Query psy12057
Match_columns 172
No_of_seqs 159 out of 1286
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 17:32:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12057.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12057hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0404 GcvT Glycine cleavage 100.0 4.2E-30 9.1E-35 226.3 14.8 135 32-171 241-378 (379)
2 PRK13579 gcvT glycine cleavage 100.0 5.2E-28 1.1E-32 211.7 15.3 121 49-169 249-370 (370)
3 PLN02319 aminomethyltransferas 100.0 9.6E-28 2.1E-32 212.5 15.9 122 50-171 283-404 (404)
4 PRK12486 dmdA putative dimethy 99.9 2.5E-27 5.4E-32 207.7 13.8 128 31-163 238-368 (368)
5 PF08669 GCV_T_C: Glycine clea 99.9 1.5E-25 3.3E-30 161.1 12.8 93 68-160 1-95 (95)
6 KOG2770|consensus 99.9 1E-25 2.2E-30 194.4 12.8 136 33-170 263-400 (401)
7 TIGR00528 gcvT glycine cleavag 99.9 8E-25 1.7E-29 190.6 14.3 114 50-164 245-360 (361)
8 PRK00389 gcvT glycine cleavage 99.9 3.3E-24 7.3E-29 186.1 14.6 122 38-167 236-358 (359)
9 TIGR01372 soxA sarcosine oxida 99.9 2.7E-24 5.8E-29 208.0 15.3 118 50-170 858-983 (985)
10 KOG2844|consensus 99.9 3.6E-22 7.9E-27 184.2 10.4 116 48-168 724-850 (856)
11 PRK09559 putative global regul 99.3 1.2E-11 2.6E-16 106.9 12.4 124 33-164 195-325 (327)
12 TIGR03317 ygfZ_signature folat 99.1 1.4E-10 3.1E-15 78.8 4.6 40 50-92 24-66 (67)
13 COG0354 Predicted aminomethylt 98.4 2.9E-07 6.2E-12 79.7 5.4 96 42-146 180-282 (305)
14 KOG2929|consensus 97.7 5.8E-05 1.3E-09 65.6 5.3 105 50-165 223-338 (348)
15 PF02470 MCE: mce related prot 86.3 8.2 0.00018 26.2 9.1 58 89-147 5-66 (81)
16 PRK10807 paraquat-inducible pr 82.0 7.1 0.00015 36.6 8.0 59 88-147 45-108 (547)
17 PF13953 PapC_C: PapC C-termin 74.3 10 0.00022 25.3 5.0 51 96-158 9-62 (68)
18 PF14578 GTP_EFTU_D4: Elongati 72.7 12 0.00025 26.5 5.1 50 87-150 20-69 (81)
19 KOG3322|consensus 59.0 11 0.00023 36.4 3.4 27 110-136 643-669 (688)
20 PRK10807 paraquat-inducible pr 57.9 45 0.00097 31.3 7.4 68 68-137 141-209 (547)
21 PF05239 PRC: PRC-barrel domai 51.9 34 0.00074 22.6 4.3 36 100-135 10-45 (79)
22 PRK13149 H/ACA RNA-protein com 47.7 88 0.0019 21.3 6.4 51 95-146 21-72 (73)
23 COG3008 PqiB Paraquat-inducibl 40.4 66 0.0014 30.4 5.5 50 88-138 163-213 (553)
24 smart00816 Amb_V_allergen Amb 39.1 15 0.00033 22.8 0.8 7 2-8 26-32 (45)
25 PF03913 Amb_V_allergen: Amb V 32.1 17 0.00037 22.5 0.2 7 2-8 25-31 (44)
26 PRK15248 fimbrial outer membra 31.3 2.4E+02 0.0052 28.0 8.0 60 85-156 769-832 (853)
27 COG3008 PqiB Paraquat-inducibl 31.2 1.7E+02 0.0036 27.8 6.6 64 81-148 44-112 (553)
28 COG3277 GAR1 RNA-binding prote 30.3 2.2E+02 0.0048 20.8 7.1 33 96-129 23-55 (98)
29 cd04088 EFG_mtEFG_II EFG_mtEFG 30.3 1.6E+02 0.0034 19.6 4.9 34 112-146 2-35 (83)
30 COG1873 Protein implicated in 29.2 2.1E+02 0.0045 20.2 6.1 51 100-150 12-66 (87)
31 PF09162 Tap-RNA_bind: Tap, RN 28.9 5.7 0.00012 28.5 -2.6 21 9-29 22-43 (88)
32 PF00571 CBS: CBS domain CBS d 28.3 67 0.0015 19.4 2.6 15 103-117 34-48 (57)
33 PRK15273 putative fimbrial out 27.8 2.7E+02 0.0058 27.8 7.7 54 85-150 742-796 (881)
34 PRK09828 putative fimbrial out 27.5 3.3E+02 0.0072 26.9 8.3 52 85-148 777-829 (865)
35 PF07620 SLEI_Leptospira: SLEI 27.4 26 0.00056 17.4 0.3 12 23-34 1-12 (16)
36 PRK15284 putative fimbrial out 25.5 2.9E+02 0.0064 27.5 7.6 55 85-151 765-820 (881)
37 PF01571 GCV_T: Aminomethyltra 24.2 35 0.00075 26.9 0.8 23 37-59 188-211 (211)
38 PF12396 DUF3659: Protein of u 23.8 68 0.0015 21.5 2.0 25 103-127 14-38 (64)
39 PF05580 Peptidase_S55: SpoIVB 23.8 69 0.0015 26.8 2.5 19 99-118 181-199 (218)
40 PF10459 Peptidase_S46: Peptid 22.3 2.7E+02 0.0058 27.2 6.4 73 56-129 582-673 (698)
41 PF01272 GreA_GreB: Transcript 21.2 38 0.00082 22.9 0.4 32 125-159 43-74 (77)
42 PRK15193 outer membrane usher 20.9 4.1E+02 0.0089 26.5 7.6 52 86-149 795-846 (876)
43 PF08308 PEGA: PEGA domain; I 20.7 2.5E+02 0.0054 18.1 5.5 14 99-113 10-23 (71)
44 PRK15217 fimbrial outer membra 20.6 5.4E+02 0.012 25.4 8.3 53 85-149 749-802 (826)
No 1
>COG0404 GcvT Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
Probab=99.97 E-value=4.2e-30 Score=226.34 Aligned_cols=135 Identities=30% Similarity=0.402 Sum_probs=118.8
Q ss_pred cccccccccchhhhccCCChhccccCccccCCCCCCCCCccHHHHHHhHhcCCCEEEEEEEecC--CCCCCCCEEEcCCC
Q psy12057 32 MAIKTSSVNTILLELFLAMDIYSRLLIFPGKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTG--VPIRPGYEIFNAND 109 (172)
Q Consensus 32 ~~~~~s~~~~~~~~~~~dtP~EaGLg~~V~~~K~~~~dFIGkeAL~~~~~~g~~r~LVgL~l~~--~~~~~g~~V~~~dg 109 (172)
+|.+.-+++-++.+ +.+|+|+||+|+|+++| .|||||+||++++++|++|++|||.+++ .++++|++|+..+|
T Consensus 241 lE~g~~l~g~d~~~--~~~P~eagl~~~v~~~k---~dFiGk~al~~~k~~g~~r~lVgl~~~~~~~~~~~g~~v~~~~g 315 (379)
T COG0404 241 LEAGLRLYGQDLDE--TITPLEAGLGWAVKLDK---DDFIGKAALLREKAKGVRRKLVGLKLDDKGPVLRGGEPVLDADG 315 (379)
T ss_pred hhcCccccccccCC--CCCHhhcCcceEecCCC---cCCcCHHHHHhhhhcCCceEEEEEEEcCCCCCCCCCCeEEecCC
Confidence 44444555555555 33699999999999987 4999999999999988877899999987 47899999994478
Q ss_pred c-EEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEECCEEEeEEEEcCCCcCCCCCCCC
Q psy12057 110 Q-RVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYHTPP 171 (172)
Q Consensus 110 ~-~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g~~~~A~V~~~Pf~dp~~~r~~ 171 (172)
+ .||+|||++|||+||++||||||+.+++..|++++|++++++++|+|+..|||||+++|+.
