Query 031421
Match_columns 160
No_of_seqs 163 out of 1143
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 13:52:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031421.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031421hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02338 OTU: OTU-like cystein 100.0 3.9E-28 8.4E-33 169.0 8.9 107 26-138 1-121 (121)
2 KOG2606 OTU (ovarian tumor)-li 99.9 2.7E-27 5.9E-32 182.4 10.7 142 2-146 141-300 (302)
3 KOG2605 OTU (ovarian tumor)-li 99.8 5.4E-19 1.2E-23 142.8 6.9 157 3-159 201-363 (371)
4 KOG3288 OTU-like cysteine prot 99.8 8.1E-19 1.7E-23 133.1 6.7 123 20-145 110-234 (307)
5 PF10275 Peptidase_C65: Peptid 99.7 1.3E-16 2.9E-21 123.6 11.7 94 49-143 141-244 (244)
6 KOG3991 Uncharacterized conser 99.7 5.1E-16 1.1E-20 116.2 9.4 94 48-144 157-256 (256)
7 COG5539 Predicted cysteine pro 99.0 6.3E-11 1.4E-15 91.9 0.4 131 7-141 158-304 (306)
8 COG5539 Predicted cysteine pro 99.0 1.9E-10 4.1E-15 89.3 1.8 110 27-142 119-230 (306)
9 PF05415 Peptidase_C36: Beet n 97.1 0.0018 3.9E-08 42.1 5.5 97 25-140 3-103 (104)
10 PF05412 Peptidase_C33: Equine 96.0 0.0062 1.3E-07 40.9 2.4 83 25-145 4-87 (108)
11 PF05381 Peptidase_C21: Tymovi 95.8 0.13 2.8E-06 34.6 8.2 91 28-140 2-94 (104)
12 PRK09784 hypothetical protein; 85.7 0.49 1.1E-05 36.9 1.7 24 16-39 196-219 (417)
13 PF05379 Peptidase_C23: Carlav 79.9 14 0.00031 24.1 8.5 86 29-139 3-88 (89)
14 KOG4345 NF-kappa B regulator A 74.1 3 6.4E-05 37.1 2.8 54 89-143 223-291 (774)
15 COG5007 Predicted transcriptio 69.3 4.2 9.2E-05 25.9 2.0 55 7-61 2-60 (80)
16 KOG3348 BolA (bacterial stress 62.6 6.7 0.00014 25.4 2.0 58 2-59 3-64 (85)
17 smart00718 DM4_12 DM4/DM12 fam 56.7 21 0.00045 23.5 3.7 48 4-59 6-54 (95)
18 PF05413 Peptidase_C34: Putati 51.9 22 0.00047 22.9 3.0 23 22-44 2-24 (92)
19 cd03346 eu_TrpOH Eukaryotic tr 43.6 15 0.00032 29.4 1.5 94 7-103 108-211 (287)
20 KOG4100 Uncharacterized conser 38.9 39 0.00084 23.2 2.8 56 32-88 15-79 (125)
21 cd00361 arom_aa_hydroxylase Bi 37.3 8.6 0.00019 29.5 -0.6 91 7-100 48-149 (221)
22 TIGR03277 methan_mark_9 putati 36.6 32 0.00069 23.3 2.1 32 30-61 77-109 (109)
23 PF01381 HTH_3: Helix-turn-hel 36.4 46 0.001 18.7 2.6 30 74-103 23-52 (55)
24 PF08715 Viral_protease: Papai 36.1 62 0.0014 26.3 4.1 48 19-67 101-150 (320)
25 TIGR02934 nifT_nitrog probable 34.5 3.8 8.2E-05 25.4 -2.4 28 65-92 13-41 (67)
26 KOG0256 1-aminocyclopropane-1- 31.5 92 0.002 26.5 4.4 57 8-67 87-146 (471)
27 TIGR01270 Trp_5_monoox tryptop 31.4 31 0.00068 29.5 1.7 90 8-100 238-337 (464)
28 PRK14670 uvrC excinuclease ABC 30.0 1.8E+02 0.0038 25.8 6.1 61 3-63 111-176 (574)
29 cd03345 eu_TyrOH Eukaryotic ty 29.1 36 0.00078 27.4 1.6 89 8-99 108-206 (298)
30 PRK12334 nucleoside triphospha 28.9 1.6E+02 0.0036 23.4 5.3 58 3-60 196-259 (277)
31 cd02665 Peptidase_C19I A subfa 28.8 80 0.0017 24.3 3.5 32 29-60 7-38 (228)
32 TIGR01268 Phe4hydrox_tetr phen 28.6 34 0.00074 29.0 1.5 93 8-103 211-313 (436)
33 PF08373 RAP: RAP domain; Int 27.5 63 0.0014 18.5 2.2 15 12-26 24-38 (58)
34 KOG3346 Phosphatidylethanolami 27.3 95 0.0021 23.2 3.5 42 118-159 44-87 (185)
35 KOG3325 Membrane coat complex 26.1 79 0.0017 23.1 2.8 25 85-109 92-116 (183)
36 COG5440 Uncharacterized conser 25.4 57 0.0012 23.6 2.0 33 6-39 5-37 (161)
37 PF03819 MazG: MazG nucleotide 25.0 1.6E+02 0.0035 17.9 3.8 35 29-63 34-72 (74)
38 cd03347 eu_PheOH Eukaryotic ph 24.8 41 0.00089 27.2 1.3 91 8-101 109-209 (306)
39 cd04240 AAK_UC AAK_UC: Unchara 24.8 1.5E+02 0.0032 22.2 4.2 35 9-44 13-51 (203)
40 PF01870 Hjc: Archaeal hollida 24.0 1.4E+02 0.003 19.4 3.4 24 8-31 3-26 (88)
41 KOG2947 Carbohydrate kinase [C 24.0 84 0.0018 24.9 2.8 24 21-44 252-275 (308)
42 PF10588 NADH-G_4Fe-4S_3: NADH 24.0 64 0.0014 17.6 1.6 17 87-103 22-38 (41)
43 KOG2605 OTU (ovarian tumor)-li 23.4 59 0.0013 27.0 2.0 45 66-110 3-47 (371)
44 cd03348 pro_PheOH Prokaryotic 23.1 27 0.00058 27.0 -0.0 90 7-100 54-155 (228)
45 TIGR00124 cit_ly_ligase [citra 23.1 1.1E+02 0.0024 25.0 3.5 55 11-78 273-327 (332)
46 TIGR01269 Tyr_3_monoox tyrosin 22.9 55 0.0012 27.9 1.7 90 7-99 231-330 (457)
47 PRK11913 phhA phenylalanine 4- 22.5 36 0.00078 27.1 0.5 90 7-99 70-170 (275)
48 PF02479 Herpes_IE68: Herpesvi 21.9 93 0.002 22.0 2.4 32 27-58 37-68 (132)
49 PF02542 YgbB: YgbB family; I 21.8 62 0.0013 23.5 1.6 17 26-42 34-50 (157)
50 cd02011 TPP_PK Thiamine pyroph 21.5 1.8E+02 0.0039 22.5 4.2 24 7-32 136-159 (227)
51 PRK13619 psbV cytochrome c-550 20.8 1.4E+02 0.0031 21.7 3.3 44 53-99 96-144 (160)
52 PRK07027 cobalamin biosynthesi 20.8 71 0.0015 22.1 1.7 33 77-109 37-69 (126)
53 PRK10963 hypothetical protein; 20.7 76 0.0016 24.2 2.0 17 52-68 6-22 (223)
54 cd05295 MDH_like Malate dehydr 20.1 85 0.0018 26.9 2.3 38 30-81 3-44 (452)
55 TIGR00160 MGSA methylglyoxal s 20.1 2.9E+02 0.0063 19.8 4.7 64 46-109 9-82 (143)
No 1
>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=99.95 E-value=3.9e-28 Score=168.96 Aligned_cols=107 Identities=35% Similarity=0.608 Sum_probs=90.1
Q ss_pred CCCCchHHHHHHHHHh----cCcchHHHHHHHHHHHHh-hccccccccccchHHHHHHhhcCCceeCcHHHHHHHHHHhC
Q 031421 26 SGDGNCQFRALSDQMY----KSPEYHKHVRKEVVKQLK-DCRSMYEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKFA 100 (160)
Q Consensus 26 ~gDGnClF~ais~~l~----~~~~~~~~lR~~~v~~i~-~n~~~f~~~i~~~~~~yl~~m~~~g~wg~~~ei~A~a~~~~ 100 (160)
||||||||||||++++ +++..|.+||+.++++|+ +|++.|.+|+..+ +|+++++||+++||+|+|++|+
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~~~~~~~lR~~~~~~l~~~~~~~~~~~~~~~------~~~~~~~Wg~~~el~a~a~~~~ 74 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGSEDNHQELRKAVVDYLRDKNRDKFEEFLEGD------KMSKPGTWGGEIELQALANVLN 74 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSSTTTHHHHHHHHHHHHHTHTTTHHHHHHHHH------HHTSTTSHEEHHHHHHHHHHHT
T ss_pred CCCccHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhccchhhhhhhhh------hhccccccCcHHHHHHHHHHhC
Confidence 7999999999999999 999999999999999999 9999998887655 8999999999999999999999
Q ss_pred CeEEEEecCCCce--eEEecC--CCCCCCCeEEEEeCC-----CCcc
Q 031421 101 AKICLLTSFRDTC--FIEIMP--QHQAPKRELWLSFWS-----EVHY 138 (160)
Q Consensus 101 v~I~V~~~~~~~~--~~~~~p--~~~~~~~~I~L~~~~-----~~HY 138 (160)
++|+|++...... .+.+.+ ......++|.|+|.. ++||
T Consensus 75 ~~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 75 RPIIVYSSSDGDNVVFIKFTGKYPPLESPPPICLCYHGHLYYTGNHY 121 (121)
T ss_dssp SEEEEECETTTBEEEEEEESCEESTTTTTTSEEEEEETEEEEETTEE
T ss_pred CeEEEEEcCCCCccceeeecCccccCCCCCeEEEEEcCCccCCCCCC
Confidence 9999998754332 233332 112447899999987 8998
No 2
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=2.7e-27 Score=182.41 Aligned_cols=142 Identities=19% Similarity=0.379 Sum_probs=123.8
Q ss_pred ChHHHHHHHHHHHHhhCCcEEeeeCCCCchHHHHHHHHHhcCc---chHHHHHHHHHHHHhhcccccccccc--------
Q 031421 2 SDASLDHQRLLQRLNVYGLYEVKVSGDGNCQFRALSDQMYKSP---EYHKHVRKEVVKQLKDCRSMYEGYVP-------- 70 (160)
Q Consensus 2 ~~~~~~~~~l~~~l~~~gl~~~~v~gDGnClF~ais~~l~~~~---~~~~~lR~~~v~~i~~n~~~f~~~i~-------- 70 (160)
++..|+.+.|.+-|...||...+||.||+|+|+||++||.... -+.+.||..+.+||++|.++|.+|+.
T Consensus 141 ~~k~~E~~k~~~il~~~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~~v~kLR~~~a~Ymr~H~~df~pf~~~eet~d~~ 220 (302)
T KOG2606|consen 141 DAKSMEKEKLAQILEERGLKMFDIPADGHCLYAAISHQLKLRSGKLLSVQKLREETADYMREHVEDFLPFLLDEETGDSL 220 (302)
T ss_pred chhhhHHHHHHHHHHhccCccccCCCCchhhHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHHHHhhhHhcCccccccC
Confidence 4678999999999999999999999999999999999997553 36899999999999999999999873
Q ss_pred --chHHHHHHhhcCCceeCcHHHHHHHHHHhCCeEEEEecCCCceeEEecCCCCCCCCeEEEEeCC-----CCcceeeec
Q 031421 71 --MKYKRYYKNMAKVGEWGDHVTLQAAADKFAAKICLLTSFRDTCFIEIMPQHQAPKRELWLSFWS-----EVHYNSLYD 143 (160)
Q Consensus 71 --~~~~~yl~~m~~~g~wg~~~ei~A~a~~~~v~I~V~~~~~~~~~~~~~p~~~~~~~~I~L~~~~-----~~HY~~l~~ 143 (160)
++|+.||+.++.++.|||++||.|+|.+|++||.||..+. +...|+++..+ .++|.|+|++ |.||+++.+
T Consensus 221 ~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~~--p~~~~geey~k-d~pL~lvY~rH~y~LGeHYNS~~~ 297 (302)
T KOG2606|consen 221 GPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQADG--PILEYGEEYGK-DKPLILVYHRHAYGLGEHYNSVTP 297 (302)
T ss_pred CHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecCC--CceeechhhCC-CCCeeeehHHhHHHHHhhhccccc
Confidence 2599999999999999999999999999999999999875 44677765543 5899999864 489999877
Q ss_pred CCC
Q 031421 144 IRD 146 (160)
Q Consensus 144 ~~~ 146 (160)
.+.
