhCCCcccHHHHHHHHHHHHhh
Q 034230 25 NLPSTLREFVGQSRISRLGCFMRVWSYIKT 54 (100)
Q Consensus 25 ~lS~~La~~lG~~~~sr~~v~~~lW~YIK~ 54 (100)
.=-++|++-||++.. +||++|+.
T Consensus 20 ~SGe~La~~LgiSRt-------aVwK~Iq~ 42 (79)
T COG1654 20 VSGEKLAEELGISRT-------AVWKHIQQ 42 (79)
T ss_pred ccHHHHHHHHCccHH-------HHHHHHHH
Confidence 334678888887544 68888865
No 18
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=51.37 E-value=12 Score=18.40 Aligned_cols=21 Identities=19% Similarity=0.241 Sum_probs=17.1
Q ss_pred cHHHHHHHHHHHHhhcCCCCC
Q 034230 40 SRLGCFMRVWSYIKTNNLQDP 60 (100)
Q Consensus 40 sr~~v~~~lW~YIK~~~Lqdp 60 (100)
.+.++...|++|...+|+.+.
T Consensus 2 ~~~~l~~lI~~yL~~~g~~~t 22 (34)
T smart00667 2 SRSELNRLILEYLLRNGYEET 22 (34)
T ss_pred cHHHHHHHHHHHHHHcCHHHH
Confidence 467889999999999997543
No 19
>PF08463 EcoEI_R_C: EcoEI R protein C-terminal; InterPro: IPR013670 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the C-terminal domain found in both the R subunit of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity [, ]. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=50.09 E-value=9.7 Score=26.33 Aligned_cols=70 Identities=13% Similarity=0.291 Sum_probs=43.5
Q ss_pred ccCCHHHHHhhCCCc--ccHHHHHHHHHHHHhhcCCCCCCCCceeecc-----hhHHhhhcCCCeeccccHHHHHhccC
Q 034230 24 VNLPSTLREFVGQSR--ISRLGCFMRVWSYIKTNNLQDPNNKNVVNCD-----QKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 24 ~~lS~~La~~lG~~~--~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cD-----e~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
-++....+.|++... ..+-+++..|-+|+..+|..++++=...-.. ..+..+| |... .+.++-.-|+.++
T Consensus 87 erv~~~~~~~l~~~~~~~~Q~~~L~~i~~~~~~~G~~~~~~l~~~pF~~~G~~~~~~~~F-g~~~-~l~~~~~~l~~~L 163 (164)
T PF08463_consen 87 ERVEEAFSKFLNQHQFNAEQREFLERILDYYAQNGIIEPEDLKEPPFSDLGGPGGIIRVF-GGKE-QLDEILNELNKNL 163 (164)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhCcccHHHhCCCchhhcCCHHHHHHHc-CCHH-HHHHHHHHHHhhc
Confidence 344556677776554 5667999999999999999886543222222 3466777 4332 4445555555443
No 20
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=48.41 E-value=15 Score=21.79 Aligned_cols=44 Identities=16% Similarity=0.291 Sum_probs=28.9
Q ss_pred cccCC-HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecch
Q 034230 23 LVNLP-STLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQ 70 (100)
Q Consensus 23 ~~~lS-~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe 70 (100)
.+.+| .+||+++|.+.. .|. .+-...++.|+.+-+.+.+++.|.
T Consensus 26 ~~~lt~~~iA~~~g~sr~---tv~-r~l~~l~~~g~I~~~~~~i~I~d~ 70 (76)
T PF13545_consen 26 PLPLTQEEIADMLGVSRE---TVS-RILKRLKDEGIIEVKRGKIIILDP 70 (76)
T ss_dssp EEESSHHHHHHHHTSCHH---HHH-HHHHHHHHTTSEEEETTEEEESSH
T ss_pred EecCCHHHHHHHHCCCHH---HHH-HHHHHHHHCCCEEEcCCEEEECCH
Confidence 34444 489999998544 333 344455667788777778877774
No 21
>PRK00071 nadD nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=47.96 E-value=14 Score=26.64 Aligned_cols=17 Identities=24% Similarity=0.157 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHhhcCCC
Q 034230 42 LGCFMRVWSYIKTNNLQ 58 (100)
Q Consensus 42 ~~v~~~lW~YIK~~~Lq 58 (100)
.-|-..+++||++|+|.
T Consensus 185 ~lvp~~V~~YI~~~~LY 201 (203)
T PRK00071 185 YLLPEAVLDYIEKHGLY 201 (203)
T ss_pred HhCCHHHHHHHHHhCcc
Confidence 33445789999999986
No 22
>PLN02945 nicotinamide-nucleotide adenylyltransferase/nicotinate-nucleotide adenylyltransferase
Probab=47.45 E-value=15 Score=27.29 Aligned_cols=17 Identities=29% Similarity=0.163 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHhhcCCC
Q 034230 42 LGCFMRVWSYIKTNNLQ 58 (100)
Q Consensus 42 ~~v~~~lW~YIK~~~Lq 58 (100)
.-|-..+++||++|||.
T Consensus 219 ~lvP~~V~~YI~~~~LY 235 (236)
T PLN02945 219 YLTPDGVIDYIKEHGLY 235 (236)
T ss_pred hhCCHHHHHHHHHcCCC
Confidence 44555789999999985
No 23
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=46.83 E-value=21 Score=18.83 Aligned_cols=25 Identities=24% Similarity=0.420 Sum_probs=18.9
Q ss_pred HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCC
Q 034230 28 STLREFVGQSRISRLGCFMRVWSYIKTNNLQD 59 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqd 59 (100)
++.|+++|++.. .|++++++..+.-
T Consensus 5 ~e~a~~lgis~~-------ti~~~~~~g~i~~ 29 (49)
T TIGR01764 5 EEAAEYLGVSKD-------TVYRLIHEGELPA 29 (49)
T ss_pred HHHHHHHCCCHH-------HHHHHHHcCCCCe
Confidence 578888987554 6899998877653
No 24
>PRK05883 acyl carrier protein; Validated
Probab=46.38 E-value=20 Score=22.93 Aligned_cols=54 Identities=19% Similarity=0.079 Sum_probs=41.7
Q ss_pred cccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 38 RISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 38 ~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
.++..+|...|-++|.+.==.++ ..|..|..|...+ |-+++.+-++.-.|..+|
T Consensus 9 ~~~~~~I~~~l~~iia~~l~v~~---~~I~~d~~l~~dl-g~DSL~~v~lv~~lE~~f 62 (91)
T PRK05883 9 TSSPSTVSATLLSILRDDLNVDL---TRVTPDARLVDDV-GLDSVAFAVGMVAIEERL 62 (91)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCh---hhCCCCCchhhcc-CCChHHHHHHHHHHHHHH
Confidence 67888999999999987532333 3689999999988 999998777766776665
No 25
>PRK07639 acyl carrier protein; Provisional
Probab=45.74 E-value=20 Score=22.64 Aligned_cols=54 Identities=13% Similarity=0.049 Sum_probs=38.7
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 39 ISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 39 ~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
|||.+|...|-+.|.+.==-++ -..|..|..|..=+ |-+++.+-++.-.|...|
T Consensus 1 M~~~ei~~~i~~il~e~l~~~~--~~~i~~d~~l~edL-~lDSld~velv~~lE~~f 54 (86)
T PRK07639 1 MRREALKNAVLKIMEEKLELKN--VTHLEETMRLNEDL-YIDSVMMLQLIVYIEMDV 54 (86)
T ss_pred CCHHHHHHHHHHHHHHHhCCCc--cccCCCCCCccccc-CCChHHHHHHHHHHHHHH
Confidence 5788888888888877531111 13578999987766 889988888877777655
No 26
>TIGR00482 nicotinate (nicotinamide) nucleotide adenylyltransferase. This model represents the predominant bacterial/eukaryotic adenylyltransferase for nicotinamide-nucleotide, its deamido form nicotinate nucleotide, or both. The first activity, nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1), synthesizes NAD by the salvage pathway, while the second, nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) synthesizes the immediate precursor of NAD by the de novo pathway. In E. coli, NadD activity is biased toward the de novo pathway while salvage activity is channeled through the multifunctional NadR protein, but this division of labor may be exceptional. The given name of this model, nicotinate (nicotinamide) nucleotide adenylyltransferase, reflects the lack of absolute specificity with respect to substrate amidation state in most species.
Probab=45.49 E-value=17 Score=25.98 Aligned_cols=17 Identities=29% Similarity=0.139 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHhhcCCC
Q 034230 42 LGCFMRVWSYIKTNNLQ 58 (100)
Q Consensus 42 ~~v~~~lW~YIK~~~Lq 58 (100)
.-|-..+++||++|+|.
T Consensus 177 ~lvP~~V~~YI~~~~LY 193 (193)
T TIGR00482 177 YLLPDPVIKYIKQHGLY 193 (193)
T ss_pred hhCCHHHHHHHHHhCCC
Confidence 33444679999999983
No 27
>PF12728 HTH_17: Helix-turn-helix domain
Probab=44.67 E-value=29 Score=19.16 Aligned_cols=26 Identities=23% Similarity=0.419 Sum_probs=19.5
Q ss_pred HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCC
Q 034230 28 STLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp 60 (100)
++.|++||++.. .++++++...+.-.