T Consensus 316 ~~~vG~VTSg~~Sptlg~~IAla~v~~~~~~~G~~~~v~i~~~~~~a~V~~~pf~dp~~~r~~ 378 (379)
T COG0404 316 EVEVGEVTSGTFSPTLGKSIALAYVDSDYAKPGTELEVEIRGKRVPARVVKPPFYDPEGERLR 378 (379)
T ss_pred CEeEEEEeeccccccCCCeeEEEEechhhccCCcEEEEEECCeEEEEEEecCCCcCccccccC
Confidence 8 4999999999999999999999999999999999999999999999999999999999863
No 2
>PRK13579 gcvT glycine cleavage system aminomethyltransferase T; Provisional
Probab=99.96 E-value=5.2e-28 Score=211.67 Aligned_cols=121 Identities=36% Similarity=0.658 Sum_probs=109.8
Q ss_pred CChhccccCccccCCCCCCCCCccHHHHHHhHhcCCCEEEEEEEecC-CCCCCCCEEEcCCCcEEEEEEeeecccccCCe
Q psy12057 49 AMDIYSRLLIFPGKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLKKN 127 (172)
Q Consensus 49 dtP~EaGLg~~V~~~K~~~~dFIGkeAL~~~~~~g~~r~LVgL~l~~-~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~ 127 (172)
++|+|+||+|+|++.|.+|+||+|||++++++..|..||+++|.+++ .++..|++|+..+|+.||+|||++|||+++++
T Consensus 249 ~~P~E~gL~~~v~~~~~~KgcyiGqEalar~~~~G~~kr~v~l~~~~~~~~~~g~~v~~~~g~~VG~VtS~~~sp~l~~~ 328 (370)
T PRK13579 249 TTPVEAALEWAIQKARREAGGFPGAKAILAALAKGASRRRVGLKPEGRAPVREGAPLFDDAGTEIGTVTSGGFGPSVGGP 328 (370)
T ss_pred CCHHHCCccceecCCCCCCCCCcCHHHHHHHHhcCCCeEEEEEEECCccCCCCCCEEEcCCCceEEEEeecCcchhcCCe
Confidence 36999999999998654468999999999999889999999999986 56778999995236999999999999999999
Q ss_pred EEEEEecCCccCCCCEEEEEECCEEEeEEEEcCCCcCCCCCC
Q psy12057 128 IAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYHT 169 (172)
Q Consensus 128 Iala~V~~~~a~~G~~l~V~i~g~~~~A~V~~~Pf~dp~~~r 169 (172)
||||||+.+++.+|++|+|++.|++++|+|+..||++++++|
T Consensus 329 iala~v~~~~~~~g~~v~v~~~g~~~~a~v~~~Pf~~~~~~~ 370 (370)
T PRK13579 329 VAMGYVPASLAAPGTAVFAEVRGKRLPVTVHALPFVPHRYKR 370 (370)
T ss_pred EEEEEEChhhcCCCCEEEEEECCEEEEEEEEcCCcccCCccC
Confidence 999999999999999999999999999999999999998765
No 3
>PLN02319 aminomethyltransferase
Probab=99.95 E-value=9.6e-28 Score=212.46 Aligned_cols=122 Identities=48% Similarity=0.784 Sum_probs=108.8
Q ss_pred ChhccccCccccCCCCCCCCCccHHHHHHhHhcCCCEEEEEEEecCCCCCCCCEEEcCCCcEEEEEEeeecccccCCeEE
Q psy12057 50 MDIYSRLLIFPGKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTGVPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIA 129 (172)
Q Consensus 50 tP~EaGLg~~V~~~K~~~~dFIGkeAL~~~~~~g~~r~LVgL~l~~~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Ia 129 (172)
+|+|+||+|+|+..+.+|+||||||++++++..|++|++++|..++.+++.|++|+..+|+.||.|||++|||+++++||
T Consensus 283 ~P~EagL~~~v~~~~~~Kg~fiGqEalar~~~~g~~rrlvgl~~~~~~~~~g~~v~~~~g~~VG~VTS~~~Sp~l~~~Ia 362 (404)
T PLN02319 283 TPVEAGLAWTIGKRRRAEGGFLGADVILKQLKEGVSRRRVGFISSGAPARSHSEILDESGEKIGEVTSGGFSPCLKKNIA 362 (404)
T ss_pred CHHHCCccceecccccCCCCCcCHHHHHHHHhcCCCeEEEEEEECCccCCCCCEEEeCCCCEEEEEeeecccccCCceEE
Confidence 69999999999843212579999999999988899999999965445668899888557999999999999999999999
Q ss_pred EEEecCCccCCCCEEEEEECCEEEeEEEEcCCCcCCCCCCCC
Q psy12057 130 MGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYHTPP 171 (172)
Q Consensus 130 la~V~~~~a~~G~~l~V~i~g~~~~A~V~~~Pf~dp~~~r~~ 171 (172)
||||+.+++.+|++++|+++|+.++|+|+..||+++.+.++|
T Consensus 363 la~v~~~~~~~g~~v~v~~~g~~~~a~v~~~Pf~~~~~~~~~ 404 (404)
T PLN02319 363 MGYVKSGFHKAGTEVKVEVRGKMYDAVVTKMPFVPTKYYKPP 404 (404)
T ss_pred EEEEChhhcCCCCEEEEEECCeEEEEEEECCCCcCcccCCCC
Confidence 999999999999999999999999999999999999987765
No 4
>PRK12486 dmdA putative dimethyl sulfoniopropionate demethylase; Reviewed
Probab=99.95 E-value=2.5e-27 Score=207.72 Aligned_cols=128 Identities=20% Similarity=0.192 Sum_probs=108.1
Q ss_pred ccccccccccchhhhccCCChhccccCccccCCCCCCCCCccHHHHHHhHhcCCCEEEEEEEecC-CCCCC--CCEEEcC
Q psy12057 31 SMAIKTSSVNTILLELFLAMDIYSRLLIFPGKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTG-VPIRP--GYEIFNA 107 (172)
Q Consensus 31 ~~~~~~s~~~~~~~~~~~dtP~EaGLg~~V~~~K~~~~dFIGkeAL~~~~~~g~~r~LVgL~l~~-~~~~~--g~~V~~~ 107 (172)
.+|.+.-.+..++.+ +.+|+|+||+|+|+++| +.|||||+||+++++++++||||+|.+++ .+++. +++|+.
T Consensus 238 RlE~G~~~~g~D~~~--~~~P~EagL~~~v~~~k--~~~FiGkeal~r~~~~g~~rrlvgl~~~~~~~~~~~~~~~V~~- 312 (368)
T PRK12486 238 RIEGGLLSYGNDMTR--DNTPHECGLGRFCNTQT--DIGCIGKDALLRVAKEGPQKQIRGIKIGGERIPPCDRAWPLLA- 312 (368)
T ss_pred HHhcccccccccCCC--CCChHHCCCceEEcCCC--CCCCcCHHHHHHHHhcCCCeEEEEEEECCCCCCCcCCceEEee-
Confidence 344444444444433 34799999999999987 24899999999998888999999999987 34542 367884
Q ss_pred CCcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEECCEEEeEEEEcCCCc
Q psy12057 108 NDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFL 163 (172)
Q Consensus 108 dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g~~~~A~V~~~Pf~ 163 (172)
+|+.||+|||++|||+++++||||||+.+++.+|++|+|++.++.++|+|+.+||+
T Consensus 313 ~g~~VG~vTS~~~sp~l~~~Iala~v~~~~~~~g~~l~v~~~~~~~~a~v~~~Pf~ 368 (368)
T PRK12486 313 GDNRVGQVTSAAYSPDFQTNVAIGMVRMTHWDPGTGLEVETPDGMRPATVREGFWI 368 (368)
T ss_pred CCeEEEEEeccCcCcccCceEEEEEEChhhcCCCCEEEEEECCceEEEEEeCCCCC
Confidence 89999999999999999999999999999888999999999999999999999996
No 5
>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=99.93 E-value=1.5e-25 Score=161.13 Aligned_cols=93 Identities=42% Similarity=0.694 Sum_probs=83.9
Q ss_pred CCCccHHHHHHhHhcCCC-EEEEEEEecC-CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEE
Q psy12057 68 GGFPGASIIQSQIKSGVS-RKRTGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELW 145 (172)
Q Consensus 68 ~dFIGkeAL~~~~~~g~~-r~LVgL~l~~-~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~ 145 (172)
+|||||+||++++.+|.. |+||+|.+++ .+++.|++|+..+|+.||+|||++|||+++++||||||+.+++.+|++++
T Consensus 1 gdfiG~eal~r~~~~g~~rr~lv~l~~~~~~~~~~g~~v~~~~g~~vG~vTS~~~sp~~~~~Iala~v~~~~~~~g~~l~ 80 (95)
T PF08669_consen 1 GDFIGQEALARQKARGVKRRRLVGLTLDGDAPPRGGEPVYDEDGKPVGRVTSGAYSPTLGKNIALAYVDREYAEPGTELE 80 (95)
T ss_dssp S-STTHHHHHHHHHHTTS-EEEEEEEESSSS--STTCEEEETTTEEEEEEEEEEEETTTTEEEEEEEEEGGGGSTTSEEE
T ss_pred CCcCCHHHHHHHHhcCCCceEEEEEEECCccCCCCCCEEEECCCcEEeEEEEEeECCCCCceEEEEEECHHHcCCCCEEE
Confidence 489999999999998884 9999999987 78999999995489999999999999999999999999999999999999
Q ss_pred EEECCEEEeEEEEcC
Q psy12057 146 VRVRDKRVDVKVTKM 160 (172)
Q Consensus 146 V~i~g~~~~A~V~~~ 160 (172)
|+++|+.++|+|+++
T Consensus 81 v~~~g~~~~a~v~~~ 95 (95)
T PF08669_consen 81 VEIRGKRVPATVVKM 95 (95)
T ss_dssp EEETTEEEEEEEE-S
T ss_pred EEECCEEEEEEEeCc
Confidence 999999999999863
No 6
>KOG2770|consensus
Probab=99.93 E-value=1e-25 Score=194.36 Aligned_cols=136 Identities=42% Similarity=0.691 Sum_probs=120.5
Q ss_pred ccccccccchhhhccCCChhccccCccccCCCCCCCCCccHHHHHHhHhcC-CCEEEEEEEecC-CCCCCCCEEEcCCCc
Q psy12057 33 AIKTSSVNTILLELFLAMDIYSRLLIFPGKRRRETGGFPGASIIQSQIKSG-VSRKRTGLTSTG-VPIRPGYEIFNANDQ 110 (172)
Q Consensus 33 ~~~~s~~~~~~~~~~~dtP~EaGLg~~V~~~K~~~~dFIGkeAL~~~~~~g-~~r~LVgL~l~~-~~~~~g~~V~~~dg~ 110 (172)
|++.-++..+|.+-++ |+||||.|.+...++.+.||.|.+.+++|.+.+ +.||+|||.+.+ .++|.|.+|+..+|+
T Consensus 263 eaGKOGyg~did~~~t--pvEa~L~W~i~krrR~~~~f~Ga~~I~~qLk~~~~~~RrvGl~~~~~p~ar~gs~I~~~~g~ 340 (401)
T KOG2770|consen 263 EAGLCLYGSDIDEETT--PVEAGLSWVIGKRRRGTYDFPGAEVILKQLKDGGISRRRVGLNLSAKPPARSGSAIFVDDGT 340 (401)
T ss_pred hcCCcccCcccccccC--hhhheeeeeeeeccccccCCCcHHHHHHHhhcCCcceEEEeeeccCCCCCCCCCeeEcCCCc
Confidence 4555566666666555 999999999988775555999999999998877 699999999987 778999999975589
Q ss_pred EEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEECCEEEeEEEEcCCCcCCCCCCC
Q psy12057 111 RVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYHTP 170 (172)
Q Consensus 111 ~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g~~~~A~V~~~Pf~dp~~~r~ 170 (172)
.||.|||++.||+++++||||||+..++++|+++.|.++++.++|+|+++||+..++++.
