Query 029403
Match_columns 194
No_of_seqs 224 out of 404
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 12:22:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029403.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029403hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3288 OTU-like cysteine prot 100.0 6.7E-34 1.5E-38 245.9 5.8 113 77-189 142-265 (307)
2 KOG3288 OTU-like cysteine prot 99.9 5.6E-28 1.2E-32 209.2 6.5 87 1-93 219-306 (307)
3 COG5539 Predicted cysteine pro 99.5 8.8E-15 1.9E-19 129.0 1.4 111 77-188 141-263 (306)
4 KOG2606 OTU (ovarian tumor)-li 99.3 1.3E-12 2.7E-17 115.6 4.8 71 77-148 193-272 (302)
5 COG5539 Predicted cysteine pro 99.3 2.6E-12 5.6E-17 113.5 3.0 85 2-92 219-304 (306)
6 PF02338 OTU: OTU-like cystein 98.8 7.5E-09 1.6E-13 78.5 4.1 58 77-141 30-88 (121)
7 PF10275 Peptidase_C65: Peptid 96.6 0.01 2.2E-07 50.9 8.1 60 77-136 143-206 (244)
8 KOG3991 Uncharacterized conser 91.9 0.32 7E-06 42.6 5.1 68 77-144 160-229 (256)
9 PHA00616 hypothetical protein 84.2 0.63 1.4E-05 30.7 1.4 25 66-90 3-27 (44)
10 PF13894 zf-C2H2_4: C2H2-type 80.0 1.5 3.2E-05 23.2 1.8 22 66-87 2-23 (24)
11 PF00096 zf-C2H2: Zinc finger, 77.0 2 4.3E-05 23.2 1.7 21 66-86 2-22 (23)
12 PF12874 zf-met: Zinc-finger o 69.9 4.4 9.5E-05 22.3 2.0 21 66-86 2-22 (25)
13 PF04959 ARS2: Arsenite-resist 67.5 2.9 6.2E-05 36.1 1.3 38 56-93 69-107 (214)
14 smart00355 ZnF_C2H2 zinc finge 66.8 5.2 0.00011 21.1 1.9 22 66-87 2-23 (26)
15 PF13912 zf-C2H2_6: C2H2-type 63.9 7 0.00015 21.8 2.1 24 65-88 2-25 (27)
16 KOG2605 OTU (ovarian tumor)-li 61.5 8.7 0.00019 35.8 3.4 56 77-133 249-306 (371)
17 PF12756 zf-C2H2_2: C2H2 type 58.3 11 0.00024 26.4 2.9 29 64-92 50-79 (100)
18 PF12171 zf-C2H2_jaz: Zinc-fin 54.4 3.8 8.2E-05 23.3 -0.2 22 65-86 2-23 (27)
19 COG4049 Uncharacterized protei 50.5 8.4 0.00018 27.0 1.0 32 61-92 14-46 (65)
20 smart00451 ZnF_U1 U1-like zinc 48.2 14 0.00031 21.6 1.7 21 65-85 4-24 (35)
21 PF00653 BIR: Inhibitor of Apo 47.1 32 0.00069 23.7 3.6 37 52-88 24-64 (70)
22 KOG2586 Pyridoxamine-phosphate 46.1 12 0.00026 32.5 1.5 38 69-116 152-189 (228)
23 PRK10144 formate-dependent nit 41.0 19 0.00042 28.7 1.9 64 38-119 28-111 (126)
24 PF05515 Viral_NABP: Viral nuc 40.2 68 0.0015 25.6 4.8 68 45-126 35-121 (124)
25 COG2051 RPS27A Ribosomal prote 39.7 16 0.00034 26.2 1.1 16 60-75 34-49 (67)
26 TIGR03147 cyt_nit_nrfF cytochr 39.0 21 0.00046 28.4 1.8 65 38-120 28-112 (126)
27 PF06107 DUF951: Bacterial pro 38.6 17 0.00038 25.2 1.1 20 61-80 28-48 (57)
28 PF06988 NifT: NifT/FixU prote 38.4 3.1 6.8E-05 29.6 -2.6 24 97-120 19-42 (64)
29 PF13909 zf-H2C2_5: C2H2-type 37.5 26 0.00057 19.0 1.6 21 66-87 2-22 (24)
30 PRK05111 acetylornithine deace 37.5 49 0.0011 29.3 4.2 48 2-54 74-129 (383)
31 PF01188 MR_MLE: Mandelate rac 35.6 25 0.00054 24.0 1.5 31 101-132 36-66 (67)
32 TIGR02934 nifT_nitrog probable 35.0 12 0.00025 26.9 -0.2 23 97-119 19-41 (67)
33 KOG2462 C2H2-type Zn-finger pr 34.8 18 0.0004 32.5 1.0 37 62-98 159-195 (279)
34 PF13913 zf-C2HC_2: zinc-finge 34.7 33 0.00071 19.5 1.7 20 65-85 3-22 (25)
35 KOG1247 Methionyl-tRNA synthet 34.3 23 0.0005 34.1 1.6 62 4-75 86-147 (567)
36 PRK13009 succinyl-diaminopimel 32.9 2.3E+02 0.005 24.9 7.7 13 2-15 61-73 (375)
37 PF07967 zf-C3HC: C3HC zinc fi 32.6 25 0.00054 27.4 1.3 24 54-77 33-56 (133)
38 PHA02768 hypothetical protein; 30.0 44 0.00094 23.0 2.0 26 66-91 7-32 (55)
39 COG3088 CcmH Uncharacterized p 29.7 55 0.0012 27.0 2.9 69 38-124 32-120 (153)
40 PRK13007 succinyl-diaminopimel 29.2 1E+02 0.0022 26.9 4.7 48 2-52 64-111 (352)
41 cd01675 RNR_III Class III ribo 26.8 51 0.0011 32.0 2.6 34 41-76 494-530 (555)
42 COG4604 CeuD ABC-type enteroch 25.5 63 0.0014 28.5 2.6 28 116-143 223-250 (252)
43 PRK08651 succinyl-diaminopimel 25.5 2.6E+02 0.0056 24.8 6.7 48 3-55 78-133 (394)
44 PRK10963 hypothetical protein; 25.2 54 0.0012 27.9 2.2 37 76-118 4-40 (223)
45 PF03918 CcmH: Cytochrome C bi 25.0 50 0.0011 26.7 1.8 56 38-107 28-103 (148)
46 cd02029 PRK_like Phosphoribulo 25.0 62 0.0013 29.1 2.6 48 1-59 120-171 (277)
47 TIGR01902 dapE-lys-deAc N-acet 24.4 1.2E+02 0.0025 26.5 4.2 47 2-55 53-101 (336)
48 cd00729 rubredoxin_SM Rubredox 24.3 27 0.00059 21.3 0.2 14 65-78 3-16 (34)
49 PRK06446 hypothetical protein; 23.8 1.8E+02 0.0039 26.7 5.5 14 2-16 65-78 (436)
50 PRK06915 acetylornithine deace 23.6 1.3E+02 0.0028 27.2 4.5 53 2-56 96-154 (422)
51 cd00022 BIR Baculoviral inhibi 23.5 1E+02 0.0022 20.7 3.0 26 52-77 22-47 (69)
52 KOG2482 Predicted C2H2-type Zn 23.3 85 0.0019 29.5 3.2 27 59-85 139-166 (423)
53 PF04780 DUF629: Protein of un 23.3 1.4E+02 0.003 28.8 4.7 68 38-113 39-110 (466)
54 cd00814 MetRS_core catalytic c 22.6 2.4E+02 0.0051 24.9 5.8 36 39-74 96-131 (319)
55 KOG2989 Uncharacterized conser 22.1 63 0.0014 28.7 2.0 15 58-72 34-48 (253)
56 PF12907 zf-met2: Zinc-binding 22.1 48 0.001 21.3 1.0 27 64-90 1-31 (40)
57 COG5134 Uncharacterized conser 21.8 83 0.0018 27.7 2.7 30 43-72 17-50 (272)
58 TIGR01246 dapE_proteo succinyl 21.2 5E+02 0.011 22.8 7.6 13 2-15 58-70 (370)
59 COG5554 NifU Nitrogen fixation 20.6 22 0.00048 25.2 -0.9 22 97-118 18-39 (69)
60 PF08867 FRG: FRG domain; Int 20.0 81 0.0018 23.4 2.0 23 117-139 61-83 (104)
No 1
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.7e-34 Score=245.87 Aligned_cols=113 Identities=38% Similarity=0.635 Sum_probs=102.2
Q ss_pred HHHHHHHHHhCcccccccccCCChhhhhhhhcCCCCcchhHHHHHHHhHhCceEEEEEcCCCceeeecCCCCccceEE--
Q 029403 77 QKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIELSILADYYGSEIAAYDIQTTRCDLYGQVSSFLESFV-- 154 (194)
Q Consensus 77 rk~aA~~I~s~p~~F~Ea~Lg~~~~eY~~~I~~~~~WGG~IEL~iLS~~~~v~I~v~d~~~~~~~~fge~~~~~~r~~-- 154 (194)
