Query psy12858
Match_columns 131
No_of_seqs 143 out of 1167
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 21:34:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12858.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12858hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0404 GcvT Glycine cleavage 99.9 1.6E-26 3.4E-31 188.7 13.0 106 5-122 271-378 (379)
2 PF08669 GCV_T_C: Glycine clea 99.9 5.2E-26 1.1E-30 152.5 12.4 91 6-108 1-93 (95)
3 KOG2844|consensus 99.9 6.7E-24 1.4E-28 181.0 11.4 113 6-123 742-854 (856)
4 PRK12486 dmdA putative dimethy 99.9 2.7E-23 5.8E-28 169.1 12.8 97 6-114 271-368 (368)
5 PRK13579 gcvT glycine cleavage 99.9 5.7E-23 1.2E-27 167.0 13.1 103 4-119 266-369 (370)
6 PLN02319 aminomethyltransferas 99.9 2.9E-22 6.3E-27 164.7 13.3 99 5-117 300-399 (404)
7 PRK00389 gcvT glycine cleavage 99.9 3.1E-21 6.7E-26 155.8 13.8 98 5-118 261-358 (359)
8 TIGR00528 gcvT glycine cleavag 99.9 1.1E-20 2.3E-25 153.0 12.9 99 4-115 260-360 (361)
9 TIGR01372 soxA sarcosine oxida 99.8 1.1E-20 2.4E-25 169.4 13.8 107 4-122 871-984 (985)
10 KOG2770|consensus 99.8 2.7E-18 5.8E-23 137.5 10.8 96 7-115 297-394 (401)
11 PRK09559 putative global regul 98.8 1.1E-07 2.4E-12 76.4 11.0 95 4-114 225-324 (327)
12 TIGR03317 ygfZ_signature folat 97.7 5.3E-05 1.2E-09 47.6 3.6 26 5-30 40-66 (67)
13 COG0354 Predicted aminomethylt 97.5 0.00027 5.8E-09 56.8 5.8 65 4-78 205-272 (305)
14 KOG2929|consensus 96.2 0.015 3.2E-07 47.1 5.9 99 4-118 238-340 (348)
15 PF02470 MCE: mce related prot 81.9 10 0.00022 23.8 8.1 38 42-79 15-52 (81)
16 PRK10807 paraquat-inducible pr 77.3 13 0.00028 32.3 7.6 61 27-97 46-108 (547)
17 PF05580 Peptidase_S55: SpoIVB 57.7 14 0.0003 28.6 3.3 19 43-61 181-199 (218)
18 KOG3322|consensus 47.1 14 0.0003 33.0 2.1 27 53-79 643-669 (688)
19 PF14578 GTP_EFTU_D4: Elongati 38.1 22 0.00048 23.2 1.5 28 25-61 20-47 (81)
20 TIGR00996 Mtu_fam_mce virulenc 37.0 81 0.0018 24.5 4.9 35 42-78 45-79 (291)
21 TIGR02860 spore_IV_B stage IV 36.8 33 0.00071 28.9 2.7 19 43-61 361-379 (402)
22 PF08248 Tryp_FSAP: Tryptophyl 34.5 22 0.00048 14.8 0.7 6 111-116 2-7 (12)
23 PF09890 DUF2117: Uncharacteri 34.0 40 0.00087 26.0 2.6 21 42-62 99-119 (215)
24 PRK10807 paraquat-inducible pr 33.5 1.6E+02 0.0035 25.7 6.5 38 42-79 171-208 (547)
25 PF00920 ILVD_EDD: Dehydratase 31.7 86 0.0019 27.4 4.4 54 52-108 428-484 (521)
26 PF03539 Spuma_A9PTase: Spumav 29.8 61 0.0013 23.8 2.8 18 95-113 50-67 (163)
27 PF05001 RNA_pol_Rpb1_R: RNA p 28.5 20 0.00043 15.7 0.1 8 59-66 3-10 (14)
28 KOG2055|consensus 24.7 55 0.0012 28.2 2.1 21 52-73 479-499 (514)
29 PHA02763 hypothetical protein; 22.0 1.7E+02 0.0037 19.5 3.6 42 66-113 12-53 (102)
30 COG3008 PqiB Paraquat-inducibl 21.4 2.7E+02 0.0058 24.6 5.6 38 42-79 174-211 (553)
31 PF04766 Baculo_p26: Nucleopol 20.7 1.3E+02 0.0029 23.5 3.3 35 26-62 97-131 (234)
32 cd03864 M14_CPN Peptidase M14 20.3 2E+02 0.0043 24.0 4.5 44 11-60 304-347 (392)
33 COG2524 Predicted transcriptio 20.2 82 0.0018 25.3 2.1 21 43-63 203-223 (294)
No 1
>COG0404 GcvT Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
Probab=99.94 E-value=1.6e-26 Score=188.67 Aligned_cols=106 Identities=34% Similarity=0.527 Sum_probs=94.5
Q ss_pred CCCCccHHHHHHhHhcCCCeEEEEEEEecCCCCCCcccCCCCcee-eCCeE-eEEEecceeccccCCeEEEEEecCCCCC
Q psy12858 5 KDYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIY-RNDQF-VGTITSAGYGFTMKKLIGLGYIRHPSEQ 82 (131)
Q Consensus 5 k~dFIGk~AL~~~~~~g~~r~lvgl~~~~~~~~~~~~~~~g~~V~-~~g~~-VG~vTSg~ySp~l~~~Iala~v~~~~~~ 82 (131)
|.|||||+||++++++|.+|+||||.+++++. .+++|++|+ .+|+. ||+|||++|||+||++||||||+.+
T Consensus 271 k~dFiGk~al~~~k~~g~~r~lVgl~~~~~~~----~~~~g~~v~~~~g~~~vG~VTSg~~Sptlg~~IAla~v~~~--- 343 (379)
T COG0404 271 KDDFIGKAALLREKAKGVRRKLVGLKLDDKGP----VLRGGEPVLDADGEVEVGEVTSGTFSPTLGKSIALAYVDSD--- 343 (379)
T ss_pred CcCCcCHHHHHhhhhcCCceEEEEEEEcCCCC----CCCCCCeEEecCCCEeEEEEeeccccccCCCeeEEEEechh---
Confidence 34899999999999988877899999999874 289999999 68884 9999999999999999999999974
Q ss_pred CcccccccCcEEEEEECCeEEEEEEEeCCCccCCCCCCcC
Q psy12858 83 NVTNDFVTEGTYTLDVAGNRFQASAHIYPPLSNVQVARPY 122 (131)
Q Consensus 83 ~v~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~dp~~~r~~ 122 (131)
....|++++|++++++++|+|+ .+|||||+++|++
T Consensus 344 ----~~~~G~~~~v~i~~~~~~a~V~-~~pf~dp~~~r~~ 378 (379)
T COG0404 344 ----YAKPGTELEVEIRGKRVPARVV-KPPFYDPEGERLR 378 (379)
T ss_pred ----hccCCcEEEEEECCeEEEEEEe-cCCCcCccccccC
Confidence 2246889999999999999999 8999999999876
No 2
>PF08669 GCV_T_C: Glycine cleavage T-protein C-terminal barrel domain; InterPro: IPR013977 This entry shows glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. ; PDB: 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 3GIR_A 1WOO_A 1WOS_A 1WOR_A ....