T Consensus 298 ~~n 300 (302)
T KOG2606|consen 298 LKN 300 (302)
T ss_pred ccc
Confidence 653
No 3
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.77 E-value=5.4e-19 Score=142.76 Aligned_cols=157 Identities=38% Similarity=0.607 Sum_probs=125.3
Q ss_pred hHHHHHHHHHHHHhhCCcEEeeeCCCCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccccccchHHHHHHhhcC
Q 031421 3 DASLDHQRLLQRLNVYGLYEVKVSGDGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPMKYKRYYKNMAK 82 (160)
Q Consensus 3 ~~~~~~~~l~~~l~~~gl~~~~v~gDGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~~i~~~~~~yl~~m~~ 82 (160)
.++-+.+++.+.+..+|+...+|.+||||+|||+|++++++.+.|..+|+.+++++..+++.|..|+++++.+|++++..
T Consensus 201 ~~~s~~~~~~~~~~~~g~e~~Kv~edGsC~fra~aDQvy~d~e~~~~~~~~~~dq~~~e~~~~~~~vt~~~~~y~k~kr~ 280 (371)
T KOG2605|consen 201 EPQSAHERSAKRKKHFGFEYKKVVEDGSCLFRALADQVYGDDEQHDHNRRECVDQLKKERDFYEDYVTEDFTSYIKRKRA 280 (371)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhcccCCchhhhccHHHhhcCHHHHHHHHHHHHHHHhhcccccccccccchhhccccccc
Confidence 45677888889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeCcHHHHHHHHH--HhCCeEEEEecCCCceeEEecCCCCCCCCeEEEEeCCCCcceeeecC---CCC-CCCCCcccc
Q 031421 83 VGEWGDHVTLQAAAD--KFAAKICLLTSFRDTCFIEIMPQHQAPKRELWLSFWSEVHYNSLYDI---RDA-PVPKKPRKK 156 (160)
Q Consensus 83 ~g~wg~~~ei~A~a~--~~~v~I~V~~~~~~~~~~~~~p~~~~~~~~I~L~~~~~~HY~~l~~~---~~~-~~~~~~~~~ 156 (160)
++.||+++|++|+|. -+..+..+++..+.+.++...|....+...+.+.+....||+..+.. .+. ..-.|.+.+
T Consensus 281 ~~~~gnhie~Qa~a~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~n~~~~~h~~~~~~~~~~~~s~~~~~~~~r~ 360 (371)
T KOG2605|consen 281 DGEPGNHIEQQAAADIYEEIEKPLNITSFKDTCYIQTPPAIEESVKMEKYNFWVEVHYNTARHSGKSADSATLEEKTKRK 360 (371)
T ss_pred CCCCcchHHHhhhhhhhhhccccceeecccccceeccCcccccchhhhhhcccchhhhhhcccccccccccchhhccCCC
Confidence 999999999999996 44555555554444555555444434445566666556899999873 222 344455566
Q ss_pred ccc
Q 031421 157 HWL 159 (160)
Q Consensus 157 ~~~ 159 (160)
+|.
T Consensus 361 ~~~ 363 (371)
T KOG2605|consen 361 SLR 363 (371)
T ss_pred chh
Confidence 664
No 4
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.77 E-value=8.1e-19 Score=133.05 Aligned_cols=123 Identities=19% Similarity=0.366 Sum_probs=101.0
Q ss_pred cEEeeeCCCCchHHHHHHHHHhcCcc-hHHHHHHHHHHHHhhcccccccc-ccchHHHHHHhhcCCceeCcHHHHHHHHH
Q 031421 20 LYEVKVSGDGNCQFRALSDQMYKSPE-YHKHVRKEVVKQLKDCRSMYEGY-VPMKYKRYYKNMAKVGEWGDHVTLQAAAD 97 (160)
Q Consensus 20 l~~~~v~gDGnClF~ais~~l~~~~~-~~~~lR~~~v~~i~~n~~~f~~~-i~~~~~~yl~~m~~~g~wg~~~ei~A~a~ 97 (160)
+.++.||.|++|||+||++.+.+.-. ...++|+.+.+.+.+||+.|..- ++..-.+||..+.++..|||-+||..+|+
T Consensus 110 l~~~vvp~DNSCLF~ai~yv~~k~~~~~~~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k~dsWGGaIElsILS~ 189 (307)
T KOG3288|consen 110 LSRRVVPDDNSCLFTAIAYVIFKQVSNRPYELREIIAQEVASNPDKYNDAILGKPNKEYCAWILKMDSWGGAIELSILSD 189 (307)
T ss_pred eEEEeccCCcchhhhhhhhhhcCccCCCcHHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHccccccCceEEeeeehh
Confidence 45677899999999999999987643 33699999999999999999864 46678999999999999999999999999
Q ss_pred HhCCeEEEEecCCCceeEEecCCCCCCCCeEEEEeCCCCcceeeecCC
Q 031421 98 KFAAKICLLTSFRDTCFIEIMPQHQAPKRELWLSFWSEVHYNSLYDIR 145 (160)
Q Consensus 98 ~~~v~I~V~~~~~~~~~~~~~p~~~~~~~~I~L~~~~~~HY~~l~~~~ 145 (160)
.|++.|++++.+. .-+.-..++......+.|.| +|-|||++....
T Consensus 190 ~ygveI~vvDiqt--~rid~fged~~~~~rv~lly-dGIHYD~l~m~~ 234 (307)
T KOG3288|consen 190 YYGVEICVVDIQT--VRIDRFGEDKNFDNRVLLLY-DGIHYDPLAMNE 234 (307)
T ss_pred hhceeEEEEecce--eeehhcCCCCCCCceEEEEe-cccccChhhhcc
Confidence 9999999999763 22322333444567799999 799999996654
No 5
>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=99.71 E-value=1.3e-16 Score=123.57 Aligned_cols=94 Identities=21% Similarity=0.324 Sum_probs=68.9
Q ss_pred HHHHHHHHHHhhcccccccccc----chHHHHHH-hhcCCceeCcHHHHHHHHHHhCCeEEEEecCCC---c--eeEEec
Q 031421 49 HVRKEVVKQLKDCRSMYEGYVP----MKYKRYYK-NMAKVGEWGDHVTLQAAADKFAAKICLLTSFRD---T--CFIEIM 118 (160)
Q Consensus 49 ~lR~~~v~~i~~n~~~f~~~i~----~~~~~yl~-~m~~~g~wg~~~ei~A~a~~~~v~I~V~~~~~~---~--~~~~~~ 118 (160)
.+|-.+..||+.|++.|.+|++ .++++||. .....+.-++++.|.|+|++|+++|.|+..+++ . ....+.
T Consensus 141 flRLlts~~l~~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v~yld~~~~~~~~~~~~~~ 220 (244)
T PF10275_consen 141 FLRLLTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALAQALGVPIRVEYLDRSVEGDEVNRHEFP 220 (244)
T ss_dssp HHHHHHHHHHHHTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--EEEEESSSSGCSTTSEEEEES
T ss_pred HHHHHHHHHHHhhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHHHHhCCeEEEEEecCCCCCCccccccCC
Confidence 5666788899999999999997 57999997 567778889999999999999999999987653 1 123343
Q ss_pred CCCCCCCCeEEEEeCCCCcceeeec
Q 031421 119 PQHQAPKRELWLSFWSEVHYNSLYD 143 (160)
Q Consensus 119 p~~~~~~~~I~L~~~~~~HY~~l~~ 143 (160)
|.+....+.|+|+| .++|||.++|
T Consensus 221 ~~~~~~~~~i~LLy-rpgHYdIly~ 244 (244)
T PF10275_consen 221 PDNESQEPQITLLY-RPGHYDILYP 244 (244)
T ss_dssp -SSTTSS-SEEEEE-ETBEEEEEEE
T ss_pred CccCCCCCEEEEEE-cCCccccccC
Confidence 33334578999999 7899999985
No 6
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.66 E-value=5.1e-16 Score=116.21 Aligned_cols=94 Identities=18% Similarity=0.284 Sum_probs=74.7
Q ss_pred HHHHHHHHHHHhhccccccccccc--hHHHHHHh-hcCCceeCcHHHHHHHHHHhCCeEEEEecCCCce---eEEecCCC
Q 031421 48 KHVRKEVVKQLKDCRSMYEGYVPM--KYKRYYKN-MAKVGEWGDHVTLQAAADKFAAKICLLTSFRDTC---FIEIMPQH 121 (160)
Q Consensus 48 ~~lR~~~v~~i~~n~~~f~~~i~~--~~~~yl~~-m~~~g~wg~~~ei~A~a~~~~v~I~V~~~~~~~~---~~~~~p~~ 121 (160)
+.+|-.+..++++|+|.|++|+++ ++.+||+. ......-+|+++|.|+|+.+++.|.|...++... .-...|+
T Consensus 157 ~ylRLvtS~~ik~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH~fpe- 235 (256)
T KOG3991|consen 157 MYLRLVTSGFIKSNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIRIRVEYVDRGSGDTVNHHDFPE- 235 (256)
T ss_pred HHHHHHHHHHHhhChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCceEEEEEecCCCCCCCCCCcCcc-
Confidence 457778889999999999999975 88999985 4555677899999999999999999988664322 1122343
Q ss_pred CCCCCeEEEEeCCCCcceeeecC
Q 031421 122 QAPKRELWLSFWSEVHYNSLYDI 144 (160)
Q Consensus 122 ~~~~~~I~L~~~~~~HY~~l~~~ 144 (160)
...+.|+|+| ..+|||.++++
T Consensus 236 -~s~P~I~LLY-rpGHYdilY~~ 256 (256)
T KOG3991|consen 236 -ASAPEIYLLY-RPGHYDILYKK 256 (256)
T ss_pred -ccCceEEEEe-cCCccccccCC
Confidence 3478899999 89999999864
No 7
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=99.01 E-value=6.3e-11 Score=91.90 Aligned_cols=131 Identities=12% Similarity=0.033 Sum_probs=94.0
Q ss_pred HHHHHHHHHhhCCcEEeeeCCCCchHHHHHHHHHhcCc-----chHHHHHHHHHHHHhhcccccccccc-------chHH
Q 031421 7 DHQRLLQRLNVYGLYEVKVSGDGNCQFRALSDQMYKSP-----EYHKHVRKEVVKQLKDCRSMYEGYVP-------MKYK 74 (160)
Q Consensus 7 ~~~~l~~~l~~~gl~~~~v~gDGnClF~ais~~l~~~~-----~~~~~lR~~~v~~i~~n~~~f~~~i~-------~~~~ 74 (160)
+...+++-+...+++-.++.|||+|.|-+||++|.-.- +..+..|-.-..|...+...|.++.= -.|+
T Consensus 158 ~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~~~~~q~~~i~f~g~hfD~~t~~m~~~d 237 (306)
T COG5539 158 AILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNSHPYVQRISILFTGIHFDEETLAMVLWD 237 (306)
T ss_pred hhcCcchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccCChhhhhhhhhhcccccchhhhhcchHH
Confidence 44556667777788888999999999999999997542 12344554444555555556655431 2699
Q ss_pred HHHHhhcCCceeCcHHHHHHHHHHhCCeEEEEecCCCceeEEecCCCCCCCCeEEEEeC----CCCcceee
Q 031421 75 RYYKNMAKVGEWGDHVTLQAAADKFAAKICLLTSFRDTCFIEIMPQHQAPKRELWLSFW----SEVHYNSL 141 (160)
Q Consensus 75 ~yl~~m~~~g~wg~~~ei~A~a~~~~v~I~V~~~~~~~~~~~~~p~~~~~~~~I~L~~~----~~~HY~~l 141 (160)
+|++.+..+..||..+|++++|..|++++.++...+ +.+.+.+.+.+. ...+.|. .-+||+.+
T Consensus 238 t~~ne~~~~a~~g~~~ei~qLas~lk~~~~~~nT~~--~~ik~n~c~~~~--~~e~~~~~Ha~a~GH~n~~ 304 (306)
T COG5539 238 TYVNEVLFDASDGITIEIQQLASLLKNPHYYTNTAS--PSIKCNICGTGF--VGEKDYYAHALATGHYNFG 304 (306)
T ss_pred HHHhhhcccccccchHHHHHHHHHhcCceEEeecCC--ceEEeecccccc--chhhHHHHHHHhhcCcccc
Confidence 999999999999999999999999999999998764 567787765422 2222221 23599876
No 8
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.97 E-value=1.9e-10 Score=89.29 Aligned_cols=110 Identities=13% Similarity=0.182 Sum_probs=91.0
Q ss_pred CCCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccccccc-hHHHHHHhhcCCceeC-cHHHHHHHHHHhCCeEE
Q 031421 27 GDGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPM-KYKRYYKNMAKVGEWG-DHVTLQAAADKFAAKIC 104 (160)
Q Consensus 27 gDGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~~i~~-~~~~yl~~m~~~g~wg-~~~ei~A~a~~~~v~I~ 104 (160)
.|..|+|++.+..++.- .-.++|..+...+.+|||.|.+.+.+ +.-.|+.++.++..|| |.+|+.++++.|++.|+
T Consensus 119 ~d~srl~q~~~~~l~~a--sv~~lrE~vs~Ev~snPDl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~ 196 (306)
T COG5539 119 DDNSRLFQAERYSLRDA--SVAKLREVVSLEVLSNPDLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIH 196 (306)
T ss_pred CchHHHHHHHHhhhhhh--hHHHHHHHHHHHHhhCccccchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeee
Confidence 46789999999998762 45899999999999999999988754 7789999999999999 99999999999999999
Q ss_pred EEecCCCceeEEecCCCCCCCCeEEEEeCCCCcceeee
Q 031421 105 LLTSFRDTCFIEIMPQHQAPKRELWLSFWSEVHYNSLY 142 (160)
Q Consensus 105 V~~~~~~~~~~~~~p~~~~~~~~I~L~~~~~~HY~~l~ 142 (160)
++..+.+. ...+.+... ...+.+.| .+.|||...
