Query 033361
Match_columns 121
No_of_seqs 125 out of 810
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 12:57:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033361.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033361hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2606 OTU (ovarian tumor)-li 99.9 2.3E-22 4.9E-27 152.8 6.3 97 7-106 188-299 (302)
2 PF02338 OTU: OTU-like cystein 99.8 3.5E-21 7.5E-26 129.8 5.6 91 3-99 21-121 (121)
3 KOG2605 OTU (ovarian tumor)-li 99.6 7.8E-16 1.7E-20 121.6 5.5 121 1-121 238-364 (371)
4 KOG3288 OTU-like cysteine prot 99.5 5.1E-15 1.1E-19 111.0 4.3 95 9-106 139-234 (307)
5 PF10275 Peptidase_C65: Peptid 99.4 6.9E-13 1.5E-17 99.7 9.3 94 10-104 141-244 (244)
6 KOG3991 Uncharacterized conser 99.3 6E-12 1.3E-16 93.3 7.3 93 9-104 157-255 (256)
7 COG5539 Predicted cysteine pro 98.8 9E-09 2E-13 78.7 6.0 67 32-102 234-304 (306)
8 COG5539 Predicted cysteine pro 96.9 0.00012 2.5E-09 56.5 -1.8 92 8-103 137-230 (306)
9 TIGR02934 nifT_nitrog probable 82.4 0.062 1.3E-06 33.0 -3.6 34 20-53 6-41 (67)
10 PF05381 Peptidase_C21: Tymovi 78.2 12 0.00027 24.8 5.9 44 53-101 49-94 (104)
11 KOG2605 OTU (ovarian tumor)-li 69.0 3.1 6.7E-05 33.6 1.7 46 26-71 2-47 (371)
12 PRK10963 hypothetical protein; 67.0 5 0.00011 29.8 2.3 17 13-29 6-22 (223)
13 PF06988 NifT: NifT/FixU prote 64.7 0.025 5.5E-07 34.4 -8.4 34 20-53 6-41 (64)
14 PF05952 ComX: Bacillus compet 57.7 2.9 6.4E-05 24.8 -0.3 18 13-30 3-20 (57)
15 COG3159 Uncharacterized protei 56.7 5.8 0.00013 29.7 1.1 17 13-29 7-23 (218)
16 PF04340 DUF484: Protein of un 54.9 4 8.7E-05 30.1 0.0 18 13-30 9-26 (225)
17 KOG3325 Membrane coat complex 48.5 23 0.0005 25.4 3.0 23 46-68 92-114 (183)
18 PF10588 NADH-G_4Fe-4S_3: NADH 48.4 12 0.00027 20.3 1.3 17 48-64 22-38 (41)
19 KOG4516 NADH:ubiquinone oxidor 47.8 20 0.00044 24.0 2.5 24 6-29 78-102 (118)
20 PF11952 DUF3469: Protein of u 45.8 47 0.001 21.2 3.9 21 3-26 8-28 (87)
21 PF06141 Phage_tail_U: Phage m 45.1 17 0.00036 25.2 1.8 19 6-24 2-20 (133)
22 smart00337 BCL BCL (B-Cell lym 39.4 12 0.00026 24.1 0.4 52 11-62 1-64 (100)
23 PF05415 Peptidase_C36: Beet n 38.5 1.1E+02 0.0024 19.9 5.1 34 32-68 34-69 (104)
24 PF04877 Hairpins: HrpZ; Inte 37.9 26 0.00057 27.5 2.1 48 9-60 164-211 (308)
25 PF07802 GCK: GCK domain; Int 37.5 20 0.00044 22.4 1.2 26 6-31 38-63 (76)
26 PF02234 CDI: Cyclin-dependent 36.6 26 0.00057 20.0 1.5 26 1-27 3-28 (51)
27 PF09494 Slx4: Slx4 endonuclea 35.7 51 0.0011 19.5 2.8 50 13-62 3-59 (64)
28 KOG4100 Uncharacterized conser 34.7 12 0.00027 25.3 -0.1 28 22-50 49-80 (125)
29 cd06845 Bcl-2_like Apoptosis r 34.1 37 0.00079 23.1 2.2 57 6-62 34-102 (144)
30 COG4479 Uncharacterized protei 33.7 52 0.0011 20.4 2.5 30 13-42 42-73 (74)
31 PF01381 HTH_3: Helix-turn-hel 33.3 48 0.001 18.2 2.3 29 36-64 24-52 (55)
32 COG5562 Phage envelope protein 30.6 27 0.00059 24.3 1.1 16 32-47 89-104 (137)
33 PRK07027 cobalamin biosynthesi 29.9 51 0.0011 22.2 2.3 33 38-70 37-69 (126)
34 PF10568 Tom37: Outer mitochon 28.8 90 0.0019 18.9 3.1 22 51-72 18-42 (72)
35 COG3426 Butyrate kinase [Energ 27.8 50 0.0011 26.2 2.2 28 32-59 314-341 (358)
36 PF02467 Whib: Transcription f 27.7 52 0.0011 19.7 1.8 10 43-52 51-60 (66)
37 PF00452 Bcl-2: Apoptosis regu 24.9 33 0.00072 21.6 0.7 50 11-60 1-63 (101)
38 COG4290 Guanyl-specific ribonu 24.7 28 0.0006 24.4 0.3 18 89-106 134-151 (152)
39 PLN02994 1-aminocyclopropane-1 24.5 69 0.0015 22.3 2.2 22 2-23 88-109 (153)
40 PF01418 HTH_6: Helix-turn-hel 23.7 83 0.0018 19.0 2.3 32 12-43 18-60 (77)
41 smart00591 RWD domain in RING 23.5 1.9E+02 0.0041 17.8 5.1 49 52-100 1-54 (107)
42 PF02865 STAT_int: STAT protei 23.2 62 0.0013 21.9 1.8 22 1-23 20-41 (124)
43 cd05295 MDH_like Malate dehydr 22.9 47 0.001 27.6 1.3 35 13-47 11-49 (452)
44 PF06374 NDUF_C2: NADH-ubiquin 22.2 66 0.0014 21.8 1.7 17 13-29 85-101 (117)
45 TIGR00160 MGSA methylglyoxal s 21.8 2.4E+02 0.0051 19.8 4.4 63 8-70 10-82 (143)
46 KOG1043 Ca2+-binding transmemb 21.2 1.3E+02 0.0028 25.5 3.5 62 10-71 224-295 (499)
47 KOG4405 GDP dissociation inhib 20.4 95 0.0021 26.1 2.5 47 15-62 205-252 (547)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.86 E-value=2.3e-22 Score=152.76 Aligned_cols=97 Identities=15% Similarity=0.343 Sum_probs=84.1
Q ss_pred hHHHHHHHHHHHHHhCccccCCCCc----------ccHHHHHHhcCCCCccCCHHHHHHHHHHhCCcEEEEecCCCceeE
Q 033361 7 YHKHVRKEVVKQLKDCRSMYEGYVP----------MKYKRYYKNMAKVGEWGDHVTLQAAADKFAAKICLLTSFRDTCFI 76 (121)
Q Consensus 7 ~h~~lR~~vv~ym~~n~~~f~~fi~----------~~~~~Yl~~m~~~g~WGg~ieL~Ala~~~~~~I~V~~~~~~~~~~ 76 (121)
.-..||..+++||++|.++|.+|+. .+|++||+.|++++.|||+|||.|+|.+|++||.|++.+.+. +
T Consensus 188 ~v~kLR~~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~~p~--~ 265 (302)
T KOG2606|consen 188 SVQKLREETADYMREHVEDFLPFLLDEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQADGPI--L 265 (302)
T ss_pred cHHHHHHHHHHHHHHHHHHhhhHhcCccccccCCHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecCCCc--e
Confidence 3568999999999999999999992 369999999999999999999999999999999999987653 6
Q ss_pred EecCCCCCCCCeEEEEecCC-----CcccceecCC
Q 033361 77 EIMPQHQAPKRELWLSFWSE-----VHYNSLYDIR 106 (121)
Q Consensus 77 ~~~~~~~~~~~~i~L~y~~~-----~HYdsv~~~~ 106 (121)
.+++...+ .++|.|+|++. +||||+.+.+
T Consensus 266 ~~geey~k-d~pL~lvY~rH~y~LGeHYNS~~~~~ 299 (302)
T KOG2606|consen 266 EYGEEYGK-DKPLILVYHRHAYGLGEHYNSVTPLK 299 (302)
T ss_pred eechhhCC-CCCeeeehHHhHHHHHhhhccccccc
Confidence 77765533 68899999875 8999997653
No 2
>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=99.84 E-value=3.5e-21 Score=129.76 Aligned_cols=91 Identities=27% Similarity=0.472 Sum_probs=77.2
Q ss_pred CChhhHHHHHHHHHHHHH-hCccccCCCCcccHHHHHHhcCCCCccCCHHHHHHHHHHhCCcEEEEecCCCc--eeEEec
Q 033361 3 KSPEYHKHVRKEVVKQLK-DCRSMYEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKFAAKICLLTSFRDT--CFIEIM 79 (121)
Q Consensus 3 g~q~~h~~lR~~vv~ym~-~n~~~f~~fi~~~~~~Yl~~m~~~g~WGg~ieL~Ala~~~~~~I~V~~~~~~~--~~~~~~ 79 (121)
|++..|.+||++|++||+ .|++.|++|+..+ +|+++|+|||++||+|||++|+++|.|++..... .++.+.