|+.+|+.|+++|+.||+|+||||+.|||.||+++++|||+|||+|||++|+++|+|+|+|++|+++|||+++|.+|++
T Consensus 142 R~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k~dsWGGaIElsILS~~ygveI~vvDiqt~rid~fged~~~~~rv~ll 221 (307)
T KOG3288|consen 142 REIIAQEVASNPDKYNDAILGKPNKEYCAWILKMDSWGGAIELSILSDYYGVEICVVDIQTVRIDRFGEDKNFDNRVLLL 221 (307)
T ss_pred HHHHHHHHhcChhhhhHHHhCCCcHHHHHHHccccccCceEEeeeehhhhceeEEEEecceeeehhcCCCCCCCceEEEE
Confidence 789999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred -----EEeeecccCC-CC-CCceeeCCchHHH--HHHHHHHHhh
Q 029403 155 -----HEILASSALL-NV-PFSSVLISRKRSI--LKELCSSMTS 189 (194)
Q Consensus 155 -----YD~l~~~~~~-~~-p~t~f~~~d~~~~--~~~l~~~l~~ 189 (194)
||+|++++.. .. |.|+||.+|+..+ +-+|++.|.+
T Consensus 222 ydGIHYD~l~m~~~~~~~~~~tifp~~dd~v~~~alqLa~~~k~ 265 (307)
T KOG3288|consen 222 YDGIHYDPLAMNEFKPTDVDNTIFPVSDDTVLTQALQLASELKR 265 (307)
T ss_pred ecccccChhhhccCCccCCcccccccccchHHHHHHHHHHHHHh
Confidence 9999999753 22 3399999987554 3677777654
No 2
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=5.6e-28 Score=209.18 Aligned_cols=87 Identities=46% Similarity=0.792 Sum_probs=83.1
Q ss_pred CeeecCcccceeeecCCCCCCCCCCeeeeeCCCCCCchHHHHHHHHHHHHHhhcccccccccceeeecccccccchHHHH
Q 029403 1 MLIYDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVIGQKAI 80 (194)
Q Consensus 1 ~liYsGIHYD~l~l~~~~~~~~~~d~tiF~~~d~~~~~~vl~~A~~La~~lk~~~~~Tdt~~F~lrC~~C~~~l~Grk~a 80 (194)
+|+|||||||+|+++++ .|.+.|.|+||.+| +.|+..|++||+++|++||||||++|+|||++|+++|+||++|
T Consensus 219 ~llydGIHYD~l~m~~~--~~~~~~~tifp~~d----d~v~~~alqLa~~~k~~r~ytdt~~ftlRC~~Cq~glvGq~ea 292 (307)
T KOG3288|consen 219 LLLYDGIHYDPLAMNEF--KPTDVDNTIFPVSD----DTVLTQALQLASELKRTRYYTDTAKFTLRCMVCQMGLVGQKEA 292 (307)
T ss_pred EEEecccccChhhhccC--CccCCccccccccc----chHHHHHHHHHHHHHhcceeccccceEEEeeecccceeeHHHH
Confidence 58999999999999976 57788999999999 8899999999999999999999999999999999999999999
Q ss_pred HHHHH-hCcccccc
Q 029403 81 AATVA-SDTVKHSE 93 (194)
Q Consensus 81 A~~I~-s~p~~F~E 93 (194)
++|.+ ++|..|.|
T Consensus 293 ~eHA~~TGH~nFge 306 (307)
T KOG3288|consen 293 AEHAKATGHVNFGE 306 (307)
T ss_pred HHHHHhcCCCcccc
Confidence 99999 99999987
No 3
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=99.47 E-value=8.8e-15 Score=128.96 Aligned_cols=111 Identities=19% Similarity=0.286 Sum_probs=88.4
Q ss_pred HHHHHHHHHhCcccccccccCCChhhhhhhhcCCCCcc-hhHHHHHHHhHhCceEEEEEcCCCceeeecCCCCccceEE-
Q 029403 77 QKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWG-GAIELSILADYYGSEIAAYDIQTTRCDLYGQVSSFLESFV- 154 (194)
Q Consensus 77 rk~aA~~I~s~p~~F~Ea~Lg~~~~eY~~~I~~~~~WG-G~IEL~iLS~~~~v~I~v~d~~~~~~~~fge~~~~~~r~~- 154 (194)
|.+|+.-+.++|+.|+++++++|.-+||+||+++++|| |.||++|||..++++|+|+|+..+++++||+.. |..|+.
T Consensus 141 rE~vs~Ev~snPDl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~~~-~~q~~~i 219 (306)
T COG5539 141 REVVSLEVLSNPDLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNSHP-YVQRISI 219 (306)
T ss_pred HHHHHHHHhhCccccchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccCCh-hhhhhhh
Confidence 67888899999999999999999999999999999999 999999999999999999999989999999876 666653
Q ss_pred ------EEeeeccc--CCCC-CCceeeCCchHHH-HHHHHHHHh
Q 029403 155 ------HEILASSA--LLNV-PFSSVLISRKRSI-LKELCSSMT 188 (194)
Q Consensus 155 ------YD~l~~~~--~~~~-p~t~f~~~d~~~~-~~~l~~~l~ 188 (194)
||..++.- .... .+..|..+|-..+ +..|+..|.
T Consensus 220 ~f~g~hfD~~t~~m~~~dt~~ne~~~~a~~g~~~ei~qLas~lk 263 (306)
T COG5539 220 LFTGIHFDEETLAMVLWDTYVNEVLFDASDGITIEIQQLASLLK 263 (306)
T ss_pred hhcccccchhhhhcchHHHHHhhhcccccccchHHHHHHHHHhc
Confidence 88887543 2211 1245554442222 467776664
No 4
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.32 E-value=1.3e-12 Score=115.60 Aligned_cols=71 Identities=20% Similarity=0.369 Sum_probs=63.4
Q ss_pred HHHHHHHHHhCcccccccccCC---------ChhhhhhhhcCCCCcchhHHHHHHHhHhCceEEEEEcCCCceeeecCCC
Q 029403 77 QKAIAATVASDTVKHSEAFIGK---------SNQDYCSWIQDPEKWGGAIELSILADYYGSEIAAYDIQTTRCDLYGQVS 147 (194)
Q Consensus 77 rk~aA~~I~s~p~~F~Ea~Lg~---------~~~eY~~~I~~~~~WGG~IEL~iLS~~~~v~I~v~d~~~~~~~~fge~~ 147 (194)
|.+.|+|+++|-++|-+.++.. .++.||+.|++|+.|||+|||.+||+.|++||.|++. .+.+..|||+.
T Consensus 193 R~~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~-~~p~~~~geey 271 (302)
T KOG2606|consen 193 REETADYMREHVEDFLPFLLDEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQA-DGPILEYGEEY 271 (302)
T ss_pred HHHHHHHHHHHHHHhhhHhcCccccccCCHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeec-CCCceeechhh
Confidence 6799999999999998766521 2899999999999999999999999999999999995 69999999875
Q ss_pred C
Q 029403 148 S 148 (194)
Q Consensus 148 ~ 148 (194)
+
T Consensus 272 ~ 272 (302)
T KOG2606|consen 272 G 272 (302)
T ss_pred C
Confidence 3
No 5
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=99.25 E-value=2.6e-12 Score=113.47 Aligned_cols=85 Identities=16% Similarity=0.309 Sum_probs=67.3
Q ss_pred eeecCcccceeeecCCCCCCCCCCeeeeeCCCCCCchHHHHHHHHHHHHHhhcccccccccceeeecccccccchHHHHH
Q 029403 2 LIYDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVIGQKAIA 81 (194)
Q Consensus 2 liYsGIHYD~l~l~~~~~~~~~~d~tiF~~~d~~~~~~vl~~A~~La~~lk~~~~~Tdt~~F~lrC~~C~~~l~Grk~aA 81 (194)
++|+|||||..++.-.+ -...++.-.|+.+| -+...+++||.-|+..+|||||+++.+||+.||++++|++++.
T Consensus 219 i~f~g~hfD~~t~~m~~-~dt~~ne~~~~a~~-----g~~~ei~qLas~lk~~~~~~nT~~~~ik~n~c~~~~~~e~~~~ 292 (306)
T COG5539 219 ILFTGIHFDEETLAMVL-WDTYVNEVLFDASD-----GITIEIQQLASLLKNPHYYTNTASPSIKCNICGTGFVGEKDYY 292 (306)
T ss_pred hhhcccccchhhhhcch-HHHHHhhhcccccc-----cchHHHHHHHHHhcCceEEeecCCceEEeeccccccchhhHHH
Confidence 47999999999865221 01123344555554 3688999999999999999999999999999999999999999
Q ss_pred HHHH-hCccccc
Q 029403 82 ATVA-SDTVKHS 92 (194)
Q Consensus 82 ~~I~-s~p~~F~ 92 (194)
+|.. .+|..|.
