Query 033766
Match_columns 112
No_of_seqs 121 out of 776
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 06:04:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033766.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033766hhsearch_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 1.7E-28 3.6E-33 186.2 5.7 97 1-103 190-301 (302)
2 KOG3288 OTU-like cysteine prot 99.8 5.4E-19 1.2E-23 132.6 4.7 94 2-101 140-234 (307)
3 PF02338 OTU: OTU-like cystein 99.7 6.1E-18 1.3E-22 113.2 5.9 85 2-94 28-121 (121)
4 PF10275 Peptidase_C65: Peptid 99.7 1.1E-16 2.3E-21 119.7 8.6 97 2-99 141-244 (244)
5 KOG3991 Uncharacterized conser 99.7 8E-17 1.7E-21 119.2 7.5 97 1-100 157-256 (256)
6 COG5539 Predicted cysteine pro 98.9 4.1E-10 8.8E-15 86.1 0.8 90 2-98 139-230 (306)
7 COG5539 Predicted cysteine pro 98.8 1.7E-09 3.8E-14 82.7 2.9 90 2-98 205-305 (306)
8 KOG2605 OTU (ovarian tumor)-li 98.8 3.7E-09 7.9E-14 83.8 4.1 95 2-100 247-344 (371)
9 PF05415 Peptidase_C36: Beet n 86.8 1.7 3.7E-05 28.4 4.3 48 25-78 35-84 (104)
10 TIGR02934 nifT_nitrog probable 80.6 0.13 2.7E-06 31.7 -2.7 33 12-44 6-40 (67)
11 PF00452 Bcl-2: Apoptosis regu 71.5 2.4 5.3E-05 27.0 1.3 51 3-53 1-64 (101)
12 PF06988 NifT: NifT/FixU prote 66.1 0.047 1E-06 33.3 -7.1 33 12-44 6-40 (64)
13 PF04877 Hairpins: HrpZ; Inte 61.7 4.8 0.0001 31.5 1.4 46 2-52 165-211 (308)
14 KOG2605 OTU (ovarian tumor)-li 60.3 4.8 0.0001 32.4 1.2 45 18-62 2-46 (371)
15 smart00337 BCL BCL (B-Cell lym 56.2 6.5 0.00014 25.4 1.2 51 3-53 1-63 (100)
16 PRK10963 hypothetical protein; 55.1 6.5 0.00014 29.1 1.1 16 5-20 6-21 (223)
17 PF05381 Peptidase_C21: Tymovi 52.8 56 0.0012 21.7 5.2 46 43-96 47-94 (104)
18 PF01381 HTH_3: Helix-turn-hel 52.2 20 0.00043 19.7 2.7 30 27-56 23-52 (55)
19 COG3159 Uncharacterized protei 49.9 8.4 0.00018 28.8 1.0 17 5-21 7-23 (218)
20 cd06845 Bcl-2_like Apoptosis r 49.1 15 0.00032 25.0 2.1 54 2-55 38-103 (144)
21 PF04340 DUF484: Protein of un 46.0 6.8 0.00015 28.8 0.0 18 5-22 9-26 (225)
22 COG4887 Uncharacterized metal- 45.9 45 0.00098 24.0 4.1 56 6-61 25-97 (191)
23 PF05159 Capsule_synth: Capsul 44.7 89 0.0019 23.1 5.9 57 38-101 5-66 (269)
24 KOG3325 Membrane coat complex 44.1 30 0.00064 24.9 3.0 22 38-59 92-113 (183)
25 COG3563 KpsC Capsule polysacch 37.5 1E+02 0.0022 26.4 5.5 60 38-109 368-428 (671)
26 COG3426 Butyrate kinase [Energ 36.2 30 0.00065 27.4 2.2 27 25-51 315-341 (358)
27 PF05952 ComX: Bacillus compet 35.7 11 0.00023 22.5 -0.3 20 4-23 2-21 (57)
28 PF07116 DUF1372: Protein of u 35.5 1.2E+02 0.0026 20.1 4.6 57 51-110 41-104 (104)
29 TIGR00865 bcl-2 Apoptosis regu 34.4 30 0.00065 25.7 1.9 53 2-54 70-133 (213)
30 PRK07027 cobalamin biosynthesi 33.2 34 0.00074 23.0 1.9 32 31-62 38-69 (126)
31 PF08960 DUF1874: Domain of un 32.6 75 0.0016 21.1 3.4 33 25-58 26-62 (105)
32 PF13734 Inhibitor_I69: Spi pr 32.0 1.1E+02 0.0025 19.8 4.1 41 50-97 37-77 (96)
33 PHA01976 helix-turn-helix prot 30.2 87 0.0019 17.8 3.1 30 28-57 30-59 (67)
34 PF07802 GCK: GCK domain; Int 27.6 30 0.00066 21.6 0.8 19 5-23 45-63 (76)
35 PF01890 CbiG_C: Cobalamin syn 26.2 55 0.0012 21.8 2.0 23 40-62 45-67 (121)
36 TIGR03070 couple_hipB transcri 25.1 1.2E+02 0.0027 16.2 3.5 29 28-56 30-58 (58)
37 COG4479 Uncharacterized protei 24.3 65 0.0014 20.0 1.8 29 6-34 43-73 (74)
38 TIGR02684 dnstrm_HI1420 probab 23.9 1.9E+02 0.0042 18.2 4.1 30 29-58 59-88 (89)
39 PF10568 Tom37: Outer mitochon 23.8 1.2E+02 0.0025 18.4 2.9 20 43-62 18-40 (72)
40 PF05182 Fip1: Fip1 motif; In 23.7 32 0.0007 19.4 0.4 16 20-35 27-42 (45)
41 cd07288 PX_SNX15 The phosphoin 23.4 52 0.0011 21.9 1.4 30 20-49 83-115 (118)
42 COG5562 Phage envelope protein 23.1 53 0.0011 22.9 1.4 14 25-38 90-103 (137)
43 COG4521 TauA ABC-type taurine 22.9 44 0.00096 26.1 1.1 49 9-57 220-269 (334)
44 cd06893 PX_SNX19 The phosphoin 22.8 43 0.00093 22.8 0.9 30 20-49 97-129 (132)
45 PHA01627 DNA binding protein 22.4 1.6E+02 0.0034 19.7 3.5 32 25-57 27-62 (107)
46 PF07166 DUF1398: Protein of u 22.2 38 0.00083 23.1 0.6 14 25-38 85-98 (125)
47 cd06879 PX_UP1_plant The phosp 21.3 57 0.0012 22.7 1.3 31 20-50 103-136 (138)
48 PF02467 Whib: Transcription f 20.3 77 0.0017 18.9 1.6 8 36-43 52-59 (66)
49 PF11952 DUF3469: Protein of u 20.3 1.1E+02 0.0023 19.5 2.3 13 40-52 31-43 (87)
50 PRK00446 cyaY frataxin-like pr 20.2 1.4E+02 0.003 19.6 3.0 17 81-97 56-73 (105)
51 TIGR00715 precor6x_red precorr 20.2 1.6E+02 0.0034 22.3 3.6 28 34-61 204-231 (256)
52 PRK09726 antitoxin HipB; Provi 20.1 2E+02 0.0043 17.6 3.6 34 28-61 40-73 (88)
53 KOG4100 Uncharacterized conser 20.1 51 0.0011 22.4 0.8 23 19-42 54-80 (125)
54 TIGR00570 cdk7 CDK-activating 20.1 71 0.0015 25.2 1.7 19 1-19 72-90 (309)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=1.7e-28 Score=186.20 Aligned_cols=97 Identities=40% Similarity=0.706 Sum_probs=85.8
Q ss_pred ChHHHHHHHHHhhCccccccccc----------cCHHHHHHHhcCCCCcCChHHHHHHHHhhCCCEEEEEecCCCCCcee
Q 033766 1 MMLLGQVADEFLLRRAETEWFVE----------GDFDAYVRQMRQPHSWGGEPELLMSSHVLKMPITVYMRDKTSGSLKN 70 (112)
Q Consensus 1 m~lR~~~~~yi~~~~~~fe~fv~----------~~~~~Y~~~m~~~~~WGg~iEl~Als~~~~~~I~V~~~~~~~~~~~~ 70 (112)
+.||.++|+||++|.++|.||+. ++|++||+.|++++.|||+|||.|||.+|++||.||+.+ ++
T Consensus 190 ~kLR~~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~---~p--- 263 (302)
T KOG2606|consen 190 QKLREETADYMREHVEDFLPFLLDEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQAD---GP--- 263 (302)
T ss_pred HHHHHHHHHHHHHHHHHhhhHhcCccccccCCHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecC---CC---
Confidence 46999999999999999999996 259999999999999999999999999999999999988 33
Q ss_pred eeecCCCCCCCCeEEEEECCC----C-cccccccCCCC
Q 033766 71 LSEYGQEYGKENPIRVLYHGY----G-HYDLLRGHDAT 103 (112)
Q Consensus 71 i~~~g~e~~~~~~i~L~Y~~~----g-HYdsv~~~~~~ 103 (112)
+..||+++++.+||.|+||++ | ||||+.+..+.