T Consensus 21 ~~~~~~~~lR~~~~~~l~~~~~~~~~~~~~~~------~~~~~~~Wg~~~el~a~a~~~~~~I~v~~~~~~~~~~~~~~~ 94 (121)
T PF02338_consen 21 GSEDNHQELRKAVVDYLRDKNRDKFEEFLEGD------KMSKPGTWGGEIELQALANVLNRPIIVYSSSDGDNVVFIKFT 94 (121)
T ss_dssp SSTTTHHHHHHHHHHHHHTHTTTHHHHHHHHH------HHTSTTSHEEHHHHHHHHHHHTSEEEEECETTTBEEEEEEES
T ss_pred CCHHHHHHHHHHHHHHHHHhccchhhhhhhhh------hhccccccCcHHHHHHHHHHhCCeEEEEEcCCCCccceeeec
Confidence 899999999999999999 9999999999766 9999999999999999999999999998875442 233433
Q ss_pred C--CCCCCCCeEEEEecC-----CCcc
Q 033361 80 P--QHQAPKRELWLSFWS-----EVHY 99 (121)
Q Consensus 80 ~--~~~~~~~~i~L~y~~-----~~HY 99 (121)
+ ......++|.|+|+. ++||
T Consensus 95 ~~~~~~~~~~~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 95 GKYPPLESPPPICLCYHGHLYYTGNHY 121 (121)
T ss_dssp CEESTTTTTTSEEEEEETEEEEETTEE
T ss_pred CccccCCCCCeEEEEEcCCccCCCCCC
Confidence 2 123457889999998 8998
No 3
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.60 E-value=7.8e-16 Score=121.63 Aligned_cols=121 Identities=37% Similarity=0.571 Sum_probs=96.6
Q ss_pred CCCChhhHHHHHHHHHHHHHhCccccCCCCcccHHHHHHhcCCCCccCCHHHHHHHHH--HhCCcEEEEecCCCceeEEe
Q 033361 1 MYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAAD--KFAAKICLLTSFRDTCFIEI 78 (121)
Q Consensus 1 lyg~q~~h~~lR~~vv~ym~~n~~~f~~fi~~~~~~Yl~~m~~~g~WGg~ieL~Ala~--~~~~~I~V~~~~~~~~~~~~ 78 (121)
||++++.|..+|+++++++..+++.|+.|++++|.+|++.|+.++.||+|+|+||+|. -+..+...++..++++++..
T Consensus 238 vy~d~e~~~~~~~~~~dq~~~e~~~~~~~vt~~~~~y~k~kr~~~~~gnhie~Qa~a~~~~~~~~~~~~~~~~~t~~~~~ 317 (371)
T KOG2605|consen 238 VYGDDEQHDHNRRECVDQLKKERDFYEDYVTEDFTSYIKRKRADGEPGNHIEQQAAADIYEEIEKPLNITSFKDTCYIQT 317 (371)
T ss_pred hhcCHHHHHHHHHHHHHHHhhcccccccccccchhhcccccccCCCCcchHHHhhhhhhhhhccccceeecccccceecc
Confidence 6999999999999999999999999999999999999999999999999999999996 44445555555556667777
Q ss_pred cCCCCCCCCeEEEEecCCCcccceecC----CCCCCCCCcccccccC
Q 033361 79 MPQHQAPKRELWLSFWSEVHYNSLYDI----RDAPVPKKPRKKHWLF 121 (121)
Q Consensus 79 ~~~~~~~~~~i~L~y~~~~HYdsv~~~----~~~p~~~~~~~~~~~~ 121 (121)
.|....+...+++.+....||+.++.- ......-+.|.++|.+
T Consensus 318 ~~~~~~~~~~~~~n~~~~~h~~~~~~~~~~~~s~~~~~~~~r~~~~~ 364 (371)
T KOG2605|consen 318 PPAIEESVKMEKYNFWVEVHYNTARHSGKSADSATLEEKTKRKSLRR 364 (371)
T ss_pred CcccccchhhhhhcccchhhhhhcccccccccccchhhccCCCchhh
Confidence 665555566677777777999999873 2222333667777754
No 4
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.54 E-value=5.1e-15 Score=111.05 Aligned_cols=95 Identities=16% Similarity=0.319 Sum_probs=77.7
Q ss_pred HHHHHHHHHHHHhCccccCCCC-cccHHHHHHhcCCCCccCCHHHHHHHHHHhCCcEEEEecCCCceeEEecCCCCCCCC
Q 033361 9 KHVRKEVVKQLKDCRSMYEGYV-PMKYKRYYKNMAKVGEWGDHVTLQAAADKFAAKICLLTSFRDTCFIEIMPQHQAPKR 87 (121)
Q Consensus 9 ~~lR~~vv~ym~~n~~~f~~fi-~~~~~~Yl~~m~~~g~WGg~ieL~Ala~~~~~~I~V~~~~~~~~~~~~~~~~~~~~~ 87 (121)
.+||+.+++-..+||+.|...| +.+-.+||+++.++.+|||-|||..||+.|++.|.|++..... .-.+++ +.....
T Consensus 139 ~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k~dsWGGaIElsILS~~ygveI~vvDiqt~r-id~fge-d~~~~~ 216 (307)
T KOG3288|consen 139 YELREIIAQEVASNPDKYNDAILGKPNKEYCAWILKMDSWGGAIELSILSDYYGVEICVVDIQTVR-IDRFGE-DKNFDN 216 (307)
T ss_pred HHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHccccccCceEEeeeehhhhceeEEEEecceee-ehhcCC-CCCCCc
Confidence 5899999999999999998555 8899999999999999999999999999999999999875432 123333 323455
Q ss_pred eEEEEecCCCcccceecCC
Q 033361 88 ELWLSFWSEVHYNSLYDIR 106 (121)
Q Consensus 88 ~i~L~y~~~~HYdsv~~~~ 106 (121)
.++|.| +|.|||++.--.
T Consensus 217 rv~lly-dGIHYD~l~m~~ 234 (307)
T KOG3288|consen 217 RVLLLY-DGIHYDPLAMNE 234 (307)
T ss_pred eEEEEe-cccccChhhhcc
Confidence 677876 799999996544
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=99.44 E-value=6.9e-13 Score=99.66 Aligned_cols=94 Identities=21% Similarity=0.323 Sum_probs=70.9
Q ss_pred HHHHHHHHHHHhCccccCCCCc----ccHHHHHHh-cCCCCccCCHHHHHHHHHHhCCcEEEEecCCC---c--eeEEec
Q 033361 10 HVRKEVVKQLKDCRSMYEGYVP----MKYKRYYKN-MAKVGEWGDHVTLQAAADKFAAKICLLTSFRD---T--CFIEIM 79 (121)
Q Consensus 10 ~lR~~vv~ym~~n~~~f~~fi~----~~~~~Yl~~-m~~~g~WGg~ieL~Ala~~~~~~I~V~~~~~~---~--~~~~~~ 79 (121)
-+|..++.||+.|++.|++|++ .++++||++ +...+.-+||+.+.|||++++++|.|+..+++ . ....+.
