Query 029459
Match_columns 193
No_of_seqs 111 out of 324
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 13:15:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029459.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029459hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1349 Gpi-anchor transamidas 100.0 6.8E-65 1.5E-69 441.5 15.2 154 40-193 26-179 (309)
2 KOG1348 Asparaginyl peptidases 100.0 3E-64 6.4E-69 454.4 18.2 156 36-193 38-195 (477)
3 PF01650 Peptidase_C13: Peptid 100.0 3.4E-60 7.3E-65 411.5 15.3 147 43-193 1-147 (256)
4 COG5206 GPI8 Glycosylphosphati 100.0 2.8E-54 6E-59 378.6 14.6 155 39-193 25-179 (382)
5 PF00656 Peptidase_C14: Caspas 97.4 9.3E-05 2E-09 61.1 2.9 75 43-165 1-78 (248)
6 KOG1546 Metacaspase involved i 91.1 2.2 4.9E-05 39.5 9.9 86 38-164 59-150 (362)
7 PRK10629 EnvZ/OmpR regulon mod 87.4 2.4 5.2E-05 33.8 6.5 68 2-81 1-70 (127)
8 KOG1017 Predicted uracil phosp 81.9 1.4 2.9E-05 38.7 3.0 23 62-84 204-226 (267)
9 COG2949 SanA Uncharacterized m 80.5 4.7 0.0001 35.4 5.8 47 36-82 51-130 (235)
10 smart00115 CASc Caspase, inter 75.2 5.1 0.00011 34.4 4.5 56 123-185 51-106 (241)
11 TIGR01653 lactococcin_972 bact 74.4 3.3 7.2E-05 31.6 2.8 26 35-60 27-52 (92)
12 PF14538 Raptor_N: Raptor N-te 68.7 8.2 0.00018 31.6 4.1 54 122-185 70-133 (154)
13 cd00032 CASc Caspase, interleu 67.8 9.9 0.00021 32.5 4.7 58 121-186 51-108 (243)
14 PF12770 CHAT: CHAT domain 64.2 14 0.0003 31.2 4.9 50 118-183 123-184 (287)
15 PRK10834 vancomycin high tempe 62.3 7.6 0.00017 34.2 3.0 34 46-82 85-118 (239)
16 PF02698 DUF218: DUF218 domain 60.5 9.9 0.00021 29.5 3.1 35 46-82 41-75 (155)
17 PF11181 YflT: Heat induced st 58.3 16 0.00034 27.4 3.7 31 57-87 6-36 (103)
18 PF13721 SecD-TM1: SecD export 57.3 49 0.0011 25.1 6.3 36 43-81 31-66 (101)
19 cd06259 YdcF-like YdcF-like. Y 56.3 9.7 0.00021 29.4 2.4 38 43-82 35-72 (150)
20 PRK14125 cell division suppres 50.3 47 0.001 25.4 5.3 45 13-60 9-53 (103)
21 PF12606 RELT: Tumour necrosis 49.6 5.1 0.00011 27.3 -0.2 32 13-63 4-35 (50)
22 PF10686 DUF2493: Protein of u 49.3 19 0.00041 25.7 2.7 22 45-66 5-26 (71)
23 PRK10494 hypothetical protein; 48.1 17 0.00036 31.9 2.8 38 43-82 121-158 (259)
24 cd06183 cyt_b5_reduct_like Cyt 46.9 12 0.00027 30.5 1.7 35 42-83 200-234 (234)
25 PRK10649 hypothetical protein; 44.5 13 0.00028 36.3 1.7 16 150-165 450-465 (577)
26 PF00233 PDEase_I: 3'5'-cyclic 39.0 20 0.00042 30.8 1.8 23 54-76 1-24 (237)
27 COG4566 TtrR Response regulato 38.9 34 0.00074 29.6 3.2 63 114-191 51-122 (202)
28 KOG1552 Predicted alpha/beta h 38.8 32 0.00069 30.8 3.1 42 60-104 112-161 (258)
29 PRK12933 secD preprotein trans 38.4 79 0.0017 31.6 6.0 36 40-80 37-72 (604)
30 PF14681 UPRTase: Uracil phosp 37.3 26 0.00056 29.5 2.2 24 61-84 135-158 (207)
31 TIGR01689 EcbF-BcbF capsule bi 36.7 66 0.0014 25.4 4.3 48 41-98 38-91 (126)
32 KOG1360 5-aminolevulinate synt 34.2 36 0.00079 33.0 2.9 33 58-90 431-467 (570)
33 PRK09598 lipid A phosphoethano 33.0 22 0.00048 34.3 1.3 14 151-164 428-441 (522)
34 PF11121 DUF2639: Protein of u 33.0 22 0.00048 23.3 0.9 16 50-76 3-18 (40)
35 PF00691 OmpA: OmpA family; I 32.8 82 0.0018 22.2 4.0 32 56-87 48-80 (97)
36 PF00884 Sulfatase: Sulfatase; 32.1 48 0.0011 27.4 3.0 14 152-165 238-251 (308)
37 COG2194 Predicted membrane-ass 29.7 30 0.00064 34.0 1.5 13 152-164 444-456 (555)
38 KOG1387 Glycosyltransferase [C 29.3 62 0.0013 30.9 3.4 28 111-138 74-102 (465)
39 PTZ00450 macrophage migration 28.6 76 0.0016 24.5 3.4 29 56-86 74-102 (113)
40 KOG1654 Microtubule-associated 28.5 54 0.0012 26.1 2.5 35 121-165 52-86 (116)
41 cd06212 monooxygenase_like The 28.4 39 0.00085 27.8 1.9 31 44-82 198-228 (232)
42 COG4669 EscJ Type III secretor 27.5 2.1E+02 0.0046 25.6 6.3 26 57-82 60-85 (246)
43 PLN02541 uracil phosphoribosyl 26.9 74 0.0016 27.9 3.4 24 61-84 171-194 (244)
44 COG4899 Uncharacterized protei 26.9 1E+02 0.0022 25.8 3.9 56 79-134 29-85 (166)
45 KOG3339 Predicted glycosyltran 25.4 4.5E+02 0.0097 23.0 7.7 39 44-88 40-78 (211)
46 PF04911 ATP-synt_J: ATP synth 24.7 18 0.00039 25.2 -0.7 19 80-98 29-47 (54)
47 PF04202 Mfp-3: Foot protein 3 24.2 57 0.0012 23.7 1.8 17 11-27 4-20 (71)
48 cd07561 Peptidase_S41_CPP_like 23.9 2.5E+02 0.0054 24.4 6.1 57 122-191 35-92 (256)
49 PRK11598 putative metal depend 23.1 52 0.0011 32.1 1.9 14 152-165 445-458 (545)
50 KOG4667 Predicted esterase [Li 22.1 78 0.0017 28.4 2.6 86 49-140 77-192 (269)
51 PF08869 XisI: XisI protein; 21.8 52 0.0011 25.9 1.3 17 68-84 81-97 (111)
52 cd04508 TUDOR Tudor domains ar 21.7 92 0.002 19.3 2.3 26 145-170 18-43 (48)
53 PF03568 Peptidase_C50: Peptid 21.3 96 0.0021 28.6 3.2 39 126-165 276-320 (383)
54 cd06209 BenDO_FAD_NAD Benzoate 21.0 61 0.0013 26.6 1.7 32 43-82 193-224 (228)
55 cd06215 FNR_iron_sulfur_bindin 20.9 48 0.001 27.1 1.0 29 45-81 199-227 (231)
56 cd08494 PBP2_NikA_DppA_OppA_li 20.9 78 0.0017 28.4 2.4 24 168-191 69-92 (448)
57 TIGR00756 PPR pentatricopeptid 20.9 59 0.0013 17.8 1.1 21 58-78 14-34 (35)
58 cd08490 PBP2_NikA_DppA_OppA_li 20.8 78 0.0017 28.6 2.5 34 154-191 56-89 (470)
59 PF00381 PTS-HPr: PTS HPr comp 20.8 94 0.002 22.1 2.4 42 109-162 27-68 (84)
60 PRK12419 riboflavin synthase s 20.6 2.8E+02 0.0061 23.0 5.5 40 41-84 10-50 (158)
61 COG2143 Thioredoxin-related pr 20.4 2E+02 0.0042 24.6 4.5 38 147-190 113-150 (182)
No 1
>KOG1349 consensus Gpi-anchor transamidase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.8e-65 Score=441.49 Aligned_cols=154 Identities=78% Similarity=1.292 Sum_probs=152.8
Q ss_pred cCCcEEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEEEecCccCCCCCCCCCCeEEeCCCCCccccCCCccccC
Q 029459 40 HTNNWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIILMLADDMACNARNKYPAQVFNNENHKLNLYGDNVEVDY 119 (193)
Q Consensus 40 ~~~~wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIlm~~DDiA~np~Np~pG~i~~~~~~~~n~Y~~~v~IDY 119 (193)
|++||||||+|||+||||||.|||+.+|+.+||.||||+|||+|++||+|||+|||+||+||++.++..|+||+.+++||
T Consensus 26 htnNwAVLv~tSRfwfNYRH~aNvl~~YrsvKrlGipDsqIilmladd~acn~RN~~pg~Vy~n~~~~~nlygd~vevdy 105 (309)
T KOG1349|consen 26 HTNNWAVLVCTSRFWFNYRHVANVLSVYRSVKRLGIPDSQIILMLADDMACNSRNPRPGTVYNNENHALNLYGDDVEVDY 105 (309)
T ss_pred ccCceEEEEecchhhhhHHHHHHHHHHHHHHHHcCCCcccEEEEeccccccccCCCCCcceeccccccccccCCcceeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCCCCeeecCCCCccCHHHHHHHHHHHHHhcC
Q 029459 120 HGYEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGGDEFLKFQDSEELQSHDLADAVKQMKEKRR 193 (193)
Q Consensus 120 ~g~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg~g~i~fpd~~~l~a~dL~~~l~~M~~~kr 193 (193)
+|.+||+|+|+++||||.+..+|++|||.+++.+|||||+|||||+|||||||.|+|+.+||+++++||+|+||
T Consensus 106 rgyevtvEnflr~LTgR~~~~tprSKrlltDe~SNIlIYmtGHGgd~FlKFqd~eelts~dLadai~qm~e~~R 179 (309)
T KOG1349|consen 106 RGYEVTVENFLRVLTGRHPNNTPRSKRLLTDEGSNILIYLTGHGGDGFLKFQDAEELTSDDLADAIQQMWEKKR 179 (309)
T ss_pred ccchhHHHHHHHHHcCCCCCCCchhhhhcccCCCcEEEEEccCCCccceecccHHHhhhHHHHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>KOG1348 consensus Asparaginyl peptidases [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3e-64 Score=454.43 Aligned_cols=156 Identities=35% Similarity=0.608 Sum_probs=147.5
Q ss_pred ccccc-CCcEEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEEEecCccCCCCCCCCCCeEEeCCCCCccccCCC
Q 029459 36 ETTMH-TNNWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIILMLADDMACNARNKYPAQVFNNENHKLNLYGDN 114 (193)
Q Consensus 36 ~~~~~-~~~wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIlm~~DDiA~np~Np~pG~i~~~~~~~~n~Y~~~ 114 (193)
+.+.. +.+||||||||+||||||||||||||||+||++|+|+||||+|||||||+||.||.||+|+|.|+++ ++|. |
T Consensus 38 d~~ddggt~waVLVAGSngyyNYRHQADvcHAYqiLrkgGikeEnIvv~MYDDIA~~~~NPrpG~iiN~P~G~-DvY~-G 115 (477)
T KOG1348|consen 38 DDDDDGGTRWAVLVAGSNGYYNYRHQADVCHAYQILRKGGIKEENIVVMMYDDIANNEENPRPGVIINRPNGK-DVYQ-G 115 (477)
T ss_pred cCCccCceeEEEEEecCCcccchhhhhhHHHHHHHHHhcCCCchhEEEEEehhhhcCCCCCCCceeecCCCch-hhhc-C
Confidence 34444 4999999999999999999999999999999999999999999999999999999999999999995 8995 9
Q ss_pred ccccCCCCCCCHHHHHHHHcCCCCCCCCC-cceecCCCCCcEEEEEeCCCCCCeeecCCCCccCHHHHHHHHHHHHHhcC
Q 029459 115 VEVDYHGYEVNAENFLRVLTGRHKAAVPR-SKRLLSDEGSHILLYMTGHGGDEFLKFQDSEELQSHDLADAVKQMKEKRR 193 (193)
Q Consensus 115 v~IDY~g~~Vt~enfl~VL~G~~~~~~p~-~k~l~s~~~dnVFiY~tgHGg~g~i~fpd~~~l~a~dL~~~l~~M~~~kr 193 (193)
|++||+|++|||+||++||.|+.+...++ +|||.|+|+||||||||||||+|.|.||+++.|+++||+++|++||+.|.
