Query gi|254780496|ref|YP_003064909.1| integration host factor subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 114
No_of_seqs 103 out of 2506
Neff 6.4
Searched_HMMs 39220
Date Sun May 29 23:26:30 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780496.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00285 ihfA integration host 100.0 1.3E-27 3.4E-32 190.7 11.7 97 3-99 2-98 (100)
2 PRK10664 transcriptional regul 99.9 2.1E-27 5.3E-32 189.5 11.3 90 5-94 1-90 (90)
3 PRK10753 transcriptional regul 99.9 4.6E-27 1.2E-31 187.4 11.3 90 5-94 1-90 (90)
4 PRK00199 ihfB integration host 99.9 7.5E-27 1.9E-31 186.1 11.4 90 5-94 1-91 (91)
5 COG0776 HimA Bacterial nucleoi 99.9 6.4E-27 1.6E-31 186.5 10.6 93 4-96 1-93 (94)
6 smart00411 BHL bacterial (prok 99.9 1.1E-25 2.9E-30 178.9 11.2 90 5-94 1-90 (90)
7 pfam00216 Bac_DNA_binding Bact 99.9 2E-25 5.2E-30 177.3 11.1 90 5-94 1-90 (90)
8 TIGR00988 hip integration host 99.9 6.7E-25 1.7E-29 174.2 7.2 92 5-96 1-93 (94)
9 cd00591 HU_IHF Integration hos 99.9 7E-24 1.8E-28 167.9 9.7 87 6-92 1-87 (87)
10 TIGR00987 himA integration hos 99.9 1.3E-21 3.4E-26 154.0 8.1 93 4-96 1-93 (96)
11 TIGR01201 HU_rel DNA-binding p 98.3 3.5E-06 8.9E-11 59.4 6.9 83 2-86 30-118 (198)
12 pfam08006 DUF1700 Protein of u 87.1 2.2 5.6E-05 23.9 5.8 49 5-53 1-52 (181)
13 PRK10428 putative stress-respo 73.3 6.1 0.00016 21.1 4.2 29 6-34 35-63 (69)
14 pfam10025 DUF2267 Uncharacteri 69.7 8 0.0002 20.4 4.1 43 5-47 1-44 (125)
15 PRK08402 replication factor A; 69.0 9.5 0.00024 20.0 4.4 32 4-35 3-34 (357)
16 COG1712 Predicted dinucleotide 67.0 3.1 8E-05 22.9 1.6 27 44-70 207-234 (255)
17 COG4709 Predicted membrane pro 66.9 9.3 0.00024 20.0 4.0 49 5-53 1-52 (195)
18 pfam02001 DUF134 Protein of un 57.9 18 0.00046 18.2 4.9 38 13-50 57-94 (100)
19 TIGR02018 his_ut_repres histid 54.6 18 0.00045 18.3 3.6 43 12-61 29-73 (234)
20 TIGR03069 PS_II_S4 photosystem 50.1 8.1 0.00021 20.4 1.3 50 10-59 186-243 (257)
21 TIGR00577 fpg formamidopyrimid 49.2 25 0.00064 17.4 3.9 32 18-50 204-235 (292)
22 PRK02955 small acid-soluble sp 46.6 10 0.00026 19.8 1.3 33 15-54 11-43 (69)
23 KOG0599 consensus 45.6 29 0.00073 17.0 3.8 61 4-65 104-180 (411)
24 TIGR03092 SASP_sspI small, aci 45.2 11 0.00028 19.6 1.3 33 15-54 8-40 (65)
25 TIGR02081 metW methionine bios 43.7 19 0.00047 18.2 2.3 48 25-72 92-142 (205)
26 TIGR02589 cas_Csd2 CRISPR-asso 42.3 27 0.0007 17.2 3.0 45 12-56 207-254 (307)
27 COG2302 Uncharacterized conser 42.1 9.6 0.00025 19.9 0.7 53 11-63 184-244 (257)
28 pfam07798 DUF1640 Protein of u 41.6 33 0.00084 16.7 4.6 33 9-42 6-38 (177)
29 pfam08142 AARP2CN AARP2CN (NUC 39.7 12 0.0003 19.4 0.8 21 39-59 54-74 (81)
30 TIGR00264 TIGR00264 alpha-NAC 38.9 34 0.00087 16.5 3.1 33 9-41 89-121 (125)
31 smart00785 AARP2CN AARP2CN (NU 36.8 14 0.00036 18.9 0.8 21 39-59 56-76 (83)
32 COG3649 CRISPR system related 36.5 40 0.001 16.2 3.1 32 10-41 178-209 (283)
33 pfam08812 YtxC YtxC-like famil 36.1 28 0.00071 17.1 2.2 32 30-61 67-98 (220)
34 TIGR01595 cas_CT1132 CRISPR-as 35.8 41 0.001 16.1 3.7 76 10-92 197-274 (310)
35 PRK11426 hypothetical protein; 35.3 41 0.0011 16.0 4.3 39 8-46 72-110 (132)
36 COG1342 Predicted DNA-binding 33.7 44 0.0011 15.9 4.7 37 14-50 55-91 (99)
37 pfam01958 DUF108 Domain of unk 33.3 27 0.00069 17.2 1.8 28 45-72 57-85 (92)
38 pfam05793 TFIIF_alpha Transcri 31.3 48 0.0012 15.6 3.4 36 1-36 475-511 (528)
39 pfam06831 H2TH Formamidopyrimi 30.1 50 0.0013 15.5 4.1 32 19-51 61-92 (93)
40 PRK13303 L-aspartate dehydroge 30.0 33 0.00085 16.6 1.8 20 51-70 226-245 (265)
41 PRK09492 treR trehalose repres 29.6 52 0.0013 15.5 3.0 27 1-31 1-27 (315)
42 KOG0193 consensus 29.2 28 0.00072 17.1 1.3 50 9-60 492-541 (678)
43 PRK04217 hypothetical protein; 29.2 52 0.0013 15.4 4.8 38 14-51 64-101 (110)
44 TIGR02834 spo_ytxC putative sp 27.9 28 0.00072 17.1 1.2 32 28-59 125-156 (283)
45 TIGR02980 SigBFG RNA polymeras 27.5 56 0.0014 15.2 4.0 28 13-40 201-228 (229)
46 PRK03660 anti-sigma F factor; 26.8 58 0.0015 15.2 7.1 38 8-45 20-57 (146)
47 PRK00414 gmhA phosphoheptose i 25.2 62 0.0016 15.0 3.0 52 1-52 1-53 (192)
48 COG3937 Uncharacterized conser 24.5 64 0.0016 14.9 4.7 35 8-42 27-61 (108)
49 PRK00188 trpD anthranilate pho 24.3 64 0.0016 14.9 3.4 29 5-33 1-29 (339)
50 PRK13304 L-aspartate dehydroge 24.2 46 0.0012 15.7 1.7 19 51-69 224-242 (265)
51 pfam00542 Ribosomal_L12 Riboso 23.9 43 0.0011 16.0 1.5 37 6-42 12-48 (68)
52 pfam10064 consensus 23.8 66 0.0017 14.8 4.6 34 10-43 10-43 (191)
53 COG2522 Predicted transcriptio 23.7 66 0.0017 14.8 2.8 36 7-43 11-46 (119)
54 TIGR00537 hemK_rel_arch methyl 23.6 63 0.0016 14.9 2.3 25 24-48 118-142 (183)
55 PRK10079 putative transcriptio 22.4 70 0.0018 14.6 4.3 39 12-57 39-77 (241)
56 pfam05066 RNA_pol_delta DNA-di 22.3 70 0.0018 14.6 5.0 52 3-58 29-80 (94)
57 PRK07738 flagellar protein Fla 22.3 26 0.00067 17.3 0.1 60 18-84 37-98 (113)
58 pfam04615 Utp14 Utp14 protein. 21.8 71 0.0018 14.6 2.2 30 28-57 597-630 (731)
59 pfam09339 HTH_IclR IclR helix- 20.7 76 0.0019 14.4 3.5 24 11-34 21-44 (52)
60 TIGR01527 arch_NMN_Atrans nico 20.7 29 0.00074 17.0 0.1 38 33-75 16-54 (171)
61 KOG1715 consensus 20.6 73 0.0019 14.5 2.1 35 6-40 131-165 (187)
62 pfam06078 DUF937 Bacterial pro 20.6 76 0.0019 14.4 5.2 33 9-41 11-43 (126)
63 PRK09764 DNA-binding transcrip 20.4 77 0.002 14.4 4.4 40 12-58 33-72 (239)
64 PTZ00095 40S ribosomal protein 20.3 38 0.00097 16.3 0.6 39 17-57 23-61 (169)
No 1
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=99.95 E-value=1.3e-27 Score=190.70 Aligned_cols=97 Identities=34% Similarity=0.614 Sum_probs=93.7
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEE
Q ss_conf 76669999999999719999999999999999999997559960000416999850267643068898889956885377
Q gi|254780496|r 3 KTITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVV 82 (114)
Q Consensus 3 ~~mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~ 82 (114)
.+|||+||++.||+++|+++.+++.+||+|+++|.++|.+|++|.|+|||+|+++.+++|.||||+|||.+.||++++|+
T Consensus 2 m~MtK~eli~~ia~~~g~s~~~a~~~v~~~~~~i~~~L~~g~~V~i~gFGtF~v~~r~~R~grNP~Tge~i~Ip~r~~v~ 81 (100)
T PRK00285 2 MALTKAELAELLFDKVGLSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQLRDKNQRPGRNPKTGEEIPITARRVVT 81 (100)
T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEEEECCCCCCCCCCCCEEEECCCCCEE
T ss_conf 96279999999999869599999999999999999999769928872238999985066145284999889975876578
Q ss_pred ECCCHHHHHHHHHHHCC
Q ss_conf 61698999997311101
Q gi|254780496|r 83 FKASSILKKRIMDDMRG 99 (114)
Q Consensus 83 Fkpsk~Lk~~in~~~~~ 99 (114)
|+||+.||+.||+...-
T Consensus 82 Fkpsk~LK~~Vn~~~~~ 98 (100)
T PRK00285 82 FRAGQKLKSRVENAHPK 98 (100)
T ss_pred EECCHHHHHHHHCCCCC
T ss_conf 71599999998460634
No 2
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=99.95 E-value=2.1e-27 Score=189.54 Aligned_cols=90 Identities=28% Similarity=0.517 Sum_probs=89.4
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114)
Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114)
|||+|||+.||+++|+++.+++.+||+|+++|.++|.+|++|+|+|||+|+++.|++|.||||+|||.|.||++++|+|+
T Consensus 1 M~K~eLi~~ia~~~~ltk~~a~~~v~~~~~~i~~~l~~g~~V~l~gFGtF~v~~r~aR~grNP~Tge~i~Ipa~~v~~Fk 80 (90)
T PRK10664 1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR 80 (90)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEEEECCCCCCCCCCCCEEEECCCCCEEEC
T ss_conf 97899999999870999999999999999999999977993998005899998766725609199988986586547774
Q ss_pred CCHHHHHHHH
Q ss_conf 6989999973
Q gi|254780496|r 85 ASSILKKRIM 94 (114)
Q Consensus 85 psk~Lk~~in 94 (114)
||+.||+.||
T Consensus 81 ~sk~LK~~vN 90 (90)
T PRK10664 81 AGKALKDAVN 90 (90)
T ss_pred CCHHHHHHHC
T ss_conf 7989998539
No 3
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=99.95 E-value=4.6e-27 Score=187.41 Aligned_cols=90 Identities=28% Similarity=0.504 Sum_probs=88.7
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114)
Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114)
|||+|||+.||+++|+++.+++.+|++|+++|.++|.+|++|.|+|||+|+++.|++|.||||+|||.|.||++++|+|+
T Consensus 1 MnK~eLi~~ia~~~~~sk~~~~~~v~~~~~~i~~~L~~g~~V~l~GFGtF~v~~r~aR~grNP~TGe~i~Ipa~~v~~Fk 80 (90)
T PRK10753 1 MNKTQLIDVIADKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFV 80 (90)
T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECEEEEEEEEECCCCCCCCCCCCEEEECCCCCEEEC
T ss_conf 97899999999873989999999999999999999976991998032899998657813508199998987587646772
Q ss_pred CCHHHHHHHH
Q ss_conf 6989999973
Q gi|254780496|r 85 ASSILKKRIM 94 (114)
Q Consensus 85 psk~Lk~~in 94 (114)
||+.||++|.
