Query T0636 YP_108324.1, BURKHOLDERIA PSEUDOMALLEI, 336 residues
Match_columns 336
No_of_seqs 141 out of 7282
Neff 8.0
Searched_HMMs 11830
Date Thu Jul 22 15:19:30 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0636.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0636.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00155 Aminotran_1_2: Aminot 100.0 0 0 364.6 26.2 315 15-329 1-363 (363)
2 PF00266 Aminotran_5: Aminotra 99.9 5.5E-20 4.7E-24 145.9 28.5 303 18-325 1-371 (371)
3 PF04864 Alliinase_C: Allinase 99.9 7.5E-23 6.4E-27 164.5 9.9 266 52-332 45-361 (362)
4 PF01053 Cys_Met_Meta_PP: Cys/ 99.6 2.5E-13 2.2E-17 102.8 18.9 303 14-333 19-385 (386)
5 PF01041 DegT_DnrJ_EryC1: DegT 99.5 6.6E-13 5.5E-17 100.1 18.5 262 31-304 5-310 (363)
6 PF00464 SHMT: Serine hydroxym 99.5 2.4E-12 2E-16 96.4 18.0 310 2-321 7-382 (399)
7 PF01212 Beta_elim_lyase: Beta 99.0 1.1E-12 9.4E-17 98.6 -5.6 243 29-279 7-283 (290)
8 PF06838 Alum_res: Aluminium r 99.0 3.1E-08 2.6E-12 69.8 15.6 255 32-294 28-328 (403)
9 PF01276 OKR_DC_1: Orn/Lys/Arg 98.9 5.1E-08 4.3E-12 68.4 16.0 220 48-272 64-326 (417)
10 PF00202 Aminotran_3: Aminotra 98.8 9.1E-09 7.7E-13 73.3 9.2 226 13-242 14-292 (339)
11 PF02347 GDC-P: Glycine cleava 98.8 2.5E-07 2.1E-11 63.9 14.8 285 30-329 80-429 (429)
12 PF00282 Pyridoxal_deC: Pyrido 98.3 0.00011 9.4E-09 46.8 17.5 223 55-279 84-368 (373)
13 PF05889 SLA_LP_auto_ag: Solub 97.7 0.0017 1.4E-07 39.2 15.0 268 62-334 68-389 (389)
14 PF03841 SelA: L-seryl-tRNA se 97.5 1.7E-05 1.4E-09 52.1 1.9 203 29-241 18-257 (367)
15 PF01282 Ribosomal_S24e: Ribos 57.1 3.2 0.00027 17.9 2.8 24 50-73 13-36 (84)
16 PF03786 UxuA: D-mannonate deh 42.4 5.8 0.00049 16.2 2.2 14 209-222 219-232 (351)
17 PF00701 DHDPS: Dihydrodipicol 36.0 9.3 0.00078 14.9 4.8 22 144-166 134-157 (289)
18 PF07021 MetW: Methionine bios 32.5 11 0.00089 14.5 10.1 158 5-189 5-184 (193)
19 PF09581 Spore_III_AF: Stage I 29.9 12 0.00098 14.3 2.7 16 319-334 163-178 (188)
20 PF05728 UPF0227: Uncharacteri 29.2 12 0.001 14.2 8.8 112 16-131 1-122 (187)
21 PF05848 CtsR: Firmicute trans 29.0 12 0.001 14.1 5.4 11 59-69 31-41 (152)
22 PF04392 ABC_sub_bind: ABC tra 28.4 12 0.001 14.1 2.7 114 51-167 43-163 (294)
23 PF06252 DUF1018: Protein of u 27.0 11 0.00092 14.4 1.6 79 255-334 25-117 (119)
24 PF04914 DltD_C: DltD C-termin 26.8 4.3 0.00037 17.0 -0.5 84 117-220 33-128 (130)
25 PF05127 DUF699: Putative ATPa 25.2 10 0.00085 14.7 1.1 23 89-111 25-48 (174)
26 PF01974 tRNA_int_endo: tRNA i 21.8 15 0.0013 13.5 1.5 20 288-307 6-25 (85)
27 PF05448 AXE1: Acetyl xylan es 21.7 16 0.0014 13.3 3.2 13 54-66 27-39 (320)
28 PF02679 ComA: (2R)-phospho-3- 21.0 17 0.0014 13.2 1.6 51 54-118 55-105 (244)
29 PF05913 DUF871: Bacterial pro 20.8 17 0.0014 13.2 2.1 37 121-162 96-132 (357)
30 PF06153 DUF970: Protein of un 20.0 18 0.0015 13.1 5.8 17 284-300 11-27 (109)
No 1
>PF00155 Aminotran_1_2: Aminotransferase class I and II 1-aminocyclopropane-1-carboxylate synthase signature aspartate aminotransferase signature; InterPro: IPR004839 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into class I and class II. This entry includes proteins from both subfamilies.; GO: 0016769 transferase activity, transferring nitrogenous groups, 0030170 pyridoxal phosphate binding, 0009058 biosynthetic process; PDB: 1u08_A 1v2f_A 1v2d_A 1v2e_B 2r5c_A 2r5e_B 1yiz_B 1yiy_A 3fvx_B 3fvs_B ....
Probab=100.00 E-value=0 Score=364.57 Aligned_cols=315 Identities=26% Similarity=0.352 Sum_probs=268.6
Q ss_pred CCCEECCCCCCCCC----CCHHHHHHHHH---HHHHHHCCCCC-CHHHHHHHHHHHHC------CCHH-HEEEECCHHHH
Q ss_conf 55357357654888----76899999999---98750058898-61899999999848------8854-38860778899
Q T0636 15 AQAVCLAFNENPEA----VEPRVQAAIAA---AAARINRYPFD-AEPRVMRKLAEHFS------CPED-NLMLVRGIDEC 79 (336)
Q Consensus 15 ~~~i~L~~Nenp~~----p~~~v~~al~~---~~~~~~~Ypd~-~~~~Lr~aia~~~~------v~~d-~I~~t~Gs~~~ 79 (336)
+++|+|++|.++++ ++|.+.+++.+ .....++|++. |+++||++++++++ ++++ +|++|+|++++
T Consensus 1 ~~~i~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~~G~~~lr~~la~~~~~~~~~~~~~~~~i~~~~G~~~~ 80 (363)
T PF00155_consen 1 KDVINLSSGDPLFDSQNPPLPEALKALLDGAADGSSILQYGPPQGYPELREALADFLGRRRGIPLDPDSNILITSGAQAA 80 (363)
T ss_dssp TEEEBESSSSTSSTTTHHHHHHHHHHHHHHHHHHGGGTSS--TTHHHHHHHHHHHHHHHHHHHHTTGGEGEEEESHHHHH
T ss_pred CCEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEE
T ss_conf 97699859879974444465999999987655444425489942119999999997876059765776228961676223
Q ss_pred HHHHHHHH---CCCCEEECCCCCHHHHHHHHHHCCCEEEECCC--CCCCCCHHHHHHHC--------CHHHHHHHCCCCC
Q ss_conf 99999984---69925763887356999999818803641554--35677889997300--------0243133036633
Q T0636 80 FDRISAEF---SSMRFVTAWPGFDGYRARIAVSGLRHFEIGLT--DDLLLDPNDLAQVS--------RDDCVVLANPSNP 146 (336)
Q Consensus 80 i~~~~~~~---~~~~vii~~P~y~~y~~~~~~~g~~~~~vp~~--~~~~~d~~~l~~~~--------~~~~i~l~nPnNP 146 (336)
+..++.++ +||.|++++|+|+.|...++..|.+++.+|++ ++|++|++++++.. ++++++++|||||
T Consensus 81 ~~~~~~~~~~~~gd~vl~~~p~y~~~~~~~~~~g~~~~~~~~~~~~~~~~d~~~l~~~l~~~~~~~~~~~~i~i~~p~NP 160 (363)
T PF00155_consen 81 LFLLFRLLKLDPGDVVLVPEPTYPSYIRIARLAGAEVVPVPLDSEDDFGLDLDALEAALEEYRKRSPRPKAILIPNPHNP 160 (363)
T ss_dssp HHHHHHHHHHTTTSEEEEEESSTTHHHHHHHHTTTEEEEEEBEETTTTEETHHHHHHHHHTHHTTTETEEEEEEESS-ST
T ss_pred EEHHHHCCCCCCCCCCCCCCCCCCCCCCCHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCC
T ss_conf 30002101135644455557755422310103684699995045555576612133333222223455413521465456
Q ss_pred CCCCCCHHHHHHH---HHHCCC-CCCCCCCCCCCCCCC------CHHHHCCCHHHHHHHHHHHCCCCCCCEEECCCHHHH
Q ss_conf 2222237999999---973787-202521002588662------003324520012023465233434531311788999
Q T0636 147 TGQALSAGELDQL---RQRAGK-LLIDETYVDYSSFRA------RGLAYGENELVFRSFSKSYGLAGLRLGALFGPSELI 216 (336)
Q Consensus 147 TG~~~~~~~l~~l---~~~~~~-~IvDeaY~~f~~~~~------~~l~~~~n~iv~~S~SK~~gl~GlRiG~~i~~~~~i 216 (336)
||.+++.+++.++ +++++. +|+||+|.+|..... ..+...+++|+++||||+||+||+|+||++++++++
T Consensus 161 tG~~~s~~~l~~l~~~~~~~~~~li~De~y~~~~~~~~~~~~~~~~~~~~~~vi~~~S~SK~~g~~GlR~G~v~~~~~~~ 240 (363)
T PF00155_consen 161 TGSVLSAEELRELAELARKYNVLLIEDEAYSDLVYGDPDFYSILSLLDEGPNVIVLGSFSKALGLPGLRVGFVVAPPELI 240 (363)
T ss_dssp T-B---HHHHHHHHHHHHHTTSEEEEEETTTTGSSSSSHTHHHGGGHHTTTTEEEEEESTTTTTBGGGT-EEEEEEHHHH
T ss_pred CHHHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCHHCHHHH
T ss_conf 31455477655588763022023430441355543897777542235788418994133223333434666400134666
Q ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHCCCEEECCC-CCEEEEECCC--HHHH
Q ss_conf 9997337877877778999999974599----9999999999999999999985897861698-6478865698--8999
Q T0636 217 AAMKRKQWFCNVGTLDLHALEAALDNDR----AREAHIAKTLAQRRRVADALRGLGYRVASSE-ANFVLVENAA--GERT 289 (336)
Q Consensus 217 ~~l~~~~~~~~~~~~~~~aa~~~l~~~~----~~~~~~~~~~~~r~~l~~~l~~lg~~~~~s~-~~Fi~~~~~~--~~~~ 289 (336)
+.+++...++..++++|.++.+++.+.. ++.+.++.++++++.+.+.|++.++++.++. +.|+|++... +.++
T Consensus 241 ~~l~~~~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 320 (363)
T PF00155_consen 241 AALRKLSRPWIISSPLQQAAAAALADPQFYDRHLRELRRRLRERRDRLREALEELGISVLPPPGGFFLWLDLDPLDAMEL 320 (363)
T ss_dssp HHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSEEEHHSSSEEEEEEETHHHHHHH
T ss_pred HHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCEEEEEECCCCHHHHH
T ss_conf 54430001223202457899875325432221100256788789999998776206243036885289996565169999
Q ss_pred HHHHHHC-CCEEEECCCCCCCCEEEEEE--CCHHHHHHHHHHH
Q ss_conf 9999876-93896077888887478874--7989999999999
Q T0636 290 LRFLRER-GIQVKDAGQFGLHHHIRISI--GREEDNDRLLAAL 329 (336)
Q Consensus 290 ~~~L~~~-gi~vr~~~~fg~~~~iRis~--~~~ee~~~l~~aL 329 (336)
++.|.++ ||.++||..|+.++|+|||+ .+++++++++++|
T Consensus 321 ~~~L~~~~gi~v~~g~~f~~~~~iRi~~a~~~~~~~~~~~~~l 363 (363)
T PF00155_consen 321 AQKLLEEHGILVVPGSYFGVPGFIRISLAGLTPEEIEEAVERL 363 (363)
T ss_dssp HHHHHHHHTEEEBEGGTTSSTTEEEEESSSSHHHHHHHHHHHH
T ss_pred HHHHHHHCCEEEEECCCCCCCCEEEEEEEECCHHHHHHHHCCC
T ss_conf 9999984999998377789999899996109999999983469
No 2
>PF00266 Aminotran_5: Aminotransferase class-V; InterPro: IPR000192 Aminotransferases share certain mechanistic features with other pyridoxal- phosphate dependent enzymes, such as the covalent binding of the pyridoxal- phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into subfamilies. This entry represents the class V aminotransferases and the related, though functionally distinct, cysteine desulphurases.; GO: 0008483 transaminase activity, 0008152 metabolic process; PDB: 2hzp_A 3e9k_A 1qz9_A 1n2t_B 1elu_A 1n31_A 1elq_B 2bkw_A 2yrr_B 2yri_A ....