T Consensus 341 kVG~vTSg~~sptl~kniamgYV~k~~~~~Gtkv~v~vr~k~~~~~VskmPfV~t~yy~~ 400 (401)
T KOG2770|consen 341 KVGQVTSGCPSPTLGKNIAMGYVKKGYHKIGTKVLVKVRNKLYPAEVSKMPFVPTNYYKS 400 (401)
T ss_pred eEeeEccCCCCCCcccceeEEEeeccccCCCCEEEEEecCcccceEEEecccccccCCCC
Confidence 999999999999999999999999999999999999999999999999999999888764
No 7
>TIGR00528 gcvT glycine cleavage system T protein. Eukaryotic forms are mitochondrial and have an N-terminal transit peptide.
Probab=99.92 E-value=8e-25 Score=190.64 Aligned_cols=114 Identities=32% Similarity=0.503 Sum_probs=104.3
Q ss_pred ChhccccCccccCCCCCCCCCccHHHHHHhHhcCCCEEEEEEEecC-CCCCCCCEEEcCCC-cEEEEEEeeecccccCCe
Q psy12057 50 MDIYSRLLIFPGKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTG-VPIRPGYEIFNAND-QRVGAITSGCPSPSLKKN 127 (172)
Q Consensus 50 tP~EaGLg~~V~~~K~~~~dFIGkeAL~~~~~~g~~r~LVgL~l~~-~~~~~g~~V~~~dg-~~VG~VTSg~ySP~lgk~ 127 (172)
+|+|+||+|++++++ +|+||+|||++++++..|..||+|++.+++ ..+..|++|+..+| +.||.|||++|||+++++
T Consensus 245 ~P~E~gl~~~v~~~f-kKgcy~GqE~lar~~~~G~~krlv~l~~~~~~~~~~g~~v~~~~g~~~vG~vtS~~~s~~~g~~ 323 (361)
T TIGR00528 245 TPLEAGLGWTIAWEP-AKRDFIGRAVLEEQKENGTEKKLVGLEMLEKGIARNGYPVFFTNGNQHVGIVTSGTFSPTLGKN 323 (361)
T ss_pred ChHHCCcccEEecCC-CCCCCcCHHHHHhHHhcCCCeEEEEEEECCCcCCCCCCEEEeCCCCeeEEEEeecCcchhcCce
Confidence 699999999999973 258999999999999889988899999876 66788999984255 999999999999999999
Q ss_pred EEEEEecCCccCCCCEEEEEECCEEEeEEEEcCCCcC
Q psy12057 128 IAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLK 164 (172)
Q Consensus 128 Iala~V~~~~a~~G~~l~V~i~g~~~~A~V~~~Pf~d 164 (172)
||||||+.+++.+|++|+|++.|++++|+|+..||++
T Consensus 324 iala~v~~~~~~~g~~~~v~~~g~~~~a~v~~~p~~~ 360 (361)
T TIGR00528 324 IGLAYVPSETEKIGTTLIVQIRNKEYPIKVVKPPFVR 360 (361)
T ss_pred EEEEEEChhhcCCCCEEEEEECCeEEEEEEecCCCcC
Confidence 9999999999999999999999999999999999986
No 8
>PRK00389 gcvT glycine cleavage system aminomethyltransferase T; Reviewed
Probab=99.92 E-value=3.3e-24 Score=186.13 Aligned_cols=122 Identities=30% Similarity=0.417 Sum_probs=106.8
Q ss_pred cccchhhhccCCChhccccCccccCCCCCCCCCccHHHHHHhHhcCCCEEEEEEEecC-CCCCCCCEEEcCCCcEEEEEE
Q psy12057 38 SVNTILLELFLAMDIYSRLLIFPGKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTG-VPIRPGYEIFNANDQRVGAIT 116 (172)
Q Consensus 38 ~~~~~~~~~~~dtP~EaGLg~~V~~~K~~~~dFIGkeAL~~~~~~g~~r~LVgL~l~~-~~~~~g~~V~~~dg~~VG~VT 116 (172)
....++.+ ..+|+|+||+|+|+++| |+||+|||+++|++..|.+|+|++|.+++ ..+..|++|+ .+|+.||.||
T Consensus 236 ~~~~d~~~--~~~P~e~gl~~~v~~~~--Kgcy~GqE~var~~~~g~krrlv~l~~~~~~~~~~g~~v~-~~g~~vG~vt 310 (359)
T PRK00389 236 LYGQDMDE--TITPLEAGLGWTVKLEE--KRDFIGREALEAQKEAGVERKLVGLELEERGIPRHGYPVL-ADGEEIGEVT 310 (359)
T ss_pred ccCccCCC--CCChHHcCcccEecCCC--CCCCcCHHHHHHHHhcCCCeEEEEEEECCCcCCCCCCEEe-eCCcEEEEEe
Confidence 33444444 23699999999999983 48999999999998888899999999975 6677899997 4899999999
Q ss_pred eeecccccCCeEEEEEecCCccCCCCEEEEEECCEEEeEEEEcCCCcCCCC
Q psy12057 117 SGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNY 167 (172)
Q Consensus 117 Sg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g~~~~A~V~~~Pf~dp~~ 167 (172)
|++|||.++++||||+|++++ |+.++|++.+++++|+|+..||+||.+
T Consensus 311 s~~~s~~~~~~iala~l~~~~---g~~~~v~~~~~~~~a~v~~~p~~~~~~ 358 (359)
T PRK00389 311 SGTFSPTLGKSIALAYVPAGV---GDEVEVEIRGKQVPAKVVKPPFVRRGK 358 (359)
T ss_pred ccCcccccCceEEEEEecCCC---CCEEEEEECCeEEEEEEecCCCcCCCC
Confidence 999999999999999999875 999999999999999999999999764
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=99.92 E-value=2.7e-24 Score=208.05 Aligned_cols=118 Identities=16% Similarity=0.217 Sum_probs=106.9
Q ss_pred ChhccccCccccCCCCCCCCCccHHHHHHhHh-cCCCEEEEEEEecC--CCCCCCCEEEcCC-----CcEEEEEEeeecc
Q psy12057 50 MDIYSRLLIFPGKRRRETGGFPGASIIQSQIK-SGVSRKRTGLTSTG--VPIRPGYEIFNAN-----DQRVGAITSGCPS 121 (172)
Q Consensus 50 tP~EaGLg~~V~~~K~~~~dFIGkeAL~~~~~-~g~~r~LVgL~l~~--~~~~~g~~V~~~d-----g~~VG~VTSg~yS 121 (172)
+|+|+||+|+|+++| +|||||++|++++. .+++|+||||.+++ .+++.|++++..+ ++.||+|||++||
T Consensus 858 tP~E~gl~~~V~~~K---g~fiGqeal~r~~~~~~~krrlvgl~~~~~~~~~~~g~~v~~~~~~~~~~~~vG~VTS~~~s 934 (985)
T TIGR01372 858 TPADLGMGWMVSKKK---PDFVGRRMLAREDLVAEDRKQLVGLLPLDPQRRLPEGAHIVADDAEAIPMNMQGHVTSSYFS 934 (985)
T ss_pred CHHHCCCcccccCCC---CCcCCHHHHHhHHhcCCCceEEEEEEEeCCCCCCCCCCEEEECCCcccCCCcEEEEeeeccc
Confidence 699999999999986 69999999998876 45699999999876 3677898887534 3789999999999
Q ss_pred cccCCeEEEEEecCCccCCCCEEEEEECCEEEeEEEEcCCCcCCCCCCC
Q psy12057 122 PSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYHTP 170 (172)
Q Consensus 122 P~lgk~Iala~V~~~~a~~G~~l~V~i~g~~~~A~V~~~Pf~dp~~~r~ 170 (172)
|+++++||||||+.+++++|++|+|++.|+.++|+|+..|||||+++|+