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 6899999999999999999996 789999976 99999999999999999999999999987643 1 122332
Q ss_pred CCCCCCCCeEEEEecCCCcccceec
Q 033361 80 PQHQAPKRELWLSFWSEVHYNSLYD 104 (121)
Q Consensus 80 ~~~~~~~~~i~L~y~~~~HYdsv~~ 104 (121)
|.+....+.|.|.| .++|||.+++
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 22334567899997 5679999975
No 6
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.31 E-value=6e-12 Score=93.27 Aligned_cols=93 Identities=19% Similarity=0.317 Sum_probs=78.0
Q ss_pred HHHHHHHHHHHHhCccccCCCCc--ccHHHHHHh-cCCCCccCCHHHHHHHHHHhCCcEEEEecCCCce---eEEecCCC
Q 033361 9 KHVRKEVVKQLKDCRSMYEGYVP--MKYKRYYKN-MAKVGEWGDHVTLQAAADKFAAKICLLTSFRDTC---FIEIMPQH 82 (121)
Q Consensus 9 ~~lR~~vv~ym~~n~~~f~~fi~--~~~~~Yl~~-m~~~g~WGg~ieL~Ala~~~~~~I~V~~~~~~~~---~~~~~~~~ 82 (121)
..+|..++.+|++|+|.|+|||+ ++.++||.. +.....-.|||+|.|||+++++.|.|...+++.. .....|+
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 36899999999999999999996 799999997 7788899999999999999999999999876532 1122332
Q ss_pred CCCCCeEEEEecCCCcccceec
Q 033361 83 QAPKRELWLSFWSEVHYNSLYD 104 (121)
Q Consensus 83 ~~~~~~i~L~y~~~~HYdsv~~ 104 (121)
.+.+.|.|.| +++|||.|++
T Consensus 236 -~s~P~I~LLY-rpGHYdilY~ 255 (256)
T KOG3991|consen 236 -ASAPEIYLLY-RPGHYDILYK 255 (256)
T ss_pred -ccCceEEEEe-cCCccccccC
Confidence 3577899987 6899999986
No 7
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.81 E-value=9e-09 Score=78.74 Aligned_cols=67 Identities=12% Similarity=0.039 Sum_probs=52.9
Q ss_pred ccHHHHHHhcCCCCccCCHHHHHHHHHHhCCcEEEEecCCCceeEEecCCCCCCCCeEEEEecCC----Ccccce
Q 033361 32 MKYKRYYKNMAKVGEWGDHVTLQAAADKFAAKICLLTSFRDTCFIEIMPQHQAPKRELWLSFWSE----VHYNSL 102 (121)
Q Consensus 32 ~~~~~Yl~~m~~~g~WGg~ieL~Ala~~~~~~I~V~~~~~~~~~~~~~~~~~~~~~~i~L~y~~~----~HYdsv 102 (121)
-+|++|++.|..+..||+.+|++|||..|++++.++....+. +.+++.+.... ..+.|+.. +|||++
T Consensus 234 ~~~dt~~ne~~~~a~~g~~~ei~qLas~lk~~~~~~nT~~~~--ik~n~c~~~~~--~e~~~~~Ha~a~GH~n~~ 304 (306)
T COG5539 234 VLWDTYVNEVLFDASDGITIEIQQLASLLKNPHYYTNTASPS--IKCNICGTGFV--GEKDYYAHALATGHYNFG 304 (306)
T ss_pred chHHHHHhhhcccccccchHHHHHHHHHhcCceEEeecCCce--EEeeccccccc--hhhHHHHHHHhhcCcccc
Confidence 389999999999999999999999999999999999876653 77776554332 33334332 599987
No 8
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=96.87 E-value=0.00012 Score=56.46 Aligned_cols=92 Identities=12% Similarity=0.198 Sum_probs=74.7
Q ss_pred HHHHHHHHHHHHHhCccccCCCCc-ccHHHHHHhcCCCCccC-CHHHHHHHHHHhCCcEEEEecCCCceeEEecCCCCCC
Q 033361 8 HKHVRKEVVKQLKDCRSMYEGYVP-MKYKRYYKNMAKVGEWG-DHVTLQAAADKFAAKICLLTSFRDTCFIEIMPQHQAP 85 (121)
Q Consensus 8 h~~lR~~vv~ym~~n~~~f~~fi~-~~~~~Yl~~m~~~g~WG-g~ieL~Ala~~~~~~I~V~~~~~~~~~~~~~~~~~~~ 85 (121)
-.+||..|+.-+.+|||.|.+.+. -+--.|+.++.++..|| |++|+.++|+.+++.|+++..+++. ..++.+.. .
T Consensus 137 v~~lrE~vs~Ev~snPDl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~-~dr~~~~~--~ 213 (306)
T COG5539 137 VAKLREVVSLEVLSNPDLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDS-EDRYNSHP--Y 213 (306)
T ss_pred HHHHHHHHHHHHhhCccccchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhH-HhhccCCh--h
Confidence 357899999999999999999995 78889999999999999 9999999999999999999988653 13344322 2
Q ss_pred CCeEEEEecCCCccccee
Q 033361 86 KRELWLSFWSEVHYNSLY 103 (121)
Q Consensus 86 ~~~i~L~y~~~~HYdsv~ 103 (121)
...+.+.| .|.|||...
T Consensus 214 ~q~~~i~f-~g~hfD~~t 230 (306)
T COG5539 214 VQRISILF-TGIHFDEET 230 (306)
T ss_pred hhhhhhhh-cccccchhh
Confidence 23356666 589999875
No 9
>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=82.37 E-value=0.062 Score=32.98 Aligned_cols=34 Identities=29% Similarity=0.489 Sum_probs=27.1
Q ss_pred HhCccc-cCCCCc-ccHHHHHHhcCCCCccCCHHHH
Q 033361 20 KDCRSM-YEGYVP-MKYKRYYKNMAKVGEWGDHVTL 53 (121)
Q Consensus 20 ~~n~~~-f~~fi~-~~~~~Yl~~m~~~g~WGg~ieL 53 (121)
|+|.+- +..||+ .|+|+=+-.|.+++.|||.+.|
T Consensus 6 R~~~~g~l~~YvpKKDLEE~Vv~~e~~~~WGG~v~L 41 (67)
T TIGR02934 6 RRNRAGELSAYVPKKDLEEVIVSVEKEELWGGWVTL 41 (67)
T ss_pred EeCCCCCEEEEEECCcchhheeeeecCccccCEEEE
Confidence 555554 778887 7899999999999999997654
No 10
>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=78.15 E-value=12 Score=24.84 Aligned_cols=44 Identities=9% Similarity=0.074 Sum_probs=33.4
Q ss_pred HHHHHHHhCCcEEEEecCCCceeEEecCCCCCCCCeEEEEecCC--Ccccc
Q 033361 53 LQAAADKFAAKICLLTSFRDTCFIEIMPQHQAPKRELWLSFWSE--VHYNS 101 (121)
Q Consensus 53 L~Ala~~~~~~I~V~~~~~~~~~~~~~~~~~~~~~~i~L~y~~~--~HYds 101 (121)
|.|||..|+....+.+.... +.++..+ +...+.|.+..| .||..
