Query psy3035
Match_columns 161
No_of_seqs 115 out of 344
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 23:50:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3035.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3035hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01401 Peptidase_M2: Angiote 100.0 4.5E-64 9.8E-69 462.6 13.0 155 1-158 114-272 (595)
2 KOG3690|consensus 100.0 2E-58 4.4E-63 420.7 15.0 158 1-158 132-294 (646)
3 cd06461 M2_ACE Peptidase famil 100.0 3.7E-50 8E-55 362.6 15.6 159 1-159 10-172 (477)
4 cd06459 M3B_Oligoendopeptidase 98.5 2.4E-06 5.2E-11 74.5 11.8 99 17-117 30-132 (427)
5 cd06258 Peptidase_M3_like The 98.3 1.9E-06 4.1E-11 74.4 8.1 76 57-134 2-77 (365)
6 PF01432 Peptidase_M3: Peptida 97.7 0.00061 1.3E-08 60.8 11.6 95 30-124 1-103 (458)
7 cd06455 M3A_TOP Peptidase M3 T 97.4 0.0019 4E-08 58.6 11.5 93 24-116 21-117 (472)
8 cd06457 M3A_MIP Peptidase M3 m 97.3 0.003 6.6E-08 57.1 10.8 90 30-120 2-94 (458)
9 PRK10911 oligopeptidase A; Pro 97.2 0.0033 7.2E-08 59.8 11.2 91 25-115 217-322 (680)
10 PRK10280 dipeptidyl carboxypep 97.2 0.006 1.3E-07 58.2 12.5 84 25-108 224-314 (681)
11 TIGR00181 pepF oligoendopeptid 96.6 0.037 8.1E-07 51.2 11.8 99 25-126 193-294 (591)
12 TIGR02289 M3_not_pepF oligoend 96.3 0.051 1.1E-06 50.2 11.0 95 21-117 144-246 (549)
13 cd06460 M32_Taq Peptidase fami 95.9 0.06 1.3E-06 48.6 9.1 79 37-115 10-90 (396)
14 TIGR02290 M3_fam_3 oligoendope 94.2 0.96 2.1E-05 42.1 12.3 101 21-126 187-290 (587)
15 KOG2089|consensus 93.0 0.95 2.1E-05 43.7 10.1 84 25-108 247-336 (718)
16 cd06456 M3A_DCP_Oligopeptidase 92.6 0.53 1.2E-05 42.5 7.6 61 56-116 3-70 (422)
17 COG0339 Dcp Zn-dependent oligo 91.3 3.4 7.4E-05 40.0 11.7 92 21-113 221-319 (683)
18 PF02074 Peptidase_M32: Carbox 68.7 40 0.00086 31.5 9.1 70 41-110 114-185 (494)
19 COG2317 Zn-dependent carboxype 66.0 40 0.00088 31.7 8.4 65 45-109 114-183 (497)
20 KOG2090|consensus 64.2 71 0.0015 31.2 9.9 96 26-122 239-337 (704)
21 COG1164 Oligoendopeptidase F [ 64.0 91 0.002 29.7 10.7 93 27-122 194-290 (598)
22 PF11593 Med3: Mediator comple 56.1 64 0.0014 29.4 7.7 91 21-113 8-102 (379)
23 PHA03102 Small T antigen; Revi 53.3 13 0.00028 29.5 2.7 46 97-142 44-89 (153)
24 TIGR02220 phg_TIGR02220 phage 47.5 17 0.00038 25.7 2.3 43 59-102 1-51 (77)
25 KOG2202|consensus 45.3 16 0.00034 31.7 2.1 72 54-142 37-115 (260)
26 PLN02498 omega-3 fatty acid de 44.3 11 0.00023 35.0 1.0 38 103-142 381-420 (450)
27 PHA02109 hypothetical protein 42.5 55 0.0012 27.3 4.8 23 100-122 210-232 (233)
28 PF10786 G6PD_bact: Glucose-6- 42.0 23 0.0005 29.8 2.6 55 56-110 149-215 (215)
29 PF14144 DOG1: Seed dormancy c 41.1 39 0.00084 23.9 3.3 56 25-88 4-60 (80)
30 PF04450 BSP: Peptidase of pla 36.6 51 0.0011 27.2 3.8 35 61-101 170-204 (205)
31 PF08880 QLQ: QLQ; InterPro: 34.7 33 0.00072 21.0 1.8 16 126-141 21-36 (37)
32 PTZ00458 acyl CoA binding prot 34.6 40 0.00086 24.5 2.5 30 41-70 54-83 (90)
33 PF02260 FATC: FATC domain; I 34.5 8 0.00017 23.0 -0.9 28 21-48 3-30 (33)
34 TIGR02453 conserved hypothetic 33.7 1.6E+02 0.0035 24.3 6.4 25 89-113 192-216 (217)
35 PF00768 Peptidase_S11: D-alan 33.7 44 0.00095 27.8 3.0 49 21-78 89-137 (240)
36 COG4493 Uncharacterized protei 33.1 52 0.0011 27.4 3.2 21 89-109 186-206 (209)
37 PF08039 Mit_proteolip: Mitoch 31.7 41 0.00089 23.0 2.0 45 91-135 2-57 (60)
38 PF05596 Taeniidae_ag: Taeniid 31.1 1.8E+02 0.0038 20.0 5.6 45 77-121 14-58 (64)
39 PRK10079 phosphonate metabolis 30.4 43 0.00093 27.2 2.4 27 103-134 11-37 (241)
40 PF00887 ACBP: Acyl CoA bindin 30.3 79 0.0017 22.0 3.5 31 41-71 54-84 (87)
41 PF15631 Imm-NTF2-2: NTF2 fold 29.1 30 0.00064 24.0 1.0 26 116-142 9-34 (66)
42 PF04749 PLAC8: PLAC8 family; 28.4 43 0.00093 23.4 1.8 14 109-122 66-79 (106)
43 PRK04196 V-type ATP synthase s 26.9 2.8E+02 0.0061 25.6 7.3 75 45-121 362-452 (460)
44 PF04174 CP_ATPgrasp_1: A circ 26.6 67 0.0014 28.5 3.1 41 97-137 7-47 (330)
45 PF13682 CZB: Chemoreceptor zi 26.3 1E+02 0.0022 19.6 3.2 19 99-117 50-68 (70)
46 PF13092 CENP-L: Kinetochore c 26.0 79 0.0017 24.9 3.1 79 36-120 39-132 (162)
47 PF02252 PA28_beta: Proteasome 25.3 1.9E+02 0.0041 22.8 5.1 58 64-121 81-139 (150)
48 PRK10001 D-alanyl-D-alanine ca 24.8 60 0.0013 29.4 2.5 48 21-78 119-167 (400)
49 cd00435 ACBP Acyl CoA binding 24.6 1E+02 0.0022 21.8 3.2 30 41-70 52-81 (85)
50 KOG3809|consensus 24.4 1E+02 0.0022 29.1 3.9 65 44-109 474-548 (583)
51 COG2187 Uncharacterized protei 24.3 1.1E+02 0.0024 27.4 4.0 58 61-122 241-304 (337)
52 KOG4771|consensus 24.1 45 0.00097 27.7 1.4 22 103-125 154-175 (210)
53 TIGR01841 phasin phasin family 23.9 2.6E+02 0.0056 19.5 6.0 56 59-115 5-60 (88)
54 PRK09532 DNA polymerase III su 23.0 1.7E+02 0.0038 29.3 5.5 44 47-105 728-771 (874)
55 TIGR01571 A_thal_Cys_rich unch 22.4 72 0.0016 23.2 2.1 13 110-122 63-75 (104)
56 PRK11397 dacD D-alanyl-D-alani 22.3 72 0.0016 28.8 2.5 48 21-78 116-164 (388)
57 COG2236 Predicted phosphoribos 21.8 67 0.0015 26.4 2.0 37 106-142 9-52 (192)
58 PRK11669 pbpG D-alanyl-D-alani 21.6 78 0.0017 27.7 2.5 48 21-78 112-160 (306)
59 PF11588 DUF3243: Protein of u 21.3 2.2E+02 0.0047 20.5 4.3 49 40-100 3-61 (81)
60 PF13021 DUF3885: Domain of un 21.2 1E+02 0.0022 19.1 2.2 15 100-114 17-31 (38)
61 COG5013 NarG Nitrate reductase 20.3 3.8E+02 0.0082 27.8 7.1 69 62-136 119-197 (1227)
62 PF09712 PHA_synth_III_E: Poly 20.3 5.7E+02 0.012 22.1 8.2 49 38-86 165-224 (293)
63 PF04328 DUF466: Protein of un 20.2 1.2E+02 0.0026 20.6 2.7 45 39-86 8-52 (65)
No 1
>PF01401 Peptidase_M2: Angiotensin-converting enzyme This Prosite motif covers only the active site.; InterPro: IPR001548 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M2 (clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The catalytic residues and zinc ligands have been identified, the zinc ion being ligated to two His residues within the motif HEXXH, showing that the enzyme belongs to the E sub-group of metalloproteases []. Pepetidyl-dipeptidase A (angiotensin-converting enzyme) is a mammalian enzyme responsible for cleavage of dipeptides from the C-termini of proteins, notably converting angiotensin I to angiotensin II []. The enzyme exists in two differentially transcribed forms, the most common of which is from lung endothelium; this contains two homologous domains that have arisen by gene duplication []. The testis-specific form contains only the C-terminal domain, arising from a duplicated promoter region present in intron 12 of the gene []. Both enzymatic forms are membrane proteins that are anchored by means of a C-terminal transmembrane domain. Both domains of the endothelial enzyme are active, but have differing kinetic constants []. ]. A number of insect enzymes have been shown to be similar to peptidyl-dipeptidase A, these containing a single catalytic domain.; GO: 0008237 metallopeptidase activity, 0008241 peptidyl-dipeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 2YDM_A 3BKL_A 2C6N_B 1UZE_A 3BKK_A 2C6F_B 2IUX_A 2IUL_A 2XYD_B 3NXQ_B ....
Probab=100.00 E-value=4.5e-64 Score=462.56 Aligned_cols=155 Identities=48% Similarity=0.878 Sum_probs=140.7
Q ss_pred CccccccceeecCCCCCCCCCCCchHHHHHHhhCCCHHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcChHH
Q psy3035 1 MESIYSTAKICQHKNEKNCNLTLEPELTEIFIGSRDPEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAAE 80 (161)
Q Consensus 1 M~~iYst~kvC~~~~~~~C~l~lepdl~~Ima~Srd~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g~ 80 (161)
|++||||||||..+ +.| +.|+|||++||++||||+||+++|++||++||+|||++|.+||+|+|+||++|||+|+|+
T Consensus 114 M~~iYst~kvC~~~--~~c-l~LePdl~~ima~Srd~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nG~~d~g~ 190 (595)
T PF01401_consen 114 MESIYSTAKVCPYD--GKC-LSLEPDLEEIMATSRDYDELLYAWEGWRDAVGPPMRPLYERYVELSNEAARLNGFKDTGE 190 (595)
T ss_dssp HHHHHHH-EEEESS--SEE-EETTTHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSHHH
T ss_pred HHHHhccccccCCC--Ccc-ccchhhHHHHHhccCCHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHcCCCCHHH
Confidence 88999999999874 568 999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCcccccccccc----ccccccccCCCCCC
Q psy3035 81 YWLDAYDTPDFRDQVAKLWDQIRPLYLQIHAYTRRRLNEKYGDKVVNRRGPIPAHLLGSCRQ----TTLEAEKPTKGAAP 156 (161)
Q Consensus 81 ~Wr~~Ye~~~~~~~~e~lw~qi~PLY~qLHayVR~~L~~~YG~~~v~~~gpIPAHLLGnmWa----ni~~~~~P~p~~~~ 156 (161)
|||+.||+++|+++|++||+||+|||+|||||||++|+++||+++|+.+||||||||||||| |||++|+|||+++.