T Consensus 116 vpkDYtg~~Vt~~Nf~aVllGd~savkGGsGKV~~SgpnDhiFiYytDHG~pGvl~mP~~~~l~akdlnevL~kmhk~k~ 195 (477)
T KOG1348|consen 116 VPKDYTGEDVTPQNFLAVLLGDASAVKGGSGKVLKSGPNDHIFIYYTDHGGPGVLGMPTSPDLYAKDLNEVLKKMHKSKT 195 (477)
T ss_pred CCCcccCCcCCHHHHHHHHhcccccccCCCceeeccCCCceEEEEEecCCCCceEecCCCcchhHHHHHHHHHHHHhccc
Confidence 99999999999999999999999988775 49999999999999999999999999999999999999999999999874
No 3
>PF01650 Peptidase_C13: Peptidase C13 family; InterPro: IPR001096 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean). The blood fluke parasite Schistosoma mansoni has two cysteine proteases in its digestive tract, one a cathepsin B-like protease, the other termed hemoglobinase [, ]. The latter has been hard to purify, free of cathepsin B, and expressed forms in Escherichia coli prove to be inactive, suggesting that hemoglobinase may act in association with cathepsin B [, ]. Plant vacuolar processing enzyme and legumain from legumes [] have been shown to have sequence and functional similarity to hemoglobinase. The catalytic residues of the family are currently unknown, but sequence alignments reveal one totally conserved cysteine and two totally conserved histidines.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=100.00 E-value=3.4e-60 Score=411.50 Aligned_cols=147 Identities=54% Similarity=0.955 Sum_probs=142.8
Q ss_pred cEEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEEEecCccCCCCCCCCCCeEEeCCCCCccccCCCccccCCCC
Q 029459 43 NWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIILMLADDMACNARNKYPAQVFNNENHKLNLYGDNVEVDYHGY 122 (193)
Q Consensus 43 ~wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIlm~~DDiA~np~Np~pG~i~~~~~~~~n~Y~~~v~IDY~g~ 122 (193)
|||||||||++|+|||||||+|++||+||++|+||||||||+|||+||||+||+||+||++|++ .|+|. |++|||+|+
T Consensus 1 ~wAvlvagS~~~~NYRh~ad~~~~Y~~l~~~G~~~~~Iil~~~dd~a~~~~Np~~g~i~~~~~~-~n~y~-~~~iDY~g~ 78 (256)
T PF01650_consen 1 NWAVLVAGSNGWFNYRHQADVCHAYQLLKRNGIPDENIILMMYDDIACNPRNPFPGKIFNDPDG-TNVYK-GVEIDYRGE 78 (256)
T ss_pred CEEEEEeccCCceeeeEehHHHHHHHHHHHcCCCCceEEEEecCCccchhhCCCCceEEeCCCc-ccccC-Ccccccccc
Confidence 7999999999999999999999999999999999999999999999999999999999999997 69996 799999999
Q ss_pred CCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCCCCeeecCCCCccCHHHHHHHHHHHHHhcC
Q 029459 123 EVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGGDEFLKFQDSEELQSHDLADAVKQMKEKRR 193 (193)
Q Consensus 123 ~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg~g~i~fpd~~~l~a~dL~~~l~~M~~~kr 193 (193)
+||+++|++||+|++. . +++|+|.++++|+|||||+||||+|+|+||+.+.|+++||+++|++|++++|
T Consensus 79 ~v~~~~fl~vL~G~~~-~-~~~kvl~s~~~D~vfiy~~~HG~~~~l~~~~~~~l~~~~L~~~L~~m~~~~~ 147 (256)
T PF01650_consen 79 DVTPENFLNVLTGDKS-V-PSGKVLNSTENDNVFIYFTGHGGPGFLKFPDGEELTADDLADALDKMHEKKR 147 (256)
T ss_pred ccCHHHHHHHhcCCCC-C-CccccccCCCCCeEEEEEeccCCCCcccCCCcccccHHHHHHHHHHHHhhCC
Confidence 9999999999999998 3 8999999999999999999999999999998899999999999999999986
No 4
>COG5206 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.8e-54 Score=378.56 Aligned_cols=155 Identities=63% Similarity=1.085 Sum_probs=152.5
Q ss_pred ccCCcEEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEEEecCccCCCCCCCCCCeEEeCCCCCccccCCCcccc
Q 029459 39 MHTNNWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIILMLADDMACNARNKYPAQVFNNENHKLNLYGDNVEVD 118 (193)
Q Consensus 39 ~~~~~wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIlm~~DDiA~np~Np~pG~i~~~~~~~~n~Y~~~v~ID 118 (193)
.+++|||||+++||+||||||.|||+.+|..+|+.||||++||+|.|||.|||.||-|||.||++.+...++|++.++||
T Consensus 25 t~tnNwAvLlstSRfwfNYRHmANVl~~Yr~vkrlGipDsQIilm~~dd~acnsRnlfpgsvf~N~Dra~dlyge~~eid 104 (382)
T COG5206 25 TNTNNWAVLLSTSRFWFNYRHMANVLVFYRVVKRLGIPDSQIILMSYDDQACNSRNLFPGSVFNNSDRAGDLYGEDSEID 104 (382)
T ss_pred ccCCceEEEEecccceeehhhhhhHHHHHHHHHHcCCCcceEEEEechhhhhhhcccCCcccccCcccccceeCcccccc
Confidence 78999999999999999999999999999999999999999999999999999999999999999998889999999999
Q ss_pred CCCCCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCCCCeeecCCCCccCHHHHHHHHHHHHHhcC
Q 029459 119 YHGYEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGGDEFLKFQDSEELQSHDLADAVKQMKEKRR 193 (193)
Q Consensus 119 Y~g~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg~g~i~fpd~~~l~a~dL~~~l~~M~~~kr 193 (193)
|+|.+||+|+|.++|+-+..+..|.+||+.+++++|||||||||||++||||||-|+|+++||++++++|+++||
T Consensus 105 Y~gyevTve~firLLt~r~~en~p~sKrlltdE~SNIfIYmtGHGgd~FlKFqdaeemtseDladai~ql~~~kR 179 (382)
T COG5206 105 YSGYEVTVEVFIRLLTARSGENHPKSKRLLTDESSNIFIYMTGHGGDAFLKFQDAEEMTSEDLADAISQLAAKKR 179 (382)
T ss_pred cccccchHHHHHHHHHhhccCCChhhhhhcccccCcEEEEEccCCCccceecccHHHhhhHHHHHHHHHHHHhhh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999997
No 5
>PF00656 Peptidase_C14: Caspase domain; InterPro: IPR011600 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences represent the p20 (20kDa) and p10 (10kDa) subunits of caspases, which together form the catalytic domain of the caspase and are derived from the p45 (45 kDa) precursor (IPR002398 from INTERPRO) []. Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases that belong to the MEROPS peptidase family C14 (caspase family, clan CD) based on the architecture of their catalytic dyad or triad []. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases act as cysteine proteases, using the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The catalytic cysteine and histidine residues are on the p20 subunit after cleavage of the p45 precursor. Caspases are mainly involved in mediating cell death (apoptosis) [, , ]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspase-mediated apoptosis follows two main pathways, one extrinsic and the other intrinsic or mitochondrial-mediated. The extrinsic pathway involves the stimulation of various TNF (tumour necrosis factor) cell surface receptors on cells targeted to die by various TNF cytokines that are produced by cells such as cytotoxic T cells. The activated receptor transmits the signal to the cytoplasm by recruiting FADD, which forms a death-inducing signalling complex (DISC) with caspase-8. The subsequent activation of caspase-8 initiates the apoptosis cascade involving caspases 3, 4, 6, 7, 9 and 10. The intrinsic pathway arises from signals that originate within the cell as a consequence of cellular stress or DNA damage. The stimulation or inhibition of different Bcl-2 family receptors results in the leakage of cytochrome c from the mitochondria, and the formation of an apoptosome composed of cytochrome c, Apaf1 and caspase-9. The subsequent activation of caspase-9 initiates the apoptosis cascade involving caspases 3 and 7, among others. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. The different caspases have different domain architectures depending upon where they fit into the apoptosis cascades, however they all carry the catalytic p10 and p20 subunits. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36 from EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1M72_C 2NN3_C 3V4L_A 3IBF_B 2QLF_D 2QLB_C 3IBC_B 2QL9_A 3R5K_B 3H1P_A ....
Probab=97.44 E-value=9.3e-05 Score=61.14 Aligned_cols=75 Identities=20% Similarity=0.400 Sum_probs=55.2
Q ss_pred cEEEEEecCCCCc-cchh--hhhHHHHHHHHHhCCCCCCCEEEEecCccCCCCCCCCCCeEEeCCCCCccccCCCccccC
Q 029459 43 NWAVLVCTSRFWF-NYRH--MANTLSLYRTVKRLGVPDERIILMLADDMACNARNKYPAQVFNNENHKLNLYGDNVEVDY 119 (193)
Q Consensus 43 ~wAVlVagS~~w~-NYRH--qadv~~~Y~~Lk~~Gipde~IIlm~~DDiA~np~Np~pG~i~~~~~~~~n~Y~~~v~IDY 119 (193)
+|||||+-+.+=. +-++ ..|+-.+.+.|++.|++.++| ++ ++
T Consensus 1 ~~AliIg~~~y~~~~~L~~~~~D~~~~~~~L~~~gf~~~~~-l~--~~-------------------------------- 45 (248)
T PF00656_consen 1 KRALIIGVNYYQNPPPLPGAVNDAEAMAEALEKLGFDVENI-LI--DN-------------------------------- 45 (248)
T ss_dssp EEEEEEEESSTSSTCHCTTHHHHHHHHHHHHHHTTEEEEEE-EE--ES--------------------------------
T ss_pred CEEEEEEeeCCCCCCCCCCHHHHHHHHHHHHHHcCCceeec-cc--cc--------------------------------
Confidence 4899999886321 2233 378999999999999999998 33 22
Q ss_pred CCCCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCCC
Q 029459 120 HGYEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGGD 165 (193)
Q Consensus 120 ~g~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg~ 165 (193)
+|.+++.+.|+--... ..++|.++|||+|||..