T Consensus 49 ltaLa~~~~~~~~~hs~~~~---~~~Gi~~--as~~~~I~ht~G~p~HFs~ 94 (104)
T PF05381_consen 49 LTALAYRYHFQCTFHSDHGV---LHYGIKD--ASTVFTITHTPGPPGHFSL 94 (104)
T ss_pred HHHHHHHHheEEEEEcCCce---EEeecCC--CceEEEEEeCCCCCCcccc
Confidence 78999999999999986654 6666433 456678877766 79988
No 11
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=69.05 E-value=3.1 Score=33.58 Aligned_cols=46 Identities=15% Similarity=0.273 Sum_probs=42.3
Q ss_pred cCCCCcccHHHHHHhcCCCCccCCHHHHHHHHHHhCCcEEEEecCC
Q 033361 26 YEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKFAAKICLLTSFR 71 (121)
Q Consensus 26 f~~fi~~~~~~Yl~~m~~~g~WGg~ieL~Ala~~~~~~I~V~~~~~ 71 (121)
|.++++++|+.|+.-+.++.+-|+-.||.+++.+++.+.+.+...+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~s~~~r~~~~~~~~~g 47 (371)
T KOG2605|consen 2 FREEVSGDFDWYLWDLGKTKTLGTILELGAMSHVYRRNVIDYEPFG 47 (371)
T ss_pred CccccCchHHHHhhcCCCCcccccchhhhhccccccCCCCCcCCcc
Confidence 6678889999999999999999999999999999999999987654
No 12
>PRK10963 hypothetical protein; Provisional
Probab=67.00 E-value=5 Score=29.81 Aligned_cols=17 Identities=18% Similarity=0.208 Sum_probs=14.8
Q ss_pred HHHHHHHHhCccccCCC
Q 033361 13 KEVVKQLKDCRSMYEGY 29 (121)
Q Consensus 13 ~~vv~ym~~n~~~f~~f 29 (121)
+.|++|+++|||+|...
T Consensus 6 ~~V~~yL~~~PdFf~~h 22 (223)
T PRK10963 6 RAVVDYLLQNPDFFIRN 22 (223)
T ss_pred HHHHHHHHHCchHHhhC
Confidence 57899999999998765
No 13
>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=64.68 E-value=0.025 Score=34.37 Aligned_cols=34 Identities=29% Similarity=0.457 Sum_probs=20.5
Q ss_pred HhCcc-ccCCCCc-ccHHHHHHhcCCCCccCCHHHH
Q 033361 20 KDCRS-MYEGYVP-MKYKRYYKNMAKVGEWGDHVTL 53 (121)
Q Consensus 20 ~~n~~-~f~~fi~-~~~~~Yl~~m~~~g~WGg~ieL 53 (121)
|+|.+ .++.||+ .|+|+=+-.|.+++.|||.++|
T Consensus 6 R~~~~G~ls~YVpKKDLEE~Vv~~E~~~~wGG~v~L 41 (64)
T PF06988_consen 6 RKNGAGGLSAYVPKKDLEEPVVSMEKPELWGGEVTL 41 (64)
T ss_dssp EE-SS--EEEEETTTTEEEEEEEESSSSS-SSEEEE
T ss_pred EeCCCcCEEEEEeCCccccceeeeeccCccCCEEEE
Confidence 44444 5666665 4555556677899999997654
No 14
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=57.75 E-value=2.9 Score=24.78 Aligned_cols=18 Identities=22% Similarity=0.257 Sum_probs=14.7
Q ss_pred HHHHHHHHhCccccCCCC
Q 033361 13 KEVVKQLKDCRSMYEGYV 30 (121)
Q Consensus 13 ~~vv~ym~~n~~~f~~fi 30 (121)
+.+|.|+.+||+......
T Consensus 3 Q~iV~YLv~nPevl~kl~ 20 (57)
T PF05952_consen 3 QEIVNYLVQNPEVLEKLK 20 (57)
T ss_pred HHHHHHHHHChHHHHHHH
Confidence 678999999999876554
No 15
>COG3159 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.72 E-value=5.8 Score=29.68 Aligned_cols=17 Identities=12% Similarity=0.249 Sum_probs=15.0
Q ss_pred HHHHHHHHhCccccCCC
Q 033361 13 KEVVKQLKDCRSMYEGY 29 (121)
Q Consensus 13 ~~vv~ym~~n~~~f~~f 29 (121)
+.|++|++.|||+|+.+
T Consensus 7 ~~VadyL~~hPeFf~~h 23 (218)
T COG3159 7 EDVADYLRQHPEFFIQH 23 (218)
T ss_pred HHHHHHHHhCcHHHHhC
Confidence 46899999999999866
No 16
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=54.88 E-value=4 Score=30.12 Aligned_cols=18 Identities=17% Similarity=0.307 Sum_probs=0.0
Q ss_pred HHHHHHHHhCccccCCCC
Q 033361 13 KEVVKQLKDCRSMYEGYV 30 (121)
Q Consensus 13 ~~vv~ym~~n~~~f~~fi 30 (121)
..|++|+++|||+|..+-
T Consensus 9 ~~V~~yL~~~PdFf~~~~ 26 (225)
T PF04340_consen 9 EDVAAYLRQHPDFFERHP 26 (225)
T ss_dssp ------------------
T ss_pred HHHHHHHHhCcHHHHhCH
Confidence 468999999999998664
No 17
>KOG3325 consensus Membrane coat complex Retromer, subunit VPS29/PEP11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=48.46 E-value=23 Score=25.42 Aligned_cols=23 Identities=30% Similarity=0.507 Sum_probs=21.2
Q ss_pred ccCCHHHHHHHHHHhCCcEEEEe
Q 033361 46 EWGDHVTLQAAADKFAAKICLLT 68 (121)
Q Consensus 46 ~WGg~ieL~Ala~~~~~~I~V~~ 68 (121)
-|||...|.++|+-++++|-+.-
T Consensus 92 P~gd~~sL~~LaRqldvDILl~G 114 (183)
T KOG3325|consen 92 PWGDPESLALLARQLDVDILLTG 114 (183)
T ss_pred cCCCHHHHHHHHHhcCCcEEEeC
Confidence 49999999999999999999874
No 18
>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=48.38 E-value=12 Score=20.29 Aligned_cols=17 Identities=18% Similarity=0.220 Sum_probs=11.7
Q ss_pred CCHHHHHHHHHHhCCcE
Q 033361 48 GDHVTLQAAADKFAAKI 64 (121)
Q Consensus 48 Gg~ieL~Ala~~~~~~I 64 (121)
.|+-|||.+|..+++.-
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 57889999999998863
No 19
>KOG4516 consensus NADH:ubiquinone oxidoreductase, NDUFC2/B14.5B subunit [Energy production and conversion]
Probab=47.81 E-value=20 Score=24.03 Aligned_cols=24 Identities=13% Similarity=-0.040 Sum_probs=19.5
Q ss_pred hhHHHHHHHHH-HHHHhCccccCCC
Q 033361 6 EYHKHVRKEVV-KQLKDCRSMYEGY 29 (121)
Q Consensus 6 ~~h~~lR~~vv-~ym~~n~~~f~~f 29 (121)
+.|-..|.++. .||+-|||+|-.+
T Consensus 78 ~~~ya~RDav~~hYmkLHPeDFp~~ 102 (118)
T KOG4516|consen 78 NEYYAKRDAVLRHYMKLHPEDFPVK 102 (118)
T ss_pred HHHHHHHHHHHHHHHhcCcccCChh
Confidence 56777887766 6899999999877
No 20
>PF11952 DUF3469: Protein of unknown function (DUF3469); InterPro: IPR021859 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 108 to 439 amino acids in length.
Probab=45.83 E-value=47 Score=21.17 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=16.5
Q ss_pred CChhhHHHHHHHHHHHHHhCcccc
Q 033361 3 KSPEYHKHVRKEVVKQLKDCRSMY 26 (121)
Q Consensus 3 g~q~~h~~lR~~vv~ym~~n~~~f 26 (121)
.-.+.|.++|+. +|.+|.+.|
T Consensus 8 ~Es~~hW~~Rr~---Fl~~~~~~~ 28 (87)
T PF11952_consen 8 WESDKHWEARRE---FLLRHKDDF 28 (87)
T ss_pred CCCHHHHHHHHH---HHHHhHhhc
Confidence 345788899985 788888888
No 21
>PF06141 Phage_tail_U: Phage minor tail protein U; InterPro: IPR009312 This entry is represented by Bacteriophage lambda, GpU, a minor tail protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a tail fibre component U of bacteriophage.; PDB: 3FZ2_D 3FZB_J 1Z1Z_A.