T Consensus 264 ~~~~geey~kd~pL~lvY~rH~y~LGeHYNS~~~~~n~ 301 (302)
T KOG2606|consen 264 ILEYGEEYGKDKPLILVYHRHAYGLGEHYNSVTPLKNK 301 (302)
T ss_pred ceeechhhCCCCCeeeehHHhHHHHHhhhccccccccc
Confidence 335899998779999999765 4 99999877654
No 2
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.76 E-value=5.4e-19 Score=132.57 Aligned_cols=94 Identities=23% Similarity=0.347 Sum_probs=84.6
Q ss_pred hHHHHHHHHHhhCcccc-ccccccCHHHHHHHhcCCCCcCChHHHHHHHHhhCCCEEEEEecCCCCCceeeeecCCCCCC
Q 033766 2 MLLGQVADEFLLRRAET-EWFVEGDFDAYVRQMRQPHSWGGEPELLMSSHVLKMPITVYMRDKTSGSLKNLSEYGQEYGK 80 (112)
Q Consensus 2 ~lR~~~~~yi~~~~~~f-e~fv~~~~~~Y~~~m~~~~~WGg~iEl~Als~~~~~~I~V~~~~~~~~~~~~i~~~g~e~~~ 80 (112)
+||+.+++.+.+|++.| ++++..+-.+||+||.++.+|||.|||..||..|++.|.|++.. ...|..||++...
T Consensus 140 elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k~dsWGGaIElsILS~~ygveI~vvDiq-----t~rid~fged~~~ 214 (307)
T KOG3288|consen 140 ELREIIAQEVASNPDKYNDAILGKPNKEYCAWILKMDSWGGAIELSILSDYYGVEICVVDIQ-----TVRIDRFGEDKNF 214 (307)
T ss_pred HHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHccccccCceEEeeeehhhhceeEEEEecc-----eeeehhcCCCCCC
Confidence 69999999999999999 89999999999999999999999999999999999999999865 3457889988655
Q ss_pred CCeEEEEECCCCcccccccCC
Q 033766 81 ENPIRVLYHGYGHYDLLRGHD 101 (112)
Q Consensus 81 ~~~i~L~Y~~~gHYdsv~~~~ 101 (112)
...+.|+|.+. |||++....
T Consensus 215 ~~rv~llydGI-HYD~l~m~~ 234 (307)
T KOG3288|consen 215 DNRVLLLYDGI-HYDPLAMNE 234 (307)
T ss_pred CceEEEEeccc-ccChhhhcc
Confidence 67899999887 999997543
No 3
>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=99.73 E-value=6.1e-18 Score=113.24 Aligned_cols=85 Identities=36% Similarity=0.579 Sum_probs=68.1
Q ss_pred hHHHHHHHHHh-hCccccccccccCHHHHHHHhcCCCCcCChHHHHHHHHhhCCCEEEEEecCCCCCceeeeecCC---C
Q 033766 2 MLLGQVADEFL-LRRAETEWFVEGDFDAYVRQMRQPHSWGGEPELLMSSHVLKMPITVYMRDKTSGSLKNLSEYGQ---E 77 (112)
Q Consensus 2 ~lR~~~~~yi~-~~~~~fe~fv~~~~~~Y~~~m~~~~~WGg~iEl~Als~~~~~~I~V~~~~~~~~~~~~i~~~g~---e 77 (112)
+||+.|++||+ +|++.|++|+.++ +|+++++|||++||+|+|.+|+++|.|++... +.......+.+ .
T Consensus 28 ~lR~~~~~~l~~~~~~~~~~~~~~~------~~~~~~~Wg~~~el~a~a~~~~~~I~v~~~~~--~~~~~~~~~~~~~~~ 99 (121)
T PF02338_consen 28 ELRKAVVDYLRDKNRDKFEEFLEGD------KMSKPGTWGGEIELQALANVLNRPIIVYSSSD--GDNVVFIKFTGKYPP 99 (121)
T ss_dssp HHHHHHHHHHHTHTTTHHHHHHHHH------HHTSTTSHEEHHHHHHHHHHHTSEEEEECETT--TBEEEEEEESCEEST
T ss_pred HHHHHHHHHHHHhccchhhhhhhhh------hhccccccCcHHHHHHHHHHhCCeEEEEEcCC--CCccceeeecCcccc
Confidence 79999999999 9999999999877 99999999999999999999999999988742 22221222322 2
Q ss_pred CCCCCeEEEEECC-----CCcc
Q 033766 78 YGKENPIRVLYHG-----YGHY 94 (112)
Q Consensus 78 ~~~~~~i~L~Y~~-----~gHY 94 (112)
....+++.|+|+. .+||
T Consensus 100 ~~~~~~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 100 LESPPPICLCYHGHLYYTGNHY 121 (121)
T ss_dssp TTTTTSEEEEEETEEEEETTEE
T ss_pred CCCCCeEEEEEcCCccCCCCCC
Confidence 2345789999986 5698
No 4
>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=99.69 E-value=1.1e-16 Score=119.67 Aligned_cols=97 Identities=23% Similarity=0.334 Sum_probs=72.7
Q ss_pred hHHHHHHHHHhhCccccccccc----cCHHHHHHH-hcCCCCcCChHHHHHHHHhhCCCEEEEEecCC-CCCceeeeecC
Q 033766 2 MLLGQVADEFLLRRAETEWFVE----GDFDAYVRQ-MRQPHSWGGEPELLMSSHVLKMPITVYMRDKT-SGSLKNLSEYG 75 (112)
Q Consensus 2 ~lR~~~~~yi~~~~~~fe~fv~----~~~~~Y~~~-m~~~~~WGg~iEl~Als~~~~~~I~V~~~~~~-~~~~~~i~~~g 75 (112)
.||..++.||+.|+++|+||++ .++++||+. +...+.-+||+.|.|||++|+++|.|+..+++ .+.....+.+.
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 5899999999999999999998 579999987 56666889999999999999999999999976 34444444554
Q ss_pred CCC-CCCCeEEEEECCCCccccccc
Q 033766 76 QEY-GKENPIRVLYHGYGHYDLLRG 99 (112)
Q Consensus 76 ~e~-~~~~~i~L~Y~~~gHYdsv~~ 99 (112)
++. ...+.|+|+|.. ||||.+++
T Consensus 221 ~~~~~~~~~i~LLyrp-gHYdIly~ 244 (244)
T PF10275_consen 221 PDNESQEPQITLLYRP-GHYDILYP 244 (244)
T ss_dssp -SSTTSS-SEEEEEET-BEEEEEEE
T ss_pred CccCCCCCEEEEEEcC-CccccccC
Confidence 322 235779999954 79999875
No 5
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.69 E-value=8e-17 Score=119.20 Aligned_cols=97 Identities=23% Similarity=0.272 Sum_probs=81.2
Q ss_pred ChHHHHHHHHHhhCcccccccccc--CHHHHHHHhcCCC-CcCChHHHHHHHHhhCCCEEEEEecCCCCCceeeeecCCC
Q 033766 1 MMLLGQVADEFLLRRAETEWFVEG--DFDAYVRQMRQPH-SWGGEPELLMSSHVLKMPITVYMRDKTSGSLKNLSEYGQE 77 (112)
Q Consensus 1 m~lR~~~~~yi~~~~~~fe~fv~~--~~~~Y~~~m~~~~-~WGg~iEl~Als~~~~~~I~V~~~~~~~~~~~~i~~~g~e 77 (112)
|.||..++.+|++|+|+|+||+++ ++++||.+-..|. +-.|||+|.|||+++++.|.|..+++..++...-+.|.+
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 689999999999999999999986 8999999988875 569999999999999999999999988665433222322
Q ss_pred CCCCCeEEEEECCCCcccccccC
Q 033766 78 YGKENPIRVLYHGYGHYDLLRGH 100 (112)
Q Consensus 78 ~~~~~~i~L~Y~~~gHYdsv~~~ 100 (112)
+..+.|.|+|. .||||.++++
T Consensus 236 -~s~P~I~LLYr-pGHYdilY~~ 256 (256)
T KOG3991|consen 236 -ASAPEIYLLYR-PGHYDILYKK 256 (256)
T ss_pred -ccCceEEEEec-CCccccccCC
Confidence 34678999995 5799999864
No 6
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.88 E-value=4.1e-10 Score=86.10 Aligned_cols=90 Identities=27% Similarity=0.251 Sum_probs=76.2
Q ss_pred hHHHHHHHHHhhCcccccccccc-CHHHHHHHhcCCCCcC-ChHHHHHHHHhhCCCEEEEEecCCCCCceeeeecCCCCC
Q 033766 2 MLLGQVADEFLLRRAETEWFVEG-DFDAYVRQMRQPHSWG-GEPELLMSSHVLKMPITVYMRDKTSGSLKNLSEYGQEYG 79 (112)
Q Consensus 2 ~lR~~~~~yi~~~~~~fe~fv~~-~~~~Y~~~m~~~~~WG-g~iEl~Als~~~~~~I~V~~~~~~~~~~~~i~~~g~e~~ 79 (112)
+||.+|+..+.+|+|.|.+.+.+ +.-.||+|++++..|| |++|+.++|..+++.|.|+.++.. .+..|++..-
T Consensus 139 ~lrE~vs~Ev~snPDl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~-----~~dr~~~~~~ 213 (306)
T COG5539 139 KLREVVSLEVLSNPDLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKD-----SEDRYNSHPY 213 (306)
T ss_pred HHHHHHHHHHhhCccccchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchh-----HHhhccCChh
Confidence 58999999999999999888875 9999999999999999 999999999999999999988832 2455776532
Q ss_pred CCCeEEEEECCCCcccccc
Q 033766 80 KENPIRVLYHGYGHYDLLR 98 (112)
Q Consensus 80 ~~~~i~L~Y~~~gHYdsv~ 98 (112)
...+.+.|.++ |||...