T Consensus 191 ~Wr~~ye~~~~~~~~~~lw~~i~PLY~~LHayVR~~L~~~Yg~~~v~~~gpIPAHLLGnmwaq~W~ni~~~~~P~p~~~~ 270 (595)
T PF01401_consen 191 YWRSSYEMPNFEQELERLWQQIKPLYKQLHAYVRRKLREKYGDDVVPPDGPIPAHLLGNMWAQSWSNIYDLVLPYPDKPS 270 (595)
T ss_dssp HHHGGG-CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS-TTS-EEGGGSSSTTSS-GGGGHHHH-STTTS--
T ss_pred HHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccCCCCCCccHHHHHHHHHHHHhhhhccccCCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999 99999999999987
Q ss_pred CC
Q psy3035 157 EE 158 (161)
Q Consensus 157 ~~ 158 (161)
+|
T Consensus 271 ~d 272 (595)
T PF01401_consen 271 LD 272 (595)
T ss_dssp S-
T ss_pred CC
Confidence 65
No 2
>KOG3690|consensus
Probab=100.00 E-value=2e-58 Score=420.71 Aligned_cols=158 Identities=42% Similarity=0.824 Sum_probs=155.1
Q ss_pred CccccccceeecCCCCCCCCCCCchHHHHHHhhCCCHHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcChHH
Q psy3035 1 MESIYSTAKICQHKNEKNCNLTLEPELTEIFIGSRDPEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAAE 80 (161)
Q Consensus 1 M~~iYst~kvC~~~~~~~C~l~lepdl~~Ima~Srd~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g~ 80 (161)
|+++|++++||++++++.|+|.|+|+|.+||++||||+||.|+|++||+++|++||+.|.+||+|+|+||++|||.+.|+
T Consensus 132 m~~~y~~~~vC~y~~p~~~~L~l~P~l~~i~~~Srd~~eL~~~W~~wr~~~g~~~r~~y~~yv~L~~e~A~lNg~~~~gd 211 (646)
T KOG3690|consen 132 MSTNYNTATVCAYDQPSACCLLLEPQLQSIMANSRDYDELQWYWVEWRRKIGKAMRQSYEEYVDLSNEAAQLNGYVNGGD 211 (646)
T ss_pred HHhhcCCceeeCCCCCCCcceecCccHHHHHhccCCHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcCCCCHHH
Confidence 78999999999999999888999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcCCc-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCcccccccccc----ccccccccCCCCC
Q psy3035 81 YWLDAYDTP-DFRDQVAKLWDQIRPLYLQIHAYTRRRLNEKYGDKVVNRRGPIPAHLLGSCRQ----TTLEAEKPTKGAA 155 (161)
Q Consensus 81 ~Wr~~Ye~~-~~~~~~e~lw~qi~PLY~qLHayVR~~L~~~YG~~~v~~~gpIPAHLLGnmWa----ni~~~~~P~p~~~ 155 (161)
|||+.||++ +|+++||++|+||+|||++||||||++|++.||++.++++||||||||||||+ |+|++++|||+++
T Consensus 212 yW~~~yE~~~~~~~~ld~i~~ei~PlY~~LHAYvRr~L~~~Ygp~~i~~~gpiPahLlgnm~gq~Ws~~y~~~~P~pe~~ 291 (646)
T KOG3690|consen 212 YWRLAYETPGDFEQDLDAIFEEIRPLYRQLHAYVRRKLRGAYGPDGISRDGPIPAHLLGNMWGQDWSNHYDLTTPFPERP 291 (646)
T ss_pred HHHHHhcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccCCCCCCcCHHHHhhhhccchHhhhhcccCCCCCC
Confidence 999999999 79999999999999999999999999999999999999999999999999987 9999999999999
Q ss_pred CCC
Q psy3035 156 PEE 158 (161)
Q Consensus 156 ~~~ 158 (161)
.+|
T Consensus 292 ~~d 294 (646)
T KOG3690|consen 292 LID 294 (646)
T ss_pred CCc
Confidence 886
No 3
>cd06461 M2_ACE Peptidase family M2 Angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor ocatapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ACE and the sperm-specific germinal ACE, both encoded by the same gene through transcription from alternative promoters. Somatic ACE has two tandem active sites with distinct catalytic properties, whereas germinal ACE, the function of which is largely unknown, has just a single active site. Recently, an ACE homolog, ACE2, has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function. ACE homologs (also known as members of the M2 gluzincin family) have been found in a wide variety of species, including those that neither h
Probab=100.00 E-value=3.7e-50 Score=362.56 Aligned_cols=159 Identities=49% Similarity=0.899 Sum_probs=153.1
Q ss_pred CccccccceeecCCCCCCCCCCCchHHHHHHhhCCCHHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcChHH
Q psy3035 1 MESIYSTAKICQHKNEKNCNLTLEPELTEIFIGSRDPEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAAE 80 (161)
Q Consensus 1 M~~iYst~kvC~~~~~~~C~l~lepdl~~Ima~Srd~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g~ 80 (161)
|++|||+++||.+.++..|++.++|+|..||++|+|+++|+++|++||+++|++|++.|.++|+|.|++|+.|||+|.++
T Consensus 10 ~~~iy~~~~v~~~~~~~~~~~~~~~~l~~i~~~s~D~~~r~~aW~~w~~~~g~~~~~~y~~lV~lrn~~A~~~Gf~n~~~ 89 (477)
T cd06461 10 METIYSTAKVCPYDDPGDCCLLLEPDLESIMAKSRDYDELLYAWEGWRDAVGPPMRPLYERYVELANEAAKLNGFVDAGE 89 (477)
T ss_pred HHHHHhceeecCCCCcccccccCHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHcCCCCHHH
Confidence 67899999999988877777999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCcccccccccc----ccccccccCCCCCC
Q psy3035 81 YWLDAYDTPDFRDQVAKLWDQIRPLYLQIHAYTRRRLNEKYGDKVVNRRGPIPAHLLGSCRQ----TTLEAEKPTKGAAP 156 (161)
Q Consensus 81 ~Wr~~Ye~~~~~~~~e~lw~qi~PLY~qLHayVR~~L~~~YG~~~v~~~gpIPAHLLGnmWa----ni~~~~~P~p~~~~ 156 (161)
|||+.||+++|.+.+++||++|+|||++||+|||++|...||.++++++||||||||||||+ |||+++.|||+++.
T Consensus 90 ~wR~~Ye~~d~~~~~e~i~~~v~Ply~~Lh~~~r~~L~~~y~~~~~d~~~~iPahl~gn~~~q~W~~~~~~~~p~p~~~~ 169 (477)
T cd06461 90 YWRSEYETPDFEQDVERLWEELKPLYLQLHAYVRRKLRKKYGDDVVNRDGPIPAHLLGNMWAQSWSNIYDLVKPYPGKPL 169 (477)
T ss_pred HhHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCCCCccccccCccccccccccccccCCCCCCC
Confidence 99999999999999999999999999999999999999999988899999999999999988 89999999999887
Q ss_pred CCC
Q psy3035 157 EEG 159 (161)
Q Consensus 157 ~~~ 159 (161)
++.
T Consensus 170 ~dv 172 (477)
T cd06461 170 LDV 172 (477)
T ss_pred CCh
Confidence 653
No 4
>cd06459 M3B_Oligoendopeptidase_F Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the PepF Bacillus amyloliquefaciens oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over expressed from a multicopy plasmid.
Probab=98.46 E-value=2.4e-06 Score=74.49 Aligned_cols=99 Identities=17% Similarity=0.127 Sum_probs=84.6
Q ss_pred CCCCCCCchHHHHHHhhCCCHHHHHHHHHHHHHhh---chhHHHhHHHHHHhHHHHHHHcCCcChHHHHhhhcCC-chHH
Q psy3035 17 KNCNLTLEPELTEIFIGSRDPEELRHYWTEFRKKS---GKQVRNHYKQYVDLENEVAVKNNFTDAAEYWLDAYDT-PDFR 92 (161)
Q Consensus 17 ~~C~l~lepdl~~Ima~Srd~~eL~~~W~~Wr~~v---g~~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~Ye~-~~~~ 92 (161)
+.+ +.|.+ ....+.++.|.+.++.+|.+|.+.. +..+.+.+.+.|++.++.|+..||++..+++...+++ ++..
T Consensus 30 G~~-~~l~~-~~~~~~~~~d~~~Rk~a~~a~~~~~~~~~~~~~~~l~~lv~~r~~~A~~~Gy~~~~~~~l~~~~~~~~~~ 107 (427)
T cd06459 30 GEE-LTLSQ-NLSNLLESPDREVRKKAFEALYKAYEKYENTLAAILNTLVKLRLTLAKLRGYDSYLEAALFNNNIPEDVY 107 (427)
T ss_pred CeE-EeccH-HHHHHHhCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHhhccCCCCHHHH
Confidence 445 88877 6777888899999999999998765 2357788999999999999999999999999999984 4788
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3035 93 DQVAKLWDQIRPLYLQIHAYTRRRL 117 (161)
Q Consensus 93 ~~~e~lw~qi~PLY~qLHayVR~~L 117 (161)
+.+.++...+.|+++++++..++.|
T Consensus 108 ~~l~~v~~~~~p~~~~~~~~~~~~l 132 (427)
T cd06459 108 DFLIAVVKENVPLLHRYLKLKKKLL 132 (427)
T ss_pred HHHHHHHHHhcHHHHHHHHHHHHHh
Confidence 8899999999999999988765443
No 5
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=98.34 E-value=1.9e-06 Score=74.44 Aligned_cols=76 Identities=17% Similarity=0.274 Sum_probs=66.9
Q ss_pred HhHHHHHHhHHHHHHHcCCcChHHHHhhhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCcc
Q psy3035 57 NHYKQYVDLENEVAVKNNFTDAAEYWLDAYDTPDFRDQVAKLWDQIRPLYLQIHAYTRRRLNEKYGDKVVNRRGPIPA 134 (161)
Q Consensus 57 ~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~Ye~~~~~~~~e~lw~qi~PLY~qLHayVR~~L~~~YG~~~v~~~gpIPA 134 (161)
+.+.++|+|.|+.|+..||++..++|...++.. -.+.|++++++|++.+..+++.++.+|.+..+.+ ....+.+|+
T Consensus 2 ~~l~~lv~lr~e~A~~lGy~~~~d~~l~~~~~~-~~e~v~~f~~~l~~~~~p~~~~~~~~l~~~~~~~-~~~~~~~~~ 77 (365)
T cd06258 2 ALLEELVSLRNQLARLLGYENFADYKLALQEAK-SPETVEGFFEELKRKLRPLLAKLREEISAAKQKE-EEIYGELPA 77 (365)
T ss_pred hHHHHHHHHHHHHHHHcCCCCHHHHHHHHHhcC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-cCCcccccc
Confidence 578999999999999999999999999999876 4679999999999999999999999999887644 445567775
No 6
>PF01432 Peptidase_M3: Peptidase family M3 This Prosite motif covers only the active site. This family belongs to family M3 of the peptidase classification.; InterPro: IPR001567 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M3 (clan MA(E)), subfamilies M3A and M3B. The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The Thimet oligopeptidase family, is a large family of archaeal, bacterial and eukaryotic oligopeptidases that cleave medium sized peptides. The group contains: mitochondrial intermediate peptidase (3.4.24.59 from EC) Neurolysin, mitochondrial precursor, (3.4.24.16 from EC) Thimet oligopeptidase (3.4.24.15 from EC) Dipeptidyl carboxypeptidase (3.4.15.5 from EC) Oligopeptidase A (3.4.24.70 from EC) Oligoendopeptidase F ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QR4_B 3CE2_A 1Y79_1 2H1J_A 2H1N_A 2O36_A 1S4B_P 2O3E_A 1I1I_P.
Probab=97.67 E-value=0.00061 Score=60.78 Aligned_cols=95 Identities=17% Similarity=0.254 Sum_probs=75.2
Q ss_pred HHhhCCCHHHHHHHHHHHHHhhch---hH--HHhHHHHHHhHHHHHHHcCCcChHHHHhhh--c-CCchHHHHHHHHHHH
Q psy3035 30 IFIGSRDPEELRHYWTEFRKKSGK---QV--RNHYKQYVDLENEVAVKNNFTDAAEYWLDA--Y-DTPDFRDQVAKLWDQ 101 (161)
Q Consensus 30 Ima~Srd~~eL~~~W~~Wr~~vg~---~~--r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~--Y-e~~~~~~~~e~lw~q 101 (161)
+|.+|.|.+.++.+|.+|.+.... .. ...+.+.+.+-++.|+..||++..++=... - ..++....++++.++
T Consensus 1 ~l~~~~d~~~Rk~~~~a~~~~~~~~~~~~~n~~~l~~l~~~R~~~A~llGy~s~~~~~l~~~m~~~~~~v~~fL~~~~~~ 80 (458)
T PF01432_consen 1 VLKYSPDRELRKKAYRAYYSRYSDNQPTLDNAAILNELLKLRNELAKLLGYPSYAEYSLQDKMAKNPENVLDFLDELVKK 80 (458)
T ss_dssp HHHC-S-HHHHHHHHHHHHTTTHHTHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHTTSTTTSHHHHHHHHHHHHHH
T ss_pred CCCcCcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhhhcCChHHHHHHHHHHHHH
Confidence 588999999999999999976532 34 888999999999999999999999974433 2 234788999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCC
Q psy3035 102 IRPLYLQIHAYTRRRLNEKYGDK 124 (161)
Q Consensus 102 i~PLY~qLHayVR~~L~~~YG~~ 124 (161)
++|+.++...-.+.-..+..|.+
T Consensus 81 ~~p~~~~~~~~l~~~~~~~~g~~ 103 (458)
T PF01432_consen 81 LKPLLERELELLKKLKKKRLGLE 103 (458)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-S
T ss_pred HHHHHHHHHHHHHHHHHHhcCCc
Confidence 99999998888888777777754
No 7
>cd06455 M3A_TOP Peptidase M3 Thimet oligopeptidase (TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase 24.15; soluble metallo-endopeptidase; EC 3.4.24.15) family also includes neurolysin (endopeptidase 24.16, microsomal endopeptidase, mitochondrial oligopeptidase M, neurotensin endopeptidase, soluble angiotensin II-binding protein, thimet oligopeptidase II) which hydrolyzes oligopeptides such as neurotensin, bradykinin and dynorphin A. TOP and neurolysin are neuropeptidases expressed abundantly in the testis, but also found in the liver, lung and kidney. They are involved in the metabolism of neuropeptides under 20 amino acid residues long and cleave most bioactive peptides at the same sites, but recognize different positions on some naturally occurring and synthetic peptides; they cleave at distinct sites on the 13-residue bioactive peptide neurotensin, which modulates central dopaminergic and cholinergic circuits. TOP has been shown to degrade peptides released by the proteasom
Probab=97.44 E-value=0.0019 Score=58.59 Aligned_cols=93 Identities=18% Similarity=0.365 Sum_probs=76.7
Q ss_pred chHHHHHHhhCCCHHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcChHHHHhhh-c--CCchHHHHHHHHHH
Q psy3035 24 EPELTEIFIGSRDPEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAAEYWLDA-Y--DTPDFRDQVAKLWD 100 (161)
Q Consensus 24 epdl~~Ima~Srd~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~-Y--e~~~~~~~~e~lw~ 100 (161)
.|.+..+|..+.|.+.++.+|.++...-....++.+.+.|++.++.|+..||++..++=... - ..+++.+.++.+.+
T Consensus 21 ~~~~~~~l~~~~d~~~Rk~~~~a~~~~~~~~n~~~l~~ll~~R~~~A~l~Gy~s~a~~~l~~~m~~s~e~v~~fl~~l~~ 100 (472)
T cd06455 21 YPDYFPVMKYAKNAETRKAMWVAFQNRGGPENVPLLEELVALRHELARLLGYKSHADYVLEDRMAKSPETVRDFLEDLSK 100 (472)
T ss_pred CccHHHHHhcCCCHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 37899999999999999999999997634778899999999999999999999999985533 2 12377788999999
Q ss_pred HHHHHHH-HHHHHHHHH
Q psy3035 101 QIRPLYL-QIHAYTRRR 116 (161)
Q Consensus 101 qi~PLY~-qLHayVR~~ 116 (161)
.++|+.+ +|+.|.+.+
T Consensus 101 ~~~p~~~~e~~~l~~~k 117 (472)
T cd06455 101 KLKPLAEKELAELLELK 117 (472)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 9999875 466665543
No 8
>cd06457 M3A_MIP Peptidase M3 mitochondrial intermediate peptidase (MIP; EC 3.4.24.59) belongs to the widespread subfamily M3A, that show similarity to the Thimet oligopeptidase (TOP). It is one of three peptidases responsible for the proteolytic processing of both, nuclear and mitochondrial encoded precursor polypeptides targeted to the various subcompartments of the mitochondria. It cleaves intermediate-size proteins initially processed by mitochondrial processing peptidase (MPP) to yield a processing intermediate with a typical N-terminal octapeptide that is sequentially cleaved by MIP to mature-size protein. MIP cleaves precursor proteins of respiratory components, including subunits of the electron transport chain and tri-carboxylic acid cycle enzymes, and components of the mitochondrial genetic machinery, including ribosomal proteins, translation factors, and proteins required for mitochondrial DNA metabolism. It has been suggested that the human MIP (HMIP polypeptide; gene symbo
Probab=97.27 E-value=0.003 Score=57.13 Aligned_cols=90 Identities=12% Similarity=0.115 Sum_probs=72.2
Q ss_pred HHhhCCCHHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcChHHHHhhh--cC-CchHHHHHHHHHHHHHHHH
Q psy3035 30 IFIGSRDPEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAAEYWLDA--YD-TPDFRDQVAKLWDQIRPLY 106 (161)
Q Consensus 30 Ima~Srd~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~--Ye-~~~~~~~~e~lw~qi~PLY 106 (161)
||+.+.|.+.++.+|.++... +....+.+.+.|.+-++.|++.||+|..+|=... -. .++..+.+++|++.++|+.