Probab=99.89 E-value=5.5e-20 Score=145.93 Aligned_cols=303 Identities=20% Similarity=0.243 Sum_probs=207.1
Q ss_pred EECCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC-----C------HHHHHHHHHHHHCCCH-HHEEEECCHHHHHHHHHH
Q ss_conf 573576548887689999999998750058898-----6------1899999999848885-438860778899999999
Q T0636 18 VCLAFNENPEAVEPRVQAAIAAAAARINRYPFD-----A------EPRVMRKLAEHFSCPE-DNLMLVRGIDECFDRISA 85 (336)
Q Consensus 18 i~L~~Nenp~~p~~~v~~al~~~~~~~~~Ypd~-----~------~~~Lr~aia~~~~v~~-d~I~~t~Gs~~~i~~~~~ 85 (336)
|.|+.+- +=++|+.|++++.+.+.+....|.. + ..+.|+.+++.+|+++ ++|+++.|+++++..+..
T Consensus 1 iYld~ag-~~~~p~~v~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~r~~la~ll~~~~~~~i~f~~~~t~~~~~~~~ 79 (371)
T PF00266_consen 1 IYLDNAG-TGPLPPSVLEAISEYLEEFFGNPHSSIHHRSQEFQEIVEEAREKLARLLGAPPPEEIAFTSNTTEALNAVLR 79 (371)
T ss_dssp EBBBTTT-S---BHHHHHHHHHHHHSTTTCTTTCSCTTSHHHHHHHHHHHHHHHHHHTSSGTGEEEEESSHHHHHHHHHH
T ss_pred CEEECCC-CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHH
T ss_conf 9703677-366979999999999987624876656753399999999999999997199853332322466554323300
Q ss_pred HH-----CCCCEEECCCCCHHHH----HHHHHHCCCEEEECCCCCCCCCHHHHHHH--CCHHHHHHHCCCCCCCCCCCHH
Q ss_conf 84-----6992576388735699----99998188036415543567788999730--0024313303663322222379
Q T0636 86 EF-----SSMRFVTAWPGFDGYR----ARIAVSGLRHFEIGLTDDLLLDPNDLAQV--SRDDCVVLANPSNPTGQALSAG 154 (336)
Q Consensus 86 ~~-----~~~~vii~~P~y~~y~----~~~~~~g~~~~~vp~~~~~~~d~~~l~~~--~~~~~i~l~nPnNPTG~~~~~~ 154 (336)
.+ +|++|++..-.|+... ...+..|.++..++.+.+..+|++++++. .++++++++.-+|-||...+.+
T Consensus 80 ~l~~~~~~g~~il~~~~e~~s~~~~~~~~~~~~g~~v~~~~~~~~~~~~~~~l~~~i~~~~~lv~~s~~~~~tG~~~pi~ 159 (371)
T PF00266_consen 80 SLRRNLKPGDEILVTNNEHPSNRLPWEELAERKGAEVREIPVDPGGEVDLEELEEAIDPRTRLVSISHVETSTGVRNPIE 159 (371)
T ss_dssp HHHHHTTSSSEEEEECTSHHHHHHHHHHHHHHCCEEEEEEEBGTTSSBSHHHHHHHHHTTEEEEEEESBETTTTEBSSHH
T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCCEEECHH
T ss_conf 01134455421022233562046799875430530269941333210114667776346862698622677775883058
Q ss_pred HHHHHHHHCCC-CCCCCCCCCCCCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEEECCCHHHHHHHHHCCCCC-------
Q ss_conf 99999973787-2025210025886620033245200120234652334345313117889999997337877-------
Q T0636 155 ELDQLRQRAGK-LLIDETYVDYSSFRARGLAYGENELVFRSFSKSYGLAGLRLGALFGPSELIAAMKRKQWFC------- 226 (336)
Q Consensus 155 ~l~~l~~~~~~-~IvDeaY~~f~~~~~~~l~~~~n~iv~~S~SK~~gl~GlRiG~~i~~~~~i~~l~~~~~~~------- 226 (336)
+|.+++++++. +++|.+.. ++.... .+...+--+++.|.-|.+|-+| +|+++.+++.++.++.....|
T Consensus 160 ~i~~~~~~~g~~~~vD~~~~-~g~~~i-d~~~~~~D~~~~s~~Kl~gp~G--~g~l~v~~~~~~~~~~~~~~~~~~~~~~ 235 (371)
T PF00266_consen 160 EIAALAREYGALVVVDAAQS-AGAIPI-DLDELGVDFLVFSSHKLFGPPG--LGFLYVSPRAIEKLEPPFPGWGYVDDPS 235 (371)
T ss_dssp HHHHHHHHTTSEEEEE-TTT-TTSS----TTTTTESEEEEESTSTTS------EEEEEEHHHHHHHHSSTCSSCTTTHTH
T ss_pred HHHHHHHCCCCEEEEECCCC-CCCCCC-CCCCCCCCEEEECCCCCCCCCC--HHHHHCCHHHHHCCCCCCCCCCCCCCCC
T ss_conf 86566620697699831356-665555-5553322468755877778973--7787705987722487457887555643
Q ss_pred ----------------CCCHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHCCC-EEECC-----CCCEEE--
Q ss_conf ----------------87777899999997459--99999999999999999999985897-86169-----864788--
Q T0636 227 ----------------NVGTLDLHALEAALDND--RAREAHIAKTLAQRRRVADALRGLGY-RVASS-----EANFVL-- 280 (336)
Q Consensus 227 ----------------~~~~~~~~aa~~~l~~~--~~~~~~~~~~~~~r~~l~~~l~~lg~-~~~~s-----~~~Fi~-- 280 (336)
+.+.++..+...+++.. .-++...++.....+++.+.|++++. .++.+ .++.+.
T Consensus 236 ~~~~~~~~~~~~f~~GT~~~~~~~al~~al~~~~~~g~~~i~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~~~iv~~~ 315 (371)
T PF00266_consen 236 LQEYGFKDDAQRFEPGTPNVPSIYALGEALKLLQEGGLEAIRERIRELAQYLREALEEIGGVRLLGPDDEPRSPSIVSFN 315 (371)
T ss_dssp HHHHHHHHTTGGSSSS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTEEESSCSGGGGGTTSEEEE
T ss_pred HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCEEEEE
T ss_conf 54420235642223555205789999999999876304789999999999999999867866994353344556548999
Q ss_pred EECCCHHHHHHHHHHCCCEEEECCCC--------CCCCEEEEEEC---CHHHHHHH
Q ss_conf 65698899999998769389607788--------88874788747---98999999
Q T0636 281 VENAAGERTLRFLRERGIQVKDAGQF--------GLHHHIRISIG---REEDNDRL 325 (336)
Q Consensus 281 ~~~~~~~~~~~~L~~~gi~vr~~~~f--------g~~~~iRis~~---~~ee~~~l 325 (336)
++..+++++.+.|.++||.++.|... +.++++|+|++ |++|+++|
T Consensus 316 ~~~~~~~~~~~~L~~~gI~~~~G~~~~~~~~~~~~~~~~iRvS~~~~nt~~dvd~l 371 (371)
T PF00266_consen 316 LPGIDAEDLVKALKERGIIISAGSACAGPSLRLLGLGGVIRVSLHYYNTEEDVDRL 371 (371)
T ss_dssp ETTSSHHHHHHHHHHHHEBEBETTTTCHHHHHHTTTTTEEEEE--TTSSHHHHHHH
T ss_pred ECCCCHHHHHHHHHCCCCEEECCCCCCHHHHHHCCCCCEEEEECCCCCCHHHHHHC
T ss_conf 64568999999985289817546640427888707998899858888999999539
No 3
>PF04864 Alliinase_C: Allinase; InterPro: IPR006948 Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulphoxide cysteine derivatives by alliinase, whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system .; GO: 0016846 carbon-sulfur lyase activity; PDB: 2hor_A 2hox_C 1lk9_A 3bwo_E 3bwn_B.
Probab=99.88 E-value=7.5e-23 Score=164.48 Aligned_cols=266 Identities=19% Similarity=0.275 Sum_probs=179.7
Q ss_pred HHHHHHHHHHHHC-----CCHH-HEEEECCHHHHHHHHHHHHCCC--------CEEECCCCCHHHHHHHHHHCCCEEEEC
Q ss_conf 1899999999848-----8854-3886077889999999984699--------257638873569999998188036415
Q T0636 52 EPRVMRKLAEHFS-----CPED-NLMLVRGIDECFDRISAEFSSM--------RFVTAWPGFDGYRARIAVSGLRHFEIG 117 (336)
Q Consensus 52 ~~~Lr~aia~~~~-----v~~d-~I~~t~Gs~~~i~~~~~~~~~~--------~vii~~P~y~~y~~~~~~~g~~~~~vp 117 (336)
.++|.+.|.+.|+ +..+ .|+++.|++|+|+.+..++..+ +|+...|.|+.|....+.+......