T Consensus 197 ~Vdv~~~~-~dr~~~~~~--~q~~~i~f-~g~hfD~~t 230 (306)
T COG5539 197 VVDVDKDS-EDRYNSHPY--VQRISILF-TGIHFDEET 230 (306)
T ss_pred eeecchhH-HhhccCChh--hhhhhhhh-cccccchhh
Confidence 99987532 234444322 34577888 799999875
No 9
>PF05415 Peptidase_C36: Beet necrotic yellow vein furovirus-type papain-like endopeptidase; InterPro: IPR008746 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 group of cysteine peptidases correspond to MEROPS peptidase family C36 (clan CA). The type example is beet necrotic yellow vein furovirus-type papain-like endopeptidase (beet necrotic yellow vein virus), which is involved in processing the viral polyprotein.
Probab=97.11 E-value=0.0018 Score=42.13 Aligned_cols=97 Identities=16% Similarity=0.165 Sum_probs=58.5
Q ss_pred eCCCCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccccccchHHHHHHhh--cCCceeCcHHHHHHHHHHhCCe
Q 031421 25 VSGDGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPMKYKRYYKNM--AKVGEWGDHVTLQAAADKFAAK 102 (160)
Q Consensus 25 v~gDGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~~i~~~~~~yl~~m--~~~g~wg~~~ei~A~a~~~~v~ 102 (160)
+..|+||+.-|||..|+-+- ..|...+.. |. ..++.|+... ..+.+|-+- ..+|+.+++.
T Consensus 3 ~sR~NNCLVVAis~~L~~T~---e~l~~~M~A----n~--------~~i~~y~~W~r~~~~STW~DC---~mFA~~LkVs 64 (104)
T PF05415_consen 3 ASRPNNCLVVAISECLGVTL---EKLDNLMQA----NV--------STIKKYHTWLRKKRPSTWDDC---RMFADALKVS 64 (104)
T ss_pred ccCCCCeEeehHHHHhcchH---HHHHHHHHh----hH--------HHHHHHHHHHhcCCCCcHHHH---HHHHHhheeE
Confidence 46799999999999998876 445443332 21 2357777754 457888543 3489999999
Q ss_pred EEEEe-cCCCceeEEecCCCCCCCCeEEEEeC-CCCccee
Q 031421 103 ICLLT-SFRDTCFIEIMPQHQAPKRELWLSFW-SEVHYNS 140 (160)
Q Consensus 103 I~V~~-~~~~~~~~~~~p~~~~~~~~I~L~~~-~~~HY~~ 140 (160)
|.+-- ++.+.. +.+...+..+.-..++..- +.+||.+
T Consensus 65 m~vkV~~~~~~~-l~~~~d~~~s~v~~~~~~Ke~dGHF~a 103 (104)
T PF05415_consen 65 MQVKVLSDKPYD-LLYFVDGAVSVVTLHLEGKESDGHFIA 103 (104)
T ss_pred EEEEEcCCCCce-eeEeecCccceehhhhhccccCCceec
Confidence 88743 333333 3333333323334444432 3478854
No 10
>PF05412 Peptidase_C33: Equine arterivirus Nsp2-type cysteine proteinase; InterPro: IPR008743 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 group of cysteine peptidases corresponds to MEROPS peptidase family C33 (clan CA). The type example is equine arteritis virus Nsp2-type cysteine proteinase, which is involved in viral polyprotein processing [].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=95.95 E-value=0.0062 Score=40.92 Aligned_cols=83 Identities=12% Similarity=0.214 Sum_probs=49.8
Q ss_pred eCCCCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccccccchHH-HHHHhhcCCceeCcHHHHHHHHHHhCCeE
Q 031421 25 VSGDGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPMKYK-RYYKNMAKVGEWGDHVTLQAAADKFAAKI 103 (160)
Q Consensus 25 v~gDGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~~i~~~~~-~yl~~m~~~g~wg~~~ei~A~a~~~~v~I 103 (160)
-|+||+|.||+||..++. | +++.|. .|-+.......|.++..+.-+-..++.|+
T Consensus 4 PP~DG~CG~H~i~aI~n~---------------m----------~~~~~t~~l~~~~r~~d~W~~dedl~~~iq~l~lPa 58 (108)
T PF05412_consen 4 PPGDGSCGWHCIAAIMNH---------------M----------MGGEFTTPLPQRNRPSDDWADDEDLYQVIQSLRLPA 58 (108)
T ss_pred CCCCCchHHHHHHHHHHH---------------h----------hccCCCccccccCCChHHccChHHHHHHHHHccCce
Confidence 589999999999988764 1 111111 12233456788999888776666667766
Q ss_pred EEEecCCCceeEEecCCCCCCCCeEEEEeCCCCcceeeecCC
Q 031421 104 CLLTSFRDTCFIEIMPQHQAPKRELWLSFWSEVHYNSLYDIR 145 (160)
Q Consensus 104 ~V~~~~~~~~~~~~~p~~~~~~~~I~L~~~~~~HY~~l~~~~ 145 (160)
.+.-..- . ...-|+.-..+.|++.-+.++
T Consensus 59 t~~~~~~------------C-p~ArYv~~l~~qHW~V~~~~g 87 (108)
T PF05412_consen 59 TLDRNGA------------C-PHARYVLKLDGQHWEVSVRKG 87 (108)
T ss_pred eccCCCC------------C-CCCEEEEEecCceEEEEEcCC
Confidence 4432211 1 123444444778887766554
No 11
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 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 entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=95.77 E-value=0.13 Score=34.65 Aligned_cols=91 Identities=12% Similarity=0.141 Sum_probs=58.7
Q ss_pred CCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccccccchHHHHHHhhcCCceeCcHHHHHHHHHHhCCeEEEEe
Q 031421 28 DGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKFAAKICLLT 107 (160)
Q Consensus 28 DGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~~i~~~~~~yl~~m~~~g~wg~~~ei~A~a~~~~v~I~V~~ 107 (160)
.-|||.-|+|.++.-.. ..|-..+...+ ||. ++. ... ++.-| -+-..+.|+|-.|+....+.+
T Consensus 2 ~~~CLL~A~s~at~~~~---~~LW~~L~~~l---PDS---lL~---n~e---i~~~G--LSTDhltaLa~~~~~~~~~hs 64 (104)
T PF05381_consen 2 ALDCLLVAISQATSISP---ETLWATLCEIL---PDS---LLD---NPE---IRTLG--LSTDHLTALAYRYHFQCTFHS 64 (104)
T ss_pred CcceeHHhhhhhhCCCH---HHHHHHHHHhC---chh---hcC---chh---hhhcC--CcHHHHHHHHHHHheEEEEEc
Confidence 35899999999998877 55555555433 111 010 001 11122 245668899999999999999
Q ss_pred cCCCceeEEecCCCCCCCCeEEEEeCCC--Cccee
Q 031421 108 SFRDTCFIEIMPQHQAPKRELWLSFWSE--VHYNS 140 (160)
Q Consensus 108 ~~~~~~~~~~~p~~~~~~~~I~L~~~~~--~HY~~ 140 (160)
..+ .+.|+..+. ...+.|.|..+ .||.+
T Consensus 65 ~~~---~~~~Gi~~a--s~~~~I~ht~G~p~HFs~ 94 (104)
T PF05381_consen 65 DHG---VLHYGIKDA--STVFTITHTPGPPGHFSL 94 (104)
T ss_pred CCc---eEEeecCCC--ceEEEEEeCCCCCCcccc
Confidence 754 467776544 56788888543 69998
No 12
>PRK09784 hypothetical protein; Provisional
Probab=85.72 E-value=0.49 Score=36.92 Aligned_cols=24 Identities=42% Similarity=0.688 Sum_probs=21.1
Q ss_pred hhCCcEEeeeCCCCchHHHHHHHH
Q 031421 16 NVYGLYEVKVSGDGNCQFRALSDQ 39 (160)
Q Consensus 16 ~~~gl~~~~v~gDGnClF~ais~~ 39 (160)
+.+||+--+|.|||-|+.|||-..
T Consensus 196 ~~~glkyapvdgdgycllrailvl 219 (417)
T PRK09784 196 KTYGLKYAPVDGDGYCLLRAILVL 219 (417)
T ss_pred hhhCceecccCCCchhHHHHHHHh
Confidence 578999999999999999998544
No 13
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 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 group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=79.86 E-value=14 Score=24.11 Aligned_cols=86 Identities=13% Similarity=0.113 Sum_probs=47.0
Q ss_pred CchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccccccchHHHHHHhhcCCceeCcHHHHHHHHHHhCCeEEEEec
Q 031421 29 GNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKFAAKICLLTS 108 (160)
Q Consensus 29 GnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~~i~~~~~~yl~~m~~~g~wg~~~ei~A~a~~~~v~I~V~~~ 108 (160)
..|..+|||.+|.+.. .+ +...+.+.. . .+..+.+. .|.=.+-..+..+.++|++.-.|...
T Consensus 3 N~Cvi~AiA~aL~R~~---~d----Vl~Vl~~~~-------~---~~~~~~l~-~G~Gl~l~~le~~f~~F~I~A~v~~~ 64 (89)
T PF05379_consen 3 NGCVIRAIAEALGRRE---QD----VLAVLSRKC-------G---EELLEELW-SGEGLDLEDLEELFELFDICAHVNFG 64 (89)
T ss_pred ccchhHHHHHHhCCCH---HH----HHHHHHhcc-------C---HHHHHHHH-cCCCcCHHHHHHHHHHcCeEEEEEEC
Confidence 5799999999999987 33 333332211 0 11122222 12212233366788999999988886
Q ss_pred CCCceeEEecCCCCCCCCeEEEEeCCCCcce
Q 031421 109 FRDTCFIEIMPQHQAPKRELWLSFWSEVHYN 139 (160)
Q Consensus 109 ~~~~~~~~~~p~~~~~~~~I~L~~~~~~HY~ 139 (160)
++ .+.+.+.+. ....... .++|..