T Consensus 935 p~lg~~iaLa~v~~~~~~~G~~v~v~~~g~~~~a~v~~~pf~dp~~~r~ 983 (985)
T TIGR01372 935 PALGRTIALALVKGGRARHGETVYVPDLGRFIAVEICDPVFFDPEGTRL 983 (985)
T ss_pred hhcCCeEEEEEECccccCCCCEEEEEECCEEEEEEEeccCCCCCCCCCc
Confidence 9999999999999999999999999999999999999999999999986
No 10
>KOG2844|consensus
Probab=99.87 E-value=3.6e-22 Score=184.19 Aligned_cols=116 Identities=22% Similarity=0.276 Sum_probs=101.5
Q ss_pred CCChhccccCccccCCCCCCCCCccHHHHHHhHhcCCCEEEEEEEecC--CCCCCCCEEEcCCCcEEEEEEeeecccccC
Q psy12057 48 LAMDIYSRLLIFPGKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTG--VPIRPGYEIFNANDQRVGAITSGCPSPSLK 125 (172)
Q Consensus 48 ~dtP~EaGLg~~V~~~K~~~~dFIGkeAL~~~~~~g~~r~LVgL~l~~--~~~~~g~~V~~~dg~~VG~VTSg~ySP~lg 125 (172)
++||+|||+.|.|+|+|+ .|||||+||++|+++|++||||.|.+++ ..+..|++|+. ||+.||.+||++||.+++
T Consensus 724 d~tPlEaGl~f~vk~k~p--~dFiGk~ALeqqra~GlkkrlV~l~l~d~d~~~~G~E~I~r-nG~~VG~ttsa~Y~ytl~ 800 (856)
T KOG2844|consen 724 DTTPLEAGLEFRVKLKKP--ADFIGKQALEQQKAEGLKKRLVCLTLDDHDPDPWGGEPIYR-NGQVVGNTTSAAYGYTLG 800 (856)
T ss_pred CCChhhccceeEEecCCC--ccchhHHHHHHHHHhhhhheEEEEEecCCCCCccCCcceee-CCEEEeeeeeccceeeec
Confidence 448999999999999974 6999999999999999999999999998 44899999995 999999999999999999
Q ss_pred CeEEEEEecC--------CccCCCCEEEEEECCEEEeEEEEcC-CCcCCCCC
Q psy12057 126 KNIAMGYIEP--------AYSKVGVELWVRVRDKRVDVKVTKM-PFLKSNYH 168 (172)
Q Consensus 126 k~Iala~V~~--------~~a~~G~~l~V~i~g~~~~A~V~~~-Pf~dp~~~ 168 (172)
|.+++|||.. ++...| +++|++.|++++|++.-. || +|...
T Consensus 801 k~v~~gyV~n~~e~~V~~d~V~sg-~yEvdi~Gkry~a~~~l~sP~-~pt~~ 850 (856)
T KOG2844|consen 801 KSVCLGYVHNFEEFPVSLDFVGSG-EYEVDIAGKRYPAKANLHSPS-LPTEK 850 (856)
T ss_pred ceEEEEEecccccCccCHHHhcCC-cEEEEecccccceeEEecCCC-CCccc
Confidence 9999999994 343334 699999999999999877 55 44433
No 11
>PRK09559 putative global regulator; Reviewed
Probab=99.35 E-value=1.2e-11 Score=106.91 Aligned_cols=124 Identities=10% Similarity=0.092 Sum_probs=89.2
Q ss_pred ccccccccchhhhccCCChhccccC--ccccCCCCCCCCCccHHHHHHhHhcCC-CEEEEEEEecC-CCCCCCCEE--Ec
Q psy12057 33 AIKTSSVNTILLELFLAMDIYSRLL--IFPGKRRRETGGFPGASIIQSQIKSGV-SRKRTGLTSTG-VPIRPGYEI--FN 106 (172)
Q Consensus 33 ~~~~s~~~~~~~~~~~dtP~EaGLg--~~V~~~K~~~~dFIGkeAL~~~~~~g~-~r~LVgL~l~~-~~~~~g~~V--~~ 106 (172)
+++.-.+...+.|.+ +|+|+||+ +.|+|+| +||+|||++.|++..|. +|+++++.+++ ..++.|++| +.
T Consensus 195 eaG~p~~g~e~~e~~--~Pqe~nL~~l~~Vsf~K---GCY~GQE~vAR~~~~G~~krrl~~l~~~~~~~~~~g~~i~~~~ 269 (327)
T PRK09559 195 EAGFPVIDAANSGQF--IPQATNLQALGGISFKK---GCYTGQEMVARAKFRGANKRALWWLAGKASRVPEAGEDLELKM 269 (327)
T ss_pred HcCCccccccccccc--CchhhChhhcCceeecC---cccccHHHHHHHHHcCCCceeEEEEecccccCCCCCCeeEEec
Confidence 333333444443333 59999999 4899986 89999999999887676 88899999886 667899965 33
Q ss_pred CC-CcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEECCEEEeEEEEcCCCcC
Q psy12057 107 AN-DQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLK 164 (172)
Q Consensus 107 ~d-g~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g~~~~A~V~~~Pf~d 164 (172)
.+ ++.||.|+|++-++. +...+++.++.+. ..++.+.+.-.+. -..++.++|+--
T Consensus 270 ~~~~~~~G~v~s~~~~~~-~~~~~l~v~~~~~-~~~~~l~~~~~~~-~~~~~~~lPy~~ 325 (327)
T PRK09559 270 GENWRRTGTVLAAVQLDD-GQVWVQVVMNNDL-EADSVFRVRDDAG-NTLHIQPLPYSL 325 (327)
T ss_pred CCCCceeEEEEEEEECCC-CCEEEEEEEecCc-CCCceEEEccCCC-CeeEecCCCCCC
Confidence 23 579999999988766 6677778888765 5566666643221 347788888754
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=99.08 E-value=1.4e-10 Score=78.83 Aligned_cols=40 Identities=18% Similarity=0.196 Sum_probs=36.9
Q ss_pred ChhccccCc--cccCCCCCCCCCccHHHHHHhHhcC-CCEEEEEEE
Q psy12057 50 MDIYSRLLI--FPGKRRRETGGFPGASIIQSQIKSG-VSRKRTGLT 92 (172)
Q Consensus 50 tP~EaGLg~--~V~~~K~~~~dFIGkeAL~~~~~~g-~~r~LVgL~ 92 (172)
+|+|+||+| +|+++| +||||||++++++..| ++|+||+|.
T Consensus 24 ~P~E~gl~~~~~v~~~K---g~yiGqe~l~r~~~~g~~~~~lv~l~ 66 (67)
T TIGR03317 24 LPQELNLDALGGVSFKK---GCYVGQEVVARMHYRGKVKRRLVRLR 66 (67)
T ss_pred CHhHcCCCccCcEeCCC---CCccCHHHHHHHHHcCCCceeEEEee
Confidence 799999999 999987 6999999999998888 699999986
No 13
>COG0354 Predicted aminomethyltransferase related to GcvT [General function prediction only]
Probab=98.44 E-value=2.9e-07 Score=79.65 Aligned_cols=96 Identities=16% Similarity=0.136 Sum_probs=72.4
Q ss_pred hhhhccCC--ChhccccCcc--ccCCCCCCCCCccHHHHHHhHhcCC-CEEEEEEEecCCCCCCCCEEEcCCCcE--EEE
Q psy12057 42 ILLELFLA--MDIYSRLLIF--PGKRRRETGGFPGASIIQSQIKSGV-SRKRTGLTSTGVPIRPGYEIFNANDQR--VGA 114 (172)
Q Consensus 42 ~~~~~~~d--tP~EaGLg~~--V~~~K~~~~dFIGkeAL~~~~~~g~-~r~LVgL~l~~~~~~~g~~V~~~dg~~--VG~ 114 (172)
.+.++..+ .|.|+||... |+|+| +||+|+|.+.|.+..|. +|+++.|.+++..+..|+.|. .+++. +|.