T Consensus 5 ~e~a~~l~is~~-------tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 5 KEAAELLGISRS-------TVYRWIRQGKIPPF 30 (51)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCCeE
Confidence 578999997544 58889988877544
No 28
>PRK06973 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=43.23 E-value=18 Score=27.32 Aligned_cols=19 Identities=32% Similarity=0.431 Sum_probs=14.5
Q ss_pred cHHHHHHHHHHHHhhcCCC
Q 034230 40 SRLGCFMRVWSYIKTNNLQ 58 (100)
Q Consensus 40 sr~~v~~~lW~YIK~~~Lq 58 (100)
-+.-|=..+++||++|+|.
T Consensus 223 i~~lvP~~V~~YI~~~~LY 241 (243)
T PRK06973 223 SAEHVPAAVWAYILQHRLY 241 (243)
T ss_pred hhHhCCHHHHHHHHHcCCC
Confidence 3444556799999999996
No 29
>PF13950 Epimerase_Csub: UDP-glucose 4-epimerase C-term subunit; PDB: 1EK5_A 1I3K_B 1I3M_B 1HZJ_A 1EK6_A 1I3N_A 1I3L_A 2CNB_B 1GY8_D 1NAI_A ....
Probab=42.67 E-value=57 Score=19.40 Aligned_cols=45 Identities=24% Similarity=0.303 Sum_probs=26.3
Q ss_pred cCCCCCCCccccccCCHHHHHhhCC-CcccHHHHHHHHHHHHhhcC
Q 034230 12 DNPKKLANLIDLVNLPSTLREFVGQ-SRISRLGCFMRVWSYIKTNN 56 (100)
Q Consensus 12 ~~~~~~~~~~~~~~lS~~La~~lG~-~~~sr~~v~~~lW~YIK~~~ 56 (100)
-.|+..+-....+.=+....+.||= .+.+-.+++...|++.+.|-
T Consensus 14 ~~~rR~GD~~~~~Ad~~kA~~~LgW~p~~~L~~~i~~~w~W~~~np 59 (62)
T PF13950_consen 14 YAPRRPGDPAHLVADISKAREELGWKPKYSLEDMIRDAWNWQKKNP 59 (62)
T ss_dssp EE---TT--SEE-B--HHHHHHC----SSSHHHHHHHHHHHHHHST
T ss_pred ECCCCCCchhhhhCCHHHHHHHhCCCcCCCHHHHHHHHHHHHHHCc
Confidence 3455655565666556666688884 56699999999999998873
No 30
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=38.88 E-value=55 Score=29.62 Aligned_cols=86 Identities=16% Similarity=0.065 Sum_probs=62.1
Q ss_pred ccccccCCCCCCCccccccCCHHHHHhhCCC-----cccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCe
Q 034230 7 KKTVIDNPKKLANLIDLVNLPSTLREFVGQS-----RISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSR 81 (100)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~lS~~La~~lG~~-----~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~ 81 (100)
.+.+.+.||..++-...-+|+++|..+||.- .....++...+.+-||...+ ...+=..|..|+..+..
T Consensus 116 ~~~s~~~~k~~~~~r~~~~l~~~l~~ll~eAN~lfarg~~eeA~~i~~EvIkqdp~-------~~~ay~tL~~IyEqrGd 188 (895)
T KOG2076|consen 116 GEKSTGTKKRGRRSRGKSKLAPELRQLLGEANNLFARGDLEEAEEILMEVIKQDPR-------NPIAYYTLGEIYEQRGD 188 (895)
T ss_pred heecccCCccCCCCCcccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcc-------chhhHHHHHHHHHHccc
Confidence 3667788888888889999999999999862 46667888888999986543 55666778888743434
Q ss_pred eccccHHHHHhccCCCCC
Q 034230 82 VELAELPALIKLHFPKDP 99 (100)
Q Consensus 82 i~~~el~~ll~~Hl~~~p 99 (100)
+.-+=...++..|+-|..
T Consensus 189 ~eK~l~~~llAAHL~p~d 206 (895)
T KOG2076|consen 189 IEKALNFWLLAAHLNPKD 206 (895)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 433444557777877653
No 31
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=38.35 E-value=79 Score=18.12 Aligned_cols=26 Identities=15% Similarity=0.288 Sum_probs=19.7
Q ss_pred HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCC
Q 034230 28 STLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp 60 (100)
.++|+.+|++.. .|+.|++..++..|
T Consensus 4 ~eva~~~gvs~~-------tlr~w~~~~g~~~~ 29 (68)
T cd01104 4 GAVARLTGVSPD-------TLRAWERRYGLPAP 29 (68)
T ss_pred HHHHHHHCcCHH-------HHHHHHHhCCCCCC
Confidence 477888887654 58889988788765
No 32
>PF07587 PSD1: Protein of unknown function (DUF1553); InterPro: IPR022655 The function is not known. It is found associated with IPR011444 from INTERPRO It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=37.70 E-value=45 Score=25.26 Aligned_cols=55 Identities=18% Similarity=0.308 Sum_probs=41.4
Q ss_pred HHHHhhCC--CcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCC--CeeccccHHHHHhccCC
Q 034230 29 TLREFVGQ--SRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGK--SRVELAELPALIKLHFP 96 (100)
Q Consensus 29 ~La~~lG~--~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~--~~i~~~el~~ll~~Hl~ 96 (100)
+||+.|-. ...+---++.+||+|.=-.||-+|-|- | |. ..-+-+|+-++|..+|.
T Consensus 5 ~LA~wlt~~~Np~faRv~VNRvW~~~fGrGlV~p~dD------------~-g~~~~~PshPeLLd~La~~F~ 63 (266)
T PF07587_consen 5 ALADWLTSPDNPLFARVIVNRVWQHLFGRGLVEPVDD------------F-GPQGNPPSHPELLDWLAAEFV 63 (266)
T ss_pred HHHHHhcCCCCcchHHHHHHHHHHHHcCCcCcCCHhh------------c-cCCCCCCCCHHHHHHHHHHHH
Confidence 57777743 566777899999999999999888754 3 43 44566788888887764
No 33
>PF13333 rve_2: Integrase core domain
Probab=37.65 E-value=34 Score=19.35 Aligned_cols=21 Identities=24% Similarity=0.075 Sum_probs=17.6
Q ss_pred CCcccHHHHHHHHHHHHhhcC
Q 034230 36 QSRISRLGCFMRVWSYIKTNN 56 (100)
Q Consensus 36 ~~~~sr~~v~~~lW~YIK~~~ 56 (100)
..-.|+.++...|++||.-.|
T Consensus 15 ~~~~t~eel~~~I~~YI~~yN 35 (52)
T PF13333_consen 15 QKFKTREELKQAIDEYIDYYN 35 (52)
T ss_pred cccchHHHHHHHHHHHHHHhc
Confidence 346799999999999998764
No 34
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=37.47 E-value=49 Score=22.94 Aligned_cols=43 Identities=19% Similarity=0.476 Sum_probs=32.0
Q ss_pred CHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCC-------CCCceeecchhHHhhh
Q 034230 27 PSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDP-------NNKNVVNCDQKLRSIL 76 (100)
Q Consensus 27 S~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp-------~~k~~I~cDe~Lk~lf 76 (100)
++|||+.+|.+.. .|-.+|++.|-... +.-|.|+-|+..+..+
T Consensus 3 ~eELA~~tG~srQ-------TINrWvRkegW~T~p~pGVkGGrARLIhId~~V~efi 52 (122)
T PF07037_consen 3 PEELAELTGYSRQ-------TINRWVRKEGWKTEPKPGVKGGRARLIHIDEQVREFI 52 (122)
T ss_pred HHHHHHHhCccHH-------HHHHHHHhcCceeccCCccccccceeeeecHHHHHHH
Confidence 4789999998544 46677877776543 2457899999999976
No 35
>TIGR02057 PAPS_reductase phosphoadenosine phosphosulfate reductase, thioredoxin dependent. Requiring thioredoxin as an electron donor, phosphoadenosine phosphosulfate reductase catalyzes the reduction of 3'-phosphoadenylylsulfate (PAPS) to sulfite and phospho-adenosine-phosphate (PAP). Found in enterobacteria, cyanobacteria, and yeast, PAPS reductase is related to a group of plant (TIGR00424) and bacterial (TIGR02055) enzymes preferring 5'-adenylylsulfate (APS) over PAPS as a substrate for reduction to sulfite.