T Consensus 81 p~k~LK~~vk 90 (90)
T PRK10753 81 SGKALKDAVK 90 (90)
T ss_pred CCHHHHHHHC
T ss_conf 6989998639
No 4
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=99.94 E-value=7.5e-27 Score=186.11 Aligned_cols=90 Identities=30% Similarity=0.549 Sum_probs=88.4
Q ss_pred CCHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEE
Q ss_conf 669999999999719-9999999999999999999975599600004169998502676430688988899568853776
Q gi|254780496|r 5 ITRSDLVKSISKEFG-LSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVF 83 (114)
Q Consensus 5 mtK~eli~~ia~~~g-~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~F 83 (114)
|||+|||+.|+++++ +++.+++.+|++|+++|.++|.+|++|+|+|||+|+++.+++|.||||+|||.+.||++++|+|
T Consensus 1 M~K~eli~~ia~~~~~l~~~~~~~iv~~~~~~i~~~l~~g~~V~i~gFGtF~~~~r~~R~gRNP~Tge~i~I~~k~~v~F 80 (91)
T PRK00199 1 MTKSELIERLATRQPHLPAKDVEDAVKTMLEEMADALAQGDRIEIRGFGSFSLHYRPPRVGRNPKTGEKVEVEGKYVPHF 80 (91)
T ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf 97899999999876998999999999999999999997699299634589999985672450849999899659765787
Q ss_pred CCCHHHHHHHH
Q ss_conf 16989999973
Q gi|254780496|r 84 KASSILKKRIM 94 (114)
Q Consensus 84 kpsk~Lk~~in 94 (114)
+||+.|++.||
T Consensus 81 kpsk~Lk~~lN 91 (91)
T PRK00199 81 KPGKELRDRVN 91 (91)
T ss_pred CCCHHHHHHHC
T ss_conf 78989998519
No 5
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=99.94 E-value=6.4e-27 Score=186.53 Aligned_cols=93 Identities=34% Similarity=0.644 Sum_probs=91.1
Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEE
Q ss_conf 66699999999997199999999999999999999975599600004169998502676430688988899568853776
Q gi|254780496|r 4 TITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVF 83 (114)
Q Consensus 4 ~mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~F 83 (114)
+|||+||++.|+++.++++.+++.+|+++++.|.++|.+|++|+|+|||+|+++.|++|.||||+|||.|.||++++|+|
T Consensus 1 ~mtKseli~~ia~~~~l~k~~a~~~v~~~~~~i~~aL~~G~~V~l~gFG~F~v~~R~aR~GRNPkTGe~i~I~a~~vp~F 80 (94)
T COG0776 1 TMTKSELIDAIAEKAGLSKKDAEEAVDAFLEEITEALAKGERVELRGFGTFEVRERAARTGRNPKTGEEIKIPAKKVPKF 80 (94)
T ss_pred CCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCC
T ss_conf 98789999999997098799999999999999999997699489830046676202787787999998686357523355
Q ss_pred CCCHHHHHHHHHH
Q ss_conf 1698999997311
Q gi|254780496|r 84 KASSILKKRIMDD 96 (114)
Q Consensus 84 kpsk~Lk~~in~~ 96 (114)
+|||.||++||..
T Consensus 81 k~gK~LK~~vn~~ 93 (94)
T COG0776 81 KPGKALKDAVNGA 93 (94)
T ss_pred CCCHHHHHHHHCC
T ss_conf 8768999988334
No 6
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=99.93 E-value=1.1e-25 Score=178.92 Aligned_cols=90 Identities=32% Similarity=0.605 Sum_probs=89.2
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114)
Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114)
|||+||+..||+++|+++.+++.+|+.|+++|.++|.+|++|+|+|||+|+++.+++|.||||+|||.++||++++|+|+
T Consensus 1 MtK~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~~~~v~i~~fG~F~~~~~~~R~grNP~Tge~i~i~~~~~v~Fk 80 (90)
T smart00411 1 MTKSELIDAIAEKAGLSKKDAKAAVDAFLEIITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKFK 80 (90)
T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECEEEEEEEEEECCEEEECCCCCCEEEECCCCCEEEC
T ss_conf 97899999999986969999999999999999999967993993404999999706613478799988997587657980
Q ss_pred CCHHHHHHHH
Q ss_conf 6989999973
Q gi|254780496|r 85 ASSILKKRIM 94 (114)
Q Consensus 85 psk~Lk~~in 94 (114)
||+.|++.||
T Consensus 81 ~sk~lk~~iN 90 (90)
T smart00411 81 PGKALKDAVN 90 (90)
T ss_pred CCHHHHHHHC
T ss_conf 6989998639
No 7
>pfam00216 Bac_DNA_binding Bacterial DNA-binding protein.
Probab=99.93 E-value=2e-25 Score=177.33 Aligned_cols=90 Identities=34% Similarity=0.656 Sum_probs=89.1
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEEC
Q ss_conf 66999999999971999999999999999999999755996000041699985026764306889888995688537761
Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFK 84 (114)
Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fk 84 (114)
|||+||++.||+++|+++++++.+|++|+++|.++|.+|++|+|+|||+|+++.+++|.||||+|||.++||++++|+|+
T Consensus 1 mtK~~li~~ia~~~~ls~~~~~~~v~~~~~~i~~~L~~~~~v~i~gfG~F~~~~~~~r~~rNP~Tge~i~i~~~~~v~Fk 80 (90)
T pfam00216 1 MTKKELIKAIAEKTGLSKKDAEAIVDAFLDVITEALKKGEKVELRGFGTFEVRERKARTGRNPKTGEEIKIPAKKVVKFK 80 (90)
T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEEEECCEEEECCCCCCEEEECCCCCEEEE
T ss_conf 97899999999864969999999999999999999967994985545899999605654288699978997597658980
Q ss_pred CCHHHHHHHH
Q ss_conf 6989999973
Q gi|254780496|r 85 ASSILKKRIM 94 (114)
Q Consensus 85 psk~Lk~~in 94 (114)
||+.|++.||
T Consensus 81 ~sk~lk~~iN 90 (90)
T pfam00216 81 PGKELKEAVN 90 (90)
T ss_pred CCHHHHHHHC
T ss_conf 6989998639
No 8
>TIGR00988 hip integration host factor, beta subunit; InterPro: IPR005685 Integration host factor (IHF) is a heterodimeric protein consisting of alpha (IPR005684 from INTERPRO) and beta subunits. IHF binds the minor groove of DNA in a sequence-specific manner to induce a large bend. This bending stabilises distinct DNA conformations that are required during several bacterial processes, such as recombination, transposition, replication and transcription .; GO: 0003677 DNA binding, 0005694 chromosome.