T Consensus 65 g~---~~~lN~~G~---i~~~F~l-~~~His 88 (89)
T PF05379_consen 65 GE---TFVLNEEGR---IKGSFRL-EDGHIS 88 (89)
T ss_pred CE---EEEECCCCc---EEEEEEE-eCCccc
Confidence 43 456666543 1222222 567753
No 14
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=74.12 E-value=3 Score=37.05 Aligned_cols=54 Identities=13% Similarity=0.214 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhCCeEEEEecCCCc--eeEEec-------------CCCCCCCCeEEEEeCCCCcceeeec
Q 031421 89 HVTLQAAADKFAAKICLLTSFRDT--CFIEIM-------------PQHQAPKRELWLSFWSEVHYNSLYD 143 (160)
Q Consensus 89 ~~ei~A~a~~~~v~I~V~~~~~~~--~~~~~~-------------p~~~~~~~~I~L~~~~~~HY~~l~~ 143 (160)
+..|..+|++++++|+|++...-. .--.|. |.......+|.|.| ..-||.++..
T Consensus 223 e~hifvl~~ilRrpivvvsd~mlR~s~~~sfap~~~ggiylpLe~p~~~c~r~pLvl~y-d~~hf~~lvs 291 (774)
T KOG4345|consen 223 EFHIFVLAHILRRPIVVVSDTMLRDSGGESFAPIPVGGIYLPLEVPAQECHRSPLVLAY-DQAHFSALVS 291 (774)
T ss_pred HHHHHHHHHHhhCCeeEecccccccCCCcccccCccCceEEeccCchhhcccchhhhhh-Hhhhhhhhhh
Confidence 344778999999999999854210 000111 22223456777888 5788888754
No 15
>COG5007 Predicted transcriptional regulator, BolA superfamily [Transcription]
Probab=69.35 E-value=4.2 Score=25.95 Aligned_cols=55 Identities=24% Similarity=0.308 Sum_probs=35.8
Q ss_pred HHHHHHHHHh-hCCcEEeeeCCCCchHHH-HHHHHHhcCc--chHHHHHHHHHHHHhhc
Q 031421 7 DHQRLLQRLN-VYGLYEVKVSGDGNCQFR-ALSDQMYKSP--EYHKHVRKEVVKQLKDC 61 (160)
Q Consensus 7 ~~~~l~~~l~-~~gl~~~~v~gDGnClF~-ais~~l~~~~--~~~~~lR~~~v~~i~~n 61 (160)
+-+.+.+.|. .+.+...+|.|||+=|+- +||..+.|-. ..++.|-.-+.+||.+|
T Consensus 2 ~~e~Ik~ll~~~L~~e~v~V~Gdg~Hf~vi~Vs~~F~g~srvkrqq~vYApL~~~i~~~ 60 (80)
T COG5007 2 DNEEIKSLLENALPLEEVEVEGDGSHFQVIAVSEEFAGKSRVKRQQLVYAPLMAYIADN 60 (80)
T ss_pred CHHHHHHHHHhcCCccEEEEecCCceEEEEEehHhhcCccHHHHHHHHHHHHHHHhhcC
Confidence 3445555553 478888999999987654 4666665543 24556666677777655
No 16
>KOG3348 consensus BolA (bacterial stress-induced morphogen)-related protein [Signal transduction mechanisms]
Probab=62.57 E-value=6.7 Score=25.38 Aligned_cols=58 Identities=17% Similarity=0.158 Sum_probs=40.0
Q ss_pred ChHHHHHHHHHHHHhhCCcEEeeeCCCCchHHHH--HHHHHhcCc--chHHHHHHHHHHHHh
Q 031421 2 SDASLDHQRLLQRLNVYGLYEVKVSGDGNCQFRA--LSDQMYKSP--EYHKHVRKEVVKQLK 59 (160)
Q Consensus 2 ~~~~~~~~~l~~~l~~~gl~~~~v~gDGnClF~a--is~~l~~~~--~~~~~lR~~~v~~i~ 59 (160)
.+..+-.+.|.+.|...-+.+.++.|.--|.|+. +|.++.|.. ..|..+-..+.+.|+
T Consensus 3 ~~e~~l~~~L~~~l~p~~v~V~D~SgGCG~~F~v~IvS~~FeGKs~L~rHRlVN~~L~Eeik 64 (85)
T KOG3348|consen 3 VTEERLEELLTEALEPEHVEVQDVSGGCGSMFDVVIVSAAFEGKSLLARHRLVNSILAEEIK 64 (85)
T ss_pred chHHHHHHHHHhhcCceEEEEEEcCCCccceEEEEEEccccCChHHHHHHHHHHHHHHHHHH
Confidence 3456667888888888899999998876678887 466666643 245555555555553
No 17
>smart00718 DM4_12 DM4/DM12 family of domains in Drosophila melanogaster proteins of unknown function.
Probab=56.71 E-value=21 Score=23.53 Aligned_cols=48 Identities=23% Similarity=0.392 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHhhCCcEEeeeCCCC-chHHHHHHHHHhcCcchHHHHHHHHHHHHh
Q 031421 4 ASLDHQRLLQRLNVYGLYEVKVSGDG-NCQFRALSDQMYKSPEYHKHVRKEVVKQLK 59 (160)
Q Consensus 4 ~~~~~~~l~~~l~~~gl~~~~v~gDG-nClF~ais~~l~~~~~~~~~lR~~~v~~i~ 59 (160)
+..-++.|++.|..+|+ || .|+.|||-..-.. ...+.-|=..++..+.
T Consensus 6 R~~lY~~lE~~l~~~G~-------~g~~ClLR~ICE~a~~-~~~~~Gll~ell~ilf 54 (95)
T smart00718 6 RRLLYEALENLLDQLGF-------NGRACLLRAICESAQK-LDDHRGLLGELLRIVL 54 (95)
T ss_pred HHHHHHHHHHHHHHcCC-------CchhhHHHHHHHcccc-cccccchHHHHHHHhh
Confidence 44567889999999995 67 8999999887653 2223335556666663
No 18
>PF05413 Peptidase_C34: Putative closterovirus papain-like endopeptidase; InterPro: IPR008744 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This signature is found in the RNA-direct RNA polymerase of apple chlorotic leaf spot virus and cherry mottle virus.; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0005524 ATP binding, 0019079 viral genome replication
Probab=51.86 E-value=22 Score=22.86 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=19.6
Q ss_pred EeeeCCCCchHHHHHHHHHhcCc
Q 031421 22 EVKVSGDGNCQFRALSDQMYKSP 44 (160)
Q Consensus 22 ~~~v~gDGnClF~ais~~l~~~~ 44 (160)
+.-|.|-=+|+|-|+|..+...+
T Consensus 2 ~kFikGk~DClf~s~a~~I~Kkp 24 (92)
T PF05413_consen 2 VKFIKGKYDCLFVSVAEIIHKKP 24 (92)
T ss_pred cceeccccccHHHHHHHHHhcCH
Confidence 34578888999999999998877
No 19
>cd03346 eu_TrpOH Eukaryotic tryptophan hydroxylase (TrpOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tyrosine hydroxylase (TyrOH). TrpOH oxidizes L-tryptophan to 5-hydroxy-L-tryptophan, the rate-limiting step in the biosynthesis of serotonin (5-hydroxytryptamine), a widely distributed hormone and neurotransmitter.
Probab=43.59 E-value=15 Score=29.41 Aligned_cols=94 Identities=10% Similarity=0.088 Sum_probs=54.8
Q ss_pred HHHHHHHHHhh-CCcEEeeeCC--CCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhcccccccc------c-cchHHHH
Q 031421 7 DHQRLLQRLNV-YGLYEVKVSG--DGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEGY------V-PMKYKRY 76 (160)
Q Consensus 7 ~~~~l~~~l~~-~gl~~~~v~g--DGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~~------i-~~~~~~y 76 (160)
+.+.+++.|++ -|..++.|+| ...=||..+|.-.+-.. ..||..-.-.-..-||-|-+. + +..+.+|
T Consensus 108 ql~dvn~~L~~~TGw~~~pV~Gli~~~~Ff~~LA~r~Fp~t---~~IR~~~~~~YtpEPDifHEl~GHvPlLadp~FA~f 184 (287)
T cd03346 108 QLEDVSRFLKERTGFTIRPVAGYLSPRDFLAGLAFRVFHCT---QYVRHSSDPFYTPEPDTCHELLGHVPLLADPSFAQF 184 (287)
T ss_pred CHHHHHHHHHhccCCEEEecCCcCCHHHHHHHHhcCcccce---eeecCccccCCCCCCchHHHHhccchhhcCHHHHHH
Confidence 34568889987 5999999998 56668888888776554 334431110011112222111 1 2367777
Q ss_pred HHhhcCCceeCcHHHHHHHHHHhCCeE
Q 031421 77 YKNMAKVGEWGDHVTLQAAADKFAAKI 103 (160)
Q Consensus 77 l~~m~~~g~wg~~~ei~A~a~~~~v~I 103 (160)
......-+-=+++.++.-+|++|=-.|
T Consensus 185 ~q~~G~~~l~a~~~~i~~LarlYWfTV 211 (287)
T cd03346 185 SQEIGLASLGASDEDIQKLATCYFFTV 211 (287)
T ss_pred HHHHHHHhcCCCHHHHHHHhHhhhhhc
Confidence 776543333357777888888774333
No 20
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.94 E-value=39 Score=23.24 Aligned_cols=56 Identities=14% Similarity=0.324 Sum_probs=30.4
Q ss_pred HHHHHHHHHhcCcc-----hHHHHHHHHHHHHhhccccccccccchHHHHHHhhc----CCceeCc
Q 031421 32 QFRALSDQMYKSPE-----YHKHVRKEVVKQLKDCRSMYEGYVPMKYKRYYKNMA----KVGEWGD 88 (160)
Q Consensus 32 lF~ais~~l~~~~~-----~~~~lR~~~v~~i~~n~~~f~~~i~~~~~~yl~~m~----~~g~wg~ 88 (160)
+|+.|-.+-.+-+. ....||.....+..-||.+-..|+ .+|+.|+..++ ..|.|-+
T Consensus 15 LYkriLrlHr~lp~~~R~lGD~YVkdEFrrHk~vnp~~~~~Fl-teW~~Ya~~l~qql~~~g~~K~ 79 (125)
T KOG4100|consen 15 LYKRILRLHRGLPAELRALGDQYVKDEFRRHKTVNPLEAQGFL-TEWERYAVALSQQLSSAGKWKG 79 (125)
T ss_pred HHHHHHHHHccCChHHHHHHHHHHHHHHHHhccCChHHHHHHH-HHHHHHHHHHHHHhhhcCcccc
Confidence 55555555444431 123444445455545566555555 57899987554 3577743
No 21
>cd00361 arom_aa_hydroxylase Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH converts L-phenylalanine to L-tyrosine, an important step in phenylalanine catabolism and neurotransmitter biosynthesis, and is linked to a severe variant of phenylketonuria in humans. TyrOH and TrpOH are involved in the biosynthesis of catecholamine and serotonin, respectively. The eukaryotic enzymes are all homotetramers.
Probab=37.32 E-value=8.6 Score=29.53 Aligned_cols=91 Identities=10% Similarity=0.127 Sum_probs=53.3
Q ss_pred HHHHHHHHHhh-CCcEEeeeCC--CCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccc------cc-cchHHHH
Q 031421 7 DHQRLLQRLNV-YGLYEVKVSG--DGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEG------YV-PMKYKRY 76 (160)
Q Consensus 7 ~~~~l~~~l~~-~gl~~~~v~g--DGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~------~i-~~~~~~y 76 (160)
+.+.+++.|++ -|..++.|+| ...=||..+|.-..-.. ..||..-.-....-||-|-+ ++ +..+.+|
T Consensus 48 ql~~in~~L~~~TGw~~~pV~gli~~~~Ff~~LA~r~Fp~t---~~iR~~~~~~YtpEPDifHe~~GH~P~L~~p~fAdf 124 (221)
T cd00361 48 QLEDVSEFLKALTGWTLVPVAGLISPRDFFALLAFRVFPVT---QYIRHPEEPDYTPEPDIFHELFGHVPLLADPSFADF 124 (221)
T ss_pred CHHHHHHHHHhhcCCEEEecCCcCCHHHHHHHHhcCCCcee---eeecCcCCCCCCCCChhHHHHhccchhhcCHHHHHH
Confidence 34568888887 8999999988 66668888887655433 33332111111111222211 11 2367788
Q ss_pred HHhhcCCceeCcH-HHHHHHHHHhC
Q 031421 77 YKNMAKVGEWGDH-VTLQAAADKFA 100 (160)
Q Consensus 77 l~~m~~~g~wg~~-~ei~A~a~~~~ 100 (160)
...+.+-+.=+.+ -++..+|++|=
T Consensus 125 ~q~~G~~~l~a~~~~~~~~LarlyW 149 (221)
T cd00361 125 SQEYGLASLGASDLEEIEKLARLYW 149 (221)
T ss_pred HHHHHHHHhCcCCHHHHHHHHHhhh
Confidence 8776554444555 67778888773
No 22
>TIGR03277 methan_mark_9 putative methanogenesis marker domain 9. A gene for a protein that contains a copy of this domain, to date, is found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. A 69-amino acid core region of this 110-amino acid domain contains eight invariant Cys residues, including two copies of a motif [WFY]CCxxKPC. These motifs could be consistent with predicted metal-binding transcription factor as was suggested for the COG4008 family. Some members of this family have an additional N-terminal domain of about 250 amino acids from the nifR3 family of predicted TIM-barrel proteins.
