Query psy15374
Match_columns 205
No_of_seqs 177 out of 268
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 19:14:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15374.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15374hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2841|consensus 100.0 1E-54 2.3E-59 376.4 11.7 142 63-204 50-196 (254)
2 TIGR00597 rad10 DNA repair pro 100.0 1.4E-54 3E-59 339.9 10.4 107 69-176 1-112 (112)
3 PF03834 Rad10: Binding domain 100.0 1.9E-37 4.1E-42 224.7 4.4 69 69-137 1-69 (69)
4 COG5241 RAD10 Nucleotide excis 100.0 1.2E-35 2.5E-40 250.7 1.0 129 66-197 31-164 (224)
5 KOG2841|consensus 99.3 3.3E-13 7.2E-18 118.0 -1.5 57 1-61 155-211 (254)
6 COG5241 RAD10 Nucleotide excis 98.8 6E-10 1.3E-14 95.0 0.4 115 64-179 83-220 (224)
7 PRK13766 Hef nuclease; Provisi 96.9 0.005 1.1E-07 61.0 9.8 115 64-183 558-691 (773)
8 PF07279 DUF1442: Protein of u 80.8 0.75 1.6E-05 40.4 1.1 135 2-170 3-152 (218)
9 TIGR00596 rad1 DNA repair prot 71.1 15 0.00033 37.9 7.5 113 67-184 585-729 (814)
10 PF15162 DUF4580: Domain of un 67.1 34 0.00074 28.9 7.5 121 66-192 4-137 (162)
11 PF02700 PurS: Phosphoribosylf 47.7 64 0.0014 23.8 5.5 50 108-157 3-64 (80)
12 TIGR03603 cyclo_dehy_ocin bact 45.9 10 0.00023 34.5 1.2 89 77-168 83-187 (318)
13 PF00899 ThiF: ThiF family; I 43.4 32 0.00069 26.6 3.5 36 133-168 91-126 (135)
14 TIGR02356 adenyl_thiF thiazole 37.3 56 0.0012 27.4 4.3 35 134-168 111-145 (202)
15 cd01492 Aos1_SUMO Ubiquitin ac 35.3 62 0.0013 27.2 4.2 34 134-167 110-143 (197)
16 cd01485 E1-1_like Ubiquitin ac 34.6 66 0.0014 27.0 4.3 34 134-167 113-146 (198)
17 PF05626 DUF790: Protein of un 34.5 44 0.00096 31.7 3.5 37 97-134 302-338 (379)
18 TIGR00036 dapB dihydrodipicoli 32.5 1.3E+02 0.0029 26.3 6.0 38 137-175 71-111 (266)
19 PTZ00399 cysteinyl-tRNA-synthe 31.9 62 0.0013 32.6 4.2 96 98-204 61-164 (651)
20 TIGR02355 moeB molybdopterin s 31.6 74 0.0016 27.7 4.2 35 134-168 114-148 (240)
21 PF02732 ERCC4: ERCC4 domain; 31.1 1.3E+02 0.0028 22.7 5.1 34 145-178 110-143 (143)
22 cd00757 ThiF_MoeB_HesA_family 30.6 75 0.0016 27.0 4.0 36 134-169 111-146 (228)
23 PRK00048 dihydrodipicolinate r 30.1 1.5E+02 0.0032 25.9 5.8 42 134-176 60-104 (257)
24 COG1948 MUS81 ERCC4-type nucle 28.3 2.7E+02 0.0058 25.2 7.2 112 67-183 26-158 (254)
25 TIGR01557 myb_SHAQKYF myb-like 27.9 50 0.0011 22.9 2.0 29 164-192 4-35 (57)
26 PF03930 Flp_N: Recombinase Fl 26.6 1.2E+02 0.0027 22.9 4.0 32 113-144 35-66 (82)
27 cd01491 Ube1_repeat1 Ubiquitin 26.6 94 0.002 28.1 4.1 33 135-167 106-138 (286)
28 PRK08328 hypothetical protein; 26.3 1E+02 0.0023 26.4 4.2 37 133-169 117-153 (231)
29 PRK08762 molybdopterin biosynt 25.5 1E+02 0.0022 28.4 4.2 100 67-169 135-260 (376)
30 PRK05690 molybdopterin biosynt 24.1 1.3E+02 0.0028 26.1 4.4 34 134-167 122-155 (245)
31 PTZ00170 D-ribulose-5-phosphat 22.9 1.6E+02 0.0034 25.4 4.7 66 110-175 66-134 (228)
32 PF00532 Peripla_BP_1: Peripla 22.2 1.5E+02 0.0032 25.8 4.4 43 139-181 9-55 (279)
33 COG3727 Vsr DNA G:T-mismatch r 21.8 71 0.0015 26.6 2.1 59 97-166 48-115 (150)
34 cd01483 E1_enzyme_family Super 21.6 1.8E+02 0.0039 22.4 4.4 35 133-167 88-122 (143)
35 PF14412 AHH: A nuclease famil 21.3 1.6E+02 0.0035 22.0 3.9 47 103-154 44-101 (109)
36 PF00249 Myb_DNA-binding: Myb- 21.0 95 0.0021 19.9 2.3 27 165-191 3-29 (48)
37 cd00291 SirA_YedF_YeeD SirA, Y 20.7 2.5E+02 0.0054 18.8 4.5 40 124-164 16-55 (69)
No 1
>KOG2841|consensus
Probab=100.00 E-value=1e-54 Score=376.35 Aligned_cols=142 Identities=57% Similarity=0.952 Sum_probs=136.3
Q ss_pred CCCCCCCeEEeCCcccCCcccccccccceeecCCCCcceeecCceeEEEEeecccccChhHHHHHHHhhcccceE-----
Q psy15374 63 GASKSSNAILVNPRQKGNPLLKHIGKVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADRIKALGKLYKL----- 137 (205)
Q Consensus 63 ~~~~~~~~I~Vs~~QkGNPlL~~i~~vpwe~~d~i~~Dy~ig~~~~vLFLSLkyH~L~P~YI~~Ri~~L~~~y~l----- 137 (205)
++..+++.|+||++|||||||+|||||+|+|+|+|.|||++|+++||||||||||++|||||++||++|+++|.+
T Consensus 50 ~~~~~~~~Ilvn~rQkGNplLk~vrnv~w~f~ddi~PDf~lg~~~cvLyLSl~yH~l~pdYi~~Ri~~l~k~yk~~VLl~ 129 (254)
T KOG2841|consen 50 PVTVPGGHILVNPRQKGNPLLKHVRNVKWEFGDDIIPDFVLGRGCCVLYLSLKYHKLHPDYIYRRIRKLGKNYKLRVLLV 129 (254)
T ss_pred CCCCCCceEEeccccccChHHHHHhcCCeEecCCCCcceEecCceEEEEeehHhhhcCcHHHHHHHHHhcccccceEEEE
Confidence 445789999999999999999999999999998899999999999999999999999999999999999999863
Q ss_pred EEcCCChHHHHHHHHHHHHhcCcEEEeecChHHHHHHHHHHHhhhCCCcchhccccCCCcccccccC
Q psy15374 138 QVDSKDPHHALKYLTRVCLLCDLTLMLAWSPEEAGEMIETYKVFENKPPDLIMEKQDVDPHSKTWNF 204 (205)
Q Consensus 138 ~VDv~d~~~~L~eL~~~c~~~~~TLilawS~eEaa~Yie~~K~~e~k~~d~i~~~~~~d~~s~~~~~ 204 (205)
+||++|++++|+||+++|+.++|||+||||.||||+|||+||.||++|+|+||++.+.||++++..|
T Consensus 130 ~vd~~e~~~~l~el~k~~~l~~~Tl~lA~s~EeaaryIE~~k~~ek~p~dli~~~~~~d~ls~~~~~ 196 (254)
T KOG2841|consen 130 HVDMEEPYKPLLELTKTCDLNDVTLVLAWSMEEAARYIETYKEYEKKPIDLIMERKDRDLLSSLLGF 196 (254)
T ss_pred EecCcchHHHHHHHHHHHHhhceeeeeeccHHHHHHHHHHHHHhhcCCchhhhhcccccHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999987654
No 2
>TIGR00597 rad10 DNA repair protein rad10. All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.4e-54 Score=339.91 Aligned_cols=107 Identities=64% Similarity=1.166 Sum_probs=104.1
Q ss_pred CeEEeCCcccCCcccccccccceeecCCCCcceeecCceeEEEEeecccccChhHHHHHHHhhcccceE-----EEcCCC
Q psy15374 69 NAILVNPRQKGNPLLKHIGKVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADRIKALGKLYKL-----QVDSKD 143 (205)
Q Consensus 69 ~~I~Vs~~QkGNPlL~~i~~vpwe~~d~i~~Dy~ig~~~~vLFLSLkyH~L~P~YI~~Ri~~L~~~y~l-----~VDv~d 143 (205)
++|+||++|||||+|++||||||||+| |+|||++|+++||||||||||+||||||++||++|+++|.+ +||++|
T Consensus 1 ~~ilvs~~QkgNPlL~~i~nv~wey~d-i~~Dy~~g~~~~vLFLSLkYH~L~peYi~~Ri~~L~~~~~lrvLL~~VDv~~ 79 (112)
T TIGR00597 1 NSILVNPRQKGNPLLKHVRNVPWEYGD-VIPDYVLGQGTCALFLSLRYHNLHPDYIHRRLQSLGKNFNLRILLVQVDVKN 79 (112)
T ss_pred CcEEeCccccCChHHHHHhcCCeEecC-cCCCEEEcCccEEEEEEhhhhccCHHHHHHHHHHhccccceeEEEEEEeCCc
Confidence 579999999999999999999999986 99999999999999999999999999999999999999864 999999
Q ss_pred hHHHHHHHHHHHHhcCcEEEeecChHHHHHHHH
Q psy15374 144 PHHALKYLTRVCLLCDLTLMLAWSPEEAGEMIE 176 (205)
Q Consensus 144 ~~~~L~eL~~~c~~~~~TLilawS~eEaa~Yie 176 (205)
++++|+||+++|+.+|||||||||+||||||||
T Consensus 80 ~~~~L~eL~k~~~~~~~TLilaws~eEaa~YlE 112 (112)
T TIGR00597 80 PQQALKELAKMCILNDCTLILAWSFEEAARYLE 112 (112)
T ss_pred hHHHHHHHHHHHHHcCcEEEEECCHHHHHHhhC
Confidence 999999999999999999999999999999997
No 3
>PF03834 Rad10: Binding domain of DNA repair protein Ercc1 (rad10/Swi10); InterPro: IPR004579 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. In yeast, Rad10 works as a heterodimer with Rad1, and is involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts or cross-linking agents. The complex forms an endonuclease which specifically degrades single-stranded DNA. Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA inter-strand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex [].; GO: 0003684 damaged DNA binding, 0004519 endonuclease activity, 0006281 DNA repair, 0005634 nucleus; PDB: 2JNW_A 2JPD_A 2A1I_A.