Probab=99.91 E-value=6.7e-25 Score=174.16 Aligned_cols=92 Identities=32% Similarity=0.553 Sum_probs=88.8
Q ss_pred CCHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEE
Q ss_conf 66999999999971-99999999999999999999975599600004169998502676430688988899568853776
Q gi|254780496|r 5 ITRSDLVKSISKEF-GLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVF 83 (114)
Q Consensus 5 mtK~eli~~ia~~~-g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~F 83 (114)
|+|+|||+.|+... .++.++|+.+|+.+++.|.++|+.|++|+|+|||+|+++.|.+|+||||+||+.+.+..|++|+|
T Consensus 1 M~kSELI~~i~~~~~~l~~k~VE~~v~~~lE~~~~alA~GdRiE~RGFGsFSl~~R~~R~GRNPkTG~~V~ld~K~VP~F 80 (94)
T TIGR00988 1 MTKSELIERIATEQSHLFAKDVEKAVKTMLEEMIEALARGDRIEIRGFGSFSLHYRAPRTGRNPKTGESVALDGKYVPHF 80 (94)
T ss_pred CCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCEEECCCCCCCCCCCCCCCEEEECCCCCCCC
T ss_conf 93378889987407875533389999999999999860798467601442000005788898899887665478042840
Q ss_pred CCCHHHHHHHHHH
Q ss_conf 1698999997311
Q gi|254780496|r 84 KASSILKKRIMDD 96 (114)
Q Consensus 84 kpsk~Lk~~in~~ 96 (114)
||||.|+|++|..
T Consensus 81 K~GK~LRDR~N~~ 93 (94)
T TIGR00988 81 KPGKELRDRLNEG 93 (94)
T ss_pred CCCCCHHCCCCCC
T ss_conf 4863011004788
No 9
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=99.90 E-value=7e-24 Score=167.90 Aligned_cols=87 Identities=36% Similarity=0.673 Sum_probs=85.2
Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEECC
Q ss_conf 69999999999719999999999999999999997559960000416999850267643068898889956885377616
Q gi|254780496|r 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFKA 85 (114)
Q Consensus 6 tK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fkp 85 (114)
||+|||..||+++|+++.+++.+|++|+++|.++|.+|++|+|+|||+|+++.+++|.||||+|||.++||++++|+|+|
T Consensus 1 TK~dLi~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~~~~V~i~~fG~F~~~~~~~r~grNP~Tge~i~i~~~~~v~Fk~ 80 (87)
T cd00591 1 TKSELIEAIAEKTGLSKKDAEAAVDAFLDVITEALAKGEKVELPGFGTFEVRERAARTGRNPKTGEEIKIPAKKVVKFKP 80 (87)
T ss_pred CHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEEEECCEEEECCCCCCEEEECCCCCEEECC
T ss_conf 98999999999869699999999999999999999779969963607999998256244888999889975976679750
Q ss_pred CHHHHHH
Q ss_conf 9899999
Q gi|254780496|r 86 SSILKKR 92 (114)
Q Consensus 86 sk~Lk~~ 92 (114)
|+.||++
T Consensus 81 sk~lK~~ 87 (87)
T cd00591 81 GKALKDA 87 (87)
T ss_pred CHHHCCC
T ss_conf 8787179
No 10
>TIGR00987 himA integration host factor, alpha subunit; InterPro: IPR005684 Integration host factor (IHF) is a heterodimeric protein consisting of alpha and beta (IPR005685 from INTERPRO) subunits. IHF binds the minor groove of DNA in a sequence-specific manner to induce a large bend. This bending stabilises distinct DNA conformations that are required during several bacterial processes, such as recombination, transposition, replication and transcription .; GO: 0003677 DNA binding, 0005694 chromosome.
Probab=99.86 E-value=1.3e-21 Score=153.95 Aligned_cols=93 Identities=35% Similarity=0.673 Sum_probs=90.6
Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEE
Q ss_conf 66699999999997199999999999999999999975599600004169998502676430688988899568853776
Q gi|254780496|r 4 TITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVF 83 (114)
Q Consensus 4 ~mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~F 83 (114)
++||.||.+.|-+..||++.++...|+.|++.|.++|..|+.|+|.|||+|.++.+..|.||||+|||.|-|.|+.+|.|
T Consensus 1 ~LT~~~~sE~~f~~~GLs~~ea~~LVE~~~~~~~~AL~~gE~VKlS~FG~F~~RDK~~R~GRNPKTGEeiPI~~RRV~~F 80 (96)
T TIGR00987 1 ALTKAELSEALFRELGLSKREAKELVELFLEEIRDALERGEQVKLSGFGNFDLRDKTQRPGRNPKTGEEIPITARRVVTF 80 (96)
T ss_pred CCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
T ss_conf 95055788999998288855778999999999999986388465303655210107778765579988788677413532
Q ss_pred CCCHHHHHHHHHH
Q ss_conf 1698999997311
Q gi|254780496|r 84 KASSILKKRIMDD 96 (114)
Q Consensus 84 kpsk~Lk~~in~~ 96 (114)
+||..||++|.+.
T Consensus 81 RP~~~lK~RV~~~ 93 (96)
T TIGR00987 81 RPGQKLKDRVEER 93 (96)
T ss_pred CCCHHHHHHHHHH
T ss_conf 7645688998751
No 11
>TIGR01201 HU_rel DNA-binding protein, putative; InterPro: IPR005902 This family of proteins is related to, but longer than, DNA-binding protein HU. It contains a distinctive domain architecture when compared to HU and related histone-like DNA-binding. Members include, so far, a protein from Bacteroides fragilis and ten from Porphyromonas gingivalis (Bacteroides gingivalis). Both species are oral pathogens. .
Probab=98.25 E-value=3.5e-06 Score=59.41 Aligned_cols=83 Identities=17% Similarity=0.294 Sum_probs=68.2
Q ss_pred CCCC-CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCC---EEEE--
Q ss_conf 8766-699999999997199999999999999999999975599600004169998502676430688988---8995--
Q gi|254780496|r 2 SKTI-TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQ---EVKI-- 75 (114)
Q Consensus 2 ~~~m-tK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge---~i~i-- 75 (114)
...| +-.+||+.||+.+++|..||.-+|+.+..+|...|.+|..|.|-++|+|.+... +|- .-+-..| .+..
T Consensus 30 ~~~~~~~~~~~~~ia~~S~~s~GDV~~i~~~L~~~l~~eL~~G~~v~lg~~G~FR~~~~-~kg-~~ve~~eGGt~v~~~~ 107 (198)
T TIGR01201 30 SGDVVDFEEIAELIAEESSLSPGDVKGILDRLAYVLRRELASGKTVRLGEIGTFRLSAT-AKG-SGVEEAEGGTEVSAEQ 107 (198)
T ss_pred CCCEECHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEECCCEEEEEEEE-ECC-CCCCCCCCCCCCCHHH
T ss_conf 77625378999998676468856899999999999999713798698747325899861-032-4364667782116765
Q ss_pred CCCCEEEECCC
Q ss_conf 68853776169
Q gi|254780496|r 76 DPRRVVVFKAS 86 (114)
Q Consensus 76 p~k~~v~Fkps 86 (114)
=.+..|.|.|.
T Consensus 108 ~~~~rv~F~p~ 118 (198)
T TIGR01201 108 VKKARVLFTPE 118 (198)
T ss_pred HCCCCEEECCC
T ss_conf 21222154223
No 12
>pfam08006 DUF1700 Protein of unknown function (DUF1700). This family contains many hypothetical bacterial proteins and two putative membrane proteins.
Probab=87.12 E-value=2.2 Score=23.89 Aligned_cols=49 Identities=6% Similarity=0.245 Sum_probs=41.0
Q ss_pred CCHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHCCCC--CCCCCCEE
Q ss_conf 66999999999971-999999999999999999999755996--00004169
Q gi|254780496|r 5 ITRSDLVKSISKEF-GLSRKDSTRFVTTLFNEICDSAVRGEA--IKISSFAT 53 (114)
Q Consensus 5 mtK~eli~~ia~~~-g~s~~~~~~~v~~~~~~i~~~L~~g~~--V~l~gfGt 53 (114)
|||.|..+++.... +++.+|.+++++..-+.+.+.+.+|.. =-+..+|+
T Consensus 1 M~k~efL~~L~~~L~~lp~~e~~~il~~y~e~f~~~~~~G~se~ei~~~LG~ 52 (181)
T pfam08006 1 MNKIEFLNELESSLKKLPEEERKDILYDYEEHFYEGEEEGKSEEEIIKELGN 52 (181)
T ss_pred CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 9899999999998865999999999999999999876689999999988299
No 13
>PRK10428 putative stress-response protein; Provisional
Probab=73.30 E-value=6.1 Score=21.12 Aligned_cols=29 Identities=21% Similarity=0.386 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf 69999999999719999999999999999
Q gi|254780496|r 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFN 34 (114)
Q Consensus 6 tK~eli~~ia~~~g~s~~~~~~~v~~~~~ 34 (114)
.+.+|+-.|.+++|.++.+|++-|+.|.+
T Consensus 35 ~re~L~GkiQerYG~sKeeae~ev~~w~~ 63 (69)
T PRK10428 35 KRDQLVGKIQERYGYQKDQAEKEVVDWET 63 (69)
T ss_pred CHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 69999879999978379999999999986
No 14
>pfam10025 DUF2267 Uncharacterized conserved protein (DUF2267). This domain, found in various hypothetical bacterial proteins, has no known function.
Probab=69.66 E-value=8 Score=20.43 Aligned_cols=43 Identities=21% Similarity=0.413 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 6699999999997199-999999999999999999975599600
Q gi|254780496|r 5 ITRSDLVKSISKEFGL-SRKDSTRFVTTLFNEICDSAVRGEAIK 47 (114)
Q Consensus 5 mtK~eli~~ia~~~g~-s~~~~~~~v~~~~~~i~~~L~~g~~V~ 47 (114)
|+-.+++..+..+.|+ +..++..++.+.+..+.+-|..++...