T Consensus 180 ~~~~~~~~~~iPqevnl~~~~gISF~K---GCYvGQE~VAR~~~rG~~kRrl~~l~~d~~~p~~g~~i~-a~~~~~~~G~ 255 (305)
T COG0354 180 GIDDATSEDFIPQEVNLDALGGISFKK---GCYVGQETVARAKYRGTNKRRLVLLALDASLPEAGEEIL-AGGEEVGLGT 255 (305)
T ss_pred cccchhccccChhhhCccccCcEeccC---cccccHHHhhHHHhcCCCceeEEEEEeCCCCCCCCCeee-cCCCcceeee
Confidence 34444433 6999998875 59986 89999999999888775 888999998865678999998 48888 899
Q ss_pred EEeeecccccCCeEEEEEecCCccCCCCEEEE
Q psy12057 115 ITSGCPSPSLKKNIAMGYIEPAYSKVGVELWV 146 (172)
Q Consensus 115 VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V 146 (172)
|+|.. -...+|+++++. ....|..+++
T Consensus 256 v~s~~----~~~~~~l~~l~~-~l~~~~~~~v 282 (305)
T COG0354 256 VLSAV----GLGPVALIRLKV-VLDNGLAIDV 282 (305)
T ss_pred EEecc----cCcchhHHHHHH-hhcccchhhh
Confidence 99873 122388999998 4445555433
No 14
>KOG2929|consensus
Probab=97.70 E-value=5.8e-05 Score=65.57 Aligned_cols=105 Identities=14% Similarity=0.184 Sum_probs=72.0
Q ss_pred ChhccccCc--cccCCCCCCCCCccHHHHHHhHhcCC-CEEEEEEEecC---CCC-----CCCCEEEcCCCcEEEEEEee
Q psy12057 50 MDIYSRLLI--FPGKRRRETGGFPGASIIQSQIKSGV-SRKRTGLTSTG---VPI-----RPGYEIFNANDQRVGAITSG 118 (172)
Q Consensus 50 tP~EaGLg~--~V~~~K~~~~dFIGkeAL~~~~~~g~-~r~LVgL~l~~---~~~-----~~g~~V~~~dg~~VG~VTSg 118 (172)
.|+|++++| .|+|+| +||+|+|-..|--..|+ ++|++.|.++. .+. .....|....|+.+|.+.|+
T Consensus 223 lPLE~N~d~lngISf~K---GCYVGQELTARThhtGViRKRl~P~r~~~~e~~p~~~~~~~~~~~v~~~~g~kvG~~~~~ 299 (348)
T KOG2929|consen 223 LPLESNFDFLNGISFDK---GCYVGQELTARTHHTGVIRKRLFPFRLDLAENEPLLVGFTNAPPEVEKKKGRKVGRVISG 299 (348)
T ss_pred cceeccccccccccccC---cceechhheehhhhcceeeeeeeeEEecccCCCccccCCCCCccceecccCceeeeeecc
Confidence 489999887 689997 89999997777666787 78999999932 222 23344555578999999997
Q ss_pred ecccccCCeEEEEEecCCccCCCCEEEEEECCEEEeEEEEcCCCcCC
Q psy12057 119 CPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKS 165 (172)
Q Consensus 119 ~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g~~~~A~V~~~Pf~dp 165 (172)
...-|||.+..+... +.-.+..+.|..+.++.. .|++-|
T Consensus 300 ------~g~~glgllr~e~~~-~~~~~l~~~g~~i~i~~~-~p~W~p 338 (348)
T KOG2929|consen 300 ------EGLRGLGLLRLEKFK-AQFYKLTTKGENIKIKPQ-KPEWWP 338 (348)
T ss_pred ------Ccceeeeeeehhhhh-ccchhhhccCccceeccC-CCcccc
Confidence 345688888877643 333445555655554443 354433
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=86.32 E-value=8.2 Score=26.17 Aligned_cols=58 Identities=17% Similarity=0.102 Sum_probs=43.0
Q ss_pred EEEEecC-CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCc---cCCCCEEEEE
Q psy12057 89 TGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAY---SKVGVELWVR 147 (172)
Q Consensus 89 VgL~l~~-~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~---a~~G~~l~V~ 147 (172)
+.+..++ .-+..|.+|.. .|-.||.|++-.+++.-++...-..|++++ ...+....|.
T Consensus 5 v~~~~~~~~GL~~gs~V~~-~Gv~VG~V~~i~l~~~~~~v~v~~~i~~~~~~~i~~~s~a~i~ 66 (81)
T PF02470_consen 5 VTVYFDDAGGLSVGSPVRY-RGVEVGKVTSIELDPDGNRVRVTLRIDPDYWHRIPDDSRASIR 66 (81)
T ss_pred EEEEECCcCCCCCcCEEEE-CCEEEEEEEEEEEcCCCCEEEEEEEEcCCcceecCCCcEEEEE
Confidence 4455555 45678899984 899999999999988888888888888887 2334444444
No 16
>PRK10807 paraquat-inducible protein B; Provisional
Probab=81.99 E-value=7.1 Score=36.55 Aligned_cols=59 Identities=20% Similarity=0.211 Sum_probs=48.5
Q ss_pred EEEEEecC-CCCCCC-CEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCc---cCCCCEEEEE
Q psy12057 88 RTGLTSTG-VPIRPG-YEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAY---SKVGVELWVR 147 (172)
Q Consensus 88 LVgL~l~~-~~~~~g-~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~---a~~G~~l~V~ 147 (172)
.+.+..++ .-+..| .+|+. .|-.||.|++..+++...+-+.-++|++++ ...++.++|.
T Consensus 45 ~itl~~~~a~gl~~GkT~I~y-rgv~VG~V~~v~l~~d~~~V~~~~~i~~~~~~ll~~~trFWvv 108 (547)
T PRK10807 45 EVTLITTNAEGIEAGKTTIKS-RSVDVGVVESVTLSDDLTHVEIKARLNSGMEKLLHKDSVFWVV 108 (547)
T ss_pred EEEEEECCCCCcCcCCceeEE-CCceEEEEEEEEECCCCCeEEEEEEECccHHHhhcCCCEEEEe
Confidence 45666665 446677 89985 899999999999999999999999999876 4678888775
No 17
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=74.34 E-value=10 Score=25.26 Aligned_cols=51 Identities=14% Similarity=0.211 Sum_probs=35.7
Q ss_pred CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEECCE---EEeEEEE
Q psy12057 96 VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDK---RVDVKVT 158 (172)
Q Consensus 96 ~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g~---~~~A~V~ 158 (172)
.+++-|+.|++.+|+.+|.|--. |++||...- ...+|.|.+.+. .+.+...
T Consensus 9 ~~lPfGA~v~~~~g~~~g~Vg~~----------G~vyl~~~~--~~~~L~V~w~~~~~~~C~~~~~ 62 (68)
T PF13953_consen 9 KPLPFGASVSDEDGNNIGIVGQD----------GQVYLSGLP--PKGTLTVKWGDGANQQCQIDYP 62 (68)
T ss_dssp EE--TT-EEEETTSSEEEEB-GC----------GEEEEEEE---TCEEEEEESTSCTTSEEEEEEE
T ss_pred CcCCCCcEEEcCCCCEEEEEcCC----------CEEEEECCC--CCcEEEEEECCCCCCeEEEEec
Confidence 67788999997789999999887 488888653 466899999876 6655543
No 18
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=72.72 E-value=12 Score=26.49 Aligned_cols=50 Identities=26% Similarity=0.407 Sum_probs=32.9
Q ss_pred EEEEEEecCCCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEECC
Q psy12057 87 KRTGLTSTGVPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRD 150 (172)
Q Consensus 87 ~LVgL~l~~~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g 150 (172)
-+|| .+.++.++.|+++ +|..+|.|.|--.. ++++ +.|..|+++-+.+.|
T Consensus 20 ~IvG-~V~~G~ik~G~~l---~G~~iG~I~sIe~~---~k~v-------~~A~~G~eVai~Ieg 69 (81)
T PF14578_consen 20 AIVG-EVLEGIIKPGYPL---DGRKIGRIKSIEDN---GKNV-------DEAKKGDEVAISIEG 69 (81)
T ss_dssp EEEE-EEEEEEEETT-EE---CSSCEEEEEEEEET---TEEE-------SEEETT-EEEEEEET
T ss_pred eEEE-EEeeeEEeCCCcc---CCEEEEEEEEeEEC---CcCc-------cccCCCCEEEEEEeC
Confidence 6788 7777788899999 57779999986321 2332 335567777777665
No 19
>KOG3322|consensus
Probab=58.97 E-value=11 Score=36.42 Aligned_cols=27 Identities=19% Similarity=0.341 Sum_probs=25.2
Q ss_pred cEEEEEEeeecccccCCeEEEEEecCC
Q psy12057 110 QRVGAITSGCPSPSLKKNIAMGYIEPA 136 (172)
Q Consensus 110 ~~VG~VTSg~ySP~lgk~Iala~V~~~ 136 (172)
..||.||+|.|+-+.|++-|+|+|+..