Probab=99.94 E-value=5.2e-26 Score=152.46 Aligned_cols=91 Identities=34% Similarity=0.543 Sum_probs=79.6
Q ss_pred CCCccHHHHHHhHhcCC-CeEEEEEEEecCCCCCCcccCCCCceee-CCeEeEEEecceeccccCCeEEEEEecCCCCCC
Q psy12858 6 DYFIGKAALQRQKDQGV-QKRLVMFVAEDLDPDTDVWLWGSEPIYR-NDQFVGTITSAGYGFTMKKLIGLGYIRHPSEQN 83 (131)
Q Consensus 6 ~dFIGk~AL~~~~~~g~-~r~lvgl~~~~~~~~~~~~~~~g~~V~~-~g~~VG~vTSg~ySp~l~~~Iala~v~~~~~~~ 83 (131)
+|||||+||++++.+|. +++||+|.+++... +++|++|+. +|+.||+|||++|||+++++||||||+.+
T Consensus 1 gdfiG~eal~r~~~~g~~rr~lv~l~~~~~~~-----~~~g~~v~~~~g~~vG~vTS~~~sp~~~~~Iala~v~~~---- 71 (95)
T PF08669_consen 1 GDFIGQEALARQKARGVKRRRLVGLTLDGDAP-----PRGGEPVYDEDGKPVGRVTSGAYSPTLGKNIALAYVDRE---- 71 (95)
T ss_dssp S-STTHHHHHHHHHHTTS-EEEEEEEESSSS-------STTCEEEETTTEEEEEEEEEEEETTTTEEEEEEEEEGG----
T ss_pred CCcCCHHHHHHHHhcCCCceEEEEEEECCccC-----CCCCCEEEECCCcEEeEEEEEeECCCCCceEEEEEECHH----
Confidence 48999999999999887 59999999985544 899999999 99999999999999999999999999873
Q ss_pred cccccccCcEEEEEECCeEEEEEEE
Q psy12858 84 VTNDFVTEGTYTLDVAGNRFQASAH 108 (131)
Q Consensus 84 v~~~~~~g~~~~V~i~g~~~~A~v~ 108 (131)
....|+.++|+++|+.++|+|+
T Consensus 72 ---~~~~g~~l~v~~~g~~~~a~v~ 93 (95)
T PF08669_consen 72 ---YAEPGTELEVEIRGKRVPATVV 93 (95)
T ss_dssp ---GGSTTSEEEEEETTEEEEEEEE
T ss_pred ---HcCCCCEEEEEECCEEEEEEEe
Confidence 3346889999999999999998
No 3
>KOG2844|consensus
Probab=99.91 E-value=6.7e-24 Score=181.01 Aligned_cols=113 Identities=47% Similarity=0.776 Sum_probs=101.8
Q ss_pred CCCccHHHHHHhHhcCCCeEEEEEEEecCCCCCCcccCCCCceeeCCeEeEEEecceeccccCCeEEEEEecCCCCCCcc
Q psy12858 6 DYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGFTMKKLIGLGYIRHPSEQNVT 85 (131)
Q Consensus 6 ~dFIGk~AL~~~~~~g~~r~lvgl~~~~~~~~~~~~~~~g~~V~~~g~~VG~vTSg~ySp~l~~~Iala~v~~~~~~~v~ 85 (131)
.|||||+||++|+++|++||||.|.+++.+.+ |++||+||+||+.||.+||+.||++++|.||++||+......|+
T Consensus 742 ~dFiGk~ALeqqra~GlkkrlV~l~l~d~d~~----~~G~E~I~rnG~~VG~ttsa~Y~ytl~k~v~~gyV~n~~e~~V~ 817 (856)
T KOG2844|consen 742 ADFIGKQALEQQKAEGLKKRLVCLTLDDHDPD----PWGGEPIYRNGQVVGNTTSAAYGYTLGKSVCLGYVHNFEEFPVS 817 (856)
T ss_pred ccchhHHHHHHHHHhhhhheEEEEEecCCCCC----ccCCcceeeCCEEEeeeeeccceeeecceEEEEEecccccCccC
Confidence 69999999999999999999999999998775 89999999999999999999999999999999999864344567
Q ss_pred cccccCcEEEEEECCeEEEEEEEeCCCccCCCCCCcCC
Q psy12858 86 NDFVTEGTYTLDVAGNRFQASAHIYPPLSNVQVARPYV 123 (131)
Q Consensus 86 ~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~dp~~~r~~~ 123 (131)
.+|...+.++|++.|++++|++....|| +|...|-++
T Consensus 818 ~d~V~sg~yEvdi~Gkry~a~~~l~sP~-~pt~~r~~~ 854 (856)
T KOG2844|consen 818 LDFVGSGEYEVDIAGKRYPAKANLHSPS-LPTEKRRKP 854 (856)
T ss_pred HHHhcCCcEEEEecccccceeEEecCCC-CCcccccCC
Confidence 6777778999999999999999988898 888777654
No 4
>PRK12486 dmdA putative dimethyl sulfoniopropionate demethylase; Reviewed
Probab=99.90 E-value=2.7e-23 Score=169.13 Aligned_cols=97 Identities=21% Similarity=0.185 Sum_probs=85.0
Q ss_pred CCCccHHHHHHhHhcCCCeEEEEEEEecCCCCCCccc-CCCCceeeCCeEeEEEecceeccccCCeEEEEEecCCCCCCc
Q psy12858 6 DYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWL-WGSEPIYRNDQFVGTITSAGYGFTMKKLIGLGYIRHPSEQNV 84 (131)
Q Consensus 6 ~dFIGk~AL~~~~~~g~~r~lvgl~~~~~~~~~~~~~-~~g~~V~~~g~~VG~vTSg~ySp~l~~~Iala~v~~~~~~~v 84 (131)
+|||||+||++++++|.+||||+|+++++.++ + .++++|+.+|+.||+|||++|||+|+++||||||+.+
T Consensus 271 ~~FiGkeal~r~~~~g~~rrlvgl~~~~~~~~----~~~~~~~V~~~g~~VG~vTS~~~sp~l~~~Iala~v~~~----- 341 (368)
T PRK12486 271 IGCIGKDALLRVAKEGPQKQIRGIKIGGERIP----PCDRAWPLLAGDNRVGQVTSAAYSPDFQTNVAIGMVRMT----- 341 (368)
T ss_pred CCCcCHHHHHHHHhcCCCeEEEEEEECCCCCC----CcCCceEEeeCCeEEEEEeccCcCcccCceEEEEEEChh-----
Confidence 37999999999988889999999999876552 2 2347899999999999999999999999999999873
Q ss_pred ccccccCcEEEEEECCeEEEEEEEeCCCcc
Q psy12858 85 TNDFVTEGTYTLDVAGNRFQASAHIYPPLS 114 (131)
Q Consensus 85 ~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~ 114 (131)
....|+.++|++++++++|+|+ .+|||
T Consensus 342 --~~~~g~~l~v~~~~~~~~a~v~-~~Pf~ 368 (368)
T PRK12486 342 --HWDPGTGLEVETPDGMRPATVR-EGFWI 368 (368)
T ss_pred --hcCCCCEEEEEECCceEEEEEe-CCCCC
Confidence 2246889999999999999999 89996
No 5
>PRK13579 gcvT glycine cleavage system aminomethyltransferase T; Provisional
Probab=99.90 E-value=5.7e-23 Score=167.01 Aligned_cols=103 Identities=21% Similarity=0.368 Sum_probs=90.1
Q ss_pred CCCCCccHHHHHHhHhcCCCeEEEEEEEecCCCCCCcccCCCCceeeC-CeEeEEEecceeccccCCeEEEEEecCCCCC
Q psy12858 4 VKDYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRN-DQFVGTITSAGYGFTMKKLIGLGYIRHPSEQ 82 (131)
Q Consensus 4 ~k~dFIGk~AL~~~~~~g~~r~lvgl~~~~~~~~~~~~~~~g~~V~~~-g~~VG~vTSg~ySp~l~~~Iala~v~~~~~~ 82 (131)
.|.||+|||++++++.+|..+|+++|.+++... +..|++|+.+ |+.||+|||++|||+++++||||||+.+
T Consensus 266 ~KgcyiGqEalar~~~~G~~kr~v~l~~~~~~~-----~~~g~~v~~~~g~~VG~VtS~~~sp~l~~~iala~v~~~--- 337 (370)
T PRK13579 266 EAGGFPGAKAILAALAKGASRRRVGLKPEGRAP-----VREGAPLFDDAGTEIGTVTSGGFGPSVGGPVAMGYVPAS--- 337 (370)
T ss_pred CCCCCcCHHHHHHHHhcCCCeEEEEEEECCccC-----CCCCCEEEcCCCceEEEEeecCcchhcCCeEEEEEEChh---
Confidence 356999999999998889999999999975433 6789999987 5999999999999999999999999873
Q ss_pred CcccccccCcEEEEEECCeEEEEEEEeCCCccCCCCC
Q psy12858 83 NVTNDFVTEGTYTLDVAGNRFQASAHIYPPLSNVQVA 119 (131)
Q Consensus 83 ~v~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~dp~~~ 119 (131)
....|+.++|++.|++++|+|+ ..|||+++..