T Consensus 293 ~Ha~a~GH~n~~ 304 (306)
T COG5539 293 AHALATGHYNFG 304 (306)
T ss_pred HHHHhhcCcccc
Confidence 9988 7766654
No 6
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=98.76 E-value=7.5e-09 Score=78.52 Aligned_cols=58 Identities=28% Similarity=0.436 Sum_probs=52.0
Q ss_pred HHHHHHHHH-hCcccccccccCCChhhhhhhhcCCCCcchhHHHHHHHhHhCceEEEEEcCCCcee
Q 029403 77 QKAIAATVA-SDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIELSILADYYGSEIAAYDIQTTRCD 141 (194)
Q Consensus 77 rk~aA~~I~-s~p~~F~Ea~Lg~~~~eY~~~I~~~~~WGG~IEL~iLS~~~~v~I~v~d~~~~~~~ 141 (194)
|+.++++++ .+++.|.+.+.+. +|+++..|||.+||.++|+.|+++|.|++...++..
T Consensus 30 R~~~~~~l~~~~~~~~~~~~~~~-------~~~~~~~Wg~~~el~a~a~~~~~~I~v~~~~~~~~~ 88 (121)
T PF02338_consen 30 RKAVVDYLRDKNRDKFEEFLEGD-------KMSKPGTWGGEIELQALANVLNRPIIVYSSSDGDNV 88 (121)
T ss_dssp HHHHHHHHHTHTTTHHHHHHHHH-------HHTSTTSHEEHHHHHHHHHHHTSEEEEECETTTBEE
T ss_pred HHHHHHHHHHhccchhhhhhhhh-------hhccccccCcHHHHHHHHHHhCCeEEEEEcCCCCcc
Confidence 788999999 9999999976555 999999999999999999999999999987666643
No 7
>PF10275 Peptidase_C65: Peptidase C65 Otubain; InterPro: IPR019400 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. ; PDB: 4DDG_C 3VON_O 2ZFY_A 4DHZ_A 4DDI_C 1TFF_A 4DHJ_I 4DHI_B.
Probab=96.62 E-value=0.01 Score=50.86 Aligned_cols=60 Identities=15% Similarity=0.193 Sum_probs=46.4
Q ss_pred HHHHHHHHHhCcccccccccC---CChhhhh-hhhcCCCCcchhHHHHHHHhHhCceEEEEEcC
Q 029403 77 QKAIAATVASDTVKHSEAFIG---KSNQDYC-SWIQDPEKWGGAIELSILADYYGSEIAAYDIQ 136 (194)
Q Consensus 77 rk~aA~~I~s~p~~F~Ea~Lg---~~~~eY~-~~I~~~~~WGG~IEL~iLS~~~~v~I~v~d~~ 136 (194)
|-.++.|+++|++.|.+.+.| .+.++|| +.+.....=.+.|.+.|||++++++|.|+-..
T Consensus 143 RLlts~~l~~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v~yld 206 (244)
T PF10275_consen 143 RLLTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALAQALGVPIRVEYLD 206 (244)
T ss_dssp HHHHHHHHHHTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--EEEEESS
T ss_pred HHHHHHHHHhhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHHHHhCCeEEEEEec
Confidence 558889999999999986655 7899999 66777777789999999999999999998654
No 8
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.86 E-value=0.32 Score=42.64 Aligned_cols=68 Identities=15% Similarity=0.166 Sum_probs=52.0
Q ss_pred HHHHHHHHHhCccccccccc-CCChhhhhhhhcCC-CCcchhHHHHHHHhHhCceEEEEEcCCCceeeec
Q 029403 77 QKAIAATVASDTVKHSEAFI-GKSNQDYCSWIQDP-EKWGGAIELSILADYYGSEIAAYDIQTTRCDLYG 144 (194)
Q Consensus 77 rk~aA~~I~s~p~~F~Ea~L-g~~~~eY~~~I~~~-~~WGG~IEL~iLS~~~~v~I~v~d~~~~~~~~fg 144 (194)
|-..+..++++++.|.+.+= |+.+.+||..=-.| ..=-+.|+|-+||+++++.|.|.++.-+.....|
T Consensus 160 RLvtS~~ik~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~ 229 (256)
T KOG3991|consen 160 RLVTSGFIKSNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIRIRVEYVDRGSGDTVN 229 (256)
T ss_pred HHHHHHHHhhChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCceEEEEEecCCCCCCCC
Confidence 44667788899999998555 48999999865554 3346899999999999999999977544444443
No 9
>PHA00616 hypothetical protein
Probab=84.23 E-value=0.63 Score=30.73 Aligned_cols=25 Identities=12% Similarity=-0.065 Sum_probs=22.8
Q ss_pred eecccccccchHHHHHHHHHhCccc
Q 029403 66 CYGVCQIGVIGQKAIAATVASDTVK 90 (194)
Q Consensus 66 rC~~C~~~l~Grk~aA~~I~s~p~~ 90 (194)
+|+-||.++.-.+....|+++++.+
T Consensus 3 qC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 3 QCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred ccchhhHHHhhHHHHHHHHHHhcCC
Confidence 7999999999999999999977765
No 10
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=79.99 E-value=1.5 Score=23.23 Aligned_cols=22 Identities=5% Similarity=0.179 Sum_probs=17.6
Q ss_pred eecccccccchHHHHHHHHHhC
Q 029403 66 CYGVCQIGVIGQKAIAATVASD 87 (194)
Q Consensus 66 rC~~C~~~l~Grk~aA~~I~s~ 87 (194)
+|..|+..+........|++++
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHhh
Confidence 6999999999999999998754
No 11
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=77.05 E-value=2 Score=23.21 Aligned_cols=21 Identities=5% Similarity=0.150 Sum_probs=19.0
Q ss_pred eecccccccchHHHHHHHHHh
Q 029403 66 CYGVCQIGVIGQKAIAATVAS 86 (194)
Q Consensus 66 rC~~C~~~l~Grk~aA~~I~s 86 (194)
+|..|++.+.-+..-..|++.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHhH
Confidence 699999999999999999875
No 12
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=69.88 E-value=4.4 Score=22.26 Aligned_cols=21 Identities=10% Similarity=0.320 Sum_probs=19.1
Q ss_pred eecccccccchHHHHHHHHHh
Q 029403 66 CYGVCQIGVIGQKAIAATVAS 86 (194)
Q Consensus 66 rC~~C~~~l~Grk~aA~~I~s 86 (194)
.|..|++.+..+....+|.++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCcCCHHHHHHHHCc
Confidence 699999999999999999764
No 13
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=67.50 E-value=2.9 Score=36.10 Aligned_cols=38 Identities=11% Similarity=0.072 Sum_probs=28.2
Q ss_pred cccccccceeeecccccccchHHHHHHHHH-hCcccccc
Q 029403 56 TYTDTANFTLCYGVCQIGVIGQKAIAATVA-SDTVKHSE 93 (194)
Q Consensus 56 ~~Tdt~~F~lrC~~C~~~l~Grk~aA~~I~-s~p~~F~E 93 (194)
+.+....-+-+|..|++.|+|..=|.+||. .|++.+.+
T Consensus 69 ~~~e~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ve~ 107 (214)
T PF04959_consen 69 NTKEEDEDKWRCPLCGKLFKGPEFVRKHIFNKHPEKVEE 107 (214)
T ss_dssp EE-SSSSEEEEE-SSS-EESSHHHHHHHHHHH-HHHHHH
T ss_pred HHHHHcCCEECCCCCCcccCChHHHHHHHhhcCHHHHHH
Confidence 344456677899999999999999999999 77777764
No 14
>smart00355 ZnF_C2H2 zinc finger.
Probab=66.83 E-value=5.2 Score=21.07 Aligned_cols=22 Identities=9% Similarity=0.098 Sum_probs=19.1
Q ss_pred eecccccccchHHHHHHHHHhC
Q 029403 66 CYGVCQIGVIGQKAIAATVASD 87 (194)
Q Consensus 66 rC~~C~~~l~Grk~aA~~I~s~ 87 (194)
+|..|++.+.++.....|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 6999999999999999988743
No 15
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=63.92 E-value=7 Score=21.82 Aligned_cols=24 Identities=13% Similarity=0.076 Sum_probs=20.6
Q ss_pred eeecccccccchHHHHHHHHHhCc
Q 029403 65 LCYGVCQIGVIGQKAIAATVASDT 88 (194)
Q Consensus 65 lrC~~C~~~l~Grk~aA~~I~s~p 88 (194)
.+|..|++.+.-+..-.+|.+.+.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 589999999999999999877654
No 16
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=61.51 E-value=8.7 Score=35.76 Aligned_cols=56 Identities=11% Similarity=0.079 Sum_probs=43.9
Q ss_pred HHHHHHHHHhCcccccccccCCChhhhhhhhcCCCCcchhHHHHHHHhH--hCceEEEE
Q 029403 77 QKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIELSILADY--YGSEIAAY 133 (194)
Q Consensus 77 rk~aA~~I~s~p~~F~Ea~Lg~~~~eY~~~I~~~~~WGG~IEL~iLS~~--~~v~I~v~ 133 (194)
+++..+..+..++.|++ +.-+....|.+.-+....||-.||+++.|.. +...+..+
T Consensus 249 ~~~~~dq~~~e~~~~~~-~vt~~~~~y~k~kr~~~~~gnhie~Qa~a~~~~~~~~~~~~ 306 (371)
T KOG2605|consen 249 RRECVDQLKKERDFYED-YVTEDFTSYIKRKRADGEPGNHIEQQAAADIYEEIEKPLNI 306 (371)
T ss_pred HHHHHHHHhhccccccc-ccccchhhcccccccCCCCcchHHHhhhhhhhhhcccccee
Confidence 45677777778888887 5667899999999999999999999999983 33444443
No 17
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=58.35 E-value=11 Score=26.44 Aligned_cols=29 Identities=10% Similarity=0.195 Sum_probs=23.4
Q ss_pred eeeecccccccchHHHHHHHHH-hCccccc
Q 029403 64 TLCYGVCQIGVIGQKAIAATVA-SDTVKHS 92 (194)
Q Consensus 64 ~lrC~~C~~~l~Grk~aA~~I~-s~p~~F~ 92 (194)
..+|..|++.+.......+|++ .+|....