Probab=36.65 E-value=32 Score=23.30 Aligned_cols=32 Identities=22% Similarity=0.368 Sum_probs=24.3
Q ss_pred chHHH-HHHHHHhcCcchHHHHHHHHHHHHhhc
Q 031421 30 NCQFR-ALSDQMYKSPEYHKHVRKEVVKQLKDC 61 (160)
Q Consensus 30 nClF~-ais~~l~~~~~~~~~lR~~~v~~i~~n 61 (160)
-|.|| ..-..++.+.+.+.++++.++++|.+|
T Consensus 77 PCplrd~aL~~igls~~EYm~lKkelae~i~~~ 109 (109)
T TIGR03277 77 PCPLRDSALQRIGMSPEEYMELKKKLAEELLKK 109 (109)
T ss_pred CCcCchHHHHHcCCCHHHHHHHHHHHHHHHhcC
Confidence 34577 555667788888999999999988653
No 23
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=36.35 E-value=46 Score=18.68 Aligned_cols=30 Identities=10% Similarity=-0.003 Sum_probs=20.9
Q ss_pred HHHHHhhcCCceeCcHHHHHHHHHHhCCeE
Q 031421 74 KRYYKNMAKVGEWGDHVTLQAAADKFAAKI 103 (160)
Q Consensus 74 ~~yl~~m~~~g~wg~~~ei~A~a~~~~v~I 103 (160)
..++.++......-+-..+..+|+.|++++
T Consensus 23 ~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~ 52 (55)
T PF01381_consen 23 RSTISRIENGKRNPSLDTLKKIAKALGVSP 52 (55)
T ss_dssp HHHHHHHHTTSSTSBHHHHHHHHHHHTSEH
T ss_pred cchhHHHhcCCCCCCHHHHHHHHHHHCCCH
Confidence 344555555555566777889999999875
No 24
>PF08715 Viral_protease: Papain like viral protease; InterPro: IPR014827 This family of viral proteases are similar to the papain protease and are required for proteolytic processing of the replicase polyprotein. The structure of this protein has shown it adopts a fold similar to that of de-ubiquitinating enzymes []. ; GO: 0004197 cysteine-type endopeptidase activity, 0008242 omega peptidase activity, 0016740 transferase activity; PDB: 3MP2_A 3EWP_B 3EWO_B 2FE8_A 3MJ5_B 3EKE_A 3EJF_A 3JZT_H 3ETI_E 3E9S_A.
Probab=36.15 E-value=62 Score=26.33 Aligned_cols=48 Identities=15% Similarity=0.086 Sum_probs=26.3
Q ss_pred CcEEeeeCCCCchHHHHHHHHHhcCcc--hHHHHHHHHHHHHhhccccccc
Q 031421 19 GLYEVKVSGDGNCQFRALSDQMYKSPE--YHKHVRKEVVKQLKDCRSMYEG 67 (160)
Q Consensus 19 gl~~~~v~gDGnClF~ais~~l~~~~~--~~~~lR~~~v~~i~~n~~~f~~ 67 (160)
|+++.. -.|+||+-.|.-.+|....- ....+..+.-+|..-++..|..
T Consensus 101 g~~~Lk-q~dNNCwVna~~~~LQ~~~~~f~~~~l~~aw~~f~~G~~~~fVa 150 (320)
T PF08715_consen 101 GFRVLK-QSDNNCWVNAACLQLQALKIKFKSPGLDEAWNEFKAGDPAPFVA 150 (320)
T ss_dssp TEEEE----TTTHHHHHHHHHHTTST--BSSHHHHHHHHHHHTT--HHHHH
T ss_pred CEEEEE-ecCCCcHHHHHHHHHHhcCCccCCHHHHHHHHHHhCCChHHHHH
Confidence 444333 37999999999888876541 1124455555655555555443
No 25
>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=34.55 E-value=3.8 Score=25.41 Aligned_cols=28 Identities=32% Similarity=0.559 Sum_probs=21.0
Q ss_pred cccccc-chHHHHHHhhcCCceeCcHHHH
Q 031421 65 YEGYVP-MKYKRYYKNMAKVGEWGDHVTL 92 (160)
Q Consensus 65 f~~~i~-~~~~~yl~~m~~~g~wg~~~ei 92 (160)
++-|++ .++++-+-.++.++.|||.+.|
T Consensus 13 l~~YvpKKDLEE~Vv~~e~~~~WGG~v~L 41 (67)
T TIGR02934 13 LSAYVPKKDLEEVIVSVEKEELWGGWVTL 41 (67)
T ss_pred EEEEEECCcchhheeeeecCccccCEEEE
Confidence 455665 4788888889999999996543
No 26
>KOG0256 consensus 1-aminocyclopropane-1-carboxylate synthase, and related proteins [Signal transduction mechanisms]
Probab=31.48 E-value=92 Score=26.49 Aligned_cols=57 Identities=12% Similarity=0.156 Sum_probs=39.7
Q ss_pred HHHHHHHHhhCCcEEeeeCCCCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhc---cccccc
Q 031421 8 HQRLLQRLNVYGLYEVKVSGDGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDC---RSMYEG 67 (160)
Q Consensus 8 ~~~l~~~l~~~gl~~~~v~gDGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n---~~~f~~ 67 (160)
.+.+..+|++ .-.......||.|-|+.+|.. .+-.....+|++++++|... +..|.+
T Consensus 87 ~DL~~~wl~k-~~~~~~~~~eg~~~f~~la~f--qdy~Gl~~frqa~A~Fm~~~r~~~v~fdP 146 (471)
T KOG0256|consen 87 FDLIESWLSK-NPEASNCTREGQSSFDELAMF--QDYHGLPSFRQAVAEFMERARGNRVKFDP 146 (471)
T ss_pred HHHHHHHHHh-ChhhhhcccccccchhhHhhc--ccccCchHHHHHHHHHHHHHhCCCCccCc
Confidence 3456667777 333445668999999998865 45556689999999888764 445544
No 27
>TIGR01270 Trp_5_monoox tryptophan 5-monooxygenase, tetrameric. This model describes tryptophan 5-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tyrosine 3-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
Probab=31.44 E-value=31 Score=29.48 Aligned_cols=90 Identities=9% Similarity=0.104 Sum_probs=52.4
Q ss_pred HHHHHHHHhh-CCcEEeeeCC--CCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhcccccccc------c-cchHHHHH
Q 031421 8 HQRLLQRLNV-YGLYEVKVSG--DGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEGY------V-PMKYKRYY 77 (160)
Q Consensus 8 ~~~l~~~l~~-~gl~~~~v~g--DGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~~------i-~~~~~~yl 77 (160)
.+.+.+.|++ -|+.++.|+| ...=||..+|.-.+... ..||..---....-||-|-+. + +..|.+|.
T Consensus 238 l~dvs~~L~~~TGw~~~pV~Gll~~r~F~~~LA~R~F~~t---qyIR~~~~~~YtpEPDi~HEl~GHvPlLadp~FA~f~ 314 (464)
T TIGR01270 238 LEDVSKFLKAKTGFRLRPVAGYLSARDFLSGLAFRVFHCT---QYVRHSADPFYTPEPDTCHELLGHMPLLADPSFAQFS 314 (464)
T ss_pred HHHHHHHHHhccCCEEEeccccCCHHHHHHHHhcCcccee---eeeccccccCcCCCCchHHHHhcccchhcCHHHHHHH
Confidence 4567888875 5999999988 55668888888777654 334431111111112222111 1 23677777
Q ss_pred HhhcCCceeCcHHHHHHHHHHhC
Q 031421 78 KNMAKVGEWGDHVTLQAAADKFA 100 (160)
Q Consensus 78 ~~m~~~g~wg~~~ei~A~a~~~~ 100 (160)
......+-=+++.++.-+|++|=
T Consensus 315 q~~G~~sl~a~~e~i~~LarlyW 337 (464)
T TIGR01270 315 QEIGLASLGASEEDIKKLATLYF 337 (464)
T ss_pred HHHHHhhcCCCHHHHHHHhHhhh
Confidence 76543333246777888888763
No 28
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=29.97 E-value=1.8e+02 Score=25.79 Aligned_cols=61 Identities=8% Similarity=0.000 Sum_probs=34.3
Q ss_pred hHHHHHHHHHHHHhhCCcEEeeeCCCCchHHHHHHHHHhcC-----cchHHHHHHHHHHHHhhccc
Q 031421 3 DASLDHQRLLQRLNVYGLYEVKVSGDGNCQFRALSDQMYKS-----PEYHKHVRKEVVKQLKDCRS 63 (160)
Q Consensus 3 ~~~~~~~~l~~~l~~~gl~~~~v~gDGnClF~ais~~l~~~-----~~~~~~lR~~~v~~i~~n~~ 63 (160)
++....+.|+..-+.++++.-.-..+.-|+...+..+++.. .+.+.+.-+.+.+++..+.+
T Consensus 111 s~~~~~~~l~~L~~~f~lR~C~~~~~rpCl~y~i~~C~gpC~g~~~~e~Y~~~v~~~~~fL~G~~~ 176 (574)
T PRK14670 111 NVKKLDLVLDLINKTFKTRKCKKKSKNPCLYFHMGQCLGVCYREDLEKEYQKEVDKIKHILNGNIS 176 (574)
T ss_pred CHHHHHHHHHHHHHHcCCCCCCCCCCCCChhhHHhcCCccccCCCCHHHHHHHHHHHHHHHcCCcH
Confidence 44444555555445566554222345789999998887654 23444555556666644433
No 29
>cd03345 eu_TyrOH Eukaryotic tyrosine hydroxylase (TyrOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tryptophan hydroxylase (TrpOH). TyrOH catalyzes the conversion of tyrosine to L-dihydroxyphenylalanine (L-DOPA), the rate-limiting step in the biosynthesis of the catecholamines dopamine, noradrenaline, and adrenaline.
Probab=29.08 E-value=36 Score=27.37 Aligned_cols=89 Identities=7% Similarity=0.110 Sum_probs=51.2
Q ss_pred HHHHHHHHhh-CCcEEeeeCC--CCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccc------cc-cchHHHHH
Q 031421 8 HQRLLQRLNV-YGLYEVKVSG--DGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEG------YV-PMKYKRYY 77 (160)
Q Consensus 8 ~~~l~~~l~~-~gl~~~~v~g--DGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~------~i-~~~~~~yl 77 (160)
.+.+++.|++ -|..++.|+| ...=||..+|.-.+-.. ..||..-.-.-..-||-|-+ ++ +..+.+|.