Probab=100.00 E-value=1.9e-37 Score=224.65 Aligned_cols=69 Identities=74% Similarity=1.325 Sum_probs=57.5
Q ss_pred CeEEeCCcccCCcccccccccceeecCCCCcceeecCceeEEEEeecccccChhHHHHHHHhhcccceE
Q psy15374 69 NAILVNPRQKGNPLLKHIGKVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADRIKALGKLYKL 137 (205)
Q Consensus 69 ~~I~Vs~~QkGNPlL~~i~~vpwe~~d~i~~Dy~ig~~~~vLFLSLkyH~L~P~YI~~Ri~~L~~~y~l 137 (205)
++|+||++|||||||++|+||||||+++|+|||++|+++||||||||||+|||+||++||++|+++|.+
T Consensus 1 ~~I~vn~~QkGNplL~~i~nv~we~~~~i~~Dy~vg~~~~vLFLSLkYH~L~P~YI~~Ri~~L~~~~~~ 69 (69)
T PF03834_consen 1 NSILVNPRQKGNPLLKHIRNVPWEYDSDIVPDYVVGSTTCVLFLSLKYHRLHPEYIHERIKKLGKNYNL 69 (69)
T ss_dssp SSEEE-GGGTT-CHHHH--SS-EEE----SSSEEEETTEEEEEEEHHHHHHSTCHHHHHHHHHTTSSS-
T ss_pred CcEEECchhcCChHHHHHhcCCeEecCCCCCCEEECCeEEEEEEeeeeecCCHHHHHHHHHHhhhhcCC
Confidence 579999999999999999999999955599999999999999999999999999999999999999864
No 4
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.2e-35 Score=250.69 Aligned_cols=129 Identities=33% Similarity=0.437 Sum_probs=123.0
Q ss_pred CCCCeEEeCCcccCCcccccccccceeecCCCCcceeecCceeEEEEeecccccChhHHHHHHHhhcccceE-----EEc
Q psy15374 66 KSSNAILVNPRQKGNPLLKHIGKVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADRIKALGKLYKL-----QVD 140 (205)
Q Consensus 66 ~~~~~I~Vs~~QkGNPlL~~i~~vpwe~~d~i~~Dy~ig~~~~vLFLSLkyH~L~P~YI~~Ri~~L~~~y~l-----~VD 140 (205)
+....|.|||+|||||+|.+.+|++|+|++-|+|||++|+..|-||||||||.+||+||+.||.+| |.|.. +||
T Consensus 31 s~s~~I~vsplQkgnp~l~~~~N~~w~y~~~i~Pd~~~~s~~~~lflslrfhs~~Peyi~~riSkl-KsYk~r~LL~hvd 109 (224)
T COG5241 31 SQSLEIDVSPLQKGNPQLSRRINSNWVYNAFIKPDEWTDSKATDLFLSLRFHSTRPEYIVLRISKL-KSYKERPLLNHVD 109 (224)
T ss_pred CeeeEEecChhhcCCCcccccccCcceeccccCcchhhcchHHHHHHHHhhhcCCCceEEEeeecc-ccccccceeeeec
Confidence 366799999999999999999999999998899999999999999999999999999999999999 67752 999
Q ss_pred CCChHHHHHHHHHHHHhcCcEEEeecChHHHHHHHHHHHhhhCCCcchhccccCCCc
Q psy15374 141 SKDPHHALKYLTRVCLLCDLTLMLAWSPEEAGEMIETYKVFENKPPDLIMEKQDVDP 197 (205)
Q Consensus 141 v~d~~~~L~eL~~~c~~~~~TLilawS~eEaa~Yie~~K~~e~k~~d~i~~~~~~d~ 197 (205)
++|++.+++||-.....+ ||+|+||.|||+||++||+.+++.++++||++...||
T Consensus 110 ~~N~~asIqElv~Tt~in--ti~l~~svee~sry~~t~~~~~~~s~~iir~~~s~d~ 164 (224)
T COG5241 110 STNWRASIQELVSTTGIN--TIYLDYSVEERSRYFLTLTYHKLYSDYIIRRMQSLDR 164 (224)
T ss_pred cccHHHHHHHHHHhcccc--eeehhhhhhHHHHHHHHhHHHhhcCHHHHHhcCCCcc
Confidence 999999999999998877 9999999999999999999999999999999999998
No 5
>KOG2841|consensus
Probab=99.27 E-value=3.3e-13 Score=118.04 Aligned_cols=57 Identities=44% Similarity=0.559 Sum_probs=54.3
Q ss_pred CcccCchhhhhhhhhhhhccCCCCCcccccCCCCCCccccccCCCCccCCCCCCCCCCCCc
Q psy15374 1 MLAWSPEEAGEMIETYKVFENKPPDLIMEKQDVDPHSKTWNFDPVPAAQNSATSESVQPSR 61 (205)
Q Consensus 1 ilaWS~eEaarylEtyK~~E~kp~d~i~e~~~~~~~~~~~~~lt~~~~~n~~~~~t~~~~~ 61 (205)
+||||.||||||||+||.||+||+|+||++.+.|+++++..|||.+|.+|| |++..+
T Consensus 155 ~lA~s~EeaaryIE~~k~~ek~p~dli~~~~~~d~ls~~~~~Lt~i~~VnK----tda~~L 211 (254)
T KOG2841|consen 155 VLAWSMEEAARYIETYKEYEKKPIDLIMERKDRDLLSSLLGFLTTIPGVNK----TDAQLL 211 (254)
T ss_pred eeeccHHHHHHHHHHHHHhhcCCchhhhhcccccHHHHHHHHHHhCCCCCc----ccHHHH
Confidence 589999999999999999999999999999999999999999999999999 777654
No 6
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=98.84 E-value=6e-10 Score=95.04 Aligned_cols=115 Identities=26% Similarity=0.533 Sum_probs=99.5
Q ss_pred CCCCCCeEEeCCcc---cCCccccccccccee-----e-----cCCCCcceeecCceeEEEEeecccccChhHHHHHHHh
Q psy15374 64 ASKSSNAILVNPRQ---KGNPLLKHIGKVPWE-----Y-----DDSIIPDYVMGRTTCALFLSIKYHALKPDYIADRIKA 130 (205)
Q Consensus 64 ~~~~~~~I~Vs~~Q---kGNPlL~~i~~vpwe-----~-----~d~i~~Dy~ig~~~~vLFLSLkyH~L~P~YI~~Ri~~ 130 (205)
...+.-.+++..+| +-||||.|+....|. + -+.|+-||.+.. .+.+|++++||.+.-+||..|+.+
T Consensus 83 s~~Peyi~~riSklKsYk~r~LL~hvd~~N~~asIqElv~Tt~inti~l~~svee-~sry~~t~~~~~~~s~~iir~~~s 161 (224)
T COG5241 83 STRPEYIVLRISKLKSYKERPLLNHVDSTNWRASIQELVSTTGINTIYLDYSVEE-RSRYFLTLTYHKLYSDYIIRRMQS 161 (224)
T ss_pred cCCCceEEEeeeccccccccceeeeeccccHHHHHHHHHHhcccceeehhhhhhH-HHHHHHHhHHHhhcCHHHHHhcCC
Confidence 44456667788889 999999999888887 3 134778999876 788999999999999999999999
Q ss_pred hc--ccceE---EEcCCChHHHHHHHHHHHHhcC-----cEEEeecChHHHHHHHHHHH
Q psy15374 131 LG--KLYKL---QVDSKDPHHALKYLTRVCLLCD-----LTLMLAWSPEEAGEMIETYK 179 (205)
Q Consensus 131 L~--~~y~l---~VDv~d~~~~L~eL~~~c~~~~-----~TLilawS~eEaa~Yie~~K 179 (205)
+. +.|+. -||-.|.++.|.++.++|..++ ++++++|.++.|++|||.+.