T Consensus 214 -~q~~~i~f~g~-hfD~~t 230 (306)
T COG5539 214 -VQRISILFTGI-HFDEET 230 (306)
T ss_pred -hhhhhhhhccc-ccchhh
Confidence 25578889775 999876
No 7
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.84 E-value=1.7e-09 Score=82.68 Aligned_cols=90 Identities=18% Similarity=0.028 Sum_probs=66.6
Q ss_pred hHHHHHHHHHhhCcccccccccc-------CHHHHHHHhcCCCCcCChHHHHHHHHhhCCCEEEEEecCCCCCceeeeec
Q 033766 2 MLLGQVADEFLLRRAETEWFVEG-------DFDAYVRQMRQPHSWGGEPELLMSSHVLKMPITVYMRDKTSGSLKNLSEY 74 (112)
Q Consensus 2 ~lR~~~~~yi~~~~~~fe~fv~~-------~~~~Y~~~m~~~~~WGg~iEl~Als~~~~~~I~V~~~~~~~~~~~~i~~~ 74 (112)
++|..-..|..++.+.|.+|.-+ +|++||..|+-+..||+.+|++|||..|++|+.++... ++. | .+
T Consensus 205 ~dr~~~~~~~q~~~i~f~g~hfD~~t~~m~~~dt~~ne~~~~a~~g~~~ei~qLas~lk~~~~~~nT~----~~~-i-k~ 278 (306)
T COG5539 205 EDRYNSHPYVQRISILFTGIHFDEETLAMVLWDTYVNEVLFDASDGITIEIQQLASLLKNPHYYTNTA----SPS-I-KC 278 (306)
T ss_pred HhhccCChhhhhhhhhhcccccchhhhhcchHHHHHhhhcccccccchHHHHHHHHHhcCceEEeecC----Cce-E-Ee
Confidence 45555667778888999888752 79999999999999999999999999999999998755 333 2 34
Q ss_pred CCCCCCCCeEEEEE--CCC--Ccccccc
Q 033766 75 GQEYGKENPIRVLY--HGY--GHYDLLR 98 (112)
Q Consensus 75 g~e~~~~~~i~L~Y--~~~--gHYdsv~ 98 (112)
++ .+......+.| |.. ||||++.
T Consensus 279 n~-c~~~~~~e~~~~~Ha~a~GH~n~~~ 305 (306)
T COG5539 279 NI-CGTGFVGEKDYYAHALATGHYNFGE 305 (306)
T ss_pred ec-cccccchhhHHHHHHHhhcCccccC
Confidence 42 12223344555 333 6999974
No 8
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.82 E-value=3.7e-09 Score=83.81 Aligned_cols=95 Identities=16% Similarity=0.152 Sum_probs=67.1
Q ss_pred hHHHHHHHHHhhCccccccccccCHHHHHHHhcCCCCcCChHHHHHHH---HhhCCCEEEEEecCCCCCceeeeecCCCC
Q 033766 2 MLLGQVADEFLLRRAETEWFVEGDFDAYVRQMRQPHSWGGEPELLMSS---HVLKMPITVYMRDKTSGSLKNLSEYGQEY 78 (112)
Q Consensus 2 ~lR~~~~~yi~~~~~~fe~fv~~~~~~Y~~~m~~~~~WGg~iEl~Als---~~~~~~I~V~~~~~~~~~~~~i~~~g~e~ 78 (112)
..|+++++++..+++.|+.|+.+++-+|+++++.++.||+|+|+||+| .....++.|.+... ..+..+.+-.++
T Consensus 247 ~~~~~~~dq~~~e~~~~~~~vt~~~~~y~k~kr~~~~~gnhie~Qa~a~~~~~~~~~~~~~~~~~--t~~~~~~~~~~~- 323 (371)
T KOG2605|consen 247 HNRRECVDQLKKERDFYEDYVTEDFTSYIKRKRADGEPGNHIEQQAAADIYEEIEKPLNITSFKD--TCYIQTPPAIEE- 323 (371)
T ss_pred HHHHHHHHHHhhcccccccccccchhhcccccccCCCCcchHHHhhhhhhhhhccccceeecccc--cceeccCccccc-
Confidence 479999999999999999999999999999999999999999999999 45566666655441 122222111111
Q ss_pred CCCCeEEEEECCCCcccccccC
Q 033766 79 GKENPIRVLYHGYGHYDLLRGH 100 (112)
Q Consensus 79 ~~~~~i~L~Y~~~gHYdsv~~~ 100 (112)
....+++.+..--||+..+..
T Consensus 324 -~~~~~~~n~~~~~h~~~~~~~ 344 (371)
T KOG2605|consen 324 -SVKMEKYNFWVEVHYNTARHS 344 (371)
T ss_pred -chhhhhhcccchhhhhhcccc
Confidence 112233333222399999875
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=86.83 E-value=1.7 Score=28.36 Aligned_cols=48 Identities=17% Similarity=0.263 Sum_probs=33.2
Q ss_pred CHHHHHHHhcCC--CCcCChHHHHHHHHhhCCCEEEEEecCCCCCceeeeecCCCC
Q 033766 25 DFDAYVRQMRQP--HSWGGEPELLMSSHVLKMPITVYMRDKTSGSLKNLSEYGQEY 78 (112)
Q Consensus 25 ~~~~Y~~~m~~~--~~WGg~iEl~Als~~~~~~I~V~~~~~~~~~~~~i~~~g~e~ 78 (112)
+++.||.|.++. .+|-| ...+|+.+++.|.|--... .+..+..+++..
T Consensus 35 ~i~~y~~W~r~~~~STW~D---C~mFA~~LkVsm~vkV~~~---~~~~l~~~~d~~ 84 (104)
T PF05415_consen 35 TIKKYHTWLRKKRPSTWDD---CRMFADALKVSMQVKVLSD---KPYDLLYFVDGA 84 (104)
T ss_pred HHHHHHHHHhcCCCCcHHH---HHHHHHhheeEEEEEEcCC---CCceeeEeecCc
Confidence 589999998765 58954 5689999999999844332 233345566543
No 10
>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=80.58 E-value=0.13 Score=31.69 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=26.0
Q ss_pred hhCccc-cccccc-cCHHHHHHHhcCCCCcCChHH
Q 033766 12 LLRRAE-TEWFVE-GDFDAYVRQMRQPHSWGGEPE 44 (112)
Q Consensus 12 ~~~~~~-fe~fv~-~~~~~Y~~~m~~~~~WGg~iE 44 (112)
+++.+- +..||. .|+|+=+-.+.+++.|||.+.
T Consensus 6 R~~~~g~l~~YvpKKDLEE~Vv~~e~~~~WGG~v~ 40 (67)
T TIGR02934 6 RRNRAGELSAYVPKKDLEEVIVSVEKEELWGGWVT 40 (67)
T ss_pred EeCCCCCEEEEEECCcchhheeeeecCccccCEEE
Confidence 455554 778887 489999999999999999643
No 11
>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=71.52 E-value=2.4 Score=26.97 Aligned_cols=51 Identities=14% Similarity=0.118 Sum_probs=41.6
Q ss_pred HHHHHHHHHhhCccccccccc-----------cCHHHHHHHhcCC-C-CcCChHHHHHHHHhhC
Q 033766 3 LLGQVADEFLLRRAETEWFVE-----------GDFDAYVRQMRQP-H-SWGGEPELLMSSHVLK 53 (112)
Q Consensus 3 lR~~~~~yi~~~~~~fe~fv~-----------~~~~~Y~~~m~~~-~-~WGg~iEl~Als~~~~ 53 (112)
||..+.+..+++++.|+.++. +.|.+-++.|-.+ + .||-=+-+-|++..+-
T Consensus 1 L~~i~~~~e~~~~~~f~~~~~~l~~~~~~~~~~~f~~v~~~lf~d~~inWGRIval~~f~~~l~ 64 (101)
T PF00452_consen 1 LRRIADELERKYEDFFENMLNQLNINTPDNAYETFNEVAEELFEDGGINWGRIVALFAFAGALA 64 (101)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCSSSTTTHHHHHHHHHHHHTTTSSTCHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHH
Confidence 688899999999999987775 1477888888888 3 8999999999887653
No 12
>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=66.14 E-value=0.047 Score=33.31 Aligned_cols=33 Identities=30% Similarity=0.485 Sum_probs=20.7
Q ss_pred hhCcc-cccccccc-CHHHHHHHhcCCCCcCChHH
Q 033766 12 LLRRA-ETEWFVEG-DFDAYVRQMRQPHSWGGEPE 44 (112)
Q Consensus 12 ~~~~~-~fe~fv~~-~~~~Y~~~m~~~~~WGg~iE 44 (112)
|++.+ .+..||.. |+|+=+-.+.+++.|||.+.