T Consensus 46 ----~t~~~i~~~l~~l~~~---------~~~~D~~~~yfsGHG~~ 78 (248)
T PF00656_consen 46 ----ATRANILKALRELLQR---------AQPGDSVVFYFSGHGIQ 78 (248)
T ss_dssp ----SSHHHHHHHHHHHHTS---------GGTCSEEEEEEESEEET
T ss_pred ----hHHHHHHHHHhhhhcc---------CCCCCeeEEEEeccccc
Confidence 6778888887744321 13789999999999965
No 6
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=91.12 E-value=2.2 Score=39.50 Aligned_cols=86 Identities=17% Similarity=0.337 Sum_probs=54.5
Q ss_pred cccCCcEEEEEecCCCCccchhh-----hhHHHHHHHH-HhCCCCCCCEEEEecCccCCCCCCCCCCeEEeCCCCCcccc
Q 029459 38 TMHTNNWAVLVCTSRFWFNYRHM-----ANTLSLYRTV-KRLGVPDERIILMLADDMACNARNKYPAQVFNNENHKLNLY 111 (193)
Q Consensus 38 ~~~~~~wAVlVagS~~w~NYRHq-----adv~~~Y~~L-k~~Gipde~IIlm~~DDiA~np~Np~pG~i~~~~~~~~n~Y 111 (193)
.-++++-||||.-+ |-|=+++ .||-+|.+.| .+.||+.|+|.+|.-+| .+|. ..|
T Consensus 59 ~~~gkrrAvLiGIN--Y~gTk~ELrGCINDv~~M~~~Lv~rfGFs~ddI~~LtDt~-----~s~~-----~~P------- 119 (362)
T KOG1546|consen 59 QMAGKRRAVLIGIN--YPGTKNELRGCINDVHRMRKLLVERFGFSEDDILMLTDTD-----ESPV-----RIP------- 119 (362)
T ss_pred cccccceEEEEeec--CCCcHHHHhhhHHHHHHHHHHHHHhhCCChhheEEEecCC-----Cccc-----ccC-------
Confidence 34677889999853 2222332 5788999985 55799999998775222 1211 112
Q ss_pred CCCccccCCCCCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCC
Q 029459 112 GDNVEVDYHGYEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGG 164 (193)
Q Consensus 112 ~~~v~IDY~g~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg 164 (193)
|.+|+.+.|.--.+ ...+.|-+|+=|||||+
T Consensus 120 -------------T~~Nir~Al~wLV~---------~aq~gD~LvfHYSGHGt 150 (362)
T KOG1546|consen 120 -------------TGKNIRRALRWLVE---------SAQPGDSLVFHYSGHGT 150 (362)
T ss_pred -------------cHHHHHHHHHHHHh---------cCCCCCEEEEEecCCCC
Confidence 23455666653322 23567999999999998
No 7
>PRK10629 EnvZ/OmpR regulon moderator; Provisional
Probab=87.44 E-value=2.4 Score=33.76 Aligned_cols=68 Identities=10% Similarity=0.018 Sum_probs=42.8
Q ss_pred cchhccccchh-hHHHHHHHHHHHHHhhhhccccccccccCCcEEEEEecC-CCCccchhhhhHHHHHHHHHhCCCCCCC
Q 029459 2 MVRFKMYNSFG-FKSLAAMLLFFILSISISYRASAETTMHTNNWAVLVCTS-RFWFNYRHMANTLSLYRTVKRLGVPDER 79 (193)
Q Consensus 2 ~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~wAVlVagS-~~w~NYRHqadv~~~Y~~Lk~~Gipde~ 79 (193)
|.+.+|-+|+- .|-+..++++. .+.+-++. -++.-||=|+++ +|=-- .|...+||.|++.||+.+.
T Consensus 1 ~~~~~m~nryp~WKylli~~vl~--~lyAlPnl------ygedpavQIs~~~~g~~~----~~~~~v~~~L~~~gI~~ks 68 (127)
T PRK10629 1 MINPRMSLRQLAWLGAVLLLLAA--LLLAWSAL------RQQESTLAIRAVHQGASL----PDGFYVYQHLDANGIHIKS 68 (127)
T ss_pred CCcchhccccHHHHHHHHHHHHH--HHHHChhc------cCCCceEEEecCCCCCcc----chHHHHHHHHHHCCCCcce
Confidence 56677777777 44431111111 23333333 344558888876 55322 8999999999999999887
Q ss_pred EE
Q 029459 80 II 81 (193)
Q Consensus 80 II 81 (193)
|.
T Consensus 69 i~ 70 (127)
T PRK10629 69 IT 70 (127)
T ss_pred EE
Confidence 75
No 8
>KOG1017 consensus Predicted uracil phosphoribosyltransferase [General function prediction only]
Probab=81.95 E-value=1.4 Score=38.72 Aligned_cols=23 Identities=35% Similarity=0.508 Sum_probs=21.2
Q ss_pred hHHHHHHHHHhCCCCCCCEEEEe
Q 029459 62 NTLSLYRTVKRLGVPDERIILML 84 (193)
Q Consensus 62 dv~~~Y~~Lk~~Gipde~IIlm~ 84 (193)
-||.+-..||++|+||++|||..
T Consensus 204 TV~~Av~VL~EhgVp~s~IiL~s 226 (267)
T KOG1017|consen 204 TVCKAVEVLKEHGVPDSNIILVS 226 (267)
T ss_pred cHHHHHHHHHHcCCCcccEEEEE
Confidence 59999999999999999999874
No 9
>COG2949 SanA Uncharacterized membrane protein [Function unknown]
Probab=80.50 E-value=4.7 Score=35.42 Aligned_cols=47 Identities=23% Similarity=0.454 Sum_probs=36.3
Q ss_pred cccccCCcEEEEEecCCC--------Cccchhhhh-------------------------HHHHHHHHHhCCCCCCCEEE
Q 029459 36 ETTMHTNNWAVLVCTSRF--------WFNYRHMAN-------------------------TLSLYRTVKRLGVPDERIIL 82 (193)
Q Consensus 36 ~~~~~~~~wAVlVagS~~--------w~NYRHqad-------------------------v~~~Y~~Lk~~Gipde~IIl 82 (193)
.++-+..+.+|+..||++ ||-||-+|- .-.|-+.|++.|+|.++|.+
T Consensus 51 ~~~lP~r~vgvVLGtsky~~~g~~N~yy~~Ri~aA~~ly~~gKV~~LLlSGDN~~~sYnEp~tM~kdL~~~GVp~~~i~l 130 (235)
T COG2949 51 IQDLPARQVGVVLGTSKYLAKGPPNRYYTYRIDAAIALYKAGKVNYLLLSGDNATVSYNEPRTMRKDLIAAGVPAKNIFL 130 (235)
T ss_pred hhhCCccceEEEEeccccccCCCccHhHHHHHHHHHHHHhcCCeeEEEEecCCCcccccchHHHHHHHHHcCCCHHHeee
Confidence 355678889999998854 455777653 45688899999999999975
No 10
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=75.16 E-value=5.1 Score=34.40 Aligned_cols=56 Identities=16% Similarity=0.198 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCCCCeeecCCCCccCHHHHHHHH
Q 029459 123 EVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGGDEFLKFQDSEELQSHDLADAV 185 (193)
Q Consensus 123 ~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg~g~i~fpd~~~l~a~dL~~~l 185 (193)
++|.+.+.+.|.--.. +..-...|-+++|+.+||+.++|.-.|++.+.-++|.+.|
T Consensus 51 dlt~~em~~~l~~~~~-------~~~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f 106 (241)
T smart00115 51 NLTAEEMLEELKEFAE-------RPEHSDSDSFVCVLLSHGEEGGIYGTDHSPLPLDEIFSLF 106 (241)
T ss_pred CCCHHHHHHHHHHHHh-------ccccCCCCEEEEEEcCCCCCCeEEEecCCEEEHHHHHHhc
Confidence 4555566666653211 1112345678899999999999998887778888877766
No 11
>TIGR01653 lactococcin_972 bacteriocin, lactococcin 972 family. This model represents bacteriocins related to lactococcin 972. Members tend to be found in association with a seven transmembrane putative immunity protein.
Probab=74.43 E-value=3.3 Score=31.56 Aligned_cols=26 Identities=23% Similarity=0.364 Sum_probs=18.3
Q ss_pred ccccccCCcEEEEEecCCCCccchhh
Q 029459 35 AETTMHTNNWAVLVCTSRFWFNYRHM 60 (193)
Q Consensus 35 ~~~~~~~~~wAVlVagS~~w~NYRHq 60 (193)
......+-.|=.-...++-|.||.|-
T Consensus 27 ~~~~~~Ggtw~~~~G~g~~ySnY~H~ 52 (92)
T TIGR01653 27 AAQSTQGGTWWKTYGMGRHYSNYWHN 52 (92)
T ss_pred ceEEecCcceEeccCCCceeeeeecC
Confidence 44556677777776667778888875
No 12
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=68.74 E-value=8.2 Score=31.58 Aligned_cols=54 Identities=19% Similarity=0.317 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCCCC------eeecCCCC----ccCHHHHHHHH
Q 029459 122 YEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGGDE------FLKFQDSE----ELQSHDLADAV 185 (193)
Q Consensus 122 ~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg~g------~i~fpd~~----~l~a~dL~~~l 185 (193)
-|.|+|.+.+.+..-.. ..+++.|++.|.|||-|. +-.|.++- .++-.||.+.+
T Consensus 70 ~dpt~e~~~~~~~~~R~----------~a~~~RvLFHYnGhGvP~Pt~~GeIw~f~~~~tqyip~si~dL~~~l 133 (154)
T PF14538_consen 70 LDPTVEDLKRLCQSLRR----------NAKDERVLFHYNGHGVPRPTENGEIWVFNKNYTQYIPLSIYDLQSWL 133 (154)
T ss_pred cCCCHHHHHHHHHHHHh----------hCCCceEEEEECCCCCCCCCCCCeEEEEcCCCCcceEEEHHHHHHhc
Confidence 46666666665554321 234688999999999983 55664431 37777776654
No 13
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=67.76 E-value=9.9 Score=32.49 Aligned_cols=58 Identities=12% Similarity=0.167 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCCCCeeecCCCCccCHHHHHHHHH
Q 029459 121 GYEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGGDEFLKFQDSEELQSHDLADAVK 186 (193)
Q Consensus 121 g~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg~g~i~fpd~~~l~a~dL~~~l~ 186 (193)
..++|.+.+.+.|.--... .....|-+++|+.+||..++|.-.|.+.+.-++|.+.|.