T Consensus 162 ~d~s~~fl~~i~~Vnksds~~~L~d~g~L~rf~gaSrdE~e~l~g~g~~ka~~~ieyln 220 (224)
T COG5241 162 LDRSNEFLILIFIVNKSDSEDTLNDIGKLCRFNGASRDEFELLLGFGFEKAAKYIEYLN 220 (224)
T ss_pred CcccccceEEEEeeccccHHHHHHHHHHHHHHhccchhHHHHHHccCHHHHHHHHHHhc
Confidence 97 45654 8999999999999999999999 99999999999999999763
No 7
>PRK13766 Hef nuclease; Provisional
Probab=96.95 E-value=0.005 Score=60.97 Aligned_cols=115 Identities=17% Similarity=0.294 Sum_probs=85.6
Q ss_pred CCCCCCeEEeCCcccCCcccccc--cccceeecCCCCcceeecCceeE-------EEEeecccccChhHHHHHHHhhccc
Q psy15374 64 ASKSSNAILVNPRQKGNPLLKHI--GKVPWEYDDSIIPDYVMGRTTCA-------LFLSIKYHALKPDYIADRIKALGKL 134 (205)
Q Consensus 64 ~~~~~~~I~Vs~~QkGNPlL~~i--~~vpwe~~d~i~~Dy~ig~~~~v-------LFLSLkyH~L~P~YI~~Ri~~L~~~ 134 (205)
+....-.|+|-.|-....+...+ ..++.+...--+.||+++..+|| |--|++-- -+++++..|++.
T Consensus 558 ~~~~~~~i~vD~RE~~~~~~~~l~~~g~~~~~~~L~~gDy~~~~~~~vERK~~~Dl~~s~~~~-----r~~~q~~~l~~~ 632 (773)
T PRK13766 558 DEPEGPKIIVDSRELRSNVARHLKRLGAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSIIDR-----RLFEQVKDLKRA 632 (773)
T ss_pred CCCCCcEEEEeCCCccchhhHHHHhCCCEEEEEecCCCCEEccCCeEEEeCcHHHHHHHhhcC-----cHHHHHHHHHhc
Confidence 34455578888886444465655 35667765545689999988877 44466643 366778888776
Q ss_pred ce---EEEcCC-------ChHHHHHHHHHHHHhcCcEEEeecChHHHHHHHHHHHhhhC
Q psy15374 135 YK---LQVDSK-------DPHHALKYLTRVCLLCDLTLMLAWSPEEAGEMIETYKVFEN 183 (205)
Q Consensus 135 y~---l~VDv~-------d~~~~L~eL~~~c~~~~~TLilawS~eEaa~Yie~~K~~e~ 183 (205)
|. |+|.-+ +++.+...|..+++..+++++.+||++|+|+||+.++..+.
T Consensus 633 ~~~~~lliE~~~~~~~~~~~~~i~~~l~~l~~~~~~~ii~~~~~~eta~~l~~l~~~~~ 691 (773)
T PRK13766 633 YERPVLIIEGDLYTIRNIHPNAIRGALASIAVDFGIPILFTRDEEETADLLKVIAKREQ 691 (773)
T ss_pred CCCcEEEEEcCchhhcccCHHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHHHHHhhcc
Confidence 64 344433 46788899999999999999999999999999999999886
No 8
>PF07279 DUF1442: Protein of unknown function (DUF1442); InterPro: IPR009902 This family consists of several hypothetical Arabidopsis thaliana proteins of around 225 residues in length. The function of this family is unknown.
Probab=80.79 E-value=0.75 Score=40.45 Aligned_cols=135 Identities=21% Similarity=0.305 Sum_probs=70.0
Q ss_pred cccCchhhhh-hhhhhhhccCCCCCcccccCCCCCCccccccCCCCccCCCCC------C--CCCCCC--c--cCCCCCC
Q psy15374 2 LAWSPEEAGE-MIETYKVFENKPPDLIMEKQDVDPHSKTWNFDPVPAAQNSAT------S--ESVQPS--R--AGASKSS 68 (205)
Q Consensus 2 laWS~eEaar-ylEtyK~~E~kp~d~i~e~~~~~~~~~~~~~lt~~~~~n~~~------~--~t~~~~--~--~~~~~~~ 68 (205)
|+||||-|.+ ||.|-|+.++.- |. ...||+-.-.+-|.++ + .+.+|+ + |+.-+.+
T Consensus 3 l~WSpe~AtkAYl~Tvk~c~~~~-----ep-------~~aEfISAlAAG~nAkliVe~~s~g~~~~ttiaLaaAAr~TgG 70 (218)
T PF07279_consen 3 LVWSPENATKAYLDTVKMCKKFK-----EP-------GVAEFISALAAGWNAKLIVEAWSSGGAISTTIALAAAARQTGG 70 (218)
T ss_pred ceeChhHHHHHHHHHHHHhhhcC-----CC-------CHHHHHHHHhccccceEEEEEecCCCchHhHHHHHHHHHhcCC
Confidence 7999999865 999999987532 21 2334443333333322 1 111222 2 2444555
Q ss_pred CeEEeCCcccC-CcccccccccceeecCCCCcceeecCceeEEEEeecccccChhHHHHHHHhhcccceEEEcCCChHHH
Q psy15374 69 NAILVNPRQKG-NPLLKHIGKVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADRIKALGKLYKLQVDSKDPHHA 147 (205)
Q Consensus 69 ~~I~Vs~~QkG-NPlL~~i~~vpwe~~d~i~~Dy~ig~~~~vLFLSLkyH~L~P~YI~~Ri~~L~~~y~l~VDv~d~~~~ 147 (205)
.-|-|-+.++. .-..+.|. +.+-...++|++|.. |+-+-.+++.+ =-++||.+. ++.
T Consensus 71 R~vCIvp~~~~~~~~~~~l~----~~~~~~~vEfvvg~~--------------~e~~~~~~~~i---DF~vVDc~~-~d~ 128 (218)
T PF07279_consen 71 RHVCIVPDEQSLSEYKKALG----EAGLSDVVEFVVGEA--------------PEEVMPGLKGI---DFVVVDCKR-EDF 128 (218)
T ss_pred eEEEEcCChhhHHHHHHHHh----hccccccceEEecCC--------------HHHHHhhccCC---CEEEEeCCc-hhH
Confidence 55666655444 22233344 333224578999873 44343333322 135888764 444
Q ss_pred HHHHHHHHHh-cCcEEEeecChHH
Q psy15374 148 LKYLTRVCLL-CDLTLMLAWSPEE 170 (205)
Q Consensus 148 L~eL~~~c~~-~~~TLilawS~eE 170 (205)
++++-++.-. ..-++++|.+.-.
T Consensus 129 ~~~vl~~~~~~~~GaVVV~~Na~~ 152 (218)
T PF07279_consen 129 AARVLRAAKLSPRGAVVVCYNAFS 152 (218)
T ss_pred HHHHHHHhccCCCceEEEEecccc
Confidence 4333333323 4567888887544
No 9
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=71.13 E-value=15 Score=37.93 Aligned_cols=113 Identities=17% Similarity=0.269 Sum_probs=81.9
Q ss_pred CCCeEEeCCcccCCcccccccc--cceeecCCCCcceeecCceeE-------EEEeecccccChhHHHHHHHhhcccce-
Q psy15374 67 SSNAILVNPRQKGNPLLKHIGK--VPWEYDDSIIPDYVMGRTTCA-------LFLSIKYHALKPDYIADRIKALGKLYK- 136 (205)
Q Consensus 67 ~~~~I~Vs~~QkGNPlL~~i~~--vpwe~~d~i~~Dy~ig~~~~v-------LFLSLkyH~L~P~YI~~Ri~~L~~~y~- 136 (205)
..-.|+|-.|-..-.|-..+.. +.-+..---+.||++++.+|| |.=||.--+ +++.++.|.+.|.