Probab=37.29 E-value=20 Score=26.58 Aligned_cols=12 Identities=25% Similarity=0.764 Sum_probs=10.3
Q ss_pred HHHHHHhhcCCC
Q 034230 47 RVWSYIKTNNLQ 58 (100)
Q Consensus 47 ~lW~YIK~~~Lq 58 (100)
-||+||++|+|-
T Consensus 172 dVw~Yi~~~~lP 183 (226)
T TIGR02057 172 QVYQYLDAHNVP 183 (226)
T ss_pred HHHHHHHHcCCC
Confidence 479999999983
No 36
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=36.49 E-value=36 Score=20.56 Aligned_cols=17 Identities=18% Similarity=0.280 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHhhcCC
Q 034230 41 RLGCFMRVWSYIKTNNL 57 (100)
Q Consensus 41 r~~v~~~lW~YIK~~~L 57 (100)
+.+|...|.+||.+||.
T Consensus 8 Q~~vL~~I~~~~~~~G~ 24 (65)
T PF01726_consen 8 QKEVLEFIREYIEENGY 24 (65)
T ss_dssp HHHHHHHHHHHHHHHSS
T ss_pred HHHHHHHHHHHHHHcCC
Confidence 57899999999999995
No 37
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=35.81 E-value=24 Score=17.65 Aligned_cols=17 Identities=12% Similarity=0.321 Sum_probs=13.1
Q ss_pred HHHHHHHHHHhhcCCCC
Q 034230 43 GCFMRVWSYIKTNNLQD 59 (100)
Q Consensus 43 ~v~~~lW~YIK~~~Lqd 59 (100)
++-..||+|...+|..+
T Consensus 2 ~Ln~lI~~YL~~~Gy~~ 18 (27)
T PF08513_consen 2 ELNQLIYDYLVENGYKE 18 (27)
T ss_dssp HHHHHHHHHHHHCT-HH
T ss_pred HHHHHHHHHHHHCCcHH
Confidence 56778999999999753
No 38
>PHA03061 putative DNA-binding virion core protein; Provisional
Probab=35.80 E-value=72 Score=25.18 Aligned_cols=60 Identities=23% Similarity=0.360 Sum_probs=44.4
Q ss_pred ccccccCCHHHHHhhCC----------CcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeecc
Q 034230 20 LIDLVNLPSTLREFVGQ----------SRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVEL 84 (100)
Q Consensus 20 ~~~~~~lS~~La~~lG~----------~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~ 84 (100)
--..|.+|++|-+++-. ..+||+ +|++|.-.--=.|...-=.|.-|++...++ |-+.+.+
T Consensus 177 KDS~Y~i~dELL~vlk~RlfrcPQVkdn~ISrt----RLyDYf~R~tk~de~kIYViLKD~~iA~iL-gieTv~i 246 (311)
T PHA03061 177 KDSMYVISDELLDVLKTRLFRCPQVKDNLISRT----RLYDYFTRVTKRDESKIYVILKDKRIADIL-GIETVKL 246 (311)
T ss_pred ccceEeccHHHHHHHHHHhccCchhhcchhhHH----HHHHHHHHhcccccceEEEEEcchhHhhhc-CcceEEe
Confidence 34578999999988842 355665 789998776655555455688899999999 9887644
No 39
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=35.59 E-value=13 Score=23.19 Aligned_cols=28 Identities=18% Similarity=0.275 Sum_probs=20.0
Q ss_pred ccCCHHHHHhhCCCcccHHHHHHHHHHH
Q 034230 24 VNLPSTLREFVGQSRISRLGCFMRVWSY 51 (100)
Q Consensus 24 ~~lS~~La~~lG~~~~sr~~v~~~lW~Y 51 (100)
+..-+.+.+.||....|..+|..+||.|
T Consensus 29 ~~~l~~vr~~Lg~~~~~e~~i~eal~~~ 56 (79)
T PF08938_consen 29 YSCLPQVREVLGDYVPPEEQIKEALWHY 56 (79)
T ss_dssp CHHCCCHHHHCCCCC--CCHHHHHHHHT
T ss_pred HHHHHHHHHHHcccCCCHHHHHHHHHHH
Confidence 3445667788887554889999999996
No 40
>PF03511 Fanconi_A: Fanconi anaemia group A protein; InterPro: IPR003516 Fanconi anaemia (FA) [, , ] is a recessive inherited disease characterised by defective DNA repair. FA cells are sensitive to DNA cross-linking agents that cause chromosomal instability and cell death. The disease is manifested clinically by progressive pancytopenia, variable physical anomalies, and predisposition to malignancy []. Four complementation groups have been identified, designated A to D. The FA group A gene (FAA) has been cloned [], but its function remains to be elucidated.
Probab=35.16 E-value=25 Score=21.76 Aligned_cols=15 Identities=13% Similarity=0.153 Sum_probs=13.7
Q ss_pred cccHHHHHhccCCCC
Q 034230 84 LAELPALIKLHFPKD 98 (100)
Q Consensus 84 ~~el~~ll~~Hl~~~ 98 (100)
||.++.+|+.|+.+.
T Consensus 10 FFSLM~LlSs~l~p~ 24 (64)
T PF03511_consen 10 FFSLMGLLSSYLAPK 24 (64)
T ss_pred HHHHHHHHHHhcCcc
Confidence 899999999999875
No 41
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=34.88 E-value=20 Score=18.71 Aligned_cols=10 Identities=30% Similarity=0.743 Sum_probs=8.1
Q ss_pred HHHhhcCCCC
Q 034230 50 SYIKTNNLQD 59 (100)
Q Consensus 50 ~YIK~~~Lqd 59 (100)
-||++|||-+
T Consensus 9 rYV~eh~ls~ 18 (28)
T PF12368_consen 9 RYVKEHGLSE 18 (28)
T ss_pred hhHHhcCCCH
Confidence 4999999854
No 42
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=34.20 E-value=33 Score=19.90 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=18.0
Q ss_pred HHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccCCC
Q 034230 46 MRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHFPK 97 (100)
Q Consensus 46 ~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl~~ 97 (100)
..||.|-+.+++..- ..++-.||...+.+||.-
T Consensus 4 ~tLrrY~~~~~l~~~-------------------~~~sK~qLa~~V~kHF~s 36 (53)
T PF13867_consen 4 PTLRRYKKHYKLPER-------------------PRSSKEQLANAVRKHFNS 36 (53)
T ss_dssp HHHHHHHHHTT-----------------------SS--HHHHHHHHHHHHTT
T ss_pred HHHHHHHHHhCCCCC-------------------CCCCHHHHHHHHHHHHhc
Confidence 468899998887532 233445666666666643
No 43
>PF05643 DUF799: Putative bacterial lipoprotein (DUF799); InterPro: IPR008517 This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative lipoproteins.
Probab=34.14 E-value=20 Score=27.00 Aligned_cols=39 Identities=31% Similarity=0.358 Sum_probs=29.2
Q ss_pred HHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHH
Q 034230 48 VWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELP 88 (100)
Q Consensus 48 lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~ 88 (100)
+-+-+|+|||.|+++-..+ .=++|+++| |-|-+-|-.|.
T Consensus 77 vde~fkqnGlt~~~~i~~v-~~~kL~eiF-GADAvLY~~I~ 115 (215)
T PF05643_consen 77 VDETFKQNGLTDAEDIHAV-PPAKLREIF-GADAVLYITIK 115 (215)
T ss_pred HHHHHHHcCCCCHHHhccC-CHHHHHHHh-CCCEEEEEEEE
Confidence 3345689999999987544 478999999 98887665443
No 44
>TIGR00517 acyl_carrier acyl carrier protein. S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site.
Probab=34.12 E-value=29 Score=20.87 Aligned_cols=50 Identities=24% Similarity=0.254 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 42 LGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 42 ~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
.++...|.+++.+.--.++ ..|.+|..|..-+ |-|++.+-+|...|..+|
T Consensus 2 ~~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dl-glDSl~~veli~~lE~~f 51 (77)
T TIGR00517 2 QEIFEKVKAIIKEQLNVDE---DQVTPDASFVEDL-GADSLDTVELVMALEEEF 51 (77)
T ss_pred hHHHHHHHHHHHHHHCCCH---HHCCCCcchhhhc-CCcHHHHHHHHHHHHHHH
Confidence 3566777888877522233 3588899987766 889988888877777655
No 45
>TIGR02055 APS_reductase thioredoxin-dependent adenylylsulfate APS reductase. This model describes recently identified adenosine 5'-phosphosulfate (APS) reductase activity found in sulfate-assimilatory prokaryotes, thus separating it from the traditionally described phosphoadenosine 5'-phosphosulfate (PAPS) reductases found in bacteria and fungi. Homologous to PAPS reductase in enterobacteria, cyanobacteria, and yeast, APS reductase here clusters with, and demonstrates greater homology to plant APS reductase. Additionally, the presence of two conserved C-terminal motifs (CCXXRKXXPL & SXGCXXCT) distinguishes APS substrate specificity and serves as a FeS cluster.