T Consensus 51 ~~nlt~~~~~~~l~~f~~~--------~~~~~d~~v~~~~sHG~~~~l~~~D~~~v~l~~i~~~f~ 108 (243)
T cd00032 51 KNNLTAEEILEELKEFASP--------DHSDSDSFVCVILSHGEEGGIYGTDGDVVPIDEITSLFN 108 (243)
T ss_pred eCCCCHHHHHHHHHHHHhc--------cCCCCCeeEEEECCCCCCCEEEEecCcEEEHHHHHHhhc
Confidence 3456666676666532210 123456688999999999999988877788788776664
No 14
>PF12770 CHAT: CHAT domain
Probab=64.19 E-value=14 Score=31.17 Aligned_cols=50 Identities=28% Similarity=0.428 Sum_probs=35.7
Q ss_pred cCCCCCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCCCC-------eeecC-----CCCccCHHHHHH
Q 029459 118 DYHGYEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGGDE-------FLKFQ-----DSEELQSHDLAD 183 (193)
Q Consensus 118 DY~g~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg~g-------~i~fp-----d~~~l~a~dL~~ 183 (193)
-..+.+.|.++++..|... .-+ .|.|+|||... .|.+. +...+++.||.+
T Consensus 123 ~~~~~~at~~~l~~~l~~~---------------~~~-ilH~a~Hg~~~~~~~~~~~l~l~~~~~~~~~~l~~~~l~~ 184 (287)
T PF12770_consen 123 VLVGPEATKDALLEALERR---------------GPD-ILHFAGHGTFDPDPPDQSGLVLSDESGQEDGLLSAEELAQ 184 (287)
T ss_pred EeeccCCCHHHHHhhhccC---------------CCC-EEEEEcccccCCCCCCCCEEEEeccCCCCCcccCHHHHHh
Confidence 3456666777777777222 222 49999999977 88886 456899999987
No 15
>PRK10834 vancomycin high temperature exclusion protein; Provisional
Probab=62.29 E-value=7.6 Score=34.16 Aligned_cols=34 Identities=15% Similarity=0.283 Sum_probs=23.6
Q ss_pred EEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEE
Q 029459 46 VLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIIL 82 (193)
Q Consensus 46 VlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIl 82 (193)
+||||.++=.. ...+-.|.+.|.++|||++.|++
T Consensus 85 ilvSGg~~~~~---~~Ea~~M~~yLi~~GVp~e~Ii~ 118 (239)
T PRK10834 85 LLLSGDNALQS---YNEPMTMRKDLIAAGVDPSDIVL 118 (239)
T ss_pred EEEeCCCCCCC---CCHHHHHHHHHHHcCCCHHHEEe
Confidence 55565443111 24566689999999999999985
No 16
>PF02698 DUF218: DUF218 domain; InterPro: IPR003848 This domain of unknown function is found in several uncharacterised proteins.; PDB: 3CA8_A.
Probab=60.53 E-value=9.9 Score=29.51 Aligned_cols=35 Identities=29% Similarity=0.330 Sum_probs=20.5
Q ss_pred EEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEE
Q 029459 46 VLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIIL 82 (193)
Q Consensus 46 VlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIl 82 (193)
||++|..+...+ ...+-.+-+.|.+.|+|+++|++
T Consensus 41 il~SGg~~~~~~--~~ea~~~~~~l~~~gvp~~~I~~ 75 (155)
T PF02698_consen 41 ILFSGGYGHGDG--RSEAEAMRDYLIELGVPEERIIL 75 (155)
T ss_dssp EEEE--SSTTHT--S-HHHHHHHHHHHT---GGGEEE
T ss_pred EEECCCCCCCCC--CCHHHHHHHHHHhcccchheeEc
Confidence 788886666553 34455556677888999999986
No 17
>PF11181 YflT: Heat induced stress protein YflT
Probab=58.30 E-value=16 Score=27.40 Aligned_cols=31 Identities=23% Similarity=0.398 Sum_probs=25.9
Q ss_pred chhhhhHHHHHHHHHhCCCCCCCEEEEecCc
Q 029459 57 YRHMANTLSLYRTVKRLGVPDERIILMLADD 87 (193)
Q Consensus 57 YRHqadv~~~Y~~Lk~~Gipde~IIlm~~DD 87 (193)
|.=+..+..+=+.|++.|+..++|.++..|+
T Consensus 6 ~~~~~E~~~~I~~L~~~Gy~~ddI~Vva~d~ 36 (103)
T PF11181_consen 6 YDNEEEALSAIEELKAQGYSEDDIYVVAKDK 36 (103)
T ss_pred ECCHHHHHHHHHHHHHcCCCcccEEEEEcCc
Confidence 3446788888999999999999999998544
No 18
>PF13721 SecD-TM1: SecD export protein N-terminal TM region
Probab=57.31 E-value=49 Score=25.10 Aligned_cols=36 Identities=17% Similarity=0.225 Sum_probs=26.1
Q ss_pred cEEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEE
Q 029459 43 NWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERII 81 (193)
Q Consensus 43 ~wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~II 81 (193)
.=||-|++++.=- ...+...+++.|++.||+.+.|.
T Consensus 31 ~pAvqIs~~~~~~---~~~~~~~v~~~L~~~~I~~k~i~ 66 (101)
T PF13721_consen 31 DPAVQISASSAGV---QLPDAFQVEQALKAAGIAVKSIE 66 (101)
T ss_pred CCcEEEecCCCCc---cCChHHHHHHHHHHCCCCcceEE
Confidence 4477788764222 34556699999999999988776
No 19
>cd06259 YdcF-like YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX, which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis.
Probab=56.30 E-value=9.7 Score=29.39 Aligned_cols=38 Identities=24% Similarity=0.198 Sum_probs=26.8
Q ss_pred cEEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEE
Q 029459 43 NWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIIL 82 (193)
Q Consensus 43 ~wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIl 82 (193)
.--||++|..+..... +.+-.+.+.|.+.|+|++.|++
T Consensus 35 ~~~ii~sGg~~~~~~~--~ea~~m~~~l~~~gv~~~~I~~ 72 (150)
T cd06259 35 APKLIVSGGQGPGEGY--SEAEAMARYLIELGVPAEAILL 72 (150)
T ss_pred CCEEEEcCCCCCCCCC--CHHHHHHHHHHHcCCCHHHeee
Confidence 3357778876655333 4444566889999999998885
No 20
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=50.32 E-value=47 Score=25.39 Aligned_cols=45 Identities=11% Similarity=0.039 Sum_probs=24.0
Q ss_pred hHHHHHHHHHHHHHhhhhccccccccccCCcEEEEEecCCCCccchhh
Q 029459 13 FKSLAAMLLFFILSISISYRASAETTMHTNNWAVLVCTSRFWFNYRHM 60 (193)
Q Consensus 13 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~wAVlVagS~~w~NYRHq 60 (193)
+..+.+++|++++.+....+.+. ...+-|.+.|....-.|..-++
T Consensus 9 ~~~ii~~~l~~~~~~~~~~~~~~---~~~~~~~~tV~~GDTLW~IA~~ 53 (103)
T PRK14125 9 HVSIFFVLTALVLLIFVYATVPV---DKNQYVEITVQEGDTLWALADQ 53 (103)
T ss_pred HHHHHHHHHHHHHHHHHHccccc---CCCCcEEEEECCCCCHHHHHHH
Confidence 34444556665555544333322 2345667777777766665544
No 21
>PF12606 RELT: Tumour necrosis factor receptor superfamily member 19; InterPro: IPR022248 The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). RELT (receptor expressed in lymphoid tissues) is a member of the TNFR superfamily. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1 []. RELT like proteins 1 and 2 (RELL1 and RELL2) are two RELT homologues that bind to RELT. The expression of RELL1 at the mRNA level is ubiquitous, whereas expression of RELL2 mRNA is more restricted to particular tissues [].
Probab=49.56 E-value=5.1 Score=27.33 Aligned_cols=32 Identities=22% Similarity=0.492 Sum_probs=19.7
Q ss_pred hHHHHHHHHHHHHHhhhhccccccccccCCcEEEEEecCCCCccchhhhhH
Q 029459 13 FKSLAAMLLFFILSISISYRASAETTMHTNNWAVLVCTSRFWFNYRHMANT 63 (193)
Q Consensus 13 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~wAVlVagS~~w~NYRHqadv 63 (193)
|..+.+++++++|..++- .+|+++ .|||..|.
T Consensus 4 ~~iV~i~iv~~lLg~~I~------------------~~~K~y-gYkht~d~ 35 (50)
T PF12606_consen 4 FLIVSIFIVMGLLGLSIC------------------TTLKAY-GYKHTVDP 35 (50)
T ss_pred hHHHHHHHHHHHHHHHHH------------------HHhhcc-ccccccCC
Confidence 455666777777776432 344443 48888775
No 22
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=49.30 E-value=19 Score=25.73 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=18.4
Q ss_pred EEEEecCCCCccchhhhhHHHH
Q 029459 45 AVLVCTSRFWFNYRHMANTLSL 66 (193)
Q Consensus 45 AVlVagS~~w~NYRHqadv~~~ 66 (193)
-|||+|||.|.++..-.++|..
T Consensus 5 rVli~GgR~~~D~~~i~~~Ld~ 26 (71)
T PF10686_consen 5 RVLITGGRDWTDHELIWAALDK 26 (71)
T ss_pred EEEEEECCccccHHHHHHHHHH
Confidence 5899999999998887777654
No 23
>PRK10494 hypothetical protein; Provisional
Probab=48.15 E-value=17 Score=31.91 Aligned_cols=38 Identities=24% Similarity=0.212 Sum_probs=26.7
Q ss_pred cEEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEE
Q 029459 43 NWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIIL 82 (193)
Q Consensus 43 ~wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIl 82 (193)
.--||++|..+..+- .+++-.+-+.+++.|+|++.|++
T Consensus 121 ~~~ii~SGg~~~~~~--~sEA~~~~~~l~~lGVp~~~Ii~ 158 (259)
T PRK10494 121 GAKLIFTGGAAKTNT--VSTAEVGARVAQSLGVPREDIIT 158 (259)
T ss_pred CCEEEEECCCCCCCC--CCHHHHHHHHHHHcCCCHHHeee
Confidence 345888887764442 34556667788899999998874
No 24
>cd06183 cyt_b5_reduct_like Cytochrome b5 reductase catalyzes the reduction of 2 molecules of cytochrome b5 using NADH as an electron donor. Like ferredoxin reductases, these proteins have an N-terminal FAD binding subdomain and a C-terminal NADH binding subdomain, separated by a cleft, which accepts FAD. The NADH-binding moiety interacts with part of the FAD and resembles a Rossmann fold. However, NAD is bound differently than in canonical Rossmann fold proteins. Nitrate reductases, flavoproteins similar to pyridine nucleotide cytochrome reductases, catalyze the reduction of nitrate to nitrite. The enzyme can be divided into three functional fragments that bind the cofactors molybdopterin, heme-iron, and FAD/NADH.