T Consensus 585 ~~~~IiVD~REfrS~lp~~L~~~G~~v~p~tL~VGDYilS~~i~VERKSi~Dli~Sl~~gR-----L~~Q~~~m~~~Y~~ 659 (814)
T TIGR00596 585 TQPKVIVDMREFRSSLPSLLHRRGIRVIPCMLTVGDYILTPDICVERKSISDLIGSLNNGR-----LYNQCEKMLRYYAY 659 (814)
T ss_pred CCceEEEecCcccchhHHHHHHCCCEEEEEecCcccEEecCCeEEEeCcHHHHHHHHhcch-----HHHHHHHHHHhcCC
Confidence 4457899988755556454433 333333334579999999999 445666555 7889999998875
Q ss_pred --E--EEcCCC---------------h--HHHHHHHHHHHHhc-CcEEEeecChHHHHHHHHHHHhhhCC
Q psy15374 137 --L--QVDSKD---------------P--HHALKYLTRVCLLC-DLTLMLAWSPEEAGEMIETYKVFENK 184 (205)
Q Consensus 137 --l--~VDv~d---------------~--~~~L~eL~~~c~~~-~~TLilawS~eEaa~Yie~~K~~e~k 184 (205)
| --|... + .++...|..+++.. ++.+|-+-|+.|-|..|..+|.-+..
T Consensus 660 PvLLIE~d~~~~f~l~~~~~~~~~~~~~~~~i~~~L~~L~l~fP~l~IiwS~s~~~TA~i~~~Lk~~e~e 729 (814)
T TIGR00596 660 PVLLIEFDQNKSFSLEPRNDLSQEISSVNNDIQQKLALLTLHFPKLRIIWSSSPYATAEIFEELKLGKEE 729 (814)
T ss_pred cEEEEEecCCcccccccccccccccCccHHHHHHHHHHHHHhcCCceEEecCCHHHHHHHHHHHHhcCCC
Confidence 2 233211 2 45556899999998 99999999999999999999999875
No 10
>PF15162 DUF4580: Domain of unknown function (DUF4580)
Probab=67.13 E-value=34 Score=28.91 Aligned_cols=121 Identities=16% Similarity=0.279 Sum_probs=84.9
Q ss_pred CCCCeEEeCCcccCCccccccc--ccceeecCCCCcceeecCceeEEEEeecccccChhH--HHHHHHhhcc----cceE
Q psy15374 66 KSSNAILVNPRQKGNPLLKHIG--KVPWEYDDSIIPDYVMGRTTCALFLSIKYHALKPDY--IADRIKALGK----LYKL 137 (205)
Q Consensus 66 ~~~~~I~Vs~~QkGNPlL~~i~--~vpwe~~d~i~~Dy~ig~~~~vLFLSLkyH~L~P~Y--I~~Ri~~L~~----~y~l 137 (205)
...-+|+||..-+|.++.+.+. +..-+|+|.+.++=++=+..||-||=+-- +|. ...||+++-. .|.+
T Consensus 4 ~w~ttvIissSl~~~ei~~~L~~~~hkiR~S~sve~~svIFpLSGvAFLL~d~----~~~~~~l~ki~kF~~ihrNsflv 79 (162)
T PF15162_consen 4 KWTTTVIISSSLQNHEIATILSNQSHKIRYSDSVEPGSVIFPLSGVAFLLMDA----QECFMFLAKIEKFIDIHRNSFLV 79 (162)
T ss_pred CCcceEEEehhccccHHHHHHhcccceEEecccccCCeEEEEcccceeeEecc----HHHhhHHHHHHHHHhccCCceEE
Confidence 3455899999999999998875 56777888788888887788888884421 222 4566666643 3444
Q ss_pred EEcC--CChH--HHHHHHHHHHHhcCcEEEeecChHHHHHHHHHHHhhhCCC-cchhccc
Q psy15374 138 QVDS--KDPH--HALKYLTRVCLLCDLTLMLAWSPEEAGEMIETYKVFENKP-PDLIMEK 192 (205)
Q Consensus 138 ~VDv--~d~~--~~L~eL~~~c~~~~~TLilawS~eEaa~Yie~~K~~e~k~-~d~i~~~ 192 (205)
++. -+++ ..+..+.++ ...|+.++.+.++.||++-+-|--.--.|| .|.|..+
T Consensus 80 -L~aalhg~~ew~~m~~iqRF-LG~nl~ilpvhn~~~~v~~M~tiAK~t~kP~~~~I~~R 137 (162)
T PF15162_consen 80 -LSAALHGPEEWKLMFRIQRF-LGSNLRILPVHNPANCVKLMCTIAKTTSKPYCDVICYR 137 (162)
T ss_pred -eehhhcCHHHHHHHHHHHHH-hcCCceEEecCCHHHHHHHHHHHHHHhcCCcHHHHHHH
Confidence 332 2222 344444333 348899999999999999988887777787 6777665
No 11
>PF02700 PurS: Phosphoribosylformylglycinamidine (FGAM) synthase; InterPro: IPR003850 Phosphoribosylformylglycinamidine(FGAM) synthetase, 6.3.5.3 from EC, catalyses the fourth step in the de novo purine biosynthetic pathway []. 5-phosphoribosylformylglycinamide (FGAR) + glutamine + ATP = FGAM + glutamate + ADP + Pi In eukaryotes and many bacterial systems (including Escherichia coli and Salmonella typhimurium), the FGAM synthetase is encoded by the large form of PurL (lgPurL), which contains an N-terminal ATPase domain and a C-terminal glutamine-binding domain. In archaeal and other bacterial systems, however, FGAM synthetase is encoded by separate genes, making it a multisubunit (rather than multidomain) enzyme. The protein is composed of the small form of PurL (smPurL), which is homologus to the ATPase domain of lgPurL, PurQ which is homologous to the glutamine-binding domain of of lgPurL, and PurS, whose function is not known. This entry represents the PurS subunit of the multisubunit FGAM synthetase. Recent studies showed that disruption of the purS gene in Bacillus subtilis resulted in a purine auxotrophic phenotype, due to defective FGAM synthetase activity. Therefore, the PurS protein appears to be required for the function of the PurL and PurQ subunits of the FGAM synthetase, but the molecular mechanism for the functional role of PurS is currently not known. For additional information please see [, ].; GO: 0016879 ligase activity, forming carbon-nitrogen bonds; PDB: 2ZW2_B 3D54_B 1VQ3_B 1GTD_A 2YX5_A 2CUW_A 1TWJ_B 1T4A_B 2DGB_B.
Probab=47.73 E-value=64 Score=23.79 Aligned_cols=50 Identities=20% Similarity=0.369 Sum_probs=37.7
Q ss_pred eEEEEeecccccChh--HHHHHHHhhcc----------cceEEEcCCChHHHHHHHHHHHHh
Q psy15374 108 CALFLSIKYHALKPD--YIADRIKALGK----------LYKLQVDSKDPHHALKYLTRVCLL 157 (205)
Q Consensus 108 ~vLFLSLkyH~L~P~--YI~~Ri~~L~~----------~y~l~VDv~d~~~~L~eL~~~c~~ 157 (205)
.-+++++|-+-+.|+ =|.+-|..||- .|.+.+|-+|.+.+..++..+|-.
T Consensus 3 ~~V~V~~K~gvlDPqG~ai~~al~~lG~~~v~~Vr~GK~~~l~~~~~~~e~a~~~v~~i~~~ 64 (80)
T PF02700_consen 3 VRVEVTLKPGVLDPQGEAIKRALHRLGYDGVKDVRVGKYIELELEADDEEEAEEQVEEICEK 64 (80)
T ss_dssp EEEEEEE-TTS--HHHHHHHHHHHHTT-TTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHH
T ss_pred EEEEEEECCCCcCcHHHHHHHHHHHcCCcccCcEEEEEEEEEEEeCCCHHHHHHHHHHHHHH
Confidence 468899999999995 59999998863 245688899999999999999976
No 12
>TIGR03603 cyclo_dehy_ocin bacteriocin biosynthesis cyclodehydratase, SagC family. Members of this protein family include enzymes related to SagC, a cyclodehydratase involved in the biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). This protein family serves as a marker for widely distributed prokaryotic systems for making a general class of heterocycle-containing bacteriocins. Note that this model does not find all possible examples of bacteriocin biosynthesis cyclodehydratases, an in particular misses the E. coli plasmid protein McbB of microcin B17 biosynthesis.