T Consensus 45 s~eLe~~Ir~LH~~VGNAvtdgr~IV~GtGsTQL~~AavyALSp~~~~~~~p~~VVa~aPyY~~y~~qT~~~~s~~y~-- 122 (362)
T PF04864_consen 45 SPELERHIRRLHRVVGNAVTDGRYIVFGTGSTQLLNAAVYALSPPATNSSPPASVVAAAPYYSVYKEQTDFFDSGLYK-- 122 (362)
T ss_dssp -HHHHHHHHHHHHH---B--TTSEEE-----HHHHHHHHHHHCHHT-TTSSSEEEEE-SS--CHHHHHCCCT-B--EE--
T ss_pred CHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCHHHHHHHCCCCCE--
T ss_conf 699999999999873452016737999277999999999970888788899631574488674328888761466833--
Q ss_pred CCCCCCCCHHHHHHHC-CHHHH-HHHCCCCCCCCCCCHHHHHHHHHH-CCCCCCCCCCC--CCCCCCCCHHHHCCCHHHH
Q ss_conf 5435677889997300-02431-330366332222237999999973-78720252100--2588662003324520012
Q T0636 118 LTDDLLLDPNDLAQVS-RDDCV-VLANPSNPTGQALSAGELDQLRQR-AGKLLIDETYV--DYSSFRARGLAYGENELVF 192 (336)
Q Consensus 118 ~~~~~~~d~~~l~~~~-~~~~i-~l~nPnNPTG~~~~~~~l~~l~~~-~~~~IvDeaY~--~f~~~~~~~l~~~~n~iv~ 192 (336)
|.-|........ ....| ++|+||||.|.+- +. .++. .+.+|.|-||. .|++-+. -.+.-|.+
T Consensus 123 ----w~Gda~~~~~~~~~~~~IElVTSPNNPDG~lr--~a---V~~g~~~k~I~D~AYYWPhyTpI~~----~aD~DiML 189 (362)
T PF04864_consen 123 ----WAGDASTFVNSDTPGPYIELVTSPNNPDGQLR--EA---VLNGSSGKAIHDLAYYWPHYTPITA----PADHDIML 189 (362)
T ss_dssp ----E---GGGGTT-S-GGGEEEEEESS-S-------------S--TTEEEEEEE-TT-STTTS---S-----B--SEEE
T ss_pred ----ECCCHHHHCCCCCCCCEEEEEECCCCCCCCHH--HH---HCCCCCCCEEEEEEEECCCCCCCCC----CCCCCEEE
T ss_conf ----42578996578998873899838999851021--45---4069975314320000555566577----66675589
Q ss_pred HHHHHHHCCCCCCCEEEC-CCHHHHHHHHHCC--CCCCCCHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHH
Q ss_conf 023465233434531311-7889999997337--87787777899999997459----------9999999999999999
Q T0636 193 RSFSKSYGLAGLRLGALF-GPSELIAAMKRKQ--WFCNVGTLDLHALEAALDND----------RAREAHIAKTLAQRRR 259 (336)
Q Consensus 193 ~S~SK~~gl~GlRiG~~i-~~~~~i~~l~~~~--~~~~~~~~~~~aa~~~l~~~----------~~~~~~~~~~~~~r~~ 259 (336)
.|+||.-|.+|-|+||++ -++++.++|.+.. ++.++|.=+|.-+...|+.. +.+.--.+.++++.++
T Consensus 190 FTlSK~TGHAGsR~GWAlVKD~~Va~km~~y~~lnt~GvS~dsQLRa~kiLk~v~~~~~~~~g~~~F~fg~~~m~~RW~~ 269 (362)
T PF04864_consen 190 FTLSKLTGHAGSRFGWALVKDEEVAKKMLKYMELNTIGVSRDSQLRALKILKVVLDGYKTNPGTEIFEFGYEVMRERWER 269 (362)
T ss_dssp --HHHH----------EEES-HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHHCCHHSTTTTTT---HHHHHHHHH
T ss_pred EEEECCCCCCCCCEEEEEEECHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 99731357664511046762399999999999761555768899999999999985116788624789999999999999
Q ss_pred HHHHHHHCC-C--------------EEECCCCCEEEEECC--CHHHHHHHHHHCCCEEEECCCCCC-CCEEEEE-ECCHH
Q ss_conf 999998589-7--------------861698647886569--889999999876938960778888-8747887-47989
Q T0636 260 VADALRGLG-Y--------------RVASSEANFVLVENA--AGERTLRFLRERGIQVKDAGQFGL-HHHIRIS-IGREE 320 (336)
Q Consensus 260 l~~~l~~lg-~--------------~~~~s~~~Fi~~~~~--~~~~~~~~L~~~gi~vr~~~~fg~-~~~iRis-~~~~e 320 (336)
|.+.++.-+ + ++.++.-.|-|++.. ..+++.+.|+++||.-|.|..||. ..|+|+| +.+.+
T Consensus 270 L~~~~~~S~rFSLq~~~~~yC~ff~~~~~psPafaWlkCe~eed~DC~~~L~~~~Iitr~G~~Fga~~ryvRlSll~~~d 349 (362)
T PF04864_consen 270 LRAAVSNSDRFSLQEIPPQYCNFFGKVREPSPAFAWLKCEWEEDEDCYAVLREAKIITRSGVLFGADSRYVRLSLLKRQD 349 (362)
T ss_dssp HHHHHCCSSSEEE---SCEEETTTTEEEE---SEEEEEE-SCGGSSHHHHHHTTTEEEB------S-TTEEEEESSS-HH
T ss_pred HHHHHHHCCCEECCCCCCHHCHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCHH
T ss_conf 99999637847558788221200053148998768886386441059999986881057887448887569987157675
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999999
Q T0636 321 DNDRLLAALAEY 332 (336)
Q Consensus 321 e~~~l~~aL~~~ 332 (336)
+.+.|++.|++.
T Consensus 350 ~Fd~l~~rL~~l 361 (362)
T PF04864_consen 350 DFDQLLERLSKL 361 (362)
T ss_dssp HHHHHHHHHHCC
T ss_pred HHHHHHHHHHHH
T ss_conf 699999999844
No 4
>PF01053 Cys_Met_Meta_PP: Cys/Met metabolism PLP-dependent enzyme; InterPro: IPR000277 Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy . PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic . A number of pyridoxal-dependent enzymes involved in the metabolism of cysteine, homocysteine and methionine have been shown , to be evolutionary related. These enzymes are proteins of about 400 amino-acid residues. The pyridoxal-P group is attached to a lysine residue located in the central section of these enzymes.; GO: 0030170 pyridoxal phosphate binding, 0006520 amino acid metabolic process; PDB: 1pff_B 1e5f_A 1e5e_A 1gc0_B 1gc2_C 1ukj_C 1pg8_D 2o7c_B 1y4i_A 2rfv_A ....
Probab=99.58 E-value=2.5e-13 Score=102.75 Aligned_cols=303 Identities=18% Similarity=0.209 Sum_probs=180.3
Q ss_pred CCCCEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCH---HHHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHH--C
Q ss_conf 655357357654888768999999999875005889861---89999999984888543886077889999999984--6
Q T0636 14 AAQAVCLAFNENPEAVEPRVQAAIAAAAARINRYPFDAE---PRVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEF--S 88 (336)
Q Consensus 14 ~~~~i~L~~Nenp~~p~~~v~~al~~~~~~~~~Ypd~~~---~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~--~ 88 (336)
..-.|..++. -.|+..... ++...-..-..|.-.+. ..|.+++|+.-|- +..++++.+..+|..++.++ +
T Consensus 19 v~pPI~~sst-f~~~~~~~~--~~~~~~~~~~~Y~R~gnPt~~~le~~la~LEg~--~~a~~~sSGmaAi~~~~~~ll~~ 93 (386)
T PF01053_consen 19 VNPPIYQSST-FAFDSAEEL--DAFAGESKGYIYSRYGNPTVRALEERLAALEGG--EAALLFSSGMAAITAALLALLRP 93 (386)
T ss_dssp SS--B---SB-BBBSSSHHH--HHHCTTT-S-SBTTTB-HHHHHHHHHHHHHHT---SEEE-B----HHHHHHHHHHS--
T ss_pred CCCCEECCCC-CCCCCHHHH--HHHCCCCCCCCEECCCCCHHHHHHHHHHHHHCC--CCEEEECCHHHHHHHHHHHHCCC
T ss_conf 3288606666-337765777--865698778724089993157999999998576--53488636089999999974789
Q ss_pred CCCEEECCCCCHHHHHHHH----HHCCCEEEECCCCCCCCCHHHHHHH--CCHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 9925763887356999999----8188036415543567788999730--002431330366332222237999999973
Q T0636 89 SMRFVTAWPGFDGYRARIA----VSGLRHFEIGLTDDLLLDPNDLAQV--SRDDCVVLANPSNPTGQALSAGELDQLRQR 162 (336)
Q Consensus 89 ~~~vii~~P~y~~y~~~~~----~~g~~~~~vp~~~~~~~d~~~l~~~--~~~~~i~l~nPnNPTG~~~~~~~l~~l~~~ 162 (336)
||+|+++...|.+....++ .+|+++..+.. -|++++++. .++++||+-+|.|||-.+.+.+.|.+++++
T Consensus 94 Gd~vv~~~~~Yg~t~~~l~~~~~~~gv~v~~~d~-----~d~~~~~~~i~~~t~~v~~EspsNP~l~v~Di~~i~~~a~~ 168 (386)
T PF01053_consen 94 GDHVVASDDLYGGTRRLLREFLPRFGVEVTFVDP-----SDLDALEAAIDPNTKLVFLESPSNPTLEVPDIEAIAEIAHE 168 (386)
T ss_dssp --EEEEESSS-HHHHHHHHHCHHH---EEEEEST-----TSHHHHHHHHCTTEEEEEEESSBTTTTB---HHHHHHHHHH
T ss_pred CCEEEEECCCCCCHHHHHHHCCCCCCEEEEEECC-----CCHHHHHHHHCCCCCEEEEECCCCCCCCCCCHHHHHHHHHH
T ss_conf 9979995775431767656336678859999688-----68899999853577589998788777524678999999998
Q ss_pred CC--CCCCCCCCCCCCCCCCCHHHHCCCHHHHHHHHHHHCCCC-CCCEEECCC--HHHHHHHHHCCCCCC--CCHHHHHH
Q ss_conf 78--720252100258866200332452001202346523343-453131178--899999973378778--77778999
Q T0636 163 AG--KLLIDETYVDYSSFRARGLAYGENELVFRSFSKSYGLAG-LRLGALFGP--SELIAAMKRKQWFCN--VGTLDLHA 235 (336)
Q Consensus 163 ~~--~~IvDeaY~~f~~~~~~~l~~~~n~iv~~S~SK~~gl~G-lRiG~~i~~--~~~i~~l~~~~~~~~--~~~~~~~a 235 (336)
++ .+|||..+... .-..++... --||+.|.||.++-.| +=.|.++.+ +++.+.++..+..++ ++......
T Consensus 169 ~g~~~vvVDnT~atp--~~~~Pl~~G-aDivv~S~TKyl~Ghsdv~~G~vv~~~~~~~~~~~~~~~~~~G~~l~p~da~l 245 (386)
T PF01053_consen 169 HGDILVVVDNTFATP--VLQRPLELG-ADIVVHSATKYLSGHSDVMGGAVVTNGSEELIERLRFLRRLLGATLSPFDAWL 245 (386)
T ss_dssp HST-EEEEEGTTTHT--TTS-GGG-----EEEEETTTTT----S--E-EEEESHHHHHHHHHHHHHHH---B--HHHHHH
T ss_pred HCCEEEEEECCCCCC--CEECCCCCC-CCEEEEECCEEECCCCCCEEEEEEECCHHHHHHHHHHHHHHCCCCCCHHHHHH
T ss_conf 597499980642276--050366567-82899847677238877435999988717889887777875388878799999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-C-EE-ECC----------------CCCEEEEECCCHH-HHHHHHHH
Q ss_conf 999974599999999999999999999998589-7-86-169----------------8647886569889-99999987
Q T0636 236 LEAALDNDRAREAHIAKTLAQRRRVADALRGLG-Y-RV-ASS----------------EANFVLVENAAGE-RTLRFLRE 295 (336)
Q Consensus 236 a~~~l~~~~~~~~~~~~~~~~r~~l~~~l~~lg-~-~~-~~s----------------~~~Fi~~~~~~~~-~~~~~L~~ 295 (336)
...-| +-+.-+.++..++...+.+.|++.. + +| ||+ .|..+-+++.+.. .+.+++..
T Consensus 246 l~rgl---~TL~lR~~~~~~nA~~lA~~L~~hp~V~~V~yPgl~s~p~h~~~~~~~~g~gg~~sf~l~~~~~~~~~f~~~ 322 (386)
T PF01053_consen 246 LLRGL---RTLALRMERHNENALALAEFLEAHPKVKRVNYPGLPSHPQHELAKRQMTGGGGMLSFELKGGEEAARRFIDA 322 (386)
T ss_dssp HH------TTHHHHHHHHHHHHHHHHHHHHTSTTEEEEEETTSTTSTTHHHHHHHCSGG--EEEEEESSHHHHHHHHHHC
T ss_pred HHHCC---CCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHHH
T ss_conf 98058---989999999999999999998517998889974778871588886023688833899928847999999984
Q ss_pred CCCE------------E-EECCC------------CCC-CCEEEEEECCHHHHHHHHHHHHHHH
Q ss_conf 6938------------9-60778------------888-8747887479899999999999998
Q T0636 296 RGIQ------------V-KDAGQ------------FGL-HHHIRISIGREEDNDRLLAALAEYS 333 (336)
Q Consensus 296 ~gi~------------v-r~~~~------------fg~-~~~iRis~~~~ee~~~l~~aL~~~~ 333 (336)
-.++ + .|... .|. ++.+|+|+|.+ +.+.|++-|++-+
T Consensus 323 l~l~~~~~slGg~~SLi~~p~~~~h~~~~~e~~~~~Gi~~~lvRlsvGlE-d~~DLi~Dl~~AL 385 (386)
T PF01053_consen 323 LKLFKIAVSLGGVESLISHPASTTHRSMPEEERAAAGIPDGLVRLSVGLE-DPEDLIADLEQAL 385 (386)
T ss_dssp -SSSEESS-----S-EEEETTTTTTTTSCHHHHHH----TTEEEEE------HHHHHHHHHHHH
T ss_pred CCCEEEECCCCCCCCCCCCCCCHHHHCCCHHHHHHCCCCCCEEEEEECCC-CHHHHHHHHHHHH
T ss_conf 35405864678777455577523231299989975699999599994579-9999999999850
No 5
>PF01041 DegT_DnrJ_EryC1: DegT/DnrJ/EryC1/StrS aminotransferase family; InterPro: IPR000653 The members of this family are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA P72454 from SWISSPROT, StsC P77952 from SWISSPROT and StsS . The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase 2.6.1.50 from EC, which catalyzes the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin .; PDB: 3gr9_D 3b8x_A 2gms_B 2gmu_B 2r0t_A 3bb8_B 3bcx_A 3dr7_C 3dr4_B 3bn1_C ....