T Consensus 6 R~~~~G~ls~YVpKKDLEE~Vv~~E~~~~wGG~v~ 40 (64)
T PF06988_consen 6 RKNGAGGLSAYVPKKDLEEPVVSMEKPELWGGEVT 40 (64)
T ss_dssp EE-SS--EEEEETTTTEEEEEEEESSSSS-SSEEE
T ss_pred EeCCCcCEEEEEeCCccccceeeeeccCccCCEEE
Confidence 34444 56677763 67766777779999999654
No 13
>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=61.66 E-value=4.8 Score=31.54 Aligned_cols=46 Identities=11% Similarity=0.013 Sum_probs=26.7
Q ss_pred hHHHHHHHHHhhCcccc-ccccccCHHHHHHHhcCCCCcCChHHHHHHHHhh
Q 033766 2 MLLGQVADEFLLRRAET-EWFVEGDFDAYVRQMRQPHSWGGEPELLMSSHVL 52 (112)
Q Consensus 2 ~lR~~~~~yi~~~~~~f-e~fv~~~~~~Y~~~m~~~~~WGg~iEl~Als~~~ 52 (112)
-|=++|++||-.||+.| .| =..+|. .++. .+..=+--|..+|-.++
T Consensus 165 ~lL~eIaqFMD~nPe~FgkP-d~~sW~---~eLk-eD~~L~~~E~~~F~~Al 211 (308)
T PF04877_consen 165 PLLKEIAQFMDQNPEQFGKP-DRKSWA---DELK-EDNGLDKAETEQFQKAL 211 (308)
T ss_pred HHHHHHHHHHhcCHhhcCCC-CCchHH---HHhh-cCCCCCHHHHHHHHHHH
Confidence 45678999999999999 55 112333 3332 23333334555555555
No 14
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=60.29 E-value=4.8 Score=32.42 Aligned_cols=45 Identities=29% Similarity=0.298 Sum_probs=41.2
Q ss_pred cccccccCHHHHHHHhcCCCCcCChHHHHHHHHhhCCCEEEEEec
Q 033766 18 TEWFVEGDFDAYVRQMRQPHSWGGEPELLMSSHVLKMPITVYMRD 62 (112)
Q Consensus 18 fe~fv~~~~~~Y~~~m~~~~~WGg~iEl~Als~~~~~~I~V~~~~ 62 (112)
|..++.++|+.|+.-+.++.+-|+-+||.+.+.+++.+...+...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~s~~~r~~~~~~~~~ 46 (371)
T KOG2605|consen 2 FREEVSGDFDWYLWDLGKTKTLGTILELGAMSHVYRRNVIDYEPF 46 (371)
T ss_pred CccccCchHHHHhhcCCCCcccccchhhhhccccccCCCCCcCCc
Confidence 667888999999999999999999999999999999999887654
No 15
>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=56.23 E-value=6.5 Score=25.39 Aligned_cols=51 Identities=16% Similarity=0.074 Sum_probs=39.8
Q ss_pred HHHHHHHHHhhCccccccccc----------cCHHHHHHHhcCCC--CcCChHHHHHHHHhhC
Q 033766 3 LLGQVADEFLLRRAETEWFVE----------GDFDAYVRQMRQPH--SWGGEPELLMSSHVLK 53 (112)
Q Consensus 3 lR~~~~~yi~~~~~~fe~fv~----------~~~~~Y~~~m~~~~--~WGg~iEl~Als~~~~ 53 (112)
||+..-+.-++|+..|..+.. +.|.+-++.+-++| .||-=+-|-+++-.+=
T Consensus 1 Lr~~~dele~~~~~~f~~~~~~l~~~~~~~~~~f~~Va~~lf~dg~inWGRIval~~F~~~la 63 (100)
T smart00337 1 LRRVGDELNKRYERAFSSFSAQLHVTPGTAIELFGEVATELFSDGNINWGRVVALLSFGGALA 63 (100)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 466777777778888887764 25777788888898 7999999999876653
No 16
>PRK10963 hypothetical protein; Provisional
Probab=55.07 E-value=6.5 Score=29.08 Aligned_cols=16 Identities=19% Similarity=-0.051 Sum_probs=13.8
Q ss_pred HHHHHHHhhCcccccc
Q 033766 5 GQVADEFLLRRAETEW 20 (112)
Q Consensus 5 ~~~~~yi~~~~~~fe~ 20 (112)
+.|++|+++|||+|+-
T Consensus 6 ~~V~~yL~~~PdFf~~ 21 (223)
T PRK10963 6 RAVVDYLLQNPDFFIR 21 (223)
T ss_pred HHHHHHHHHCchHHhh
Confidence 5789999999999863
No 17
>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=52.83 E-value=56 Score=21.73 Aligned_cols=46 Identities=15% Similarity=0.176 Sum_probs=31.9
Q ss_pred HHHHHHHHhhCCCEEEEEecCCCCCceeeeecCCCCCCCCeEEEEECCC--Ccccc
Q 033766 43 PELLMSSHVLKMPITVYMRDKTSGSLKNLSEYGQEYGKENPIRVLYHGY--GHYDL 96 (112)
Q Consensus 43 iEl~Als~~~~~~I~V~~~~~~~~~~~~i~~~g~e~~~~~~i~L~Y~~~--gHYds 96 (112)
-.+.|||..|+....|+... .. ..||-..+ ...+.|.+... |||..
T Consensus 47 DhltaLa~~~~~~~~~hs~~----~~---~~~Gi~~a-s~~~~I~ht~G~p~HFs~ 94 (104)
T PF05381_consen 47 DHLTALAYRYHFQCTFHSDH----GV---LHYGIKDA-STVFTITHTPGPPGHFSL 94 (104)
T ss_pred HHHHHHHHHHheEEEEEcCC----ce---EEeecCCC-ceEEEEEeCCCCCCcccc
Confidence 45779999999999998755 22 25887643 35566666332 59998
No 18
>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=52.23 E-value=20 Score=19.75 Aligned_cols=30 Identities=7% Similarity=0.004 Sum_probs=23.8
Q ss_pred HHHHHHhcCCCCcCChHHHHHHHHhhCCCE
Q 033766 27 DAYVRQMRQPHSWGGEPELLMSSHVLKMPI 56 (112)
Q Consensus 27 ~~Y~~~m~~~~~WGg~iEl~Als~~~~~~I 56 (112)
..++.++.+....-.--.+.++|++|++++
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 456666666677788889999999999875
No 19
>COG3159 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.89 E-value=8.4 Score=28.85 Aligned_cols=17 Identities=18% Similarity=-0.111 Sum_probs=14.1
Q ss_pred HHHHHHHhhCccccccc
Q 033766 5 GQVADEFLLRRAETEWF 21 (112)
Q Consensus 5 ~~~~~yi~~~~~~fe~f 21 (112)
+.|++|++.|||+|..+
T Consensus 7 ~~VadyL~~hPeFf~~h 23 (218)
T COG3159 7 EDVADYLRQHPEFFIQH 23 (218)
T ss_pred HHHHHHHHhCcHHHHhC
Confidence 46899999999998633
No 20
>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=49.05 E-value=15 Score=25.03 Aligned_cols=54 Identities=17% Similarity=0.107 Sum_probs=42.9
Q ss_pred hHHHHHHHHHhhCccccccccc----------cCHHHHHHHhcCC-C-CcCChHHHHHHHHhhCCC
Q 033766 2 MLLGQVADEFLLRRAETEWFVE----------GDFDAYVRQMRQP-H-SWGGEPELLMSSHVLKMP 55 (112)
Q Consensus 2 ~lR~~~~~yi~~~~~~fe~fv~----------~~~~~Y~~~m~~~-~-~WGg~iEl~Als~~~~~~ 55 (112)
.||+.+.+..++|++.|+.... +.|.+=++.+-++ + .||-=+-|.|+|-.+-+.