Probab=45.87 E-value=10 Score=34.54 Aligned_cols=89 Identities=12% Similarity=0.099 Sum_probs=56.6
Q ss_pred ccCCcccccccc-ccee-ecCCCCcceeecCceeEEEEeecccccChhHHHHHHHhhccc------------ceEEEcCC
Q psy15374 77 QKGNPLLKHIGK-VPWE-YDDSIIPDYVMGRTTCALFLSIKYHALKPDYIADRIKALGKL------------YKLQVDSK 142 (205)
Q Consensus 77 QkGNPlL~~i~~-vpwe-~~d~i~~Dy~ig~~~~vLFLSLkyH~L~P~YI~~Ri~~L~~~------------y~l~VDv~ 142 (205)
-=|+|++.++-. |.-= ..| .|++--+.-.+||-.----+.+-+-..+||..+... |.++||..
T Consensus 83 GLGs~va~~La~GVg~L~ivD---~D~Ve~SNL~~L~~~~diG~~K~~~a~~~L~~lnp~v~i~~~~~li~~~DlVid~t 159 (318)
T TIGR03603 83 KFGANIAYNLCNNVGALFISD---KTYFQETAEIDLYSKEFILKKDIRDLTSNLDALELTKNVDELKDLLKDYNYIIICT 159 (318)
T ss_pred cchHHHHHHHhCCCCEEEEEc---CCEechhhHHHHhChhhcCcHHHHHHHHHHHHhCCCCEEeeHHHHhCCCCEEEECC
Confidence 346777766543 2211 123 566654443345543333444567788888888642 45699988
Q ss_pred ChHH--HHHHHHHHHHhcCcEEEeecCh
Q psy15374 143 DPHH--ALKYLTRVCLLCDLTLMLAWSP 168 (205)
Q Consensus 143 d~~~--~L~eL~~~c~~~~~TLilawS~ 168 (205)
|... .|+++|+.|...+..+|.+|-.
T Consensus 160 Dn~~~r~L~~iN~ac~~~~~PlV~gav~ 187 (318)
T TIGR03603 160 EHSNISLLRGLNKLSKETKKPNTIAFID 187 (318)
T ss_pred CCccHhHHHHHHHHHHHHCCCEEEEEEc
Confidence 8754 6789999999999998877544
No 13
>PF00899 ThiF: ThiF family; InterPro: IPR000594 Ubiquitin-activating enzyme (E1 enzyme) [, ] activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin- conjugating enzymes (E2). The family of ubiquitin-activating enzymes shares in its catalytic domain significant similarity with a large family of NAD/FAD-binding proteins. This domain is based on the common NAD/FAD-binding fold and finds members of several families, including UBA ubiquitin activating enzymes; the hesA/moeB/thiF family; NADH peroxidases; the LDH family; sarcosin oxidase; phytoene dehydrogenases; alanine dehydrogenases; hydroxyacyl-CoA dehydrogenases and many other NAD/FAD dependent dehydrogenases and oxidases.; GO: 0003824 catalytic activity; PDB: 1ZKM_D 1ZUD_3 1ZFN_D 1R4M_G 2NVU_A 1R4N_C 3DBR_A 3DBH_C 3DBL_G 1YOV_A ....
Probab=43.41 E-value=32 Score=26.58 Aligned_cols=36 Identities=22% Similarity=0.275 Sum_probs=29.5
Q ss_pred ccceEEEcCCChHHHHHHHHHHHHhcCcEEEeecCh
Q psy15374 133 KLYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWSP 168 (205)
Q Consensus 133 ~~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS~ 168 (205)
+.+.+.||..|...+...|++.|...+.-+|.+|..
T Consensus 91 ~~~d~vi~~~d~~~~~~~l~~~~~~~~~p~i~~~~~ 126 (135)
T PF00899_consen 91 KDYDIVIDCVDSLAARLLLNEICREYGIPFIDAGVN 126 (135)
T ss_dssp HTSSEEEEESSSHHHHHHHHHHHHHTT-EEEEEEEE
T ss_pred cCCCEEEEecCCHHHHHHHHHHHHHcCCCEEEEEee
Confidence 345678998888889999999999999999988864
No 14
>TIGR02356 adenyl_thiF thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with the Escherichia. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ThiF. This model represents the more widely distributed clade of ThiF proteins such found in E. coli.
Probab=37.31 E-value=56 Score=27.41 Aligned_cols=35 Identities=17% Similarity=0.171 Sum_probs=30.8
Q ss_pred cceEEEcCCChHHHHHHHHHHHHhcCcEEEeecCh
Q psy15374 134 LYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWSP 168 (205)
Q Consensus 134 ~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS~ 168 (205)
.+.++||..|..++-..|++.|..++..+|.+|..
T Consensus 111 ~~D~Vi~~~d~~~~r~~l~~~~~~~~ip~i~~~~~ 145 (202)
T TIGR02356 111 NVDLVLDCTDNFATRYLINDACVALGTPLISAAVV 145 (202)
T ss_pred CCCEEEECCCCHHHHHHHHHHHHHcCCCEEEEEec
Confidence 46679999998888899999999999999999865
No 15
>cd01492 Aos1_SUMO Ubiquitin activating enzyme (E1) subunit Aos1. Aos1 is part of the heterodimeric activating enzyme (E1), specific for the SUMO family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by SUMO family of ubiquitin-like proteins (Ublps) is involved in cell division, nuclear transport, the stress response and signal transduction. Aos1 contains part of the adenylation domain.
Probab=35.30 E-value=62 Score=27.21 Aligned_cols=34 Identities=9% Similarity=0.158 Sum_probs=29.4
Q ss_pred cceEEEcCCChHHHHHHHHHHHHhcCcEEEeecC
Q psy15374 134 LYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWS 167 (205)
Q Consensus 134 ~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS 167 (205)
.|.+.||..+..+...+|++.|...+..++.|.+
T Consensus 110 ~~dvVi~~~~~~~~~~~ln~~c~~~~ip~i~~~~ 143 (197)
T cd01492 110 QFDVVVATELSRAELVKINELCRKLGVKFYATGV 143 (197)
T ss_pred CCCEEEECCCCHHHHHHHHHHHHHcCCCEEEEEe
Confidence 4567888888889999999999999999988876
No 16
>cd01485 E1-1_like Ubiquitin activating enzyme (E1), repeat 1-like. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. A set of novel molecules with a structural similarity to Ub, called Ub-like proteins (Ubls), have similar conjugation cascades. In contrast to ubiquitin-E1, which is a single-chain protein with a weakly conserved two-fold repeat, many of the Ubls-E1are a heterodimer where each subunit corresponds to one half of a single-chain E1. This CD represents the family homol
Probab=34.60 E-value=66 Score=27.01 Aligned_cols=34 Identities=9% Similarity=0.218 Sum_probs=28.4
Q ss_pred cceEEEcCCChHHHHHHHHHHHHhcCcEEEeecC
Q psy15374 134 LYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWS 167 (205)
Q Consensus 134 ~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS 167 (205)
.|.+.||..|+.++...|+++|..++.-++.|-+
T Consensus 113 ~~dvVi~~~d~~~~~~~ln~~c~~~~ip~i~~~~ 146 (198)
T cd01485 113 KFTLVIATEENYERTAKVNDVCRKHHIPFISCAT 146 (198)
T ss_pred CCCEEEECCCCHHHHHHHHHHHHHcCCCEEEEEe
Confidence 4667899988888999999999999988777644
No 17
>PF05626 DUF790: Protein of unknown function (DUF790); InterPro: IPR008508 This family consists of several hypothetical bacterial and archaeal proteins whose functions have not been experimentally verified. Computational analysis of sequence, predicted structure and genomic context suggests that these proteins may be endonucleases involved in either restriction-modification and/or DNA excision repair [].
Probab=34.46 E-value=44 Score=31.65 Aligned_cols=37 Identities=24% Similarity=0.550 Sum_probs=28.9
Q ss_pred CCcceeecCceeEEEEeecccccChhHHHHHHHhhccc
Q psy15374 97 IIPDYVMGRTTCALFLSIKYHALKPDYIADRIKALGKL 134 (205)
Q Consensus 97 i~~Dy~ig~~~~vLFLSLkyH~L~P~YI~~Ri~~L~~~ 134 (205)
++|||.+.++.--+|+=+ .|--+||||..|+++|.+.
T Consensus 302 ~IPDF~~~~~g~~vylEI-vGfWtpeYL~rKl~kl~~~ 338 (379)
T PF05626_consen 302 MIPDFRFEHDGRRVYLEI-VGFWTPEYLERKLEKLRKA 338 (379)
T ss_pred EccceeEEECCEEEEEEE-ecCCCHHHHHHHHHHHhhC
Confidence 569999987544555543 5778999999999999864
No 18
>TIGR00036 dapB dihydrodipicolinate reductase.