Probab=45.10 E-value=17 Score=25.24 Aligned_cols=19 Identities=32% Similarity=0.482 Sum_probs=15.7
Q ss_pred hhHHHHHHHHHHHHHhCcc
Q 033361 6 EYHKHVRKEVVKQLKDCRS 24 (121)
Q Consensus 6 ~~h~~lR~~vv~ym~~n~~ 24 (121)
..|.+||++|++-|+++..
T Consensus 2 ~~ht~IR~aVld~L~~~~~ 20 (133)
T PF06141_consen 2 KIHTQIRKAVLDALKANIP 20 (133)
T ss_dssp -HHHHHHHHHHHHHHHH-S
T ss_pred chHHHHHHHHHHHHHhcCC
Confidence 4699999999999999853
No 22
>smart00337 BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions. (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulation
Probab=39.37 E-value=12 Score=24.15 Aligned_cols=52 Identities=15% Similarity=0.266 Sum_probs=38.2
Q ss_pred HHHHHHHHHHhCccccCCCCc----------ccHHHHHHhcCCCC--ccCCHHHHHHHHHHhCC
Q 033361 11 VRKEVVKQLKDCRSMYEGYVP----------MKYKRYYKNMAKVG--EWGDHVTLQAAADKFAA 62 (121)
Q Consensus 11 lR~~vv~ym~~n~~~f~~fi~----------~~~~~Yl~~m~~~g--~WGg~ieL~Ala~~~~~ 62 (121)
||+..-+.-++++..|+.+.. ..|.+=+++|-++| .||==+.|.|+|-.+-+
T Consensus 1 Lr~~~dele~~~~~~f~~~~~~l~~~~~~~~~~f~~Va~~lf~dg~inWGRIval~~F~~~la~ 64 (100)
T smart00337 1 LRRVGDELNKRYERAFSSFSAQLHVTPGTAIELFGEVATELFSDGNINWGRVVALLSFGGALAV 64 (100)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 466666677778888877752 45555667788888 89999999999766543
No 23
>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=38.51 E-value=1.1e+02 Score=19.90 Aligned_cols=34 Identities=18% Similarity=0.300 Sum_probs=25.5
Q ss_pred ccHHHHHHhcC--CCCccCCHHHHHHHHHHhCCcEEEEe
Q 033361 32 MKYKRYYKNMA--KVGEWGDHVTLQAAADKFAAKICLLT 68 (121)
Q Consensus 32 ~~~~~Yl~~m~--~~g~WGg~ieL~Ala~~~~~~I~V~~ 68 (121)
...+.||++++ .+.||-|-+ -+|+.+++.|.+--
T Consensus 34 ~~i~~y~~W~r~~~~STW~DC~---mFA~~LkVsm~vkV 69 (104)
T PF05415_consen 34 STIKKYHTWLRKKRPSTWDDCR---MFADALKVSMQVKV 69 (104)
T ss_pred HHHHHHHHHHhcCCCCcHHHHH---HHHHhheeEEEEEE
Confidence 35788998855 578997654 68899999987754
No 24
>PF04877 Hairpins: HrpZ; InterPro: IPR006961 HrpZ (harpin elicitor) from the plant pathogen Pseudomonas syringae binds to lipid bilayers and forms a cation-conducting pore in vivo. This pore-forming activity may allow nutrient release or delivery of virulence factors during bacterial colonisation of host plants []. The entry also represents hairpinN which is a virulence determinant which elicits lesion formation in Arabidopsis and tobacco and triggers systemic resistance in Arabidopsis [].
Probab=37.92 E-value=26 Score=27.51 Aligned_cols=48 Identities=8% Similarity=0.057 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhCccccCCCCcccHHHHHHhcCCCCccCCHHHHHHHHHHh
Q 033361 9 KHVRKEVVKQLKDCRSMYEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKF 60 (121)
Q Consensus 9 ~~lR~~vv~ym~~n~~~f~~fi~~~~~~Yl~~m~~~g~WGg~ieL~Ala~~~ 60 (121)
..+=++|++||-.||+.|-+==..+|.+ ++ +.+..=+--|..+|-..+
T Consensus 164 ~~lL~eIaqFMD~nPe~FgkPd~~sW~~---eL-keD~~L~~~E~~~F~~Al 211 (308)
T PF04877_consen 164 MPLLKEIAQFMDQNPEQFGKPDRKSWAD---EL-KEDNGLDKAETEQFQKAL 211 (308)
T ss_pred HHHHHHHHHHHhcCHhhcCCCCCchHHH---Hh-hcCCCCCHHHHHHHHHHH
Confidence 3566789999999999996443344433 33 233333444554444433
No 25
>PF07802 GCK: GCK domain; InterPro: IPR012891 This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways (such as IPR001806 from INTERPRO) indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this family (such as Q9LMF3 from SWISSPROT); this may indicate that these domains are able to interact with one another, raising the possibility that this domain mediates heterodimerisation.
Probab=37.47 E-value=20 Score=22.39 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHHHHHhCccccCCCCc
Q 033361 6 EYHKHVRKEVVKQLKDCRSMYEGYVP 31 (121)
Q Consensus 6 ~~h~~lR~~vv~ym~~n~~~f~~fi~ 31 (121)
....+.....-+-|..|+|.|+|++.
T Consensus 38 ~kC~e~~~~L~kCM~ahsdYY~P~La 63 (76)
T PF07802_consen 38 EKCFEATAALRKCMEAHSDYYEPILA 63 (76)
T ss_pred HHHHHHHHHHHHHHHhchhHHHHHHH
Confidence 45567888899999999999999985
No 26
>PF02234 CDI: Cyclin-dependent kinase inhibitor; InterPro: IPR003175 Cell cycle progression is negatively controlled by cyclin-dependent kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.; GO: 0004861 cyclin-dependent protein kinase inhibitor activity, 0007050 cell cycle arrest, 0005634 nucleus; PDB: 1H27_E 1JSU_C.