T Consensus 38 ~Lr~~~dele~~~~~~f~~~~~~l~~~~~~~~~~f~~v~~~lf~dg~inWGRIval~~f~~~la~~ 103 (144)
T cd06845 38 TLRRVGDELEEKHRRLFENMCRQLNISPDNAYEVFQEVARELFEDGGINWGRIVALFAFGGRLAVK 103 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHH
Confidence 4788888999999999877664 3588888888888 4 899999999888765443
No 21
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=45.97 E-value=6.8 Score=28.77 Aligned_cols=18 Identities=17% Similarity=-0.099 Sum_probs=0.0
Q ss_pred HHHHHHHhhCcccccccc
Q 033766 5 GQVADEFLLRRAETEWFV 22 (112)
Q Consensus 5 ~~~~~yi~~~~~~fe~fv 22 (112)
..|++|+++|||+|.-+-
T Consensus 9 ~~V~~yL~~~PdFf~~~~ 26 (225)
T PF04340_consen 9 EDVAAYLRQHPDFFERHP 26 (225)
T ss_dssp ------------------
T ss_pred HHHHHHHHhCcHHHHhCH
Confidence 468999999999996444
No 22
>COG4887 Uncharacterized metal-binding protein conserved in archaea [General function prediction only]
Probab=45.87 E-value=45 Score=23.96 Aligned_cols=56 Identities=16% Similarity=0.049 Sum_probs=39.8
Q ss_pred HHHHHHhhCcccc--ccccc----------cCHHHHHHHhcCC--C-C--cCChHHHHHHHHhhCCCEEEEEe
Q 033766 6 QVADEFLLRRAET--EWFVE----------GDFDAYVRQMRQP--H-S--WGGEPELLMSSHVLKMPITVYMR 61 (112)
Q Consensus 6 ~~~~yi~~~~~~f--e~fv~----------~~~~~Y~~~m~~~--~-~--WGg~iEl~Als~~~~~~I~V~~~ 61 (112)
.+-+|=+.|-..| .++++ +...+||.+|.-- | . -|-+-|..|+++++.+-+.||++
T Consensus 25 ~~eeY~~enlk~~~~sa~iE~~~ymk~TrlEEIae~ckrm~ykkiGiAFCigle~EAr~l~~iLsr~fEVySV 97 (191)
T COG4887 25 TVEEYRRENLKLFRSSAEIEVEGYMKWTRLEEIAELCKRMVYKKIGIAFCIGLEEEARALCEILSRGFEVYSV 97 (191)
T ss_pred HHHHHhhhhHHHhhhhhhhhhhhhHHHHhHHHHHHHHHHhhhhhcceeeeeccHHHHHHHHHHHHhcceeeee
Confidence 3444555555555 34454 4678999998643 3 1 37789999999999999999986
No 23
>PF05159 Capsule_synth: Capsule polysaccharide biosynthesis protein; InterPro: IPR007833 This family includes export proteins involved in capsule polysaccharide biosynthesis, such as KpsS P42218 from SWISSPROT and LipB P57038 from SWISSPROT. Capsule polysaccharide modification protein lipB/A is involved in the phospholipid modification of the capsular polysaccharide and is a strong requirement for its translocation to the cell surface. The capsule of Neisseria meningitidis serogroup B and of other meningococcal serogroups and other Gram-negative bacterial pathogens, are anchored in the outer membrane through a 1,2-diacylglycerol moiety. The lipA and lipB genes are located on the 3' end of the ctr operon. lipA and lipB do not encode proteins responsible for diacylglycerophosphatidic acid substitution of the meningococcal capsule polymer, but they are required for proper translocation and surface expression of the lipidated polymer []. KpsS is an unusual sulphate-modified form of the capsular polysaccharide in Rhizobium loti (Mesorhizobium loti). Many plants, including R. loti, enter into symbiotic relationships with bacteria that allow survival in nutrient-limiting environments. KpsS functions as a fucosyl sulphotransferase in vitro. The kpsS gene product shares no significant amino acid similarity with previously identified sulphotransferases []. Sulphated cell surface polysaccharides are required for optimum nodule formation but limit growth rate and nodule colonisation in M. loti [].; GO: 0000271 polysaccharide biosynthetic process, 0015774 polysaccharide transport
Probab=44.67 E-value=89 Score=23.10 Aligned_cols=57 Identities=18% Similarity=0.314 Sum_probs=36.5
Q ss_pred CcCCh----HHHHHHHHhhCCCEEEEEecCCCCCceeeeecCCCCCCCCeEEEEECCCC-cccccccCC
Q 033766 38 SWGGE----PELLMSSHVLKMPITVYMRDKTSGSLKNLSEYGQEYGKENPIRVLYHGYG-HYDLLRGHD 101 (112)
Q Consensus 38 ~WGg~----iEl~Als~~~~~~I~V~~~~~~~~~~~~i~~~g~e~~~~~~i~L~Y~~~g-HYdsv~~~~ 101 (112)
.|||. -.+..+|+.+++++.++..+ -+..+ .++. ...+|..+.+...| +++|-.+..
T Consensus 5 ~wg~~~~~~~~~~~~a~~~~i~~~~~E~G----~lR~~-~~~~--~~~~P~s~~~D~~Gv~~~s~~~~~ 66 (269)
T PF05159_consen 5 VWGDKRPYHRAAIEVAKELGIPVIFFEDG----FLRSI-GLGS--DGYPPDSLTIDPQGVNADSSLPSD 66 (269)
T ss_pred EECCCccHHHHHHHHHHHhCCCEEEEecC----ccccc-cccc--cCCCCeEEEECCCCccCCCCCccc
Confidence 58885 24556789999999988643 22112 1222 23578888887777 888876543
No 24
>KOG3325 consensus Membrane coat complex Retromer, subunit VPS29/PEP11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=44.14 E-value=30 Score=24.92 Aligned_cols=22 Identities=23% Similarity=0.489 Sum_probs=20.3
Q ss_pred CcCChHHHHHHHHhhCCCEEEE
Q 033766 38 SWGGEPELLMSSHVLKMPITVY 59 (112)
Q Consensus 38 ~WGg~iEl~Als~~~~~~I~V~ 59 (112)
-|||..-|.+|++-++++|-|.
T Consensus 92 P~gd~~sL~~LaRqldvDILl~ 113 (183)
T KOG3325|consen 92 PWGDPESLALLARQLDVDILLT 113 (183)
T ss_pred cCCCHHHHHHHHHhcCCcEEEe
Confidence 3999999999999999999885
No 25
>COG3563 KpsC Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]
Probab=37.53 E-value=1e+02 Score=26.42 Aligned_cols=60 Identities=27% Similarity=0.454 Sum_probs=39.1
Q ss_pred CcC-ChHHHHHHHHhhCCCEEEEEecCCCCCceeeeecCCCCCCCCeEEEEECCCCcccccccCCCCchhhhh
Q 033766 38 SWG-GEPELLMSSHVLKMPITVYMRDKTSGSLKNLSEYGQEYGKENPIRVLYHGYGHYDLLRGHDATTQSRLC 109 (112)
Q Consensus 38 ~WG-g~iEl~Als~~~~~~I~V~~~~~~~~~~~~i~~~g~e~~~~~~i~L~Y~~~gHYdsv~~~~~~~~~~~~ 109 (112)
.|| |..+|.++|+..++|+.-. .| ++.. +.|....-.+|+.|+..+-|=| . +..+||+|.
T Consensus 368 aWG~~~~~lv~~A~~h~iPl~~~-ED----GFlR--Sv~LGs~ltPPlSLv~Dd~~iY----F-da~~pS~LE 428 (671)
T COG3563 368 AWGNGKEALVEFAEQHHIPLLRM-ED----GFLR--SVGLGSNLTPPLSLVLDDMGIY----F-DANTPSRLE 428 (671)
T ss_pred EecCCcHHHHHHHHHhCCCeeee-cc----ccee--eccccccCCCCeeEEEcCceeE----e-cCCCchhHH
Confidence 497 5699999999999996543 33 3542 3455444468999999876422 2 234466663
No 26
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=36.17 E-value=30 Score=27.44 Aligned_cols=27 Identities=19% Similarity=0.134 Sum_probs=21.4
Q ss_pred CHHHHHHHhcCCCCcCChHHHHHHHHh
Q 033766 25 DFDAYVRQMRQPHSWGGEPELLMSSHV 51 (112)
Q Consensus 25 ~~~~Y~~~m~~~~~WGg~iEl~Als~~ 51 (112)
-.++|+.++..--.++|+.|+.|||.=
T Consensus 315 ~I~~~v~~iapv~v~PGE~EleALA~G 341 (358)
T COG3426 315 AIEDRVSWIAPVIVYPGEDELEALAEG 341 (358)
T ss_pred HHHHHHhhhcceEecCCchHHHHHHhh
Confidence 366777777776778999999999863
No 27
>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=35.72 E-value=11 Score=22.46 Aligned_cols=20 Identities=10% Similarity=0.064 Sum_probs=16.1
Q ss_pred HHHHHHHHhhCccccccccc
Q 033766 4 LGQVADEFLLRRAETEWFVE 23 (112)
Q Consensus 4 R~~~~~yi~~~~~~fe~fv~ 23 (112)
-|.++.|+.+||+-.+-..+
T Consensus 2 ~Q~iV~YLv~nPevl~kl~~ 21 (57)
T PF05952_consen 2 KQEIVNYLVQNPEVLEKLKE 21 (57)
T ss_pred hHHHHHHHHHChHHHHHHHc
Confidence 37889999999998766655
No 28
>PF07116 DUF1372: Protein of unknown function (DUF1372); InterPro: IPR010779 This entry is represented by Streptococcus phage Sfi11, Gp93. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several Streptococcus bacteriophage sequences and related proteins from Streptococcus species. Members of this family are typically around 100 residues in length and their function is unknown.