T Consensus 1 m~~~~fl~~V~~~~~~~~r~~A~~a~raVL~tL~~Rl~~~ea~~ 44 (125)
T pfam10025 1 MDYDEFLKEVQERAGLDSREEAERAARAVLETLADRLSGEEAAD 44 (125)
T ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf 98999999999880899889999999999999998878878999
No 15
>PRK08402 replication factor A; Reviewed
Probab=69.00 E-value=9.5 Score=19.96 Aligned_cols=32 Identities=25% Similarity=0.561 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Q ss_conf 66699999999997199999999999999999
Q gi|254780496|r 4 TITRSDLVKSISKEFGLSRKDSTRFVTTLFNE 35 (114)
Q Consensus 4 ~mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~ 35 (114)
-+||.+|++.|.+++|+|.+++++-++.+.+.
T Consensus 3 vltkEeIiekI~~e~G~S~eEIeekI~ei~ee 34 (357)
T PRK08402 3 VLTKEEIIERIERETGLSREEIEEEIREIMEE 34 (357)
T ss_pred CCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 12299999999987288899999999999986
No 16
>COG1712 Predicted dinucleotide-utilizing enzyme [General function prediction only]
Probab=66.97 E-value=3.1 Score=22.91 Aligned_cols=27 Identities=22% Similarity=0.452 Sum_probs=20.6
Q ss_pred CCCCCCC-CEEEEEEECCCCCCCCCCCC
Q ss_conf 9600004-16999850267643068898
Q gi|254780496|r 44 EAIKISS-FATFHVKQKGSRVGRNLQTN 70 (114)
Q Consensus 44 ~~V~l~g-fGtF~~~~~~~R~~rNP~Tg 70 (114)
..|+++| ||+|+++.+.-...-||+|.
T Consensus 207 Hev~v~g~fG~~~~~~eN~p~~~NPKTS 234 (255)
T COG1712 207 HEVEVRGAFGTFEIKIENVPLPENPKTS 234 (255)
T ss_pred EEEEEEECCCEEEEEEECCCCCCCCCHH
T ss_conf 5999983244289998366278896058
No 17
>COG4709 Predicted membrane protein [Function unknown]
Probab=66.89 E-value=9.3 Score=20.02 Aligned_cols=49 Identities=12% Similarity=0.313 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHCC--CCCCCCCCEE
Q ss_conf 66999999999971-9999999999999999999997559--9600004169
Q gi|254780496|r 5 ITRSDLVKSISKEF-GLSRKDSTRFVTTLFNEICDSAVRG--EAIKISSFAT 53 (114)
Q Consensus 5 mtK~eli~~ia~~~-g~s~~~~~~~v~~~~~~i~~~L~~g--~~V~l~gfGt 53 (114)
|||.|.+.++-... ++++++-.++++.+.+.-.++-.+| +.=-+..+|.
T Consensus 1 Mtk~efL~eL~~yL~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~ 52 (195)
T COG4709 1 MTKTEFLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGD 52 (195)
T ss_pred CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 9788999999999871998889999999999998650348988999988199
No 18
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=57.91 E-value=18 Score=18.24 Aligned_cols=38 Identities=32% Similarity=0.462 Sum_probs=33.1
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 99997199999999999999999999975599600004
Q gi|254780496|r 13 SISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISS 50 (114)
Q Consensus 13 ~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~g 50 (114)
.-|++-|+|+..+..+++.-=.-|.++|.+|..+.|.|
T Consensus 57 eaA~~MgVSR~Tf~ril~~ARkKvA~aLv~Gk~l~IeG 94 (100)
T pfam02001 57 EAAKLMGISRRTVWRLLTSARKKIADALVEGRIIIIKG 94 (100)
T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf 99988497699999999999999999986798499967
No 19
>TIGR02018 his_ut_repres histidine utilization repressor; InterPro: IPR010248 This entry represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0006547 histidine metabolic process, 0045892 negative regulation of transcription DNA-dependent.
Probab=54.64 E-value=18 Score=18.32 Aligned_cols=43 Identities=23% Similarity=0.328 Sum_probs=33.9
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEE--ECCC
Q ss_conf 9999971999999999999999999999755996000041699985--0267
Q gi|254780496|r 12 KSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVK--QKGS 61 (114)
Q Consensus 12 ~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~--~~~~ 61 (114)
.+|....|+|+-.|.+.+-.|. .+|--+..+|.|||--. .+..
T Consensus 29 ~EL~~~~G~SRMTvnrALreLt-------~~G~l~R~qg~GTFVA~ae~k~~ 73 (234)
T TIGR02018 29 NELVAQFGVSRMTVNRALRELT-------DAGLLERRQGVGTFVARAEPKAQ 73 (234)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH-------HCCCEEEECCCEEEECCCCCCCC
T ss_conf 9999774872335789999887-------56818812785004417776531
No 20
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=50.11 E-value=8.1 Score=20.37 Aligned_cols=50 Identities=14% Similarity=0.192 Sum_probs=37.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHH--------HHHHHHHHHCCCCCCCCCCEEEEEEEC
Q ss_conf 99999997199999999999999--------999999975599600004169998502
Q gi|254780496|r 10 LVKSISKEFGLSRKDSTRFVTTL--------FNEICDSAVRGEAIKISSFATFHVKQK 59 (114)
Q Consensus 10 li~~ia~~~g~s~~~~~~~v~~~--------~~~i~~~L~~g~~V~l~gfGtF~~~~~ 59 (114)
|=..+|.-.++|+..+...+++= .+--...+..|..|.++|+|.|.+...
T Consensus 186 LDavvs~~~~~SRska~~lI~~g~V~vN~~~v~~~s~~v~~gDiiSvRG~GR~~i~ei 243 (257)
T TIGR03069 186 IDAIASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGKGRLEILEL 243 (257)
T ss_pred HHHHHHHHHCCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEEECCCEEEEEEC
T ss_conf 8999998866579999999884968989999057875668999999906717999975
No 21
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR000191 Formamidopyrimidine-DNA glycosylase (3.2.2.23 from EC) (Fapy-DNA glycosylase) (gene fpg) is a bacterial enzyme involved in DNA repair and which excise oxidized purine bases to release 2,6-diamino-4-hydroxy-5N-methylformamido- pyrimidine (Fapy) and 7,8-dihydro-8-oxoguanine (8-OxoG) residues. In addition to its glycosylase activity, FPG can also nick DNA at apurinic/apyrimidinic sites (AP sites). FPG is a monomeric protein of about 32 Kd which binds and require zinc for its activity. The C-terminal region is the zinc binding site in the enzyme where four conserved and essential cysteines are located ..
Probab=49.23 E-value=25 Score=17.38 Aligned_cols=32 Identities=13% Similarity=0.162 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 199999999999999999999975599600004
Q gi|254780496|r 18 FGLSRKDSTRFVTTLFNEICDSAVRGEAIKISS 50 (114)
Q Consensus 18 ~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~g 50 (114)
..|+.++++.+.+++.++|.+|++.|+. +|+.
T Consensus 204 ~~L~~~~~~~L~~~i~~vL~~Aie~GGt-t~~~ 235 (292)
T TIGR00577 204 NQLSKEECELLHKAIKEVLRKAIEAGGT-TIRD 235 (292)
T ss_pred HCCCHHHHHHHHHHHHHHHHHHHHCCCC-CCCC
T ss_conf 0158889999999999999999864897-0002
No 22
>PRK02955 small acid-soluble spore protein SspI; Provisional
Probab=46.56 E-value=10 Score=19.81 Aligned_cols=33 Identities=18% Similarity=0.277 Sum_probs=24.6
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEE
Q ss_conf 9971999999999999999999999755996000041699
Q gi|254780496|r 15 SKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATF 54 (114)
Q Consensus 15 a~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF 54 (114)
+.-.|-++.+++ +.|.+++..|++=.|||+|++
T Consensus 11 ~nv~g~s~~elk-------~tI~daI~sgEEk~LPGLGVl 43 (69)
T PRK02955 11 ANVSGNSQEQLE-------ETIVDAIQSGEEKMLPGLGVL 43 (69)
T ss_pred HHHCCCCHHHHH-------HHHHHHHHCCCHHCCCCCHHH
T ss_conf 983189999999-------999999864630137740678
No 23
>KOG0599 consensus
Probab=45.56 E-value=29 Score=17.03 Aligned_cols=61 Identities=25% Similarity=0.350 Sum_probs=44.9
Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH----------------HHCCCCCCCCCCEEEEEEECCCCCCC
Q ss_conf 666999999999971999999999999999999999----------------75599600004169998502676430
Q gi|254780496|r 4 TITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDS----------------AVRGEAIKISSFATFHVKQKGSRVGR 65 (114)
Q Consensus 4 ~mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~----------------L~~g~~V~l~gfGtF~~~~~~~R~~r 65 (114)
-|-|-||-..+.....+|.+++..++..+|+.+.-- |..+..|.|.+|| |....-++..-|
T Consensus 104 l~prGELFDyLts~VtlSEK~tR~iMrqlfegVeylHa~~IVHRDLKpENILlddn~~i~isDFG-Fa~~l~~GekLr 180 (411)
T KOG0599 104 LMPRGELFDYLTSKVTLSEKETRRIMRQLFEGVEYLHARNIVHRDLKPENILLDDNMNIKISDFG-FACQLEPGEKLR 180 (411)
T ss_pred HCCCCHHHHHHHHHEEECHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHEEECCCCCEEEECCC-EEECCCCCHHHH
T ss_conf 33451288775431441178899999999999999987434422368645643156635873254-021268741688
No 24
>TIGR03092 SASP_sspI small, acid-soluble spore protein I. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspI. The gene in Bacillus subtilis previously was designated ysfA.