Probab=36.59 E-value=26 Score=19.98 Aligned_cols=26 Identities=15% Similarity=0.434 Sum_probs=18.2
Q ss_pred CCCChhhHHHHHHHHHHHHHhCccccC
Q 033361 1 MYKSPEYHKHVRKEVVKQLKDCRSMYE 27 (121)
Q Consensus 1 lyg~q~~h~~lR~~vv~ym~~n~~~f~ 27 (121)
||| +..|.++++-+...|++..+.|+
T Consensus 3 LFg-p~d~~e~~~~~~~~l~~~~e~~~ 28 (51)
T PF02234_consen 3 LFG-PVDHEELERFFQEELQEQREEFS 28 (51)
T ss_dssp SS-----HHHHHHHHHHHHTTTTHHHH
T ss_pred CCC-CCCHHHHHHHHHHHHHHHHHHHH
Confidence 567 67789999999999998887653
No 27
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=35.72 E-value=51 Score=19.48 Aligned_cols=50 Identities=16% Similarity=0.206 Sum_probs=32.3
Q ss_pred HHHHHHHHhCccccCCCC---cccHHHHHHhcCCCCc----cCCHHHHHHHHHHhCC
Q 033361 13 KEVVKQLKDCRSMYEGYV---PMKYKRYYKNMAKVGE----WGDHVTLQAAADKFAA 62 (121)
Q Consensus 13 ~~vv~ym~~n~~~f~~fi---~~~~~~Yl~~m~~~g~----WGg~ieL~Ala~~~~~ 62 (121)
.++.++|+++|+.++..+ |-.+++..+.+...|. =.+.-.|...++.-++
T Consensus 3 ~~lt~~I~~~p~l~ekIL~YePI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD~~gI 59 (64)
T PF09494_consen 3 EALTKLIRSDPELYEKILMYEPINLEELHAWLKASGIGFDRKVDPSKLKEWLDSQGI 59 (64)
T ss_pred HHHHHHHHcCHHHHHHHHcCCCccHHHHHHHHHHcCCCccceeCHHHHHHHHHHCCc
Confidence 355677889999877555 4566666666665565 5555666666665443
No 28
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.72 E-value=12 Score=25.31 Aligned_cols=28 Identities=18% Similarity=0.564 Sum_probs=18.1
Q ss_pred CccccCCCCcccHHHHHHhcCC----CCccCCH
Q 033361 22 CRSMYEGYVPMKYKRYYKNMAK----VGEWGDH 50 (121)
Q Consensus 22 n~~~f~~fi~~~~~~Yl~~m~~----~g~WGg~ 50 (121)
||+.-..|+ .+|+.||..+++ .|+|-|+
T Consensus 49 np~~~~~Fl-teW~~Ya~~l~qql~~~g~~K~~ 80 (125)
T KOG4100|consen 49 NPLEAQGFL-TEWERYAVALSQQLSSAGKWKGE 80 (125)
T ss_pred ChHHHHHHH-HHHHHHHHHHHHHhhhcCccccc
Confidence 444444554 479999987665 5777654
No 29
>cd06845 Bcl-2_like Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting
Probab=34.11 E-value=37 Score=23.13 Aligned_cols=57 Identities=19% Similarity=0.339 Sum_probs=44.4
Q ss_pred hhHHHHHHHHHHHHHhCccccCCCCc----------ccHHHHHHhcCCC-C-ccCCHHHHHHHHHHhCC
Q 033361 6 EYHKHVRKEVVKQLKDCRSMYEGYVP----------MKYKRYYKNMAKV-G-EWGDHVTLQAAADKFAA 62 (121)
Q Consensus 6 ~~h~~lR~~vv~ym~~n~~~f~~fi~----------~~~~~Yl~~m~~~-g-~WGg~ieL~Ala~~~~~ 62 (121)
.-...||+.+-+..++|++.|..... ..|.+=+++|-++ + .||==+.|.|+|-.+-+
T Consensus 34 ~~~~~Lr~~~dele~~~~~~f~~~~~~l~~~~~~~~~~f~~v~~~lf~dg~inWGRIval~~f~~~la~ 102 (144)
T cd06845 34 EVAETLRRVGDELEEKHRRLFENMCRQLNISPDNAYEVFQEVARELFEDGGINWGRIVALFAFGGRLAV 102 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHH
Confidence 45678999999999999999987752 4566667777777 3 89999999988766544
No 30
>COG4479 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.73 E-value=52 Score=20.37 Aligned_cols=30 Identities=10% Similarity=0.211 Sum_probs=21.4
Q ss_pred HHHHHHHHhCccccCCCC--cccHHHHHHhcC
Q 033361 13 KEVVKQLKDCRSMYEGYV--PMKYKRYYKNMA 42 (121)
Q Consensus 13 ~~vv~ym~~n~~~f~~fi--~~~~~~Yl~~m~ 42 (121)
..+++||+.|.+..-+.- +.-|++|+..+.
T Consensus 42 ~~is~YLE~~a~f~~~m~~FDeiwe~Yle~~~ 73 (74)
T COG4479 42 HEISDYLETNADFLFNMSVFDEIWEEYLEHLK 73 (74)
T ss_pred HHHHHHHHhcCCcccchhhHHHHHHHHHHHhc
Confidence 467899999987544333 478999988653
No 31
>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=33.33 E-value=48 Score=18.16 Aligned_cols=29 Identities=10% Similarity=-0.034 Sum_probs=20.6
Q ss_pred HHHHhcCCCCccCCHHHHHHHHHHhCCcE
Q 033361 36 RYYKNMAKVGEWGDHVTLQAAADKFAAKI 64 (121)
Q Consensus 36 ~Yl~~m~~~g~WGg~ieL~Ala~~~~~~I 64 (121)
.++.++.+....=+--.+.++|+.|++++
T Consensus 24 ~~i~~~~~g~~~~~~~~~~~ia~~l~~~~ 52 (55)
T PF01381_consen 24 STISRIENGKRNPSLDTLKKIAKALGVSP 52 (55)
T ss_dssp HHHHHHHTTSSTSBHHHHHHHHHHHTSEH
T ss_pred chhHHHhcCCCCCCHHHHHHHHHHHCCCH
Confidence 34555555556667778999999999875
No 32
>COG5562 Phage envelope protein [General function prediction only]
Probab=30.55 E-value=27 Score=24.29 Aligned_cols=16 Identities=13% Similarity=0.530 Sum_probs=14.2
Q ss_pred ccHHHHHHhcCCCCcc
Q 033361 32 MKYKRYYKNMAKVGEW 47 (121)
Q Consensus 32 ~~~~~Yl~~m~~~g~W 47 (121)
.+|++||+.|.+.|..
T Consensus 89 ttF~ef~~~la~AGVf 104 (137)
T COG5562 89 TTFEEFCSALAEAGVF 104 (137)
T ss_pred ccHHHHHHHHHhCCeE
Confidence 5899999999998875
No 33
>PRK07027 cobalamin biosynthesis protein CbiG; Provisional
Probab=29.89 E-value=51 Score=22.20 Aligned_cols=33 Identities=12% Similarity=0.084 Sum_probs=28.4
Q ss_pred HHhcCCCCccCCHHHHHHHHHHhCCcEEEEecC
Q 033361 38 YKNMAKVGEWGDHVTLQAAADKFAAKICLLTSF 70 (121)
Q Consensus 38 l~~m~~~g~WGg~ieL~Ala~~~~~~I~V~~~~ 70 (121)
+..+.....-.++.-|..+|+.+++|+..++..
T Consensus 37 i~~lasi~~K~~E~~L~~~A~~lg~pl~~~~~~ 69 (126)
T PRK07027 37 VRVVATLDLKADEAGLLALCARHGWPLRAFSAA 69 (126)
T ss_pred hheeEehhhhcCCHHHHHHHHHhCCCeEEeCHH
Confidence 556777788899999999999999999999643
No 34
>PF10568 Tom37: Outer mitochondrial membrane transport complex protein; InterPro: IPR019564 Tom37 is one of the outer membrane proteins that make up the TOM complex for guiding cytosolic mitochondrial beta-barrel proteins from the cytosol across the outer mitochondrial membrane into the intramembrane space. In conjunction with Tom70, it guides peptides without an mitochondrial targeting sequence (MTS) into Tom40, the protein that forms the passage through the outer membrane []. It has homology with metaxin, also part of the outer mitochondrial membrane beta-barrel protein transport complex []. This entry represents outer mitochondrial membrane transport complex proteins Tom37 and metaxin.; GO: 0006626 protein targeting to mitochondrion, 0005741 mitochondrial outer membrane
Probab=28.78 E-value=90 Score=18.91 Aligned_cols=22 Identities=14% Similarity=-0.011 Sum_probs=18.6
Q ss_pred HHHHHHHHHhCCc---EEEEecCCC
Q 033361 51 VTLQAAADKFAAK---ICLLTSFRD 72 (121)
Q Consensus 51 ieL~Ala~~~~~~---I~V~~~~~~ 72 (121)
+.++|++++...+ +.|+.++.+
T Consensus 18 La~~~yl~~~~~~~~~~~vv~s~n~ 42 (72)
T PF10568_consen 18 LAVIAYLKFAGAPEQQFKVVPSNNP 42 (72)
T ss_pred HHHHHHHHhCCCCCceEEEEEcCCC
Confidence 6688889999999 999987754
No 35
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=27.83 E-value=50 Score=26.21 Aligned_cols=28 Identities=18% Similarity=0.033 Sum_probs=24.4
Q ss_pred ccHHHHHHhcCCCCccCCHHHHHHHHHH
Q 033361 32 MKYKRYYKNMAKVGEWGDHVTLQAAADK 59 (121)
Q Consensus 32 ~~~~~Yl~~m~~~g~WGg~ieL~Ala~~ 59 (121)
.-.++|+++++.-=.+.|+.||.|||+-
T Consensus 314 ~~I~~~v~~iapv~v~PGE~EleALA~G 341 (358)
T COG3426 314 DAIEDRVSWIAPVIVYPGEDELEALAEG 341 (358)
T ss_pred HHHHHHHhhhcceEecCCchHHHHHHhh
Confidence 3567889999999999999999999864
No 36
>PF02467 Whib: Transcription factor WhiB; InterPro: IPR003482 WhiB is a putative transcription factor in Actinobacteria, required for differentiation and sporulation. The process of mycelium formation in Streptomyces, which occurs in response to nutrient limitation, is controlled by a number of whi genes, named for the white colour of aerial hyphae when mutations occur in these genes. The normal colour is grey. The exact role of WhiB is not clear, but a mutation in the gene results in white, tightly coiled aerial hyphae.