Probab=35.52 E-value=1.2e+02 Score=20.15 Aligned_cols=57 Identities=16% Similarity=0.179 Sum_probs=31.7
Q ss_pred hhCCCEEEEEecCCCCCceeeeecCCCCCCCCeEEEEECCC-------CcccccccCCCCchhhhhh
Q 033766 51 VLKMPITVYMRDKTSGSLKNLSEYGQEYGKENPIRVLYHGY-------GHYDLLRGHDATTQSRLCK 110 (112)
Q Consensus 51 ~~~~~I~V~~~~~~~~~~~~i~~~g~e~~~~~~i~L~Y~~~-------gHYdsv~~~~~~~~~~~~~ 110 (112)
--+.||.||++|..+ ....-+..+-..-..-..+..+.+ +-||++. .++.-|+=|++
T Consensus 41 e~~~piiIykaDN~G--~ei~GkVt~K~~ig~~yTvti~~YGkFlVtkeqY~~i~-iGDdiP~yLkg 104 (104)
T PF07116_consen 41 EEKKPIIIYKADNAG--AEIFGKVTEKEIIGGLYTVTIGAYGKFLVTKEQYESIK-IGDDIPDYLKG 104 (104)
T ss_pred cccCcEEEEEecCCC--cEEEEEEeeceeECCEEEEEecCceEEEEehhhcceee-cCCcchhhhcC
Confidence 356899999998442 221111111101123344555555 3899986 66777888764
No 29
>TIGR00865 bcl-2 Apoptosis regulator. in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.
Probab=34.39 E-value=30 Score=25.72 Aligned_cols=53 Identities=11% Similarity=0.018 Sum_probs=41.4
Q ss_pred hHHHHHHHHHhhCccccccccc----------cCHHHHHHHhcCCC-CcCChHHHHHHHHhhCC
Q 033766 2 MLLGQVADEFLLRRAETEWFVE----------GDFDAYVRQMRQPH-SWGGEPELLMSSHVLKM 54 (112)
Q Consensus 2 ~lR~~~~~yi~~~~~~fe~fv~----------~~~~~Y~~~m~~~~-~WGg~iEl~Als~~~~~ 54 (112)
.||+..-+.-++|+..|..++. ..|.+-.+.+-++| .||-=+-|-|++-.+-+
T Consensus 70 ~Lr~igdEle~~~~~~f~~m~~qL~it~~~a~~~F~~Va~elF~DGiNWGRIVaLfaFgg~La~ 133 (213)
T TIGR00865 70 ALRRAGDEFERRYRRAFSDMTSQLHITPFTARQSFFQVAAELFRDGVNWGRIVAFFSFGGALCV 133 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence 4777788888888888987764 25777888888888 79999999888866543
No 30
>PRK07027 cobalamin biosynthesis protein CbiG; Provisional
Probab=33.22 E-value=34 Score=23.02 Aligned_cols=32 Identities=16% Similarity=0.127 Sum_probs=26.2
Q ss_pred HHhcCCCCcCChHHHHHHHHhhCCCEEEEEec
Q 033766 31 RQMRQPHSWGGEPELLMSSHVLKMPITVYMRD 62 (112)
Q Consensus 31 ~~m~~~~~WGg~iEl~Als~~~~~~I~V~~~~ 62 (112)
..+.......++.-|..+|+.+++|+..|+.+
T Consensus 38 ~~lasi~~K~~E~~L~~~A~~lg~pl~~~~~~ 69 (126)
T PRK07027 38 RVVATLDLKADEAGLLALCARHGWPLRAFSAA 69 (126)
T ss_pred heeEehhhhcCCHHHHHHHHHhCCCeEEeCHH
Confidence 34455566799999999999999999999654
No 31
>PF08960 DUF1874: Domain of unknown function (DUF1874); InterPro: IPR015055 This entry is represented by Acidianus two-tailed virus, Orf117. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2J85_A 2X4I_C.
Probab=32.64 E-value=75 Score=21.12 Aligned_cols=33 Identities=15% Similarity=0.269 Sum_probs=21.4
Q ss_pred CHHHHHHHhcCCCCc----CChHHHHHHHHhhCCCEEE
Q 033766 25 DFDAYVRQMRQPHSW----GGEPELLMSSHVLKMPITV 58 (112)
Q Consensus 25 ~~~~Y~~~m~~~~~W----Gg~iEl~Als~~~~~~I~V 58 (112)
+.++.|+.+ ..+.| |-+-..++++++|+++|-+
T Consensus 26 t~~Ea~~~l-~~~~~vSaIGH~sTa~lls~llg~~ip~ 62 (105)
T PF08960_consen 26 TVEEAKELL-QNEGFVSAIGHDSTAQLLSELLGVNIPM 62 (105)
T ss_dssp -HHHHHHHH-CTTTEEE----HHHHHHHHHHHT-----
T ss_pred CHHHHHHHH-hcCceEEeeCcHHHHHHHHHHhCCcccc
Confidence 899999999 44455 7778999999999999865
No 32
>PF13734 Inhibitor_I69: Spi protease inhibitor; PDB: 1PVJ_A 1DKI_D 2UZJ_A 2JTC_A 4D8E_A 4D8I_A 4D8B_A.
Probab=32.01 E-value=1.1e+02 Score=19.78 Aligned_cols=41 Identities=17% Similarity=0.344 Sum_probs=22.0
Q ss_pred HhhCCCEEEEEecCCCCCceeeeecCCCCCCCCeEEEEECCCCccccc
Q 033766 50 HVLKMPITVYMRDKTSGSLKNLSEYGQEYGKENPIRVLYHGYGHYDLL 97 (112)
Q Consensus 50 ~~~~~~I~V~~~~~~~~~~~~i~~~g~e~~~~~~i~L~Y~~~gHYdsv 97 (112)
.-.+.|+.|+..+ .++++.| -|++. -.+| |+|...|++|..
T Consensus 37 ~~~~~~~YI~N~~--~~GFVIV--SgDdr--~~~I-LaYS~~G~fd~~ 77 (96)
T PF13734_consen 37 TPSDTPYYIFNDN--NKGFVIV--SGDDR--MGPI-LAYSDEGSFDTN 77 (96)
T ss_dssp TT-SSSEEEEEET--TS-EEEE--ESBTT--S-SE-EEEESSS----T
T ss_pred CCCCCcEEEEEcC--CCEEEEE--ECCCC--ccce-eEEcCCCCcCcc
Confidence 3445699999883 3467755 35432 2455 999888899853
No 33
>PHA01976 helix-turn-helix protein
Probab=30.16 E-value=87 Score=17.84 Aligned_cols=30 Identities=10% Similarity=0.142 Sum_probs=20.2
Q ss_pred HHHHHhcCCCCcCChHHHHHHHHhhCCCEE
Q 033766 28 AYVRQMRQPHSWGGEPELLMSSHVLKMPIT 57 (112)
Q Consensus 28 ~Y~~~m~~~~~WGg~iEl~Als~~~~~~I~ 57 (112)
..+.++.+...=-..-.+..+|++|++++.
T Consensus 30 ~~v~~~e~g~~~p~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 30 SLIYDFEADKRLPNLKTLLRLADALGVTLD 59 (67)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence 444455544444455679999999999874
No 34
>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=27.59 E-value=30 Score=21.63 Aligned_cols=19 Identities=5% Similarity=-0.111 Sum_probs=15.0
Q ss_pred HHHHHHHhhCccccccccc
Q 033766 5 GQVADEFLLRRAETEWFVE 23 (112)
Q Consensus 5 ~~~~~yi~~~~~~fe~fv~ 23 (112)
...-.=|..|+|+|+||+.
T Consensus 45 ~~L~kCM~ahsdYY~P~La 63 (76)
T PF07802_consen 45 AALRKCMEAHSDYYEPILA 63 (76)
T ss_pred HHHHHHHHhchhHHHHHHH
Confidence 3444568899999999997
No 35
>PF01890 CbiG_C: Cobalamin synthesis G C-terminus; InterPro: IPR002750 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CbiG proteins are specific for anaerobic cobalamin biosynthesis. CbiG, which shows homology with CobE of the aerobic pathway, participates in the conversion of cobalt-precorrin 5 into cobalt-precorrin 6 []. CbiG is responsible for the opening of the delta-lactone ring and extrusion of the C2-unit []. The aerobic pathway uses molecular oxygen to trigger the events at C-20 leading to contraction and expulsion of the C2-unit as acetic acid from a metal-free intermediate, whereas the anaerobic route involves the internal delivery of oxygen from a carboxylic acid terminus to C-20 followed by extrusion of the C2-unit as acetaldehyde, using cobalt complexes as substrates []. This entry represents the core domain of CibG.; GO: 0009236 cobalamin biosynthetic process; PDB: 3BY5_A 2W6K_A 2W6L_A 3EEQ_B.