Probab=32.77 E-value=26 Score=25.10 Aligned_cols=11 Identities=55% Similarity=1.138 Sum_probs=10.2
Q ss_pred HHHHHHhhcCC
Q 034230 47 RVWSYIKTNNL 57 (100)
Q Consensus 47 ~lW~YIK~~~L 57 (100)
-||+||++|||
T Consensus 136 dVw~Yi~~~~l 146 (191)
T TIGR02055 136 DVWEYIADNEL 146 (191)
T ss_pred HHHHHHHHcCC
Confidence 58999999998
No 46
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=32.68 E-value=55 Score=20.22 Aligned_cols=50 Identities=24% Similarity=0.364 Sum_probs=32.3
Q ss_pred cCC-HHHHHhhCCCcccHHHHHHHHHH--HHhhcCCCCCCCCc--eeecchhHHhhh
Q 034230 25 NLP-STLREFVGQSRISRLGCFMRVWS--YIKTNNLQDPNNKN--VVNCDQKLRSIL 76 (100)
Q Consensus 25 ~lS-~~La~~lG~~~~sr~~v~~~lW~--YIK~~~Lqdp~~k~--~I~cDe~Lk~lf 76 (100)
..+ .+|++.+|.+..+-+.+++.|++ ||... .||.|+| .|..-++=+.++
T Consensus 36 ~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~--~~~~DrR~~~l~lT~~G~~~~ 90 (126)
T COG1846 36 GITVKELAERLGLDRSTVTRLLKRLEDKGLIERL--RDPEDRRAVLVRLTEKGRELL 90 (126)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeec--CCccccceeeEEECccHHHHH
Confidence 345 89999999988888888888887 55544 3455544 344433333333
No 47
>PF03289 Pox_I1: Poxvirus protein I1; InterPro: IPR004969 Proteins in this group show homology to vaccinia virus I1L (Late) encoded protein.
Probab=32.50 E-value=91 Score=24.64 Aligned_cols=59 Identities=24% Similarity=0.370 Sum_probs=44.1
Q ss_pred cccccCCHHHHHhhCC----------CcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeecc
Q 034230 21 IDLVNLPSTLREFVGQ----------SRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVEL 84 (100)
Q Consensus 21 ~~~~~lS~~La~~lG~----------~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~ 84 (100)
-..|.++++|-+++-. ..+||. +|++|.-.--=.|...-=.|.-|++...++ |-+.+.+
T Consensus 179 Ds~Y~i~dELL~vlk~RlfR~PQVkdn~ISrt----RLyDYf~R~tk~de~kIYViLKD~~iA~iL-gieTv~i 247 (312)
T PF03289_consen 179 DSMYIISDELLDVLKTRLFRCPQVKDNIISRT----RLYDYFTRVTKRDESKIYVILKDKKIADIL-GIETVKI 247 (312)
T ss_pred cceEecCHHHHHHHHHHhccCCccccchhhHH----HHHHHHHHhcccccceEEEEEcchhHhhhc-CcceEEe
Confidence 4578999999988842 355665 789998776655555555688899999999 9887644
No 48
>COG0021 TktA Transketolase [Carbohydrate transport and metabolism]
Probab=32.41 E-value=79 Score=27.73 Aligned_cols=32 Identities=16% Similarity=0.293 Sum_probs=27.0
Q ss_pred cccHHHHHHHHHHHHhhcCCCCC---CCCceeecc
Q 034230 38 RISRLGCFMRVWSYIKTNNLQDP---NNKNVVNCD 69 (100)
Q Consensus 38 ~~sr~~v~~~lW~YIK~~~Lqdp---~~k~~I~cD 69 (100)
.|.-.++...||.++..+|=.|| ++-|+|..-
T Consensus 32 pmG~A~ia~~L~~~~l~~nP~nP~W~nRDRFVLSa 66 (663)
T COG0021 32 PMGAADIAYVLWTRFLKHNPDNPKWINRDRFVLSA 66 (663)
T ss_pred CccHHHHHHHHHHHHhcCCCCCCCCCCCccEEecC
Confidence 67788999999999999999999 566777654
No 49
>PRK12563 sulfate adenylyltransferase subunit 2; Provisional
Probab=32.20 E-value=26 Score=27.68 Aligned_cols=24 Identities=21% Similarity=0.479 Sum_probs=17.2
Q ss_pred HHHHHHhhcCCCCC-----C-------CCceeecch
Q 034230 47 RVWSYIKTNNLQDP-----N-------NKNVVNCDQ 70 (100)
Q Consensus 47 ~lW~YIK~~~Lqdp-----~-------~k~~I~cDe 70 (100)
-||+||+.|||--. . ++..|.||+
T Consensus 203 DVW~YI~~~~IP~~pLY~~~~r~~~~~~g~~~~~~~ 238 (312)
T PRK12563 203 DVWQYIAREKIPLVPLYFAKRRPVVERDGLLIMVDD 238 (312)
T ss_pred HHHHHHHHcCCCCCcchhcCCCceEEECCeEEeccc
Confidence 48999999998532 1 455677777
No 50
>cd09286 NMNAT_Eukarya Nicotinamide/nicotinate mononucleotide adenylyltransferase, Eukaryotic. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis. This subfamily consists strictly of eukaryotic members and includes secondary structural elements not found in all NMNATs.
Probab=32.13 E-value=36 Score=25.23 Aligned_cols=17 Identities=24% Similarity=0.108 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHhhcCCC
Q 034230 42 LGCFMRVWSYIKTNNLQ 58 (100)
Q Consensus 42 ~~v~~~lW~YIK~~~Lq 58 (100)
..|-..+.+||++|+|.
T Consensus 209 ~llp~~V~~YI~~~~LY 225 (225)
T cd09286 209 YLLPDPVIEYIEQHQLY 225 (225)
T ss_pred hcCCHHHHHHHHHcCCC
Confidence 44555688999999984
No 51
>cd02165 NMNAT Nicotinamide/nicotinate mononucleotide adenylyltransferase. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis.
Probab=31.41 E-value=39 Score=23.91 Aligned_cols=17 Identities=29% Similarity=0.127 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHhhcCCC
Q 034230 42 LGCFMRVWSYIKTNNLQ 58 (100)
Q Consensus 42 ~~v~~~lW~YIK~~~Lq 58 (100)
.-|-..+.+||++|+|.
T Consensus 176 ~lvp~~V~~yI~~~~lY 192 (192)
T cd02165 176 YLLPPAVADYIKEHGLY 192 (192)
T ss_pred HhCCHHHHHHHHHccCC
Confidence 34555688999999984
No 52
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=31.14 E-value=61 Score=22.38 Aligned_cols=45 Identities=13% Similarity=0.110 Sum_probs=29.5
Q ss_pred HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecch-hHHhhh
Q 034230 28 STLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQ-KLRSIL 76 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe-~Lk~lf 76 (100)
.+||+++|.+..|=+ ..+ .-.++.|+..-+.++++++|- .|+++.
T Consensus 153 ~~iA~~lG~tretvs---R~l-~~l~~~g~I~~~~~~i~I~d~~~L~~~~ 198 (202)
T PRK13918 153 DELAAAVGSVRETVT---KVI-GELSREGYIRSGYGKIQLLDLKGLEELA 198 (202)
T ss_pred HHHHHHhCccHHHHH---HHH-HHHHHCCCEEcCCCEEEEECHHHHHHHH
Confidence 489999998544333 333 334578888877777877775 565554
No 53
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=30.39 E-value=50 Score=17.49 Aligned_cols=21 Identities=10% Similarity=0.333 Sum_probs=13.3
Q ss_pred HHHHHhhCCCcccHHHHHHHH
Q 034230 28 STLREFVGQSRISRLGCFMRV 48 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~l 48 (100)
.++|+.+|....|=+.+++.+
T Consensus 6 ~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp HHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHhCCcHHHHHHHHHHH
Confidence 478999998665555555443
No 54
>KOG4144 consensus Arylalkylamine N-acetyltransferase [General function prediction only]
Probab=30.19 E-value=33 Score=25.19 Aligned_cols=33 Identities=15% Similarity=0.350 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhcCCCCCCCCceeecchhHHhhh
Q 034230 44 CFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSIL 76 (100)
Q Consensus 44 v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf 76 (100)
....||+|+..-+-|.-.++...+|-+.|-.-.
T Consensus 119 a~~Ll~~ylq~l~~q~i~~r~~Li~h~pLvPFY 151 (190)
T KOG4144|consen 119 APILLWRYLQHLGSQPIVRRAALICHDPLVPFY 151 (190)
T ss_pred chhHHHHHHHHhhcCccccceeeeecCCccchh
Confidence 456799999999988888999999999987754
No 55
>PRK08887 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=29.43 E-value=51 Score=23.33 Aligned_cols=18 Identities=17% Similarity=-0.047 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHhhcCCCC
Q 034230 42 LGCFMRVWSYIKTNNLQD 59 (100)
Q Consensus 42 ~~v~~~lW~YIK~~~Lqd 59 (100)
.-|-..+.+||++|+|.-
T Consensus 154 ~lvp~~V~~yI~~~~LY~ 171 (174)
T PRK08887 154 HLTTPGVARLLKEHQLYT 171 (174)
T ss_pred HhCCHHHHHHHHHccccC
Confidence 445556899999999974
No 56
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=28.68 E-value=1.2e+02 Score=19.13 Aligned_cols=41 Identities=10% Similarity=0.043 Sum_probs=29.7
Q ss_pred CHHHHHhhCCC---cccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHH
Q 034230 27 PSTLREFVGQS---RISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLR 73 (100)
Q Consensus 27 S~~La~~lG~~---~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk 73 (100)
-..+++.+|.. ..+..++...+++++..++- ..|+.||.=.