T Consensus 338 ----~~~~g~~v~v~~~g~~~~a~v~-~~Pf~~~~~~ 369 (370)
T PRK13579 338 ----LAAPGTAVFAEVRGKRLPVTVH-ALPFVPHRYK 369 (370)
T ss_pred ----hcCCCCEEEEEECCEEEEEEEE-cCCcccCCcc
Confidence 1246889999999999999999 8999988743
No 6
>PLN02319 aminomethyltransferase
Probab=99.88 E-value=2.9e-22 Score=164.70 Aligned_cols=99 Identities=23% Similarity=0.420 Sum_probs=85.6
Q ss_pred CCCCccHHHHHHhHhcCCCeEEEEEEEecCCCCCCcccCCCCcee-eCCeEeEEEecceeccccCCeEEEEEecCCCCCC
Q psy12858 5 KDYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIY-RNDQFVGTITSAGYGFTMKKLIGLGYIRHPSEQN 83 (131)
Q Consensus 5 k~dFIGk~AL~~~~~~g~~r~lvgl~~~~~~~~~~~~~~~g~~V~-~~g~~VG~vTSg~ySp~l~~~Iala~v~~~~~~~ 83 (131)
|.||||||+|++++.+|.++|+|+|.. +..+ +..|+.|+ .+|+.||+|||++|||+++++||||||+.+
T Consensus 300 Kg~fiGqEalar~~~~g~~rrlvgl~~-~~~~-----~~~g~~v~~~~g~~VG~VTS~~~Sp~l~~~Iala~v~~~---- 369 (404)
T PLN02319 300 EGGFLGADVILKQLKEGVSRRRVGFIS-SGAP-----ARSHSEILDESGEKIGEVTSGGFSPCLKKNIAMGYVKSG---- 369 (404)
T ss_pred CCCCcCHHHHHHHHhcCCCeEEEEEEE-CCcc-----CCCCCEEEeCCCCEEEEEeeecccccCCceEEEEEEChh----
Confidence 569999999999988899999999954 3334 56777777 478999999999999999999999999873
Q ss_pred cccccccCcEEEEEECCeEEEEEEEeCCCccCCC
Q psy12858 84 VTNDFVTEGTYTLDVAGNRFQASAHIYPPLSNVQ 117 (131)
Q Consensus 84 v~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~dp~ 117 (131)
....|+.++|+++|+.++|+|+ ..|||+|+
T Consensus 370 ---~~~~g~~v~v~~~g~~~~a~v~-~~Pf~~~~ 399 (404)
T PLN02319 370 ---FHKAGTEVKVEVRGKMYDAVVT-KMPFVPTK 399 (404)
T ss_pred ---hcCCCCEEEEEECCeEEEEEEE-CCCCcCcc
Confidence 2236889999999999999999 89999987
No 7
>PRK00389 gcvT glycine cleavage system aminomethyltransferase T; Reviewed
Probab=99.87 E-value=3.1e-21 Score=155.76 Aligned_cols=98 Identities=27% Similarity=0.432 Sum_probs=88.6
Q ss_pred CCCCccHHHHHHhHhcCCCeEEEEEEEecCCCCCCcccCCCCceeeCCeEeEEEecceeccccCCeEEEEEecCCCCCCc
Q psy12858 5 KDYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGFTMKKLIGLGYIRHPSEQNV 84 (131)
Q Consensus 5 k~dFIGk~AL~~~~~~g~~r~lvgl~~~~~~~~~~~~~~~g~~V~~~g~~VG~vTSg~ySp~l~~~Iala~v~~~~~~~v 84 (131)
|.||+|||++++++..|.+||||+|.+++... +..|++|+.+|+.||+|||++|||.++++||||+|+.
T Consensus 261 Kgcy~GqE~var~~~~g~krrlv~l~~~~~~~-----~~~g~~v~~~g~~vG~vts~~~s~~~~~~iala~l~~------ 329 (359)
T PRK00389 261 KRDFIGREALEAQKEAGVERKLVGLELEERGI-----PRHGYPVLADGEEIGEVTSGTFSPTLGKSIALAYVPA------ 329 (359)
T ss_pred CCCCcCHHHHHHHHhcCCCeEEEEEEECCCcC-----CCCCCEEeeCCcEEEEEeccCcccccCceEEEEEecC------
Confidence 77999999999998888999999999975433 7889999999999999999999999999999999987
Q ss_pred ccccccCcEEEEEECCeEEEEEEEeCCCccCCCC
Q psy12858 85 TNDFVTEGTYTLDVAGNRFQASAHIYPPLSNVQV 118 (131)
Q Consensus 85 ~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~dp~~ 118 (131)
++ |+.++|++.|++++|+|+ ..|||||+.
T Consensus 330 --~~--g~~~~v~~~~~~~~a~v~-~~p~~~~~~ 358 (359)
T PRK00389 330 --GV--GDEVEVEIRGKQVPAKVV-KPPFVRRGK 358 (359)
T ss_pred --CC--CCEEEEEECCeEEEEEEe-cCCCcCCCC
Confidence 22 788999999999999999 799999865
No 8
>TIGR00528 gcvT glycine cleavage system T protein. Eukaryotic forms are mitochondrial and have an N-terminal transit peptide.