T Consensus 2 ~l~~~~d~~~Rk~a~~a~~~~-~~~n~~il~~l~~lR~e~A~llGy~sya~~~l~~~ma~spe~v~~fL~~l~~~~~p~~ 80 (458)
T cd06457 2 LLASVPNESVRELVYRAFHSS-SAEQLELLEELLSSRAELAQLLGFESYAHRALRGKMAKNPENVMEFLTELSEKLRPRA 80 (458)
T ss_pred ccccCCCHHHHHHHHHHHhhh-hhhHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence 688999999999999999975 5778899999999999999999999999975432 22 2478889999999999998
Q ss_pred HHHHHHHHHHHHHH
Q psy3035 107 LQIHAYTRRRLNEK 120 (161)
Q Consensus 107 ~qLHayVR~~L~~~ 120 (161)
++=..-++....+.
T Consensus 81 ~~e~~~L~~~~~~~ 94 (458)
T cd06457 81 EEELAVLRDMKRKV 94 (458)
T ss_pred HHHHHHHHHHHHHh
Confidence 66444344433333
No 9
>PRK10911 oligopeptidase A; Provisional
Probab=97.23 E-value=0.0033 Score=59.84 Aligned_cols=91 Identities=14% Similarity=0.226 Sum_probs=76.1
Q ss_pred hHHHHHHhhCCCHHHHHHHHHHHHHhhch--------hHHHhHHHHHHhHHHHHHHcCCcChHHHHhhh---cCCchHHH
Q psy3035 25 PELTEIFIGSRDPEELRHYWTEFRKKSGK--------QVRNHYKQYVDLENEVAVKNNFTDAAEYWLDA---YDTPDFRD 93 (161)
Q Consensus 25 pdl~~Ima~Srd~~eL~~~W~~Wr~~vg~--------~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~---Ye~~~~~~ 93 (161)
|.+.-+|..+.|.+.++.+|.++...... ...+.+.+.|.|-++.|++.||++..+|=... +..++..+
T Consensus 217 p~~~p~L~~~~drelRk~~y~A~~~r~~~~~~~~~~~dN~~il~eil~lR~e~AkLLGy~syAd~~L~~kma~spe~V~~ 296 (680)
T PRK10911 217 PSYLPVMTYCDNQALREEMYRAYSTRASDQGPNAGKWDNSEVMEEILALRHELAQLLGFENYADKSLATKMAENPQQVLD 296 (680)
T ss_pred CcHHHHHhhCCCHHHHHHHHHHHHhhhhhccCcccccchHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHhCCCHHHHHH
Confidence 78888999999999999999999965432 25789999999999999999999999985542 33458899
Q ss_pred HHHHHHHHHHHHHH----HHHHHHHH
Q psy3035 94 QVAKLWDQIRPLYL----QIHAYTRR 115 (161)
Q Consensus 94 ~~e~lw~qi~PLY~----qLHayVR~ 115 (161)
.+++|+..++|+.+ +|+++-+.
T Consensus 297 fL~~l~~~~~p~a~~El~~L~~~~k~ 322 (680)
T PRK10911 297 FLTDLAKRARPQGEKELAQLRAFAKA 322 (680)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999986 56666554
No 10
>PRK10280 dipeptidyl carboxypeptidase II; Provisional
Probab=97.20 E-value=0.006 Score=58.23 Aligned_cols=84 Identities=12% Similarity=0.099 Sum_probs=72.7
Q ss_pred hHHHHHHhhCCCHHHHHHHHHHHHHhhch----hHHHhHHHHHHhHHHHHHHcCCcChHHHHhh---hcCCchHHHHHHH
Q psy3035 25 PELTEIFIGSRDPEELRHYWTEFRKKSGK----QVRNHYKQYVDLENEVAVKNNFTDAAEYWLD---AYDTPDFRDQVAK 97 (161)
Q Consensus 25 pdl~~Ima~Srd~~eL~~~W~~Wr~~vg~----~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~---~Ye~~~~~~~~e~ 97 (161)
|+..-+|+.++|.+.++.+|.++...... ...+.+.+.|+|-++.|++.||++..+|=.. .+..++....++.
T Consensus 224 ~~~~p~l~~~~dr~~Re~~~~A~~~r~~~~~~~dn~~il~~ll~lR~e~A~lLGf~~yA~~~l~~kMa~spe~V~~FL~~ 303 (681)
T PRK10280 224 TTQQPALAELRDRQTRENLFAAGWTRAEKGDANDTRAIIQRLVEIRAQQAKLLGFPHYAAWKIADQMAKTPEAALNFMRE 303 (681)
T ss_pred CcHhHHHhcCCCHHHHHHHHHHHHhhhccCCchhHHHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHCCCHHHHHHHHHH
Confidence 79999999999999999999999987543 5788999999999999999999999998543 3455688888999
Q ss_pred HHHHHHHHHHH
Q psy3035 98 LWDQIRPLYLQ 108 (161)
Q Consensus 98 lw~qi~PLY~q 108 (161)
|+..++|.-++
T Consensus 304 L~~~~~~~a~~ 314 (681)
T PRK10280 304 IVPAARQRASD 314 (681)
T ss_pred HHHHHHHHHHH
Confidence 99999888753
No 11
>TIGR00181 pepF oligoendopeptidase F. This family represents the oligoendopeptidase F clade of the family of larger M3 or thimet (for thiol-dependent metallopeptidase) oligopeptidase family. Lactococcus lactis PepF hydrolyzed peptides of 7 and 17 amino acids with fairly broad specificity. The homolog of lactococcal PepF in group B Streptococcus was named PepB (PubMed:8757883), with the name difference reflecting a difference in species of origin rather activity; substrate profiles were quite similar. Differences in substrate specificity should be expected in other species. The gene is duplicated in Lactococcus lactis on the plasmid that bears it. A shortened second copy is found in Bacillus subtilis.
Probab=96.55 E-value=0.037 Score=51.20 Aligned_cols=99 Identities=16% Similarity=0.142 Sum_probs=75.4
Q ss_pred hHHHHHHhhCCCHHHHHHHHHHHHHhhch---hHHHhHHHHHHhHHHHHHHcCCcChHHHHhhhcCCchHHHHHHHHHHH
Q psy3035 25 PELTEIFIGSRDPEELRHYWTEFRKKSGK---QVRNHYKQYVDLENEVAVKNNFTDAAEYWLDAYDTPDFRDQVAKLWDQ 101 (161)
Q Consensus 25 pdl~~Ima~Srd~~eL~~~W~~Wr~~vg~---~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~Ye~~~~~~~~e~lw~q 101 (161)
|....+|++|.|.+.++.+|+++.+.-.. .+...|...|.+.++.|+..||++.-++=...=+. =++.++.|++.
T Consensus 193 ~~~~~~l~~~~dr~~Rk~a~~a~~~~~~~~~~~~a~~l~~~v~~r~~~A~lrGy~s~~~~~l~~~~i--~~~v~~~l~~~ 270 (591)
T TIGR00181 193 STYENFLQKNKDREIRKKAYESFYKAYRKHKNTFAALYYGNVQKNVFLAKLRNYESYIDASLFSDEV--PREVYDNLYDT 270 (591)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHhccCCC--CHHHHHHHHHH
Confidence 57888999999999999999999876543 57888999999999999999999999865433222 23456777787
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCC
Q psy3035 102 IRPLYLQIHAYTRRRLNEKYGDKVV 126 (161)
Q Consensus 102 i~PLY~qLHayVR~~L~~~YG~~~v 126 (161)
|+..+..+|.|.+.|= +..|-+.+
T Consensus 271 v~~~~~~~~~y~~~k~-k~lg~~~l 294 (591)
T TIGR00181 271 IKKNAPVLQRYYKLRK-KVLKLDKM 294 (591)
T ss_pred HHHhhHHHHHHHHHHH-HHhCCCcc
Confidence 8877788888887553 34464433
No 12
>TIGR02289 M3_not_pepF oligoendopeptidase, M3 family. This family consists of probable oligoendopeptidases in the M3 family, related to lactococcal PepF and group B streptococcal PepB (TIGR00181) but in a distinct clade with considerable sequence differences. The likely substrate is small peptides and not whole proteins, as with PepF, but members are not characterized and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family.
Probab=96.28 E-value=0.051 Score=50.20 Aligned_cols=95 Identities=16% Similarity=0.355 Sum_probs=74.6
Q ss_pred CCCchHHHHHHhhCCCHHHHHHHHHHHHHhh---chhHHHhHHHHHHhHHHHHHHcCCcChHHHHh---hh--cCCchHH
Q psy3035 21 LTLEPELTEIFIGSRDPEELRHYWTEFRKKS---GKQVRNHYKQYVDLENEVAVKNNFTDAAEYWL---DA--YDTPDFR 92 (161)
Q Consensus 21 l~lepdl~~Ima~Srd~~eL~~~W~~Wr~~v---g~~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr---~~--Ye~~~~~ 92 (161)
+.+ .++..+|.. .|.+.++.+|.+..+.. ...+...|.+.|.+.++.|+..||++..++=. .. |..+++.
T Consensus 144 ~~l-~~~~~~l~~-~dr~~Rk~a~~a~~~~~~~~~~~~~~il~~lv~~R~~~Akl~Gy~s~~e~~~~~~~r~~~~~e~v~ 221 (549)
T TIGR02289 144 KTL-SQLKPYLQD-PNRSTRKKAWYARSEFFAVVEEELDRIYDELVQIRTQIALNLGFSNYRDYMYKLKNRTDYSAEDCY 221 (549)
T ss_pred ccH-HHhhHHhhC-CCHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcccCCCHHHHH
Confidence 556 578777775 89999999999998643 34577899999999999999999999999842 23 5666788
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3035 93 DQVAKLWDQIRPLYLQIHAYTRRRL 117 (161)
Q Consensus 93 ~~~e~lw~qi~PLY~qLHayVR~~L 117 (161)
+.++.+.+.+.|+.+.+...-+++|
T Consensus 222 ~~l~~v~~~~~p~~~~~~~~k~k~l 246 (549)
T TIGR02289 222 KYRESILKYVVPLWTKLRKIKKKRL 246 (549)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHhC
Confidence 8888899999999877666544433
No 13
>cd06460 M32_Taq Peptidase family M32 is a subclass of metallocarboxypeptidases which are distributed mainly in bacteria and archaea, and contain a HEXXH motif that coordinates a divalent cation such as Zn2+ or Co2+, so far only observed in the active site of neutral metallopeptidases but not in carboxypeptidases. M32 includes the thermostable carboxypeptidases (E.C. 3.4.17.19) from Thermus aquaticus (TaqCP) and Pyrococcus furiosus (PfuCP), which have broad specificities toward a wide range of C-terminal substrates that include basic, aromatic, neutral and polar amino acids. These enzymes have a similar fold to the M3 peptidases such as neurolysin and the M2 angiotensin converting enzyme (ACE). Novel peptidases from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, are the first eukaryotic M32 enzymes identified so far, thus making these enzymes an attractive potential target for drug development against these o
Probab=95.85 E-value=0.06 Score=48.61 Aligned_cols=79 Identities=16% Similarity=0.269 Sum_probs=67.7
Q ss_pred HHHHHHHHHHHHHhhc-hhHHHhHHHHHHhHHHHHHHcCC-cChHHHHhhhcCCchHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3035 37 PEELRHYWTEFRKKSG-KQVRNHYKQYVDLENEVAVKNNF-TDAAEYWLDAYDTPDFRDQVAKLWDQIRPLYLQIHAYTR 114 (161)
Q Consensus 37 ~~eL~~~W~~Wr~~vg-~~~r~~y~~~V~L~N~aA~~nGf-~d~g~~Wr~~Ye~~~~~~~~e~lw~qi~PLY~qLHayVR 114 (161)
-.+-..+|..-|.+.. ...+|.+++.|+|..+.|...|+ .+.-+.+...||..--.+.++.+|.+|++....|.+-|.