Probab=32.49 E-value=1.3e+02 Score=26.33 Aligned_cols=38 Identities=16% Similarity=0.255 Sum_probs=17.0
Q ss_pred EEEcCCChHHHHHHHHHHHHhcCcEEEe---ecChHHHHHHH
Q psy15374 137 LQVDSKDPHHALKYLTRVCLLCDLTLML---AWSPEEAGEMI 175 (205)
Q Consensus 137 l~VDv~d~~~~L~eL~~~c~~~~~TLil---awS~eEaa~Yi 175 (205)
++||.+ +.+...++.+.|+.+++-+++ +|+.+|+.+..
T Consensus 71 vVIdfT-~p~~~~~~~~~al~~g~~vVigttg~~~e~~~~l~ 111 (266)
T TIGR00036 71 VLIDFT-TPEGVLNHLKFALEHGVRLVVGTTGFSEEDKQELA 111 (266)
T ss_pred EEEECC-ChHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHH
Confidence 344444 334444444555555444443 34444444433
No 19
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=31.87 E-value=62 Score=32.59 Aligned_cols=96 Identities=21% Similarity=0.255 Sum_probs=64.3
Q ss_pred CcceeecCceeEEEEeecccccCh-hH----HHHHHHh-hcccceE--EEcCCChHHHHHHHHHHHHhcCcEEEeecChH
Q psy15374 98 IPDYVMGRTTCALFLSIKYHALKP-DY----IADRIKA-LGKLYKL--QVDSKDPHHALKYLTRVCLLCDLTLMLAWSPE 169 (205)
Q Consensus 98 ~~Dy~ig~~~~vLFLSLkyH~L~P-~Y----I~~Ri~~-L~~~y~l--~VDv~d~~~~L~eL~~~c~~~~~TLilawS~e 169 (205)
+-=|+||+|+- -.-|.=|- .| |..|+.. + ..|.| +..++|+.+-|-.= +...++++...++..
T Consensus 61 v~~Y~CGPTvY-----d~~HiGhart~v~~Dil~R~l~~~-~Gy~V~~v~nitDidDKIi~~---A~~~g~~~~~el~~~ 131 (651)
T PTZ00399 61 VRWYTCGPTVY-----DSSHLGHARTYVTFDIIRRILEDY-FGYDVFYVMNITDIDDKIIKR---AREEKLSIFLELARK 131 (651)
T ss_pred eEEEEeCCCcc-----CCcccccchHHHHHHHHHHHHHHh-cCCceEEEeCCCCcchHHHHH---HHHhCCCcHHHHHHH
Confidence 34499999653 45677673 56 6778887 4 35666 77888887644332 334666655555556
Q ss_pred HHHHHHHHHHhhhCCCcchhccccCCCcccccccC
Q psy15374 170 EAGEMIETYKVFENKPPDLIMEKQDVDPHSKTWNF 204 (205)
Q Consensus 170 Eaa~Yie~~K~~e~k~~d~i~~~~~~d~~s~~~~~ 204 (205)
-.++|.+.++...-.+|+.+..- ++|...|++|
T Consensus 132 ~~~~f~~d~~~Lni~~p~~~~r~--tehi~~ii~~ 164 (651)
T PTZ00399 132 WEKEFFEDMKALNVRPPDVITRV--SEYVPEIVDF 164 (651)
T ss_pred HHHHHHHHHHHcCCCCCccccCc--CccHHHHHHH
Confidence 66677888888888888886655 6777776654
No 20
>TIGR02355 moeB molybdopterin synthase sulfurylase MoeB. This model describes the molybdopterin biosynthesis protein MoeB in E. coli and related species. The enzyme covalently modifies the molybdopterin synthase MoaD by sulfurylation. This enzyme is closely related to ThiF, a thiamine biosynthesis enzyme that modifies ThiS by an analogous adenylation. Both MoeB and ThiF belong to the HesA/MoeB/ThiF family (pfam00899).
Probab=31.65 E-value=74 Score=27.68 Aligned_cols=35 Identities=20% Similarity=0.250 Sum_probs=29.7
Q ss_pred cceEEEcCCChHHHHHHHHHHHHhcCcEEEeecCh
Q psy15374 134 LYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWSP 168 (205)
Q Consensus 134 ~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS~ 168 (205)
.+.++||..|..++-..|++.|..++.-+|.+.+.
T Consensus 114 ~~DlVvd~~D~~~~r~~ln~~~~~~~ip~v~~~~~ 148 (240)
T TIGR02355 114 EHDIVVDCTDNVEVRNQLNRQCFAAKVPLVSGAAI 148 (240)
T ss_pred cCCEEEEcCCCHHHHHHHHHHHHHcCCCEEEEEec
Confidence 45679999999999999999999999988877543
No 21
>PF02732 ERCC4: ERCC4 domain; InterPro: IPR006166 This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases (3.1.22 from EC) [], and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006259 DNA metabolic process; PDB: 2BHN_D 2BGW_B 1J22_A 1J25_A 1J24_A 1J23_A 2ZIU_A 2ZIW_A 2ZIV_A 2ZIX_A ....
Probab=31.10 E-value=1.3e+02 Score=22.69 Aligned_cols=34 Identities=15% Similarity=0.228 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhcCcEEEeecChHHHHHHHHHH
Q psy15374 145 HHALKYLTRVCLLCDLTLMLAWSPEEAGEMIETY 178 (205)
Q Consensus 145 ~~~L~eL~~~c~~~~~TLilawS~eEaa~Yie~~ 178 (205)
.++..-|..+-+..++.++.+=|.+|.|++|-.|
T Consensus 110 ~~i~~~L~~lq~~~~~~v~~~~~~~et~~~l~~f 143 (143)
T PF02732_consen 110 SAIEEALVELQLRYGISVIFTESWEETADWLASF 143 (143)
T ss_dssp HHHHHHHHHHHHCSS-EEEEESSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCeEEEEECCHHHHHHHhhhC
Confidence 5667788888888999999999999999999765
No 22
>cd00757 ThiF_MoeB_HesA_family ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1).
Probab=30.59 E-value=75 Score=27.01 Aligned_cols=36 Identities=17% Similarity=0.182 Sum_probs=28.7
Q ss_pred cceEEEcCCChHHHHHHHHHHHHhcCcEEEeecChH
Q psy15374 134 LYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWSPE 169 (205)
Q Consensus 134 ~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS~e 169 (205)
.+.++||..|....-..|++.|..++..+|.++...
T Consensus 111 ~~DvVi~~~d~~~~r~~l~~~~~~~~ip~i~~g~~g 146 (228)
T cd00757 111 GYDLVLDCTDNFATRYLINDACVKLGKPLVSGAVLG 146 (228)
T ss_pred CCCEEEEcCCCHHHHHHHHHHHHHcCCCEEEEEecc
Confidence 355688877777788889999999999998887643
No 23
>PRK00048 dihydrodipicolinate reductase; Provisional
Probab=30.12 E-value=1.5e+02 Score=25.87 Aligned_cols=42 Identities=17% Similarity=0.167 Sum_probs=32.0
Q ss_pred cceEEEcCCChHHHHHHHHHHHHhcCcEEEe---ecChHHHHHHHH
Q psy15374 134 LYKLQVDSKDPHHALKYLTRVCLLCDLTLML---AWSPEEAGEMIE 176 (205)
Q Consensus 134 ~y~l~VDv~d~~~~L~eL~~~c~~~~~TLil---awS~eEaa~Yie 176 (205)
...++||...|.. ..++.+.|+.+++-+++ +||.+|+.+..+
T Consensus 60 ~~DvVid~t~p~~-~~~~~~~al~~G~~vvigttG~s~~~~~~l~~ 104 (257)
T PRK00048 60 DADVLIDFTTPEA-TLENLEFALEHGKPLVIGTTGFTEEQLAELEE 104 (257)
T ss_pred CCCEEEECCCHHH-HHHHHHHHHHcCCCEEEECCCCCHHHHHHHHH
Confidence 3557888885544 59999999999999998 567777655554
No 24
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=28.27 E-value=2.7e+02 Score=25.19 Aligned_cols=112 Identities=21% Similarity=0.252 Sum_probs=80.1
Q ss_pred CCCeEEeCCcccCCccccccc--ccceeecCCCCcceeecCceeEE-------EEeecccccChhHHHHHHHhhcccceE
Q psy15374 67 SSNAILVNPRQKGNPLLKHIG--KVPWEYDDSIIPDYVMGRTTCAL-------FLSIKYHALKPDYIADRIKALGKLYKL 137 (205)
Q Consensus 67 ~~~~I~Vs~~QkGNPlL~~i~--~vpwe~~d~i~~Dy~ig~~~~vL-------FLSLkyH~L~P~YI~~Ri~~L~~~y~l 137 (205)
-.-.|+|-.|-.-+++.+++. .|.-+..---+.||+++.++||= --||..= -++...+.|.+.|.-
T Consensus 26 ~~~~viVD~RE~rs~v~~~L~~~gv~v~~~~LevGDYvvs~~v~VERKs~~Dfv~Si~dg-----RlfeQ~~rL~~~y~r 100 (254)
T COG1948 26 FEVVVIVDSRELRSEVPRLLKRLGVKVEVRTLEVGDYVVSDDVIVERKSISDFVSSIIDG-----RLFEQAKRLKKSYER 100 (254)
T ss_pred cceEEEEecchhcccchHHHHhCCCeEEEEecccccEEeecCeeEEeccHHHHHHHHhcc-----hHHHHHHHHHhcCCc
Confidence 455889999999999988875 45555655456899999988883 2233333 255667778777752
Q ss_pred ---EEcCC---------ChHHHHHHHHHHHHhcCcEEEeecChHHHHHHHHHHHhhhC
Q psy15374 138 ---QVDSK---------DPHHALKYLTRVCLLCDLTLMLAWSPEEAGEMIETYKVFEN 183 (205)
Q Consensus 138 ---~VDv~---------d~~~~L~eL~~~c~~~~~TLilawS~eEaa~Yie~~K~~e~ 183 (205)
.|-=+ .++.+..-|.-+.+..++-+|-.=|++|-|.+|..++.-++
T Consensus 101 pvliVegd~~~~~~~~i~~~av~~al~s~~vdfg~~vi~t~~~~~Ta~~i~~la~req 158 (254)
T COG1948 101 PVLIVEGDDSFSRRPKIHPNAVRGALASLAVDFGLPVIWTRSPEETAELIHELARREQ 158 (254)
T ss_pred cEEEEEcccccccccccCHHHHHHHHHHHHhhcCceEEEeCCHHHHHHHHHHHHHHHH
Confidence 22111 33555567777878888888888889999999999988777
No 25
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=27.86 E-value=50 Score=22.89 Aligned_cols=29 Identities=14% Similarity=0.433 Sum_probs=23.1
Q ss_pred eecChHHHHHHHHHHHhhhC---CCcchhccc
Q psy15374 164 LAWSPEEAGEMIETYKVFEN---KPPDLIMEK 192 (205)
Q Consensus 164 lawS~eEaa~Yie~~K~~e~---k~~d~i~~~ 192 (205)
+.||.||-.++|+.++.+.. ..|..|.+.