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~ 79 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRN 79 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCcc
Confidence 6899999999999999999999 4555554
No 18
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=54.36 E-value=3.8 Score=23.34 Aligned_cols=22 Identities=9% Similarity=0.211 Sum_probs=18.7
Q ss_pred eeecccccccchHHHHHHHHHh
Q 029403 65 LCYGVCQIGVIGQKAIAATVAS 86 (194)
Q Consensus 65 lrC~~C~~~l~Grk~aA~~I~s 86 (194)
..|..|++.+..+....+|+.+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 3699999999999998888664
No 19
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=50.49 E-value=8.4 Score=27.03 Aligned_cols=32 Identities=13% Similarity=0.008 Sum_probs=26.0
Q ss_pred ccceeeecccccccchHHHHHHHHH-hCccccc
Q 029403 61 ANFTLCYGVCQIGVIGQKAIAATVA-SDTVKHS 92 (194)
Q Consensus 61 ~~F~lrC~~C~~~l~Grk~aA~~I~-s~p~~F~ 92 (194)
..--+||.-|+..+.-++.-..||. +|--.|+
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~~~~~ 46 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHGWLFG 46 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhhhhhc
Confidence 3456899999999999999999998 5555555
No 20
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=48.17 E-value=14 Score=21.61 Aligned_cols=21 Identities=10% Similarity=0.363 Sum_probs=18.1
Q ss_pred eeecccccccchHHHHHHHHH
Q 029403 65 LCYGVCQIGVIGQKAIAATVA 85 (194)
Q Consensus 65 lrC~~C~~~l~Grk~aA~~I~ 85 (194)
..|..|++.+.+.....+|+.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 469999999999888888876
No 21
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=47.08 E-value=32 Score=23.71 Aligned_cols=37 Identities=8% Similarity=0.032 Sum_probs=23.7
Q ss_pred hhcccccccccceeeecccccccch----HHHHHHHHHhCc
Q 029403 52 QRKKTYTDTANFTLCYGVCQIGVIG----QKAIAATVASDT 88 (194)
Q Consensus 52 k~~~~~Tdt~~F~lrC~~C~~~l~G----rk~aA~~I~s~p 88 (194)
-+++-|-.-.+.+++|-.|+..+.+ .....+|.+..|
T Consensus 24 A~aGFyy~~~~d~v~C~~C~~~l~~w~~~Ddp~~~H~~~sp 64 (70)
T PF00653_consen 24 ARAGFYYTGTGDRVRCFYCGLELDNWEPNDDPWEEHKRHSP 64 (70)
T ss_dssp HHTTEEEESSTTEEEETTTTEEEES-STT--HHHHHHHHST
T ss_pred HHCCCEEcCCCCEEEEeccCCEEeCCCCCCCHHHHHHHHCc
Confidence 3445444334899999999998864 445566766554
No 22
>KOG2586 consensus Pyridoxamine-phosphate oxidase [Coenzyme transport and metabolism]
Probab=46.05 E-value=12 Score=32.53 Aligned_cols=38 Identities=16% Similarity=0.242 Sum_probs=28.6
Q ss_pred ccccccchHHHHHHHHHhCcccccccccCCChhhhhhhhcCCCCcchh
Q 029403 69 VCQIGVIGQKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWGGA 116 (194)
Q Consensus 69 ~C~~~l~Grk~aA~~I~s~p~~F~Ea~Lg~~~~eY~~~I~~~~~WGG~ 116 (194)
-|+..+.+|..-+++-+...++|.+. +-|..|++|||-
T Consensus 152 ~qs~vI~~re~l~k~~e~l~~~~~~~----------~~IpkP~swgg~ 189 (228)
T KOG2586|consen 152 PQSEVIPDREELEKKDEELTELFGDE----------QSIPKPDSWGGY 189 (228)
T ss_pred CCCCccCCHHHHHHHHHHHHHHhccc----------ccccCCCcccce
Confidence 36666778888888877777777762 567889999994
No 23
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=41.00 E-value=19 Score=28.71 Aligned_cols=64 Identities=14% Similarity=0.156 Sum_probs=43.6
Q ss_pred hHHHHHHHHHHHHHhhcccccccccceeeecccccccch----------HHHHHHHHHhCcc----------cccccccC
Q 029403 38 GPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVIG----------QKAIAATVASDTV----------KHSEAFIG 97 (194)
Q Consensus 38 ~~vl~~A~~La~~lk~~~~~Tdt~~F~lrC~~C~~~l~G----------rk~aA~~I~s~p~----------~F~Ea~Lg 97 (194)
+...+.|.+|+++ |||.+|+--=.- |.++.+.++++.. .|++.+|-
T Consensus 28 ~~~e~r~~~L~~~--------------LRC~vCqnqsiadSna~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~ 93 (126)
T PRK10144 28 PQQQQQALNIASQ--------------LRCPQCQNQNLLESNAPVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGDFVRY 93 (126)
T ss_pred HHHHHHHHHHHHc--------------CCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEe
Confidence 4556777777665 589999643221 5667777765543 48899999
Q ss_pred CChhhhhhhhcCCCCcchhHHH
Q 029403 98 KSNQDYCSWIQDPEKWGGAIEL 119 (194)
Q Consensus 98 ~~~~eY~~~I~~~~~WGG~IEL 119 (194)
+|+-+-..|+. |.|-+=+
T Consensus 94 ~Pp~~~~t~~L----W~~P~~l 111 (126)
T PRK10144 94 NPPLTGQTLVL----WALPVVL 111 (126)
T ss_pred cCCCCcchHHH----HHHHHHH
Confidence 99888888775 7665433
No 24
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=40.24 E-value=68 Score=25.63 Aligned_cols=68 Identities=18% Similarity=0.213 Sum_probs=47.4
Q ss_pred HHHHHHHhhccccccccccee--------eecccccccc--h---------HHHHHHHHHhCcccccccccCCChhhhhh
Q 029403 45 LKLVKEQQRKKTYTDTANFTL--------CYGVCQIGVI--G---------QKAIAATVASDTVKHSEAFIGKSNQDYCS 105 (194)
Q Consensus 45 ~~La~~lk~~~~~Tdt~~F~l--------rC~~C~~~l~--G---------rk~aA~~I~s~p~~F~Ea~Lg~~~~eY~~ 105 (194)
-++.+++.+...|+-|+++.. +|-.||..+. | +.++-+.|..+|..|.. +
T Consensus 35 ~k~~R~~~q~kp~~G~SksA~KRRAkR~~~C~~CG~~l~~~~~C~~~~T~sq~d~~~~I~~G~~r~~t---E-------- 103 (124)
T PF05515_consen 35 CKLGRKLSQNKPFNGTSKSAAKRRAKRYNRCFKCGRYLHNNGNCRRNTTRSQSDVLEVIREGPIRLLT---E-------- 103 (124)
T ss_pred HHHHHHHHhcCCcCCCcHHHHHHHHHHhCccccccceeecCCcCCCccchhHHHHHHHHhcccceeec---c--------
Confidence 466677777777888988876 7888888762 3 45777778888887763 1
Q ss_pred hhcCCCCcchhHHHHHHHhHh
Q 029403 106 WIQDPEKWGGAIELSILADYY 126 (194)
Q Consensus 106 ~I~~~~~WGG~IEL~iLS~~~ 126 (194)
++-.-|..+|..|+++..
T Consensus 104 ---~~~R~~s~a~~l~~~dl~ 121 (124)
T PF05515_consen 104 ---NPYRKNSNAEQLILSDLE 121 (124)
T ss_pred ---CCCCcchHHHHHHHHHhh
Confidence 223446677777777654
No 25
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=39.71 E-value=16 Score=26.24 Aligned_cols=16 Identities=13% Similarity=0.212 Sum_probs=12.6
Q ss_pred cccceeeecccccccc
Q 029403 60 TANFTLCYGVCQIGVI 75 (194)
Q Consensus 60 t~~F~lrC~~C~~~l~ 75 (194)
-+.+.++|+.||..|.