Probab=46.89 E-value=12 Score=30.48 Aligned_cols=35 Identities=20% Similarity=0.303 Sum_probs=25.7
Q ss_pred CcEEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEEE
Q 029459 42 NNWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIILM 83 (193)
Q Consensus 42 ~~wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIlm 83 (193)
..-.+.|||+.++-+ -.+.+.|++.|+|+++|.+|
T Consensus 200 ~~~~~~icGp~~~~~-------~~~~~~l~~~G~~~~~i~~~ 234 (234)
T cd06183 200 EDTLVLVCGPPPMIE-------GAVKGLLKELGYKKDNVFKF 234 (234)
T ss_pred CCeEEEEECCHHHHH-------HHHHHHHHHcCCCHHHEEeC
Confidence 345678888876542 15667788999999999875
No 25
>PRK10649 hypothetical protein; Provisional
Probab=44.53 E-value=13 Score=36.28 Aligned_cols=16 Identities=25% Similarity=0.686 Sum_probs=13.4
Q ss_pred CCCCcEEEEEeCCCCC
Q 029459 150 DEGSHILLYMTGHGGD 165 (193)
Q Consensus 150 ~~~dnVFiY~tgHGg~ 165 (193)
..++.++||++|||..
T Consensus 450 ~~~nt~iiy~SDHGe~ 465 (577)
T PRK10649 450 TDPNGFLVYFSDHGEE 465 (577)
T ss_pred CCCCeEEEEECCCCcc
Confidence 3478899999999975
No 26
>PF00233 PDEase_I: 3'5'-cyclic nucleotide phosphodiesterase; InterPro: IPR002073 The cyclic nucleotide phosphodiesterases (PDE) comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They are divided into 11 families. They regulate the localisation, duration and amplitude of cyclic nucleotide signalling within subcellular domains. PDEs are therefore important for signal transduction. PDE enzymes are often targets for pharmacological inhibition due to their unique tissue distribution, structural properties, and functional properties. Inhibitors include: Roflumilast for chronic obstructive pulmonary disease and asthma [], Sildenafil for erectile dysfunction [] and Cilostazol for peripheral arterial occlusive disease [], amongst others. Retinal 3',5'-cGMP phosphodiesterase is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction. In rod cells, PDE is oligomeric, comprising an alpha-, a beta- and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion. This entry represents the catalytic domain of PDE which is multihelical and can be divided into three subdomains.; GO: 0004114 3',5'-cyclic-nucleotide phosphodiesterase activity, 0007165 signal transduction; PDB: 3I8V_A 3TVX_A 2QYK_A 1ZKL_A 3G3N_A 4DFF_B 2OUS_B 3SNL_A 2OUY_A 2OUP_B ....
Probab=39.03 E-value=20 Score=30.81 Aligned_cols=23 Identities=30% Similarity=0.631 Sum_probs=19.0
Q ss_pred CccchhhhhHHH-HHHHHHhCCCC
Q 029459 54 WFNYRHMANTLS-LYRTVKRLGVP 76 (193)
Q Consensus 54 w~NYRHqadv~~-~Y~~Lk~~Gip 76 (193)
|.|.+|.+||++ +|.+|++.++.
T Consensus 1 yHN~~Ha~dV~q~~~~ll~~~~~~ 24 (237)
T PF00233_consen 1 YHNFRHAADVLQFVYYLLSNGGLR 24 (237)
T ss_dssp SSSHHHHHHHHHHHHHHHHHGGGG
T ss_pred CCCHHHHHHHHHHHHHHHHccCcc
Confidence 689999999999 77778877753
No 27
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=38.88 E-value=34 Score=29.61 Aligned_cols=63 Identities=21% Similarity=0.325 Sum_probs=42.1
Q ss_pred CccccCCCCCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCC---------CCeeecCCCCccCHHHHHHH
Q 029459 114 NVEVDYHGYEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGG---------DEFLKFQDSEELQSHDLADA 184 (193)
Q Consensus 114 ~v~IDY~g~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg---------~g~i~fpd~~~l~a~dL~~~ 184 (193)
++..|-+--..+--.|.+-|..+... -=-|++||||- .|-+-|=. ..+..++|.++
T Consensus 51 clllDvrMPg~sGlelq~~L~~~~~~--------------~PVIfiTGhgDIpmaV~AmK~GAvDFLe-KP~~~q~Llda 115 (202)
T COG4566 51 CLLLDVRMPGMSGLELQDRLAERGIR--------------LPVIFLTGHGDIPMAVQAMKAGAVDFLE-KPFSEQDLLDA 115 (202)
T ss_pred eEEEecCCCCCchHHHHHHHHhcCCC--------------CCEEEEeCCCChHHHHHHHHcchhhHHh-CCCchHHHHHH
Confidence 34455555555556666666655432 11389999997 36666654 47899999999
Q ss_pred HHHHHHh
Q 029459 185 VKQMKEK 191 (193)
Q Consensus 185 l~~M~~~ 191 (193)
++...+.
T Consensus 116 v~~Al~~ 122 (202)
T COG4566 116 VERALAR 122 (202)
T ss_pred HHHHHHH
Confidence 9988764
No 28
>KOG1552 consensus Predicted alpha/beta hydrolase [General function prediction only]
Probab=38.80 E-value=32 Score=30.79 Aligned_cols=42 Identities=31% Similarity=0.464 Sum_probs=31.4
Q ss_pred hhhHHHHHHHHHh-CCCCCCCEEEEecC-------ccCCCCCCCCCCeEEeCC
Q 029459 60 MANTLSLYRTVKR-LGVPDERIILMLAD-------DMACNARNKYPAQVFNNE 104 (193)
Q Consensus 60 qadv~~~Y~~Lk~-~Gipde~IIlm~~D-------DiA~np~Np~pG~i~~~~ 104 (193)
.+|+-++|+.||+ .| ++|+|||+-.- |.| .|+|..|.|-..|
T Consensus 112 y~Di~avye~Lr~~~g-~~~~Iil~G~SiGt~~tv~La--sr~~~~alVL~SP 161 (258)
T KOG1552|consen 112 YADIKAVYEWLRNRYG-SPERIILYGQSIGTVPTVDLA--SRYPLAAVVLHSP 161 (258)
T ss_pred hhhHHHHHHHHHhhcC-CCceEEEEEecCCchhhhhHh--hcCCcceEEEecc
Confidence 5999999999988 57 99999998532 223 2455777777766
No 29
>PRK12933 secD preprotein translocase subunit SecD; Reviewed
Probab=38.44 E-value=79 Score=31.57 Aligned_cols=36 Identities=22% Similarity=0.220 Sum_probs=28.6
Q ss_pred cCCcEEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCE
Q 029459 40 HTNNWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERI 80 (193)
Q Consensus 40 ~~~~wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~I 80 (193)
-++.-||-|++.++ .++....+.+.|++.||+.+.+
T Consensus 37 y~~~pavqis~~~~-----~~~~~~~~~~~l~~~~i~~~~~ 72 (604)
T PRK12933 37 YGEDAAVQVSAKAG-----LLLNVVELRQLLQAQGINVKRI 72 (604)
T ss_pred cCCCCeEEEecCCC-----CcchHHHHHHHHHHCCCCCceE
Confidence 34455888998876 6788899999999999876554
No 30
>PF14681 UPRTase: Uracil phosphoribosyltransferase; PDB: 1V9S_B 1UPF_A 1UPU_D 1JLR_B 1BD4_A 1BD3_C 1JLS_D 1XTV_C 1XTU_H 3G6W_C ....
Probab=37.32 E-value=26 Score=29.47 Aligned_cols=24 Identities=29% Similarity=0.581 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHhCCCCCCCEEEEe
Q 029459 61 ANTLSLYRTVKRLGVPDERIILML 84 (193)
Q Consensus 61 adv~~~Y~~Lk~~Gipde~IIlm~ 84 (193)
..+|.+.+.|+++|+++++|+++.
T Consensus 135 ~s~~~ai~~L~~~G~~~~~I~~v~ 158 (207)
T PF14681_consen 135 GSAIAAIEILKEHGVPEENIIIVS 158 (207)
T ss_dssp HHHHHHHHHHHHTTG-GGEEEEEE
T ss_pred hhHHHHHHHHHHcCCCcceEEEEE
Confidence 578999999999999999999885
No 31
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=36.70 E-value=66 Score=25.39 Aligned_cols=48 Identities=13% Similarity=0.235 Sum_probs=33.8
Q ss_pred CCcEEEEEecCCCCccch------hhhhHHHHHHHHHhCCCCCCCEEEEecCccCCCCCCCCCC
Q 029459 41 TNNWAVLVCTSRFWFNYR------HMANTLSLYRTVKRLGVPDERIILMLADDMACNARNKYPA 98 (193)
Q Consensus 41 ~~~wAVlVagS~~w~NYR------Hqadv~~~Y~~Lk~~Gipde~IIlm~~DDiA~np~Np~pG 98 (193)
.+.+-|+++|+|....+. .+...-...+.|.++|+|-++|++ +-|++|
T Consensus 38 ~~G~~IiiaTGR~~~~~~~n~~~i~~~~~~~t~~wL~k~~ipYd~l~~----------~kp~~~ 91 (126)
T TIGR01689 38 ALGFEIVISSSRNMRTYEGNVGKINIHTLPIIILWLNQHNVPYDEIYV----------GKPWCG 91 (126)
T ss_pred HCCCEEEEECCCCchhhhccccccchhhHHHHHHHHHHcCCCCceEEe----------CCCcCC
Confidence 345679999999877655 111222345778999999999984 468888
No 32
>KOG1360 consensus 5-aminolevulinate synthase [Coenzyme transport and metabolism]
Probab=34.21 E-value=36 Score=32.99 Aligned_cols=33 Identities=27% Similarity=0.385 Sum_probs=28.4
Q ss_pred hhhhhHHHHHHHHHhCCCC----CCCEEEEecCccCC
Q 029459 58 RHMANTLSLYRTVKRLGVP----DERIILMLADDMAC 90 (193)
Q Consensus 58 RHqadv~~~Y~~Lk~~Gip----de~IIlm~~DDiA~ 90 (193)
-||.+|-++-|.|.+.||| ++|||-.+--|-+-
T Consensus 431 ~hqrnv~~~kq~l~~~GiPVi~~pSHIiPv~vgda~l 467 (570)
T KOG1360|consen 431 QHQRNVKYVKQLLMELGIPVIPNPSHIIPVRVGDAAL 467 (570)
T ss_pred HHHHHHHHHHHHHHHcCCcccCCCcceeeeeccCHHH
Confidence 4889999999999999997 89999988766543
No 33
>PRK09598 lipid A phosphoethanolamine transferase; Reviewed
Probab=32.97 E-value=22 Score=34.33 Aligned_cols=14 Identities=21% Similarity=0.767 Sum_probs=12.0
Q ss_pred CCCcEEEEEeCCCC
Q 029459 151 EGSHILLYMTGHGG 164 (193)
Q Consensus 151 ~~dnVFiY~tgHGg 164 (193)
+.++++||++|||.
T Consensus 428 ~~~t~iIy~SDHGe 441 (522)
T PRK09598 428 KQPALMIYLSDHGE 441 (522)
T ss_pred CCCeEEEEEccCcc
Confidence 34889999999996
No 34
>PF11121 DUF2639: Protein of unknown function (DUF2639); InterPro: IPR022580 This family is conserved in the Bacillaceae family. Several members are named as being YflJ, but the function is not known.