T Consensus 4 ~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~ 35 (57)
T TIGR01557 4 VVWTEDLHDRFLQAVQKLGGPDWATPKRILEL 35 (57)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcccchHHHHHH
Confidence 46999999999999999986 445666543
No 26
>PF03930 Flp_N: Recombinase Flp protein N-terminus; InterPro: IPR022647 This entry describes the N-terminal domain of Recombinase Flp protein and is found in fungi. FLP proteins catalyse recombination between large inverted repetitions of the plasmid.; PDB: 1P4E_C 1FLO_C 1M6X_A.
Probab=26.59 E-value=1.2e+02 Score=22.93 Aligned_cols=32 Identities=25% Similarity=0.421 Sum_probs=24.7
Q ss_pred eecccccChhHHHHHHHhhcccceEEEcCCCh
Q psy15374 113 SIKYHALKPDYIADRIKALGKLYKLQVDSKDP 144 (205)
Q Consensus 113 SLkyH~L~P~YI~~Ri~~L~~~y~l~VDv~d~ 144 (205)
+.+||.-+|+=+.+-|++.-..|...|-+.-.
T Consensus 35 ~F~Yhlk~~~~L~~~L~~~~~p~~F~I~~~Kk 66 (82)
T PF03930_consen 35 SFEYHLKKPQELQEGLEKAFPPYKFVIKSHKK 66 (82)
T ss_dssp EEEES-S-HHHHHHHHHHHSTTSEEEESTT-S
T ss_pred EEEEecCCHHHHHHHHHHhcCCeEEEEecccC
Confidence 77999999999999999999988886654444
No 27
>cd01491 Ube1_repeat1 Ubiquitin activating enzyme (E1), repeat 1. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Ubiquitin-E1 is a single-chain protein with a weakly conserved two-fold repeat. This CD represents the first repeat of Ub-E1.
Probab=26.58 E-value=94 Score=28.14 Aligned_cols=33 Identities=9% Similarity=0.134 Sum_probs=28.1
Q ss_pred ceEEEcCCChHHHHHHHHHHHHhcCcEEEeecC
Q psy15374 135 YKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWS 167 (205)
Q Consensus 135 y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS 167 (205)
|.++|+.+++.+...+|+++|..++.-+|.|-+
T Consensus 106 fdvVV~~~~~~~~~~~in~~c~~~~ipfI~a~~ 138 (286)
T cd01491 106 FQVVVLTDASLEDQLKINEFCHSPGIKFISADT 138 (286)
T ss_pred CCEEEEecCCHHHHHHHHHHHHHcCCEEEEEec
Confidence 446888888889999999999999988887754
No 28
>PRK08328 hypothetical protein; Provisional
Probab=26.29 E-value=1e+02 Score=26.43 Aligned_cols=37 Identities=16% Similarity=0.022 Sum_probs=30.9
Q ss_pred ccceEEEcCCChHHHHHHHHHHHHhcCcEEEeecChH
Q psy15374 133 KLYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWSPE 169 (205)
Q Consensus 133 ~~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS~e 169 (205)
+.+.++||..|..++-..++..|..++.-+|-+|...
T Consensus 117 ~~~D~Vid~~d~~~~r~~l~~~~~~~~ip~i~g~~~g 153 (231)
T PRK08328 117 KGVDVIVDCLDNFETRYLLDDYAHKKGIPLVHGAVEG 153 (231)
T ss_pred hcCCEEEECCCCHHHHHHHHHHHHHcCCCEEEEeecc
Confidence 4567899988887888899999999999999888653
No 29
>PRK08762 molybdopterin biosynthesis protein MoeB; Validated
Probab=25.50 E-value=1e+02 Score=28.37 Aligned_cols=100 Identities=19% Similarity=0.149 Sum_probs=58.6
Q ss_pred CCCeEEeCCcccCCcccccccccce---eecCCCCcceeecCc--eeEEEEeecccccChhHHHHHHHhhcc--------
Q psy15374 67 SSNAILVNPRQKGNPLLKHIGKVPW---EYDDSIIPDYVMGRT--TCALFLSIKYHALKPDYIADRIKALGK-------- 133 (205)
Q Consensus 67 ~~~~I~Vs~~QkGNPlL~~i~~vpw---e~~d~i~~Dy~ig~~--~~vLFLSLkyH~L~P~YI~~Ri~~L~~-------- 133 (205)
....++|---=-|..+++.+-.... ..-| .|.+--++ ..+||-.---.+.+-+-+.+||+++..
T Consensus 135 ~~~VlvvG~GG~Gs~ia~~La~~Gvg~i~lvD---~d~v~~sNl~Rq~l~~~~diG~~Ka~~~~~~l~~~np~v~v~~~~ 211 (376)
T PRK08762 135 EARVLLIGAGGLGSPAALYLAAAGVGTLGIVD---HDVVDRSNLQRQILHTEDRVGQPKVDSAAQRLAALNPDVQVEAVQ 211 (376)
T ss_pred cCcEEEECCCHHHHHHHHHHHHcCCCeEEEEe---CCEecchhhccccccchhhCCCcHHHHHHHHHHHHCCCCEEEEEe
Confidence 3345555444567777776543332 2222 44332111 233433211223445566666665532
Q ss_pred -------------cceEEEcCCChHHHHHHHHHHHHhcCcEEEeecChH
Q psy15374 134 -------------LYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWSPE 169 (205)
Q Consensus 134 -------------~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS~e 169 (205)
.+.++||..|...+-..|+..|...+..+|.+|...
T Consensus 212 ~~~~~~~~~~~~~~~D~Vv~~~d~~~~r~~ln~~~~~~~ip~i~~~~~g 260 (376)
T PRK08762 212 ERVTSDNVEALLQDVDVVVDGADNFPTRYLLNDACVKLGKPLVYGAVFR 260 (376)
T ss_pred ccCChHHHHHHHhCCCEEEECCCCHHHHHHHHHHHHHcCCCEEEEEecc
Confidence 244689988887777789999999999999998654
No 30
>PRK05690 molybdopterin biosynthesis protein MoeB; Provisional
Probab=24.07 E-value=1.3e+02 Score=26.12 Aligned_cols=34 Identities=21% Similarity=0.234 Sum_probs=28.8
Q ss_pred cceEEEcCCChHHHHHHHHHHHHhcCcEEEeecC
Q psy15374 134 LYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWS 167 (205)
Q Consensus 134 ~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS 167 (205)
.|.++||..|..++...|+..|..++..+|.+..