Probab=99.85 E-value=1.1e-20 Score=153.05 Aligned_cols=99 Identities=28% Similarity=0.439 Sum_probs=87.3
Q ss_pred CCCCCccHHHHHHhHhcCCCeEEEEEEEecCCCCCCcccCCCCceee-CC-eEeEEEecceeccccCCeEEEEEecCCCC
Q psy12858 4 VKDYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYR-ND-QFVGTITSAGYGFTMKKLIGLGYIRHPSE 81 (131)
Q Consensus 4 ~k~dFIGk~AL~~~~~~g~~r~lvgl~~~~~~~~~~~~~~~g~~V~~-~g-~~VG~vTSg~ySp~l~~~Iala~v~~~~~ 81 (131)
+|.||+|||++++++..|..||+|++.+++... +..|++|+. +| +.||.|||++|||+++++||||||+.+
T Consensus 260 kKgcy~GqE~lar~~~~G~~krlv~l~~~~~~~-----~~~g~~v~~~~g~~~vG~vtS~~~s~~~g~~iala~v~~~-- 332 (361)
T TIGR00528 260 AKRDFIGRAVLEEQKENGTEKKLVGLEMLEKGI-----ARNGYPVFFTNGNQHVGIVTSGTFSPTLGKNIGLAYVPSE-- 332 (361)
T ss_pred CCCCCcCHHHHHhHHhcCCCeEEEEEEECCCcC-----CCCCCEEEeCCCCeeEEEEeecCcchhcCceEEEEEEChh--
Confidence 467999999999999889999999999876444 788999997 76 999999999999999999999999973
Q ss_pred CCcccccccCcEEEEEECCeEEEEEEEeCCCccC
Q psy12858 82 QNVTNDFVTEGTYTLDVAGNRFQASAHIYPPLSN 115 (131)
Q Consensus 82 ~~v~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~d 115 (131)
....|+.++|++.|++++|+|+ ..|||+
T Consensus 333 -----~~~~g~~~~v~~~g~~~~a~v~-~~p~~~ 360 (361)
T TIGR00528 333 -----TEKIGTTLIVQIRNKEYPIKVV-KPPFVR 360 (361)
T ss_pred -----hcCCCCEEEEEECCeEEEEEEe-cCCCcC
Confidence 2236889999999999999999 799975
No 9
>TIGR01372 soxA sarcosine oxidase, alpha subunit family, heterotetrameric form. This model describes the alpha subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members are share the same function. The model is designated as subfamily rather than equivalog for this reason.Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) forms
Probab=99.85 E-value=1.1e-20 Score=169.37 Aligned_cols=107 Identities=20% Similarity=0.198 Sum_probs=90.0
Q ss_pred CCCCCccHHHHHHhHh-cCCCeEEEEEEEecCCCCCCcccCCCCceeeCC------eEeEEEecceeccccCCeEEEEEe
Q psy12858 4 VKDYFIGKAALQRQKD-QGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRND------QFVGTITSAGYGFTMKKLIGLGYI 76 (131)
Q Consensus 4 ~k~dFIGk~AL~~~~~-~g~~r~lvgl~~~~~~~~~~~~~~~g~~V~~~g------~~VG~vTSg~ySp~l~~~Iala~v 76 (131)
.|.|||||++|++++. .+++++||+|.+++.+.. ++.|..++.++ +.||+|||++|||+++++||||||
T Consensus 871 ~Kg~fiGqeal~r~~~~~~~krrlvgl~~~~~~~~----~~~g~~v~~~~~~~~~~~~vG~VTS~~~sp~lg~~iaLa~v 946 (985)
T TIGR01372 871 KKPDFVGRRMLAREDLVAEDRKQLVGLLPLDPQRR----LPEGAHIVADDAEAIPMNMQGHVTSSYFSPALGRTIALALV 946 (985)
T ss_pred CCCCcCCHHHHHhHHhcCCCceEEEEEEEeCCCCC----CCCCCEEEECCCcccCCCcEEEEeeeccchhcCCeEEEEEE
Confidence 3459999999998876 457999999998865321 56777777553 689999999999999999999999
Q ss_pred cCCCCCCcccccccCcEEEEEECCeEEEEEEEeCCCccCCCCCCcC
Q psy12858 77 RHPSEQNVTNDFVTEGTYTLDVAGNRFQASAHIYPPLSNVQVARPY 122 (131)
Q Consensus 77 ~~~~~~~v~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~dp~~~r~~ 122 (131)
+.+ ....|+.++|++.|++++|+|+ .+|||||+++|++
T Consensus 947 ~~~-------~~~~G~~v~v~~~g~~~~a~v~-~~pf~dp~~~r~~ 984 (985)
T TIGR01372 947 KGG-------RARHGETVYVPDLGRFIAVEIC-DPVFFDPEGTRLH 984 (985)
T ss_pred Ccc-------ccCCCCEEEEEECCEEEEEEEe-ccCCCCCCCCCcC
Confidence 873 1236889999999999999999 8999999999986
No 10
>KOG2770|consensus
Probab=99.77 E-value=2.7e-18 Score=137.52 Aligned_cols=96 Identities=21% Similarity=0.289 Sum_probs=86.3
Q ss_pred CCccHHHHHHhHhcC-CCeEEEEEEEecCCCCCCcccCCCCceeeC-CeEeEEEecceeccccCCeEEEEEecCCCCCCc
Q psy12858 7 YFIGKAALQRQKDQG-VQKRLVMFVAEDLDPDTDVWLWGSEPIYRN-DQFVGTITSAGYGFTMKKLIGLGYIRHPSEQNV 84 (131)
Q Consensus 7 dFIGk~AL~~~~~~g-~~r~lvgl~~~~~~~~~~~~~~~g~~V~~~-g~~VG~vTSg~ySp~l~~~Iala~v~~~~~~~v 84 (131)
||.|.+.+++|..++ ..+|+|||.+.+..+ ++.|.+|+.+ |+.||.|||++.||+++++||||||+..
T Consensus 297 ~f~Ga~~I~~qLk~~~~~~RrvGl~~~~~p~-----ar~gs~I~~~~g~kVG~vTSg~~sptl~kniamgYV~k~----- 366 (401)
T KOG2770|consen 297 DFPGAEVILKQLKDGGISRRRVGLNLSAKPP-----ARSGSAIFVDDGTKVGQVTSGCPSPTLGKNIAMGYVKKG----- 366 (401)
T ss_pred CCCcHHHHHHHhhcCCcceEEEeeeccCCCC-----CCCCCeeEcCCCceEeeEccCCCCCCcccceeEEEeecc-----
Confidence 899999999988766 899999999988644 7999999987 7999999999999999999999999984
Q ss_pred ccccccCcEEEEEECCeEEEEEEEeCCCccC
Q psy12858 85 TNDFVTEGTYTLDVAGNRFQASAHIYPPLSN 115 (131)
Q Consensus 85 ~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~d 115 (131)
....|+.+.|.++++.++++|+ ++||+.
T Consensus 367 --~~~~Gtkv~v~vr~k~~~~~Vs-kmPfV~ 394 (401)
T KOG2770|consen 367 --YHKIGTKVLVKVRNKLYPAEVS-KMPFVP 394 (401)
T ss_pred --ccCCCCEEEEEecCcccceEEE-eccccc
Confidence 3358999999999999999999 899953
No 11
>PRK09559 putative global regulator; Reviewed
Probab=98.76 E-value=1.1e-07 Score=76.41 Aligned_cols=95 Identities=13% Similarity=0.070 Sum_probs=66.9
Q ss_pred CCCCCccHHHHHHhHhcC-CCeEEEEEEEecCCCCCCcccCCCCcee--eC--CeEeEEEecceeccccCCeEEEEEecC
Q psy12858 4 VKDYFIGKAALQRQKDQG-VQKRLVMFVAEDLDPDTDVWLWGSEPIY--RN--DQFVGTITSAGYGFTMKKLIGLGYIRH 78 (131)
Q Consensus 4 ~k~dFIGk~AL~~~~~~g-~~r~lvgl~~~~~~~~~~~~~~~g~~V~--~~--g~~VG~vTSg~ySp~l~~~Iala~v~~ 78 (131)
.|.||+|+|++.|.+..| .+|++++|.+++..+ ++.|++|. .+ ++.||.|+|++-++. +...+++.++.