Probab=99.55 E-value=6.6e-13 Score=100.09 Aligned_cols=262 Identities=16% Similarity=0.183 Sum_probs=168.2
Q ss_pred HHHHHHHHHHHHHHHCCCC-C-CHHHHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHH---CCCCEEECCCCCHHHHHH
Q ss_conf 8999999999875005889-8-6189999999984888543886077889999999984---699257638873569999
Q T0636 31 PRVQAAIAAAAARINRYPF-D-AEPRVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEF---SSMRFVTAWPGFDGYRAR 105 (336)
Q Consensus 31 ~~v~~al~~~~~~~~~Ypd-~-~~~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~---~~~~vii~~P~y~~y~~~ 105 (336)
...++++.+.+..- .|.. . .-.++.+++|+++|+ ...+.++.++.|+.+++.++ +||+|+++.-+|......
T Consensus 5 ~~~~~~v~~vl~sg-~~~~~g~~~~~fE~~~a~~~g~--~~av~~~sgt~AL~~al~al~~~~gdeVi~p~~t~~at~~a 81 (363)
T PF01041_consen 5 EEELEAVLEVLRSG-WLTNYGPEVREFEKEFAEYFGV--KYAVAVSSGTSALHLALRALGVGPGDEVIVPAFTFPATASA 81 (363)
T ss_dssp HHHHHHHHHHHHHT-TCB----HHHHHHHHHHHHCTS--SEEE-BSSCHHHHHHHHHH-S-BTT-EEEEESSS-THHHHH
T ss_pred HHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHHHCC--CEEEEECCHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHH
T ss_conf 99999999999809-9626998999999999998497--96999679999999999984178999899788655777999
Q ss_pred HHHHCCCEEEECCC-CCCCCCHHHHHHH--CCHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCC-CCCCCCCCCCCCC
Q ss_conf 99818803641554-3567788999730--002431330366332222237999999973787202-5210025886620
Q T0636 106 IAVSGLRHFEIGLT-DDLLLDPNDLAQV--SRDDCVVLANPSNPTGQALSAGELDQLRQRAGKLLI-DETYVDYSSFRAR 181 (336)
Q Consensus 106 ~~~~g~~~~~vp~~-~~~~~d~~~l~~~--~~~~~i~l~nPnNPTG~~~~~~~l~~l~~~~~~~Iv-DeaY~~f~~~~~~ 181 (336)
+...|..++.+..+ ++|.+|++++++. .++|+|++. +.-|...+.++|.++++++++.|| |.+..-.+...-.
T Consensus 82 i~~~G~~pv~~Dvd~~t~~~d~~~~~~~i~~~t~aii~v---h~~G~~~d~~~i~~~~~~~~i~vIEDaa~a~g~~~~g~ 158 (363)
T PF01041_consen 82 ILQAGAKPVFVDVDPDTLNIDPEALEKAITPKTKAIIPV---HLFGQPADMDEIREIARKHGIPVIEDAAQALGATYKGK 158 (363)
T ss_dssp HHHTT-EEEEE-BETTTSSB-HHHHHHHHHTTEEEEEEE-----------HHHHHHHHHHCT-EEEEE-TT----EETTE
T ss_pred HHHCCCEEEEEECCCCCCCCCHHHHHHHHHCCCEEEEEE---CCCCCCCCHHHHHHHHHHHCCEEEECCCCCCCCEECCE
T ss_conf 998299899982698989839999997621698799998---88678148999999999959999871757656725997
Q ss_pred HHHHCCCHHHHHHH--HHHHCCCCCCCEEECC-CHHHHHHHHHCCCCC-------------------CCCHHHHHHHHHH
Q ss_conf 03324520012023--4652334345313117-889999997337877-------------------8777789999999
Q T0636 182 GLAYGENELVFRSF--SKSYGLAGLRLGALFG-PSELIAAMKRKQWFC-------------------NVGTLDLHALEAA 239 (336)
Q Consensus 182 ~l~~~~n~iv~~S~--SK~~gl~GlRiG~~i~-~~~~i~~l~~~~~~~-------------------~~~~~~~~aa~~~ 239 (336)
.+-... .+.+.|| +|.+... -=|.++. ++++.++++.++... .++.+....+...
T Consensus 159 ~~G~~g-d~~~fSF~~~K~i~~g--eGG~v~t~d~~~~~~~~~lr~~G~~~~~~~~~~~~~~~G~n~rm~~~~AAig~~Q 235 (363)
T PF01041_consen 159 KVGTFG-DAGVFSFHPTKNITTG--EGGAVVTNDEELAERARSLRNHGRSRDSFDRYEHELPIGYNYRMSELQAAIGLAQ 235 (363)
T ss_dssp B----S-SBEE---STTSSS-S-------EEES-HHHHHHHHHHCBTCEETSSSSTTB-S-S---B-B-BHHHHHHHHHH
T ss_pred ECCCCC-CEEEEECCCCCCCEEC--CCCCEEECCHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHH
T ss_conf 556888-8899968998766106--9980653749999986577745876566652332105865567668999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CEEE--CCCC---C---E-EEEECC---CHHHHHHHHHHCCCEEEECC
Q ss_conf 74599999999999999999999998589-7861--6986---4---7-886569---88999999987693896077
Q T0636 240 LDNDRAREAHIAKTLAQRRRVADALRGLG-YRVA--SSEA---N---F-VLVENA---AGERTLRFLRERGIQVKDAG 304 (336)
Q Consensus 240 l~~~~~~~~~~~~~~~~r~~l~~~l~~lg-~~~~--~s~~---~---F-i~~~~~---~~~~~~~~L~~~gi~vr~~~ 304 (336)
|+. +.+.+++-++..+++.+.|+++. +... +.+. . | +.++.. +-+.+.+.|.++||-++...
T Consensus 236 L~~---l~~~~~~R~~~a~~y~~~L~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~Rd~l~~~L~~~GI~t~~~y 310 (363)
T PF01041_consen 236 LKR---LDEIIARRRENAERYREALADLPGLRPLPIPPGNSEHSYHRYPIRLPEEALADRDELIEALRARGIETRVHY 310 (363)
T ss_dssp HHC---HHHHHHHHHHHHHHHHHHHTTGSSEEEEGCGTTTEEEEESSEEEEETTTCHHCHHHHHHHHHHTTEB-BSST
T ss_pred HHH---HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCHHHHHHHHHHHHHCCCCEECCC
T ss_conf 999---999999999999999998558999656777888765212799999545322579999999998799634115
No 6
>PF00464 SHMT: Serine hydroxymethyltransferase; InterPro: IPR001085 Synonym(s): Serine hydroxymethyltransferase, Serine aldolase, Threonine aldolase Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP) dependent enzyme and belongs to the aspartate aminotransferase superfamily (fold type I) . The pyridoxal-P group is attached to a lysine residue around which the sequence is highly conserved in all forms of the enzyme . The enzyme carries out interconversion of serine and glycine using PLP as the cofactor. SHMT catalyses the transfer of a hydroxymethyl group from N5, N10- methylene tetrahydrofolate to glycine, resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers and the mammalian enzyme forms a homotetramer , . PLP dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalysed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), D-amino acid superfamily (fold type IV) and glycogen phophorylase family (fold type V) , . In vertebrates, glycine hydroxymethyltransferase exists in a cytoplasmic and a mitochondrial form whereas only one form is found in prokaryotes.; GO: 0004372 glycine hydroxymethyltransferase activity, 0006544 glycine metabolic process, 0006563 L-serine metabolic process; PDB: 3ecd_D 2dkj_A 2a7v_A 1bj4_A 1eji_C 1rv3_A 1ls3_C 1cj0_B 1rvu_A 1rvy_A ....
Probab=99.50 E-value=2.4e-12 Score=96.43 Aligned_cols=310 Identities=19% Similarity=0.249 Sum_probs=195.4
Q ss_pred CHHHHHHHHHCCCCCCEECCCCCCCCCCCHHHHHHHHHHHHH--HHCCCCC------CHHHHHHHHH-----HHHCCCHH
Q ss_conf 511578975036655357357654888768999999999875--0058898------6189999999-----98488854
Q T0636 2 SVGEAMDTEVRAAAQAVCLAFNENPEAVEPRVQAAIAAAAAR--INRYPFD------AEPRVMRKLA-----EHFSCPED 68 (336)
Q Consensus 2 ~~~~~~~~~~~~~~~~i~L~~Nenp~~p~~~v~~al~~~~~~--~~~Ypd~------~~~~Lr~aia-----~~~~v~~d 68 (336)
+|.++++++...-...|.|--.||- .+|.+++++...+.. ...||.. .+....|.+| +.++.+++
T Consensus 7 ei~~~i~~e~~rq~~~l~LIASEN~--~S~~v~~algS~ltnkYaeG~pg~ryy~G~~~vD~iE~la~~ra~~lF~a~~~ 84 (399)
T PF00464_consen 7 EIFELIEKEEERQRDTLNLIASENF--TSPAVLEALGSDLTNKYAEGYPGKRYYGGCEYVDEIEELAIERAKKLFGAEPK 84 (399)
T ss_dssp HHHHHHHHHHHHHHHSEB--TT-------HHHHHH---GGGGS--------------HHHHHHHHHHHHHHHHHTT--TT
T ss_pred HHHHHHHHHHHHHHCCEEEECCCCC--CCHHHHHHHCCCHHCCCCCCCCCCCCCCCCEEHHHHHHHHHHHHHHHHCCCCC
T ss_conf 9999999999988658657557565--89999998637130447788898677688774999999999999998599854
Q ss_pred ----HEEEECCHHHHHHHHHHHH-CCCCEEECCCCCHHHHHHHHH----------HCCCEEEECCC-CCCCCCHHHHHHH
Q ss_conf ----3886077889999999984-699257638873569999998----------18803641554-3567788999730
Q T0636 69 ----NLMLVRGIDECFDRISAEF-SSMRFVTAWPGFDGYRARIAV----------SGLRHFEIGLT-DDLLLDPNDLAQV 132 (336)
Q Consensus 69 ----~I~~t~Gs~~~i~~~~~~~-~~~~vii~~P~y~~y~~~~~~----------~g~~~~~vp~~-~~~~~d~~~l~~~ 132 (336)
+|-.-+|++..+...+..+ +||+|+.+.+...++...-.. ...+.+.++.+ ++..+|.+++++.