T Consensus 34 hast~V~C~~CG~~l~ 49 (67)
T COG2051 34 HASTVVTCLICGTTLA 49 (67)
T ss_pred cCceEEEecccccEEE
Confidence 3457789999998875
No 26
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=38.97 E-value=21 Score=28.43 Aligned_cols=65 Identities=14% Similarity=0.162 Sum_probs=43.5
Q ss_pred hHHHHHHHHHHHHHhhcccccccccceeeecccccccch----------HHHHHHHHHhCcc----------cccccccC
Q 029403 38 GPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVIG----------QKAIAATVASDTV----------KHSEAFIG 97 (194)
Q Consensus 38 ~~vl~~A~~La~~lk~~~~~Tdt~~F~lrC~~C~~~l~G----------rk~aA~~I~s~p~----------~F~Ea~Lg 97 (194)
+...+.+.+|.++ |||.+|+---.. |+++.+.|+++.. .|++.+|-
T Consensus 28 ~~~e~r~~~L~~~--------------LRC~vCqnqsiadS~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~~Vly 93 (126)
T TIGR03147 28 PEQRTRAVALAKS--------------LRCPQCQNQNLVESNSPIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGDFVLY 93 (126)
T ss_pred HHHHHHHHHHHHh--------------CCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEe
Confidence 4567778888665 589999644322 5677777775543 48888998
Q ss_pred CChhhhhhhhcCCCCcchhHHHH
Q 029403 98 KSNQDYCSWIQDPEKWGGAIELS 120 (194)
Q Consensus 98 ~~~~eY~~~I~~~~~WGG~IEL~ 120 (194)
+|+-+-..|+. |.|-+=+.
T Consensus 94 ~Pp~~~~t~~L----W~~P~lll 112 (126)
T TIGR03147 94 NPPFKWQTLLL----WLLPVLLL 112 (126)
T ss_pred cCCCCcchHHH----HHHHHHHH
Confidence 88877777764 66654433
No 27
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=38.56 E-value=17 Score=25.23 Aligned_cols=20 Identities=10% Similarity=0.187 Sum_probs=14.2
Q ss_pred ccceeeeccccccc-chHHHH
Q 029403 61 ANFTLCYGVCQIGV-IGQKAI 80 (194)
Q Consensus 61 ~~F~lrC~~C~~~l-~Grk~a 80 (194)
+.|.|+|..|+..+ .-|...
T Consensus 28 aDikikC~gCg~~imlpR~~f 48 (57)
T PF06107_consen 28 ADIKIKCLGCGRQIMLPRSKF 48 (57)
T ss_pred CcEEEEECCCCCEEEEeHHHH
Confidence 56999999998764 344433
No 28
>PF06988 NifT: NifT/FixU protein; InterPro: IPR009727 This family consists of several NifT and FixU bacterial proteins. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in Klebsiella pneumoniae has only a limited effect on nitrogen fixation [].; GO: 0009399 nitrogen fixation; PDB: 2JN4_A.
Probab=38.43 E-value=3.1 Score=29.56 Aligned_cols=24 Identities=29% Similarity=0.638 Sum_probs=17.6
Q ss_pred CCChhhhhhhhcCCCCcchhHHHH
Q 029403 97 GKSNQDYCSWIQDPEKWGGAIELS 120 (194)
Q Consensus 97 g~~~~eY~~~I~~~~~WGG~IEL~ 120 (194)
=|+.+|=+-.+.+++.|||.+.|.
T Consensus 19 KKDLEE~Vv~~E~~~~wGG~v~L~ 42 (64)
T PF06988_consen 19 KKDLEEPVVSMEKPELWGGEVTLA 42 (64)
T ss_dssp TTTEEEEEEEESSSSS-SSEEEET
T ss_pred CCccccceeeeeccCccCCEEEEC
Confidence 456777777788999999987653
No 29
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=37.46 E-value=26 Score=18.99 Aligned_cols=21 Identities=5% Similarity=0.115 Sum_probs=15.9
Q ss_pred eecccccccchHHHHHHHHHhC
Q 029403 66 CYGVCQIGVIGQKAIAATVASD 87 (194)
Q Consensus 66 rC~~C~~~l~Grk~aA~~I~s~ 87 (194)
+|..|...-. ++...+|++.+
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHHhh
Confidence 7999998888 88899998853
No 30
>PRK05111 acetylornithine deacetylase; Provisional
Probab=37.46 E-value=49 Score=29.31 Aligned_cols=48 Identities=17% Similarity=0.293 Sum_probs=26.3
Q ss_pred eeecCcccceeeecCCC--CCC---CCCCeeee---eCCCCCCchHHHHHHHHHHHHHhhc
Q 029403 2 LIYDGLHYDALAISPFE--GAP---EEFDQTIF---PVQKGRTIGPAEDLALKLVKEQQRK 54 (194)
Q Consensus 2 liYsGIHYD~l~l~~~~--~~~---~~~d~tiF---~~~d~~~~~~vl~~A~~La~~lk~~ 54 (194)
|++.| |||+++..+.. ..| ...|-.+| ..+++ .-+..++..++.|++.
T Consensus 74 il~~~-H~Dvvp~~~~~W~~~Pf~~~~~~g~i~GrG~~D~K----g~~a~~l~a~~~l~~~ 129 (383)
T PRK05111 74 LLLAG-HTDTVPFDEGRWTRDPFTLTEHDGKLYGLGTADMK----GFFAFILEALRDIDLT 129 (383)
T ss_pred EEEEe-eeceecCCCCcCcCCCCccEEECCEEEeccccccc----HHHHHHHHHHHHHhhc
Confidence 45666 99999764311 111 12355778 34453 3355666666666653
No 31
>PF01188 MR_MLE: Mandelate racemase / muconate lactonizing enzyme, C-terminal domain; InterPro: IPR013342 Mandelate racemase 5.1.2.2 from EC (MR) and muconate lactonising enzyme 5.5.1.1 from EC (MLE) are two bacterial enzymes involved in aromatic acid catabolism. They catalyse mechanistically distinct reactions yet they are related at the level of their primary, quaternary (homooctamer) and tertiary structures [, ]. A number of other proteins also seem to be evolutionary related to these two enzymes. These include, various plasmid-encoded chloromuconate cycloisomerases 5.5.1.7 from EC, Escherichia coli protein rspA [], E. coli bifunctional DGOA protein, E. coli hypothetical proteins ycjG, yfaW and yidU and a hypothetical protein from Streptomyces ambofaciens []. This entry represents the C-terminal region of these proteins.; PDB: 3QLD_B 3CYJ_C 2QDD_B 3FVD_A 3H7V_A 2OZT_A 3NXL_A 1JDF_D 1JCT_B 1EC9_C ....
Probab=35.62 E-value=25 Score=23.97 Aligned_cols=31 Identities=32% Similarity=0.446 Sum_probs=24.1
Q ss_pred hhhhhhhcCCCCcchhHHHHHHHhHhCceEEE
Q 029403 101 QDYCSWIQDPEKWGGAIELSILADYYGSEIAA 132 (194)
Q Consensus 101 ~eY~~~I~~~~~WGG~IEL~iLS~~~~v~I~v 132 (194)
++| .||.+|-....--++..|++..++||++
T Consensus 36 ~~~-~~iEeP~~~~d~~~~~~l~~~~~~pia~ 66 (67)
T PF01188_consen 36 EDY-EWIEEPLPPDDLDGLAELRQQTSVPIAA 66 (67)
T ss_dssp GGG-SEEESSSSTTSHHHHHHHHHHCSSEEEE
T ss_pred Chh-heeecCCCCCCHHHHHHHHHhCCCCEEe
Confidence 345 7787777776667888899999999874
No 32
>TIGR02934 nifT_nitrog probable nitrogen fixation protein FixT. This largely uncharacterized protein family is assigned a role in nitrogen fixation by two criteria. First, its gene occurs, generally, among genes essential for expression of active nitrogenase. Second, its phylogenetic profile closely matches that of nitrogen-fixing bacteria. However, mutational studies in Klebsiella pneumoniae failed to demonstrate any phenotype for deletion or overexpression of the protein.