T Consensus 225 ~KGCY~GQE~vAR~~~~G~~krrl~~l~~~~~~~-----~~~g~~i~~~~~~~~~~~G~v~s~~~~~~-~~~~~l~v~~~ 298 (327)
T PRK09559 225 KKGCYTGQEMVARAKFRGANKRALWWLAGKASRV-----PEAGEDLELKMGENWRRTGTVLAAVQLDD-GQVWVQVVMNN 298 (327)
T ss_pred cCcccccHHHHHHHHHcCCCceeEEEEecccccC-----CCCCCeeEEecCCCCceeEEEEEEEECCC-CCEEEEEEEec
Confidence 467999999999988777 588999999876655 78899763 22 579999999987666 66667777775
Q ss_pred CCCCCcccccccCcEEEEEECCeEEEEEEEeCCCcc
Q psy12858 79 PSEQNVTNDFVTEGTYTLDVAGNRFQASAHIYPPLS 114 (131)
Q Consensus 79 ~~~~~v~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~ 114 (131)
+ ...++.+.+.-... -..++. .+||-
T Consensus 299 ~--------~~~~~~l~~~~~~~-~~~~~~-~lPy~ 324 (327)
T PRK09559 299 D--------LEADSVFRVRDDAG-NTLHIQ-PLPYS 324 (327)
T ss_pred C--------cCCCceEEEccCCC-CeeEec-CCCCC
Confidence 3 23344555532221 236666 68873
No 12
>TIGR03317 ygfZ_signature folate-binding protein YgfZ. YgfZ is a protein from Escherichia coli, homologous to the glycine cleavage system T protein, or aminomethyltransferase, GcvT (TIGR00528). Homologs of YgfZ other than members of the GcvT family share a well-conserved signature region that includes the motif, KGCYxGQE. Elsewhere, sequence diverge and length variation are substantial. Members of this family are mostly bacterial, largely absent from the Firmicutes and otherwise usually present. A few eukaryotic examples are found among the Apicomplexa, and a few archaeal sequences are found. Two functions implicated for this folate-binding protein are RNA modification (a function likely to be conserved) and replication initiation (a function likely to be highly variable). Many members of this family are, at the time of construction of this model, misnamed as the glycine cleavage system T protein.
Probab=97.69 E-value=5.3e-05 Score=47.58 Aligned_cols=26 Identities=31% Similarity=0.621 Sum_probs=23.3
Q ss_pred CCCCccHHHHHHhHhcC-CCeEEEEEE
Q psy12858 5 KDYFIGKAALQRQKDQG-VQKRLVMFV 30 (131)
Q Consensus 5 k~dFIGk~AL~~~~~~g-~~r~lvgl~ 30 (131)
|.||||||++++++.+| ++++||+|.
T Consensus 40 Kg~yiGqe~l~r~~~~g~~~~~lv~l~ 66 (67)
T TIGR03317 40 KGCYVGQEVVARMHYRGKVKRRLVRLR 66 (67)
T ss_pred CCCccCHHHHHHHHHcCCCceeEEEee
Confidence 46999999999998888 799999986
No 13
>COG0354 Predicted aminomethyltransferase related to GcvT [General function prediction only]
Probab=97.47 E-value=0.00027 Score=56.79 Aligned_cols=65 Identities=23% Similarity=0.293 Sum_probs=52.6
Q ss_pred CCCCCccHHHHHHhHhcC-CCeEEEEEEEecCCCCCCcccCCCCceeeCCeE--eEEEecceeccccCCeEEEEEecC
Q psy12858 4 VKDYFIGKAALQRQKDQG-VQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQF--VGTITSAGYGFTMKKLIGLGYIRH 78 (131)
Q Consensus 4 ~k~dFIGk~AL~~~~~~g-~~r~lvgl~~~~~~~~~~~~~~~g~~V~~~g~~--VG~vTSg~ySp~l~~~Iala~v~~ 78 (131)
.|+||+|+|...|.+..| .+|+|+.|.+++. . |..|+.|..+++. +|.|+|..- ...+|++++..
T Consensus 205 ~KGCYvGQE~VAR~~~rG~~kRrl~~l~~d~~-~-----p~~g~~i~a~~~~~~~G~v~s~~~----~~~~~l~~l~~ 272 (305)
T COG0354 205 KKGCYVGQETVARAKYRGTNKRRLVLLALDAS-L-----PEAGEEILAGGEEVGLGTVLSAVG----LGPVALIRLKV 272 (305)
T ss_pred cCcccccHHHhhHHHhcCCCceeEEEEEeCCC-C-----CCCCCeeecCCCcceeeeEEeccc----CcchhHHHHHH
Confidence 678999999999988777 7889999999875 3 7889999999888 889988741 12377888775
No 14
>KOG2929|consensus
Probab=96.17 E-value=0.015 Score=47.12 Aligned_cols=99 Identities=20% Similarity=0.296 Sum_probs=63.6
Q ss_pred CCCCCccHHHHHHhHhcC-CCeEEEEEEEecCCCCC--CcccCCCCcee-eCCeEeEEEecceeccccCCeEEEEEecCC
Q psy12858 4 VKDYFIGKAALQRQKDQG-VQKRLVMFVAEDLDPDT--DVWLWGSEPIY-RNDQFVGTITSAGYGFTMKKLIGLGYIRHP 79 (131)
Q Consensus 4 ~k~dFIGk~AL~~~~~~g-~~r~lvgl~~~~~~~~~--~~~~~~g~~V~-~~g~~VG~vTSg~ySp~l~~~Iala~v~~~ 79 (131)
.|.+|+|+|--.+-...| .++||+.|.++..+-.+ ...+.....|. ..|+.||.+.|+. ..-|||.+...