T Consensus 85 ~w~anVqp~SGs~An~av~~ALl~pgD~im~l~l~~GGHlthg~~~~~~k~~~~g~~~~~~~Y~~d~~~~~IDyd~l~~~ 164 (399)
T PF00464_consen 85 EWYANVQPHSGSQANLAVYFALLKPGDRIMGLSLPHGGHLTHGYKVNFKKVSASGKFYESVPYGVDPETGLIDYDELEKL 164 (399)
T ss_dssp T-EEE-------HHHHHHHHHHT-S-EEEE---TT----TT---TTSSSBSSHHHHHSEE----B-TTTSSB-HHHHHHH
T ss_pred CCEEEEECCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCHHHHHHH
T ss_conf 55378845875899999999975347838953655687767676666532344354379998652466796679999999
Q ss_pred ---CCHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCC-CCCCCCCC-CC--CCCCCCHHHHCCCHHHHHHHHHHHCCCCCC
Q ss_conf ---002431330366332222237999999973787-20252100-25--886620033245200120234652334345
Q T0636 133 ---SRDDCVVLANPSNPTGQALSAGELDQLRQRAGK-LLIDETYV-DY--SSFRARGLAYGENELVFRSFSKSYGLAGLR 205 (336)
Q Consensus 133 ---~~~~~i~l~nPnNPTG~~~~~~~l~~l~~~~~~-~IvDeaY~-~f--~~~~~~~l~~~~n~iv~~S~SK~~gl~GlR 205 (336)
.++|+|++.-=+.| ..++-++++++++..+. +++|-+.. .+ ++..+.++.. -+ ||..|.-|+| +|=|
T Consensus 165 a~~~kPklIi~G~S~y~--r~~d~~~~reIad~vga~l~~D~aH~aGLIA~g~~p~P~~~-AD-vVt~tTHKTl--rGPr 238 (399)
T PF00464_consen 165 AKEFKPKLIICGASAYP--RPIDFKRFREIADEVGAYLMADIAHIAGLIAGGLFPSPLPY-AD-VVTTTTHKTL--RGPR 238 (399)
T ss_dssp HHHH--SEEEE--TS-S--S---HHHHHHHHHHTT-EEEEE-TTT---TTTTSS--GTTT-SS-EEE--SSGGG------
T ss_pred HHHCCCCEEEECCHHCC--CCCCHHHHHHHHHHCCCEEEEEHHHHHHHEECCCCCCCCCC-CC-EEECCCCCCC--CCCC
T ss_conf 98769999998904437--77799999999987798999614556665127777998787-72-8976666566--6887
Q ss_pred CEEECCC--------------HHHHHHHHHCCCCCCCCH--HHHHHHHH-HHHH--HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3131178--------------899999973378778777--78999999-9745--999999999999999999999985
Q T0636 206 LGALFGP--------------SELIAAMKRKQWFCNVGT--LDLHALEA-ALDN--DRAREAHIAKTLAQRRRVADALRG 266 (336)
Q Consensus 206 iG~~i~~--------------~~~i~~l~~~~~~~~~~~--~~~~aa~~-~l~~--~~~~~~~~~~~~~~r~~l~~~l~~ 266 (336)
-|.++.+ +++.+++++..-|...+. ....++++ ++.. ...++++.+++..+.+.|.+.|.+
T Consensus 239 gGiIl~~~g~~~~~~~~~~~~~~~~~kI~~avFPg~qggp~~h~iAa~Ava~~Ea~~~~fk~Ya~qVv~NAkaLA~~L~~ 318 (399)
T PF00464_consen 239 GGIILTNKGYKNVDKQGKEIDEELAKKIDSAVFPGLQGGPHMHRIAALAVAFKEALSPEFKEYAKQVVKNAKALAEALNE 318 (399)
T ss_dssp ---EEES----EE-T---EE-HHHHHHHHHHHTTTT-----HHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 06999805655555555521799999873241876434640768999999999865843899999999999999999976
Q ss_pred CCCEEECCC--CCEEEEECC----CHHHHHHHHHHCCCEEE----ECCCCC-CCCEEEEEECCHHH
Q ss_conf 897861698--647886569----88999999987693896----077888-88747887479899
Q T0636 267 LGYRVASSE--ANFVLVENA----AGERTLRFLRERGIQVK----DAGQFG-LHHHIRISIGREED 321 (336)
Q Consensus 267 lg~~~~~s~--~~Fi~~~~~----~~~~~~~~L~~~gi~vr----~~~~fg-~~~~iRis~~~~ee 321 (336)
.|+++...+ ...+|+++. ++..+.+.|.+.||.+. |++... .+..||| ||++-
T Consensus 319 ~G~~vv~ggTdnHlvlvD~~~~g~~g~~a~~~L~~agI~~Nkn~iP~d~~~~~~sGiRi--GT~~~ 382 (399)
T PF00464_consen 319 RGFRVVSGGTDNHLVLVDLRSKGLTGKEAEKLLEEAGITVNKNTIPGDKSPFVPSGIRI--GTPAL 382 (399)
T ss_dssp ---EE------SS-EEEEGGGGT----HHHHHHHHTTEB-B----TT-STTTT----EE----HHH
T ss_pred CCCEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHCCEEEECCCCCCCCCCCCCCEEEE--CCHHH
T ss_conf 79748616987737999755356899999999997794760451578776768886896--88789
No 7
>PF01212 Beta_elim_lyase: Beta-eliminating lyase; InterPro: IPR001597 This family includes tryptophanase (tryptophan indole-lyase, TNase) (4.1.99.1 from EC), tyrosine phenol-lyase (TPL) (4.1.99.2 from EC), threonine aldolase (4.1.2.5 from EC).; GO: 0016829 lyase activity, 0006520 amino acid metabolic process; PDB: 1svv_B 1v72_A 1c7g_A 1tpl_B 2vlh_B 2vlf_B 2tpl_B 2ez2_A 2ez1_A 1ax4_B ....
Probab=99.01 E-value=1.1e-12 Score=98.62 Aligned_cols=243 Identities=24% Similarity=0.239 Sum_probs=141.0
Q ss_pred CCHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHH--CCCCEEECCCCCH-HHH-
Q ss_conf 76899999999987500588-986189999999984888543886077889999999984--6992576388735-699-
Q T0636 29 VEPRVQAAIAAAAARINRYP-FDAEPRVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEF--SSMRFVTAWPGFD-GYR- 103 (336)
Q Consensus 29 p~~~v~~al~~~~~~~~~Yp-d~~~~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~--~~~~vii~~P~y~-~y~- 103 (336)
|.|.++++|.++...-..|. |+...+|.+.+++.+|.+. -+++.+| +.+=.++++++ +++.|+...++-. .++
T Consensus 7 ~t~~m~~a~a~a~~gd~~Yg~D~~~~~le~~ia~l~g~e~-a~f~~sG-T~AN~lal~~~~~~~~~vi~~~~~Hi~~~E~ 84 (290)
T PF01212_consen 7 PTPAMLEAMAAANVGDDAYGEDPTTNRLEERIAELFGKEA-ALFVPSG-TMANQLALRAHCRPGQSVICHDPAHIHFDET 84 (290)
T ss_dssp --HHEEHHHHHTT---TT----HHHHHHHHHHHHHHTSTE-EEEE-----HHHHHHHHHHHHHHHEEEEETTESSHHCHH
T ss_pred CCHHHHHHHHHCCCCCHHHCCCHHHHHHHHHHHHHHCCCE-EEECCCC-HHHHHHHHHHHHCCCCEEEECCCCCCCEECC
T ss_conf 6799999997203453220679889999999999859986-9996885-6899999999606698899745761321174
Q ss_pred -HHHHHHCCCEEEECCCCCCCCCHHHHHHHC--------CHHHHHHHCCCCCC-CCCCCHHHHHHH---HHHCCC-CCCC
Q ss_conf -999981880364155435677889997300--------02431330366332-222237999999---973787-2025
Q T0636 104 -ARIAVSGLRHFEIGLTDDLLLDPNDLAQVS--------RDDCVVLANPSNPT-GQALSAGELDQL---RQRAGK-LLID 169 (336)
Q Consensus 104 -~~~~~~g~~~~~vp~~~~~~~d~~~l~~~~--------~~~~i~l~nPnNPT-G~~~~~~~l~~l---~~~~~~-~IvD 169 (336)
....+.|.+++.++-+++..++++++++.. ++++|+|.||+|-- |++++.++|+++ ++++++ +.+|
T Consensus 85 ga~~~~~G~~~~~l~~~~~G~l~~~~l~~~~~~~~~h~~~~~~v~le~t~~~~gG~v~~~~el~~i~~~a~~~gl~lhmD 164 (290)
T PF01212_consen 85 GAPEELSGAKLVPLPGDDDGKLTPEDLEAAIEEHGDHAPQPALVSLENTTNSAGGTVYSLEELRAISELAREHGLPLHMD 164 (290)
T ss_dssp HHHHHH---EEEEEB-GCGT-B-HHHHHHHHHHS-TTSTTEEEEEEESS-ST-------HHHHHHHHHHHHHTT-EEEEE
T ss_pred CHHHHHHCCEEEEECCCCCCCCCHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCCEECCHHHHHHHHHHHHHCCCEEEEE
T ss_conf 68999829789970785457769999999833566767874079998077687988588999999999999829989997
Q ss_pred CCCCC----CCCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEEECCCHHHHHHHHHCCCCC--CCC---HHH-----HHH
Q ss_conf 21002----5886620033245200120234652334345313117889999997337877--877---778-----999
Q T0636 170 ETYVD----YSSFRARGLAYGENELVFRSFSKSYGLAGLRLGALFGPSELIAAMKRKQWFC--NVG---TLD-----LHA 235 (336)
Q Consensus 170 eaY~~----f~~~~~~~l~~~~n~iv~~S~SK~~gl~GlRiG~~i~~~~~i~~l~~~~~~~--~~~---~~~-----~~a 235 (336)
.|=.- ....+...+..+-+.++ -|+||..|+|+= +.++++++.++..++.+... .+. .++ +.+
T Consensus 165 GARl~na~~~~~~~~~e~~~~~D~v~-~~~tK~~ga~~G--avl~~~~~~i~~~~~~~k~~Gg~m~q~G~laa~~~~~~~ 241 (290)
T PF01212_consen 165 GARLANAAAALGCTLAELAAGADSVS-FSLTKGGGAPGG--AVLAGSDDFIEEARRQRKRLGGGMRQAGILAAAELYQEA 241 (290)
T ss_dssp -TTHHHHHSHHHHHHHHHHGG-SEEE-E-TTSTT-SS-E--EEEEESSGHHHHHHHHHHHHH-HHHHTHHCBCHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHCCCCEEE-EEEEECCCCCCC--EEEECCHHHHHHHHHHHHHHCCCEEECCCEEEECHHHHH
T ss_conf 23377654330579999960789999-961704766644--599827899999999999965870205611331012688
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEE-ECCCCCEE
Q ss_conf 999974599999999999999999999998589786-16986478
Q T0636 236 LEAALDNDRAREAHIAKTLAQRRRVADALRGLGYRV-ASSEANFV 279 (336)
Q Consensus 236 a~~~l~~~~~~~~~~~~~~~~r~~l~~~l~~lg~~~-~~s~~~Fi 279 (336)
+..++++. .....+-.+.-+++.+.|+.++... .|+++|-+
T Consensus 242 ~l~~le~~---~~~~~~~~~~A~~la~~l~~~~~~~~~~~~tn~~ 283 (290)
T PF01212_consen 242 GLRALELW---LERLAHDHAMAKRLAEGLEELGGALPRPVETNQV 283 (290)
T ss_dssp HHBCEEEC---CTTHHHHSHHHHHHHHSHHEEEEEEETTSS-HHH
T ss_pred HHHHHHHH---HHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCEE
T ss_conf 88888741---6889999999999999999789811189977557
No 8
>PF06838 Alum_res: Aluminium resistance protein ; InterPro: IPR009651 This family represents the aluminium resistance protein, which confers resistance to aluminium in bacteria .; PDB: 3ht4_A 3gwp_B 3fd0_B.