T Consensus 55 ~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~~~~------~~lviDe~~~ 98 (131)
T PF13401_consen 55 AQEILEALGLPLKSRQTSDELRSLLIDALDRRRV------VLLVIDEADH 98 (131)
T ss_dssp HHHHHHHHT-SSSSTS-HHHHHHHHHHHHHHCTE------EEEEEETTHH
T ss_pred HHHHHHHhCccccccCCHHHHHHHHHHHHHhcCC------eEEEEeChHh
Confidence 44666666654 35688999999999999885 6888888733
No 57
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=28.59 E-value=59 Score=22.17 Aligned_cols=43 Identities=19% Similarity=0.350 Sum_probs=28.9
Q ss_pred ccCC-HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecch
Q 034230 24 VNLP-STLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQ 70 (100)
Q Consensus 24 ~~lS-~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe 70 (100)
+.++ .+||+++|.+ |..|. ++-.-.++.|+..-..++++++|.
T Consensus 142 ~~~t~~~iA~~lG~t---retvs-R~l~~l~~~g~I~~~~~~i~I~d~ 185 (193)
T TIGR03697 142 LRLSHQAIAEAIGST---RVTIT-RLLGDLRKKKLISIHKKKITVHDP 185 (193)
T ss_pred CCCCHHHHHHHhCCc---HHHHH-HHHHHHHHCCCEEecCCEEEEeCH
Confidence 4444 5899999964 43333 344456778888877888888875
No 58
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=28.30 E-value=1.2e+02 Score=18.62 Aligned_cols=40 Identities=13% Similarity=0.184 Sum_probs=27.9
Q ss_pred HHHHHhh--CCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhh
Q 034230 28 STLREFV--GQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSIL 76 (100)
Q Consensus 28 ~~La~~l--G~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf 76 (100)
+++.+++ |.-++|+++|...+-. ++++....|++.+-.-|
T Consensus 17 ~~m~~if~l~~~~vs~~el~a~lrk---------e~~~~y~~c~D~~L~~F 58 (68)
T PF07308_consen 17 DDMIEIFALAGFEVSKAELSAWLRK---------EDEKGYKECSDQLLRNF 58 (68)
T ss_pred HHHHHHHHHcCCccCHHHHHHHHCC---------CCCccccccChHHHHHH
Confidence 4666665 5578999988766543 66777888877765555
No 59
>PRK05253 sulfate adenylyltransferase subunit 2; Provisional
Probab=27.41 E-value=36 Score=26.58 Aligned_cols=12 Identities=33% Similarity=1.035 Sum_probs=10.5
Q ss_pred HHHHHHhhcCCC
Q 034230 47 RVWSYIKTNNLQ 58 (100)
Q Consensus 47 ~lW~YIK~~~Lq 58 (100)
-||+||+.+|+-
T Consensus 193 DIw~Yi~~~~IP 204 (301)
T PRK05253 193 DIWQYIERENIP 204 (301)
T ss_pred HHHHHHHHcCCC
Confidence 489999999875
No 60
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.14 E-value=84 Score=16.65 Aligned_cols=24 Identities=21% Similarity=0.257 Sum_probs=17.9
Q ss_pred HHHHHhhCCCcccHHHHHHHHHHHHhhcCCC
Q 034230 28 STLREFVGQSRISRLGCFMRVWSYIKTNNLQ 58 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lq 58 (100)
.++|+++|++.. .|+.|+++-.+.
T Consensus 4 ~e~a~~~gv~~~-------tlr~~~~~g~l~ 27 (49)
T cd04761 4 GELAKLTGVSPS-------TLRYYERIGLLS 27 (49)
T ss_pred HHHHHHHCcCHH-------HHHHHHHCCCCC
Confidence 467888888655 588888777665
No 61
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=27.02 E-value=89 Score=17.49 Aligned_cols=18 Identities=22% Similarity=0.479 Sum_probs=16.1
Q ss_pred CcccHHHHHHHHHHHHhh
Q 034230 37 SRISRLGCFMRVWSYIKT 54 (100)
Q Consensus 37 ~~~sr~~v~~~lW~YIK~ 54 (100)
...|+.+|+....+||+.
T Consensus 36 ~k~~K~~iL~~ai~yI~~ 53 (55)
T PF00010_consen 36 RKLSKASILQKAIDYIKQ 53 (55)
T ss_dssp SSSSHHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHHH
Confidence 478999999999999985
No 62
>TIGR00434 cysH phosophoadenylyl-sulfate reductase (thioredoxin). This enzyme, involved in the assimilation of inorganic sulfate, is designated cysH in Bacteria and MET16 in Saccharomyces cerevisiae. Synonyms include phosphoadenosine phosphosulfate reductase, PAPS reductase, and PAPS reductase, thioredoxin-dependent. In a reaction requiring reduced thioredoxin and NADPH, it converts 3(prime)-phosphoadenylylsulfate (PAPS) to sulfite and adenosine 3(prime),5(prime) diphosphate (PAP). A related family of plant enzymes, scoring below the trusted cutoff, differs in having a thioredoxin-like C-terminal domain, not requiring thioredoxin, and in having a preference for 5(prime)-adenylylsulfate (APS) over PAPS.
Probab=26.80 E-value=38 Score=24.29 Aligned_cols=12 Identities=42% Similarity=0.808 Sum_probs=10.5
Q ss_pred HHHHHHhhcCCC
Q 034230 47 RVWSYIKTNNLQ 58 (100)
Q Consensus 47 ~lW~YIK~~~Lq 58 (100)
-||+||.++||-
T Consensus 157 dVw~Yi~~~~lp 168 (212)
T TIGR00434 157 DVYQYIDAHNLP 168 (212)
T ss_pred HHHHHHHHcCCC
Confidence 479999999985
No 63
>PRK00982 acpP acyl carrier protein; Provisional
Probab=26.43 E-value=40 Score=20.14 Aligned_cols=49 Identities=20% Similarity=0.209 Sum_probs=34.6
Q ss_pred HHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhccC
Q 034230 43 GCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLHF 95 (100)
Q Consensus 43 ~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~Hl 95 (100)
++...++++|.+.==.+ ...|..|..|..-+ |-|++.+-+|...|...|
T Consensus 3 ~i~~~l~~~l~~~l~~~---~~~i~~d~~l~~dl-glDSl~~~~li~~le~~f 51 (78)
T PRK00982 3 EIFEKVKKIIVEQLGVD---EEEVTPEASFVDDL-GADSLDTVELVMALEEEF 51 (78)
T ss_pred HHHHHHHHHHHHHHCCC---HHHCCCCcchHhhc-CCCHHHHHHHHHHHHHHH
Confidence 56777888886643222 33588999996666 999988888877776655
No 64
>PLN02309 5'-adenylylsulfate reductase
Probab=25.79 E-value=39 Score=28.06 Aligned_cols=12 Identities=25% Similarity=0.933 Sum_probs=10.6
Q ss_pred HHHHHHhhcCCC
Q 034230 47 RVWSYIKTNNLQ 58 (100)
Q Consensus 47 ~lW~YIK~~~Lq 58 (100)
-||.||++|+|-
T Consensus 262 dVw~Yi~~~~lP 273 (457)
T PLN02309 262 EVWNFLRTMDVP 273 (457)
T ss_pred HHHHHHHHcCCC
Confidence 589999999984
No 65
>smart00224 GGL G protein gamma subunit-like motifs.
Probab=25.75 E-value=1.6e+02 Score=17.60 Aligned_cols=34 Identities=21% Similarity=0.291 Sum_probs=27.5
Q ss_pred HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCC
Q 034230 28 STLREFVGQSRISRLGCFMRVWSYIKTNNLQDPN 61 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~ 61 (100)
..|..=++...+.-+.+...|-+|+.++.-.||-
T Consensus 9 e~Lr~el~~~RikvS~a~~~li~y~e~~~~~DP~ 42 (63)
T smart00224 9 EQLRKELSRERIKVSKAAEELLAYCEQHAEEDPL 42 (63)
T ss_pred HHHHHHHCCceehHHHHHHHHHHHHHcCCCCCCC
Confidence 3455557788888899999999999998877774
No 66
>COG1137 YhbG ABC-type (unclassified) transport system, ATPase component [General function prediction only]
Probab=25.46 E-value=81 Score=24.23 Aligned_cols=27 Identities=19% Similarity=0.410 Sum_probs=23.0
Q ss_pred CCceeecchhHHhhhcCCCeeccccHHHHHh
Q 034230 62 NKNVVNCDQKLRSILMGKSRVELAELPALIK 92 (100)
Q Consensus 62 ~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~ 92 (100)
+.+++..||. |.|.|.+...+|+.++.