T Consensus 238 ~KGCYVGQELTARThhtGViRKRl~P~r~~~~e~~p~~~~~~~~~~~v~~~~g~kvG~~~~~~------g~~glgllr~e 311 (348)
T KOG2929|consen 238 DKGCYVGQELTARTHHTGVIRKRLFPFRLDLAENEPLLVGFTNAPPEVEKKKGRKVGRVISGE------GLRGLGLLRLE 311 (348)
T ss_pred cCcceechhheehhhhcceeeeeeeeEEecccCCCccccCCCCCccceecccCceeeeeeccC------cceeeeeeehh
Confidence 578999999888777778 68899999994322110 00112333343 5688999999874 35577788762
Q ss_pred CCCCcccccccCcEEEEEECCeEEEEEEEeCCCccCCCC
Q psy12858 80 SEQNVTNDFVTEGTYTLDVAGNRFQASAHIYPPLSNVQV 118 (131)
Q Consensus 80 ~~~~v~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf~dp~~ 118 (131)
.......+..+.|..+.++.. .|+|=|+-
T Consensus 312 --------~~~~~~~~l~~~g~~i~i~~~--~p~W~p~~ 340 (348)
T KOG2929|consen 312 --------KFKAQFYKLTTKGENIKIKPQ--KPEWWPDW 340 (348)
T ss_pred --------hhhccchhhhccCccceeccC--CCcccccc
Confidence 223444556677877776664 57665543
No 15
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=81.90 E-value=10 Score=23.79 Aligned_cols=38 Identities=18% Similarity=0.030 Sum_probs=32.2
Q ss_pred cCCCCceeeCCeEeEEEecceeccccCCeEEEEEecCC
Q psy12858 42 LWGSEPIYRNDQFVGTITSAGYGFTMKKLIGLGYIRHP 79 (131)
Q Consensus 42 ~~~g~~V~~~g~~VG~vTSg~ySp~l~~~Iala~v~~~ 79 (131)
+..|.+|...|-.||.|++-.+++.-++...-..|+++
T Consensus 15 L~~gs~V~~~Gv~VG~V~~i~l~~~~~~v~v~~~i~~~ 52 (81)
T PF02470_consen 15 LSVGSPVRYRGVEVGKVTSIELDPDGNRVRVTLRIDPD 52 (81)
T ss_pred CCCcCEEEECCEEEEEEEEEEEcCCCCEEEEEEEEcCC
Confidence 67789999999999999999987777777777777763
No 16
>PRK10807 paraquat-inducible protein B; Provisional
Probab=77.30 E-value=13 Score=32.30 Aligned_cols=61 Identities=8% Similarity=0.113 Sum_probs=44.8
Q ss_pred EEEEEecCCCCCCcccCCC-CceeeCCeEeEEEecceeccccCCeEEEEEecCCCCCCcccccc-cCcEEEEE
Q psy12858 27 VMFVAEDLDPDTDVWLWGS-EPIYRNDQFVGTITSAGYGFTMKKLIGLGYIRHPSEQNVTNDFV-TEGTYTLD 97 (131)
Q Consensus 27 vgl~~~~~~~~~~~~~~~g-~~V~~~g~~VG~vTSg~ySp~l~~~Iala~v~~~~~~~v~~~~~-~g~~~~V~ 97 (131)
+.+..++.+- ...| .+|+-.|..||.|++-.+++...+-+.-++|+.+ .. .+. .+++|++.
T Consensus 46 itl~~~~a~g-----l~~GkT~I~yrgv~VG~V~~v~l~~d~~~V~~~~~i~~~-~~----~ll~~~trFWvv 108 (547)
T PRK10807 46 VTLITTNAEG-----IEAGKTTIKSRSVDVGVVESVTLSDDLTHVEIKARLNSG-ME----KLLHKDSVFWVV 108 (547)
T ss_pred EEEEECCCCC-----cCcCCceeEECCceEEEEEEEEECCCCCeEEEEEEECcc-HH----HhhcCCCEEEEe
Confidence 4455544333 5667 8999999999999999999999999999999875 21 222 45666554
No 17
>PF05580 Peptidase_S55: SpoIVB peptidase S55; InterPro: IPR008763 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 the MEROPS peptidase family S55 (SpoIVB peptidase family, clan PA(S)). The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis [, ].
Probab=57.73 E-value=14 Score=28.57 Aligned_cols=19 Identities=21% Similarity=0.597 Sum_probs=17.0
Q ss_pred CCCCceeeCCeEeEEEecc
Q psy12858 43 WGSEPIYRNDQFVGTITSA 61 (131)
Q Consensus 43 ~~g~~V~~~g~~VG~vTSg 61 (131)
..|+||+.||+.||-||..
T Consensus 181 MSGSPI~qdGKLiGAVthv 199 (218)
T PF05580_consen 181 MSGSPIIQDGKLIGAVTHV 199 (218)
T ss_pred ccCCCEEECCEEEEEEEEE
Confidence 4579999999999999987
No 18
>KOG3322|consensus
Probab=47.10 E-value=14 Score=33.04 Aligned_cols=27 Identities=22% Similarity=0.520 Sum_probs=24.9
Q ss_pred eEeEEEecceeccccCCeEEEEEecCC
Q psy12858 53 QFVGTITSAGYGFTMKKLIGLGYIRHP 79 (131)
Q Consensus 53 ~~VG~vTSg~ySp~l~~~Iala~v~~~ 79 (131)
..||.||+|.|+-..|++-|+|+|+..
T Consensus 643 ~ligfvT~g~~~ln~g~~~~i~~v~~~ 669 (688)
T KOG3322|consen 643 GLIGFVTLGLFALNYGKGKGIGFVRNS 669 (688)
T ss_pred eeEEEEeechhhhhcCCCceeeEEecc
Confidence 578999999999999999999999873
No 19
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=38.11 E-value=22 Score=23.16 Aligned_cols=28 Identities=18% Similarity=0.175 Sum_probs=18.9
Q ss_pred EEEEEEEecCCCCCCcccCCCCceeeCCeEeEEEecc
Q psy12858 25 RLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSA 61 (131)
Q Consensus 25 ~lvgl~~~~~~~~~~~~~~~g~~V~~~g~~VG~vTSg 61 (131)
-+|| ++.+. . .+.|.++ +|..+|.|.|-
T Consensus 20 ~IvG-~V~~G-~-----ik~G~~l--~G~~iG~I~sI 47 (81)
T PF14578_consen 20 AIVG-EVLEG-I-----IKPGYPL--DGRKIGRIKSI 47 (81)
T ss_dssp EEEE-EEEEE-E-----EETT-EE--CSSCEEEEEEE
T ss_pred eEEE-EEeee-E-----EeCCCcc--CCEEEEEEEEe
Confidence 5777 66543 2 6778888 77778888875
No 20
>TIGR00996 Mtu_fam_mce virulence factor Mce family protein. Members of this paralogous family are found as six tandem homologous proteins in the same orientation per cassette, in four separate cassettes in Mycobacterium tuberculosis. The six members of each cassette represent six subfamilies. One subfamily includes the protein mce (mycobacterial cell entry), a virulence protein required for invasion of non-phagocytic cells.
Probab=36.95 E-value=81 Score=24.46 Aligned_cols=35 Identities=11% Similarity=-0.016 Sum_probs=25.5
Q ss_pred cCCCCceeeCCeEeEEEecceeccccCCeEEEEEecC
Q psy12858 42 LWGSEPIYRNDQFVGTITSAGYGFTMKKLIGLGYIRH 78 (131)
Q Consensus 42 ~~~g~~V~~~g~~VG~vTSg~ySp~l~~~Iala~v~~ 78 (131)
+..|.+|...|..||.|++-...+ ++...-..|+.
T Consensus 45 L~~g~~V~~~Gv~VG~V~~i~~~~--~~v~v~~~i~~ 79 (291)
T TIGR00996 45 LYPGSKVRVRGVPVGKVTAISLPG--NGARVTFSLDR 79 (291)
T ss_pred CCCCCceEEcceEEEEEEEEEecC--CEEEEEEEecC
Confidence 678999999999999999998633 33334444444
No 21
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=36.82 E-value=33 Score=28.89 Aligned_cols=19 Identities=26% Similarity=0.592 Sum_probs=16.7
Q ss_pred CCCCceeeCCeEeEEEecc
Q psy12858 43 WGSEPIYRNDQFVGTITSA 61 (131)
Q Consensus 43 ~~g~~V~~~g~~VG~vTSg 61 (131)
..|+||+.||+.||-||..