Probab=45.17 E-value=11 Score=19.58 Aligned_cols=33 Identities=12% Similarity=0.200 Sum_probs=24.2
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEE
Q ss_conf 9971999999999999999999999755996000041699
Q gi|254780496|r 15 SKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATF 54 (114)
Q Consensus 15 a~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF 54 (114)
+.-.|-++.+++ +.|.+++..|++=.|||+|++
T Consensus 8 ~nv~~~s~~elk-------~tI~daI~sgEEk~LPGLGVl 40 (65)
T TIGR03092 8 ANISNNTKEQLE-------ATIVDAIQSGEEKMLPGLGVL 40 (65)
T ss_pred HHCCCCCHHHHH-------HHHHHHHHCCCHHCCCCCHHH
T ss_conf 980189999999-------999999864730037740678
No 25
>TIGR02081 metW methionine biosynthesis protein MetW; InterPro: IPR010743 This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, Gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In Pseudomonas putida, as in Gram-positive bacteria and certain fungi, the second and third steps are a direct sulphydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells . .
Probab=43.70 E-value=19 Score=18.17 Aligned_cols=48 Identities=13% Similarity=0.071 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHHH--CCCCCCCCCCEEEEEEECCCCCCCCC-CCCCE
Q ss_conf 99999999999999975--59960000416999850267643068-89888
Q gi|254780496|r 25 STRFVTTLFNEICDSAV--RGEAIKISSFATFHVKQKGSRVGRNL-QTNQE 72 (114)
Q Consensus 25 ~~~~v~~~~~~i~~~L~--~g~~V~l~gfGtF~~~~~~~R~~rNP-~Tge~ 72 (114)
+-..++.--.+|-|-|. +..-|.+||||-|.++-.=.+.||=| -|++-
T Consensus 92 TLQa~~Np~~iL~EmLRvg~~aIVSFPNFGyW~~R~~i~~~GRMPkVt~~l 142 (205)
T TIGR02081 92 TLQATRNPEEILDEMLRVGRRAIVSFPNFGYWRVRWSILTGGRMPKVTDEL 142 (205)
T ss_pred HHHHHHCHHHHHHHHHHHCCEEEEECCCCCCHHCHHHEECCCCCCCCCCCC
T ss_conf 566422568999887767385156058877110103111078588788787
No 26
>TIGR02589 cas_Csd2 CRISPR-associated protein, Csd2 family; InterPro: IPR013418 This entry represents one of two closely related subfamilies that belong to the larger family of CRISPR-associated protein TM1801. Members are the Csd2 proteins of the Dvulg subtype of the CRISPR/cas system. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. A related entry is IPR013419 from INTERPRO, the Csh2 protein of the Hmari CRISPR subtype..
Probab=42.30 E-value=27 Score=17.15 Aligned_cols=45 Identities=13% Similarity=0.208 Sum_probs=31.6
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC---CCCCCCCCCEEEEE
Q ss_conf 9999971999999999999999999999755---99600004169998
Q gi|254780496|r 12 KSISKEFGLSRKDSTRFVTTLFNEICDSAVR---GEAIKISSFATFHV 56 (114)
Q Consensus 12 ~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~---g~~V~l~gfGtF~~ 56 (114)
-.||++||+|.+|++.+-++|+..-..--.. .+.-..+++-.|+=
T Consensus 207 a~lA~~TGFs~eDl~~~~~~L~~lFE~D~SaARP~G~M~~r~v~~F~H 254 (307)
T TIGR02589 207 AQLAEKTGFSDEDLELIKEALVNLFENDRSAARPEGSMSVRKVYVFKH 254 (307)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEEE
T ss_conf 577742488888999999998634005652368688743114888830
No 27
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=42.09 E-value=9.6 Score=19.93 Aligned_cols=53 Identities=21% Similarity=0.340 Sum_probs=37.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHH--------HHHHHHHHHCCCCCCCCCCEEEEEEECCCCC
Q ss_conf 9999997199999999999999--------9999999755996000041699985026764
Q gi|254780496|r 11 VKSISKEFGLSRKDSTRFVTTL--------FNEICDSAVRGEAIKISSFATFHVKQKGSRV 63 (114)
Q Consensus 11 i~~ia~~~g~s~~~~~~~v~~~--------~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~ 63 (114)
=..+|.-.++|+..+...++.= .+--...+..|.-|.++|||.|++......+
T Consensus 184 D~vis~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~GR~~i~~i~g~T 244 (257)
T COG2302 184 DVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGFGRLKILEINGVT 244 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCEECCCCEEEEECCCCEEEEEECCCC
T ss_conf 9999988765599999987737327712991266633224989998404517898625823
No 28
>pfam07798 DUF1640 Protein of unknown function (DUF1640). This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Probab=41.61 E-value=33 Score=16.65 Aligned_cols=33 Identities=27% Similarity=0.385 Sum_probs=28.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999999971999999999999999999999755
Q gi|254780496|r 9 DLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVR 42 (114)
Q Consensus 9 eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~ 42 (114)
.+++.+ +..|++..+++.++.++.+++.+.+..
T Consensus 6 ~~Vk~L-e~~Gft~~QAe~i~~~l~~~l~~~l~~ 38 (177)
T pfam07798 6 ALVQLL-EENGFTEEQAEAIVSALTEVINDSIEN 38 (177)
T ss_pred HHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999-887999999999999999999989999
No 29
>pfam08142 AARP2CN AARP2CN (NUC121) domain. This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU.
Probab=39.73 E-value=12 Score=19.37 Aligned_cols=21 Identities=10% Similarity=0.292 Sum_probs=16.9
Q ss_pred HHHCCCCCCCCCCEEEEEEEC
Q ss_conf 975599600004169998502
Q gi|254780496|r 39 SAVRGEAIKISSFATFHVKQK 59 (114)
Q Consensus 39 ~L~~g~~V~l~gfGtF~~~~~ 59 (114)
.|..+.-|+|+|+|-|.+...
T Consensus 54 ~l~~n~lVHIpG~GDfqi~~I 74 (81)
T pfam08142 54 GLNANQLVHIPGVGDFQIEKI 74 (81)
T ss_pred CCCCCCEEEECCCCCEEEEEE
T ss_conf 889999898688476395475
No 30
>TIGR00264 TIGR00264 alpha-NAC homolog; InterPro: IPR005231 Eukaryotic NAC, an abundant heterodimer composed of two homologous subunits, reversibly binds eukaryotic ribosomes and is located in direct proximity to nascent polypeptides as they emerge from the ribosome . Despite being implicated in diverse cellular functions, its role in vivo is still not completely understood. It is thought that NAC may function as a shield protecting the nascent chain from inappropriate interactions with cytosolic factors, and could regulate further translation of the polypeptide through its interaction with the ribosome. Archaeal NAC is a homodimer which appears to be functionally analogous to the eukaryotic form, associating with ribosomes and contacting the nascent polypeptide chain emerging on the ribosome . It has two domains; the NAC domain, which it shares with eukaryotic NAC, and a C-terminal UBA domain also found on the alpha, but not beta, subunit of eukaryotic NAC. The NAC domain forms a six-stranded beta-barrel structure which shows some similarities to the OB fold. This domain appears to be responsible for dimerisation, nucleic acid binding, and nascent polypeptide binding. The UBA domain is typical of ubiquitin or polyubquitin-binding proteins; its physiological role is unclear but it was suggested that it may compete with the proteosome for ubiquitin, thus inhibiting ubiquitin-mediated protein degradation. .
Probab=38.88 E-value=34 Score=16.55 Aligned_cols=33 Identities=9% Similarity=0.261 Sum_probs=27.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999997199999999999999999999975
Q gi|254780496|r 9 DLVKSISKEFGLSRKDSTRFVTTLFNEICDSAV 41 (114)
Q Consensus 9 eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~ 41 (114)
|=|+.|+.++|.|+++|.++++..--=|+|||-
T Consensus 89 dDieLvm~Q~nvs~E~ArrALeE~gGDlAEAim 121 (125)
T TIGR00264 89 DDIELVMEQANVSKEEARRALEEAGGDLAEAIM 121 (125)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHH
T ss_conf 579999976599988989998631851888987
No 31
>smart00785 AARP2CN AARP2CN (NUC121) domain. This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU PUBMED:15112237.
Probab=36.77 E-value=14 Score=18.91 Aligned_cols=21 Identities=10% Similarity=0.305 Sum_probs=16.6
Q ss_pred HHHCCCCCCCCCCEEEEEEEC
Q ss_conf 975599600004169998502
Q gi|254780496|r 39 SAVRGEAIKISSFATFHVKQK 59 (114)
Q Consensus 39 ~L~~g~~V~l~gfGtF~~~~~ 59 (114)
.|..+..|+|+|+|-|.+...
T Consensus 56 ~l~~n~lVHIpG~GDfqi~~I 76 (83)
T smart00785 56 GLNANQLVHIPGLGDFQISKI 76 (83)
T ss_pred CCCCCCEEEECCCCCEEEEEE
T ss_conf 889999898588476395475
No 32
>COG3649 CRISPR system related protein [Defense mechanisms]
Probab=36.55 E-value=40 Score=16.16 Aligned_cols=32 Identities=9% Similarity=0.233 Sum_probs=24.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999997199999999999999999999975
Q gi|254780496|r 10 LVKSISKEFGLSRKDSTRFVTTLFNEICDSAV 41 (114)
Q Consensus 10 li~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~ 41 (114)
|-...|++||++.++++++.++++-...+.+.
T Consensus 178 IN~~~AekTGft~EDaekike~l~~lfeNd~s 209 (283)
T COG3649 178 INQNSAEKTGFTEEDAEKIKEGLWMLFENDIS 209 (283)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHH
T ss_conf 42324755288677799999999998404400
No 33
>pfam08812 YtxC YtxC-like family. This family includes proteins similar to B. subtilis YtxC an uncharacterized protein.