T Consensus 157 ~P~fiLLDEP----FAGVDPiaV~dIq~iI~ 183 (243)
T COG1137 157 NPKFILLDEP----FAGVDPIAVIDIQRIIK 183 (243)
T ss_pred CCCEEEecCC----ccCCCchhHHHHHHHHH
Confidence 5569999999 66889999999998876
No 67
>COG4380 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.19 E-value=40 Score=24.98 Aligned_cols=35 Identities=26% Similarity=0.283 Sum_probs=26.9
Q ss_pred HHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeecc
Q 034230 48 VWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVEL 84 (100)
Q Consensus 48 lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~ 84 (100)
+-+-.|.|||-+..|-.. ..-++|++|| |.|-+-+
T Consensus 76 veETFkQNGlT~AgDih~-v~paKL~qIf-GaDA~LY 110 (216)
T COG4380 76 VEETFKQNGLTNAGDIHA-VRPAKLHQIF-GADAVLY 110 (216)
T ss_pred hHHHHHHcCCCccccccc-CCHHHHHHHh-CcceEEE
Confidence 445689999999987654 4568999999 8877544
No 68
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=25.07 E-value=73 Score=22.82 Aligned_cols=45 Identities=11% Similarity=0.150 Sum_probs=29.0
Q ss_pred HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecch-hHHhhh
Q 034230 28 STLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQ-KLRSIL 76 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe-~Lk~lf 76 (100)
.+||+++|.+..|=+.+ |-+ .++.|+...+.+++.++|- .|..+.
T Consensus 173 ~~lA~~lG~sretvsR~---L~~-L~~~G~I~~~~~~i~I~d~~~L~~~~ 218 (226)
T PRK10402 173 TQAAEYLGVSYRHLLYV---LAQ-FIQDGYLKKSKRGYLIKNRKQLSGLA 218 (226)
T ss_pred HHHHHHHCCcHHHHHHH---HHH-HHHCCCEEeeCCEEEEeCHHHHHHHH
Confidence 68899999754443433 333 3567777777778888874 455543
No 69
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=24.99 E-value=1.1e+02 Score=22.11 Aligned_cols=48 Identities=10% Similarity=0.245 Sum_probs=30.9
Q ss_pred ccCC-HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCC-Cceeecch-hHHhh
Q 034230 24 VNLP-STLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNN-KNVVNCDQ-KLRSI 75 (100)
Q Consensus 24 ~~lS-~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~-k~~I~cDe-~Lk~l 75 (100)
..++ .+||+.+|++..|=+.+ -.-.++.|+.+-.. ++++++|. .|.++
T Consensus 178 i~lt~~~IA~~lGisretlsR~----L~~L~~~GlI~~~~~~~i~I~D~~~L~~l 228 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRA----LSQLQDRGLIGLSGARQIELRNRQALRNL 228 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHH----HHHHHHCCcEEecCCceEEEcCHHHHHHh
Confidence 3444 68999999865544433 34567778887654 67888885 44443
No 70
>cd07212 Pat_PNPLA9 Patatin-like phospholipase domain containing protein 9. PNPLA9 is a Ca-independent phospholipase that catalyzes the hydrolysis of glycerophospholipids at the sn-2 position. PNPLA9 is also known as PLA2G6 (phospholipase A2 group VI) or iPLA2beta. PLA2G6 is stimulated by ATP and inhibited by bromoenol lactone (BEL). In humans, PNPLA9 in expressed ubiquitously and is involved in signal transduction, cell proliferation, and apoptotic cell death. Mutations in human PLA2G6 leads to infantile neuroaxonal dystrophy (INAD) and idiopathic neurodegeneration with brain iron accumulation (NBIA). This family includes PLA2G6 from Homo sapiens and Rattus norvegicus.
Probab=24.90 E-value=48 Score=25.74 Aligned_cols=12 Identities=0% Similarity=-0.155 Sum_probs=4.6
Q ss_pred CcccHHHHHHHH
Q 034230 37 SRISRLGCFMRV 48 (100)
Q Consensus 37 ~~~sr~~v~~~l 48 (100)
++.+...+.+.+
T Consensus 290 de~~~~~l~~l~ 301 (312)
T cd07212 290 DETDDEDLVNML 301 (312)
T ss_pred CcCCHHHHHHHH
Confidence 333333333333
No 71
>PF10924 DUF2711: Protein of unknown function (DUF2711); InterPro: IPR024250 Some members in this family of proteins are annotated as ywbB. The function of these proteins is unknown.
Probab=24.60 E-value=71 Score=24.20 Aligned_cols=48 Identities=19% Similarity=0.258 Sum_probs=35.5
Q ss_pred CcccHHHHHHHHHHHHhhcCCCCCC-CCceeecchhHHhhhc--CCCeeccc
Q 034230 37 SRISRLGCFMRVWSYIKTNNLQDPN-NKNVVNCDQKLRSILM--GKSRVELA 85 (100)
Q Consensus 37 ~~~sr~~v~~~lW~YIK~~~Lqdp~-~k~~I~cDe~Lk~lf~--g~~~i~~~ 85 (100)
.+-.|.+..+.|-.|++. +|..|. +.--+..=..|.++|. |.+++.+.
T Consensus 86 ~ey~r~dla~~L~~~~~~-dlyyP~ED~~s~Fl~~~l~kvl~skG~~~i~y~ 136 (217)
T PF10924_consen 86 KEYARPDLAEKLNSYIDE-DLYYPSEDHTSLFLIPSLLKVLKSKGAEKIYYS 136 (217)
T ss_pred hhhcChHHHHHHHhhccc-ccCCCCccCcchhhHHHHHHHHHhCCCCeEEEe
Confidence 577899999999999986 699997 4555666677788874 34555443
No 72
>PTZ00411 transaldolase-like protein; Provisional
Probab=24.36 E-value=1.3e+02 Score=24.03 Aligned_cols=54 Identities=11% Similarity=0.170 Sum_probs=33.4
Q ss_pred cHHHHHHHHHHHHhhcCCCCCCCCc-eeecchhHHhhhcCCCeeccc-cHHHHHhccC
Q 034230 40 SRLGCFMRVWSYIKTNNLQDPNNKN-VVNCDQKLRSILMGKSRVELA-ELPALIKLHF 95 (100)
Q Consensus 40 sr~~v~~~lW~YIK~~~Lqdp~~k~-~I~cDe~Lk~lf~g~~~i~~~-el~~ll~~Hl 95 (100)
.--..++.+++|++.++....--.. +-..++-+. +. |++.++++ .+.+-|..|=
T Consensus 211 ~Gv~~v~~i~~~~k~~g~~T~Im~ASfRn~~qi~~-la-G~D~lTi~p~ll~~L~~~~ 266 (333)
T PTZ00411 211 PGVISVTKIYNYYKKHGYKTIVMGASFRNTGEILE-LA-GCDKLTISPKLLEELANTE 266 (333)
T ss_pred chHHHHHHHHHHHHHcCCCeEEEecccCCHHHHHH-HH-CCCEEeCCHHHHHHHHhCC
Confidence 3457889999999999874321111 122344443 55 99999874 6666555554
No 73
>PF09626 DHC: Dihaem cytochrome c; InterPro: IPR018588 Dihaem cytochrome c (DHC) is a soluble c-type cytochrome that folds into two distinct domains, each binding a single haem group and connected by a small linker region. Despite little sequence similarity, the N-terminal domain (residues 12-75) is a class I type cytochrome c, that binds one of the haems, but the domain surrounding the other haem is structurally unique. DHC binds electrostatically to an oxygen-binding protein, sphaeroides haem protein (SHP), as a component of a conserved electron transfer pathway. DHC acts as the physiological electron donor for SHP during phototrophic growth []. In certain species DHC is found upstream of IPR011577 from INTERPRO. ; PDB: 2FWT_A 2FW5_A.
Probab=23.72 E-value=1.4e+02 Score=20.29 Aligned_cols=57 Identities=21% Similarity=0.428 Sum_probs=29.1
Q ss_pred hCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCeeccccHHHHHhcc
Q 034230 34 VGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSRVELAELPALIKLH 94 (100)
Q Consensus 34 lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~i~~~el~~ll~~H 94 (100)
+|....-..+-...||+|...|-......+ ..-.-++.+ .+.....+.+.+-.+..|
T Consensus 33 FG~~a~Ld~~~~~~I~~YL~~nAa~~~~~~---~~~~~~~~~-~~~~p~RITe~~~f~~~H 89 (120)
T PF09626_consen 33 FGEDASLDPATQAEIWAYLQANAADRSQTK---RSRKILRSL-PGPPPLRITESPYFKRKH 89 (120)
T ss_dssp TTB-----HHHHHHHHHHHHHTSTTTTS--------GGGTT--TT---S-GGGSHHHHHHH
T ss_pred cCCCCCCCHHHHHHHHHHHHHcccccccch---hHHHHHhcc-CCCCCceeeccHHHHHHc
Confidence 344333345667889999999998766654 333444555 355556666776666665
No 74
>TIGR02039 CysD sulfate adenylyltransferase, small subunit. In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules.