Probab=32.96 E-value=22 Score=23.28 Aligned_cols=16 Identities=31% Similarity=0.831 Sum_probs=12.3
Q ss_pred cCCCCccchhhhhHHHHHHHHHhCCCC
Q 029459 50 TSRFWFNYRHMANTLSLYRTVKRLGVP 76 (193)
Q Consensus 50 gS~~w~NYRHqadv~~~Y~~Lk~~Gip 76 (193)
||+||| -+.||+.||.
T Consensus 3 gSKGw~-----------V~eLKk~GI~ 18 (40)
T PF11121_consen 3 GSKGWY-----------VKELKKLGIR 18 (40)
T ss_pred CcchHH-----------HHHHHHhCcc
Confidence 688887 3678888874
No 35
>PF00691 OmpA: OmpA family; InterPro: IPR006665 This entry represents domain with a beta/alpha/beta/alpha-beta(2) structure found in the C-terminal region of many Gram-negative bacterial outer membrane proteins [], such as porin-like integral membrane proteins (such as ompA) [], small lipid-anchored proteins (such as pal) [], and MotB proton channels []. The N-terminal half is variable although some of the proteins in this group have the OmpA-like transmembrane domain IPR000498 from INTERPRO at the N terminus. OmpA from Escherichia coli is required for pathogenesis, and can interact with host receptor molecules []. MotB (and MotA) serves two functions in E. coli, the MotA(4)-MotB(2) complex attaches to the cell wall via MotB to form the stator of the flagellar motor, and the MotA-MotB complex couples the flow of ions across the cell membrane to movement of the rotor [].; GO: 0009279 cell outer membrane; PDB: 1OAP_A 2W8B_G 2HQS_C 4ERH_A 2ZF8_A 2ZOV_A 2ZVZ_B 2ZVY_A 3TD4_B 3TD5_D ....
Probab=32.77 E-value=82 Score=22.24 Aligned_cols=32 Identities=19% Similarity=0.228 Sum_probs=23.4
Q ss_pred cchhhhh-HHHHHHHHHhCCCCCCCEEEEecCc
Q 029459 56 NYRHMAN-TLSLYRTVKRLGVPDERIILMLADD 87 (193)
Q Consensus 56 NYRHqad-v~~~Y~~Lk~~Gipde~IIlm~~DD 87 (193)
|.+-... +-.+-+.|...||++++|.+..+-+
T Consensus 48 n~~LS~~RA~~V~~~L~~~gi~~~ri~~~~~G~ 80 (97)
T PF00691_consen 48 NQELSQRRAEAVKQYLVENGIPPERISVVGYGE 80 (97)
T ss_dssp HHHHHHHHHHHHHHHHHHTTSSGGGEEEEEETT
T ss_pred HhHHHHHHHHHHHHHHHHcCCChHhEEEEEEcc
Confidence 4444332 5567788999999999999877655
No 36
>PF00884 Sulfatase: Sulfatase; InterPro: IPR000917 Sulphatases 3.1.6. from EC are enzymes that hydrolyze various sulphate esters. The sequence of different types of sulphatases are available and have shown to be structurally related [, , ]; these include: arylsulphatase A 3.1.6.8 from EC (ASA), a lysosomal enzyme which hydrolyses cerebroside sulphate; arylsulphatase B 3.1.6.12 from EC (ASB), which hydrolyses the sulphate ester group from N-acetylgalactosamine 4-sulphate residues of dermatan sulphate; arylsulphatase C (ASD) and E (ASE); steryl-sulphatase 3.1.6.2 from EC (STS), a membrane bound microsomal enzyme which hydrolyses 3-beta-hydroxy steroid sulphates; iduronate 2-sulphatase precursor 3.1.6.13 from EC (IDS), a lysosomal enzyme that hydrolyses the 2-sulphate groups from non-reducing-terminal iduronic acid residues in dermatan sulphate and heparan sulphate; N-acetylgalactosamine-6-sulphatase 3.1.6.4 from EC, which hydrolyses the 6-sulphate groups of the N-acetyl-d-galactosamine 6-sulphate units of chondroitin sulphate and the D-galactose 6-sulphate units of keratan sulphate; glucosamine-6-sulphatase 3.1.6.14 from EC (G6S), which hydrolyses the N-acetyl-D-glucosamine 6-sulphate units of heparan sulphate and keratan sulphate; N-sulphoglucosamine sulphohydrolase 3.10.1.1 from EC (sulphamidase), the lysosomal enzyme that catalyses the hydrolysis of N-sulpho-d-glucosamine into glucosamine and sulphate; sea urchin embryo arylsulphatase 3.1.6.1 from EC; green algae arylsulphatase 3.1.6.1 from EC, which plays an important role in the mineralisation of sulphates; and arylsulphatase 3.1.6.1 from EC from Escherichia coli (aslA), Klebsiella aerogenes (gene atsA) and Pseudomonas aeruginosa (gene atsA). ; GO: 0008484 sulfuric ester hydrolase activity, 0008152 metabolic process; PDB: 1P49_A 1FSU_A 2QZU_A 2W5Q_A 2W5T_A 2W5S_A 2W5R_A 3LXQ_A 1HDH_B 1E33_P ....
Probab=32.12 E-value=48 Score=27.38 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=12.1
Q ss_pred CCcEEEEEeCCCCC
Q 029459 152 GSHILLYMTGHGGD 165 (193)
Q Consensus 152 ~dnVFiY~tgHGg~ 165 (193)
++.++|+.+|||..
T Consensus 238 d~TiiiitsDHG~~ 251 (308)
T PF00884_consen 238 DNTIIIITSDHGES 251 (308)
T ss_dssp GGEEEEEEESSSSS
T ss_pred ccceeEEecCcCcc
Confidence 56799999999984
No 37
>COG2194 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]
Probab=29.69 E-value=30 Score=33.95 Aligned_cols=13 Identities=31% Similarity=0.731 Sum_probs=11.4
Q ss_pred CCcEEEEEeCCCC
Q 029459 152 GSHILLYMTGHGG 164 (193)
Q Consensus 152 ~dnVFiY~tgHGg 164 (193)
.+..+||++|||-
T Consensus 444 ~~~~liY~SDHGE 456 (555)
T COG2194 444 DNTSLIYFSDHGE 456 (555)
T ss_pred CCeEEEEEcCccH
Confidence 3779999999997
No 38
>KOG1387 consensus Glycosyltransferase [Cell wall/membrane/envelope biogenesis]
Probab=29.30 E-value=62 Score=30.93 Aligned_cols=28 Identities=32% Similarity=0.509 Sum_probs=21.7
Q ss_pred cCCCccccCCCC-CCCHHHHHHHHcCCCC
Q 029459 111 YGDNVEVDYHGY-EVNAENFLRVLTGRHK 138 (193)
Q Consensus 111 Y~~~v~IDY~g~-~Vt~enfl~VL~G~~~ 138 (193)
|+..+-+=|+|+ +||||++|+=-+.+.+
T Consensus 74 ~~n~~~viYsGD~n~t~~~IL~k~k~~F~ 102 (465)
T KOG1387|consen 74 FPNNVIVIYSGDFNVTPENILNKVKNKFD 102 (465)
T ss_pred CCCceEEEEeCCCCCCHHHHHHHHHHhcC
Confidence 444566789998 9999999987776654
No 39
>PTZ00450 macrophage migration inhibitory factor-like protein; Provisional
Probab=28.62 E-value=76 Score=24.52 Aligned_cols=29 Identities=21% Similarity=0.272 Sum_probs=21.6
Q ss_pred cchhhhhHHHHHHHHHhCCCCCCCEEEEecC
Q 029459 56 NYRHMANTLSLYRTVKRLGVPDERIILMLAD 86 (193)
Q Consensus 56 NYRHqadv~~~Y~~Lk~~Gipde~IIlm~~D 86 (193)
|=.|.+.+|.+.+ ++.|||.++|.+-..|
T Consensus 74 n~~~s~~i~~~l~--~~LgIp~dRiYI~f~d 102 (113)
T PTZ00450 74 PKMMTPRITAAIT--KECGIPAERIYVFYYS 102 (113)
T ss_pred HHHHHHHHHHHHH--HHcCCCcccEEEEEEc
Confidence 4456666666644 6789999999988876
No 40
>KOG1654 consensus Microtubule-associated anchor protein involved in autophagy and membrane trafficking [Cytoskeleton]
Probab=28.50 E-value=54 Score=26.07 Aligned_cols=35 Identities=9% Similarity=0.310 Sum_probs=28.8
Q ss_pred CCCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCCCCC
Q 029459 121 GYEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGHGGD 165 (193)
Q Consensus 121 g~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgHGg~ 165 (193)
.+++|+..|+.|++-| +...|++-+|++..+|--+
T Consensus 52 P~dltvgqfi~iIRkR----------iqL~~~kA~flfVn~~~p~ 86 (116)
T KOG1654|consen 52 PDDLTVGQFIKIIRKR----------IQLSPEKAFFLFVNNTSPP 86 (116)
T ss_pred cccccHHHHHHHHHHH----------hccChhHeEEEEEcCcCCc
Confidence 6889999999999844 6678888899999888543
No 41
>cd06212 monooxygenase_like The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is incorportated into the aromatic compond, while the other is used to form a molecule of water. In contrast dioxygenases add both atoms of oxygen to the substrate.
Probab=28.37 E-value=39 Score=27.80 Aligned_cols=31 Identities=19% Similarity=0.310 Sum_probs=23.3
Q ss_pred EEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEE
Q 029459 44 WAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIIL 82 (193)
Q Consensus 44 wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIl 82 (193)
.-|.++|+.++ +-.+.+.|++.|+|.+||..
T Consensus 198 ~~v~~CGp~~~--------~~~v~~~l~~~G~~~~~i~~ 228 (232)
T cd06212 198 CDVYLCGPPPM--------IDAALPVLEMSGVPPDQIFY 228 (232)
T ss_pred CEEEEECCHHH--------HHHHHHHHHHcCCCHHHeee
Confidence 35777777655 34677889999999999863
No 42
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=27.45 E-value=2.1e+02 Score=25.55 Aligned_cols=26 Identities=8% Similarity=0.179 Sum_probs=21.9
Q ss_pred chhhhhHHHHHHHHHhCCCCCCCEEE
Q 029459 57 YRHMANTLSLYRTVKRLGVPDERIIL 82 (193)
Q Consensus 57 YRHqadv~~~Y~~Lk~~Gipde~IIl 82 (193)
+--.+|...+-.+|+.+|+|.+.-+.
T Consensus 60 ~Ve~~~fa~Av~iL~~~GlPr~~f~~ 85 (246)
T COG4669 60 LVEESDFAEAVEILNQNGLPRKKFTT 85 (246)
T ss_pred EEcHHHHHHHHHHHHhcCCCCCCCCc
Confidence 33478999999999999999988774
No 43
>PLN02541 uracil phosphoribosyltransferase
Probab=26.93 E-value=74 Score=27.95 Aligned_cols=24 Identities=13% Similarity=0.162 Sum_probs=21.5
Q ss_pred hhHHHHHHHHHhCCCCCCCEEEEe
Q 029459 61 ANTLSLYRTVKRLGVPDERIILML 84 (193)
Q Consensus 61 adv~~~Y~~Lk~~Gipde~IIlm~ 84 (193)
+.++.+.+.|+++|.+.++|+++.