T Consensus 10 ~~~~~~~W~~ar~~~df~~f~p~L~~~v~l~re~a~~~~~~~~~YdaLLd~ye~g~~~~~id~~F~~lk~~l~~l~~~v~ 89 (396)
T cd06460 10 TSEAEQAWREARKKNDFALFAPYLEKIVELSREIAEYLGYEKHPYDALLDLYEPGMTTAKLDAIFAELKAGLVPLLKKVL 89 (396)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556788999998776 56889999999999999999988 666778999999877789999999999999999888775
Q ss_pred H
Q psy3035 115 R 115 (161)
Q Consensus 115 ~ 115 (161)
.
T Consensus 90 ~ 90 (396)
T cd06460 90 E 90 (396)
T ss_pred h
Confidence 5
No 14
>TIGR02290 M3_fam_3 oligoendopeptidase, pepF/M3 family. The M3 family of metallopeptidases contains several distinct clades. Oligoendopeptidase F as characterized in Lactococcus, the functionally equivalent oligoendopeptidase B of group B Streptococcus, and closely related sequences are described by TIGR00181. The present family is quite similar but forms a distinct clade, and a number of species have one member of each. A greater sequence difference separates members of TIGR02289, probable oligoendopeptidases of the M3 family that probably should not be designated PepF.
Probab=94.23 E-value=0.96 Score=42.07 Aligned_cols=101 Identities=11% Similarity=0.129 Sum_probs=70.2
Q ss_pred CCCchHHHHHHhhCCCHHHHHHHHHHHHHhhc---hhHHHhHHHHHHhHHHHHHHcCCcChHHHHhhhcCCchHHHHHHH
Q psy3035 21 LTLEPELTEIFIGSRDPEELRHYWTEFRKKSG---KQVRNHYKQYVDLENEVAVKNNFTDAAEYWLDAYDTPDFRDQVAK 97 (161)
Q Consensus 21 l~lepdl~~Ima~Srd~~eL~~~W~~Wr~~vg---~~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~Ye~~~~~~~~e~ 97 (161)
+++ ..+..+ .+|.|.+.++.+|++..+... ..+-..|...|...++.||.-||++.-++=...-+.+ .+.++.
T Consensus 187 ~t~-~~~~~~-l~~~dr~~Rk~a~~~~~~~~~~~~~~~a~~l~~~v~~~~~~a~~rgy~s~~e~~l~~~~i~--~~~~~~ 262 (587)
T TIGR02290 187 LSL-EQALNL-LRDPDAEVRKKAFKALLKAWEKNAPTLAAILNALAGDRLTEYRLRGYDHPLEPRLLYNRID--QETLDA 262 (587)
T ss_pred cCH-HHHHHH-HhCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHhhccCCCC--HHHHHH
Confidence 444 467775 467799999999998887542 3455566889999999999999999988544333333 355666
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Q psy3035 98 LWDQIRPLYLQIHAYTRRRLNEKYGDKVV 126 (161)
Q Consensus 98 lw~qi~PLY~qLHayVR~~L~~~YG~~~v 126 (161)
+++.|+--+..+|.|.+.+ ++..|-+.+
T Consensus 263 l~~~v~~~~p~~~~y~~~k-~~~lgl~~l 290 (587)
T TIGR02290 263 MLEAIKENYPLFRRYYKLK-AKLLGKEKL 290 (587)
T ss_pred HHHHHHHhhHHHHHHHHHH-HHHhCCCcc
Confidence 7776666666678887654 445674443
No 15
>KOG2089|consensus
Probab=93.01 E-value=0.95 Score=43.70 Aligned_cols=84 Identities=15% Similarity=0.294 Sum_probs=71.7
Q ss_pred hHHHHHHhhCCCHHHHHHHHHHHHHhhch---hHHHhHHHHHHhHHHHHHHcCCcChHHHHhhh--c-CCchHHHHHHHH
Q psy3035 25 PELTEIFIGSRDPEELRHYWTEFRKKSGK---QVRNHYKQYVDLENEVAVKNNFTDAAEYWLDA--Y-DTPDFRDQVAKL 98 (161)
Q Consensus 25 pdl~~Ima~Srd~~eL~~~W~~Wr~~vg~---~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~--Y-e~~~~~~~~e~l 98 (161)
|++--+|..-.+...++.+|.+|-...|. ..-..-.+.+.|--+-|+..||+...+|=... - .+++....++.|
T Consensus 247 p~~~pvmk~c~~r~tR~~v~~A~~~ra~~~~~eNs~ii~~l~~lR~~lAklLGY~t~Ad~~L~~kMa~ss~tv~~fl~dL 326 (718)
T KOG2089|consen 247 PHYFPVMKHCKIRQTRKTVWRAYNSRASEGDLENSAIIEQLLKLRLELAKLLGYSTYADYSLAMKMAKSSETVVEFLDDL 326 (718)
T ss_pred cchhHHHHhCCcHHHHHHHHHHHhccCCcccccccHHHHHHHHHHHHHHHHhCchhHHHHHHHHHhhcCcHHHHHHHHHH
Confidence 79999999999999999999999998887 57778899999999999999999999984422 1 223677889999
Q ss_pred HHHHHHHHHH
Q psy3035 99 WDQIRPLYLQ 108 (161)
Q Consensus 99 w~qi~PLY~q 108 (161)
-+.|+||=..
T Consensus 327 ~~kL~pl~~~ 336 (718)
T KOG2089|consen 327 SQKLRPLGID 336 (718)
T ss_pred HHHhhhcchh
Confidence 9999998655
No 16
>cd06456 M3A_DCP_Oligopeptidase_A Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and proteins, the smallest substrate being N-blocked tripeptides and unblocked tetrapeptides. DCP from E. coli is inhibited by the anti-hypertensive drug captopril, an inhibitor of the mammalian angiotensin converting enzyme (ACE, also called peptidyl dipeptidase A). Oligopeptidase A (OpdA) may play a specific role in the degradation of signal peptides after they are released from precursor forms of secreted proteins. It can also cleave N-acetyl-L-Ala.
Probab=92.56 E-value=0.53 Score=42.46 Aligned_cols=61 Identities=20% Similarity=0.272 Sum_probs=49.7
Q ss_pred HHhHHHHHHhHHHHHHHcCCcChHHHHhh-hc--CCchHHHHHHHHHHHHHHHHHH----HHHHHHHH
Q psy3035 56 RNHYKQYVDLENEVAVKNNFTDAAEYWLD-AY--DTPDFRDQVAKLWDQIRPLYLQ----IHAYTRRR 116 (161)
Q Consensus 56 r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~-~Y--e~~~~~~~~e~lw~qi~PLY~q----LHayVR~~ 116 (161)
.+.+.+.|+|-++.|+..||++..+|=.. .. ..++..+.+++|++.++|+-++ |.++.+..
T Consensus 3 ~~~l~~l~~lR~e~A~llG~~s~a~~~l~~~ma~sp~~v~~Fl~~l~~~~~p~~~~e~~~L~~~~~~~ 70 (422)
T cd06456 3 RPLIEEILALRAEKAKLLGFENYAEYSLADKMAKSPEAVLEFLEDLAPKAKPQAKKELAELQAFAKEE 70 (422)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 56789999999999999999999998433 22 2348889999999999999987 77666543
No 17
>COG0339 Dcp Zn-dependent oligopeptidases [Amino acid transport and metabolism]
Probab=91.30 E-value=3.4 Score=40.03 Aligned_cols=92 Identities=18% Similarity=0.244 Sum_probs=72.3
Q ss_pred CCCchHHHHHHhhCCCHHHHHHHHHHHHHhhchh----HHHhHHHHHHhHHHHHHHcCCcChHHHHhhh--cCCc-hHHH
Q psy3035 21 LTLEPELTEIFIGSRDPEELRHYWTEFRKKSGKQ----VRNHYKQYVDLENEVAVKNNFTDAAEYWLDA--YDTP-DFRD 93 (161)
Q Consensus 21 l~lepdl~~Ima~Srd~~eL~~~W~~Wr~~vg~~----~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~--Ye~~-~~~~ 93 (161)
+.. |...-+|+.+.|.+-+..+|.+|......- .++.-.+++.|--+-|++.||+++.+|=... =+++ ....
T Consensus 221 l~~-p~~~p~l~~~~~r~lRe~~y~A~~~ra~~~~~~~n~~ii~~~L~LR~E~A~LLGf~~yA~~~L~~kMA~~p~~Vl~ 299 (683)
T COG0339 221 LDI-PSYLPVLTYADNRALREKLYRAYVTRASEGGPNDNRAIIEEILKLRAELAKLLGFSNYAEYSLADKMAKTPEAVLN 299 (683)
T ss_pred ecc-cchhHHHHhcccHHHHHHHHHHHhhhccccCCcccHHHHHHHHHHHHHHHHHcCcccHHHHhHHHHhhcCHHHHHH
Confidence 444 789999999999999999999999765222 5688999999999999999999999975532 2333 4667
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy3035 94 QVAKLWDQIRPLYLQIHAYT 113 (161)
Q Consensus 94 ~~e~lw~qi~PLY~qLHayV 113 (161)
.++.||..-+|..++--+=+
T Consensus 300 fL~~l~~ka~~~a~~e~a~L 319 (683)
T COG0339 300 FLNDLAEKARPQAEKELAEL 319 (683)
T ss_pred HHHHHHHHhHHHHHHHHHHH
Confidence 78999998888875433333
No 18
>PF02074 Peptidase_M32: Carboxypeptidase Taq (M32) metallopeptidase; InterPro: IPR001333 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M32 (carboxypeptidase Taq family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. Carboxypeptidase Taq is a zinc-containing thermostable metallopeptidase. It was originally discovered and purified from Thermus aquaticus; optimal enzymatic activity occurs at 80 celcius. Although very little is known about this enzyme, it is thought either to be associated with a membrane or to be particle bound.; GO: 0004181 metallocarboxypeptidase activity, 0006508 proteolysis; PDB: 1K9X_A 1KA4_A 1KA2_A 3DWC_A 1WGZ_A 3HQ2_A 3HOA_B.