Probab=35.00 E-value=12 Score=26.89 Aligned_cols=23 Identities=26% Similarity=0.502 Sum_probs=18.5
Q ss_pred CCChhhhhhhhcCCCCcchhHHH
Q 029403 97 GKSNQDYCSWIQDPEKWGGAIEL 119 (194)
Q Consensus 97 g~~~~eY~~~I~~~~~WGG~IEL 119 (194)
=|+.+|=+-.+.+++.|||.+-|
T Consensus 19 KKDLEE~Vv~~e~~~~WGG~v~L 41 (67)
T TIGR02934 19 KKDLEEVIVSVEKEELWGGWVTL 41 (67)
T ss_pred CCcchhheeeeecCccccCEEEE
Confidence 46788888889999999997543
No 33
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=34.84 E-value=18 Score=32.49 Aligned_cols=37 Identities=14% Similarity=0.195 Sum_probs=23.0
Q ss_pred cceeeecccccccchHHHHHHHHHhCcccccccccCC
Q 029403 62 NFTLCYGVCQIGVIGQKAIAATVASDTVKHSEAFIGK 98 (194)
Q Consensus 62 ~F~lrC~~C~~~l~Grk~aA~~I~s~p~~F~Ea~Lg~ 98 (194)
.=.-+|.+|++..|---+-+-||++|.--+.=.+.||
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGK 195 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGK 195 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccCCCcccccccc
Confidence 3445777777777766666677777764444334444
No 34
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=34.72 E-value=33 Score=19.49 Aligned_cols=20 Identities=5% Similarity=0.114 Sum_probs=15.4
Q ss_pred eeecccccccchHHHHHHHHH
Q 029403 65 LCYGVCQIGVIGQKAIAATVA 85 (194)
Q Consensus 65 lrC~~C~~~l~Grk~aA~~I~ 85 (194)
+.|..||..+ +......|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 5799999988 6677777754
No 35
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=34.30 E-value=23 Score=34.14 Aligned_cols=62 Identities=15% Similarity=0.196 Sum_probs=39.0
Q ss_pred ecCcccceeeecCCCCCCCCCCeeeeeCCCCCCchHHHHHHHHHHHHHhhcccccccccceeeecccccccc
Q 029403 4 YDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVI 75 (194)
Q Consensus 4 YsGIHYD~l~l~~~~~~~~~~d~tiF~~~d~~~~~~vl~~A~~La~~lk~~~~~Tdt~~F~lrC~~C~~~l~ 75 (194)
|.||||++--.-. .++|.--+-+.+.+ -+-++.+-.++.+++|..-.+-=.|.|++|++-|-
T Consensus 86 yh~ihk~vy~Wf~-----IdfD~fgrtTT~~q-----T~i~Q~iF~kl~~ng~~se~tv~qLyC~vc~~fla 147 (567)
T KOG1247|consen 86 YHGIHKVVYDWFK-----IDFDEFGRTTTKTQ-----TEICQDIFSKLYDNGYLSEQTVKQLYCEVCDTFLA 147 (567)
T ss_pred cchhHHHHHHhhc-----ccccccCcccCcch-----hHHHHHHhhchhhcCCcccceeeeEEehhhccccc
Confidence 7899998864421 12232222222322 35677777788888888777777888888876654
No 36
>PRK13009 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=32.92 E-value=2.3e+02 Score=24.88 Aligned_cols=13 Identities=31% Similarity=0.593 Sum_probs=9.4
Q ss_pred eeecCcccceeeec
Q 029403 2 LIYDGLHYDALAIS 15 (194)
Q Consensus 2 liYsGIHYD~l~l~ 15 (194)
|++.| |+|+++..
T Consensus 61 i~l~~-H~D~Vp~g 73 (375)
T PRK13009 61 LCFAG-HTDVVPPG 73 (375)
T ss_pred EEEEe-ecccCCCC
Confidence 45566 99999653
No 37
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=32.59 E-value=25 Score=27.42 Aligned_cols=24 Identities=8% Similarity=0.112 Sum_probs=20.8
Q ss_pred cccccccccceeeecccccccchH
Q 029403 54 KKTYTDTANFTLCYGVCQIGVIGQ 77 (194)
Q Consensus 54 ~~~~Tdt~~F~lrC~~C~~~l~Gr 77 (194)
++..+++...+|+|..|+..+.-.
T Consensus 33 ~~GW~~~~~d~l~C~~C~~~l~~~ 56 (133)
T PF07967_consen 33 RRGWICVSKDMLKCESCGARLCVK 56 (133)
T ss_pred HcCCCcCCCCEEEeCCCCCEEEEe
Confidence 478999999999999999887655
No 38
>PHA02768 hypothetical protein; Provisional
Probab=30.03 E-value=44 Score=23.01 Aligned_cols=26 Identities=12% Similarity=0.156 Sum_probs=22.0
Q ss_pred eecccccccchHHHHHHHHHhCcccc
Q 029403 66 CYGVCQIGVIGQKAIAATVASDTVKH 91 (194)
Q Consensus 66 rC~~C~~~l~Grk~aA~~I~s~p~~F 91 (194)
+|..||+.+.-...-..|.+.|+.-|
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~H~k~~ 32 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRKHNTNL 32 (55)
T ss_pred CcchhCCeeccHHHHHHHHHhcCCcc
Confidence 89999999998888899999887444
No 39
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=29.73 E-value=55 Score=27.01 Aligned_cols=69 Identities=20% Similarity=0.220 Sum_probs=47.2
Q ss_pred hHHHHHHHHHHHHHhhcccccccccceeeecccccccc----------hHHHHHHHHHhCc----------ccccccccC
Q 029403 38 GPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVI----------GQKAIAATVASDT----------VKHSEAFIG 97 (194)
Q Consensus 38 ~~vl~~A~~La~~lk~~~~~Tdt~~F~lrC~~C~~~l~----------Grk~aA~~I~s~p----------~~F~Ea~Lg 97 (194)
..-.+.|..|.++ |||.+|+--=. =|.++-+-++++. ..|+|.++=
T Consensus 32 ~~qe~ra~~Lt~~--------------LRCp~CQNqsIadSnA~IA~DlR~~V~e~l~eGkS~~qIid~mVaRYG~FVly 97 (153)
T COG3088 32 PAQEQRARALTEE--------------LRCPQCQNQSIADSNAPIARDLRHQVYELLQEGKSDQQIIDYMVARYGEFVLY 97 (153)
T ss_pred HHHHHHHHHHHHh--------------cCCCcCCCCChhhhccHHHHHHHHHHHHHHHcCCcHHHHHHHHHHhhcceeee
Confidence 3446677777665 58999953211 1445555555443 348899999
Q ss_pred CChhhhhhhhcCCCCcchhHHHHHHHh
Q 029403 98 KSNQDYCSWIQDPEKWGGAIELSILAD 124 (194)
Q Consensus 98 ~~~~eY~~~I~~~~~WGG~IEL~iLS~ 124 (194)
+||-.+..|+. ||+=+=+.+|.-
T Consensus 98 ~Pp~~~~T~lL----W~~Pv~llllG~ 120 (153)
T COG3088 98 KPPLTGQTLLL----WGLPVVLLLLGG 120 (153)
T ss_pred cCCCchhHHHH----HHhHHHHHHHHH
Confidence 99999999987 999887776653
No 40
>PRK13007 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=29.25 E-value=1e+02 Score=26.93 Aligned_cols=48 Identities=10% Similarity=0.221 Sum_probs=25.8
Q ss_pred eeecCcccceeeecCCCCCCCCCCeeeeeCCCCCCchHHHHHHHHHHHHHh
Q 029403 2 LIYDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQ 52 (194)
Q Consensus 2 liYsGIHYD~l~l~~~~~~~~~~d~tiF~~~d~~~~~~vl~~A~~La~~lk 52 (194)
|+++| |||+++... +-.+...|-.+|...-.+. ..-+..++.+++.++
T Consensus 64 i~l~~-H~Dtvp~~~-~~~~~~~~g~i~GrG~~D~-Kg~~a~~l~a~~~l~ 111 (352)
T PRK13007 64 VVLAG-HLDTVPVAD-NLPSRREGDRLYGCGASDM-KSGLAVMLHLAATLA 111 (352)
T ss_pred EEEEc-cccccCCCC-CCCcceeCCEEEccCcccc-cHHHHHHHHHHHHhh
Confidence 56677 999998652 1112234567776331111 233555566666663
No 41
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=26.84 E-value=51 Score=32.01 Aligned_cols=34 Identities=18% Similarity=0.045 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhhc--cc-ccccccceeeecccccccch
Q 029403 41 EDLALKLVKEQQRK--KT-YTDTANFTLCYGVCQIGVIG 76 (194)
Q Consensus 41 l~~A~~La~~lk~~--~~-~Tdt~~F~lrC~~C~~~l~G 76 (194)
.++.++|++.+-++ +| +++|..+ +|+.||...+|
T Consensus 494 ~~al~~lv~~a~~~~~~y~~~~~p~~--~C~~CG~~~~~ 530 (555)
T cd01675 494 PEALEALVKKAAKRGVIYFGINTPID--ICNDCGYIGEG 530 (555)
T ss_pred HHHHHHHHHHHHHcCCceEEEecCCc--cCCCCCCCCcC
Confidence 56666666665443 55 7788877 99999976544
No 42
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=25.51 E-value=63 Score=28.53 Aligned_cols=28 Identities=25% Similarity=0.468 Sum_probs=23.2