Probab=23.57 E-value=46 Score=26.00 Aligned_cols=12 Identities=33% Similarity=1.002 Sum_probs=10.6
Q ss_pred HHHHHHhhcCCC
Q 034230 47 RVWSYIKTNNLQ 58 (100)
Q Consensus 47 ~lW~YIK~~~Lq 58 (100)
-||.||..+|+-
T Consensus 185 DVW~YI~~~~IP 196 (294)
T TIGR02039 185 DIWRYIAAENIP 196 (294)
T ss_pred HHHHHHHHcCCC
Confidence 589999999985
No 75
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=23.44 E-value=68 Score=23.97 Aligned_cols=51 Identities=16% Similarity=0.221 Sum_probs=37.9
Q ss_pred ccccccCCCCCCCccccccCCHHHHHhhCCCcccHHHHHHHHHHHHhhcCC
Q 034230 7 KKTVIDNPKKLANLIDLVNLPSTLREFVGQSRISRLGCFMRVWSYIKTNNL 57 (100)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~L 57 (100)
+||-...=+-.+|+..+|..++.=.-.+.....|-.+.+..|++|+++++.
T Consensus 144 kKAr~GeI~~fTGid~pYE~P~~Pel~l~t~~~~vee~v~~i~~~l~~~~~ 194 (197)
T COG0529 144 KKARAGEIKNFTGIDSPYEAPENPELHLDTDRNSVEECVEQILDLLKERKI 194 (197)
T ss_pred HHHHcCCCCCCcCCCCCCCCCCCCeeEeccccCCHHHHHHHHHHHHHhccc
Confidence 445555555667888888776554445677788889999999999998775
No 76
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=23.39 E-value=1.2e+02 Score=21.58 Aligned_cols=44 Identities=11% Similarity=0.153 Sum_probs=28.0
Q ss_pred HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecc-hhHHhhh
Q 034230 28 STLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCD-QKLRSIL 76 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cD-e~Lk~lf 76 (100)
.++|+++|.. |..|...+-+ .++.|+ .-..++++++| +.|+.+.
T Consensus 177 ~~iA~~lG~t---retvsR~l~~-L~~~gl-~~~~~~i~I~d~~~L~~~~ 221 (236)
T PRK09392 177 RVLASYLGMT---PENLSRAFAA-LASHGV-HVDGSAVTITDPAGLARFA 221 (236)
T ss_pred HHHHHHhCCC---hhHHHHHHHH-HHhCCe-EeeCCEEEEcCHHHHHHhh
Confidence 6899999984 4444444444 455667 45556777777 4566654
No 77
>COG4389 Site-specific recombinase [DNA replication, recombination, and repair]
Probab=23.22 E-value=77 Score=27.25 Aligned_cols=23 Identities=35% Similarity=0.414 Sum_probs=20.5
Q ss_pred CCCcccHHHHHHHHHHHHhhcCC
Q 034230 35 GQSRISRLGCFMRVWSYIKTNNL 57 (100)
Q Consensus 35 G~~~~sr~~v~~~lW~YIK~~~L 57 (100)
|.+-.|+.+|++.+|.-||.+-|
T Consensus 637 ~t~i~s~r~I~~~VW~~Ik~~PL 659 (677)
T COG4389 637 GTKIGSIRNIIKSVWNQIKSNPL 659 (677)
T ss_pred cccchhHHHHHHHHHHHHhcCCc
Confidence 56788999999999999998876
No 78
>cd00957 Transaldolase_TalAB Transaldolases including both TalA and TalB. The enzyme catalyses the reversible transfer of a dyhydroxyacetone moiety, derived from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. The catalytic mechanism is similar to other class I aldolases. The enzyme is found in the non-oxidative branch of the pentose phosphate pathway and forms a dimer in solution.
Probab=23.08 E-value=1.6e+02 Score=23.30 Aligned_cols=54 Identities=15% Similarity=0.182 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHhhcCCCCCCCCcee-ecchhHHhhhcCCCeeccc-cHHHHHhccCC
Q 034230 41 RLGCFMRVWSYIKTNNLQDPNNKNVV-NCDQKLRSILMGKSRVELA-ELPALIKLHFP 96 (100)
Q Consensus 41 r~~v~~~lW~YIK~~~Lqdp~~k~~I-~cDe~Lk~lf~g~~~i~~~-el~~ll~~Hl~ 96 (100)
=-..++.+++|++.++..-.--...+ ..++-+. +. |++.++++ .+.+-|..|-.
T Consensus 200 Gv~~v~~i~~~~~~~~~~T~vmaASfRn~~~v~~-la-G~d~~Ti~p~ll~~L~~~~~ 255 (313)
T cd00957 200 GVASVKKIYNYYKKFGYKTKVMGASFRNIGQILA-LA-GCDYLTISPALLEELKNSTA 255 (313)
T ss_pred HHHHHHHHHHHHHHcCCCcEEEecccCCHHHHHH-Hh-CCCeEEcCHHHHHHHHhCCC
Confidence 45779999999999997432111112 3455444 55 99998874 66666655544
No 79
>PF01507 PAPS_reduct: Phosphoadenosine phosphosulfate reductase family; InterPro: IPR002500 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases []. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) [, ]. It is also found in NodP nodulation protein P from Rhizobium meliloti (Sinorhizobium meliloti) which has ATP sulphurylase activity (sulphate adenylate transferase) [].; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2GOY_C 3G5A_C 3G6K_D 3G59_A 3FWK_A 2WSI_A 2OQ2_B 1SUR_A 2O8V_A 1ZUN_A.
Probab=22.87 E-value=44 Score=22.39 Aligned_cols=12 Identities=58% Similarity=1.149 Sum_probs=8.9
Q ss_pred HHHHHHhhcCCC
Q 034230 47 RVWSYIKTNNLQ 58 (100)
Q Consensus 47 ~lW~YIK~~~Lq 58 (100)
-+|+||+.+|+.
T Consensus 143 dV~~yi~~~~l~ 154 (174)
T PF01507_consen 143 DVWDYIKANGLP 154 (174)
T ss_dssp HHHHHHHHHT--
T ss_pred HHHHHHHHhcCC
Confidence 489999999983
No 80
>PF14838 INTS5_C: Integrator complex subunit 5 C-terminus
Probab=22.77 E-value=41 Score=29.60 Aligned_cols=43 Identities=21% Similarity=0.409 Sum_probs=25.1
Q ss_pred CCHHHHHhhCC-CcccHHHH---HHH-HHHHHhhcCCCCCCCCceeecchh
Q 034230 26 LPSTLREFVGQ-SRISRLGC---FMR-VWSYIKTNNLQDPNNKNVVNCDQK 71 (100)
Q Consensus 26 lS~~La~~lG~-~~~sr~~v---~~~-lW~YIK~~~Lqdp~~k~~I~cDe~ 71 (100)
++|.|+.+.+. +..|-.|| ... ||+|+++|. |..-.++.||+.
T Consensus 618 LPppL~~~~el~~~ltp~Ei~~lL~~cIW~y~kdh~---Psp~~f~~~~~~ 665 (696)
T PF14838_consen 618 LPPPLSYIHELFPYLTPHEIYLLLLSCIWNYMKDHV---PSPALFVFNDET 665 (696)
T ss_pred CCchHHHHHHHHHhcCHHHHHHHHHHHHHHHHhhCC---CCHHHHhcCccc
Confidence 34444444432 34555444 445 999999987 444445666665
No 81
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.35 E-value=1e+02 Score=22.51 Aligned_cols=23 Identities=13% Similarity=0.302 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHhhcCCCCCCCCc
Q 034230 42 LGCFMRVWSYIKTNNLQDPNNKN 64 (100)
Q Consensus 42 ~~v~~~lW~YIK~~~Lqdp~~k~ 64 (100)
.+++..||+|....|+-+|.|++
T Consensus 68 ~~~i~~Il~~l~k~g~~e~~Dk~ 90 (174)
T KOG4068|consen 68 QEFIDEILEELEKKGLAEPTDKR 90 (174)
T ss_pred HHHHHHHHHHHHHccCCcccccC
Confidence 58899999999999999999887
No 82
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=22.24 E-value=1.6e+02 Score=19.64 Aligned_cols=36 Identities=14% Similarity=0.254 Sum_probs=22.8
Q ss_pred ccccccCCHHHHHhhCCCc---ccHHHHHHHH---HHHHhhc
Q 034230 20 LIDLVNLPSTLREFVGQSR---ISRLGCFMRV---WSYIKTN 55 (100)
Q Consensus 20 ~~~~~~lS~~La~~lG~~~---~sr~~v~~~l---W~YIK~~ 55 (100)
|.....--.++..+||... -|+.+|+..| .+||++|
T Consensus 42 f~g~lv~~kEi~~ilG~~~~i~Rt~~Qvv~~l~RRiDYV~~N 83 (99)
T PF13758_consen 42 FGGSLVTEKEIKEILGEGQGITRTREQVVDVLSRRIDYVQQN 83 (99)
T ss_pred cCcccccHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHHH
Confidence 3333334457888898743 3666666655 5698876
No 83
>PF08225 Antimicrobial19: Pseudin antimicrobial peptide; InterPro: IPR013156 Pseudins are a subfamily of the FSAP family (Frog Secreted Active Peptides) extracted from the skin of the paradoxical frog Pseudis paradoxa (Paradoxical frog). The pseudins belong to the class of cationic, amphipathic-helical antimicrobial peptides [].; GO: 0006952 defense response
Probab=22.17 E-value=53 Score=16.12 Aligned_cols=19 Identities=32% Similarity=0.485 Sum_probs=12.7
Q ss_pred hHHhhhcCCCeeccccHHHHHhcc
Q 034230 71 KLRSILMGKSRVELAELPALIKLH 94 (100)
Q Consensus 71 ~Lk~lf~g~~~i~~~el~~ll~~H 94 (100)
.|+++|. .+.|..++++.|
T Consensus 4 tlkkv~q-----glhe~ikli~nh 22 (23)
T PF08225_consen 4 TLKKVFQ-----GLHEVIKLINNH 22 (23)
T ss_pred HHHHHHH-----HHHHHHHHHhcC
Confidence 4667762 366777777776
No 84
>TIGR00424 APS_reduc 5'-adenylylsulfate reductase, thioredoxin-independent. This enzyme, involved in the assimilation of inorganic sulfate, is closely related to the thioredoxin-dependent PAPS reductase of Bacteria (CysH) and Saccharomyces cerevisiae. However, it has its own C-terminal thioredoxin-like domain and is not thioredoxin-dependent. Also, it has a substrate preference for 5'-adenylylsulfate (APS) over 3'-phosphoadenylylsulfate (PAPS) so the pathway does not require an APS kinase (CysC) to convert APS to PAPS. Arabidopsis thaliana appears to have three isozymes, all able to complement E. coli CysH mutants (even in backgrounds lacking thioredoxin or APS kinase) but likely localized to different compartments in Arabidopsis.