T Consensus 361 MSGSPi~q~gkliGAvtHV 379 (402)
T TIGR02860 361 MSGSPIIQNGKVIGAVTHV 379 (402)
T ss_pred ccCCCEEECCEEEEEEEEE
Confidence 4579999999999999975
No 22
>PF08248 Tryp_FSAP: Tryptophyllin-3 skin active peptide; InterPro: IPR013266 PdT-3 or Tryptophyllin-3 peptide is a subfamily of the family Tryptophyllin and of the superfamily FSAP (Frog Skin Active Peptide). Originally identified in skin extracts of Neotropical leaf frogs, Phyllomedusa sp. This subfamily has an average length of 13 amino acids. The pharmacological activity of the tryptophyllins remains to be established [] but it seems that these peptides possess an action on liver protein synthesis and body weight []. It is thought to possesses insulin-releasing activity [].
Probab=34.47 E-value=22 Score=14.81 Aligned_cols=6 Identities=17% Similarity=0.168 Sum_probs=4.7
Q ss_pred CCccCC
Q psy12858 111 PPLSNV 116 (131)
Q Consensus 111 ~Pf~dp 116 (131)
.|||+|
T Consensus 2 kpfw~p 7 (12)
T PF08248_consen 2 KPFWPP 7 (12)
T ss_pred CccCCC
Confidence 588887
No 23
>PF09890 DUF2117: Uncharacterized protein conserved in archaea (DUF2117); InterPro: IPR012032 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=34.03 E-value=40 Score=26.00 Aligned_cols=21 Identities=29% Similarity=0.365 Sum_probs=18.3
Q ss_pred cCCCCceeeCCeEeEEEecce
Q psy12858 42 LWGSEPIYRNDQFVGTITSAG 62 (131)
Q Consensus 42 ~~~g~~V~~~g~~VG~vTSg~ 62 (131)
...||.|+.||-+||..||..
T Consensus 99 v~pGE~I~VNGiVIG~A~s~~ 119 (215)
T PF09890_consen 99 VSPGENIFVNGIVIGRATSSE 119 (215)
T ss_pred cCCCCCEEEeeEEEEEEcCCe
Confidence 456899999999999999874
No 24
>PRK10807 paraquat-inducible protein B; Provisional
Probab=33.48 E-value=1.6e+02 Score=25.66 Aligned_cols=38 Identities=16% Similarity=0.256 Sum_probs=31.5
Q ss_pred cCCCCceeeCCeEeEEEecceeccccCCeEEEEEecCC
Q psy12858 42 LWGSEPIYRNDQFVGTITSAGYGFTMKKLIGLGYIRHP 79 (131)
Q Consensus 42 ~~~g~~V~~~g~~VG~vTSg~ySp~l~~~Iala~v~~~ 79 (131)
+..|+||+-.|-.||.|++..+++.-....=-++|..+
T Consensus 171 L~~GaPV~yrgi~VG~V~~~~l~~~~~~v~~~~fI~~~ 208 (547)
T PRK10807 171 LSPGDPVLFRGYRVGSVETSTFDPQKRLMSYQLFINAP 208 (547)
T ss_pred CCCCCceEECCcEEEEEEEEEecCCCCEEEEEEEEcch
Confidence 67899999999999999999997765555556788875
No 25
>PF00920 ILVD_EDD: Dehydratase family; InterPro: IPR000581 Two dehydratases, dihydroxy-acid dehydratase (4.2.1.9 from EC) (gene ilvD or ILV3) and 6-phosphogluconate dehydratase (4.2.1.12 from EC) (gene edd) have been shown to be evolutionary related []. Dihydroxy-acid dehydratase catalyses the fourth step in the biosynthesis of isoleucine and valine, the dehydratation of 2,3-dihydroxy-isovaleic acid into alpha-ketoisovaleric acid. 6-Phosphogluconate dehydratase catalyses the first step in the Entner-Doudoroff pathway, the dehydratation of 6-phospho-D-gluconate into 6-phospho-2-dehydro-3-deoxy-D-gluconate. Another protein containing this signature is the Escherichia coli hypothetical protein yjhG. The N-terminal part of the proteins contains a cysteine that could be involved in the binding of a 2Fe-2S iron-sulphur cluster [].; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2GP4_B.
Probab=31.71 E-value=86 Score=27.37 Aligned_cols=54 Identities=17% Similarity=0.209 Sum_probs=36.2
Q ss_pred CeEeEEEecceeccccCCeEEEEEecCCCCCCcccccc---cCcEEEEEECCeEEEEEEE
Q psy12858 52 DQFVGTITSAGYGFTMKKLIGLGYIRHPSEQNVTNDFV---TEGTYTLDVAGNRFQASAH 108 (131)
Q Consensus 52 g~~VG~vTSg~ySp~l~~~Iala~v~~~~~~~v~~~~~---~g~~~~V~i~g~~~~A~v~ 108 (131)
|+.|..||-|-||=. .+....++|.+ ++++|-.++ .|+.++|++..+++...|.
T Consensus 428 g~~valITDGRfSG~-t~G~~vgHvsP--EAa~GGpIalV~dGD~I~IDi~~r~l~l~v~ 484 (521)
T PF00920_consen 428 GKSVALITDGRFSGA-TRGPCVGHVSP--EAAVGGPIALVRDGDRITIDIPNRRLDLLVS 484 (521)
T ss_dssp T--EEEEESSB-SSS--SS-EEEEEES---GGGT-GGGC--TT-EEEEETTTTEEEE-S-
T ss_pred CCceeEeecCccCCc-ccCCEEEEECc--cccCCCCeEEEcCCCEEEEECCCCEEEEecC
Confidence 578999999999988 77888999998 455554544 6789999999988887765
No 26
>PF03539 Spuma_A9PTase: Spumavirus aspartic protease (A9); InterPro: IPR001641 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to MEROPS peptidase family A9 (spumapepsin family, clan AA). Foamy viruses are single-stranded enveloped retroviruses that have been noted to infect monkeys, cats and humans. In the human virus, the aspartic protease is encoded by the retroviral gag gene [], and in monkeys by the pol gene []. At present, the virus has not been proven to cause any particular disease. However, studies have shown Human foamy virus causes neurological disorders in infected mice []. It is not clear whether the Foamy virus/spumavirus proteases share a common evolutionary origin with other aspartic proteases. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 2JYS_A.
Probab=29.75 E-value=61 Score=23.78 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=14.2
Q ss_pred EEEECCeEEEEEEEeCCCc
Q psy12858 95 TLDVAGNRFQASAHIYPPL 113 (131)
Q Consensus 95 ~V~i~g~~~~A~v~~~~Pf 113 (131)
+..+.|+.+.|+|. ..||
T Consensus 50 ~fKi~grkv~aEVi-~s~~ 67 (163)
T PF03539_consen 50 TFKINGRKVEAEVI-ASPY 67 (163)
T ss_dssp EEEESS-EEEEEEE-EESS
T ss_pred EEEEcCeEEEEEEe-cCcc
Confidence 55689999999999 6776
No 27
>PF05001 RNA_pol_Rpb1_R: RNA polymerase Rpb1 C-terminal repeat ; InterPro: IPR000684 RNA polymerase II (2.7.7.6 from EC) [, ] is one of the three forms of RNA polymerase that exist in eukaryotic nuclei. The C-terminal region of the largest subunit of this oligomeric enzyme consists of the tandem repeat of a conserved heptapeptide []. The number of repeats varies according to the species (for example there are 17 in Plasmodium, 26 in yeast, 44 in Drosophila, and 52 in mammals). The region containing these repeats is essential for the function of polymerase II. This repeated heptapeptide (called CT7n or CTD) is rich in hydroxyl groups. It probably projects out of the globular catalytic domain and may interact with the acidic activator domains of transcriptional regulatory proteins. It is also known to bind by intercalation to DNA. RNA polymerase II is activated by phosphorylation. The serine and threonine residues in the CT7n repeats are the target of such phosphorylation.; GO: 0003677 DNA binding, 0006366 transcription from RNA polymerase II promoter, 0005665 DNA-directed RNA polymerase II, core complex; PDB: 2L0I_B 2GHQ_C 2GHT_C.