Probab=98.96 E-value=3.1e-08 Score=69.82 Aligned_cols=255 Identities=15% Similarity=0.214 Sum_probs=148.7
Q ss_pred HHHHHHHHH-HHHH-----HCC--CCCCHHHHHHHHHHHHCCCHH--HEEEECCHHHHHHHHH-HHH-CCCCEEEC--CC
Q ss_conf 999999999-8750-----058--898618999999998488854--3886077889999999-984-69925763--88
Q T0636 32 RVQAAIAAA-AARI-----NRY--PFDAEPRVMRKLAEHFSCPED--NLMLVRGIDECFDRIS-AEF-SSMRFVTA--WP 97 (336)
Q Consensus 32 ~v~~al~~~-~~~~-----~~Y--pd~~~~~Lr~aia~~~~v~~d--~I~~t~Gs~~~i~~~~-~~~-~~~~vii~--~P 97 (336)
.|++|+++. +.+. ..| -|.|...|-+..|+.++-..- +..+.+|+ ++|..++ ..+ +||+.+.. .|
T Consensus 28 KVL~Af~~~~vs~~hf~~stGYGy~D~GRd~Le~vyA~vfgaE~ALVR~q~vSGT-HAi~~aLfg~LrPGD~ll~itG~P 106 (403)
T PF06838_consen 28 KVLKAFQEHRVSESHFNGSTGYGYDDIGRDKLERVYADVFGAEDALVRPQFVSGT-HAIATALFGVLRPGDELLSITGKP 106 (403)
T ss_dssp HHHHHHHHTT--GGGSS------------HHHHHHHHHHCT-S--B-STTS-----HHHHHHH--------EEEE-----
T ss_pred HHHHHHHHCCCCHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHCCCCCCHH-HHHHHHHHHCCCCCCEEEECCCCC
T ss_conf 9999999839787666888867878756899999999995635553012004408-899999973678998688716997
Q ss_pred CCHHHH----------HHHHHHCCCEEEECCCCCCCCCHHHHHHH--CCHHHHHHH-CCCCCCCCCCCHHHHHHHHH---
Q ss_conf 735699----------99998188036415543567788999730--002431330-36633222223799999997---
Q T0636 98 GFDGYR----------ARIAVSGLRHFEIGLTDDLLLDPNDLAQV--SRDDCVVLA-NPSNPTGQALSAGELDQLRQ--- 161 (336)
Q Consensus 98 ~y~~y~----------~~~~~~g~~~~~vp~~~~~~~d~~~l~~~--~~~~~i~l~-nPnNPTG~~~~~~~l~~l~~--- 161 (336)
|.-.+ -.++-+|+.+.++|+.+|..+|.+.+.+. .++|++.|- +.---+=..++.++|.++++
T Consensus 107 -YDTL~eVIGi~g~~~GSL~e~GI~Y~~v~L~~dg~~D~~~i~~~i~~~tk~v~IQRS~GYs~R~slsi~~I~~~i~~ik 185 (403)
T PF06838_consen 107 -YDTLEEVIGIRGSGQGSLKEFGIKYDEVDLTEDGEIDYEAIKKAIKPKTKMVLIQRSRGYSWRPSLSIEEIKEIIKFIK 185 (403)
T ss_dssp --CCHHHH----S-----TGGGT-EEEE--B-----B-HHHHHHHHHTTEEEEEEE------SS----HHHHHHHHHHHH
T ss_pred -CHHHHHHHCCCCCCCCCHHHHCCCEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf -0767987287999988889939752899753799828999998617565599995278876789859999999999999
Q ss_pred -H--CCCCCCCCCCCCCCCCCCCHHHHCCCHHHHHHHHHHHCCCCC-C-CEEECCCHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf -3--787202521002588662003324520012023465233434-5-3131178899999973378778777789999
Q T0636 162 -R--AGKLLIDETYVDYSSFRARGLAYGENELVFRSFSKSYGLAGL-R-LGALFGPSELIAAMKRKQWFCNVGTLDLHAL 236 (336)
Q Consensus 162 -~--~~~~IvDeaY~~f~~~~~~~l~~~~n~iv~~S~SK~~gl~Gl-R-iG~~i~~~~~i~~l~~~~~~~~~~~~~~~aa 236 (336)
. +.++.||..|.||.....+.-...| ++.+|+=|.-| .|+ . =||+++.++++++...+.. ...++-..+
T Consensus 186 ~~~p~~ivfVDNCYGEFvE~~EP~~vGAD--liaGSLIKNpG-GgiAptGGYIaGr~dlVe~aa~RLT---aPGiG~e~G 259 (403)
T PF06838_consen 186 EINPDVIVFVDNCYGEFVETKEPTEVGAD--LIAGSLIKNPG-GGIAPTGGYIAGRKDLVEQAAYRLT---APGIGKEVG 259 (403)
T ss_dssp HH-TTSEEEEE------SSSS-GGG------EEE--TTS-------------BB--HHHHHHHHHHHS------------
T ss_pred HHCCCEEEEEECCCCCCCCCCCCCCCCHH--HEECCCEECCC-CCCCCCCCEEECHHHHHHHHHHHCC---CCCCCCCCC
T ss_conf 75898399997886120156585301644--40120124798-8736757778536999999864005---885564457
Q ss_pred HHHHHHHH-----HHH-HHHHHHHHHHHHHHHHHHHCCCEEECCCC----CE-EEEECCCHHHHHHHHH
Q ss_conf 99974599-----999-99999999999999999858978616986----47-8865698899999998
Q T0636 237 EAALDNDR-----ARE-AHIAKTLAQRRRVADALRGLGYRVASSEA----NF-VLVENAAGERTLRFLR 294 (336)
Q Consensus 237 ~~~l~~~~-----~~~-~~~~~~~~~r~~l~~~l~~lg~~~~~s~~----~F-i~~~~~~~~~~~~~L~ 294 (336)
...-.... ++. ....+-.+........|+++|+++.|.-. -- --+++.+.+.+..+++
T Consensus 260 at~~~~r~~~QGlFlAP~vv~eAlKgAif~A~~~e~lG~~v~P~~~~~R~DiIQav~lg~~e~liaFC~ 328 (403)
T PF06838_consen 260 ATLGSNRLMYQGLFLAPHVVGEALKGAIFAAALFEKLGFEVSPKPDEPRTDIIQAVKLGSPEKLIAFCQ 328 (403)
T ss_dssp --TTTHHHHH---TSHHHHHHHHH---HHHHHHHHH---EEES-TTS--SSS-EEEE-SSHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCHHHHHHHHH
T ss_conf 680378999878600249999999999999999998499568999998672578886799899999999
No 9
>PF01276 OKR_DC_1: Orn/Lys/Arg decarboxylase, major domain; InterPro: IPR000310 Pyridoxal-dependent decarboxylases are bacterial proteins acting on ornithine, lysine, arginine and related substrates . One of the regions of sequence similarity contains a conserved lysine residue, which is the site of attachment of the pyridoxal-phosphate group.; GO: 0003824 catalytic activity; PDB: 2vyc_G 1ord_A 1c4k_A.
Probab=98.94 E-value=5.1e-08 Score=68.39 Aligned_cols=220 Identities=17% Similarity=0.222 Sum_probs=129.6
Q ss_pred CCCCHHHHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHH--CCCCEEECCCCCHHHHHHHHHHCCCEEEECCC-CCC--
Q ss_conf 8986189999999984888543886077889999999984--69925763887356999999818803641554-356--
Q T0636 48 PFDAEPRVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEF--SSMRFVTAWPGFDGYRARIAVSGLRHFEIGLT-DDL-- 122 (336)
Q Consensus 48 pd~~~~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~--~~~~vii~~P~y~~y~~~~~~~g~~~~~vp~~-~~~-- 122 (336)
|+.--.+..+..|+.||.+ ...+++||++.++..++.+. +||.|+++--+=-.....+.+.|...++++.+ +++
T Consensus 64 p~G~I~eaq~~aA~~fgad-~t~f~vnGsT~~n~a~i~a~~~~gd~vLv~RN~HKSv~~alil~ga~Pvyl~p~~~~~Gi 142 (417)
T PF01276_consen 64 PEGIIKEAQELAARAFGAD-RTYFLVNGSTGGNQAMIMALCRPGDKVLVDRNCHKSVYHALILSGAKPVYLYPERNEYGI 142 (417)
T ss_dssp T---HHHHHHHHHHHHT-S-EEEEE----HHHHHHHHHHH--TT-EEEEETT--HHHHHHTTT---EEEEE---------
T ss_pred CCCHHHHHHHHHHHHCCCC-CEEEEECCCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHCCCEEEEECCCCCCCCC
T ss_conf 8719999999999863998-379995782189999999842899989970764899999999879978994378667886
Q ss_pred --CCCH-----HHHHHH----CCHHH---HHHHCCCCCCCCCCCHHHHHHHHHHCC-CCCCCCCCCC---CCCCCCCHH-
Q ss_conf --7788-----999730----00243---133036633222223799999997378-7202521002---588662003-
Q T0636 123 --LLDP-----NDLAQV----SRDDC---VVLANPSNPTGQALSAGELDQLRQRAG-KLLIDETYVD---YSSFRARGL- 183 (336)
Q Consensus 123 --~~d~-----~~l~~~----~~~~~---i~l~nPnNPTG~~~~~~~l~~l~~~~~-~~IvDeaY~~---f~~~~~~~l- 183 (336)
.+++ +.+++. ...+. ++|+||+- -|.+.+.++|.+++++.+ .++||||... |.+.....+
T Consensus 143 ~~~i~~~~~~~e~i~~~l~~~p~~ka~~~vvlt~pTY-~G~~~d~~~i~~~~h~~~~~llvDEAhGah~~F~~lp~~a~~ 221 (417)
T PF01276_consen 143 IGGIPPSEFTPESIEKALAEHPDAKAPRAVVLTSPTY-DGVCYDLKEIADICHKYGIPLLVDEAHGAHFRFHPLPKSALA 221 (417)
T ss_dssp -----GGGCSHHHHHHHHHHGCCCHCECEEEEESS------EE-HHHHHHHHTTTECEEEEE-TT---CCCSGGGCCCSS
T ss_pred CCCCCHHHCCHHHHHHHHHHCCCCCCCEEEEEECCCC-CEEEECHHHHHHHHHHCCCEEEEECCCHHHHCCCCCCCCHHH
T ss_conf 0477836437999999998486435831899977986-637408999999985459959997857676553867547756
Q ss_pred -----HHCCCHHHHHHHHHHHCCCCCCCE-EECCC-H-----HHH-HHHHHCCCCCCCCH--HHHHHHHHHH---HHHHH
Q ss_conf -----324520012023465233434531-31178-8-----999-99973378778777--7899999997---45999
Q T0636 184 -----AYGENELVFRSFSKSYGLAGLRLG-ALFGP-S-----ELI-AAMKRKQWFCNVGT--LDLHALEAAL---DNDRA 245 (336)
Q Consensus 184 -----~~~~n~iv~~S~SK~~gl~GlRiG-~~i~~-~-----~~i-~~l~~~~~~~~~~~--~~~~aa~~~l---~~~~~ 245 (336)
...+.++++.|.=|+. |++.-+ |+... . +.+ +.+...+.+.+... .|.-++.+.+ ...+.
T Consensus 222 ~gaD~~~~~~~~vvqS~HKtL--~alTQ~S~LH~~~~~~vd~~~~~~al~~~qTTSPSY~LmASLD~A~~~m~~~~G~~l 299 (417)
T PF01276_consen 222 MGADDPEDPAILVVQSTHKTL--PALTQASMLHVKGDRIVDHERVNEALMMLQTTSPSYLLMASLDVARAMMEAEEGREL 299 (417)
T ss_dssp TT-------EEEEEEEHHHHS--S--TT-EEEEEE-GGG--HHHHHHHHHHCS-SS--CHHHHHHHHHHHHH------HH
T ss_pred CCCCCCCCCCEEEEEEHHHCC--CCCCHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 479655676326886221125--674600377877997777999999999875888389999999999999750451999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHC-CCEEE
Q ss_conf 9999999999999999999858-97861
Q T0636 246 REAHIAKTLAQRRRVADALRGL-GYRVA 272 (336)
Q Consensus 246 ~~~~~~~~~~~r~~l~~~l~~l-g~~~~ 272 (336)
+++.++....-|+++.. +++. +++++
T Consensus 300 ~~~~i~~a~~~R~~l~~-~~~~~~f~~~ 326 (417)
T PF01276_consen 300 LEEAIELAIDFRKKLAR-LNDIWGFKPW 326 (417)
T ss_dssp HHHHHHHHHHHHHHHHH-HH----SEES
T ss_pred HHHHHHHHHHHHHHHHC-CCCCCEEEEC
T ss_conf 99999999999997513-3568867747
No 10
>PF00202 Aminotran_3: Aminotransferase class-III; InterPro: IPR005814 Aminotransferases share certain mechanistic features with other pyridoxalphosphate-dependent enzymes, such as the covalent binding of the pyridoxalphosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into subfamilies. One of these, called class-III, includes acetylornithine aminotransferase (2.6.1.11 from EC), which catalyzes the transfer of an amino group from acetylornithine to alpha-ketoglutarate, yielding N-acetyl-glutamic-5-semi-aldehyde and glutamic acid; ornithine aminotransferase (2.6.1.13 from EC), which catalyzes the transfer of an amino group from ornithine to alpha-ketoglutarate, yielding glutamic-5-semi-aldehyde and glutamic acid; omega-amino acid--pyruvate aminotransferase (2.6.1.18 from EC), which catalyzes transamination between a variety of omega-amino acids, mono- and diamines, and pyruvate; 4-aminobutyrate aminotransferase (2.6.1.19 from EC) (GABA transaminase), which catalyzes the transfer of an amino group from GABA to alpha-ketoglutarate, yielding succinate semialdehyde and glutamic acid; DAPA aminotransferase (2.6.1.62 from EC), a bacterial enzyme (bioA), which catalyzes an intermediate step in the biosynthesis of biotin, the transamination of 7-keto-8-aminopelargonic acid to form 7,8-diaminopelargonic acid; 2,2-dialkylglycine decarboxylase (4.1.1.64 from EC), a Burkholderia cepacia (Pseudomonas cepacia) enzyme (dgdA) that catalyzes the decarboxylating amino transfer of 2,2-dialkylglycine and pyruvate to dialkyl ketone, alanine and carbon dioxide; glutamate-1-semialdehyde aminotransferase (5.4.3.8 from EC) (GSA); Bacillus subtilis aminotransferases yhxA and yodT; Haemophilus influenzae aminotransferase HI0949; and Caenorhabditis elegans aminotransferase T01B11.2.; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding; PDB: 2pb2_A 2pb0_B 1wkg_A 1wkh_B 1vef_B 2can_A 1gbn_B 1oat_C 2byj_A 2byl_B ....