T Consensus 108 l~dvn~~L~~~TGw~~~pV~Gli~~~~Ff~~LA~R~Fp~t---~yIR~~~~~~YtpEPDi~HEl~GHvPlLadp~FA~f~ 184 (298)
T cd03345 108 LEDVSEFLKERTGFQLRPVAGLLSARDFLASLAFRVFQCT---QYIRHASSPMHSPEPDCCHELLGHVPMLADPTFAQFS 184 (298)
T ss_pred HHHHHHHHHhccCCEEEecCccCCHHHHHHHHhcCccccc---ceecCCcccCCCCCCchHHHHhccchhhCCHHHHHHH
Confidence 4567888887 8999999988 55568888887766544 33332110000011222211 11 23677777
Q ss_pred HhhcCCceeCcHHHHHHHHHHh
Q 031421 78 KNMAKVGEWGDHVTLQAAADKF 99 (160)
Q Consensus 78 ~~m~~~g~wg~~~ei~A~a~~~ 99 (160)
..+..-+-=+++.++.-+|++|
T Consensus 185 q~~G~~~l~a~~~~i~~LarlY 206 (298)
T cd03345 185 QDIGLASLGASDEEIEKLSTLY 206 (298)
T ss_pred HHHHHHhcCCCHHHHHHHhHhh
Confidence 7654333335677777788776
No 30
>PRK12334 nucleoside triphosphate pyrophosphohydrolase; Reviewed
Probab=28.95 E-value=1.6e+02 Score=23.42 Aligned_cols=58 Identities=14% Similarity=0.067 Sum_probs=46.4
Q ss_pred hHHHHHHHHHHHHhhCCcEEeeeCCC------CchHHHHHHHHHhcCcchHHHHHHHHHHHHhh
Q 031421 3 DASLDHQRLLQRLNVYGLYEVKVSGD------GNCQFRALSDQMYKSPEYHKHVRKEVVKQLKD 60 (160)
Q Consensus 3 ~~~~~~~~l~~~l~~~gl~~~~v~gD------GnClF~ais~~l~~~~~~~~~lR~~~v~~i~~ 60 (160)
|+.+--+++.++..+.|+.--.+++- |+.||..+..+-...-+.-..||+...+|++.
T Consensus 196 PaL~~A~ki~~ra~~~Gf~~~~~~~~~~e~e~GdlLf~lv~~ar~~~idpE~aLr~a~~kf~~r 259 (277)
T PRK12334 196 PALALAAKVLSRARKAGLPVPLAPAEDSEDELGALLLALVAVAVAAGVDAEAALRAAVRDFRDR 259 (277)
T ss_pred CHHHHHHHHHHHHHhcCCCCCCccchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 66777889999999999987777666 88999988877666666678899998888743
No 31
>cd02665 Peptidase_C19I A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=28.81 E-value=80 Score=24.25 Aligned_cols=32 Identities=16% Similarity=0.360 Sum_probs=22.5
Q ss_pred CchHHHHHHHHHhcCcchHHHHHHHHHHHHhh
Q 031421 29 GNCQFRALSDQMYKSPEYHKHVRKEVVKQLKD 60 (160)
Q Consensus 29 GnClF~ais~~l~~~~~~~~~lR~~~v~~i~~ 60 (160)
+.|.|.|+...++..|.+..+.=..+.+.|++
T Consensus 7 ~~~~~~~~~~~~~~~QQDa~Ef~~~Lld~Le~ 38 (228)
T cd02665 7 NTCWFSAVIQSLFSQQQDVSEFTHLLLDWLED 38 (228)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34999999999998876666655555554443
No 32
>TIGR01268 Phe4hydrox_tetr phenylalanine-4-hydroxylase, tetrameric form. The member of this family from Drosophila has been described as having both phenylalanine-4-hydroxylase and tryptophan 5-monoxygenase activity (PubMed:1371286). However, a Drosophila member of the tryptophan 5-monoxygenase clade has subsequently been discovered.
Probab=28.58 E-value=34 Score=29.04 Aligned_cols=93 Identities=11% Similarity=0.116 Sum_probs=53.0
Q ss_pred HHHHHHHHhh-CCcEEeeeCC--CCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccc------cc-cchHHHHH
Q 031421 8 HQRLLQRLNV-YGLYEVKVSG--DGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEG------YV-PMKYKRYY 77 (160)
Q Consensus 8 ~~~l~~~l~~-~gl~~~~v~g--DGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~------~i-~~~~~~yl 77 (160)
.+.+.+.|++ -|..++.|+| ...=||..+|.-.+... ..||..---....-||-|-+ ++ +..+.+|.
T Consensus 211 l~dvs~~L~~~TGw~~~pV~Gll~~~~F~~~LA~r~F~~t---~yiR~~~~~~YtpEPDi~Hel~GHvPlla~p~fA~f~ 287 (436)
T TIGR01268 211 LEDVSQFLQDCTGFTLRPVAGLLSSRDFLAGLAFRVFHST---QYIRHHSKPMYTPEPDICHELLGHVPLFADVEFAQFS 287 (436)
T ss_pred HHHHHHHHHhccCCEEEecCCcCCHHHHHHHHhcCcccee---eeecccccccCCCCChhHHHHhccchhhCCHHHHHHH
Confidence 4567888888 5999999988 55568888888776654 33443111001111222211 11 23677777
Q ss_pred HhhcCCceeCcHHHHHHHHHHhCCeE
Q 031421 78 KNMAKVGEWGDHVTLQAAADKFAAKI 103 (160)
Q Consensus 78 ~~m~~~g~wg~~~ei~A~a~~~~v~I 103 (160)
.....-+-=+.+.++.-+|++|=-.|
T Consensus 288 q~~G~~~l~a~~~~i~~LarlyWfTV 313 (436)
T TIGR01268 288 QEIGLASLGAPDDYIEKLATLYWFTI 313 (436)
T ss_pred HHHHHhhcCCCHHHHHHHhhhheeee
Confidence 76544333345667777887774333
No 33
>PF08373 RAP: RAP domain; InterPro: IPR013584 The ~60-residue RAP (an acronym for RNA-binding domain abundant in Apicomplexans) domain is found in various proteins in eukaryotes. It is particularly abundant in apicomplexans and might mediate a range of cellular functions through its potential interactions with RNA []. The RAP domain consists of multiple blocks of charged and aromatics residues and is predicted to be composed of alpha helical and beta strand structures. Two predicted loop regions that are dominated by glycine and tryptophan residues are found before and after the central beta sheet []. Some proteins known to contain a RAP domain are listed below: Human hypothetical protein MGC5297, Mammalian FAST kinase domain-containing proteins (FASTKDs), Chlamydomonas reinhardtii chloroplastic trans-splicing factor Raa3.
Probab=27.46 E-value=63 Score=18.54 Aligned_cols=15 Identities=13% Similarity=0.321 Sum_probs=12.4
Q ss_pred HHHHhhCCcEEeeeC
Q 031421 12 LQRLNVYGLYEVKVS 26 (160)
Q Consensus 12 ~~~l~~~gl~~~~v~ 26 (160)
.+.|+++|+.++.||
T Consensus 24 ~r~L~~~G~~Vi~Ip 38 (58)
T PF08373_consen 24 HRHLKALGYKVISIP 38 (58)
T ss_pred HHHHHHCCCEEEEec
Confidence 356788999999997
No 34
>KOG3346 consensus Phosphatidylethanolamine binding protein [General function prediction only]
Probab=27.35 E-value=95 Score=23.20 Aligned_cols=42 Identities=19% Similarity=0.294 Sum_probs=29.3
Q ss_pred cCCCCCCCCeEEEE--eCCCCcceeeecCCCCCCCCCccccccc
Q 031421 118 MPQHQAPKRELWLS--FWSEVHYNSLYDIRDAPVPKKPRKKHWL 159 (160)
Q Consensus 118 ~p~~~~~~~~I~L~--~~~~~HY~~l~~~~~~~~~~~~~~~~~~ 159 (160)
.|+.....+.|... -..+++|.+|..-.|.|.+.-|+.|-|+
T Consensus 44 ~pt~~~~~P~v~~~~~a~~~~~yTLvm~DPDaPsr~~p~~rE~l 87 (185)
T KOG3346|consen 44 TPTQVKNRPIVSWDGFADPGSLYTLVMTDPDAPSRSDPKFREWL 87 (185)
T ss_pred CchhhccCCeEEEcCcCCCCCeEEEEEeCCCCCCCCCCcceeEE
Confidence 34333334444443 1356899999999999999999998664
No 35
>KOG3325 consensus Membrane coat complex Retromer, subunit VPS29/PEP11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.10 E-value=79 Score=23.06 Aligned_cols=25 Identities=28% Similarity=0.434 Sum_probs=21.9
Q ss_pred eeCcHHHHHHHHHHhCCeEEEEecC
Q 031421 85 EWGDHVTLQAAADKFAAKICLLTSF 109 (160)
Q Consensus 85 ~wg~~~ei~A~a~~~~v~I~V~~~~ 109 (160)
-||+-..+.++|+-+.+.|.+.-.+
T Consensus 92 P~gd~~sL~~LaRqldvDILl~G~T 116 (183)
T KOG3325|consen 92 PWGDPESLALLARQLDVDILLTGHT 116 (183)
T ss_pred cCCCHHHHHHHHHhcCCcEEEeCCc
Confidence 6899999999999999999887544
No 36
>COG5440 Uncharacterized conserved protein [Function unknown]
Probab=25.38 E-value=57 Score=23.63 Aligned_cols=33 Identities=27% Similarity=0.270 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhhCCcEEeeeCCCCchHHHHHHHH
Q 031421 6 LDHQRLLQRLNVYGLYEVKVSGDGNCQFRALSDQ 39 (160)
Q Consensus 6 ~~~~~l~~~l~~~gl~~~~v~gDGnClF~ais~~ 39 (160)
+-...+..||+..|+....| .|+|-.||-++..
T Consensus 5 ~~d~~I~~WL~EeG~~~~kv-~~~na~fH~~v~~ 37 (161)
T COG5440 5 DSDNMILDWLAEEGNVSVKV-PDENAPFHFVVKP 37 (161)
T ss_pred hHHHHHHHHHHHhCceeecc-CCCCCceeEEecC
Confidence 44567889999999987776 6889899865544
No 37
>PF03819 MazG: MazG nucleotide pyrophosphohydrolase domain; InterPro: IPR004518 This domain is found in a group of prokaryotic proteins which includes Escherichia coli MazG. The domain is about 100 amino acid residues in length and contains four conserved negatively charged residues that probably form an active site or metal binding site.; PDB: 1VMG_A 2YXH_B 2OIE_B 2OIG_C 2Q4P_A 2A3Q_B 2Q9L_C 2Q5Z_B 2Q73_A 3CRC_B ....
Probab=24.97 E-value=1.6e+02 Score=17.94 Aligned_cols=35 Identities=11% Similarity=0.130 Sum_probs=18.2
Q ss_pred CchHHHHHHHHHh----cCcchHHHHHHHHHHHHhhccc
Q 031421 29 GNCQFRALSDQMY----KSPEYHKHVRKEVVKQLKDCRS 63 (160)
Q Consensus 29 GnClF~ais~~l~----~~~~~~~~lR~~~v~~i~~n~~ 63 (160)
|+|+|..+..+-. ..-+-...+...+.++.+++|.
T Consensus 34 gDvl~~l~~la~~~~~~~~idle~~~~~~~~K~~~R~p~ 72 (74)
T PF03819_consen 34 GDVLFYLLQLARILEERLGIDLEEALERKMEKLERRYPH 72 (74)
T ss_dssp HHHHHHHHHHHHHHHCHTTSHHHHHHHHHHHHHHHHSGG
T ss_pred HHHHHHHHHHHHHHhHcCCCCHHHHHHHHHHHHhccCCC
Confidence 5677777666553 3333334455555555554443
No 38
>cd03347 eu_PheOH Eukaryotic phenylalanine-4-hydroxylase (eu_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic phenylalanine-4-hydroxylase (pro_PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH catalyzes the first and rate-limiting step in the metabolism of the amino acid L-phenylalanine (L-Phe), the hydroxylation of L-Phe to L-tyrosine (L-Tyr). It uses (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the physiological electron donor. The catalytic activity of the tetrameric enzyme is tightly regulated by the binding of L-Phe and BH4 as well as by phosphorylation. Mutations in the human enzyme are linked to a severe variant of phenylketonuria.
Probab=24.85 E-value=41 Score=27.15 Aligned_cols=91 Identities=9% Similarity=0.091 Sum_probs=51.3
Q ss_pred HHHHHHHHhh-CCcEEeeeCC--CCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccc------cc-cchHHHHH
Q 031421 8 HQRLLQRLNV-YGLYEVKVSG--DGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEG------YV-PMKYKRYY 77 (160)
Q Consensus 8 ~~~l~~~l~~-~gl~~~~v~g--DGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~------~i-~~~~~~yl 77 (160)
.+.+++.|++ -|..++.|+| ...=||..+|.-.+-.. ..||..---.-..-||-|-+ ++ +..+.+|.