T Consensus 643 ~ligfvT~g~~~ln~g~~~~i~~v~~~ 669 (688)
T KOG3322|consen 643 GLIGFVTLGLFALNYGKGKGIGFVRNS 669 (688)
T ss_pred eeEEEEeechhhhhcCCCceeeEEecc
Confidence 579999999999999999999999974
No 20
>PRK10807 paraquat-inducible protein B; Provisional
Probab=57.89 E-value=45 Score=31.32 Aligned_cols=68 Identities=16% Similarity=0.158 Sum_probs=45.2
Q ss_pred CCCccHHHHHHhHhcCCCEEEEEEEecC-CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCc
Q psy12057 68 GGFPGASIIQSQIKSGVSRKRTGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAY 137 (172)
Q Consensus 68 ~dFIGkeAL~~~~~~g~~r~LVgL~l~~-~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~ 137 (172)
..|.|-+.-.... .+.+.....|.-++ .-+..|+||+. .|-.||.|++..+++.-+...=-++|+++|
T Consensus 141 ~~F~~~~~~p~~~-~~~~g~~~~L~~~~~~~L~~GaPV~y-rgi~VG~V~~~~l~~~~~~v~~~~fI~~~y 209 (547)
T PRK10807 141 DKYDLLDSPPLAP-PDAKGIRIILDSKKAGQLSPGDPVLF-RGYRVGSVETSTFDPQKRLMSYQLFINAPY 209 (547)
T ss_pred ceeEeccCCcccc-CCCCceEEEEECCCCCCCCCCCceEE-CCcEEEEEEEEEecCCCCEEEEEEEEcchH
Confidence 3587765432111 12222233444333 66789999985 899999999999977666666679999887
No 21
>PF05239 PRC: PRC-barrel domain; InterPro: IPR007903 The PRC-barrel is an all beta barrel domain found in photosynthetic reaction centre subunit H of the purple bacteria. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the C terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain [].; PDB: 2QGG_A 3H9N_A 2WJN_H 2PRC_H 5PRC_H 2X5V_H 1DXR_H 1R2C_H 3G7F_H 1PRC_H ....
Probab=51.89 E-value=34 Score=22.59 Aligned_cols=36 Identities=14% Similarity=0.266 Sum_probs=27.8
Q ss_pred CCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecC
Q psy12057 100 PGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEP 135 (172)
Q Consensus 100 ~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~ 135 (172)
-|.+|++.+|+.+|.|.--.+.+.-++..++..=..
T Consensus 10 ~g~~V~~~~G~~iG~V~di~id~~~~~i~~i~v~~~ 45 (79)
T PF05239_consen 10 IGKEVIDRDGEKIGKVKDIVIDPKTGKIVGIVVSSG 45 (79)
T ss_dssp TTSEEEETTSCEEEEEEEEEEETTTTEEEEEEEEET
T ss_pred cCCEEEcCCCCEEEEEEEEEEeCCCCCEEEEEEcCC
Confidence 367888878999999999988888777666554443
No 22
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=47.69 E-value=88 Score=21.30 Aligned_cols=51 Identities=14% Similarity=0.182 Sum_probs=35.6
Q ss_pred CCCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCcc-CCCCEEEE
Q psy12057 95 GVPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYS-KVGVELWV 146 (172)
Q Consensus 95 ~~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a-~~G~~l~V 146 (172)
+..|+-|+.|++++.+.||.|--- |+|.-+-.+..-..+...+ ..|+++.|
T Consensus 21 ~~~P~~n~~V~~~~~~~IGkV~dI-fGPV~~pY~~Vk~~~~~~~~~~g~k~yi 72 (73)
T PRK13149 21 DKQPPIGSVVYDKKLKKIGKVVDV-FGPVKEPYVLVKPDKKDPPELVGEKLYV 72 (73)
T ss_pred CCCCCCCCEeECCCCCEeEEEEEE-ECCCCCcEEEEEeCCCCCccccCCEEEe
Confidence 356788999998788999999876 7886666665555444333 25666655
No 23
>COG3008 PqiB Paraquat-inducible protein B [General function prediction only]
Probab=40.44 E-value=66 Score=30.42 Aligned_cols=50 Identities=20% Similarity=0.262 Sum_probs=40.6
Q ss_pred EEEEEecC-CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCcc
Q psy12057 88 RTGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYS 138 (172)
Q Consensus 88 LVgL~l~~-~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a 138 (172)
++.|.-++ +.+..|++|+. .+-.||.|+|..|-|.-++-.=-.+|+++|+
T Consensus 163 ~i~L~a~dlGsL~~GspVyf-r~i~VGqV~sy~~d~d~~~V~i~vfI~~py~ 213 (553)
T COG3008 163 RIHLDAKDLGSLNVGSPVYF-RKIPVGQVESYQFDPDKQGVTIQVFIEAPYD 213 (553)
T ss_pred EEEEecCccCCcCCCCeeEE-eceeeeeEEEEEEcCCCCeEEEEEEecChhh
Confidence 34444445 77889999995 7889999999999998888777889998873
No 24
>smart00816 Amb_V_allergen Amb V Allergen. Amb V is an Ambrosia sp (ragweed) pollen allergen. Amb t V has been shown to contain a C-terminal helix as the major T cell epitope. Free sulphhydryl groups also play a major role in the T cell recognition of cross-reactivity T cell epitopes within these related allergens.
Probab=39.07 E-value=15 Score=22.81 Aligned_cols=7 Identities=71% Similarity=1.815 Sum_probs=5.8
Q ss_pred CCCceEe
Q psy12057 2 SCPWTVV 8 (172)
Q Consensus 2 ~~~~~~~ 8 (172)
-|||.||
T Consensus 26 YCpwqvV 32 (45)
T smart00816 26 YCPWQVV 32 (45)
T ss_pred cCCceEE
Confidence 3999987
No 25
>PF03913 Amb_V_allergen: Amb V Allergen; InterPro: IPR005611 Amb V is an Ambrosia sp (ragweed) pollen allergen. Amb t V has been shown to contain a C-terminal helix as the major T cell epitope. Free sulphydryl groups also play a major role in the T cell recognition of cross-reactivity T cell epitopes within these related allergens [].; PDB: 2BBG_A 3BBG_A 1BBG_A.
Probab=32.11 E-value=17 Score=22.50 Aligned_cols=7 Identities=71% Similarity=1.815 Sum_probs=1.1
Q ss_pred CCCceEe
Q psy12057 2 SCPWTVV 8 (172)
Q Consensus 2 ~~~~~~~ 8 (172)
-|||.||
T Consensus 25 YCpwqvV 31 (44)
T PF03913_consen 25 YCPWQVV 31 (44)
T ss_dssp S-----E
T ss_pred cccceee
Confidence 3999986
No 26
>PRK15248 fimbrial outer membrane usher protein StbC; Provisional
Probab=31.29 E-value=2.4e+02 Score=27.97 Aligned_cols=60 Identities=18% Similarity=0.189 Sum_probs=41.5
Q ss_pred CEEEEEEEecC-CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEECC---EEEeEE
Q psy12057 85 SRKRTGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRD---KRVDVK 156 (172)
Q Consensus 85 ~r~LVgL~l~~-~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g---~~~~A~ 156 (172)
++-|+.+...+ .+++.|..|.+.+|+.+|.|--. |..||... .+..++.|.+.+ +.+.++
T Consensus 769 ~~~l~~l~~~dG~~lP~Ga~V~~~~g~~~g~Vg~~----------G~vyl~~~--~~~~~l~V~wg~~~~~~C~~~ 832 (853)
T PRK15248 769 KAVLISVKMPDGGIPPMGADVFNGEGTNIGMVGQS----------GQIYARIA--HPSGSLLVRWGTGANQRCRVA 832 (853)
T ss_pred eEEEEEEEcCCCCcCCCceEEECCCCcEEEEEcCC----------CEEEEEcC--CCCceEEEEECCCCCCeEEEE
Confidence 44455666544 67788999886678888988876 57888853 345679999965 445444
No 27
>COG3008 PqiB Paraquat-inducible protein B [General function prediction only]
Probab=31.17 E-value=1.7e+02 Score=27.81 Aligned_cols=64 Identities=20% Similarity=0.094 Sum_probs=48.4
Q ss_pred hcCCCEEEEEEEecC--CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCc---cCCCCEEEEEE
Q psy12057 81 KSGVSRKRTGLTSTG--VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAY---SKVGVELWVRV 148 (172)
Q Consensus 81 ~~g~~r~LVgL~l~~--~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~---a~~G~~l~V~i 148 (172)
+.|+. +.+..+. ++-.+-.+|.. .|-.||.||+...|-.+.+-...|-|++|. ...+|.++|.-
T Consensus 44 ~~G~~---Itl~f~saeGIeaGKT~Iry-~gvdVG~V~~v~LsdDl~~V~V~a~i~~da~~~L~~dT~FWvVk 112 (553)
T COG3008 44 DRGPE---ITLTFESAEGIEAGKTPIRY-QGVDVGVVTDIKLSDDLKGVEVTAQINSDAKDLLREDTRFWVVK 112 (553)
T ss_pred hcCCe---EEEEecCccccccCcceEEe-cceeeeEEEEEEeccCccceEEEEEeChhHHHHhhcCcEEEEEe
Confidence 45653 4444443 55555577863 788999999999999999999999999864 56788888753
No 28
>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=30.34 E-value=2.2e+02 Score=20.81 Aligned_cols=33 Identities=18% Similarity=0.173 Sum_probs=26.2
Q ss_pred CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEE
Q psy12057 96 VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIA 129 (172)
Q Consensus 96 ~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Ia 129 (172)
.+|.-+++|++.+++.||.|-.. |+|.-.-.+.