Q ss_pred hHHHHHHHhHhCceEEEEEcCCCceeee
Q 029403 116 AIELSILADYYGSEIAAYDIQTTRCDLY 143 (194)
Q Consensus 116 ~IEL~iLS~~~~v~I~v~d~~~~~~~~f 143 (194)
=|.-.+|++.|+++|.|.+++++++-.|
T Consensus 223 ii~~~~L~eiydm~i~v~~i~g~kIcvy 250 (252)
T COG4604 223 IIQPEILSEIYDMDIPVEEINGKKICVY 250 (252)
T ss_pred hcCHHHHHHHhcCCceeEEeCCcEEEEE
Confidence 4667899999999999999987776544
No 43
>PRK08651 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=25.46 E-value=2.6e+02 Score=24.83 Aligned_cols=48 Identities=15% Similarity=0.156 Sum_probs=25.0
Q ss_pred eecCcccceeeecCCC--CCCC---CCCeeeee---CCCCCCchHHHHHHHHHHHHHhhcc
Q 029403 3 IYDGLHYDALAISPFE--GAPE---EFDQTIFP---VQKGRTIGPAEDLALKLVKEQQRKK 55 (194)
Q Consensus 3 iYsGIHYD~l~l~~~~--~~~~---~~d~tiF~---~~d~~~~~~vl~~A~~La~~lk~~~ 55 (194)
++.| |+|+++..... ..|- ..|..++. .+++. -+..++..++.+++.+
T Consensus 78 ll~~-HlDtvp~~~~~~~~~Pf~~~~~~~~~~grG~~D~k~----~~~~~l~a~~~l~~~~ 133 (394)
T PRK08651 78 HFNG-HYDVVPPGEGWSVNVPFEPKVKDGKVYGRGASDMKG----GIAALLAAFERLDPAG 133 (394)
T ss_pred EEEe-eeeeecCCCCccccCCCCcEEECCEEEecCccccch----HHHHHHHHHHHHHhcC
Confidence 4444 99999765221 1111 12446665 33332 3566666666666554
No 44
>PRK10963 hypothetical protein; Provisional
Probab=25.21 E-value=54 Score=27.88 Aligned_cols=37 Identities=11% Similarity=0.170 Sum_probs=30.3
Q ss_pred hHHHHHHHHHhCcccccccccCCChhhhhhhhcCCCCcchhHH
Q 029403 76 GQKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIE 118 (194)
Q Consensus 76 Grk~aA~~I~s~p~~F~Ea~Lg~~~~eY~~~I~~~~~WGG~IE 118 (194)
.++.+++|.+.||+-|.. ..+-...|+-|..+||+|=
T Consensus 4 ~~~~V~~yL~~~PdFf~~------h~~Ll~~L~lph~~~gaVS 40 (223)
T PRK10963 4 DDRAVVDYLLQNPDFFIR------NARLVEQMRVPHPVRGTVS 40 (223)
T ss_pred CHHHHHHHHHHCchHHhh------CHHHHHhccCCCCCCCeec
Confidence 368899999999998886 5666778988988998763
No 45
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=24.98 E-value=50 Score=26.73 Aligned_cols=56 Identities=21% Similarity=0.283 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHHHhhcccccccccceeeecccccc-cch---------HHHHHHHHHhCcc----------cccccccC
Q 029403 38 GPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIG-VIG---------QKAIAATVASDTV----------KHSEAFIG 97 (194)
Q Consensus 38 ~~vl~~A~~La~~lk~~~~~Tdt~~F~lrC~~C~~~-l~G---------rk~aA~~I~s~p~----------~F~Ea~Lg 97 (194)
+..-+.+.+|.+ .|||.+|+-. +-. |+++.+.++++-. .|+|.+|-
T Consensus 28 ~~~e~r~~~l~~--------------~LrCp~Cq~qsi~~s~a~~A~dmR~~I~~~l~~G~s~~eI~~~~v~rYG~~Vl~ 93 (148)
T PF03918_consen 28 PEQEARARELAK--------------ELRCPVCQNQSIADSNAPIARDMRREIREMLAEGKSDEEIIDYFVERYGEFVLY 93 (148)
T ss_dssp HHHHHHHHHHHH--------------CCE-TTTTS-CTTT--SHHHHHHHHHHHHHHHHT--HHHHHHHHHHHHTTT-EE
T ss_pred hhHHHHHHHHHh--------------cccCCCCCCCchhhcCcHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCcceee
Confidence 445666666654 3689998532 221 4666666665443 47788888
Q ss_pred CChhhhhhhh
Q 029403 98 KSNQDYCSWI 107 (194)
Q Consensus 98 ~~~~eY~~~I 107 (194)
+|+.+-..|+
T Consensus 94 ~Pp~~~~~~~ 103 (148)
T PF03918_consen 94 EPPFKGFTWL 103 (148)
T ss_dssp S--S------
T ss_pred cCCCCccHHH
Confidence 8876555554
No 46
>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=24.96 E-value=62 Score=29.09 Aligned_cols=48 Identities=17% Similarity=0.254 Sum_probs=33.4
Q ss_pred CeeecCcc--cce--eeecCCCCCCCCCCeeeeeCCCCCCchHHHHHHHHHHHHHhhcccccc
Q 029403 1 MLIYDGLH--YDA--LAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKTYTD 59 (194)
Q Consensus 1 ~liYsGIH--YD~--l~l~~~~~~~~~~d~tiF~~~d~~~~~~vl~~A~~La~~lk~~~~~Td 59 (194)
+|+|.||| |.. ..+. .-+|-.|| ++. +.-++..+++-+..++++|..+
T Consensus 120 vIivEGLhg~~~~~~~~lr------~~~DlkIf-Vd~----~~dlr~irRI~RD~~ERGrs~E 171 (277)
T cd02029 120 LLFYEGLHGGVVTEGYNVA------QHADLLVG-VVP----IINLEWIQKIHRDTAERGYSAE 171 (277)
T ss_pred EEEECCCCcccccccHHHH------HhCCeEEE-ecC----cHHHHHHHHHHhhhHhhCCCHH
Confidence 47899999 321 1222 12688999 332 4558999999999999999874
No 47
>TIGR01902 dapE-lys-deAc N-acetyl-ornithine/N-acetyl-lysine deacetylase. This clade of mainly archaeal and related bacterial species contains two characterized enzymes, an deacetylase with specificity for both N-acetyl-ornithine and N-acetyl-lysine from Thermus which is found within a lysine biosynthesis operon, and a fusion protein with acetyl-glutamate kinase (an enzyme of ornithine biosynthesis) from Lactobacillus. It is possible that all of the sequences within this clade have dual specificity, or that a mix of specificities have evolved within this clade.
Probab=24.42 E-value=1.2e+02 Score=26.55 Aligned_cols=47 Identities=9% Similarity=-0.065 Sum_probs=24.0
Q ss_pred eeecCcccceeeecCCCCCCCCCCeeeeeCC--CCCCchHHHHHHHHHHHHHhhcc
Q 029403 2 LIYDGLHYDALAISPFEGAPEEFDQTIFPVQ--KGRTIGPAEDLALKLVKEQQRKK 55 (194)
Q Consensus 2 liYsGIHYD~l~l~~~~~~~~~~d~tiF~~~--d~~~~~~vl~~A~~La~~lk~~~ 55 (194)
|+++| |||+++- .-.+...|-.+|-.. |. ..-+.+.+...+.+++.+
T Consensus 53 i~~~~-H~D~vp~---~~~~~~~~g~i~GrG~~D~---Kg~~aa~l~a~~~l~~~~ 101 (336)
T TIGR01902 53 ILLAG-HVDTVPG---YIPVKIEGGLLYGRGAVDA---KGPLIAMIFATWLLNEKG 101 (336)
T ss_pred EEEEc-cccccCC---CcccEEeCCEEEEecccCC---CcHHHHHHHHHHHHHhCC
Confidence 56677 9999952 111223355788632 31 223444444445555443
No 48
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=24.32 E-value=27 Score=21.32 Aligned_cols=14 Identities=21% Similarity=0.256 Sum_probs=11.3
Q ss_pred eeecccccccchHH
Q 029403 65 LCYGVCQIGVIGQK 78 (194)
Q Consensus 65 lrC~~C~~~l~Grk 78 (194)
-+|.+||.+..|++
T Consensus 3 ~~C~~CG~i~~g~~ 16 (34)
T cd00729 3 WVCPVCGYIHEGEE 16 (34)
T ss_pred EECCCCCCEeECCc
Confidence 48999999888753
No 49
>PRK06446 hypothetical protein; Provisional
Probab=23.83 E-value=1.8e+02 Score=26.66 Aligned_cols=14 Identities=36% Similarity=0.767 Sum_probs=10.3
Q ss_pred eeecCcccceeeecC
Q 029403 2 LIYDGLHYDALAISP 16 (194)
Q Consensus 2 liYsGIHYD~l~l~~ 16 (194)
|++.| |||+++..+
T Consensus 65 vll~g-H~DvVp~~~ 78 (436)
T PRK06446 65 LLIYN-HYDVQPVDP 78 (436)
T ss_pred EEEEe-cccCCCCCc
Confidence 45666 999997643
No 50
>PRK06915 acetylornithine deacetylase; Validated
Probab=23.59 E-value=1.3e+02 Score=27.16 Aligned_cols=53 Identities=13% Similarity=0.114 Sum_probs=25.7
Q ss_pred eeecCcccceeeecCCC------CCCCCCCeeeeeCCCCCCchHHHHHHHHHHHHHhhccc
Q 029403 2 LIYDGLHYDALAISPFE------GAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKT 56 (194)
Q Consensus 2 liYsGIHYD~l~l~~~~------~~~~~~d~tiF~~~d~~~~~~vl~~A~~La~~lk~~~~ 56 (194)
|++.| |||+++..... -.+...|-++|...-.+. ..-+..++..++.|++++.