Probab=36.13 E-value=28 Score=17.10 Aligned_cols=32 Identities=22% Similarity=0.340 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCEEEEEEECCC
Q ss_conf 99999999997559960000416999850267
Q gi|254780496|r 30 TTLFNEICDSAVRGEAIKISSFATFHVKQKGS 61 (114)
Q Consensus 30 ~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~ 61 (114)
+.+.+.|.+.|..+..+.+.||-+|.++.-..
T Consensus 67 ~~I~~~i~~~l~e~~~i~idgFitFRLk~y~~ 98 (220)
T pfam08812 67 NLIIKKILEFLEENNEINIDGFVTFRLKDYLE 98 (220)
T ss_pred HHHHHHHHHHHCCCCEEEECCCEEEEHHHHHH
T ss_conf 99999999997359979460001451299999
No 34
>TIGR01595 cas_CT1132 CRISPR-associated protein, CT1132 family; InterPro: IPR006482 This protein is found in at least five species that contain CRISPR loci being found exclusively next to other cas proteins. Its function is unknown..
Probab=35.81 E-value=41 Score=16.09 Aligned_cols=76 Identities=20% Similarity=0.271 Sum_probs=48.9
Q ss_pred HHHHHHHHCCCC--HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEEECCCH
Q ss_conf 999999971999--999999999999999999755996000041699985026764306889888995688537761698
Q gi|254780496|r 10 LVKSISKEFGLS--RKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFKASS 87 (114)
Q Consensus 10 li~~ia~~~g~s--~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~Tge~i~ip~k~~v~Fkpsk 87 (114)
+-.-+|+++|++ .+|++.+.++|+..+.+....-..=+.|-+=. +|.. +.++|-..|+.-+. -.+.|.-+.
T Consensus 197 ~n~n~A~~tG~~ts~eD~~~~~~aL~~~~~n~~s~ak~eh~PRLL~-~V~Y---KE~~ny~~G~l~~~---~~~~f~~~~ 269 (310)
T TIGR01595 197 INANLAKKTGFSTSEEDLEKFLEALLNGFENDRSAAKNEHNPRLLV-RVVY---KEGVNYIDGELSYL---VKVVFEHES 269 (310)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE-EEEE---ECCCEEECCCEEEE---EEEEEECCH
T ss_conf 5344353148764588899999999987653354300026872577-8887---53721112503234---666540303
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780496|r 88 ILKKR 92 (114)
Q Consensus 88 ~Lk~~ 92 (114)
.|-..
T Consensus 270 ~~~~~ 274 (310)
T TIGR01595 270 ELGRD 274 (310)
T ss_pred HHHHH
T ss_conf 44212
No 35
>PRK11426 hypothetical protein; Provisional
Probab=35.28 E-value=41 Score=16.04 Aligned_cols=39 Identities=10% Similarity=0.322 Sum_probs=34.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 999999999719999999999999999999997559960
Q gi|254780496|r 8 SDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAI 46 (114)
Q Consensus 8 ~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V 46 (114)
.|-|..+|.++|++..++...+..++=.+.+.|.-++.|
T Consensus 72 ~d~v~~lA~q~G~~~~~~~~~LA~~LP~~VD~lTP~G~v 110 (132)
T PRK11426 72 TNAVSDLGQKLGVDTSTASSLLAEQLPKIIDALSPQGEV 110 (132)
T ss_pred CHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 099999999979399999999999837888563989978
No 36
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=33.68 E-value=44 Score=15.88 Aligned_cols=37 Identities=30% Similarity=0.455 Sum_probs=30.3
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 9997199999999999999999999975599600004
Q gi|254780496|r 14 ISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISS 50 (114)
Q Consensus 14 ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~g 50 (114)
-|.+.|+|+...-..+++--.-+..+|.+|.-+.|.|
T Consensus 55 AA~rMgISr~Tfwr~l~sAR~KvA~aLveGkaI~i~G 91 (99)
T COG1342 55 AALRMGISRQTFWRLLTSARKKVADALVEGKAIIIKG 91 (99)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECC
T ss_conf 9998464299999999999999999985587488638
No 37
>pfam01958 DUF108 Domain of unknown function DUF108. This family has no known function. It is found to compose the complete protein in archaebacteria and a single domain in a large C. elegans protein.
Probab=33.34 E-value=27 Score=17.17 Aligned_cols=28 Identities=18% Similarity=0.309 Sum_probs=21.6
Q ss_pred CCCCCC-CEEEEEEECCCCCCCCCCCCCE
Q ss_conf 600004-1699985026764306889888
Q gi|254780496|r 45 AIKISS-FATFHVKQKGSRVGRNLQTNQE 72 (114)
Q Consensus 45 ~V~l~g-fGtF~~~~~~~R~~rNP~Tge~ 72 (114)
+|++.| ||.|.++...--..-||+|+..
T Consensus 57 eI~~~g~~G~~~~~i~n~P~~~NPkTS~l 85 (92)
T pfam01958 57 EIEVEGDFGEFVIRVENVPSPDNPKTSAL 85 (92)
T ss_pred EEEEEECCEEEEEEEECCCCCCCCCHHHH
T ss_conf 99999375899999967638999830888
No 38
>pfam05793 TFIIF_alpha Transcription initiation factor IIF, alpha subunit (TFIIF-alpha). Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II.
Probab=31.34 E-value=48 Score=15.64 Aligned_cols=36 Identities=25% Similarity=0.475 Sum_probs=21.6
Q ss_pred CCCCCCHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHH
Q ss_conf 9876669999999999-71999999999999999999
Q gi|254780496|r 1 MSKTITRSDLVKSISK-EFGLSRKDSTRFVTTLFNEI 36 (114)
Q Consensus 1 m~~~mtK~eli~~ia~-~~g~s~~~~~~~v~~~~~~i 36 (114)
|.+-||-.||+..... ++||+..+.-.+|..++.-|
T Consensus 475 ~rKPmTt~dLl~KFK~kktglsseq~v~~~a~ILKkI 511 (528)
T pfam05793 475 MRKPMTTKELLKKFKAKKTGLSSEEDVNALAQILKRI 511 (528)
T ss_pred HHCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHC
T ss_conf 6289619999998602678888499999999999862
No 39
>pfam06831 H2TH Formamidopyrimidine-DNA glycosylase H2TH domain. Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.
Probab=30.15 E-value=50 Score=15.52 Aligned_cols=32 Identities=22% Similarity=0.335 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 999999999999999999999755996000041
Q gi|254780496|r 19 GLSRKDSTRFVTTLFNEICDSAVRGEAIKISSF 51 (114)
Q Consensus 19 g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gf 51 (114)
.++..+++.+.++.-.++.++++.|+. +|+.|
T Consensus 61 ~Ls~~~~~~L~~~i~~vl~~ai~~gGt-ti~dy 92 (93)
T pfam06831 61 SLSKKECEALHTVIKDVLQKAIEMGGG-GIRTF 92 (93)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCC-CCCCC
T ss_conf 199999999999999999999994999-73018
No 40
>PRK13303 L-aspartate dehydrogenase; Provisional
Probab=30.03 E-value=33 Score=16.63 Aligned_cols=20 Identities=25% Similarity=0.456 Sum_probs=7.6
Q ss_pred CEEEEEEECCCCCCCCCCCC
Q ss_conf 16999850267643068898
Q gi|254780496|r 51 FATFHVKQKGSRVGRNLQTN 70 (114)
Q Consensus 51 fGtF~~~~~~~R~~rNP~Tg 70 (114)
||.|..+...--..-||+|+
T Consensus 226 ~g~~~~~i~n~p~~~NPkTS 245 (265)
T PRK13303 226 FGEFEFEMSGKPLPDNPKTS 245 (265)
T ss_pred CEEEEEEEECCCCCCCCCHH
T ss_conf 57899999677489998308
No 41
>PRK09492 treR trehalose repressor; Provisional
Probab=29.60 E-value=52 Score=15.46 Aligned_cols=27 Identities=22% Similarity=0.433 Sum_probs=19.9
Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9876669999999999719999999999999
Q gi|254780496|r 1 MSKTITRSDLVKSISKEFGLSRKDSTRFVTT 31 (114)
Q Consensus 1 m~~~mtK~eli~~ia~~~g~s~~~~~~~v~~ 31 (114)
|+++||-+| ||+..|+|...|..+++.
T Consensus 1 M~kkvTikD----IA~~aGVS~aTVSrvLn~ 27 (315)
T PRK09492 1 MQNKLTIKD----IARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CCCCCCHHH----HHHHHCCCHHHHHHHHCC
T ss_conf 989887999----999989799999999789
No 42
>KOG0193 consensus
Probab=29.23 E-value=28 Score=17.05 Aligned_cols=50 Identities=16% Similarity=0.198 Sum_probs=32.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECC
Q ss_conf 9999999971999999999999999999999755996000041699985026
Q gi|254780496|r 9 DLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKG 60 (114)
Q Consensus 9 eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~ 60 (114)
||.++++. |+..-.++.|++-=+..=-=-|.++.+|.|-+||-|.++.+-
T Consensus 492 dIAqQiaq--GM~YLHAK~IIHrDLKSnNIFl~~~~kVkIgDFGLatvk~~w 541 (678)
T KOG0193 492 DIAQQIAQ--GMDYLHAKNIIHRDLKSNNIFLHEDLKVKIGDFGLATVKTRW 541 (678)
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHCCCCCEEECCCCCEEEECCCCEEEEEEE
T ss_conf 99999987--650565531443110226468705884898313204542122
No 43
>PRK04217 hypothetical protein; Provisional
Probab=29.19 E-value=52 Score=15.42 Aligned_cols=38 Identities=24% Similarity=0.295 Sum_probs=31.4
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 99971999999999999999999999755996000041
Q gi|254780496|r 14 ISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSF 51 (114)
Q Consensus 14 ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gf 51 (114)
-|.+.|+|+.....+++.--.-|.++|.+|..+.|..=
T Consensus 64 aA~~M~VSR~Tf~ril~~AR~KvA~aLv~Gkal~I~~~ 101 (110)
T PRK04217 64 AGKRMGVSRGTVWRALTSARKKVAQMLVEGRELIILPQ 101 (110)
T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECC
T ss_conf 99884976999999999999999999867974899748
No 44
>TIGR02834 spo_ytxC putative sporulation protein YtxC; InterPro: IPR014199 This uncharacterised protein is one of a number of proteins conserved in all known endospore-forming Firmicutes (low-GC Gram-positive bacteria), including Carboxydothermus hydrogenoformans, and it is not found in non-endospore forming species. It is uniformly distributed in the mother cell cytoplasm in Bacillus subtilis ..