T Consensus 23 ~iP~l~~~V~~~~~k~IG~V~dV-fGPv~~PY~~ 55 (98)
T COG3277 23 RIPPLNAPVYDANLKRIGKVVDV-FGPVDEPYIL 55 (98)
T ss_pred CCCCCCCeeEecCCCEEEEEEEE-EccCCCCEEE
Confidence 67889999998889999999886 7885555443
No 29
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=30.28 E-value=1.6e+02 Score=19.59 Aligned_cols=34 Identities=18% Similarity=0.218 Sum_probs=20.9
Q ss_pred EEEEEeeecccccCCeEEEEEecCCccCCCCEEEE
Q psy12057 112 VGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWV 146 (172)
Q Consensus 112 VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V 146 (172)
+++|....|.|..++ ++++.|-..-.+.|+.+.+
T Consensus 2 ~a~Vfk~~~d~~~G~-~~~~Rv~sG~l~~g~~v~~ 35 (83)
T cd04088 2 VALVFKTIHDPFVGK-LSFVRVYSGTLKAGSTLYN 35 (83)
T ss_pred EEEEEEcccCCCCce-EEEEEEecCEEcCCCEEEE
Confidence 355666666666665 5666666666666666644
No 30
>COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only]
Probab=29.20 E-value=2.1e+02 Score=20.19 Aligned_cols=51 Identities=18% Similarity=0.137 Sum_probs=37.3
Q ss_pred CCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecC--CccCCCC--EEEEEECC
Q psy12057 100 PGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEP--AYSKVGV--ELWVRVRD 150 (172)
Q Consensus 100 ~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~--~~a~~G~--~l~V~i~g 150 (172)
.|-+|++.+|+.+|.|.--..-..-++-.+++..+. +....+. .+.|.+..
T Consensus 12 ~gk~V~~~~G~~vG~V~dv~ld~~~g~i~~l~v~~~~~~l~~~~k~~~v~IP~~~ 66 (87)
T COG1873 12 LGKEVITNDGKYVGTVSDVVLDIKEGKITGLLVIPTNKGLFLFGKGKEVIVPYEY 66 (87)
T ss_pred cCcEEEcCCCeEEEEEEeEEEEccCCcEEEEEEecCCccccccCCCcEEEEehhH
Confidence 456787668999999999999888898888888866 3333333 67776653
No 31
>PF09162 Tap-RNA_bind: Tap, RNA-binding; InterPro: IPR015245 This domain adopts a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. It is mainly found in mRNA export factors, which mediate the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element []. ; GO: 0003723 RNA binding, 0006406 mRNA export from nucleus, 0005634 nucleus, 0005737 cytoplasm; PDB: 1FT8_A 1KOH_C 1KOO_C 3RW6_B 3RW7_C 1FO1_A.
Probab=28.88 E-value=5.7 Score=28.53 Aligned_cols=21 Identities=33% Similarity=0.830 Sum_probs=13.0
Q ss_pred Eeeeeeccce-ecccccccccc
Q psy12057 9 WVLISIHNMC-FKFQPIAWLST 29 (172)
Q Consensus 9 ~~~~~~~~~~-~~~~~~~~~~~ 29 (172)
|+|-+|+++| --|.|++|--.
T Consensus 22 wLl~~iq~~c~v~F~Pv~fh~~ 43 (88)
T PF09162_consen 22 WLLNSIQSHCSVPFTPVDFHYE 43 (88)
T ss_dssp HHHHHHHHHSSS----EEEEEE
T ss_pred HHHHHHHHHCCCCeeeeeeeee
Confidence 6777889999 58999988544
No 32
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=28.29 E-value=67 Score=19.36 Aligned_cols=15 Identities=20% Similarity=0.468 Sum_probs=11.9
Q ss_pred EEEcCCCcEEEEEEe
Q psy12057 103 EIFNANDQRVGAITS 117 (172)
Q Consensus 103 ~V~~~dg~~VG~VTS 117 (172)
+|.+.+|+.+|.+|-
T Consensus 34 ~V~d~~~~~~G~is~ 48 (57)
T PF00571_consen 34 PVVDEDGKLVGIISR 48 (57)
T ss_dssp EEESTTSBEEEEEEH
T ss_pred EEEecCCEEEEEEEH
Confidence 567667899999985
No 33
>PRK15273 putative fimbrial outer membrane usher protein SteB; Provisional
Probab=27.79 E-value=2.7e+02 Score=27.83 Aligned_cols=54 Identities=17% Similarity=0.138 Sum_probs=38.8
Q ss_pred CEEEEEEEecC-CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEECC
Q psy12057 85 SRKRTGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRD 150 (172)
Q Consensus 85 ~r~LVgL~l~~-~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g 150 (172)
++-++.+...+ .+++-|+.|.+.+|+.+|.|-.. |..||.-. .++.+|.|.+.+
T Consensus 742 ~~~l~~l~~~dG~~lPfGa~V~~~~g~~~giVg~~----------G~vyl~g~--~~~~~l~V~wg~ 796 (881)
T PRK15273 742 EKMMAVFRLADGDFPPFGAEVKNERQQQLGLVADD----------GNAWLAGV--KAGETLKVFWDG 796 (881)
T ss_pred eEEEEEEEccCCCcCCCceEEEcCCCcEEEEEcCC----------CEEEEecC--CCCceEEEEeCC
Confidence 34455555544 67788999986678889999887 57888864 345678998865
No 34
>PRK09828 putative fimbrial outer membrane usher protein; Provisional
Probab=27.45 E-value=3.3e+02 Score=26.95 Aligned_cols=52 Identities=13% Similarity=0.261 Sum_probs=37.9
Q ss_pred CEEEEEEEecC-CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEE
Q psy12057 85 SRKRTGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRV 148 (172)
Q Consensus 85 ~r~LVgL~l~~-~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i 148 (172)
++-++-+...+ .+++-|..|.+.+|+.+|.|--. |.+||.-- .+..+|.|.+
T Consensus 777 ~~~ll~l~~~~G~~lP~Ga~V~~~~g~~~g~Vg~~----------G~vyl~gl--~~~~~l~v~w 829 (865)
T PRK09828 777 RSAIMNITRSDGKNIPFAADVYDEQGNVIGNVGQG----------GQAFVRGI--EDQGELRIRW 829 (865)
T ss_pred eEEEEEEECCCCCcCCCceEEECCCCcEEEEEeCC----------CEEEEEcC--CCCceEEEEE
Confidence 44455666544 67788999986577888988877 58888864 3456799998
No 35
>PF07620 SLEI_Leptospira: SLEI; InterPro: IPR011512 This entry represents a highly conserved sequence motif found at the C-terminal of some hypothetical proteins from Leptospira interrogans.
Probab=27.37 E-value=26 Score=17.44 Aligned_cols=12 Identities=42% Similarity=0.924 Sum_probs=9.3
Q ss_pred cccccccccccc
Q psy12057 23 PIAWLSTHSMAI 34 (172)
Q Consensus 23 ~~~~~~~~~~~~ 34 (172)
|+.|+..+|.|+
T Consensus 1 ~~~~~rdNsLeI 12 (16)
T PF07620_consen 1 PQRWLRDNSLEI 12 (16)
T ss_pred CcccccCCeEEE
Confidence 577888888775
No 36
>PRK15284 putative fimbrial outer membrane usher protein StfC; Provisional
Probab=25.52 E-value=2.9e+02 Score=27.51 Aligned_cols=55 Identities=22% Similarity=0.184 Sum_probs=39.2
Q ss_pred CEEEEEEEecC-CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEECCE
Q psy12057 85 SRKRTGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDK 151 (172)
Q Consensus 85 ~r~LVgL~l~~-~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~g~ 151 (172)
++-++-|...+ .+++-|..|.+.+|+.+|.|--. |..||.-- .+..++.|.+.++
T Consensus 765 ~~~l~~l~~~dG~~lPfGa~V~~~~g~~~giVg~~----------G~vyL~gl--~~~~~l~V~w~~~ 820 (881)
T PRK15284 765 QKAMAVLRLRDGSHPPFGAEVKNDNQQQVGLVDDD----------GNVYLAGV--KPGEHMQVFWEGV 820 (881)
T ss_pred eEEEEEEEcCCCCcCCCceEEEcCCCceEEEEcCC----------CEEEEEcc--CCCceEEEEECCC
Confidence 44456666644 67788999986678889999877 57788753 3456788888654
No 37
>PF01571 GCV_T: Aminomethyltransferase folate-binding domain; InterPro: IPR006222 This is a family of 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 2.1.2.10 from EC that catalyses the following reaction: (6S)-tetrahydrofolate + S-aminomethyldihydrolipoylprotein = (6R)-5,10-methylenetetrahydrofolate + NH3 + dihydrolipoylprotein ; GO: 0004047 aminomethyltransferase activity, 0006546 glycine catabolic process, 0005737 cytoplasm; PDB: 3TFJ_B 3TFI_B 3TFH_A 1YX2_B 3GIR_A 3A8K_D 3A8I_B 3A8J_C 1VLO_A 1WOO_A ....