T Consensus 171 gS~~~ai~~L~~~Gv~~~~I~~v~ 194 (244)
T PLN02541 171 GTIVAAIDELVSRGASVEQIRVVC 194 (244)
T ss_pred HHHHHHHHHHHHcCCCcccEEEEE
Confidence 468999999999999999999875
No 44
>COG4899 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.88 E-value=1e+02 Score=25.76 Aligned_cols=56 Identities=27% Similarity=0.402 Sum_probs=40.9
Q ss_pred CEEEEecCccCCCCCCCCCCeEEeCCCCCccccCCCccccCCC-CCCCHHHHHHHHc
Q 029459 79 RIILMLADDMACNARNKYPAQVFNNENHKLNLYGDNVEVDYHG-YEVNAENFLRVLT 134 (193)
Q Consensus 79 ~IIlm~~DDiA~np~Np~pG~i~~~~~~~~n~Y~~~v~IDY~g-~~Vt~enfl~VL~ 134 (193)
.|.-.-|||-.|--+||.|-+-|....-..-+-|.....||-+ -+|..+.|.+-|.
T Consensus 29 ~~AQv~~DdD~Cqi~~p~~~r~FIr~~lpIPi~G~~~~l~yG~WveVe~~~f~~Yl~ 85 (166)
T COG4899 29 LDAQVRYDDDMCQILNPKPKRHFIRSNLPIPIDGGKKKLDYGGWVEVEHSDFMTYLN 85 (166)
T ss_pred hhhhheecccceeecCCCccceeeeecccceecCccceeccceEEEEeHHHHHHHHH
Confidence 3445578999999999999999987543222223334577877 6899999999887
No 45
>KOG3339 consensus Predicted glycosyltransferase [General function prediction only]
Probab=25.43 E-value=4.5e+02 Score=22.96 Aligned_cols=39 Identities=23% Similarity=0.243 Sum_probs=28.6
Q ss_pred EEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEEEecCcc
Q 029459 44 WAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIILMLADDM 88 (193)
Q Consensus 44 wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIlm~~DDi 88 (193)
--.+|.||-| |++..|..-+.|.+. +.+..+|+--.|..
T Consensus 40 ~~lVvlGSGG-----HT~EMlrLl~~l~~~-y~~r~yI~a~tD~m 78 (211)
T KOG3339|consen 40 STLVVLGSGG-----HTGEMLRLLEALQDL-YSPRSYIAADTDEM 78 (211)
T ss_pred eEEEEEcCCC-----cHHHHHHHHHHHHhh-cCceEEEEecCchh
Confidence 3566778877 999999998888554 78888885444444
No 46
>PF04911 ATP-synt_J: ATP synthase j chain; InterPro: IPR006995 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit J found in the F0 complex of F-ATPases from fungal mitochondria. This subunit does not appear to display sequence similarity with subunits of F-ATPases found in other organisms []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o)
Probab=24.68 E-value=18 Score=25.16 Aligned_cols=19 Identities=26% Similarity=0.347 Sum_probs=14.7
Q ss_pred EEEEecCccCCCCCCCCCC
Q 029459 80 IILMLADDMACNARNKYPA 98 (193)
Q Consensus 80 IIlm~~DDiA~np~Np~pG 98 (193)
-.+|-+|+-.+|||||.-.
T Consensus 29 ~a~~ns~E~~NDPRNP~~~ 47 (54)
T PF04911_consen 29 NAMMNSDEFKNDPRNPRAA 47 (54)
T ss_pred HHHhcCHHHhcCCCChhhh
Confidence 3456788889999999754
No 47
>PF04202 Mfp-3: Foot protein 3; InterPro: IPR007328 Mytilus foot protein-3 (Mfp-3) is a highly polymorphic protein family located in the byssal adhesive plaques of blue mussels.
Probab=24.21 E-value=57 Score=23.75 Aligned_cols=17 Identities=18% Similarity=0.315 Sum_probs=12.4
Q ss_pred hhhHHHHHHHHHHHHHh
Q 029459 11 FGFKSLAAMLLFFILSI 27 (193)
Q Consensus 11 ~~~~~~~~~~l~~~~~~ 27 (193)
+-..+|.|+||+++++.
T Consensus 4 ~Si~VLlaLvLIg~fAV 20 (71)
T PF04202_consen 4 LSIAVLLALVLIGSFAV 20 (71)
T ss_pred hhHHHHHHHHHHhhhee
Confidence 44567778899997765
No 48
>cd07561 Peptidase_S41_CPP_like C-terminal processing peptidase-like; serine protease family S41. Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP). CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at variable distance from the C-terminus. The CPP active site consists of a serine/lysine catalytic dyad. Conservation of these residues is seen in the CPP-like proteins of this group. CPP proteins contain a PDZ domain that promotes protein-protein interactions and is important for substrate recognition however, most of CPP-like proteins only have an internal fragment or lack the PDZ domain.
Probab=23.94 E-value=2.5e+02 Score=24.41 Aligned_cols=57 Identities=19% Similarity=0.324 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEe-CCCCCCeeecCCCCccCHHHHHHHHHHHHHh
Q 029459 122 YEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMT-GHGGDEFLKFQDSEELQSHDLADAVKQMKEK 191 (193)
Q Consensus 122 ~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~t-gHGg~g~i~fpd~~~l~a~dL~~~l~~M~~~ 191 (193)
..-+|+.|+.-|+=..+.. ..|=|++ +.+.-|+|.+..-..-++++|.++|++|.++
T Consensus 35 ~~~~p~~~~~~l~~~~~~~-------------~~fs~~~~~~~~IGYi~i~~F~~~~~~~l~~a~~~l~~~ 92 (256)
T cd07561 35 YFDDPEDFLESLLSEKDGK-------------DRFSYIVDGGKKVGYLVYNSFTSGYDDELNQAFAEFKAQ 92 (256)
T ss_pred ccCCHHHHHHHhhCccccC-------------CceEEEeeCCCcEEEEEECccccchHHHHHHHHHHHHHc
Confidence 3457899999887655421 2344443 5555699999765455789999999999865
No 49
>PRK11598 putative metal dependent hydrolase; Provisional
Probab=23.10 E-value=52 Score=32.10 Aligned_cols=14 Identities=29% Similarity=0.570 Sum_probs=11.7
Q ss_pred CCcEEEEEeCCCCC
Q 029459 152 GSHILLYMTGHGGD 165 (193)
Q Consensus 152 ~dnVFiY~tgHGg~ 165 (193)
++.++||++|||..
T Consensus 445 ~nT~iIy~SDHGe~ 458 (545)
T PRK11598 445 FNTSLVYLSDHGES 458 (545)
T ss_pred CCeEEEEECcCCCc
Confidence 46799999999963
No 50
>KOG4667 consensus Predicted esterase [Lipid transport and metabolism]
Probab=22.07 E-value=78 Score=28.39 Aligned_cols=86 Identities=15% Similarity=0.148 Sum_probs=48.5
Q ss_pred ecCCCCccchhhhhHHH-HHHHHHhCCCCCCCEEEEe-------------cCccCCCCCCC--CCCeEEeCCCC-----C
Q 029459 49 CTSRFWFNYRHMANTLS-LYRTVKRLGVPDERIILML-------------ADDMACNARNK--YPAQVFNNENH-----K 107 (193)
Q Consensus 49 agS~~w~NYRHqadv~~-~Y~~Lk~~Gipde~IIlm~-------------~DDiA~np~Np--~pG~i~~~~~~-----~ 107 (193)
.||-+|-|||+.||-+| +||.+.. .|+++=. |-.=..+|+|- -||+-.-...- +
T Consensus 77 ~gsf~~Gn~~~eadDL~sV~q~~s~-----~nr~v~vi~gHSkGg~Vvl~ya~K~~d~~~viNcsGRydl~~~I~eRlg~ 151 (269)
T KOG4667|consen 77 EGSFYYGNYNTEADDLHSVIQYFSN-----SNRVVPVILGHSKGGDVVLLYASKYHDIRNVINCSGRYDLKNGINERLGE 151 (269)
T ss_pred CCccccCcccchHHHHHHHHHHhcc-----CceEEEEEEeecCccHHHHHHHHhhcCchheEEcccccchhcchhhhhcc
Confidence 46778899999999887 8999876 4544321 11111224432 24432221110 0
Q ss_pred ---ccccCCCccccCCC------CCCCHHHHHHHHcCCCCCC
Q 029459 108 ---LNLYGDNVEVDYHG------YEVNAENFLRVLTGRHKAA 140 (193)
Q Consensus 108 ---~n~Y~~~v~IDY~g------~~Vt~enfl~VL~G~~~~~ 140 (193)
.-.-.+| -|||.. .-||+|-+..-|.++-.+.
T Consensus 152 ~~l~~ike~G-fid~~~rkG~y~~rvt~eSlmdrLntd~h~a 192 (269)
T KOG4667|consen 152 DYLERIKEQG-FIDVGPRKGKYGYRVTEESLMDRLNTDIHEA 192 (269)
T ss_pred cHHHHHHhCC-ceecCcccCCcCceecHHHHHHHHhchhhhh
Confidence 0000012 256653 6799999999999997654
No 51
>PF08869 XisI: XisI protein; InterPro: IPR014968 The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required []. ; PDB: 3D7Q_A 2NWV_A 2NVM_A 2NLV_B.
Probab=21.80 E-value=52 Score=25.86 Aligned_cols=17 Identities=35% Similarity=0.600 Sum_probs=12.5
Q ss_pred HHHHhCCCCCCCEEEEe
Q 029459 68 RTVKRLGVPDERIILML 84 (193)
Q Consensus 68 ~~Lk~~Gipde~IIlm~ 84 (193)
+-|-+.|+|+++|+|=+
T Consensus 81 ~eLve~GVpk~dIVLgF 97 (111)
T PF08869_consen 81 EELVEAGVPKEDIVLGF 97 (111)
T ss_dssp HHHHHTT--GGGEEETT
T ss_pred HHHHHcCCCHHHEEEcc
Confidence 67889999999999854
No 52
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=21.69 E-value=92 Score=19.31 Aligned_cols=26 Identities=12% Similarity=0.175 Sum_probs=19.2
Q ss_pred ceecCCCCCcEEEEEeCCCCCCeeec
Q 029459 145 KRLLSDEGSHILLYMTGHGGDEFLKF 170 (193)
Q Consensus 145 k~l~s~~~dnVFiY~tgHGg~g~i~f 170 (193)
+++...+++.+.|+|.|.|....+..