T Consensus 109 l~dvn~~L~~~TGw~~~pV~Gli~~~~Ff~~LA~R~Fp~t---~yIR~~~~~~YtpEPDifHEl~GHvPlLadp~FA~f~ 185 (306)
T cd03347 109 LEDVSNFLQTCTGFRLRPVAGLLSSRDFLAGLAFRVFHST---QYIRHPSKPMYTPEPDICHELLGHVPLFADPSFAQFS 185 (306)
T ss_pred HHHHHHHHHhccCCEEEecCccCCHHHHHHHHhcCcccee---eeecCccccCCCCCCchHHHHhccchhhcCHHHHHHH
Confidence 4567888887 6999999988 55568888887766544 33332110000011222211 11 23677777
Q ss_pred HhhcCCceeCcHHHHHHHHHHhCC
Q 031421 78 KNMAKVGEWGDHVTLQAAADKFAA 101 (160)
Q Consensus 78 ~~m~~~g~wg~~~ei~A~a~~~~v 101 (160)
.....-+.=+.+.++.-+|++|=-
T Consensus 186 q~~G~~~l~a~~~~i~~LarlYWf 209 (306)
T cd03347 186 QEIGLASLGAPDEYIEKLATVYWF 209 (306)
T ss_pred HHHHHHhcCCCHHHHHHHhhheee
Confidence 765443333456677778877633
No 39
>cd04240 AAK_UC AAK_UC: Uncharacterized (UC) amino acid kinase-like proteins found mainly in archaea and a few bacteria. Sequences in this CD are members of the Amino Acid Kinase (AAK) superfamily.
Probab=24.81 E-value=1.5e+02 Score=22.19 Aligned_cols=35 Identities=31% Similarity=0.284 Sum_probs=26.4
Q ss_pred HHHHHHHhhC-CcEEeeeCCCCchH---HHHHHHHHhcCc
Q 031421 9 QRLLQRLNVY-GLYEVKVSGDGNCQ---FRALSDQMYKSP 44 (160)
Q Consensus 9 ~~l~~~l~~~-gl~~~~v~gDGnCl---F~ais~~l~~~~ 44 (160)
..|.++|.+. |.++.=|+|.|| | ||.+...++.+.
T Consensus 13 ~~~~~~l~~~~~~~v~iV~GGG~-~A~~~r~~~~~~g~~~ 51 (203)
T cd04240 13 VRLLRWLKTLSGGGVVIVPGGGP-FADVVRRYQERKGLSD 51 (203)
T ss_pred HHHHHHHHhccCCCEEEEcCCcH-HHHHHHHHHHHcCCCh
Confidence 4566677665 778888999999 6 888887665554
No 40
>PF01870 Hjc: Archaeal holliday junction resolvase (hjc); InterPro: IPR002732 This entry represents Holliday junction resolvases (hjc gene) and related proteins, primarily from archaeal species []. The Holliday junction is an essential intermediate of homologous recombination. Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. In the presence of divalent cations, these junctions exist predominantly as the stacked-X form in which the double-helical segments are coaxially stacked and twisted by 60 degrees in a right-handed direction across the junction cross-over. In this structure, the stacked arms resemble two adjacent double-helices, but are linked at the junction by two common strands that cross-over between the duplexes []. During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within the four-way Holliday structure. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back to two double strands.; PDB: 2WJ0_A 2WIZ_B 2WIW_B 2WCW_C 2WCZ_A 1HH1_A 1GEF_D 1IPI_B 2EO0_B 1OB9_A ....
Probab=24.03 E-value=1.4e+02 Score=19.40 Aligned_cols=24 Identities=25% Similarity=0.387 Sum_probs=20.7
Q ss_pred HHHHHHHHhhCCcEEeeeCCCCch
Q 031421 8 HQRLLQRLNVYGLYEVKVSGDGNC 31 (160)
Q Consensus 8 ~~~l~~~l~~~gl~~~~v~gDGnC 31 (160)
+..|.+.|...|+.+...++.|.+
T Consensus 3 Erel~~~L~~~Gf~v~R~~~Sg~~ 26 (88)
T PF01870_consen 3 ERELVKILWERGFAVVRAAGSGGG 26 (88)
T ss_dssp HHHHHHHHHHTT-EEEEBSCCSSS
T ss_pred HHHHHHHHHhCCcEEEEecCCCCc
Confidence 567888999999999999999998
No 41
>KOG2947 consensus Carbohydrate kinase [Carbohydrate transport and metabolism]
Probab=24.03 E-value=84 Score=24.90 Aligned_cols=24 Identities=17% Similarity=0.116 Sum_probs=19.2
Q ss_pred EEeeeCCCCchHHHHHHHHHhcCc
Q 031421 21 YEVKVSGDGNCQFRALSDQMYKSP 44 (160)
Q Consensus 21 ~~~~v~gDGnClF~ais~~l~~~~ 44 (160)
+++++.|+|+||-.++-+++...+
T Consensus 252 kvVD~lg~~DtF~A~vIyA~lk~~ 275 (308)
T KOG2947|consen 252 KVVDTLGAGDTFNAGVIYALLKQG 275 (308)
T ss_pred cceeeccCCCcchHHHHHHHHHhh
Confidence 468899999999888888865544
No 42
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=24.00 E-value=64 Score=17.64 Aligned_cols=17 Identities=18% Similarity=0.220 Sum_probs=11.6
Q ss_pred CcHHHHHHHHHHhCCeE
Q 031421 87 GDHVTLQAAADKFAAKI 103 (160)
Q Consensus 87 g~~~ei~A~a~~~~v~I 103 (160)
.|+.||+.+|..+++.-
T Consensus 22 ~G~CeLQ~~~~~~gv~~ 38 (41)
T PF10588_consen 22 NGNCELQDLAYEYGVDE 38 (41)
T ss_dssp GGG-HHHHHHHHH-S--
T ss_pred CCCCHHHHHHHHhCCCc
Confidence 57899999999998853
No 43
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=23.36 E-value=59 Score=27.03 Aligned_cols=45 Identities=16% Similarity=0.242 Sum_probs=39.7
Q ss_pred cccccchHHHHHHhhcCCceeCcHHHHHHHHHHhCCeEEEEecCC
Q 031421 66 EGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKFAAKICLLTSFR 110 (160)
Q Consensus 66 ~~~i~~~~~~yl~~m~~~g~wg~~~ei~A~a~~~~v~I~V~~~~~ 110 (160)
.+.+..+++.|+.-+.++.+-|+-.++.+.+.+++.+.+.+.+.+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~s~~~r~~~~~~~~~g 47 (371)
T KOG2605|consen 3 REEVSGDFDWYLWDLGKTKTLGTILELGAMSHVYRRNVIDYEPFG 47 (371)
T ss_pred ccccCchHHHHhhcCCCCcccccchhhhhccccccCCCCCcCCcc
Confidence 345677899999999999999999999999999999999888754
No 44
>cd03348 pro_PheOH Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH), tyrosine hydroxylase (TyrOH) and tryptophan hydroxylase (TrpOH). PheOH catalyzes the hydroxylation of L-Phe to L-tyrosine (L-Tyr). It uses (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the physiological electron donor.
Probab=23.12 E-value=27 Score=27.00 Aligned_cols=90 Identities=16% Similarity=0.225 Sum_probs=50.9
Q ss_pred HHHHHHHHHhh-CCcEEeeeCC--CCchHHHHHHHHHhcCcchHHHHHHHH-HHHHhhccccccccc-------cchHHH
Q 031421 7 DHQRLLQRLNV-YGLYEVKVSG--DGNCQFRALSDQMYKSPEYHKHVRKEV-VKQLKDCRSMYEGYV-------PMKYKR 75 (160)
Q Consensus 7 ~~~~l~~~l~~-~gl~~~~v~g--DGnClF~ais~~l~~~~~~~~~lR~~~-v~~i~~n~~~f~~~i-------~~~~~~ 75 (160)
+.+.+++.|++ -|..++.|+| ...=||..+|.-.+-.. ..||..- .+|+ .-||-|-+.+ +..+.+
T Consensus 54 ql~~vn~~L~~~TGw~~~pV~Glip~~~Ff~~LA~r~Fp~t---~~iR~~~~~~Yt-pEPDifHe~fGHvPmL~~p~fAd 129 (228)
T cd03348 54 DFADVSERLKAATGWTVVAVPGLIPDDEFFEHLANRRFPVT---NFIRRPEELDYL-QEPDIFHDIFGHVPMLTNPVFAD 129 (228)
T ss_pred CHHHHHHHHHhccCCEEEecCCcCCHHHHHHHHhcCCCcee---eeecCccccCCC-CCcHHHHHHhcccHhhcCHHHHH
Confidence 34568888877 8999999987 56668888877655443 3333311 1111 1222222111 236777
Q ss_pred HHHhhcCCceeCcH-HHHHHHHHHhC
Q 031421 76 YYKNMAKVGEWGDH-VTLQAAADKFA 100 (160)
Q Consensus 76 yl~~m~~~g~wg~~-~ei~A~a~~~~ 100 (160)
|......-|.=+.+ -++..+|++|=
T Consensus 130 f~q~~G~~~l~a~~~~~~~~LarlyW 155 (228)
T cd03348 130 FMQAYGKGGLKATGLEDRALLARLYW 155 (228)
T ss_pred HHHHHHHHHhCCCCHHHHHHHhHhhh
Confidence 77765443333444 66777887763
No 45
>TIGR00124 cit_ly_ligase [citrate (pro-3S)-lyase] ligase. ATP is cleaved to AMP and pyrophosphate during the reaction. The carboxyl end is homologous to a number of cytidyltransferases that also release pyrophosphate.
Probab=23.07 E-value=1.1e+02 Score=24.95 Aligned_cols=55 Identities=15% Similarity=0.119 Sum_probs=32.2
Q ss_pred HHHHHhhCCcEEeeeCCCCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccccccchHHHHHH
Q 031421 11 LLQRLNVYGLYEVKVSGDGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPMKYKRYYK 78 (160)
Q Consensus 11 l~~~l~~~gl~~~~v~gDGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~~i~~~~~~yl~ 78 (160)
|...|...++.+..|+.-|. .+...+...||+.+.+ .+.+...++++....+++.