Probab=27.72 E-value=52 Score=19.70 Aligned_cols=10 Identities=30% Similarity=0.760 Sum_probs=6.9
Q ss_pred CCCccCCHHH
Q 033361 43 KVGEWGDHVT 52 (121)
Q Consensus 43 ~~g~WGg~ie 52 (121)
..|.|||-.+
T Consensus 51 ~~GVWGG~t~ 60 (66)
T PF02467_consen 51 EHGVWGGLTE 60 (66)
T ss_pred CeEEECCCcH
Confidence 3588988654
No 37
>PF00452 Bcl-2: Apoptosis regulator proteins, Bcl-2 family; InterPro: IPR000712 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 2WH6_A 1K3K_A 1AF3_A 3PK1_B 2K7W_A 1F16_A 3PL7_C 2VM6_A 3I1H_A 3MQP_A ....
Probab=24.93 E-value=33 Score=21.65 Aligned_cols=50 Identities=16% Similarity=0.280 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhCccccCCCCc-----------ccHHHHHHhcCCC--CccCCHHHHHHHHHHh
Q 033361 11 VRKEVVKQLKDCRSMYEGYVP-----------MKYKRYYKNMAKV--GEWGDHVTLQAAADKF 60 (121)
Q Consensus 11 lR~~vv~ym~~n~~~f~~fi~-----------~~~~~Yl~~m~~~--g~WGg~ieL~Ala~~~ 60 (121)
||+.+-+..+++++.|++++. ..|.+=+++|-.+ =+||==+.|.|+|..+
T Consensus 1 L~~i~~~~e~~~~~~f~~~~~~l~~~~~~~~~~~f~~v~~~lf~d~~inWGRIval~~f~~~l 63 (101)
T PF00452_consen 1 LRRIADELERKYEDFFENMLNQLNINTPDNAYETFNEVAEELFEDGGINWGRIVALFAFAGAL 63 (101)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCSSSTTTHHHHHHHHHHHHTTTSSTCHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHH
Confidence 688888888999988887762 2456666777665 6899999998887655
No 38
>COG4290 Guanyl-specific ribonuclease Sa [Nucleotide transport and metabolism]
Probab=24.68 E-value=28 Score=24.36 Aligned_cols=18 Identities=22% Similarity=0.381 Sum_probs=14.7
Q ss_pred EEEEecCCCcccceecCC
Q 033361 89 LWLSFWSEVHYNSLYDIR 106 (121)
Q Consensus 89 i~L~y~~~~HYdsv~~~~ 106 (121)
-.++|+...||+|.+.+.
T Consensus 134 ~e~~YYT~dHY~SFrri~ 151 (152)
T COG4290 134 PEVWYYTSDHYESFRRIT 151 (152)
T ss_pred cceeEEecchhhhhhccc
Confidence 357789999999998764
No 39
>PLN02994 1-aminocyclopropane-1-carboxylate synthase
Probab=24.49 E-value=69 Score=22.34 Aligned_cols=22 Identities=14% Similarity=0.289 Sum_probs=17.4
Q ss_pred CCChhhHHHHHHHHHHHHHhCc
Q 033361 2 YKSPEYHKHVRKEVVKQLKDCR 23 (121)
Q Consensus 2 yg~q~~h~~lR~~vv~ym~~n~ 23 (121)
|++..-..++|+++++||.+..
T Consensus 88 Y~~~~G~~~lR~AiA~~l~~~~ 109 (153)
T PLN02994 88 FQDYHGLANFRKAIANFMAEAR 109 (153)
T ss_pred CCCCCCcHHHHHHHHHHHHHHh
Confidence 5666667899999999997653
No 40
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=23.65 E-value=83 Score=19.01 Aligned_cols=32 Identities=13% Similarity=0.170 Sum_probs=20.9
Q ss_pred HHHHHHHHHhCccccCCCC-----------cccHHHHHHhcCC
Q 033361 12 RKEVVKQLKDCRSMYEGYV-----------PMKYKRYYKNMAK 43 (121)
Q Consensus 12 R~~vv~ym~~n~~~f~~fi-----------~~~~~~Yl~~m~~ 43 (121)
-+.+++||.+|++.+...- +.+.-.+|++|.-
T Consensus 18 e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~ 60 (77)
T PF01418_consen 18 EKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGF 60 (77)
T ss_dssp HHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTT
T ss_pred HHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCC
Confidence 3679999999999875432 1566677777743
No 41
>smart00591 RWD domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain.
Probab=23.55 E-value=1.9e+02 Score=17.82 Aligned_cols=49 Identities=14% Similarity=0.143 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCcEEEEecCCC--ceeEEecCCCC---CCCCeEEEEecCCCccc
Q 033361 52 TLQAAADKFAAKICLLTSFRD--TCFIEIMPQHQ---APKRELWLSFWSEVHYN 100 (121)
Q Consensus 52 eL~Ala~~~~~~I~V~~~~~~--~~~~~~~~~~~---~~~~~i~L~y~~~~HYd 100 (121)
|+.||..+|.-.+........ ...+.+.+... .....+.|.+.-...|=
T Consensus 1 EieaL~sIy~~~~~~~~~~~~~~~~~i~l~~~~~~~~~~~~~~~l~~~~p~~YP 54 (107)
T smart00591 1 ELEALESIYPEDFEVIDEDARIPEITIKLSPSSDEGEDQYVSLTLQVKLPENYP 54 (107)
T ss_pred ChHHHHhhccceeEEecCCCCccEEEEEEecCCCCCCccceEEEEEEECCCCCC
Confidence 688999999998877765433 23344433221 12234555554444553
No 42
>PF02865 STAT_int: STAT protein, protein interaction domain; InterPro: IPR013799 The STAT protein (Signal Transducers and Activators of Transcription) family contains transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors, hence they act as signal transducers in the cytoplasm and transcription activators in the nucleus []. Binding of these factors to cell-surface receptors leads to receptor autophosphorylation at a tyrosine, the phosphotyrosine being recognised by the STAT SH2 domain, which mediates the recruitment of STAT proteins from the cytosol and their association with the activated receptor. The STAT proteins are then activated by phosphorylation via members of the JAK family of protein kinases, causing them to dimerise and translocated to the nucleus, where they bind to specific promoter sequences in target genes. In mammals, STATs comprise a family of seven structurally and functionally related proteins: Stat1, Stat2, Stat3, Stat4, Stat5a and Stat5b, Stat6. STAT proteins play a critical role in regulating innate and acquired host immune responses. Dysregulation of at least two STAT signalling cascades (i.e. Stat3 and Stat5) is associated with cellular transformation. Signalling through the JAK/STAT pathway is initiated when a cytokine binds to its corresponding receptor. This leads to conformational changes in the cytoplasmic portion of the receptor, initiating activation of receptor associated members of the JAK family of kinases. The JAKs, in turn, mediate phosphorylation at the specific receptor tyrosine residues, which then serve as docking sites for STATs and other signalling molecules. Once recruited to the receptor, STATs also become phosphorylated by JAKs, on a single tyrosine residue. Activated STATs dissociate from the receptor, dimerise, translocate to the nucleus and bind to members of the GAS (gamma activated site) family of enhancers. The seven STAT proteins identified in mammals range in size from 750 and 850 amino acids. The chromosomal distribution of these STATs, as well as the identification of STATs in more primitive eukaryotes, suggest that this family arose from a single primordial gene. STATs share structurally and functionally conserved domains including: an N-terminal domain that strengthens interactions between STAT dimers on adjacent DNA-binding sites; a coiled-coil STAT domain that is implicated in protein-protein interactions; a DNA-binding domain with an immunoglobulin-like fold similar to p53 tumour suppressor protein; an EF-hand-like linker domain connecting the DNA-binding and SH2 domains; an SH2 domain (IPR000980 from INTERPRO) that acts as a phosphorylation-dependent switch to control receptor recognition and DNA-binding; and a C-terminal transactivation domain []. The crystal structure of the N terminus of Stat4 reveals a dimer. The interface of this dimer is formed by a ring-shaped element consisting of five short helices. Several studies suggest that this N-terminal dimerisation promotes cooperativity of binding to tandem GAS elements and with the transcriptional coactivator CBP/p300. This entry represents the N-terminal domain, which is responsible for protein interactions. This domain has a multi-helical structure that can be subdivided into two structural sub-domains.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0004871 signal transducer activity, 0006355 regulation of transcription, DNA-dependent, 0007165 signal transduction; PDB: 1BGF_A 1YVL_A.