Probab=26.20 E-value=55 Score=21.82 Aligned_cols=23 Identities=26% Similarity=0.523 Sum_probs=18.5
Q ss_pred CChHHHHHHHHhhCCCEEEEEec
Q 033766 40 GGEPELLMSSHVLKMPITVYMRD 62 (112)
Q Consensus 40 Gg~iEl~Als~~~~~~I~V~~~~ 62 (112)
.++.-|.++|+.+++|++.|..+
T Consensus 45 ~~E~~l~~~A~~l~~~~~~~~~e 67 (121)
T PF01890_consen 45 ADEPGLLELAEELGIPLRFFSAE 67 (121)
T ss_dssp S--HHHHHHHHHCTSEEEEE-HH
T ss_pred CCCHHHHHHHHHhCCCeEEECHH
Confidence 67899999999999999999865
No 36
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=25.13 E-value=1.2e+02 Score=16.19 Aligned_cols=29 Identities=10% Similarity=0.171 Sum_probs=17.3
Q ss_pred HHHHHhcCCCCcCChHHHHHHHHhhCCCE
Q 033766 28 AYVRQMRQPHSWGGEPELLMSSHVLKMPI 56 (112)
Q Consensus 28 ~Y~~~m~~~~~WGg~iEl~Als~~~~~~I 56 (112)
.++.++.+...=-.--++..++++|++++
T Consensus 30 ~~vs~~e~g~~~~~~~~~~~i~~~lgv~l 58 (58)
T TIGR03070 30 RFIRDVENGKPTVRLDKVLRVLDALGLEL 58 (58)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHHHcCCCC
Confidence 34444444332234556888999998864
No 37
>COG4479 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.35 E-value=65 Score=20.03 Aligned_cols=29 Identities=7% Similarity=0.186 Sum_probs=18.5
Q ss_pred HHHHHHhhCcccc--ccccccCHHHHHHHhc
Q 033766 6 QVADEFLLRRAET--EWFVEGDFDAYVRQMR 34 (112)
Q Consensus 6 ~~~~yi~~~~~~f--e~fv~~~~~~Y~~~m~ 34 (112)
.+++||+.|.++. ..-.++=|++|+....
T Consensus 43 ~is~YLE~~a~f~~~m~~FDeiwe~Yle~~~ 73 (74)
T COG4479 43 EISDYLETNADFLFNMSVFDEIWEEYLEHLK 73 (74)
T ss_pred HHHHHHHhcCCcccchhhHHHHHHHHHHHhc
Confidence 5778888887743 2222356888887653
No 38
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=23.88 E-value=1.9e+02 Score=18.23 Aligned_cols=30 Identities=10% Similarity=0.029 Sum_probs=15.6
Q ss_pred HHHHhcCCCCcCChHHHHHHHHhhCCCEEE
Q 033766 29 YVRQMRQPHSWGGEPELLMSSHVLKMPITV 58 (112)
Q Consensus 29 Y~~~m~~~~~WGg~iEl~Als~~~~~~I~V 58 (112)
.+.+|.+...=-.--.|..+|++|++++.|
T Consensus 59 tLs~iE~g~~~Ps~~tL~kI~~aLgi~l~v 88 (89)
T TIGR02684 59 SLYKALSGKGNPTFDTILKVTKALGLKLTA 88 (89)
T ss_pred HHHHHHcCCCCCCHHHHHHHHHHcCCceee
Confidence 333344333333345566666677666654
No 39
>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=23.81 E-value=1.2e+02 Score=18.38 Aligned_cols=20 Identities=10% Similarity=0.100 Sum_probs=17.4
Q ss_pred HHHHHHHHhhCCC---EEEEEec
Q 033766 43 PELLMSSHVLKMP---ITVYMRD 62 (112)
Q Consensus 43 iEl~Als~~~~~~---I~V~~~~ 62 (112)
|.++|++++...+ +.|+..+
T Consensus 18 La~~~yl~~~~~~~~~~~vv~s~ 40 (72)
T PF10568_consen 18 LAVIAYLKFAGAPEQQFKVVPSN 40 (72)
T ss_pred HHHHHHHHhCCCCCceEEEEEcC
Confidence 7788899999999 9998766
No 40
>PF05182 Fip1: Fip1 motif; InterPro: IPR007854 This short motif is about 40 amino acids in length and is found in the Fip1 protein that is a component of a Saccharomyces cerevisiae pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase []. This region of Fip1 is needed for the interaction with the Yth1 subunit of the complex and for specific polyadenylation of the cleaved mRNA precursor [].
Probab=23.70 E-value=32 Score=19.41 Aligned_cols=16 Identities=31% Similarity=0.528 Sum_probs=12.4
Q ss_pred cccccCHHHHHHHhcC
Q 033766 20 WFVEGDFDAYVRQMRQ 35 (112)
Q Consensus 20 ~fv~~~~~~Y~~~m~~ 35 (112)
-|-|.+|.+||++..+
T Consensus 27 Gf~E~tW~~Y~~kq~~ 42 (45)
T PF05182_consen 27 GFNEETWREYCKKQRQ 42 (45)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 4556799999998764
No 41
>cd07288 PX_SNX15 The phosphoinositide binding Phox Homology domain of Sorting Nexin 15. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX15 contains an N-terminal PX domain and a C-terminal Microtubule Interacting and Trafficking (MIT) domain. It plays a role in protein trafficking processes in the endocytic pathway and the trans-Golgi network. The PX domain of SNX15 interacts with the PDGF receptor and is responsible for the membrane association of t
Probab=23.41 E-value=52 Score=21.94 Aligned_cols=30 Identities=13% Similarity=-0.034 Sum_probs=24.5
Q ss_pred ccccc---CHHHHHHHhcCCCCcCChHHHHHHH
Q 033766 20 WFVEG---DFDAYVRQMRQPHSWGGEPELLMSS 49 (112)
Q Consensus 20 ~fv~~---~~~~Y~~~m~~~~~WGg~iEl~Als 49 (112)
.||++ .+++|++.+...-.|.++.+++.+-
T Consensus 83 ~fIeeRR~~Le~fL~~i~~~p~l~~s~~~~~FL 115 (118)
T cd07288 83 AVIEERRNAAEAMLLFTVNIPALYNSPQLKEFF 115 (118)
T ss_pred HHHHHHHHHHHHHHHHHhCChhhcCChHHHHHH
Confidence 35553 7999999999998999999988763
No 42
>COG5562 Phage envelope protein [General function prediction only]
Probab=23.11 E-value=53 Score=22.92 Aligned_cols=14 Identities=7% Similarity=0.387 Sum_probs=12.7
Q ss_pred CHHHHHHHhcCCCC
Q 033766 25 DFDAYVRQMRQPHS 38 (112)
Q Consensus 25 ~~~~Y~~~m~~~~~ 38 (112)
+|++||+.|.+-|.
T Consensus 90 tF~ef~~~la~AGV 103 (137)
T COG5562 90 TFEEFCSALAEAGV 103 (137)
T ss_pred cHHHHHHHHHhCCe
Confidence 89999999999884
No 43
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=22.90 E-value=44 Score=26.06 Aligned_cols=49 Identities=14% Similarity=0.186 Sum_probs=41.0
Q ss_pred HHHhhCccccccccccCHHHHHHHhcCCCCc-CChHHHHHHHHhhCCCEE
Q 033766 9 DEFLLRRAETEWFVEGDFDAYVRQMRQPHSW-GGEPELLMSSHVLKMPIT 57 (112)
Q Consensus 9 ~yi~~~~~~fe~fv~~~~~~Y~~~m~~~~~W-Gg~iEl~Als~~~~~~I~ 57 (112)
||-++|++.-..|.--..+.|...+.++..| .+...++-|+++-+++-.