Probab=27.94 E-value=28 Score=17.06 Aligned_cols=32 Identities=25% Similarity=0.396 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEC
Q ss_conf 99999999999975599600004169998502
Q gi|254780496|r 28 FVTTLFNEICDSAVRGEAIKISSFATFHVKQK 59 (114)
Q Consensus 28 ~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~ 59 (114)
--..+.+.+.+.|..+..+.+.||=||.++.-
T Consensus 125 r~~~I~~~~~~~l~e~~~i~~~gFvtFRLk~y 156 (283)
T TIGR02834 125 RKNEILDEINEFLEENDEINIEGFVTFRLKPY 156 (283)
T ss_pred HHHHHHHHHHHHCCCCCEEEECCCHHHCCHHH
T ss_conf 89999999997436788786324210000678
No 45
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=27.54 E-value=56 Score=15.24 Aligned_cols=28 Identities=14% Similarity=0.405 Sum_probs=16.1
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999719999999999999999999997
Q gi|254780496|r 13 SISKEFGLSRKDSTRFVTTLFNEICDSA 40 (114)
Q Consensus 13 ~ia~~~g~s~~~~~~~v~~~~~~i~~~L 40 (114)
+||+..|+|+-+|..+..-.+.-|.+.|
T Consensus 201 eiA~~lGiSQMhVSRl~~~~L~~LR~~l 228 (229)
T TIGR02980 201 EIAERLGISQMHVSRLLRRALKRLREQL 228 (229)
T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 9997818436788999999999999860
No 46
>PRK03660 anti-sigma F factor; Provisional
Probab=26.78 E-value=58 Score=15.15 Aligned_cols=38 Identities=11% Similarity=0.194 Sum_probs=33.1
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999999971999999999999999999999755996
Q gi|254780496|r 8 SDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEA 45 (114)
Q Consensus 8 ~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~ 45 (114)
+..+..++.+.|++..++..+.=++-+.+.+++..+..
T Consensus 20 R~~v~~~a~~~g~~~~~~~di~lAV~EA~tNaI~H~y~ 57 (146)
T PRK03660 20 RVTVAAFAAQLDPTLEELTEIKTAVSEAVTNAIIHGYE 57 (146)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 99999999973999999999999999999999986036
No 47
>PRK00414 gmhA phosphoheptose isomerase; Reviewed
Probab=25.15 E-value=62 Score=14.97 Aligned_cols=52 Identities=13% Similarity=0.115 Sum_probs=32.3
Q ss_pred CCCCCCHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCE
Q ss_conf 98766699999999997199-99999999999999999997559960000416
Q gi|254780496|r 1 MSKTITRSDLVKSISKEFGL-SRKDSTRFVTTLFNEICDSAVRGEAIKISSFA 52 (114)
Q Consensus 1 m~~~mtK~eli~~ia~~~g~-s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfG 52 (114)
|.+..-+..|-+.++-...+ +.+.--..++...+.|.+++.+|++|.+-|=|
T Consensus 1 m~~~~I~~~~~~~~~~~~~~~~~~~~~~~I~~aa~~i~~~~~~g~kI~~cGNG 53 (192)
T PRK00414 1 MYQDLIRNELNEAAETLANFLKDDANIHAIQRAAVLIADSFKAGGKVLSCGNG 53 (192)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf 92799999999999999999715644999999999999999879979999685
No 48
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=24.47 E-value=64 Score=14.89 Aligned_cols=35 Identities=23% Similarity=0.369 Sum_probs=29.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999971999999999999999999999755
Q gi|254780496|r 8 SDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVR 42 (114)
Q Consensus 8 ~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~ 42 (114)
++|+..+.++-.++..++.++|+.++..+.++-..
T Consensus 27 ~klvDelVkkGeln~eEak~~vddl~~q~k~~~~e 61 (108)
T COG3937 27 QKLVDELVKKGELNAEEAKRFVDDLLRQAKEAQGE 61 (108)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999827878999999999999998987602
No 49
>PRK00188 trpD anthranilate phosphoribosyltransferase; Provisional
Probab=24.32 E-value=64 Score=14.87 Aligned_cols=29 Identities=14% Similarity=0.346 Sum_probs=16.7
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf 66999999999971999999999999999
Q gi|254780496|r 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLF 33 (114)
Q Consensus 5 mtK~eli~~ia~~~g~s~~~~~~~v~~~~ 33 (114)
|+=+++++++...-.|+++++..+++.++
T Consensus 1 M~~~~~i~k~~~g~~Lt~eEa~~~~~~i~ 29 (339)
T PRK00188 1 MTMKELLNKLLEGEDLSEEEAEELMDQIM 29 (339)
T ss_pred CCHHHHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf 98799999997699979999999999998
No 50
>PRK13304 L-aspartate dehydrogenase; Reviewed
Probab=24.18 E-value=46 Score=15.75 Aligned_cols=19 Identities=26% Similarity=0.389 Sum_probs=6.3
Q ss_pred CEEEEEEECCCCCCCCCCC
Q ss_conf 1699985026764306889
Q gi|254780496|r 51 FATFHVKQKGSRVGRNLQT 69 (114)
Q Consensus 51 fGtF~~~~~~~R~~rNP~T 69 (114)
||.|..+...--.--||+|
T Consensus 224 ~g~~~~~i~n~p~~~NPkT 242 (265)
T PRK13304 224 FGTFKTRVENVPCPDNPKT 242 (265)
T ss_pred CEEEEEEEECCCCCCCCCH
T ss_conf 5169999966608899840
No 51
>pfam00542 Ribosomal_L12 Ribosomal protein L7/L12 C-terminal domain.
Probab=23.89 E-value=43 Score=15.96 Aligned_cols=37 Identities=16% Similarity=0.243 Sum_probs=30.6
Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 6999999999971999999999999999999999755
Q gi|254780496|r 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVR 42 (114)
Q Consensus 6 tK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~ 42 (114)
+|-.+|+.|-+-+|++-.++..+++..=..|.+.+..
T Consensus 12 ~Ki~vIK~VR~itglgLkeAK~lVe~~P~~ike~v~k 48 (68)
T pfam00542 12 KKIAVIKVVREITGLGLKEAKDLVEGAPKVIKEGVSK 48 (68)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHCCCCH
T ss_conf 2449999999976998899999987288999839999
No 52
>pfam10064 consensus
Probab=23.76 E-value=66 Score=14.81 Aligned_cols=34 Identities=18% Similarity=0.323 Sum_probs=28.7
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999999719999999999999999999997559
Q gi|254780496|r 10 LVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRG 43 (114)
Q Consensus 10 li~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g 43 (114)
=+..+|.++|++..+++..+.+.+-.|...|.+.
T Consensus 10 ~i~~lA~qlG~~~~q~~~av~aalP~llggl~~n 43 (191)
T pfam10064 10 PIQQIAQQLGLDEEQVTAAVEAALPALLGGLKRN 43 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 0999999959899999999999999999999872
No 53
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=23.68 E-value=66 Score=14.80 Aligned_cols=36 Identities=19% Similarity=0.220 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999999999719999999999999999999997559
Q gi|254780496|r 7 RSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRG 43 (114)
Q Consensus 7 K~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g 43 (114)
|+.|++.+.++ |+|+.++.+.+..--..++..|...
T Consensus 11 Ra~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~k 46 (119)
T COG2522 11 RALLAKELIEE-GLSQYRIAKLLGLTQAAVSQYLSGK 46 (119)
T ss_pred HHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHCCC
T ss_conf 99999999995-8869999999688899999997367
No 54
>TIGR00537 hemK_rel_arch methylase, putative; InterPro: IPR004557 These proteins exhibit homology to the Saccharomyces cerevisiae (yeast) ORF YDR140w (FYV9). No known function has been described for this yeast ORF though the null mutant is viable and exhibits K1 killer toxin hypersensitivity. Members of this entry are weakly related to the yeast ORF YNL063w which is a putative S-adenosyl-methionine-dependent methyltransferase . Members of this entry are found in archaeal, bacterial and eukaryotic lineages.; GO: 0008168 methyltransferase activity.
Probab=23.63 E-value=63 Score=14.94 Aligned_cols=25 Identities=12% Similarity=0.414 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 9999999999999999755996000
Q gi|254780496|r 24 DSTRFVTTLFNEICDSAVRGEAIKI 48 (114)
Q Consensus 24 ~~~~~v~~~~~~i~~~L~~g~~V~l 48 (114)
+=.++++-|++.+-+.|+.|++|.|
T Consensus 118 dGr~vidrFldelp~~lk~gGrv~l 142 (183)
T TIGR00537 118 DGRKVIDRFLDELPEYLKEGGRVQL 142 (183)
T ss_pred CCHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf 3057888887656888705998999
No 55
>PRK10079 putative transcriptional regulator; Provisional
Probab=22.37 E-value=70 Score=14.64 Aligned_cols=39 Identities=15% Similarity=0.278 Sum_probs=30.6
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEE
Q ss_conf 9999971999999999999999999999755996000041699985
Q gi|254780496|r 12 KSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVK 57 (114)
Q Consensus 12 ~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~ 57 (114)
..|++..|+|+..+.+.++.|. .+|--...+|-|||-..