Probab=98.83 E-value=9.1e-09 Score=73.27 Aligned_cols=226 Identities=19% Similarity=0.230 Sum_probs=130.2
Q ss_pred CCCCCEECCCC--CCCCC-CCHHHHHHHHHHHHHHHC-----CCCCCHHHHHHHHHHHHCCCHHHEEEECCHHHHHHHHH
Q ss_conf 66553573576--54888-768999999999875005-----88986189999999984888543886077889999999
Q T0636 13 AAAQAVCLAFN--ENPEA-VEPRVQAAIAAAAARINR-----YPFDAEPRVMRKLAEHFSCPEDNLMLVRGIDECFDRIS 84 (336)
Q Consensus 13 ~~~~~i~L~~N--enp~~-p~~~v~~al~~~~~~~~~-----Ypd~~~~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~ 84 (336)
.+++.||+.++ -+.+| -.|.+.+|+.+.+.++.. ++.+...+|-+.|++...-..++++.+++++|+...++
T Consensus 14 dG~~ylD~~~g~~~~~lGh~~p~v~~ai~~q~~~~~~~~~~~~~~~~~~~lae~L~~~~p~~~~~v~f~~SGseAve~Ai 93 (339)
T PF00202_consen 14 DGNEYLDFTSGYGVVNLGHNHPEVVEAIKEQLERLNHVSFFGFPHPPAVELAEKLAELAPPGLDRVFFANSGSEAVEAAI 93 (339)
T ss_dssp TEEEEEBSSHHHHTT------HHHHHHHHHHHHHCSHHSTTTSEEHHHHHHHHHHHHHS-TTESEEEEE----HHHHHHH
T ss_pred CCCEEEECCCCHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHH
T ss_conf 99999986655230057888199999999999753234322457679999999997108997567987568857999999
Q ss_pred H---------HHCCC-CEEECCCCCHHHHHHHHH-HCC------------CEEEECCCCCCC-----CCHHHH---H-HH
Q ss_conf 9---------84699-257638873569999998-188------------036415543567-----788999---7-30
Q T0636 85 A---------EFSSM-RFVTAWPGFDGYRARIAV-SGL------------RHFEIGLTDDLL-----LDPNDL---A-QV 132 (336)
Q Consensus 85 ~---------~~~~~-~vii~~P~y~~y~~~~~~-~g~------------~~~~vp~~~~~~-----~d~~~l---~-~~ 132 (336)
+ ...+. +|+...-+|-+....+.. .+. .+..+|..+... ...+.+ . +.
T Consensus 94 klAr~y~~~~~~tgr~~ii~~~~~yHG~t~~~~s~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 173 (339)
T PF00202_consen 94 KLARQYHKKRGYTGRSKIISFEGSYHGRTLGALSVTGNPGYRKPFGPLLPGVIFVPFPDLYADEEEQACLEYLEELIAAL 173 (339)
T ss_dssp HHHHHHHHHHHHTT--EEEEECT------HHHCTTTTSHHHHGCCSSSSS-EEEEETTEHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHCCCCCCCCCCEEEEECCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99866400247888747999368657787461565578755566545676530013797134567888899999999974
Q ss_pred CCHH-HHHHHCCC-CCCCCCCCHH----HHHHHHHHCCCCC-CCCCCCCCCCCCC----CHHHHCCCHHHHHHHHHHHCC
Q ss_conf 0024-31330366-3322222379----9999997378720-2521002588662----003324520012023465233
Q T0636 133 SRDD-CVVLANPS-NPTGQALSAG----ELDQLRQRAGKLL-IDETYVDYSSFRA----RGLAYGENELVFRSFSKSYGL 201 (336)
Q Consensus 133 ~~~~-~i~l~nPn-NPTG~~~~~~----~l~~l~~~~~~~I-vDeaY~~f~~~~~----~~l~~~~n~iv~~S~SK~~gl 201 (336)
...+ +.+|.-|= ...|.....+ .+.+++++++.++ +||+...|+..-. ......|+++ +|||..|
T Consensus 174 ~~~~iAAviiEPiqg~gG~~~~~~~yl~~lr~lc~~~g~llI~DEV~tG~GRtG~~~a~~~~gv~PDiv---~~gK~l~- 249 (339)
T PF00202_consen 174 GPDDIAAVIIEPIQGEGGVIPPPPGYLQALRELCREHGILLIFDEVQTGFGRTGKMFAFEHFGVEPDIV---TFGKGLG- 249 (339)
T ss_dssp CCTTEEEEEEESEE-----EEB-HHHHHHHHHHHHHTT-EEEEE-S------SSTTSGGGGGT--SSEE---EE-TTT--
T ss_pred CCCCEEEEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCHHHCCCCCCHHH---HHHHHCC-
T ss_conf 799789999940124689626898999858987356727999976886765767862200248711499---9876426-
Q ss_pred CCCCCEEECCCHHHHHHHHHCC--CCCCCCHHHHHHHHHHHHH
Q ss_conf 4345313117889999997337--8778777789999999745
Q T0636 202 AGLRLGALFGPSELIAAMKRKQ--WFCNVGTLDLHALEAALDN 242 (336)
Q Consensus 202 ~GlRiG~~i~~~~~i~~l~~~~--~~~~~~~~~~~aa~~~l~~ 242 (336)
.|+-+|.+++.+++.+.+.... .+|+-|.++..++.+.|+.
T Consensus 250 gG~P~sav~~~~~i~~~~~~~~~~~T~~gnpl~~aaa~a~L~~ 292 (339)
T PF00202_consen 250 GGLPISAVVGREEIMDAFDPGSHGSTFGGNPLACAAALATLDI 292 (339)
T ss_dssp E-EEEEEEEEEHHHHTTCTTTSS--TTTT-HHHHHHHHHHHHH
T ss_pred CCCEEEEEECCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 8613422440488887751488666467896999889999999
No 11
>PF02347 GDC-P: Glycine cleavage system P-protein; InterPro: IPR003437 This family consists of glycine cleavage system P-proteins (1.4.4.2 from EC) from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex (2.1.2.10 from EC (GDC) also annotated as glycine cleavage system or glycine synthase. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. GDC consists of four proteins P, H, L and T . The reaction catalysed by this protein is: Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2 ; GO: 0004375 glycine dehydrogenase (decarboxylating) activity, 0006544 glycine metabolic process, 0005961 glycine dehydrogenase complex (decarboxylating); PDB: 1wyv_A 1wyu_E 1wyt_C.
Probab=98.77 E-value=2.5e-07 Score=63.92 Aligned_cols=285 Identities=17% Similarity=0.193 Sum_probs=148.4
Q ss_pred CHHHHHHHHHHHHHHHCC-CC-----CCHH----HHHHHHHHHHCCCHHHEEEECCH---HHHHHHHHHHHCCC--CEEE
Q ss_conf 689999999998750058-89-----8618----99999999848885438860778---89999999984699--2576
Q T0636 30 EPRVQAAIAAAAARINRY-PF-----DAEP----RVMRKLAEHFSCPEDNLMLVRGI---DECFDRISAEFSSM--RFVT 94 (336)
Q Consensus 30 ~~~v~~al~~~~~~~~~Y-pd-----~~~~----~Lr~aia~~~~v~~d~I~~t~Gs---~~~i~~~~~~~~~~--~vii 94 (336)
|+.+.+.+.+...-+..| |- .|.. ++-..|++..|.+.-+.-+-.|+ -|++.++.+...+. ++++
T Consensus 80 P~~i~~~i~~~~ef~TaytPYQpEisQG~Lq~l~e~Qt~i~eLTGmdvanaSl~d~atA~aEa~~ma~r~~~~~~~kvlv 159 (429)
T PF02347_consen 80 PAVIDRNILSRPEFYTAYTPYQPEISQGRLQALFEYQTMICELTGMDVANASLYDGATAAAEAMLMAVRITRRKRNKVLV 159 (429)
T ss_dssp -HHHHH-HHCHHHTTTS-STTSGGGB---HHHHHHHHHHHHHH----EE-SB-----HHHH---HHHHHHH-----EEEE
T ss_pred CHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 77772243346210015799994788999999999999999976978557788860679999999999983788738997
Q ss_pred CCCCCHHHHH----HHHHHCCCEEEECCCCCCCCCHHHHHHHCCHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 3887356999----999818803641554356778899973000243133036633222223799999997378720252
Q T0636 95 AWPGFDGYRA----RIAVSGLRHFEIGLTDDLLLDPNDLAQVSRDDCVVLANPSNPTGQALSAGELDQLRQRAGKLLIDE 170 (336)
Q Consensus 95 ~~P~y~~y~~----~~~~~g~~~~~vp~~~~~~~d~~~l~~~~~~~~i~l~nPnNPTG~~~~~~~l~~l~~~~~~~IvDe 170 (336)
+.-..+.+.. .++..|.+++.++.+++...| ..++.++++.|||. .|.+-+.+++.++++.++-+++-.