T Consensus 18 ~V~~~~~~~~~~V~f~DyG~~~~v~~ 43 (48)
T cd04508 18 KITSILSDGKVEVFFVDYGNTEVVPL 43 (48)
T ss_pred EEEEECCCCcEEEEEEcCCCcEEEeH
Confidence 44444557889999999998876554
No 53
>PF03568 Peptidase_C50: Peptidase family C50; InterPro: IPR005314 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C50 (separase family, clan CD). The active site residues for members of this family and family C14 occur in the same order in the sequence: H,C. The separases are caspase-like proteases, which plays a central role in the chromosome segregation. In yeast they cleave the rad21 subunit of the cohesin complex at the onset of anaphase. During most of the cell cycle, separase is inactivated by the securin/cut2 protein, which probably covers its active site. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0005634 nucleus
Probab=21.31 E-value=96 Score=28.56 Aligned_cols=39 Identities=23% Similarity=0.463 Sum_probs=21.5
Q ss_pred HHHHHHHHcCCC-CCC----CCCcceec-CCCCCcEEEEEeCCCCC
Q 029459 126 AENFLRVLTGRH-KAA----VPRSKRLL-SDEGSHILLYMTGHGGD 165 (193)
Q Consensus 126 ~enfl~VL~G~~-~~~----~p~~k~l~-s~~~dnVFiY~tgHGg~ 165 (193)
-+.|...++... +++ .|...-+. .-.+.++||| .||||-
T Consensus 276 ~~~~~~~~~~~~~w~g~~g~~P~~~e~~~~l~~~dlf~Y-~GHG~G 320 (383)
T PF03568_consen 276 EKRFEPFFKSWKGWKGIIGRAPTEEEFLQALTSSDLFLY-CGHGSG 320 (383)
T ss_pred HHHHHHHHhcccCCCceECCCCCHHHHHHHHHhCCeEEE-ecCCcH
Confidence 456777777665 433 22222121 2236679985 599983
No 54
>cd06209 BenDO_FAD_NAD Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal ferredoxin at the end fused to an FAD/NADP(P) domain. In dioxygenase FAD/NAD(P) binding domain, the reductase transfers 2 electrons from NAD(P)H to the oxygenase which insert into an aromatic substrate, an initial step in microbial aerobic degradation of aromatic rings. Flavin oxidoreductases use flavins as substrates, unlike flavoenzymes which have a flavin prosthetic group.
Probab=21.02 E-value=61 Score=26.58 Aligned_cols=32 Identities=9% Similarity=0.140 Sum_probs=21.6
Q ss_pred cEEEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEEE
Q 029459 43 NWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERIIL 82 (193)
Q Consensus 43 ~wAVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~IIl 82 (193)
++.|.++|+.++ +-.+.+.|++.|+|+++|..
T Consensus 193 ~~~v~icGp~~m--------~~~~~~~l~~~G~~~~~i~~ 224 (228)
T cd06209 193 DVDVYLCGPPPM--------VDAVRSWLDEQGIEPANFYY 224 (228)
T ss_pred CcEEEEeCCHHH--------HHHHHHHHHHcCCCHHHEee
Confidence 445667776544 33466778888999888863
No 55
>cd06215 FNR_iron_sulfur_binding_1 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal portion of the FAD/NAD binding domain contains most of the NADP(H) binding residues and the N-terminal sub-domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. In this ferredoxin like sub-group, the FAD/NAD sub-domains is typically fused to a C-terminal iron-sulfur binding domain. Iron-sulfur pr
Probab=20.90 E-value=48 Score=27.06 Aligned_cols=29 Identities=24% Similarity=0.408 Sum_probs=22.5
Q ss_pred EEEEecCCCCccchhhhhHHHHHHHHHhCCCCCCCEE
Q 029459 45 AVLVCTSRFWFNYRHMANTLSLYRTVKRLGVPDERII 81 (193)
Q Consensus 45 AVlVagS~~w~NYRHqadv~~~Y~~Lk~~Gipde~II 81 (193)
.|.|||+.+. +-.+.+.|++.|+|.+||.
T Consensus 199 ~v~icGp~~m--------~~~~~~~l~~~gv~~~~i~ 227 (231)
T cd06215 199 TVFVCGPAGF--------MKAVKSLLAELGFPMSRFH 227 (231)
T ss_pred eEEEECCHHH--------HHHHHHHHHHcCCCHHHee
Confidence 5777777544 5578888999999999885
No 56
>cd08494 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=20.87 E-value=78 Score=28.44 Aligned_cols=24 Identities=13% Similarity=0.372 Sum_probs=21.2
Q ss_pred eecCCCCccCHHHHHHHHHHHHHh
Q 029459 168 LKFQDSEELQSHDLADAVKQMKEK 191 (193)
Q Consensus 168 i~fpd~~~l~a~dL~~~l~~M~~~ 191 (193)
++|.|++.|+++|+..+++.+.+.
T Consensus 69 ~~fsdG~pvTA~Dv~~s~~~~~~~ 92 (448)
T cd08494 69 VTFHDGTPFDAADVKFSLQRARAP 92 (448)
T ss_pred CEecCcCCCCHHHHHhHHHHHhCC
Confidence 689999999999999999988653
No 57
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=20.86 E-value=59 Score=17.79 Aligned_cols=21 Identities=14% Similarity=0.438 Sum_probs=16.7
Q ss_pred hhhhhHHHHHHHHHhCCCCCC
Q 029459 58 RHMANTLSLYRTVKRLGVPDE 78 (193)
Q Consensus 58 RHqadv~~~Y~~Lk~~Gipde 78 (193)
....++..+++.+++.|++++
T Consensus 14 ~~~~~a~~~~~~M~~~g~~p~ 34 (35)
T TIGR00756 14 GRVEEALELFKEMLERGIEPD 34 (35)
T ss_pred CCHHHHHHHHHHHHHcCCCCC
Confidence 345678889999999998765
No 58
>cd08490 PBP2_NikA_DppA_OppA_like_3 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=20.84 E-value=78 Score=28.62 Aligned_cols=34 Identities=18% Similarity=0.343 Sum_probs=25.6
Q ss_pred cEEEEEeCCCCCCeeecCCCCccCHHHHHHHHHHHHHh
Q 029459 154 HILLYMTGHGGDEFLKFQDSEELQSHDLADAVKQMKEK 191 (193)
Q Consensus 154 nVFiY~tgHGg~g~i~fpd~~~l~a~dL~~~l~~M~~~ 191 (193)
..+.|---.| ++|.|++.|+++|+.-+++.+...
T Consensus 56 ~~~tf~Lr~~----~~wsDG~plTA~Dv~~s~~~~~~~ 89 (470)
T cd08490 56 TTWEFTLRDG----VKFHDGTPLTAEAVKASLERALAK 89 (470)
T ss_pred CEEEEEECCC----CCccCCCCCCHHHHHHHHHHHhcc
Confidence 3444444444 589999999999999999987653
No 59
>PF00381 PTS-HPr: PTS HPr component phosphorylation site; InterPro: IPR005698 The histidine-containing phosphocarrier protein (HPr) is a central component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species [, ]. PTS catalyses the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is as follows: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to Enzyme I (EI) of the PTS, which in turn transfers it to the phosphoryl carrier protein (HPr) [, ]. Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease complex (enzymes EII/EIII). HPr [, ] is a small cytoplasmic protein of 70 to 90 amino acid residues. In some bacteria, HPr is a domain in a larger protein that includes a EIII(Fru) (IIA) domain and in some cases also the EI domain. A conserved histidine in the N-terminal section of HPr serves as an acceptor for the phosphoryl group of EI. In the central part of HPr, there is a conserved serine which (in Gram-positive bacteria only) is phosphorylated by an ATP-dependent protein kinase; a process which probably play a regulatory role in sugar transport. The overall architecture of the HPr domain has been described as an open faced beta-sandwich in which a beta-sheet is packed against three alpha-helices. Regulatory phosphorylation at the conserved Ser residue does not appear to induce large structural changes to the HPr domain, in particular in the region of the active site [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TXE_A 1QR5_A 1RZR_S 2NZU_L 2OEN_L 2NZV_L 1Y51_B 1Y4Y_A 1Y50_A 2HPR_A ....
Probab=20.78 E-value=94 Score=22.10 Aligned_cols=42 Identities=17% Similarity=0.351 Sum_probs=31.1
Q ss_pred cccCCCccccCCCCCCCHHHHHHHHcCCCCCCCCCcceecCCCCCcEEEEEeCC
Q 029459 109 NLYGDNVEVDYHGYEVNAENFLRVLTGRHKAAVPRSKRLLSDEGSHILLYMTGH 162 (193)
Q Consensus 109 n~Y~~~v~IDY~g~~Vt~enfl~VL~G~~~~~~p~~k~l~s~~~dnVFiY~tgH 162 (193)
+-|++.+.|.+.+..|++++++.+|+-.. .+.+.|-|+..|-
T Consensus 27 ~~~~~~i~i~~~~~~vdakSil~l~~L~~------------~~G~~i~i~~~G~ 68 (84)
T PF00381_consen 27 SKFDSDITIRKGGKTVDAKSILGLMSLGA------------KKGDEIEIEAEGE 68 (84)
T ss_dssp HTSSSEEEEEETTEEEETTSHHHHHHHTB------------STTEEEEEEEEST
T ss_pred hhCCCEEEEEeCceeEecCCHHHHhhhhc------------CCCCEEEEEEECc
Confidence 34667788999999999999999998443 3356676666553
No 60
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=20.56 E-value=2.8e+02 Score=22.98 Aligned_cols=40 Identities=8% Similarity=0.116 Sum_probs=27.0
Q ss_pred CCcEEEEEecCCCCccchhhhhHHH-HHHHHHhCCCCCCCEEEEe
Q 029459 41 TNNWAVLVCTSRFWFNYRHMANTLS-LYRTVKRLGVPDERIILML 84 (193)
Q Consensus 41 ~~~wAVlVagS~~w~NYRHqadv~~-~Y~~Lk~~Gipde~IIlm~ 84 (193)
+-+.+|++| + ||.......+. +.+.|+++|+++++|-++-
T Consensus 10 ~~riaIV~s--r--fn~~It~~Ll~gA~~~l~~~G~~~~~i~v~~ 50 (158)
T PRK12419 10 PQRIAFIQA--R--WHADIVDQARKGFVAEIAARGGAASQVDIFD 50 (158)
T ss_pred CCEEEEEEe--c--CCHHHHHHHHHHHHHHHHHcCCCccceEEEE
Confidence 346666665 3 44444444443 7889999999999998773
No 61
>COG2143 Thioredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.41 E-value=2e+02 Score=24.56 Aligned_cols=38 Identities=11% Similarity=0.218 Sum_probs=30.1
Q ss_pred ecCCCCCcEEEEEeCCCCCCeeecCCCCccCHHHHHHHHHHHHH
Q 029459 147 LLSDEGSHILLYMTGHGGDEFLKFQDSEELQSHDLADAVKQMKE 190 (193)
Q Consensus 147 l~s~~~dnVFiY~tgHGg~g~i~fpd~~~l~a~dL~~~l~~M~~ 190 (193)
+.|+|. +.|.||-|.+++..|. +|-.+++...|++-.+
T Consensus 113 vrstPt----fvFfdk~Gk~Il~lPG--Y~ppe~Fl~vlkYVa~ 150 (182)
T COG2143 113 VRSTPT----FVFFDKTGKTILELPG--YMPPEQFLAVLKYVAD 150 (182)
T ss_pred cccCce----EEEEcCCCCEEEecCC--CCCHHHHHHHHHHHHH
Confidence 335555 5677888999999996 8999999999887654
Done!