Probab=28.48 E-value=20 Score=15.74 Aligned_cols=8 Identities=63% Similarity=0.771 Sum_probs=3.2
Q ss_pred ecceeccc
Q psy12858 59 TSAGYGFT 66 (131)
Q Consensus 59 TSg~ySp~ 66 (131)
||..|||+
T Consensus 3 ~SP~ysPt 10 (14)
T PF05001_consen 3 TSPGYSPT 10 (14)
T ss_dssp TB---BTT
T ss_pred CCCCCCcc
Confidence 46677775
No 28
>KOG2055|consensus
Probab=24.66 E-value=55 Score=28.20 Aligned_cols=21 Identities=14% Similarity=0.301 Sum_probs=16.5
Q ss_pred CeEeEEEecceeccccCCeEEE
Q psy12858 52 DQFVGTITSAGYGFTMKKLIGL 73 (131)
Q Consensus 52 g~~VG~vTSg~ySp~l~~~Ial 73 (131)
+..||+||+-+|||.-| .+|+
T Consensus 479 n~~vg~vtc~aFSP~sG-~lAv 499 (514)
T KOG2055|consen 479 NTKVGHVTCMAFSPNSG-YLAV 499 (514)
T ss_pred CCcccceEEEEecCCCc-eEEe
Confidence 56789999999999765 4443
No 29
>PHA02763 hypothetical protein; Provisional
Probab=21.97 E-value=1.7e+02 Score=19.52 Aligned_cols=42 Identities=17% Similarity=0.250 Sum_probs=30.9
Q ss_pred ccCCeEEEEEecCCCCCCcccccccCcEEEEEECCeEEEEEEEeCCCc
Q psy12858 66 TMKKLIGLGYIRHPSEQNVTNDFVTEGTYTLDVAGNRFQASAHIYPPL 113 (131)
Q Consensus 66 ~l~~~Iala~v~~~~~~~v~~~~~~g~~~~V~i~g~~~~A~v~~~~Pf 113 (131)
-|+..=+.|-|+.- . .|..|+.+.+.+++++++++|....|+
T Consensus 12 iLn~aK~vATIRk~--~----~YK~gqkv~l~v~dr~f~gKvIa~ap~ 53 (102)
T PHA02763 12 ILNNAKAVATIRKK--S----FYKIGQKVILKVGDKRFPGKVIAKAPV 53 (102)
T ss_pred HhcCceeEEeeeeh--h----hhccCcEEEEEecCccccceEEEecCc
Confidence 34555567777752 1 466888898999999999999876665
No 30
>COG3008 PqiB Paraquat-inducible protein B [General function prediction only]
Probab=21.42 E-value=2.7e+02 Score=24.61 Aligned_cols=38 Identities=21% Similarity=0.253 Sum_probs=33.6
Q ss_pred cCCCCceeeCCeEeEEEecceeccccCCeEEEEEecCC
Q psy12858 42 LWGSEPIYRNDQFVGTITSAGYGFTMKKLIGLGYIRHP 79 (131)
Q Consensus 42 ~~~g~~V~~~g~~VG~vTSg~ySp~l~~~Iala~v~~~ 79 (131)
+..|++||-.+-+||.|+|..|-|--.+-.=-.+|+.+
T Consensus 174 L~~GspVyfr~i~VGqV~sy~~d~d~~~V~i~vfI~~p 211 (553)
T COG3008 174 LNVGSPVYFRKIPVGQVESYQFDPDKQGVTIQVFIEAP 211 (553)
T ss_pred cCCCCeeEEeceeeeeEEEEEEcCCCCeEEEEEEecCh
Confidence 67899999999999999999999988877777888875
No 31
>PF04766 Baculo_p26: Nucleopolyhedrovirus p26 protein; InterPro: IPR006853 This entry represents Baculovirus p26 and Vaccinia virus B2 proteins.
Probab=20.66 E-value=1.3e+02 Score=23.47 Aligned_cols=35 Identities=29% Similarity=0.487 Sum_probs=23.6
Q ss_pred EEEEEEecCCCCCCcccCCCCceeeCCeEeEEEecce
Q psy12858 26 LVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAG 62 (131)
Q Consensus 26 lvgl~~~~~~~~~~~~~~~g~~V~~~g~~VG~vTSg~ 62 (131)
|-.|++++.+.. ..+.-|+||+++++.|-.||---
T Consensus 97 lpaf~~~d~~~a--~~lyiGAPIf~~~kLVSVVT~r~ 131 (234)
T PF04766_consen 97 LPAFVVDDFELA--NKLYIGAPIFDNNKLVSVVTDRY 131 (234)
T ss_pred eeEEEEcchhhh--hhEeccCceecCCceEEEEEEEe
Confidence 334566553221 12678999999999999998653
No 32
>cd03864 M14_CPN Peptidase M14 Carboxypeptidase N (CPN, also known as kininase I, creatine kinase conversion factor, plasma carboxypeptidase B, arginine carboxypeptidase, and protaminase; EC 3.4.17.3) is an extracellular glycoprotein synthesized in the liver and released into the blood, where it is present in high concentrations. CPN belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPN plays an important role in protecting the body from excessive buildup of potentially deleterious peptides that normally act as local autocrine or paracrine hormones. It specifically removes C-terminal basic residues. As CPN can cleave lysine more avidly than arginine residues it is also called lysine carboxypeptidase. CPN substrates inclu
Probab=20.26 E-value=2e+02 Score=24.03 Aligned_cols=44 Identities=14% Similarity=0.077 Sum_probs=32.4
Q ss_pred HHHHHHhHhcCCCeEEEEEEEecCCCCCCcccCCCCceeeCCeEeEEEec
Q psy12858 11 KAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITS 60 (131)
Q Consensus 11 k~AL~~~~~~g~~r~lvgl~~~~~~~~~~~~~~~g~~V~~~g~~VG~vTS 60 (131)
|+||++.-++ .++-+.|++.+..+. |-.+..|...|...|.+|.
T Consensus 304 ~~all~~~~~-~~~gI~G~V~D~~g~-----pi~~A~V~v~g~~~~~~T~ 347 (392)
T cd03864 304 REALISYIEQ-VHQGIKGMVTDENNN-----GIANAVISVSGISHDVTSG 347 (392)
T ss_pred HHHHHHHHHH-hcCeEEEEEECCCCC-----ccCCeEEEEECCccceEEC
Confidence 7888876554 677888998886554 7778888887766676664
No 33
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=20.15 E-value=82 Score=25.32 Aligned_cols=21 Identities=29% Similarity=0.487 Sum_probs=17.6
Q ss_pred CCCCceeeCCeEeEEEeccee
Q psy12858 43 WGSEPIYRNDQFVGTITSAGY 63 (131)
Q Consensus 43 ~~g~~V~~~g~~VG~vTSg~y 63 (131)
-.|.||..+|++||.+|-..-
T Consensus 203 i~GaPVvd~dk~vGiit~~dI 223 (294)
T COG2524 203 IRGAPVVDDDKIVGIITLSDI 223 (294)
T ss_pred ccCCceecCCceEEEEEHHHH
Confidence 358999999999999997653
Done!