T Consensus 220 dfAekhPe~v~aFakv~~da~a~Y~anp~~W~~~s~~v~k~arL~G~~~e 269 (334)
T COG4521 220 DFAEKHPEVVAAFAKVALDAQADYLANPDVWLADSEQVSKLARLSGVPEE 269 (334)
T ss_pred HhhHhChHHHHHHHHHHHHhhHHHhcChhhhccCchhhhhhhhhcCCChh
Confidence 5667888877778777888899999999999 777888889999998864
No 44
>cd06893 PX_SNX19 The phosphoinositide binding Phox Homology domain of Sorting Nexin 19. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX19 contains an N-terminal PXA domain, a central PX domain, and a C-terminal domain that is conserved in some SNXs. These domains are also found in SNX13 and SNX14, which also contain a regulator of G protein signaling (RGS) domain in between the PXA and PX domains. SNX19 interacts with IA-2, a major autoantigen found
Probab=22.81 E-value=43 Score=22.85 Aligned_cols=30 Identities=13% Similarity=0.082 Sum_probs=24.2
Q ss_pred ccccc---CHHHHHHHhcCCCCcCChHHHHHHH
Q 033766 20 WFVEG---DFDAYVRQMRQPHSWGGEPELLMSS 49 (112)
Q Consensus 20 ~fv~~---~~~~Y~~~m~~~~~WGg~iEl~Als 49 (112)
.||++ .+++|++++...-.|....+++++-
T Consensus 97 ~fie~Rr~~Le~fL~~l~~~p~l~~s~~l~~FL 129 (132)
T cd06893 97 DKIEARRGLLETFLRQLCSIPEISNSEEVQEFL 129 (132)
T ss_pred HHHHHHHHHHHHHHHHHHcCHhhhcCHHHHHHH
Confidence 36653 7999999998888899988888763
No 45
>PHA01627 DNA binding protein
Probab=22.42 E-value=1.6e+02 Score=19.68 Aligned_cols=32 Identities=9% Similarity=0.224 Sum_probs=27.3
Q ss_pred CHHHHHHHhcCCCCc----CChHHHHHHHHhhCCCEE
Q 033766 25 DFDAYVRQMRQPHSW----GGEPELLMSSHVLKMPIT 57 (112)
Q Consensus 25 ~~~~Y~~~m~~~~~W----Gg~iEl~Als~~~~~~I~ 57 (112)
+.++.|+.+.+. .| |-+-.+++++.+++++|-
T Consensus 27 ~~~Eak~~v~~~-~~vSaIGH~sTA~lls~llg~~ip 62 (107)
T PHA01627 27 DIEEAKELLENE-EFVSAIGHDATANLLSNLCGVNLP 62 (107)
T ss_pred CHHHHHHHhccc-CeEEeeccHHHHHHHHHHhCcccc
Confidence 899999999654 44 778999999999999875
No 46
>PF07166 DUF1398: Protein of unknown function (DUF1398); InterPro: IPR009833 This entry is represented by Bacteriophage DE3, Orf: ECD_10033. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Escherichia coli and Salmonella species. The function of this family is unknown.; PDB: 2HH8_A.
Probab=22.16 E-value=38 Score=23.13 Aligned_cols=14 Identities=14% Similarity=0.501 Sum_probs=11.4
Q ss_pred CHHHHHHHhcCCCC
Q 033766 25 DFDAYVRQMRQPHS 38 (112)
Q Consensus 25 ~~~~Y~~~m~~~~~ 38 (112)
+|.+||+.+.+.|.
T Consensus 85 df~tfC~~~A~AGI 98 (125)
T PF07166_consen 85 DFETFCKDAAKAGI 98 (125)
T ss_dssp -HHHHHHHHHHTT-
T ss_pred cHHHHHHHHHhcCC
Confidence 89999999999873
No 47
>cd06879 PX_UP1_plant The phosphoinositide binding Phox Homology domain of uncharacterized plant proteins. The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to PI-enriched membranes. Members in this subfamily are uncharacterized fungal proteins containing a PX domain. PX domain harboring proteins have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction.
Probab=21.34 E-value=57 Score=22.67 Aligned_cols=31 Identities=3% Similarity=0.047 Sum_probs=24.8
Q ss_pred ccccc---CHHHHHHHhcCCCCcCChHHHHHHHH
Q 033766 20 WFVEG---DFDAYVRQMRQPHSWGGEPELLMSSH 50 (112)
Q Consensus 20 ~fv~~---~~~~Y~~~m~~~~~WGg~iEl~Als~ 50 (112)
.|+++ .+++|++++..+-.|..+.+++.+-+
T Consensus 103 ~fiEeRR~gLE~fLq~Ll~~p~l~~s~~v~~FLe 136 (138)
T cd06879 103 ALLEERRHSLEEWMGKLLSDIDLSRSVPVASFLE 136 (138)
T ss_pred HHHHHHHHHHHHHHHHHHcCccccCCHHHHHHhC
Confidence 45553 79999999999989999988887643
No 48
>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=20.31 E-value=77 Score=18.94 Aligned_cols=8 Identities=38% Similarity=0.883 Sum_probs=5.8
Q ss_pred CCCcCChH
Q 033766 36 PHSWGGEP 43 (112)
Q Consensus 36 ~~~WGg~i 43 (112)
.|.|||--
T Consensus 52 ~GVWGG~t 59 (66)
T PF02467_consen 52 HGVWGGLT 59 (66)
T ss_pred eEEECCCc
Confidence 58898853
No 49
>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=20.26 E-value=1.1e+02 Score=19.48 Aligned_cols=13 Identities=38% Similarity=0.342 Sum_probs=7.6
Q ss_pred CChHHHHHHHHhh
Q 033766 40 GGEPELLMSSHVL 52 (112)
Q Consensus 40 Gg~iEl~Als~~~ 52 (112)
++.-+|.+||+++
T Consensus 31 ~~~d~L~~Ls~v~ 43 (87)
T PF11952_consen 31 APEDRLLCLSQVW 43 (87)
T ss_pred chHHHHHHHHHHH
Confidence 3445666666654
No 50
>PRK00446 cyaY frataxin-like protein; Provisional
Probab=20.25 E-value=1.4e+02 Score=19.58 Aligned_cols=17 Identities=18% Similarity=0.292 Sum_probs=11.9
Q ss_pred CCeEEEEECCCC-ccccc
Q 033766 81 ENPIRVLYHGYG-HYDLL 97 (112)
Q Consensus 81 ~~~i~L~Y~~~g-HYdsv 97 (112)
.+.|+|+-.+.| ||+-.
T Consensus 56 ~~QIWlas~sG~~hf~~~ 73 (105)
T PRK00446 56 LHELWLAAKSGGFHFDYK 73 (105)
T ss_pred hhheeEecCCCCccceec
Confidence 356999985544 99864
No 51
>TIGR00715 precor6x_red precorrin-6x reductase. This enzyme was found to be a monomer by gel filtration.
Probab=20.19 E-value=1.6e+02 Score=22.28 Aligned_cols=28 Identities=21% Similarity=0.316 Sum_probs=21.7
Q ss_pred cCCCCcCChHHHHHHHHhhCCCEEEEEe
Q 033766 34 RQPHSWGGEPELLMSSHVLKMPITVYMR 61 (112)
Q Consensus 34 ~~~~~WGg~iEl~Als~~~~~~I~V~~~ 61 (112)
+++|.=||-.|-...|+.+++|+.|+.-
T Consensus 204 K~SG~~Gg~~eKi~AA~~lgi~vivI~R 231 (256)
T TIGR00715 204 KASGEQGGELEKVKAAEALGINVIRIAR 231 (256)
T ss_pred cCCCCccchHHHHHHHHHcCCcEEEEeC
Confidence 3456667888888888888888888763
No 52
>PRK09726 antitoxin HipB; Provisional
Probab=20.11 E-value=2e+02 Score=17.64 Aligned_cols=34 Identities=9% Similarity=0.068 Sum_probs=22.1
Q ss_pred HHHHHhcCCCCcCChHHHHHHHHhhCCCEEEEEe
Q 033766 28 AYVRQMRQPHSWGGEPELLMSSHVLKMPITVYMR 61 (112)
Q Consensus 28 ~Y~~~m~~~~~WGg~iEl~Als~~~~~~I~V~~~ 61 (112)
..+.++.+...--.--.|..+|++|++++.++..
T Consensus 40 ~tis~~e~g~~~ps~~~l~~ia~~lgv~~~~~~~ 73 (88)
T PRK09726 40 ATISNFENNPDNTTLTTFFKILQSLELSMTLCDA 73 (88)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHHHcCCCcchhcc
Confidence 3444444433333445689999999999998543
No 53
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.10 E-value=51 Score=22.43 Aligned_cols=23 Identities=26% Similarity=0.697 Sum_probs=15.6
Q ss_pred ccccccCHHHHHHHhcC----CCCcCCh
Q 033766 19 EWFVEGDFDAYVRQMRQ----PHSWGGE 42 (112)
Q Consensus 19 e~fv~~~~~~Y~~~m~~----~~~WGg~ 42 (112)
.+|+. +|+.||..+.+ .|+|-|+
T Consensus 54 ~~Flt-eW~~Ya~~l~qql~~~g~~K~~ 80 (125)
T KOG4100|consen 54 QGFLT-EWERYAVALSQQLSSAGKWKGE 80 (125)
T ss_pred HHHHH-HHHHHHHHHHHHhhhcCccccc
Confidence 45553 69999987765 5777553
No 54
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.09 E-value=71 Score=25.22 Aligned_cols=19 Identities=11% Similarity=0.085 Sum_probs=15.6
Q ss_pred ChHHHHHHHHHhhCccccc
Q 033766 1 MMLLGQVADEFLLRRAETE 19 (112)
Q Consensus 1 m~lR~~~~~yi~~~~~~fe 19 (112)
+.+|+.|..-+-+..++|.
T Consensus 72 V~iRkrv~~i~Nk~e~dF~ 90 (309)
T TIGR00570 72 VDIRKRVLKIYNKREEDFP 90 (309)
T ss_pred HHHHHHHHHHHccchhccC
Confidence 4688888888888888886
Done!