Probab=24.23 E-value=35 Score=26.86 Aligned_cols=23 Identities=9% Similarity=-0.143 Sum_probs=12.9
Q ss_pred ccccchhhhccCC-ChhccccCcc
Q psy12057 37 SSVNTILLELFLA-MDIYSRLLIF 59 (172)
Q Consensus 37 s~~~~~~~~~~~d-tP~EaGLg~~ 59 (172)
+.+..--.|+..+ +|+|+||+|+
T Consensus 188 ~G~p~~~~d~~~~~~P~E~~l~w~ 211 (211)
T PF01571_consen 188 AGIPLYGQDLDEEFLPQEANLDWA 211 (211)
T ss_dssp TT---TTTSSCTTS-TTTTTGGGG
T ss_pred cCCcccccccCCCCCHHHcCCCcC
Confidence 3344444455434 7999999995
No 38
>PF12396 DUF3659: Protein of unknown function (DUF3659) ; InterPro: IPR022124 This domain family is found in bacteria and eukaryotes, and is approximately 70 amino acids in length.
Probab=23.83 E-value=68 Score=21.54 Aligned_cols=25 Identities=20% Similarity=0.438 Sum_probs=17.7
Q ss_pred EEEcCCCcEEEEEEeeecccccCCe
Q psy12057 103 EIFNANDQRVGAITSGCPSPSLKKN 127 (172)
Q Consensus 103 ~V~~~dg~~VG~VTSg~ySP~lgk~ 127 (172)
.|++.+|+.||.|+.+-..--.|+.
T Consensus 14 ~V~d~~G~~vG~vveGd~k~L~G~~ 38 (64)
T PF12396_consen 14 NVVDDDGNVVGRVVEGDPKKLVGKK 38 (64)
T ss_pred eEECCCCCEEEEEecCCHHHhcCCc
Confidence 4666689999999999544444443
No 39
>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=23.82 E-value=69 Score=26.76 Aligned_cols=19 Identities=26% Similarity=0.413 Sum_probs=16.4
Q ss_pred CCCCEEEcCCCcEEEEEEee
Q psy12057 99 RPGYEIFNANDQRVGAITSG 118 (172)
Q Consensus 99 ~~g~~V~~~dg~~VG~VTSg 118 (172)
..|+||+ .||+.||-||..
T Consensus 181 MSGSPI~-qdGKLiGAVthv 199 (218)
T PF05580_consen 181 MSGSPII-QDGKLIGAVTHV 199 (218)
T ss_pred ccCCCEE-ECCEEEEEEEEE
Confidence 4678999 499999999987
No 40
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 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 entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=22.25 E-value=2.7e+02 Score=27.20 Aligned_cols=73 Identities=19% Similarity=0.128 Sum_probs=46.2
Q ss_pred cCccccCCCCCCCCCccHHHHHHhHhcCC--------CEEEEEEEecCCC--CCCCCEEEcCCCcEEEEEEeee------
Q psy12057 56 LLIFPGKRRRETGGFPGASIIQSQIKSGV--------SRKRTGLTSTGVP--IRPGYEIFNANDQRVGAITSGC------ 119 (172)
Q Consensus 56 Lg~~V~~~K~~~~dFIGkeAL~~~~~~g~--------~r~LVgL~l~~~~--~~~g~~V~~~dg~~VG~VTSg~------ 119 (172)
|.-++... ..+.+|.--+.+++..+.+. ...-|.|+.+..+ =..|+||++.+|+.||.+=-+.
T Consensus 582 l~G~~eK~-~g~~~F~lP~~~~~l~~~~dfG~y~~~~g~~pv~FlstnDitGGNSGSPvlN~~GeLVGl~FDgn~Esl~~ 660 (698)
T PF10459_consen 582 LAGLYEKE-TGDEPFDLPARWLELYEAKDFGRYDPELGSVPVNFLSTNDITGGNSGSPVLNAKGELVGLAFDGNWESLSG 660 (698)
T ss_pred HHHHHHhc-CCCCCCcCCHHHHHHHhcccccccccccCCeeeEEEeccCcCCCCCCCccCCCCceEEEEeecCchhhccc
Confidence 44445544 33567999888887766433 4456677665322 1467899988899999876543
Q ss_pred ---cccccCCeEE
Q psy12057 120 ---PSPSLKKNIA 129 (172)
Q Consensus 120 ---ySP~lgk~Ia 129 (172)
|.|.+.++|+
T Consensus 661 D~~fdp~~~R~I~ 673 (698)
T PF10459_consen 661 DIAFDPELNRTIH 673 (698)
T ss_pred ccccccccceeEE
Confidence 4555555554
No 41
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=21.22 E-value=38 Score=22.92 Aligned_cols=32 Identities=16% Similarity=0.217 Sum_probs=22.6
Q ss_pred CCeEEEEEecCCccCCCCEEEEEECCEEEeEEEEc
Q psy12057 125 KKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTK 159 (172)
Q Consensus 125 gk~Iala~V~~~~a~~G~~l~V~i~g~~~~A~V~~ 159 (172)
..+||.|++-. +.|+.+++...+.....+|..
T Consensus 43 ~SPLG~ALlG~---~~Gd~v~~~~~~g~~~~~I~~ 74 (77)
T PF01272_consen 43 DSPLGKALLGK---KVGDEVEVELPGGERKYEILE 74 (77)
T ss_dssp TSHHHHHHTT----BTT-EEEEEETTBEEEEEEEE
T ss_pred cCHHHHHhcCC---CCCCEEEEEeCCceEEEEEEE
Confidence 34567777765 579999999998877777753
No 42
>PRK15193 outer membrane usher protein; Provisional
Probab=20.88 E-value=4.1e+02 Score=26.49 Aligned_cols=52 Identities=19% Similarity=0.264 Sum_probs=36.6
Q ss_pred EEEEEEEecCCCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEEC
Q psy12057 86 RKRTGLTSTGVPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVR 149 (172)
Q Consensus 86 r~LVgL~l~~~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~ 149 (172)
+-++.+..++.+++.|..|.+.+|+.+|.|--. |..||.-. .+...|.|.+.
T Consensus 795 ~~ll~l~~~G~plPfGa~V~~~~g~~~g~Vg~~----------G~vyl~gl--~~~~~l~v~w~ 846 (876)
T PRK15193 795 RALMTLSHQGIPLPFGATVTLDDQHNSGIVDDD----------GSVYLSGL--PAQGVLHVRWG 846 (876)
T ss_pred EEEEEEccCCcCCCCceEEECCCCceEEEEcCC----------CEEEEEcc--CCCceEEEEEC
Confidence 334444333467788999986677888888777 57888864 34567999986
No 43
>PF08308 PEGA: PEGA domain; InterPro: IPR013229 This domain is found in both archaea and bacteria and has similarity to S-layer (surface layer) proteins. It is named after the characteristic PEGA sequence motif found in this domain. The secondary structure of this domain is predicted to be beta-strands.
Probab=20.67 E-value=2.5e+02 Score=18.07 Aligned_cols=14 Identities=21% Similarity=0.655 Sum_probs=11.6
Q ss_pred CCCCEEEcCCCcEEE
Q psy12057 99 RPGYEIFNANDQRVG 113 (172)
Q Consensus 99 ~~g~~V~~~dg~~VG 113 (172)
..|+.|+ .||+.+|
T Consensus 10 p~gA~V~-vdg~~~G 23 (71)
T PF08308_consen 10 PSGAEVY-VDGKYIG 23 (71)
T ss_pred CCCCEEE-ECCEEec
Confidence 4688898 4999999
No 44
>PRK15217 fimbrial outer membrane usher protein; Provisional
Probab=20.56 E-value=5.4e+02 Score=25.41 Aligned_cols=53 Identities=15% Similarity=0.227 Sum_probs=36.9
Q ss_pred CEEEEEEEecC-CCCCCCCEEEcCCCcEEEEEEeeecccccCCeEEEEEecCCccCCCCEEEEEEC
Q psy12057 85 SRKRTGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVR 149 (172)
Q Consensus 85 ~r~LVgL~l~~-~~~~~g~~V~~~dg~~VG~VTSg~ySP~lgk~Iala~V~~~~a~~G~~l~V~i~ 149 (172)
++-|+-+...+ .+++.|..|.+++|+.+|.|--. |..||.-.- ..+ .+.|.+.
T Consensus 749 ~~~ll~l~~~~G~~lP~Ga~V~~~~g~~~g~Vg~~----------G~vyl~g~~-~~~-~l~v~wg 802 (826)
T PRK15217 749 KPWFIKALRADGQPLTFGYEVNDIHGHNIGVVGQG----------SQLFIRTNE-VPP-SVKVAID 802 (826)
T ss_pred eEEEEEEEcCCCCcCCCceEEECCCCcEEEEEcCC----------CeEEEEcCC-CCc-eEEEEEC
Confidence 44455555544 67788999987678889998877 588887532 233 5888875
Done!