T Consensus 122 ~~DiVi~~~D~~~~r~~ln~~~~~~~ip~v~~~~ 155 (245)
T PRK05690 122 GHDLVLDCTDNVATRNQLNRACFAAKKPLVSGAA 155 (245)
T ss_pred cCCEEEecCCCHHHHHHHHHHHHHhCCEEEEeee
Confidence 3557999999888888999999999999988744
No 31
>PTZ00170 D-ribulose-5-phosphate 3-epimerase; Provisional
Probab=22.91 E-value=1.6e+02 Score=25.36 Aligned_cols=66 Identities=12% Similarity=0.182 Sum_probs=48.0
Q ss_pred EEEeecccccChhHHHHHHHhhcccce-EEEcCCC--hHHHHHHHHHHHHhcCcEEEeecChHHHHHHH
Q psy15374 110 LFLSIKYHALKPDYIADRIKALGKLYK-LQVDSKD--PHHALKYLTRVCLLCDLTLMLAWSPEEAGEMI 175 (205)
Q Consensus 110 LFLSLkyH~L~P~YI~~Ri~~L~~~y~-l~VDv~d--~~~~L~eL~~~c~~~~~TLilawS~eEaa~Yi 175 (205)
+|+.++.|--+|+..-+.+.+.|-.+. ++....+ ...+++.+.+.=...+.+|..+|+.++...|+
T Consensus 66 ~~lDvHLm~~~p~~~i~~~~~~Gad~itvH~ea~~~~~~~~l~~ik~~G~~~gval~p~t~~e~l~~~l 134 (228)
T PTZ00170 66 TFLDCHLMVSNPEKWVDDFAKAGASQFTFHIEATEDDPKAVARKIREAGMKVGVAIKPKTPVEVLFPLI 134 (228)
T ss_pred CCEEEEECCCCHHHHHHHHHHcCCCEEEEeccCCchHHHHHHHHHHHCCCeEEEEECCCCCHHHHHHHH
Confidence 667999998899877788888886543 4666433 34566655555556778888889888888776
No 32
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=22.22 E-value=1.5e+02 Score=25.80 Aligned_cols=43 Identities=16% Similarity=0.180 Sum_probs=29.3
Q ss_pred EcCCCh--HHHHHHHHHHHHhcCcEEEeecChHHHH--HHHHHHHhh
Q psy15374 139 VDSKDP--HHALKYLTRVCLLCDLTLMLAWSPEEAG--EMIETYKVF 181 (205)
Q Consensus 139 VDv~d~--~~~L~eL~~~c~~~~~TLilawS~eEaa--~Yie~~K~~ 181 (205)
=|+.|| .+++..+.+.|-.+|+.|+|+.+..+.. +||+.+...
T Consensus 9 p~~~npff~~ii~gIe~~a~~~Gy~l~l~~t~~~~~~e~~i~~l~~~ 55 (279)
T PF00532_consen 9 PDISNPFFAEIIRGIEQEAREHGYQLLLCNTGDDEEKEEYIELLLQR 55 (279)
T ss_dssp SSSTSHHHHHHHHHHHHHHHHTTCEEEEEEETTTHHHHHHHHHHHHT
T ss_pred CCCCCcHHHHHHHHHHHHHHHcCCEEEEecCCCchHHHHHHHHHHhc
Confidence 356666 5788888888888888888876443222 666665443
No 33
>COG3727 Vsr DNA G:T-mismatch repair endonuclease [DNA replication, recombination, and repair]
Probab=21.76 E-value=71 Score=26.62 Aligned_cols=59 Identities=22% Similarity=0.535 Sum_probs=36.1
Q ss_pred CCcceeecCceeEEEE-eecccccChhHHHH--------HHHhhcccceEEEcCCChHHHHHHHHHHHHhcCcEEEeec
Q psy15374 97 IIPDYVMGRTTCALFL-SIKYHALKPDYIAD--------RIKALGKLYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAW 166 (205)
Q Consensus 97 i~~Dy~ig~~~~vLFL-SLkyH~L~P~YI~~--------Ri~~L~~~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilaw 166 (205)
..||+|+....||+|+ ..=.|. |+-|+-. =++++++ .|+-.+..++.|.. .|+.+++.|
T Consensus 48 GkPDiVl~~y~~viFvHGCFWh~-H~c~~a~vPksnt~fWleKi~k------NveRD~r~~~~L~~----~GwrvlvVW 115 (150)
T COG3727 48 GKPDIVLPKYRCVIFVHGCFWHG-HHCYLAKVPKSNTEFWLEKIGK------NVERDERDIKRLQQ----LGWRVLVVW 115 (150)
T ss_pred CCCCEeecCceEEEEEeeeeccC-CccccccCCCcchHHHHHHHhh------hhhhhHHHHHHHHH----cCCeEEEEE
Confidence 4599999999999999 444443 3333211 1233333 34445566666655 488888888
No 34
>cd01483 E1_enzyme_family Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS.
Probab=21.63 E-value=1.8e+02 Score=22.45 Aligned_cols=35 Identities=20% Similarity=0.197 Sum_probs=28.1
Q ss_pred ccceEEEcCCChHHHHHHHHHHHHhcCcEEEeecC
Q psy15374 133 KLYKLQVDSKDPHHALKYLTRVCLLCDLTLMLAWS 167 (205)
Q Consensus 133 ~~y~l~VDv~d~~~~L~eL~~~c~~~~~TLilawS 167 (205)
+.+.+.||..|.......|++.|..++..++-+-+
T Consensus 88 ~~~diVi~~~d~~~~~~~l~~~~~~~~i~~i~~~~ 122 (143)
T cd01483 88 DGVDLVIDAIDNIAVRRALNRACKELGIPVIDAGG 122 (143)
T ss_pred cCCCEEEECCCCHHHHHHHHHHHHHcCCCEEEEcC
Confidence 35667888888888888899999998888777654
No 35
>PF14412 AHH: A nuclease family of the HNH/ENDO VII superfamily with conserved AHH
Probab=21.30 E-value=1.6e+02 Score=21.98 Aligned_cols=47 Identities=15% Similarity=0.361 Sum_probs=30.6
Q ss_pred ecCceeEEEEe------ecccc-cChh-H---HHHHHHhhcccceEEEcCCChHHHHHHHHHH
Q psy15374 103 MGRTTCALFLS------IKYHA-LKPD-Y---IADRIKALGKLYKLQVDSKDPHHALKYLTRV 154 (205)
Q Consensus 103 ig~~~~vLFLS------LkyH~-L~P~-Y---I~~Ri~~L~~~y~l~VDv~d~~~~L~eL~~~ 154 (205)
++...-.+||. +-+|+ -||. | |.+||..+.. --..+.+..+.+|.++
T Consensus 44 in~~~Ngv~Lp~~~~~~~~~H~g~H~~~Y~~~V~~~L~~~~~-----~~~~~~~~~~~~l~~i 101 (109)
T PF14412_consen 44 INDPENGVWLPNSEKPGRPPHRGRHPNEYNKYVRERLDKIEN-----SKKENREEFRKELQKI 101 (109)
T ss_pred cCCccceeeeeccCCCCcCCcCCCCcHHHHHHHHHHHHHHHH-----HhhcCHHHHHHHHHHH
Confidence 55566677776 66887 8886 5 8999998875 0012345566666554
No 36
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=20.96 E-value=95 Score=19.88 Aligned_cols=27 Identities=22% Similarity=0.441 Sum_probs=20.7
Q ss_pred ecChHHHHHHHHHHHhhhCCCcchhcc
Q psy15374 165 AWSPEEAGEMIETYKVFENKPPDLIME 191 (205)
Q Consensus 165 awS~eEaa~Yie~~K~~e~k~~d~i~~ 191 (205)
.||.||-...++.++.|....-+.|-.
T Consensus 3 ~Wt~eE~~~l~~~v~~~g~~~W~~Ia~ 29 (48)
T PF00249_consen 3 PWTEEEDEKLLEAVKKYGKDNWKKIAK 29 (48)
T ss_dssp SS-HHHHHHHHHHHHHSTTTHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhCCcHHHHHHH
Confidence 599999999999999998874444433
No 37
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=20.66 E-value=2.5e+02 Score=18.78 Aligned_cols=40 Identities=15% Similarity=0.072 Sum_probs=27.1
Q ss_pred HHHHHHhhcccceEEEcCCChHHHHHHHHHHHHhcCcEEEe
Q psy15374 124 IADRIKALGKLYKLQVDSKDPHHALKYLTRVCLLCDLTLML 164 (205)
Q Consensus 124 I~~Ri~~L~~~y~l~VDv~d~~~~L~eL~~~c~~~~~TLil 164 (205)
+...|+++...-.+.|.++|+. +...+.++|-..|+.++-
T Consensus 16 ~~~~l~~l~~g~~l~v~~d~~~-~~~~i~~~~~~~g~~~~~ 55 (69)
T cd00291 16 TKKALEKLKSGEVLEVLLDDPG-AVEDIPAWAKETGHEVLE 55 (69)
T ss_pred HHHHHhcCCCCCEEEEEecCCc-HHHHHHHHHHHcCCEEEE
Confidence 3455666665555555555554 888889999999998643
Done!