Probab=68.69 E-value=40 Score=31.54 Aligned_cols=70 Identities=14% Similarity=0.362 Sum_probs=50.9
Q ss_pred HHHHHHHHHhhc-hhHHHhHHHHHHhHHHHHHHcCCc-ChHHHHhhhcCCchHHHHHHHHHHHHHHHHHHHH
Q psy3035 41 RHYWTEFRKKSG-KQVRNHYKQYVDLENEVAVKNNFT-DAAEYWLDAYDTPDFRDQVAKLWDQIRPLYLQIH 110 (161)
Q Consensus 41 ~~~W~~Wr~~vg-~~~r~~y~~~V~L~N~aA~~nGf~-d~g~~Wr~~Ye~~~~~~~~e~lw~qi~PLY~qLH 110 (161)
..+|..=|.+.. ...+|..++.|+|..+.|..-|+. +.-|.+...||..--.+.++.++.+||+.-..|=
T Consensus 114 ~~~W~~AR~~nDf~~F~P~Le~iv~l~re~a~~~~~~~~~YDaLLd~yEpg~t~~~ld~~F~~lk~~l~~l~ 185 (494)
T PF02074_consen 114 EQAWEEARENNDFSAFAPYLEKIVELQREIAEYLGYELSPYDALLDDYEPGMTTEKLDEIFAELKAFLVPLL 185 (494)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHCTSTTSHHHHHHHHHSTT--HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 345666554433 337888899999999999999975 4667799999876666889999998886555543
No 19
>COG2317 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]
Probab=65.98 E-value=40 Score=31.68 Aligned_cols=65 Identities=15% Similarity=0.303 Sum_probs=48.3
Q ss_pred HHHHHhhch----hHHHhHHHHHHhHHHHHHHcCCcC-hHHHHhhhcCCchHHHHHHHHHHHHHHHHHHH
Q psy3035 45 TEFRKKSGK----QVRNHYKQYVDLENEVAVKNNFTD-AAEYWLDAYDTPDFRDQVAKLWDQIRPLYLQI 109 (161)
Q Consensus 45 ~~Wr~~vg~----~~r~~y~~~V~L~N~aA~~nGf~d-~g~~Wr~~Ye~~~~~~~~e~lw~qi~PLY~qL 109 (161)
.+||++-.+ -.++.-++.|+|+.+.|..-|+.. .=+.-...||.....+++++++..|+|--..|
T Consensus 114 ~aWreAr~knDf~~F~p~Lekiv~l~re~A~~~~~~~~pYdaLld~yEpG~t~~~i~~vF~~Lk~~L~~l 183 (497)
T COG2317 114 HAWREAREKNDFSIFKPYLEKIVELKREFAEYRGYEEHPYDALLDLYEPGLTVRDVDRVFAELKKELVPL 183 (497)
T ss_pred HHHHHHhhcccHhhhhHHHHHHHHHHHHHHHhcccccCcHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHH
Confidence 455654322 267777888999999999999865 34557788887788899999999988755444
No 20
>KOG2090|consensus
Probab=64.20 E-value=71 Score=31.16 Aligned_cols=96 Identities=11% Similarity=0.079 Sum_probs=79.7
Q ss_pred HHHHHHhhCCCHHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcChHHHHhhhc--CC-chHHHHHHHHHHHH
Q psy3035 26 ELTEIFIGSRDPEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAAEYWLDAY--DT-PDFRDQVAKLWDQI 102 (161)
Q Consensus 26 dl~~Ima~Srd~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~Y--e~-~~~~~~~e~lw~qi 102 (161)
.+..++++|-|.+.++-+|...+.- ...-...-..++...-+.|++-||+...++-...= +. ....+.+++|-+.+
T Consensus 239 ~i~~ll~~~~d~~vRk~vY~~~~~~-~~~q~~~L~~Li~sRheLa~l~G~~SfA~~al~~~~a~~pk~V~~Fl~~Ls~k~ 317 (704)
T KOG2090|consen 239 IIYGLLSSSEDESVRKMVYNTFHSP-SDIQVKLLEHLISSRHELAKLVGKSSFAHRALEGKLAKNPKTVRSFLEELSEKL 317 (704)
T ss_pred eeehhhhcCCCHHHHHHHHHHhcCC-cHHHHHHHHHHHHHHHHHHHHhCcchHHHHHhhccccCChHHHHHHHHHHHHhh
Confidence 5778889999999999999999953 35556778899999999999999999999866432 22 36778899999999
Q ss_pred HHHHHHHHHHHHHHHHHHhC
Q psy3035 103 RPLYLQIHAYTRRRLNEKYG 122 (161)
Q Consensus 103 ~PLY~qLHayVR~~L~~~YG 122 (161)
+|--++-.+.+|.-.++.-|
T Consensus 318 ~~~~~kel~~i~~mk~k~~~ 337 (704)
T KOG2090|consen 318 SEKTDKELAVIRDMKKKENN 337 (704)
T ss_pred hHHHHHHHHHHHHHHhhhcC
Confidence 99999999999987666554
No 21
>COG1164 Oligoendopeptidase F [Amino acid transport and metabolism]
Probab=63.97 E-value=91 Score=29.67 Aligned_cols=93 Identities=17% Similarity=0.223 Sum_probs=63.1
Q ss_pred HHHHHhhCCCHHHHHHHHHHHHHhhc---hhHHHhHHHHHHhHHHHHHHcCCcChHHHHhhhcCCchHHHHHHHHHHHHH
Q psy3035 27 LTEIFIGSRDPEELRHYWTEFRKKSG---KQVRNHYKQYVDLENEVAVKNNFTDAAEYWLDAYDTPDFRDQVAKLWDQIR 103 (161)
Q Consensus 27 l~~Ima~Srd~~eL~~~W~~Wr~~vg---~~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~Ye~~~~~~~~e~lw~qi~ 103 (161)
-...+.+|.|-+.++.+|++|-+... ..+-..+...|...+.-|+.-||.|.-+.=...-+. =++.++++++.|+
T Consensus 194 ~~~~ll~~~Dr~~Rk~A~~a~~~~~~~~~~t~a~~l~~~~~~~~~~a~~r~y~~~~~~~l~~~~i--~~~~~d~l~~~v~ 271 (598)
T COG1164 194 QLLNLLEDPDREVRKAAYEALYKAYEKHRNTLAALLNTLVKVLAFLARARNYDDVIDSALLRNEV--DREVVDNLIESVK 271 (598)
T ss_pred HHHHHhhCCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhcCcchHHHHHHHhCCC--CHHHHHHHHHHHH
Confidence 44667789999999999999986542 234455556667778888999999987754333222 2356778888888
Q ss_pred HHHH-HHHHHHHHHHHHHhC
Q psy3035 104 PLYL-QIHAYTRRRLNEKYG 122 (161)
Q Consensus 104 PLY~-qLHayVR~~L~~~YG 122 (161)
--+. -+|.|+..+ ++.-|
T Consensus 272 ~~~~~l~~ry~~~r-~k~Lg 290 (598)
T COG1164 272 EAFLPLLHRYYKLR-AKVLG 290 (598)
T ss_pred HhcchHHHHHHHHH-HHHhC
Confidence 4443 566666665 55556
No 22
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=56.07 E-value=64 Score=29.41 Aligned_cols=91 Identities=15% Similarity=0.307 Sum_probs=53.1
Q ss_pred CCCchHHHHHHhhCCCH-HHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcChHHH--Hhhhc-CCchHHHHHH
Q psy3035 21 LTLEPELTEIFIGSRDP-EELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAAEY--WLDAY-DTPDFRDQVA 96 (161)
Q Consensus 21 l~lepdl~~Ima~Srd~-~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g~~--Wr~~Y-e~~~~~~~~e 96 (161)
+.|| +|++.++..-+. +.+...=..=|+.+ -|||-.|-+|+++.=..=+...-+....| -|+.. |..+=.+.+-
T Consensus 8 ~~Le-eLe~kLa~~d~~Kd~V~~~I~ea~~sI-LPlRL~FNeFi~tma~Ie~~~~~s~qeKFl~IR~KlleL~~~lQ~lS 85 (379)
T PF11593_consen 8 LKLE-ELEEKLASNDNSKDSVMDKISEAQDSI-LPLRLQFNEFIQTMANIEEMNNKSPQEKFLLIRSKLLELYNKLQELS 85 (379)
T ss_pred CcHH-HHHHHHhcCCchHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHHhhcccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7886 999999954333 55555556666666 79999999999876544222222222222 22221 1112223444
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy3035 97 KLWDQIRPLYLQIHAYT 113 (161)
Q Consensus 97 ~lw~qi~PLY~qLHayV 113 (161)
+=+++++||+.-+-.|-
T Consensus 86 ~df~~LqPLF~Ti~eys 102 (379)
T PF11593_consen 86 SDFQKLQPLFDTIPEYS 102 (379)
T ss_pred HHHHHhchHHhhhHHHh
Confidence 45677788887776664
No 23
>PHA03102 Small T antigen; Reviewed
Probab=53.30 E-value=13 Score=29.53 Aligned_cols=46 Identities=9% Similarity=0.177 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCcccccccccc
Q psy3035 97 KLWDQIRPLYLQIHAYTRRRLNEKYGDKVVNRRGPIPAHLLGSCRQ 142 (161)
Q Consensus 97 ~lw~qi~PLY~qLHayVR~~L~~~YG~~~v~~~gpIPAHLLGnmWa 142 (161)
+.+++|.-+|+.|-..+.+..-..+|.+.++..++.|+-.||.+++
T Consensus 44 e~~k~in~Ay~~L~d~~~r~~yd~~g~~~~~~~~~~~~~~f~~~fg 89 (153)
T PHA03102 44 EKMKELNTLYKKFRESVKSLRDLDGEEDSSSEEEDVPSGYVGATFG 89 (153)
T ss_pred HHHHHHHHHHHHHhhHHHhccccccCCcccccccccHHHHhhhhcC
Confidence 4778899999999999999998999987777777889999988876
No 24
>TIGR02220 phg_TIGR02220 phage conserved hypothetical protein, C-terminal domain. This model represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=47.53 E-value=17 Score=25.74 Aligned_cols=43 Identities=28% Similarity=0.513 Sum_probs=32.1
Q ss_pred HHHHHHhHHHHHHHcCCc-ChHHH-------HhhhcCCchHHHHHHHHHHHH
Q psy3035 59 YKQYVDLENEVAVKNNFT-DAAEY-------WLDAYDTPDFRDQVAKLWDQI 102 (161)
Q Consensus 59 y~~~V~L~N~aA~~nGf~-d~g~~-------Wr~~Ye~~~~~~~~e~lw~qi 102 (161)
|.+.++..|+.|-.+ |. +.+.. |.+.|..++|...++..-.+-
T Consensus 1 ~~eii~yLN~ktg~~-y~~~~k~~~~lI~aR~~eg~~~~dfk~VId~k~~~W 51 (77)
T TIGR02220 1 YKEIIEYLNEKAGKS-FKHTTAKHKKLIKARWNEGYTLEDFKKVIDNKVSEW 51 (77)
T ss_pred ChHHHHHHHHhcCcc-cccccHhHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 467788889888776 76 44444 889998889998888665554
No 25
>KOG2202|consensus
Probab=45.29 E-value=16 Score=31.66 Aligned_cols=72 Identities=19% Similarity=0.415 Sum_probs=41.2
Q ss_pred hHHHhHHHHHHhHHHHHHHcCCcChHHHHh------hhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CCC
Q psy3035 54 QVRNHYKQYVDLENEVAVKNNFTDAAEYWL------DAYDTPDFRDQVAKLWDQIRPLYLQIHAYTRRRLNEKYGD-KVV 126 (161)
Q Consensus 54 ~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr------~~Ye~~~~~~~~e~lw~qi~PLY~qLHayVR~~L~~~YG~-~~v 126 (161)
.-+|.|...|-|.| =|.....-|. ..+..+.++. +..-+|+.+|. +|.++||+ +.+
T Consensus 37 h~kpt~s~t~ll~n------myq~P~~~~~~~d~~~~~~~de~~q~-------~~defyEd~f~----E~~~kygEiee~ 99 (260)
T KOG2202|consen 37 HEKPTFSQTVLLKN------MYQNPENSWERRDAQGQFLTDEELQR-------HEDEFYEDVFT----ELEDKYGEIEEL 99 (260)
T ss_pred hcccccchHHHHHH------HHhCCCCCchhhhhccccccHHHHHH-------HHHHHHHHHHH----HHHHHhhhhhhh
Confidence 34788899999998 3445555554 1222222222 33345666654 56778884 222
Q ss_pred CCCCCCcccccccccc
Q psy3035 127 NRRGPIPAHLLGSCRQ 142 (161)
Q Consensus 127 ~~~gpIPAHLLGnmWa 142 (161)
+--.-+=.||.||+.+
T Consensus 100 ~Vc~Nl~~hl~GNVYV 115 (260)
T KOG2202|consen 100 NVCDNLGDHLVGNVYV 115 (260)
T ss_pred hhhcccchhhhhhhhh
Confidence 2233456899999865
No 26
>PLN02498 omega-3 fatty acid desaturase
Probab=44.29 E-value=11 Score=35.00 Aligned_cols=38 Identities=32% Similarity=0.593 Sum_probs=29.9
Q ss_pred HHHH--HHHHHHHHHHHHHHhCCCCCCCCCCCcccccccccc
Q psy3035 103 RPLY--LQIHAYTRRRLNEKYGDKVVNRRGPIPAHLLGSCRQ 142 (161)
Q Consensus 103 ~PLY--~qLHayVR~~L~~~YG~~~v~~~gpIPAHLLGnmWa 142 (161)
-|.| ++=|+-++..|.+.|-++. ..||||-|+++.||.
T Consensus 381 IPhYhl~eAt~aiK~~lg~yy~e~~--~~~~~p~~~~~~l~r 420 (450)
T PLN02498 381 IPHYHLVEATEAAKPVLGKYYREPK--KSGPLPFHLLGSLIR 420 (450)
T ss_pred CCCcCHHHHHHHHHHHhHHheecCC--CCCCchhHHHHHHHH
Confidence 4777 5667778888888886543 349999999999997
No 27
>PHA02109 hypothetical protein
Probab=42.50 E-value=55 Score=27.28 Aligned_cols=23 Identities=35% Similarity=0.609 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhC
Q psy3035 100 DQIRPLYLQIHAYTRRRLNEKYG 122 (161)
Q Consensus 100 ~qi~PLY~qLHayVR~~L~~~YG 122 (161)
-|++-=-+.+-+|||+.|.++||
T Consensus 210 ~Q~~~Ki~N~R~~Vk~~LSE~F~ 232 (233)
T PHA02109 210 CQVKHKILNLRAEVKRRLSEDFG 232 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcC
Confidence 36777778899999999999997
No 28
>PF10786 G6PD_bact: Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49); InterPro: IPR019722 This entry represents proteins conserved in Firmicutes and Proteobacteria. Several members are annotated as being glucose-6-phosphate 1-dehydrogenase (1.1.1.49 from EC) but this could not be confirmed.
Probab=42.01 E-value=23 Score=29.84 Aligned_cols=55 Identities=18% Similarity=0.399 Sum_probs=34.9
Q ss_pred HHhHHHHHHhHHHHH-----HHcCCcChHHHHh-------hhcCCchHHHHHHHHHHHHHHHHHHHH
Q psy3035 56 RNHYKQYVDLENEVA-----VKNNFTDAAEYWL-------DAYDTPDFRDQVAKLWDQIRPLYLQIH 110 (161)
Q Consensus 56 r~~y~~~V~L~N~aA-----~~nGf~d~g~~Wr-------~~Ye~~~~~~~~e~lw~qi~PLY~qLH 110 (161)
..-|..+..|+...| +...-.+..++|+ ..-+..+.++-+-+--.++.|||+.+|
T Consensus 149 e~Ey~Dh~~l~~~l~~~~~~~~~~~~~~~d~f~iGK~~~r~~l~~~d~~~~i~~~i~~L~PLYe~~h 215 (215)
T PF10786_consen 149 ESEYADHLSLAEYLSDTSKQKQLNLRSGDDFFCIGKHAFRDQLAQEDMEEFIAETIRELLPLYEACH 215 (215)
T ss_pred hhhhcchHHHHHHhcccccchhhhhhcccceeeeccccccchhccccHHHHHHHHHHHHHHHHHhhC
Confidence 456777777777621 2222334444443 222344777888888899999999998
No 29
>PF14144 DOG1: Seed dormancy control
Probab=41.15 E-value=39 Score=23.88 Aligned_cols=56 Identities=21% Similarity=0.356 Sum_probs=44.5
Q ss_pred hHHHHHHhhCC-CHHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcChHHHHhhhcCC
Q psy3035 25 PELTEIFIGSR-DPEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAAEYWLDAYDT 88 (161)
Q Consensus 25 pdl~~Ima~Sr-d~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~Ye~ 88 (161)
++|..-+.... +-++|.- -| ...-..|.+|.++...||+.+-|.=..-.|++..|-
T Consensus 4 ~eLr~al~~~~~~~~~L~~-------lV-~~~~~Hy~~y~~~K~~aa~~DV~~~~s~~W~sp~Er 60 (80)
T PF14144_consen 4 NELRAALQSHADSDDELRS-------LV-DKVMSHYDEYYRAKSAAAKADVFHLLSPPWKSPLER 60 (80)
T ss_pred HHHHHHHHhcCCCHHHHHH-------HH-HHHHHHHHHHHHHHHHHHhcchHHHhCCCCCCHHHH
Confidence 57777777776 6666654 33 566788999999999999999998888889888754
No 30
>PF04450 BSP: Peptidase of plants and bacteria; InterPro: IPR007541 These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens [].