T Consensus 96 l~l~~-H~Dtvp~~~~~~W~~~Pf~~~~~~g~lyGrG~~D~-Kgg~aa~l~a~~~l~~~~~ 154 (422)
T PRK06915 96 MILNG-HIDVVPEGDVNQWDHHPYSGEVIGGRIYGRGTTDM-KGGNVALLLAMEALIESGI 154 (422)
T ss_pred EEEEe-eccccCCCCcccCcCCCCCceEECCEEEecCcccc-hHHHHHHHHHHHHHHHcCC
Confidence 45666 99999764221 111123556776331100 1233444555566666553
No 51
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=23.51 E-value=1e+02 Score=20.74 Aligned_cols=26 Identities=8% Similarity=-0.000 Sum_probs=17.4
Q ss_pred hhcccccccccceeeecccccccchH
Q 029403 52 QRKKTYTDTANFTLCYGVCQIGVIGQ 77 (194)
Q Consensus 52 k~~~~~Tdt~~F~lrC~~C~~~l~Gr 77 (194)
-..+-|-.-.+..++|-.|+..+.+.
T Consensus 22 a~~Gfyy~~~~d~v~C~~C~~~~~~w 47 (69)
T cd00022 22 AEAGFYYTGRGDEVKCFFCGLELKNW 47 (69)
T ss_pred HHcCCeEcCCCCEEEeCCCCCCccCC
Confidence 34444433335789999999988763
No 52
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=23.31 E-value=85 Score=29.47 Aligned_cols=27 Identities=19% Similarity=0.299 Sum_probs=21.7
Q ss_pred ccccceeeecccccccch-HHHHHHHHH
Q 029403 59 DTANFTLCYGVCQIGVIG-QKAIAATVA 85 (194)
Q Consensus 59 dt~~F~lrC~~C~~~l~G-rk~aA~~I~ 85 (194)
.-++|.+.|+-|+....| |.+.-+|.-
T Consensus 139 edt~fslqClFCn~e~lgnRs~~l~Hlf 166 (423)
T KOG2482|consen 139 EDTIFSLQCLFCNNEGLGNRSEILEHLF 166 (423)
T ss_pred cCCeeeeEEEEecchhcccHHHHHHHHH
Confidence 556799999999998887 677777754
No 53
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=23.26 E-value=1.4e+02 Score=28.81 Aligned_cols=68 Identities=13% Similarity=0.167 Sum_probs=50.7
Q ss_pred hHHHHHHHHHHHHHhhcccccccccceeeecccccccchHHHHHHHHH-hCcccccc---cccCCChhhhhhhhcCCCCc
Q 029403 38 GPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVIGQKAIAATVA-SDTVKHSE---AFIGKSNQDYCSWIQDPEKW 113 (194)
Q Consensus 38 ~~vl~~A~~La~~lk~~~~~Tdt~~F~lrC~~C~~~l~Grk~aA~~I~-s~p~~F~E---a~Lg~~~~eY~~~I~~~~~W 113 (194)
..++..|+.+|++-++=+ | -.|..|.+.+.-...-..|+. .|+..+.+ .++.+.+++.-..+.....|
T Consensus 39 ~~~Lseal~fak~n~sWr-------F-WiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~~w~e~I~~~~W 110 (466)
T PF04780_consen 39 ADALSEALSFAKENKSWR-------F-WICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDDDWAEMISVGSW 110 (466)
T ss_pred HHHHHHHHHHHHhcCcee-------E-eeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCHHHHHHHhcCCC
Confidence 567888888887733322 2 268889999999999999999 88888865 45666666666666677888
No 54
>cd00814 MetRS_core catalytic core domain of methioninyl-tRNA synthetases. Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function.
Probab=22.59 E-value=2.4e+02 Score=24.95 Aligned_cols=36 Identities=8% Similarity=0.047 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHhhcccccccccceeeeccccccc
Q 029403 39 PAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGV 74 (194)
Q Consensus 39 ~vl~~A~~La~~lk~~~~~Tdt~~F~lrC~~C~~~l 74 (194)
.-...+.++.++|+++++..-...=..-|..|+.-|
T Consensus 96 ~~~~~v~~i~~~L~ekG~iY~~~~~~~yc~~~~~~l 131 (319)
T cd00814 96 RHKEIVQEFFKKLYENGYIYEGEYEGLYCVSCERFL 131 (319)
T ss_pred HHHHHHHHHHHHHHHCCCEEeeeeeeeECCCCCcEe
Confidence 345678899999999988754444455788888655
No 55
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.14 E-value=63 Score=28.70 Aligned_cols=15 Identities=20% Similarity=0.250 Sum_probs=11.8
Q ss_pred cccccceeeeccccc
Q 029403 58 TDTANFTLCYGVCQI 72 (194)
Q Consensus 58 Tdt~~F~lrC~~C~~ 72 (194)
-=.+-|++||+.||-
T Consensus 34 Rlm~Pf~~rC~tCge 48 (253)
T KOG2989|consen 34 RLMTPFRLRCNTCGE 48 (253)
T ss_pred eecccceeecccccc
Confidence 456779999999953
No 56
>PF12907 zf-met2: Zinc-binding
Probab=22.11 E-value=48 Score=21.34 Aligned_cols=27 Identities=4% Similarity=0.204 Sum_probs=20.0
Q ss_pred eeeeccccccc---chHHHHHHHHH-hCccc
Q 029403 64 TLCYGVCQIGV---IGQKAIAATVA-SDTVK 90 (194)
Q Consensus 64 ~lrC~~C~~~l---~Grk~aA~~I~-s~p~~ 90 (194)
.++|.+|...+ .-+..-.+|.. .||..
T Consensus 1 ~i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 1 NIICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred CcCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 36899998544 45788889988 77764
No 57
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=21.76 E-value=83 Score=27.73 Aligned_cols=30 Identities=13% Similarity=0.181 Sum_probs=19.0
Q ss_pred HHHHHHHHHhhccc---ccc-cccceeeeccccc
Q 029403 43 LALKLVKEQQRKKT---YTD-TANFTLCYGVCQI 72 (194)
Q Consensus 43 ~A~~La~~lk~~~~---~Td-t~~F~lrC~~C~~ 72 (194)
.+..-++++|.++. ++- .+-|++||+.|+.
T Consensus 17 L~~~~~~KlK~arprglSiRL~TPF~~RCL~C~~ 50 (272)
T COG5134 17 LAKRKFDKLKNARPRGLSIRLETPFPVRCLNCEN 50 (272)
T ss_pred hHHHHHHHhcccCcccceEEeccCcceeecchhh
Confidence 44555556666444 333 3569999999963
No 58
>TIGR01246 dapE_proteo succinyl-diaminopimelate desuccinylase, proteobacterial clade. This model describes a proteobacterial subset of succinyl-diaminopimelate desuccinylases. An experimentally confirmed Gram-positive lineage succinyl-diaminopimelate desuccinylase has been described for Corynebacterium glutamicum, and a neighbor-joining tree shows the seed members, SP:Q59284, and putative archaeal members such as TrEMBL:O58003 in a single clade. However, the archaeal members differ substantially, share a number of motifs with acetylornithine deacetylases rather than succinyl-diaminopimelate desuccinylases, and are not taken as trusted examples of succinyl-diaminopimelate desuccinylases. This model is limited to proteobacterial members for this reason.
Probab=21.23 E-value=5e+02 Score=22.80 Aligned_cols=13 Identities=31% Similarity=0.647 Sum_probs=9.9
Q ss_pred eeecCcccceeeec
Q 029403 2 LIYDGLHYDALAIS 15 (194)
Q Consensus 2 liYsGIHYD~l~l~ 15 (194)
|++.| |+|+++..
T Consensus 58 i~~~~-H~DtVp~~ 70 (370)
T TIGR01246 58 LAFAG-HTDVVPAG 70 (370)
T ss_pred EEEEc-cccccCCC
Confidence 45666 99999764
No 59
>COG5554 NifU Nitrogen fixation protein [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.56 E-value=22 Score=25.21 Aligned_cols=22 Identities=23% Similarity=0.463 Sum_probs=16.5
Q ss_pred CCChhhhhhhhcCCCCcchhHH
Q 029403 97 GKSNQDYCSWIQDPEKWGGAIE 118 (194)
Q Consensus 97 g~~~~eY~~~I~~~~~WGG~IE 118 (194)
-|+.+|=.-...+.+-|||.|=
T Consensus 18 KKDLEEpii~V~nedlwGG~il 39 (69)
T COG5554 18 KKDLEEPIIVVKNEDLWGGKIL 39 (69)
T ss_pred ccccccceEEEeccccccceEE
Confidence 3556666667788999999874
No 60
>PF08867 FRG: FRG domain; InterPro: IPR014966 This entry contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised.
Probab=20.01 E-value=81 Score=23.39 Aligned_cols=23 Identities=26% Similarity=0.310 Sum_probs=20.4
Q ss_pred HHHHHHHhHhCceEEEEEcCCCc
Q 029403 117 IELSILADYYGSEIAAYDIQTTR 139 (194)
Q Consensus 117 IEL~iLS~~~~v~I~v~d~~~~~ 139 (194)
+|+++|++|||+|-.-+|..+..
T Consensus 61 ~~~lal~QHyGlpTrLLDwT~np 83 (104)
T PF08867_consen 61 LEWLALAQHYGLPTRLLDWTSNP 83 (104)
T ss_pred HHHHHHHhhcCCCccceeecCCH
Confidence 89999999999999999985543
Done!