T Consensus 273 ~~~~~~~~~I~~~~I~R~~~----------~~~~~SASaIR~~L~~---~~~~~i~~~VP~~t~~~l~ 327 (332)
T TIGR00124 273 LEEPNDAPPIEVVEIQRKLA----------AGGPISASTVRELLAK---GDWAAWAKLVPETTLHFLQ 327 (332)
T ss_pred hhccCCCCCcEEEEEeeecC----------CCCeeCHHHHHHHHHc---CCHHHHHHhCCHHHHHHHH
Confidence 44455556777777777665 2444578899998732 2233445566655445443
No 46
>TIGR01269 Tyr_3_monoox tyrosine 3-monooxygenase, tetrameric. This model describes tyrosine 3-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tryptophan 5-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
Probab=22.92 E-value=55 Score=27.93 Aligned_cols=90 Identities=8% Similarity=0.125 Sum_probs=51.4
Q ss_pred HHHHHHHHHhh-CCcEEeeeCC--CCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccc------cc-cchHHHH
Q 031421 7 DHQRLLQRLNV-YGLYEVKVSG--DGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEG------YV-PMKYKRY 76 (160)
Q Consensus 7 ~~~~l~~~l~~-~gl~~~~v~g--DGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~------~i-~~~~~~y 76 (160)
+.+.+.+.|++ -|+.++.|+| ...=||..+|.-.+... ..||..---....-||-|-+ ++ +..|.+|
T Consensus 231 qL~dvs~~L~~~TGw~l~pV~GLl~~rdF~~~LA~RvFp~T---qyIR~~~~~~YtpEPDi~HEl~GHvPlLadp~FA~F 307 (457)
T TIGR01269 231 QLQTISEFLHRTTGFRLRPVAGLLSARDFLASLAFRVFQCT---QYIRHHSSPMHTPEPDCIHELLGHMPMLADRQFAQF 307 (457)
T ss_pred CHHHHHHHHHhccCCEEEeccccCCHHHHHHHHhcCcccce---eeecCccccCCCCCCchHHHHhcccccccCHHHHHH
Confidence 34568888887 5999999998 55668888888776654 33332111000011222211 11 2367777
Q ss_pred HHhhcCCceeCcHHHHHHHHHHh
Q 031421 77 YKNMAKVGEWGDHVTLQAAADKF 99 (160)
Q Consensus 77 l~~m~~~g~wg~~~ei~A~a~~~ 99 (160)
...+..-+-=+++.+|.-+|.+|
T Consensus 308 ~q~~G~asl~As~e~i~~LarlY 330 (457)
T TIGR01269 308 SQEIGLASLGASEEEIEKLSTLY 330 (457)
T ss_pred HHHHHHHhcCCCHHHHHHHhHhH
Confidence 77654333324566677777766
No 47
>PRK11913 phhA phenylalanine 4-monooxygenase; Reviewed
Probab=22.49 E-value=36 Score=27.09 Aligned_cols=90 Identities=12% Similarity=0.182 Sum_probs=51.2
Q ss_pred HHHHHHHHHhh-CCcEEeeeCC--CCchHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccc------cc-cchHHHH
Q 031421 7 DHQRLLQRLNV-YGLYEVKVSG--DGNCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEG------YV-PMKYKRY 76 (160)
Q Consensus 7 ~~~~l~~~l~~-~gl~~~~v~g--DGnClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~------~i-~~~~~~y 76 (160)
+.+.+++.|++ -|..++.|+| ...=||..+|.-.+-.. ..||..-.-.-..-||-|-+ ++ +..+.+|
T Consensus 70 ql~~in~~L~~~TGw~~~pV~Glip~~~Ff~~LA~r~Fp~t---~~IR~~~~~~YtpEPDifHevfGHvPmL~~p~FAdf 146 (275)
T PRK11913 70 QLDEINRVLQAATGWQVVPVPGLIPFDVFFELLANRRFPVA---TFIRRPEELDYLQEPDIFHDVFGHVPLLTNPVFADF 146 (275)
T ss_pred CHHHHHHHHHhhcCCEEEecCccCCHHHHHHHHhcCcccee---eeecCccccCCCCCCchHHHHhccchhhcCHHHHHH
Confidence 44568888886 8999999998 66778888887766544 33332111001111222211 11 2367777
Q ss_pred HHhhcCCceeCcHHHHH-HHHHHh
Q 031421 77 YKNMAKVGEWGDHVTLQ-AAADKF 99 (160)
Q Consensus 77 l~~m~~~g~wg~~~ei~-A~a~~~ 99 (160)
...+.+-|.=+.+.+.. .+|++|
T Consensus 147 ~q~~G~~~l~a~~~~~~~~Larly 170 (275)
T PRK11913 147 MQAYGKLGLRASKEGRLEFLARLY 170 (275)
T ss_pred HHHHHHHHhCcChhhHHHHHhhhe
Confidence 77665444334444444 677766
No 48
>PF02479 Herpes_IE68: Herpesvirus immediate early protein; InterPro: IPR003403 This regulatory protein is expressed from an immediate early gene in the cell cycle of Herpesviridae. The protein is known by various names including IE-68, US1, ICP22 and IR4.
Probab=21.91 E-value=93 Score=21.96 Aligned_cols=32 Identities=16% Similarity=0.206 Sum_probs=25.7
Q ss_pred CCCchHHHHHHHHHhcCcchHHHHHHHHHHHH
Q 031421 27 GDGNCQFRALSDQMYKSPEYHKHVRKEVVKQL 58 (160)
Q Consensus 27 gDGnClF~ais~~l~~~~~~~~~lR~~~v~~i 58 (160)
.|=|=+||+|+..-.....++..+|..+.++.
T Consensus 37 ~dvN~lFRci~r~s~n~~~~~~aLRR~l~D~Y 68 (132)
T PF02479_consen 37 RDVNRLFRCIARSSINVTGDARALRRLLLDFY 68 (132)
T ss_pred HHHHHHHHHHHhcCCCCchHHHHHHHHHHHHH
Confidence 45566999998886666678899999999865
No 49
>PF02542 YgbB: YgbB family; InterPro: IPR003526 MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[]. A number of proteins from eukaryotes and prokaryotes share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme of this type [].; GO: 0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity, 0016114 terpenoid biosynthetic process; PDB: 3T80_B 3GHZ_A 2PMP_A 3F6M_A 3FPI_A 3RE3_A 1T0A_C 1W57_A 1W55_A 3B6N_A ....
Probab=21.83 E-value=62 Score=23.54 Aligned_cols=17 Identities=24% Similarity=0.477 Sum_probs=12.9
Q ss_pred CCCCchHHHHHHHHHhc
Q 031421 26 SGDGNCQFRALSDQMYK 42 (160)
Q Consensus 26 ~gDGnClF~ais~~l~~ 42 (160)
-.||+.++|||.++|.|
T Consensus 34 HSDgDVl~HAi~DAlLG 50 (157)
T PF02542_consen 34 HSDGDVLLHAIIDALLG 50 (157)
T ss_dssp SSS--HHHHHHHHHHHH
T ss_pred cChHHHHHHHHHHHHHH
Confidence 36999999999999865
No 50
>cd02011 TPP_PK Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent magnesium ions and TPP for activity.
Probab=21.53 E-value=1.8e+02 Score=22.45 Aligned_cols=24 Identities=25% Similarity=0.344 Sum_probs=19.9
Q ss_pred HHHHHHHHHhhCCcEEeeeCCCCchH
Q 031421 7 DHQRLLQRLNVYGLYEVKVSGDGNCQ 32 (160)
Q Consensus 7 ~~~~l~~~l~~~gl~~~~v~gDGnCl 32 (160)
..+.|.++++.+|+....| ||+.+
T Consensus 136 ~~e~l~~~~~~yG~~~~~V--DG~D~ 159 (227)
T cd02011 136 SHEELEALFRGYGYEPYFV--EGDDP 159 (227)
T ss_pred CchhHHHHHHhCCCceEEE--CCCCH
Confidence 3577999999999999988 77764
No 51
>PRK13619 psbV cytochrome c-550; Provisional
Probab=20.83 E-value=1.4e+02 Score=21.73 Aligned_cols=44 Identities=18% Similarity=0.165 Sum_probs=24.2
Q ss_pred HHHHHHhhccccccccccchHHHHHHhhcCCce-----eCcHHHHHHHHHHh
Q 031421 53 EVVKQLKDCRSMYEGYVPMKYKRYYKNMAKVGE-----WGDHVTLQAAADKF 99 (160)
Q Consensus 53 ~~v~~i~~n~~~f~~~i~~~~~~yl~~m~~~g~-----wg~~~ei~A~a~~~ 99 (160)
.+|+|| +||..|...- +..+....+...+. |-++.++.++|-..
T Consensus 96 aLVdym-k~PtsyDG~~--~~a~~hpsi~~~di~P~mr~LtdedL~~iAg~I 144 (160)
T PRK13619 96 ALVDYL-KHPTSYDGED--DYSELHPNVSRPDIFPELRNFTEDDLYDVAGYM 144 (160)
T ss_pred HHHHHH-hCCcccccch--hhhhhcccccccccccccCCCCHHHHHHHHHHH
Confidence 578887 4566553321 12222234544444 67888888777543
No 52
>PRK07027 cobalamin biosynthesis protein CbiG; Provisional
Probab=20.76 E-value=71 Score=22.06 Aligned_cols=33 Identities=12% Similarity=0.084 Sum_probs=26.0
Q ss_pred HHhhcCCceeCcHHHHHHHHHHhCCeEEEEecC
Q 031421 77 YKNMAKVGEWGDHVTLQAAADKFAAKICLLTSF 109 (160)
Q Consensus 77 l~~m~~~g~wg~~~ei~A~a~~~~v~I~V~~~~ 109 (160)
+..+.......++..|..+|+.+++|+.+|+.+
T Consensus 37 i~~lasi~~K~~E~~L~~~A~~lg~pl~~~~~~ 69 (126)
T PRK07027 37 VRVVATLDLKADEAGLLALCARHGWPLRAFSAA 69 (126)
T ss_pred hheeEehhhhcCCHHHHHHHHHhCCCeEEeCHH
Confidence 344455566678899999999999999999754
No 53
>PRK10963 hypothetical protein; Provisional
Probab=20.72 E-value=76 Score=24.18 Aligned_cols=17 Identities=18% Similarity=0.208 Sum_probs=13.8
Q ss_pred HHHHHHHhhcccccccc
Q 031421 52 KEVVKQLKDCRSMYEGY 68 (160)
Q Consensus 52 ~~~v~~i~~n~~~f~~~ 68 (160)
+.+++|+++|||.|...
T Consensus 6 ~~V~~yL~~~PdFf~~h 22 (223)
T PRK10963 6 RAVVDYLLQNPDFFIRN 22 (223)
T ss_pred HHHHHHHHHCchHHhhC
Confidence 56889999999988653
No 54
>cd05295 MDH_like Malate dehydrogenase-like. These MDH-like proteins are related to other groups in the MDH family but do not have conserved substrate and cofactor binding residues. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subgroup are uncharacterized MDH-like proteins from animals. They are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=20.14 E-value=85 Score=26.86 Aligned_cols=38 Identities=11% Similarity=0.349 Sum_probs=24.2
Q ss_pred chHHHHHHHHHhcCcchHHHHHHHHHHHHhhccccccccc----cchHHHHHHhhc
Q 031421 30 NCQFRALSDQMYKSPEYHKHVRKEVVKQLKDCRSMYEGYV----PMKYKRYYKNMA 81 (160)
Q Consensus 30 nClF~ais~~l~~~~~~~~~lR~~~v~~i~~n~~~f~~~i----~~~~~~yl~~m~ 81 (160)
||=|.|-+.. +.+|+..|-.+|.-.. ++.|+++++.+.
T Consensus 3 ~cp~ya~~el--------------lad~l~~~l~~f~~~ki~~~p~~w~~wl~~~c 44 (452)
T cd05295 3 DCPYYAKAEL--------------LADYLQKNLPDFRVHKIVKHPDEWEDWLQDLC 44 (452)
T ss_pred CCchhHHHHH--------------HHHHHHhhCCCceEEEccCChHHHHHHHHHHH
Confidence 6767665554 4567888866664321 467888887664
No 55
>TIGR00160 MGSA methylglyoxal synthase. Methylglyoxal synthase (MGS) generates methylglyoxal (MG), a toxic metabolite (that may also be a regulatory metabolite and) that is detoxified, prinicipally, through a pathway involving glutathione and glyoxylase I. Totemeyer, et al. (MUID:98149311) propose that, during a loss of control over carbon flux, with accumulation of phosphorylated sugars and depletion of phosphate, as might happen during a rapid shift to a richer medium, MGS aids the cell by converting some dihydroxyacetone phosphate (DHAP) to MG and phosphate. This is therefore an alternative to triosephosphate isomerase and the remainder of the glycolytic pathway for the disposal of DHAP during the stress of a sudden increase in available sugars.
Probab=20.14 E-value=2.9e+02 Score=19.76 Aligned_cols=64 Identities=8% Similarity=0.041 Sum_probs=44.6
Q ss_pred hHHHHHHHHHHHHhhccccccccc---cchHHHHHHh-------hcCCceeCcHHHHHHHHHHhCCeEEEEecC
Q 031421 46 YHKHVRKEVVKQLKDCRSMYEGYV---PMKYKRYYKN-------MAKVGEWGDHVTLQAAADKFAAKICLLTSF 109 (160)
Q Consensus 46 ~~~~lR~~~v~~i~~n~~~f~~~i---~~~~~~yl~~-------m~~~g~wg~~~ei~A~a~~~~v~I~V~~~~ 109 (160)
.|..-|..+++|...|.+.++.+- .++--..+.. ...+|-.||+..|.|...-=++...|+..+
T Consensus 9 AHD~kK~~l~~f~~~~~~~L~~h~L~ATgTTG~~i~~~tgL~V~~~~SGplGGDqQIga~Ia~g~id~vIFf~D 82 (143)
T TIGR00160 9 AHDKKKQDLVNFVQQHKPLLSQHDLYATGTTGNLISRATGLNINAMLSGPMGGDQQIGALIAEGKIDAVIFFWD 82 (143)
T ss_pred ecccchHHHHHHHHHHHHHHcCCCEEECccHHHHHHHHHCCCeEEeccCCccHHHHHHHHHHhCCCCEEEEecC
Confidence 456678899999999988766542 2332223322 235688899999998887778888888754
Done!