Probab=36.62 E-value=51 Score=27.19 Aligned_cols=35 Identities=20% Similarity=0.614 Sum_probs=25.6
Q ss_pred HHHHhHHHHHHHcCCcChHHHHhhhcCCchHHHHHHHHHHH
Q psy3035 61 QYVDLENEVAVKNNFTDAAEYWLDAYDTPDFRDQVAKLWDQ 101 (161)
Q Consensus 61 ~~V~L~N~aA~~nGf~d~g~~Wr~~Ye~~~~~~~~e~lw~q 101 (161)
.||...|++.+..+| +...+|..-.-. .|++||++
T Consensus 170 gfV~~LN~~m~~~~y-~~~~~~~~l~G~-----~v~~LW~e 204 (205)
T PF04450_consen 170 GFVRRLNEAMRRDKY-SSDDFWKELLGK-----PVDELWAE 204 (205)
T ss_pred cHHHHHHHHHhhCCC-CcHhHHHHHHCc-----CHHHHHhh
Confidence 577778999999999 455677755533 38899975
No 31
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=34.73 E-value=33 Score=20.99 Aligned_cols=16 Identities=25% Similarity=0.588 Sum_probs=12.5
Q ss_pred CCCCCCCccccccccc
Q psy3035 126 VNRRGPIPAHLLGSCR 141 (161)
Q Consensus 126 v~~~gpIPAHLLGnmW 141 (161)
+.++.|||.||+--+|
T Consensus 21 l~~~~pVP~~l~~~I~ 36 (37)
T PF08880_consen 21 LARNQPVPPQLQQAIQ 36 (37)
T ss_pred HHcCCCCCHHHHHhhh
Confidence 5568899999986655
No 32
>PTZ00458 acyl CoA binding protein; Provisional
Probab=34.62 E-value=40 Score=24.46 Aligned_cols=30 Identities=17% Similarity=0.351 Sum_probs=22.8
Q ss_pred HHHHHHHHHhhchhHHHhHHHHHHhHHHHH
Q psy3035 41 RHYWTEFRKKSGKQVRNHYKQYVDLENEVA 70 (161)
Q Consensus 41 ~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA 70 (161)
+.=|.+|...-|-.-..--.+||+|.++..
T Consensus 54 raKw~AW~~l~~ms~~eA~~~YI~l~~~l~ 83 (90)
T PTZ00458 54 RKKYEAWKSIENLNREDAKKRYVEIVTELF 83 (90)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Confidence 456999998767666677788888888754
No 33
>PF02260 FATC: FATC domain; InterPro: IPR003152 The FATC domain is found at the C-terminal end of the PIK-related kinases. Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding; PDB: 2KIT_A 1W1N_A 2KIO_A.
Probab=34.50 E-value=8 Score=23.04 Aligned_cols=28 Identities=25% Similarity=0.538 Sum_probs=23.5
Q ss_pred CCCchHHHHHHhhCCCHHHHHHHHHHHH
Q psy3035 21 LTLEPELTEIFIGSRDPEELRHYWTEFR 48 (161)
Q Consensus 21 l~lepdl~~Ima~Srd~~eL~~~W~~Wr 48 (161)
|+.+-.+.++++...|.+-|...+.||.
T Consensus 3 lsv~~qV~~LI~~At~~~nLa~my~GW~ 30 (33)
T PF02260_consen 3 LSVEQQVDELISEATDPENLARMYIGWM 30 (33)
T ss_dssp S-STHHHHHHHHHHHHHHHHHHHCTSS-
T ss_pred CCHHHHHHHHHHHHcCHHHHHHHhcchh
Confidence 5667889999999999999999998885
No 34
>TIGR02453 conserved hypothetical protein TIGR02453. Members of this family are widely (though sparsely) distributed bacterial proteins about 230 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown. In several fungi, this model identifies a conserved region of a longer protein. Therefore, it may be incorrect to speculate that all members share a common function.
Probab=33.73 E-value=1.6e+02 Score=24.33 Aligned_cols=25 Identities=24% Similarity=0.495 Sum_probs=21.5
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHH
Q psy3035 89 PDFRDQVAKLWDQIRPLYLQIHAYT 113 (161)
Q Consensus 89 ~~~~~~~e~lw~qi~PLY~qLHayV 113 (161)
++|.++|.+.|..++||+.=|...+
T Consensus 192 ~~~~~~l~~~f~~l~P~~~~L~~~l 216 (217)
T TIGR02453 192 EDLVERIADAFERLRPLMDYLNAAL 216 (217)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4799999999999999998887653
No 35
>PF00768 Peptidase_S11: D-alanyl-D-alanine carboxypeptidase This is family S11 in the peptidase classification. ; InterPro: IPR001967 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S11 (D-Ala-D-Ala carboxypeptidase A family, clan SE). The protein fold of the peptidase domain for members of this family resembles that of D-Ala-D-Ala-carboxypeptidase B, the type example for clan SE. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endo-peptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S27) of serine protease have been identified, these being grouped into 6 clans (SA, SB, SC, SE, SF and SG) on the basis of structural similarity and other functional evidence. Structures are known for four of the clans (SA, SB, SC and SE): these appear to be totally unrelated, suggesting at least four evolutionary origins of serine peptidases and possibly many more []. Not with standing their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C clans have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (SA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. Bacterial cell walls are complex structures containing amino acids and amino sugars, with alternating chains of N-acetylglucosamine and N-acetyl-muramic acid units linked by short peptides []: the link peptide in Escherichia coli is L-alanyl-D-isoglutamyl-L-meso-diaminopimelyl-D-alanine. The chains are usually cross-linked between the carboxyl of D-alanine and the free amino group of diaminopimelate. During the synthesis of peptidoglycan, the precursor has the described tetramer sequence with an added C-terminal D-alanine []. D-Ala-D-Ala carboxypeptidase A is involved in the metabolism of cell components []; it is synthesised with a leader peptide to target it to the cell membrane []. After cleavage of the leader peptide, the enzyme is retained in the membrane by a C-terminal anchor. There are three families of serine-type D-Ala-D-Ala peptidase, which are also known as low molecular weight penicillin-binding proteins. Family S11 contains only D-Ala-D-Ala peptidases, unlike families S12 and S13, which contain other enzymes, such as class C beta-lactamases and D-amino-peptidases []. Although these enzymes are serine proteases, some members of family S11 are partially inhibited by thiol-blocking agents [].; GO: 0009002 serine-type D-Ala-D-Ala carboxypeptidase activity, 0006508 proteolysis; PDB: 2BCF_A 1TVF_A 3MFD_B 1ES3_A 1ESI_A 1ES4_A 1ES2_A 1SKF_A 1ES5_A 1J9M_A ....
Probab=33.66 E-value=44 Score=27.80 Aligned_cols=49 Identities=16% Similarity=0.234 Sum_probs=28.8
Q ss_pred CCCchHHHHHHhhCCCHHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcCh
Q psy3035 21 LTLEPELTEIFIGSRDPEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDA 78 (161)
Q Consensus 21 l~lepdl~~Ima~Srd~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~ 78 (161)
++++.=|..+|-.|-|-.-.. ++..+-..-..||+++|+-|++.|..++
T Consensus 89 ~tv~dLL~alll~S~NdAA~a---------LA~~i~gs~~~Fv~~MN~~A~~lG~~~T 137 (240)
T PF00768_consen 89 YTVRDLLYALLLPSANDAAYA---------LAEHIGGSEEAFVAMMNEKAKELGMTNT 137 (240)
T ss_dssp EEHHHHHHHHHHS--HHHHHH---------HHHHHHSSHHHHHHHHHHHHHHTT-TT-
T ss_pred eeHHHHHHHhhhcCchHHHHH---------HHHHcCCCHHHHHHHHHHHHHHcCCCcc
Confidence 455444555666665543332 2233334459999999999999998775
No 36
>COG4493 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.11 E-value=52 Score=27.45 Aligned_cols=21 Identities=29% Similarity=0.528 Sum_probs=18.8
Q ss_pred chHHHHHHHHHHHHHHHHHHH
Q psy3035 89 PDFRDQVAKLWDQIRPLYLQI 109 (161)
Q Consensus 89 ~~~~~~~e~lw~qi~PLY~qL 109 (161)
..|.++++..++|+-|||+.+
T Consensus 186 ~~fl~~~eetfdqllplY~~~ 206 (209)
T COG4493 186 KIFLAEIEETFDQLLPLYQAA 206 (209)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 379999999999999999865
No 37
>PF08039 Mit_proteolip: Mitochondrial proteolipid; InterPro: IPR012574 This family consists of proteins with similarity to the mitochondrial proteolipids. Mitochondrial proteolipid consists of about 60 amino acids residues and is about 6.8 kDa in size [].; GO: 0005739 mitochondrion
Probab=31.67 E-value=41 Score=22.97 Aligned_cols=45 Identities=24% Similarity=0.513 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHH------hCCCC---CCCCCCCccc
Q psy3035 91 FRDQVAKLWDQIRPLYLQIHA--YTRRRLNEK------YGDKV---VNRRGPIPAH 135 (161)
Q Consensus 91 ~~~~~e~lw~qi~PLY~qLHa--yVR~~L~~~------YG~~~---v~~~gpIPAH 135 (161)
|+..+.++|-.+||.|.|+-. +|+-.|-.. +++.. ....+|-|||
T Consensus 2 ~qs~iknvWvpmkpYytqvYqEIWVGmGlm~fivYKi~sadkrskalkasspapah 57 (60)
T PF08039_consen 2 LQSLIKNVWVPMKPYYTQVYQEIWVGMGLMGFIVYKIRSADKRSKALKASSPAPAH 57 (60)
T ss_pred hHHHHHHhhhcchHHHHHHHHHHHHhhhhheeEEEeecccchhHHHHhccCCCCcc
Confidence 567799999999999999875 667666554 23221 3345688887
No 38
>PF05596 Taeniidae_ag: Taeniidae antigen; InterPro: IPR008860 This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.
Probab=31.12 E-value=1.8e+02 Score=19.97 Aligned_cols=45 Identities=13% Similarity=0.108 Sum_probs=37.7
Q ss_pred ChHHHHhhhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3035 77 DAAEYWLDAYDTPDFRDQVAKLWDQIRPLYLQIHAYTRRRLNEKY 121 (161)
Q Consensus 77 d~g~~Wr~~Ye~~~~~~~~e~lw~qi~PLY~qLHayVR~~L~~~Y 121 (161)
..-++++..|+.+=+-+.|-.|..++.-....++.=||..|.+.-
T Consensus 14 K~i~~v~~FF~~DPlGqkIa~l~kdw~~~~~~~r~KiR~~L~ey~ 58 (64)
T PF05596_consen 14 KWIEEVRNFFYEDPLGQKIAQLAKDWNEICQEVRKKIRAALAEYC 58 (64)
T ss_pred HHHHHHHHHhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344678888888888899999999999999999999999888653
No 39
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=30.35 E-value=43 Score=27.23 Aligned_cols=27 Identities=26% Similarity=0.364 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCCCCCCcc
Q psy3035 103 RPLYLQIHAYTRRRLNEKYGDKVVNRRGPIPA 134 (161)
Q Consensus 103 ~PLY~qLHayVR~~L~~~YG~~~v~~~gpIPA 134 (161)
.|+|+||...+|.++...|. ....||.
T Consensus 11 ~p~Y~qi~~~L~~~I~~~~~-----~G~~LPs 37 (241)
T PRK10079 11 PTRYQEIAAKLEQELRQHYR-----CGDYLPA 37 (241)
T ss_pred CCHHHHHHHHHHHHHhcccC-----CCCcCCC
Confidence 48999999999999975553 3445664
No 40
>PF00887 ACBP: Acyl CoA binding protein; InterPro: IPR000582 Acyl-CoA-binding protein (ACBP) is a small (10 Kd) protein that binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters []. ACBP is also known as diazepam binding inhibitor (DBI) or endozepine (EP) because of its ability to displace diazepam from the benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore possible that this protein also acts as a neuropeptide to modulate the action of the GABA receptor []. ACBP is a highly conserved protein of about 90 residues that is found in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and in some eubacterial species []. Although ACBP occurs as a completely independent protein, intact ACB domains have been identified in a number of large, multifunctional proteins in a variety of eukaryotic species. These include large membrane-associated proteins with N-terminal ACB domains, multifunctional enzymes with both ACB and peroxisomal enoyl-CoA Delta(3), Delta(2)-enoyl-CoA isomerase domains, and proteins with both an ACB domain and ankyrin repeats (IPR002110 from INTERPRO) []. The ACB domain consists of four alpha-helices arranged in a bowl shape with a highly exposed acyl-CoA-binding site. The ligand is bound through specific interactions with residues on the protein, most notably several conserved positive charges that interact with the phosphate group on the adenosine-3'phosphate moiety, and the acyl chain is sandwiched between the hydrophobic surfaces of CoA and the protein []. Other proteins containing an ACB domain include: Endozepine-like peptide (ELP) (gene DBIL5) from mouse []. ELP is a testis-specific ACBP homologue that may be involved in the energy metabolism of the mature sperm. MA-DBI, a transmembrane protein of unknown function which has been found in mammals. MA-DBI contains a N-terminal ACB domain. DRS-1 [], a human protein of unknown function that contains a N-terminal ACB domain and a C-terminal enoyl-CoA isomerase/hydratase domain. ; GO: 0000062 fatty-acyl-CoA binding; PDB: 2CB8_A 2FJ9_A 2LBB_A 1ST7_A 3EPY_B 2FDQ_C 1NTI_A 1HB8_A 1ACA_A 1NVL_A ....
Probab=30.28 E-value=79 Score=21.98 Aligned_cols=31 Identities=19% Similarity=0.514 Sum_probs=24.2
Q ss_pred HHHHHHHHHhhchhHHHhHHHHHHhHHHHHH
Q psy3035 41 RHYWTEFRKKSGKQVRNHYKQYVDLENEVAV 71 (161)
Q Consensus 41 ~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~ 71 (161)
+.-|.+|+..-|-.-..-=.+||++.++...