Probab=23.25 E-value=62 Score=21.93 Aligned_cols=22 Identities=14% Similarity=0.323 Sum_probs=16.6
Q ss_pred CCCChhhHHHHHHHHHHHHHhCc
Q 033361 1 MYKSPEYHKHVRKEVVKQLKDCR 23 (121)
Q Consensus 1 lyg~q~~h~~lR~~vv~ym~~n~ 23 (121)
|||+ ....+||.-.+.+|++.+
T Consensus 20 lY~~-~FPiEvRh~LA~WIE~Q~ 41 (124)
T PF02865_consen 20 LYGD-HFPIEVRHYLAQWIESQD 41 (124)
T ss_dssp C-BT-TC-HHHHHHTHHHHHHS-
T ss_pred Hhcc-cCCHHHHHHHHHHHHhCc
Confidence 6886 469999999999999964
No 43
>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=22.89 E-value=47 Score=27.56 Aligned_cols=35 Identities=11% Similarity=0.371 Sum_probs=27.7
Q ss_pred HHHHHHHHhCccccCCC-C---cccHHHHHHhcCCCCcc
Q 033361 13 KEVVKQLKDCRSMYEGY-V---PMKYKRYYKNMAKVGEW 47 (121)
Q Consensus 13 ~~vv~ym~~n~~~f~~f-i---~~~~~~Yl~~m~~~g~W 47 (121)
.+++|||..|-.+|.-. | |+.|++|+..+-+..-|
T Consensus 11 ellad~l~~~l~~f~~~ki~~~p~~w~~wl~~~c~~~~w 49 (452)
T cd05295 11 ELLADYLQKNLPDFRVHKIVKHPDEWEDWLQDLCKKNGW 49 (452)
T ss_pred HHHHHHHHhhCCCceEEEccCChHHHHHHHHHHHHhcCC
Confidence 46899999998888744 2 68999999987776666
No 44
>PF06374 NDUF_C2: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2); InterPro: IPR009423 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 family consists of several NADH-ubiquinone oxidoreductase subunit b14.5b proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0006120 mitochondrial electron transport, NADH to ubiquinone, 0005743 mitochondrial inner membrane
Probab=22.23 E-value=66 Score=21.78 Aligned_cols=17 Identities=6% Similarity=-0.007 Sum_probs=13.8
Q ss_pred HHHHHHHHhCccccCCC
Q 033361 13 KEVVKQLKDCRSMYEGY 29 (121)
Q Consensus 13 ~~vv~ym~~n~~~f~~f 29 (121)
..+-+||+.|||+|..-
T Consensus 85 ~~m~~YI~lHPEDFp~~ 101 (117)
T PF06374_consen 85 ADMRHYIKLHPEDFPEK 101 (117)
T ss_pred hhHHHHHHhCcccCCCc
Confidence 34568999999999864
No 45
>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=21.79 E-value=2.4e+02 Score=19.83 Aligned_cols=63 Identities=8% Similarity=0.054 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHhCccccCCCC---cccHHHHHHh-------cCCCCccCCHHHHHHHHHHhCCcEEEEecC
Q 033361 8 HKHVRKEVVKQLKDCRSMYEGYV---PMKYKRYYKN-------MAKVGEWGDHVTLQAAADKFAAKICLLTSF 70 (121)
Q Consensus 8 h~~lR~~vv~ym~~n~~~f~~fi---~~~~~~Yl~~-------m~~~g~WGg~ieL~Ala~~~~~~I~V~~~~ 70 (121)
|..-....++|..+|.+.++.+- +++--..+.+ --.+|--||..+|-|+-..=+++..|+-.+
T Consensus 10 HD~kK~~l~~f~~~~~~~L~~h~L~ATgTTG~~i~~~tgL~V~~~~SGplGGDqQIga~Ia~g~id~vIFf~D 82 (143)
T TIGR00160 10 HDKKKQDLVNFVQQHKPLLSQHDLYATGTTGNLISRATGLNINAMLSGPMGGDQQIGALIAEGKIDAVIFFWD 82 (143)
T ss_pred cccchHHHHHHHHHHHHHHcCCCEEECccHHHHHHHHHCCCeEEeccCCccHHHHHHHHHHhCCCCEEEEecC
Confidence 56667889999999999888764 3333333332 225799999999999998888888888654
No 46
>KOG1043 consensus Ca2+-binding transmembrane protein LETM1/MRS7 [Function unknown]
Probab=21.21 E-value=1.3e+02 Score=25.47 Aligned_cols=62 Identities=19% Similarity=0.187 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHhC----ccccCCCC----cc--cHHHHHHhcCCCCccCCHHHHHHHHHHhCCcEEEEecCC
Q 033361 10 HVRKEVVKQLKDC----RSMYEGYV----PM--KYKRYYKNMAKVGEWGDHVTLQAAADKFAAKICLLTSFR 71 (121)
Q Consensus 10 ~lR~~vv~ym~~n----~~~f~~fi----~~--~~~~Yl~~m~~~g~WGg~ieL~Ala~~~~~~I~V~~~~~ 71 (121)
.+|..++++|.+- ...|...- .. .|+.++.+++..|.-+.+=||.++|.+|+-.+.+=...+
T Consensus 224 ~~r~~~sk~Lq~tl~~~~~~~k~~~~~e~~qs~~fd~f~~kvr~~~~~~S~eeii~~aklf~de~~LdnLsR 295 (499)
T KOG1043|consen 224 VERSEASKFLQKTLQQMIDRIKTWSNLETSQSIEFDRFLGKVRFIGLGVSTEEIIAFAKLFSDEITLDNLSR 295 (499)
T ss_pred HHHHHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhcccCCCccHHHHHHHHHHhccchhhhccCH
Confidence 4666666666544 44454422 12 699999999998888899999999999999988865443
No 47
>KOG4405 consensus GDP dissociation inhibitor [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.36 E-value=95 Score=26.07 Aligned_cols=47 Identities=17% Similarity=0.169 Sum_probs=31.1
Q ss_pred HHHHH-HhCccccCCCCcccHHHHHHhcCCCCccCCHHHHHHHHHHhCC
Q 033361 15 VVKQL-KDCRSMYEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKFAA 62 (121)
Q Consensus 15 vv~ym-~~n~~~f~~fi~~~~~~Yl~~m~~~g~WGg~ieL~Ala~~~~~ 62 (121)
|-+|+ +++++.+..|-+.+|-+|++.|+-+-. =-.+-|+|+|.+=..
T Consensus 205 c~~y~tEk~~~~~~~~~e~~F~EyL~~~rltp~-lqs~vl~aIaM~~~~ 252 (547)
T KOG4405|consen 205 CQEYLTEKDPDEYVEFRERPFSEYLKTMRLTPK-LQSIVLHAIAMLSES 252 (547)
T ss_pred HHHhhhccCcHHHHHhhcCcHHHHHHhcCCChh-hHHHHHHHHHhcCcc
Confidence 44554 456778888888999999999865433 245556666655433
Done!