Probab=22.17 E-value=50 Score=27.47 Aligned_cols=11 Identities=27% Similarity=1.005 Sum_probs=10.0
Q ss_pred HHHHHhhcCCC
Q 034230 48 VWSYIKTNNLQ 58 (100)
Q Consensus 48 lW~YIK~~~Lq 58 (100)
+|.||++|+|-
T Consensus 268 Vw~Yi~~~~LP 278 (463)
T TIGR00424 268 VWNFLRTMDVP 278 (463)
T ss_pred HHHHHHHcCCC
Confidence 99999999984
No 85
>cd04382 RhoGAP_MgcRacGAP RhoGAP_MgcRacGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in MgcRacGAP proteins. MgcRacGAP plays an important dual role in cytokinesis: i) it is part of centralspindlin-complex, together with the mitotic kinesin MKLP1, which is critical for the structure of the central spindle by promoting microtuble bundling. ii) after phosphorylation by aurora B MgcRacGAP becomes an effective regulator of RhoA and plays an important role in the assembly of the contractile ring and the initiation of cytokinesis. MgcRacGAP-like proteins contain a N-terminal C1-like domain, and a C-terminal RhoGAP domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway
Probab=22.07 E-value=88 Score=22.54 Aligned_cols=72 Identities=14% Similarity=0.149 Sum_probs=45.2
Q ss_pred HHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCce---eecchhHHhhhc-CCC-----eeccccHHHHHhccCCCC
Q 034230 28 STLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNV---VNCDQKLRSILM-GKS-----RVELAELPALIKLHFPKD 98 (100)
Q Consensus 28 ~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~---I~cDe~Lk~lf~-g~~-----~i~~~el~~ll~~Hl~~~ 98 (100)
-+|++|-+.....=+.++....+||.++|+..++==|. ..-=+.|++.|. |.. ......+..+|+..|...
T Consensus 4 ~~~~~~~~~~~~~IP~~l~~ci~~ie~~gl~~EGIFRv~G~~~~i~~l~~~~~~~~~~~~~~~~d~h~vaslLK~fLReL 83 (193)
T cd04382 4 GELADFDPSTSPMIPALIVHCVNEIEARGLTEEGLYRVSGSEREVKALKEKFLRGKTVPNLSKVDIHVICGCLKDFLRSL 83 (193)
T ss_pred ccccccCCCCCCCccHHHHHHHHHHHHcCCCCCCeeecCCcHHHHHHHHHHHHcCCCCcccccCCHHHHHHHHHHHHHhC
Confidence 46778877777777889999999999999986641110 111124455553 211 124456777888777666
Q ss_pred C
Q 034230 99 P 99 (100)
Q Consensus 99 p 99 (100)
|
T Consensus 84 P 84 (193)
T cd04382 84 K 84 (193)
T ss_pred C
Confidence 5
No 86
>COG5577 Spore coat protein [Cell envelope biogenesis, outer membrane]
Probab=21.44 E-value=94 Score=21.95 Aligned_cols=37 Identities=16% Similarity=0.201 Sum_probs=26.4
Q ss_pred CCHHHHHhhCCCcccHHHHHHHHHHHHhhcCCCCCCC
Q 034230 26 LPSTLREFVGQSRISRLGCFMRVWSYIKTNNLQDPNN 62 (100)
Q Consensus 26 lS~~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~ 62 (100)
-+|+|..+|-..-..--+--..||+|...||-.-|.+
T Consensus 85 ~tP~lR~vL~~~l~~~i~~~~~v~~ym~~~g~Y~py~ 121 (145)
T COG5577 85 ATPELRAVLKDQLNQAIEMHKEVSEYMVQKGYYPPYN 121 (145)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCcCCCC
Confidence 3667777765544444456788999999999887764
No 87
>PF10265 DUF2217: Uncharacterized conserved protein (DUF2217); InterPro: IPR019392 This is a family of conserved proteins varying in length from 500-600 residues. Their function is not known.
Probab=20.84 E-value=92 Score=26.50 Aligned_cols=64 Identities=16% Similarity=0.264 Sum_probs=41.2
Q ss_pred cccccCCCCCCCccccc-----cCCHHHH-HhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCceeecchhHHhhhcCCCe
Q 034230 8 KTVIDNPKKLANLIDLV-----NLPSTLR-EFVGQSRISRLGCFMRVWSYIKTNNLQDPNNKNVVNCDQKLRSILMGKSR 81 (100)
Q Consensus 8 ~~~~~~~~~~~~~~~~~-----~lS~~La-~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp~~k~~I~cDe~Lk~lf~g~~~ 81 (100)
|+.+...+.+.||+..| .|||.|| .|||..+ -.+.++.|.|+.=+ .-|+.|| .-++
T Consensus 425 kakr~~l~~~~Gf~ahfY~i~e~isPvlawGflGp~~-----~l~~~c~~Fk~qv~------------~fl~diF-~~~~ 486 (514)
T PF10265_consen 425 KAKRRMLKYPDGFMAHFYSISEHISPVLAWGFLGPDE-----SLRELCHYFKEQVI------------SFLKDIF-DFDK 486 (514)
T ss_pred HHHhhccCCCCchhhhhhhhhccccHHHHhhccCCch-----HHHHHHHHHHHHHH------------HHHHHHH-hcCc
Confidence 55666677777876654 3566666 5667644 34568888887532 4578888 7777
Q ss_pred eccccHHH
Q 034230 82 VELAELPA 89 (100)
Q Consensus 82 i~~~el~~ 89 (100)
+.+..+.+
T Consensus 487 ~ryts~~~ 494 (514)
T PF10265_consen 487 VRYTSVEE 494 (514)
T ss_pred cccccHHH
Confidence 76654433
No 88
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=20.67 E-value=1.9e+02 Score=16.82 Aligned_cols=32 Identities=22% Similarity=0.345 Sum_probs=25.4
Q ss_pred HHHHhhCCCcccHHHHHHHHHHHHhhcCCCCC
Q 034230 29 TLREFVGQSRISRLGCFMRVWSYIKTNNLQDP 60 (100)
Q Consensus 29 ~La~~lG~~~~sr~~v~~~lW~YIK~~~Lqdp 60 (100)
.|..=++...+.-+.+...|-+|+.++.-.||
T Consensus 10 qLr~el~~~RikvS~a~~~l~~y~e~~~~~Dp 41 (57)
T cd00068 10 QLRKELSRERLKVSKAAAELLKYCEQNAENDP 41 (57)
T ss_pred HHHHHHCCchhhHHHHHHHHHHHHHhcCCCCC
Confidence 45555677788889999999999999976665
No 89
>COG0175 CysH 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=20.49 E-value=58 Score=24.65 Aligned_cols=12 Identities=58% Similarity=1.024 Sum_probs=10.4
Q ss_pred HHHHHHhhcCCC
Q 034230 47 RVWSYIKTNNLQ 58 (100)
Q Consensus 47 ~lW~YIK~~~Lq 58 (100)
-||.||..||+-
T Consensus 184 dVw~Yi~~~~lp 195 (261)
T COG0175 184 DVWLYILANNLP 195 (261)
T ss_pred HHHHHHHHhCCC
Confidence 589999999974
Done!