T Consensus 54 ~~K~~AW~~l~gms~~eA~~~Yi~~v~~~~~ 84 (87)
T PF00887_consen 54 RAKWDAWKALKGMSKEEAMREYIELVEELIP 84 (87)
T ss_dssp HHHHHHHHTTTTTHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHccCCCHHHHHHHHHHHHHHHHH
Confidence 3459999988787777778889999887653
No 41
>PF15631 Imm-NTF2-2: NTF2 fold immunity protein
Probab=29.12 E-value=30 Score=24.00 Aligned_cols=26 Identities=23% Similarity=0.382 Sum_probs=22.4
Q ss_pred HHHHHhCCCCCCCCCCCcccccccccc
Q psy3035 116 RLNEKYGDKVVNRRGPIPAHLLGSCRQ 142 (161)
Q Consensus 116 ~L~~~YG~~~v~~~gpIPAHLLGnmWa 142 (161)
-|..+||... ...-|.-+-+.||+|.
T Consensus 9 ~l~~iYG~~~-~~ekP~~v~~~~~~Wi 34 (66)
T PF15631_consen 9 YLKPIYGKEI-EEEKPYRVTLDGDSWI 34 (66)
T ss_pred HHHHHcCchh-hhcCCeEEecCCCeEE
Confidence 4778999776 7788999999999997
No 42
>PF04749 PLAC8: PLAC8 family; InterPro: IPR006461 This group of sequences are described by a region of about 170 amino acids. These proteins have highly divergent N-terminal regions rich in low complexity sequence. PSI-BLAST reveals no clear similarity to any characterised protein. It is common in plants but found also in Homo sapiens (Human), Dictyostelium, and Leishmania; at least 12 distinct members are found in Arabidopsis. Most members of this family contain more than 10 per cent Cys, but no Cys residue is invariant across the family.
Probab=28.36 E-value=43 Score=23.42 Aligned_cols=14 Identities=29% Similarity=0.636 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHhC
Q psy3035 109 IHAYTRRRLNEKYG 122 (161)
Q Consensus 109 LHayVR~~L~~~YG 122 (161)
++..+|.++|++||
T Consensus 66 ~~~~~R~~iR~ry~ 79 (106)
T PF04749_consen 66 YGCSLRQQIRERYG 79 (106)
T ss_pred hhhhHHHHHHHHhC
Confidence 66999999999998
No 43
>PRK04196 V-type ATP synthase subunit B; Provisional
Probab=26.88 E-value=2.8e+02 Score=25.65 Aligned_cols=75 Identities=13% Similarity=0.182 Sum_probs=52.6
Q ss_pred HHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcChH---------------HHHhhh-cCCchHHHHHHHHHHHHHHHHHH
Q psy3035 45 TEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAA---------------EYWLDA-YDTPDFRDQVAKLWDQIRPLYLQ 108 (161)
Q Consensus 45 ~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g---------------~~Wr~~-Ye~~~~~~~~e~lw~qi~PLY~q 108 (161)
..|++.++. ++..|+++-+|.+-++=. |-.+.. +|-+.. ++..++++.++.+|.-+..+-.+
T Consensus 362 ~~~~~~a~~-l~~~y~~~~~l~~~~~~~-G~~~l~d~~~~~~~~~~~~~~~fL~Q~~~~~~~~~~~~~~l~~~l~~~~~~ 439 (460)
T PRK04196 362 EDHKDVANQ-LYAAYARGKDLRELAAIV-GEEALSERDRKYLKFADAFEREFVNQGFDENRSIEETLDLGWELLSILPES 439 (460)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHhc-CCCcCCHHHHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHhhCCHH
Confidence 567765544 999999999999999887 643322 222222 24458899999999988888766
Q ss_pred HHHHHHHHHHHHh
Q psy3035 109 IHAYTRRRLNEKY 121 (161)
Q Consensus 109 LHayVR~~L~~~Y 121 (161)
-=..+..+|.++|
T Consensus 440 ~l~~~~~~l~~~~ 452 (460)
T PRK04196 440 ELKRIKDEYIEKY 452 (460)
T ss_pred HHHHHHHHHHHHh
Confidence 6666666666665
No 44
>PF04174 CP_ATPgrasp_1: A circularly permuted ATPgrasp ; InterPro: IPR007302 This is a domain of unknown function. It sometimes occurs in combination with IPR007296 from INTERPRO) and (IPR007297 from INTERPRO).; PDB: 3N6X_A.
Probab=26.55 E-value=67 Score=28.50 Aligned_cols=41 Identities=24% Similarity=0.404 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCccccc
Q psy3035 97 KLWDQIRPLYLQIHAYTRRRLNEKYGDKVVNRRGPIPAHLL 137 (161)
Q Consensus 97 ~lw~qi~PLY~qLHayVR~~L~~~YG~~~v~~~gpIPAHLL 137 (161)
.-|.+|.-=-.|=..-+-.-|...||+..+=++|.||+.++
T Consensus 7 ~eW~~l~~Gl~QRa~~L~~~l~DlYg~q~il~~g~~P~~lv 47 (330)
T PF04174_consen 7 EEWAELEAGLAQRARALNAFLADLYGPQRILRDGVLPAELV 47 (330)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTT-HHHHTTSS-GGGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhcCCCCHHHH
Confidence 34666666666666777777999999988888999999996
No 45
>PF13682 CZB: Chemoreceptor zinc-binding domain
Probab=26.34 E-value=1e+02 Score=19.63 Aligned_cols=19 Identities=11% Similarity=0.282 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy3035 99 WDQIRPLYLQIHAYTRRRL 117 (161)
Q Consensus 99 w~qi~PLY~qLHayVR~~L 117 (161)
|.+|..+.+++|..++.-+
T Consensus 50 ~~~l~~~H~~~H~~a~~i~ 68 (70)
T PF13682_consen 50 FKELEEPHEEFHELAREII 68 (70)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 8999999999999988754
No 46
>PF13092 CENP-L: Kinetochore complex Sim4 subunit Fta1
Probab=25.99 E-value=79 Score=24.94 Aligned_cols=79 Identities=14% Similarity=0.138 Sum_probs=42.8
Q ss_pred CHHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcCh-HHHHhhhcCCchHHHHHHHHHHHH------------
Q psy3035 36 DPEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDA-AEYWLDAYDTPDFRDQVAKLWDQI------------ 102 (161)
Q Consensus 36 d~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~-g~~Wr~~Ye~~~~~~~~e~lw~qi------------ 102 (161)
....|.|.|+.|=+.++.+-+. .+.-+..-..+|.-. ..-=....+..==.+++.++|+.+
T Consensus 39 ~~~~L~~~~e~w~~~~~~~~~~------~~~k~~~l~L~f~~p~~~~~L~~i~i~Ip~~dl~~~~~~~~~~~~~~~~~~~ 112 (162)
T PF13092_consen 39 PSSFLCWMLEMWIATLTSSSPG------PVIKEVQLTLSFSVPPESPGLKSIDITIPPEDLRAFWRSGDDDWESREETQE 112 (162)
T ss_pred CHHHHHHHHHHHHHhcCCCCCC------ccccceEEEEEecCCCCCCCcCeEEEEECHHHHHHHHHhhcccccccccccc
Confidence 4578999999999888765444 111111112344411 100001111100124455555555
Q ss_pred --HHHHHHHHHHHHHHHHHH
Q psy3035 103 --RPLYLQIHAYTRRRLNEK 120 (161)
Q Consensus 103 --~PLY~qLHayVR~~L~~~ 120 (161)
.||+..|..|+.+-+.=.
T Consensus 113 ~~~~F~~aL~~y~~~hl~l~ 132 (162)
T PF13092_consen 113 EVSPFMEALSSYFYRHLALD 132 (162)
T ss_pred cccHHHHHHHHHHHHHhCCC
Confidence 999999999999866533
No 47
>PF02252 PA28_beta: Proteasome activator pa28 beta subunit; InterPro: IPR003186 PA28 activator complex (also known as 11S regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha (PA28alpha) and beta (PA28beta) subunits. The catalytic properties of PA28alpha and PA28beta-activated proteosome are similar [, ]. This entry represents the beta subunit. The activator complex binds to the 20S proteasome and stimulates peptidase activity in and ATP-independent manner.; GO: 0008537 proteasome activator complex; PDB: 1AVO_N.
Probab=25.28 E-value=1.9e+02 Score=22.77 Aligned_cols=58 Identities=7% Similarity=0.087 Sum_probs=43.4
Q ss_pred HhHHHHHHHcCCcChHHHHhhhcCCch-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3035 64 DLENEVAVKNNFTDAAEYWLDAYDTPD-FRDQVAKLWDQIRPLYLQIHAYTRRRLNEKY 121 (161)
Q Consensus 64 ~L~N~aA~~nGf~d~g~~Wr~~Ye~~~-~~~~~e~lw~qi~PLY~qLHayVR~~L~~~Y 121 (161)
+-.-.+++..-++...||++.-.|.+. -...+.....+|+-.|-.||..+-..+-+.=
T Consensus 81 ~Ra~~v~k~~K~p~v~DY~~~v~e~Dek~~~~lr~~~~elRn~Y~~l~D~i~KN~eKi~ 139 (150)
T PF02252_consen 81 ARAKAVSKAAKYPHVEDYRQAVHELDEKEYISLRLIVLELRNNYATLYDIISKNFEKIK 139 (150)
T ss_dssp HHHHHHHHHHH-TTBTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHhc
Confidence 344445566678889999998887653 3366788888999999999999998876653
No 48
>PRK10001 D-alanyl-D-alanine carboxypeptidase fraction C; Provisional
Probab=24.80 E-value=60 Score=29.45 Aligned_cols=48 Identities=15% Similarity=0.143 Sum_probs=29.9
Q ss_pred CCCchHHHHHHhhCCC-HHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcCh
Q psy3035 21 LTLEPELTEIFIGSRD-PEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDA 78 (161)
Q Consensus 21 l~lepdl~~Ima~Srd-~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~ 78 (161)
++++.=|..+|-.|-| ....+--+ +| ..-..||+++|+-|++.|..|+
T Consensus 119 ~tv~dLl~a~li~SaNDAA~aLAe~------i~----Gs~~~Fv~~MN~kAkeLGm~nT 167 (400)
T PRK10001 119 VSVADLNKGVIIQSGNDACIALADY------VA----GSQESFIGLMNGYAKKLGLTNT 167 (400)
T ss_pred EEHHHHHHHHHHhChHHHHHHHHHH------cC----CCHHHHHHHHHHHHHHcCCCCC
Confidence 5554345555555544 33333222 22 2357899999999999998775
No 49
>cd00435 ACBP Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
Probab=24.59 E-value=1e+02 Score=21.80 Aligned_cols=30 Identities=20% Similarity=0.428 Sum_probs=22.4
Q ss_pred HHHHHHHHHhhchhHHHhHHHHHHhHHHHH
Q psy3035 41 RHYWTEFRKKSGKQVRNHYKQYVDLENEVA 70 (161)
Q Consensus 41 ~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA 70 (161)
+.-|.+|+.--|-.-..--..||++.++..
T Consensus 52 ~~K~~AW~~l~~ms~~eA~~~YV~~~~~l~ 81 (85)
T cd00435 52 RAKWDAWNSLKGMSKEDAMKAYIAKVEELI 81 (85)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Confidence 456999997666666666788888888754
No 50
>KOG3809|consensus
Probab=24.36 E-value=1e+02 Score=29.14 Aligned_cols=65 Identities=18% Similarity=0.332 Sum_probs=32.9
Q ss_pred HHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcCh--------HHHHhhhcCC--chHHHHHHHHHHHHHHHHHHH
Q psy3035 44 WTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDA--------AEYWLDAYDT--PDFRDQVAKLWDQIRPLYLQI 109 (161)
Q Consensus 44 W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~--------g~~Wr~~Ye~--~~~~~~~e~lw~qi~PLY~qL 109 (161)
=.+||..+ ..+|..-+.+..-.=-.+++..|-.- =++||+.|-- ..++++-.--+..+.|||.+|
T Consensus 474 ~sa~~~~~-~~lr~~~Q~LtkSa~PLgkl~D~i~eD~daMq~EL~mWrse~rq~~~elq~eq~~t~~a~epL~~~l 548 (583)
T KOG3809|consen 474 MSAEREKM-KQLREKLQDLTKSAYPLGKLFDFINEDIDAMQKELEMWRSEQRQNEQELQNEQAATFGASEPLYNIL 548 (583)
T ss_pred HHHHHHHH-HHHHHHHHHHHHhhccHHHHHhhhhhhHHHHHHHHHHHHHHHHHhHHHHHhhhhcccccchHHHHHH
Confidence 34555555 45566555555544455566666322 3689998843 233333222333444444433
No 51
>COG2187 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.28 E-value=1.1e+02 Score=27.39 Aligned_cols=58 Identities=21% Similarity=0.300 Sum_probs=39.2
Q ss_pred HHHHhHHHHHHH------cCCcChHHHHhhhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q psy3035 61 QYVDLENEVAVK------NNFTDAAEYWLDAYDTPDFRDQVAKLWDQIRPLYLQIHAYTRRRLNEKYG 122 (161)
Q Consensus 61 ~~V~L~N~aA~~------nGf~d~g~~Wr~~Ye~~~~~~~~e~lw~qi~PLY~qLHayVR~~L~~~YG 122 (161)
+|+...+-.|=+ -|.+|.+.+-.+.|=. +.=+----++.|||..--||||.+....=.