T Consensus 39 ~eLa~~y~VSR~TVR~Al~~L~-------~eGli~r~~G~GtfV~~ 77 (241)
T PRK10079 39 QQLAARFEVNRHTLRRAIDQLV-------ERGWVQRRQGVGVLVLM 77 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH-------HCCCEEEECCCCEEEEC
T ss_conf 9999997988999999999999-------77987997696259935
No 56
>pfam05066 RNA_pol_delta DNA-directed RNA polymerase delta subunit. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich carboxyl-terminal region.
Probab=22.34 E-value=70 Score=14.63 Aligned_cols=52 Identities=17% Similarity=0.278 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEE
Q ss_conf 76669999999999719999999999999999999997559960000416999850
Q gi|254780496|r 3 KTITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQ 58 (114)
Q Consensus 3 ~~mtK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~ 58 (114)
+.|+=.||+..|++..|++..++...+..|..-| --++++.--|=+.|-++.
T Consensus 29 ~~m~F~dL~~ev~~~~g~s~ee~~~~iaqfYTdl----n~DgRFi~lGen~WgLR~ 80 (94)
T pfam05066 29 KPMTFDDLVNEIQKLLGISDEEIRERLAQFYTDL----NIDGRFISLGENRWGLRS 80 (94)
T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH----HCCCCEEECCCCCCCCCC
T ss_conf 9413999999999995989889999999999998----514520463688414532
No 57
>PRK07738 flagellar protein FlaG; Provisional
Probab=22.31 E-value=26 Score=17.26 Aligned_cols=60 Identities=17% Similarity=0.228 Sum_probs=40.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC-CCCEEEEEEECCCCCCCCCCCCCEE-EECCCCEEEEC
Q ss_conf 1999999999999999999999755996000-0416999850267643068898889-95688537761
Q gi|254780496|r 18 FGLSRKDSTRFVTTLFNEICDSAVRGEAIKI-SSFATFHVKQKGSRVGRNLQTNQEV-KIDPRRVVVFK 84 (114)
Q Consensus 18 ~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l-~gfGtF~~~~~~~R~~rNP~Tge~i-~ip~k~~v~Fk 84 (114)
..+++.+++++++.+-+.+.. +..+=++.+ ..+|.+.++.. +..|||.| .||+...+.|-
T Consensus 37 ~evskeeLeeaV~kLN~~l~~-~~~~l~F~~~e~~~~~~VkVv------D~~T~eVIReIPpEe~Ld~~ 98 (113)
T PRK07738 37 TEVSKEDLEETVDGMNELLEP-SQTHLKFELHEKLNEYYVKVV------DNRTNEVVREIPPKKLLDMY 98 (113)
T ss_pred CCCCHHHHHHHHHHHHHHHHH-CCCCEEEEEECCCCCEEEEEE------ECCCCHHHHHCCCHHHHHHH
T ss_conf 666999999999999999972-277538998256684899999------78863788978809999999
No 58
>pfam04615 Utp14 Utp14 protein. This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome.
Probab=21.80 E-value=71 Score=14.62 Aligned_cols=30 Identities=7% Similarity=0.130 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHH----HCCCCCCCCCCEEEEEE
Q ss_conf 9999999999997----55996000041699985
Q gi|254780496|r 28 FVTTLFNEICDSA----VRGEAIKISSFATFHVK 57 (114)
Q Consensus 28 ~v~~~~~~i~~~L----~~g~~V~l~gfGtF~~~ 57 (114)
+|..|...=.+.+ .......|||||.|.=.
T Consensus 597 Vv~eF~~EK~~~~e~e~pke~d~tLPGWGsW~G~ 630 (731)
T pfam04615 597 VVADFEKEKREVIEEEDPKEIDLTLPGWGSWAGA 630 (731)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf 7999999899998740663224688887655677
No 59
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=20.73 E-value=76 Score=14.43 Aligned_cols=24 Identities=25% Similarity=0.538 Sum_probs=19.8
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf 999999719999999999999999
Q gi|254780496|r 11 VKSISKEFGLSRKDSTRFVTTLFN 34 (114)
Q Consensus 11 i~~ia~~~g~s~~~~~~~v~~~~~ 34 (114)
+..||+.+|+++..+-+++..+.+
T Consensus 21 l~eia~~~gl~kstv~RlL~tL~~ 44 (52)
T pfam09339 21 LTEIARRTGLPKSTAHRLLQTLVE 44 (52)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 999999989199999999999998
No 60
>TIGR01527 arch_NMN_Atrans nicotinamide-nucleotide adenylyltransferase; InterPro: IPR006418 This family of archaeal proteins exhibits NAD salvage biosynthesis enzyme nicotinamide-nucleotide adenylyltransferase (2.7.7.1 from EC) activity. In some cases, the enzyme was tested and found also to have the activity of nicotinate-nucleotide adenylyltransferase (2.7.7.18 from EC), an enzyme of NAD de novo biosynthesis, although with a higher Km. In some archaeal species, a number of proteins which are uncharacterised with respect to activity, are also present.; GO: 0000309 nicotinamide-nucleotide adenylyltransferase activity, 0009435 NAD biosynthetic process, 0005737 cytoplasm.
Probab=20.72 E-value=29 Score=17.00 Aligned_cols=38 Identities=16% Similarity=0.116 Sum_probs=23.8
Q ss_pred HHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCC-CCEEEE
Q ss_conf 9999999755996000041699985026764306889-888995
Q gi|254780496|r 33 FNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNLQT-NQEVKI 75 (114)
Q Consensus 33 ~~~i~~~L~~g~~V~l~gfGtF~~~~~~~R~~rNP~T-ge~i~i 75 (114)
.++|...|.+=.++ |=|.|+ -..+++.+||.| ||.|..
T Consensus 16 ~~Vik~~l~~VDEL-iiGiGS----Aq~SHt~~NPFTAGERv~M 54 (171)
T TIGR01527 16 LEVIKKILEEVDEL-IIGIGS----AQESHTLENPFTAGERVLM 54 (171)
T ss_pred HHHHHHHHHHCCEE-EEEEEC----CCCCCCCCCCCCCCHHHHH
T ss_conf 79999887354777-987404----8862022289761307899
No 61
>KOG1715 consensus
Probab=20.62 E-value=73 Score=14.54 Aligned_cols=35 Identities=14% Similarity=0.278 Sum_probs=17.5
Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 69999999999719999999999999999999997
Q gi|254780496|r 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSA 40 (114)
Q Consensus 6 tK~eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L 40 (114)
+|--+|+.|-.-+|++-+++.++|+.+=.++.+.+
T Consensus 131 ~KIkVIKEVR~~tgL~LkeAKklVE~aP~ilKegv 165 (187)
T KOG1715 131 SKIKVIKEVRALTGLGLKEAKKLVEKAPKILKEGV 165 (187)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHCCC
T ss_conf 21368999987624457999999996509987678
No 62
>pfam06078 DUF937 Bacterial protein of unknown function (DUF937). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=20.59 E-value=76 Score=14.41 Aligned_cols=33 Identities=12% Similarity=0.233 Sum_probs=21.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999997199999999999999999999975
Q gi|254780496|r 9 DLVKSISKEFGLSRKDSTRFVTTLFNEICDSAV 41 (114)
Q Consensus 9 eli~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~ 41 (114)
..+..++...|.+...+...+...+-.+...+.
T Consensus 11 ~~~~~la~~lG~~~~~~~~~~~~~lp~llggl~ 43 (126)
T pfam06078 11 PLISQLAAQLGLGGAQAEGGLGALLPALLGGLG 43 (126)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 999999998299999999999999899999873
No 63
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=20.38 E-value=77 Score=14.39 Aligned_cols=40 Identities=20% Similarity=0.280 Sum_probs=29.8
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEE
Q ss_conf 99999719999999999999999999997559960000416999850
Q gi|254780496|r 12 KSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQ 58 (114)
Q Consensus 12 ~~ia~~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~~ 58 (114)
..|++..|+|...+.+.++.|. .+|--...+|-|||-...
T Consensus 33 ~eLa~~~~VSR~TvR~Al~~L~-------~eGli~r~~G~GTfV~~~ 72 (239)
T PRK09764 33 SALQTEFGVSRVTVRQALRQLV-------EQQILESIQGSGTYVKEE 72 (239)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH-------HCCCEEEECCCEEEECCC
T ss_conf 9999997979999999999999-------789999986877898887
No 64
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=20.35 E-value=38 Score=16.28 Aligned_cols=39 Identities=8% Similarity=-0.009 Sum_probs=32.5
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEE
Q ss_conf 71999999999999999999999755996000041699985
Q gi|254780496|r 17 EFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVK 57 (114)
Q Consensus 17 ~~g~s~~~~~~~v~~~~~~i~~~L~~g~~V~l~gfGtF~~~ 57 (114)
+.|.|.+|+.. +.|+..+++.|...+++++|.|-.|-..
T Consensus 23 ~~g~TVkDV~~--~~fi~a~A~~LKk~gKi~~P~W~d~VKT 61 (169)
T PTZ00095 23 RKNATLKDVSP--WRFIKAFAQHFKLEGKIFVPKCTEIVKT 61 (169)
T ss_pred CCCCEEECCCH--HHHHHHHHHHHHHCCCCCCCCHHHHHCC
T ss_conf 48971016899--9999999999987599789722666302
Done!