T Consensus 241 r~iDv~~D~AFl~MDLe~~gr~dla~~~ln~Yl~----~tgD~~gl~lLpfyla~rA~VRakV~sf~l 304 (337)
T COG2187 241 RFIDVLYDLAFLAMDLEFRGRKDLARRFLNTYLE----ETGDWDGLELLPFYLAYRAYVRAKVTSFLL 304 (337)
T ss_pred hHHHHHHHHHHHHhhHhhcCChHHHHHHHHHHHH----HhCCccHHHHhHHHHHHHHHHHHheeEEec
Confidence 577777777733 4788888777777711 111111127899999999999998765543
No 52
>KOG4771|consensus
Probab=24.14 E-value=45 Score=27.69 Aligned_cols=22 Identities=36% Similarity=0.487 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCC
Q psy3035 103 RPLYLQIHAYTRRRLNEKYGDKV 125 (161)
Q Consensus 103 ~PLY~qLHayVR~~L~~~YG~~~ 125 (161)
.|+-+-=|+|+|+ |.++||+|.
T Consensus 154 l~~s~rehewi~r-L~~KhGdD~ 175 (210)
T KOG4771|consen 154 LTTSQREHEWIRR-LVEKHGDDI 175 (210)
T ss_pred cchHHHHHHHHHH-HHHHhchhH
Confidence 4556677999987 999999653
No 53
>TIGR01841 phasin phasin family protein. This model describes a family of small proteins found associated with inclusions in bacterial cells. Most associate with polyhydroxyalkanoate (PHA) inclusions, the most common of which consist of polyhydroxybutyrate (PHB). These are designated granule-associate proteins or phasins; the member from Rhodospirillum rubrum is an activator of polyhydroxybutyrate (PHB) degradation. However, the member from Magnetospirillum sp. AMB-1 is called a magnetic particle membrane-specific GTPase.
Probab=23.93 E-value=2.6e+02 Score=19.50 Aligned_cols=56 Identities=14% Similarity=0.156 Sum_probs=34.1
Q ss_pred HHHHHHhHHHHHHHcCCcChHHHHhhhcCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3035 59 YKQYVDLENEVAVKNNFTDAAEYWLDAYDTPDFRDQVAKLWDQIRPLYLQIHAYTRR 115 (161)
Q Consensus 59 y~~~V~L~N~aA~~nGf~d~g~~Wr~~Ye~~~~~~~~e~lw~qi~PLY~qLHayVR~ 115 (161)
++++++|.-+++|. .+++..+..+.-....+..+.++--=+-++|..++..+|.|+
T Consensus 5 ~e~l~~ln~~~~r~-~l~e~~~~~k~l~~ak~p~e~~~lQ~~~~~~~~eka~a~~r~ 60 (88)
T TIGR01841 5 VERLVKLQLQALRA-TLDESVAASQRLASAGDPQELIALQTEFAKPAAEKLLAYSRE 60 (88)
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHHHhcCCCHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 45555555555544 355555556655555566666666566677777777777775
No 54
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=22.96 E-value=1.7e+02 Score=29.25 Aligned_cols=44 Identities=20% Similarity=0.280 Sum_probs=26.8
Q ss_pred HHHhhchhHHHhHHHHHHhHHHHHHHcCCcChHHHHhhhcCCchHHHHHHHHHHHHHHH
Q psy3035 47 FRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAAEYWLDAYDTPDFRDQVAKLWDQIRPL 105 (161)
Q Consensus 47 Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~Ye~~~~~~~~e~lw~qi~PL 105 (161)
.|++.|++-+....++-+.-=++|+.||++. +..+++|++|+.|
T Consensus 728 lRram~kK~~~~m~~~~~~F~~ga~~~g~~~---------------~~a~~i~~~i~~F 771 (874)
T PRK09532 728 LRRAMGKKKISEMQKHREKFIDGAAKNGVSK---------------KVAENLFDQMVKF 771 (874)
T ss_pred HHHHhccCCHHHHHHHHHHHHHHHHHcCCCH---------------HHHHHHHHHHHHh
Confidence 4667776644434333333335888899864 3467777777664
No 55
>TIGR01571 A_thal_Cys_rich uncharacterized Cys-rich domain. This model describes an uncharacterized domain of about 100 residues. It is common in plants but found also in Homo sapiens, Dictyostelium, and Leishmania; at least 12 distinct members are found in Arabidopsis. Most members of this family contain more than 10 per cent Cys, but no Cys residue is invariant across the family.
Probab=22.45 E-value=72 Score=23.20 Aligned_cols=13 Identities=46% Similarity=0.902 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHhC
Q psy3035 110 HAYTRRRLNEKYG 122 (161)
Q Consensus 110 HayVR~~L~~~YG 122 (161)
...+|.+++++||
T Consensus 63 ~~~~R~~~R~ry~ 75 (104)
T TIGR01571 63 TCFIRIKLREKYG 75 (104)
T ss_pred HHHHHHHHHHHhC
Confidence 4689999999998
No 56
>PRK11397 dacD D-alanyl-D-alanine carboxypeptidase; Provisional
Probab=22.25 E-value=72 Score=28.82 Aligned_cols=48 Identities=15% Similarity=0.199 Sum_probs=30.6
Q ss_pred CCCchHHHHHHhhCC-CHHHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcCh
Q psy3035 21 LTLEPELTEIFIGSR-DPEELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDA 78 (161)
Q Consensus 21 l~lepdl~~Ima~Sr-d~~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~ 78 (161)
++++.=|..+|-.|- |....+--+. -..-..||+++|+-|++.|-.|+
T Consensus 116 ~tv~dLL~~llv~SaNDAA~aLAe~i----------~Gs~~~Fv~~MN~kAkeLGm~~T 164 (388)
T PRK11397 116 VSVRDLSRGLIVDSGNDACVALADYI----------AGGQRQFVEMMNNYVEKLHLKDT 164 (388)
T ss_pred EEHHHHHHHHHHhChhHHHHHHHHHh----------cCCHHHHHHHHHHHHHHcCCCCC
Confidence 555534455554554 4444443332 23467999999999999998765
No 57
>COG2236 Predicted phosphoribosyltransferases [General function prediction only]
Probab=21.77 E-value=67 Score=26.40 Aligned_cols=37 Identities=27% Similarity=0.442 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHH----hCCCC---CCCCCCCcccccccccc
Q psy3035 106 YLQIHAYTRRRLNEK----YGDKV---VNRRGPIPAHLLGSCRQ 142 (161)
Q Consensus 106 Y~qLHayVR~~L~~~----YG~~~---v~~~gpIPAHLLGnmWa 142 (161)
|..+|.-+|.-=.+. |-+|+ +...|-|||++|.+.+.
T Consensus 9 w~~I~~~~~~lA~kI~~s~~~PDvIiaiaRGG~~pariLsd~L~ 52 (192)
T COG2236 9 WEEIHRLCRALAEKIRASGFKPDVIVAIARGGLIPARILSDFLG 52 (192)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCEEEEEcCCceehHHHHHHHhC
Confidence 344555554433333 44555 45789999999988876
No 58
>PRK11669 pbpG D-alanyl-D-alanine endopeptidase; Provisional
Probab=21.60 E-value=78 Score=27.73 Aligned_cols=48 Identities=15% Similarity=0.138 Sum_probs=30.0
Q ss_pred CCCchHHHHHHhhCCCH-HHHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcCh
Q psy3035 21 LTLEPELTEIFIGSRDP-EELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDA 78 (161)
Q Consensus 21 l~lepdl~~Ima~Srd~-~eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~ 78 (161)
++++.=|.-+|-.|-|- ...+-.+ + -.....||+++|+-|++.|..++
T Consensus 112 ~tv~dLL~amli~S~NDAA~aLAe~------v----~Gs~~~Fv~~MN~kAkeLGm~~T 160 (306)
T PRK11669 112 ISRKDMLLLALMSSENRAAASLAHH------Y----PGGYKAFIKAMNAKAKALGMTNT 160 (306)
T ss_pred EEHHHHHHHHHHhCcHHHHHHHHHH------c----CCCHHHHHHHHHHHHHHcCCCCC
Confidence 56653455556556543 3222211 2 12457999999999999998775
No 59
>PF11588 DUF3243: Protein of unknown function (DUF3243); InterPro: IPR021637 This family of proteins with unknown function includes uncharacterised proteins ymfJ and yflH. The family appears to be restricted to Firmicutes.; PDB: 3D0W_B.
Probab=21.28 E-value=2.2e+02 Score=20.49 Aligned_cols=49 Identities=18% Similarity=0.378 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCc---------ChHHHHhhhcCCchHH-HHHHHHHH
Q psy3035 40 LRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFT---------DAAEYWLDAYDTPDFR-DQVAKLWD 100 (161)
Q Consensus 40 L~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~---------d~g~~Wr~~Ye~~~~~-~~~e~lw~ 100 (161)
.+..|..|.+-.|..+. .|+..|-+ ..|+|--...|..|=+ ..+.+||+
T Consensus 3 vl~nf~~wK~~Lg~~v~------------~ae~~Gms~e~i~~~A~~iGdyLA~~vdP~N~EerlLkELW~ 61 (81)
T PF11588_consen 3 VLENFDQWKDFLGDRVE------------QAEKLGMSEETIANLAYQIGDYLAKNVDPKNPEERLLKELWD 61 (81)
T ss_dssp HHHHHHHHHHHHHHHHH------------HHHHHHHHTT----HHHHHHHHHHT-----SHHHHHHHHHHH
T ss_pred HhhhHHHHHHHHHHHHH------------HHHHcCCCHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence 45679999988776643 23333333 3578776777766655 44889997
No 60
>PF13021 DUF3885: Domain of unknown function (DUF3885)
Probab=21.18 E-value=1e+02 Score=19.10 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHH
Q psy3035 100 DQIRPLYLQIHAYTR 114 (161)
Q Consensus 100 ~qi~PLY~qLHayVR 114 (161)
+.|+|||++-|.++-
T Consensus 17 ~~i~~ly~~y~~WIl 31 (38)
T PF13021_consen 17 ERIRPLYEKYNDWIL 31 (38)
T ss_pred HHHHHHHHHHHHHHH
Confidence 368899999888763
No 61
>COG5013 NarG Nitrate reductase alpha subunit [Energy production and conversion]
Probab=20.31 E-value=3.8e+02 Score=27.83 Aligned_cols=69 Identities=29% Similarity=0.520 Sum_probs=47.4
Q ss_pred HHHhHHHHHHHcCCcChHHHHhhhcCCchHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCC
Q psy3035 62 YVDLENEVAVKNNFTDAAEYWLDAYDTPDFRD----------QVAKLWDQIRPLYLQIHAYTRRRLNEKYGDKVVNRRGP 131 (161)
Q Consensus 62 ~V~L~N~aA~~nGf~d~g~~Wr~~Ye~~~~~~----------~~e~lw~qi~PLY~qLHayVR~~L~~~YG~~~v~~~gp 131 (161)
+|+|-.+|-.. +.|.-+-|++--|.++=.. .|..-|+++.-+--.-|.|.- ++||+|.|-.=.|
T Consensus 119 L~emwREAk~~--~gDPV~AWa~IvedP~krk~Yk~aRGkGG~VR~~W~E~~EiIAAA~vyTI----k~YGPDRv~GFSP 192 (1227)
T COG5013 119 LIEMWREAKAR--HGDPVEAWASIVEDPDKRKSYKQARGKGGFVRSSWDEVNELIAAANVYTI----KTYGPDRVAGFSP 192 (1227)
T ss_pred HHHHHHHHHHh--hCCHHHHHHHHHhCHHHHHHHHHhccCCceEEecHHHHHHHHHHhhhhhh----hhcCCccccCcCC
Confidence 33444444333 5677778887776663221 145568888888888888865 4899999988899
Q ss_pred Ccccc
Q psy3035 132 IPAHL 136 (161)
Q Consensus 132 IPAHL 136 (161)
|||--
T Consensus 193 IPAMS 197 (1227)
T COG5013 193 IPAMS 197 (1227)
T ss_pred cchhh
Confidence 99953
No 62
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=20.28 E-value=5.7e+02 Score=22.09 Aligned_cols=49 Identities=20% Similarity=0.413 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhh-------chhHHHhHHHHHHhHHHHHHHcC-CcChHH---HHhhhc
Q psy3035 38 EELRHYWTEFRKKS-------GKQVRNHYKQYVDLENEVAVKNN-FTDAAE---YWLDAY 86 (161)
Q Consensus 38 ~eL~~~W~~Wr~~v-------g~~~r~~y~~~V~L~N~aA~~nG-f~d~g~---~Wr~~Y 86 (161)
.+|..+|.....+. .......+.++.+-.++.+.... +++.-+ .|....
T Consensus 165 ~~l~~a~~~~~~a~~ey~~~l~~~~~~a~~~~~~~l~~~~~~g~~~~s~re~~d~Wi~~a 224 (293)
T PF09712_consen 165 QALFDAWMEYQRASQEYQAQLSEAWMKAFERMMEKLQERAEEGEQIKSWREFYDIWIDAA 224 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcCHHHHHHHHHHHH
Confidence 44555566655544 34556677777777777665543 444444 477544
No 63
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=20.21 E-value=1.2e+02 Score=20.61 Aligned_cols=45 Identities=16% Similarity=0.175 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHhhchhHHHhHHHHHHhHHHHHHHcCCcChHHHHhhhc
Q psy3035 39 ELRHYWTEFRKKSGKQVRNHYKQYVDLENEVAVKNNFTDAAEYWLDAY 86 (161)
Q Consensus 39 eL~~~W~~Wr~~vg~~~r~~y~~~V~L~N~aA~~nGf~d~g~~Wr~~Y 86 (161)
-++.+|..+|.-+|. ++|.+||+=..+.=-.----+..||||...
T Consensus 8 ~~~~~~~~~r~l~G~---~~Ye~Yv~H~~~~HP~~p~ms~~eF~r~r~ 52 (65)
T PF04328_consen 8 AWRRVRWYARLLVGE---PDYERYVEHMRRHHPDEPPMSEREFFRERQ 52 (65)
T ss_pred HHHHHHHHHHHhcCc---HHHHHHHHHHHHHCcCCCCCCHHHHHHHHH
Confidence 356788888988885 579999873322111112345567777553
Done!