T Consensus 160 ~~~~hp~~~~v~~t~a~~~g~~iv~~~~~~~~~~d------~~~~a~v~vq~Pn~-~G~~ed~~~i~~~~h~~gal~~~~ 232 (429)
T PF02347_consen 160 PDSVHPQNRAVLRTYAEGAGIEIVTVPLDDDGMDD------DDDTAAVMVQYPNT-FGVFEDIEEIAEIAHEAGALVYVG 232 (429)
T ss_dssp ETT--HHHHHHHHHHHHHEEEEEEEE------------------EEEEEEESS--------THHHHHHHHHH---EEEEE
T ss_pred CCCCCCCCHHHHHHHEEECCCEEEEECCCCCCCCC------CCCEEEEEEECCCC-CEEEEEHHHHHHHHHHCCCEEEEE
T ss_conf 68889888999984045068189997630147776------63748998746998-747801999999999859999999
Q ss_pred CCC-CCCCCCCCHHHHCCCHHHHHHHHHHHCCC----CCCCEEECCCHHHH----------------------------H
Q ss_conf 100-25886620033245200120234652334----34531311788999----------------------------9
Q T0636 171 TYV-DYSSFRARGLAYGENELVFRSFSKSYGLA----GLRLGALFGPSELI----------------------------A 217 (336)
Q Consensus 171 aY~-~f~~~~~~~l~~~~n~iv~~S~SK~~gl~----GlRiG~~i~~~~~i----------------------------~ 217 (336)
+.. -.+....+. ...-+++ +++ +|.||+| |=-.|++...++++ +
T Consensus 233 an~~Al~~l~~Pg-e~GADI~-vg~-~Q~fgiP~g~GGP~~G~~a~~~~l~r~lPGRiVG~t~D~~G~~~~~LtLqtREQ 309 (429)
T PF02347_consen 233 ANPNALGGLKSPG-EMGADIA-VGE-HQTFGIPHGFGGPGAGFFAVRKELVRQLPGRIVGVTKDADGKRAYRLTLQTREQ 309 (429)
T ss_dssp --CCCT--B----------EE-E-T-TTTT-------------BEE-GGGGGGS-S-EEEB--BE------EEE-GGGTC
T ss_pred ECHHHHCCCCCHH-HCCCCEE-EEC-CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCCC
T ss_conf 5878870878831-1676679-407-987776767888760167658988866898845531136677136753256765
Q ss_pred HHHHCCCCCCCCH---H-HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCC--CEEEEECCCHHH--
Q ss_conf 9973378778777---7-89999999-7459999999999999999999999858978616986--478865698899--
Q T0636 218 AMKRKQWFCNVGT---L-DLHALEAA-LDNDRAREAHIAKTLAQRRRVADALRGLGYRVASSEA--NFVLVENAAGER-- 288 (336)
Q Consensus 218 ~l~~~~~~~~~~~---~-~~~aa~~~-l~~~~~~~~~~~~~~~~r~~l~~~l~~lg~~~~~s~~--~Fi~~~~~~~~~-- 288 (336)
.+++-+...|+.+ + +..++..+ +..++=+.+.-+.......++.+.|+++.-..+++.. .|+.....+ ..
T Consensus 310 hIrReKAtSNIctnqaL~A~~A~~Y~~~~Gp~GL~~iA~~~~~~A~yl~~~L~~~~~~~~~~~~f~e~v~~~~~~-~~~~ 388 (429)
T PF02347_consen 310 HIRREKATSNICTNQALLALAAAMYASYHGPEGLKEIAERIHLNANYLAKRLKEIFGLPFPGPFFFEFVTVFPKD-KKVE 388 (429)
T ss_dssp HHHGGCSS----S--HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHCC--BECTS-SS-SSEEEEESS--HHHH
T ss_pred CCHHCCCEECCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCC-HHHH
T ss_conf 210000000024418999999999999879789999999999999999999887538666797811144212873-6699
Q ss_pred -HHHHHHHCCCEEEECCCCCCCCEEEEEEC---CHHHHHHHHHHH
Q ss_conf -99999876938960778888874788747---989999999999
Q T0636 289 -TLRFLRERGIQVKDAGQFGLHHHIRISIG---REEDNDRLLAAL 329 (336)
Q Consensus 289 -~~~~L~~~gi~vr~~~~fg~~~~iRis~~---~~ee~~~l~~aL 329 (336)
+.+.+.+.|+-.+ +-..+.+-+|+. |++|+++|+++|
T Consensus 389 ~l~~~~~~~gl~~~----~~~~~~~~i~~tE~~t~~~id~l~~~~ 429 (429)
T PF02347_consen 389 ELLKRGIAGGLNLR----YPDDGALLICVTETRTKEDIDALVQAF 429 (429)
T ss_dssp HHHH------EEET----T----EEEEE--TT--HHHHHHHHH--
T ss_pred HHHHHHHHCCCCCC----CCCCCEEEEEECCCCCHHHHHHHHHCC
T ss_conf 99999996698754----058997999834799999999998539
No 12
>PF00282 Pyridoxal_deC: Pyridoxal-dependent decarboxylase conserved domain; InterPro: IPR002129 Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy . PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic . A number of pyridoxal-dependent decarboxylases share regions of sequence similarity, particularly in the vicinity of a conserved lysine residue, which provides the attachment site for the pyridoxal-phosphate (PLP) group , . Among these enzymes are aromatic-L-amino-acid decarboxylase (L-dopa decarboxylase or tryptophan decarboxylase), which catalyses the decarboxylation of tryptophan to tryptamine ; tyrosine decarboxylase, which converts tyrosine into tyramine; and histidine decarboxylase, which catalyses the decarboxylation of histidine to histamine . These enzymes belong to the group II decarboxylases , .; GO: 0016831 carboxy-lyase activity, 0030170 pyridoxal phosphate binding, 0019752 carboxylic acid metabolic process; PDB: 2qma_B 2okk_A 1es0_B 2okj_A 2jis_B 1xey_B 2dgk_D 1pmm_F 3fz6_E 2dgl_C ....
Probab=98.27 E-value=0.00011 Score=46.77 Aligned_cols=223 Identities=17% Similarity=0.143 Sum_probs=126.0
Q ss_pred HHHHHHHHHCCCHHH-------EEEECCHHHHHHHHHHHH----------CC----C--CEEECC-CCCHHHHHHHHHHC
Q ss_conf 999999984888543-------886077889999999984----------69----9--257638-87356999999818
Q T0636 55 VMRKLAEHFSCPEDN-------LMLVRGIDECFDRISAEF----------SS----M--RFVTAW-PGFDGYRARIAVSG 110 (336)
Q Consensus 55 Lr~aia~~~~v~~d~-------I~~t~Gs~~~i~~~~~~~----------~~----~--~vii~~-P~y~~y~~~~~~~g 110 (336)
..+.+++.+|.+.+. =++|+|++++.-..+.+. .+ . .+++.+ .-| ....++...|
T Consensus 84 vi~wl~~l~g~~~~~~~~~~~~G~~tsGgs~anl~al~aAR~~~~~~~~~~~~~~~~~~~i~~s~~aH~-s~~Kaa~~lG 162 (373)
T PF00282_consen 84 VIDWLAELLGLPASFYDSGEAGGIFTSGGSEANLTALLAARDRALPRVKAEGVREIGRPVIYCSEQAHY-SIKKAARILG 162 (373)
T ss_dssp HHHHHHHHTT--GGG-TTTT-B--EE--HHHHHHHHHHHHHHHHHHHHHCH-TTTSSSEEEEEETTS-T-HHHHHHHHTT
T ss_pred HHHHHHHHHCCCCCCCCCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECHHHH-HHHHHHHHCC
T ss_conf 999999995897420025788428835538999999999999986654214665567605876212147-9999998579
Q ss_pred CCEEEECCCCCCCCCHHHHHHHCC---HH-----HHHHHCCCCCCCCCCCHHHHHHHHHHCCCCC-CCCCCCCC---CCC
Q ss_conf 803641554356778899973000---24-----3133036633222223799999997378720-25210025---886
Q T0636 111 LRHFEIGLTDDLLLDPNDLAQVSR---DD-----CVVLANPSNPTGQALSAGELDQLRQRAGKLL-IDETYVDY---SSF 178 (336)
Q Consensus 111 ~~~~~vp~~~~~~~d~~~l~~~~~---~~-----~i~l~nPnNPTG~~~~~~~l~~l~~~~~~~I-vDeaY~~f---~~~ 178 (336)
..++.||.++++++|++++++..+ .+ +|+.+-..-.||.+=+.++|.+++++++.++ ||-||..+ +++
T Consensus 163 lgv~~Vp~d~~~~md~~~L~~~i~~~~~~G~~p~~VvataGtT~~GaiD~l~~i~~i~~~~~~wlHVDaA~GG~~~~~~~ 242 (373)
T PF00282_consen 163 LGVRVVPTDENGRMDVDALEKAIEEDRAAGKTPFAVVATAGTTNTGAIDPLEEIADICRKYNLWLHVDAAYGGSALLSPF 242 (373)
T ss_dssp -EEEEE-B-TTSSB-HHHHHHHHHHHHHT--EEEEEEEE---TTT-----HHHHHHHHHHHT-EEEEEES----GGGHTT
T ss_pred CCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCEEEECHHHHHHHHCCC
T ss_conf 73289323866573899999998873025665358885268866553200999988986369756862354552443023
Q ss_pred CCCHHHHCCCH-HHHHHHHHHHCCCCCCCEEECC-CHHHHH-HHHH----CC----------CC--CCC--CH-HHHHHH
Q ss_conf 62003324520-0120234652334345313117-889999-9973----37----------87--787--77-789999
Q T0636 179 RARGLAYGENE-LVFRSFSKSYGLAGLRLGALFG-PSELIA-AMKR----KQ----------WF--CNV--GT-LDLHAL 236 (336)
Q Consensus 179 ~~~~l~~~~n~-iv~~S~SK~~gl~GlRiG~~i~-~~~~i~-~l~~----~~----------~~--~~~--~~-~~~~aa 236 (336)
....+..-+.. -+.-.+-|..+.| .-+|+++. +++... .+.. +. .. +++ +. ......
T Consensus 243 ~r~~~~gle~aDSit~d~HK~l~~p-~~~~~ll~r~~~~l~~~~~~~a~Yl~~~~~~~~~~~d~~~~tl~~sR~~~alk~ 321 (373)
T PF00282_consen 243 YRHLLFGLERADSITIDPHKWLYVP-YGCGVLLVRDKELLRSAFSINADYLFHPDRESDDSYDYGDWTLEGSRRFRALKL 321 (373)
T ss_dssp TGGGGTTSTTESEEEE-TTSTTS---SS-EEEEESSGGGHHGGG-EEBTTSS-S-SSS-GGGSBCCTSS--S-B-CHHHH
T ss_pred CCHHHCCCCCCEEEEECHHHHCCCC-CCCEEEEECCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf 1011048744405888828845666-146577744777777765269230257410044777736756899832379999
Q ss_pred HHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHCC-CEEE-CCCCCEE
Q ss_conf 99974--599999999999999999999998589-7861-6986478
Q T0636 237 EAALD--NDRAREAHIAKTLAQRRRVADALRGLG-YRVA-SSEANFV 279 (336)
Q Consensus 237 ~~~l~--~~~~~~~~~~~~~~~r~~l~~~l~~lg-~~~~-~s~~~Fi 279 (336)
...|+ ..+-+.+.+++..+..+++.+.+++.+ +.+. +++-+-+
T Consensus 322 W~~l~~~G~~g~~~~i~~~~~~A~~~~~~i~~~~~~el~~~~~l~~V 368 (373)
T PF00282_consen 322 WASLRSLGREGYREMIERCIELARYFAELIRASPDFELVNPPELNIV 368 (373)
T ss_dssp HHHHHH------HHHHHHHHHHHHHHHHHHHTTTTEEESST-SSSEE
T ss_pred HHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCEEE
T ss_conf 99999968998999999999999999999974889799758983189
No 13
>PF05889 SLA_LP_auto_ag: Soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen); InterPro: IPR008829 This family consists of several eukaryotic and archaeal proteins which are related to the Homo sapiens soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis . The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway . The archaeal sequences Q8TXK0 from SWISSPROT and Q8TYR3 from SWISSPROT are annotated as being pyridoxal phosphate-dependent enzymes.; PDB: 2e7j_B 2e7i_B 2z67_B 3bcb_A 3bc8_A 3bca_A.
Probab=97.68 E-value=0.0017 Score=39.15 Aligned_cols=268 Identities=15% Similarity=0.112 Sum_probs=136.4
Q ss_pred HHCCC-HHHEEEECCHHH-HHHHHHHHHC----CCCEEECC-CCCHHHHHHHHHHCCCEEEECC--CCC-CCCCHHHHHH
Q ss_conf 84888-543886077889-9999999846----99257638-8735699999981880364155--435-6778899973
Q T0636 62 HFSCP-EDNLMLVRGIDE-CFDRISAEFS----SMRFVTAW-PGFDGYRARIAVSGLRHFEIGL--TDD-LLLDPNDLAQ 131 (336)
Q Consensus 62 ~~~v~-~d~I~~t~Gs~~-~i~~~~~~~~----~~~vii~~-P~y~~y~~~~~~~g~~~~~vp~--~~~-~~~d~~~l~~ 131 (336)
..|++ ....++.+-++. .|.++++++. ++-|+.+. =-|..|. ++...|.+++.+|. ..| ...|.+++++
T Consensus 68 ~~G~~~~~~~~~vP~aTGm~l~l~l~a~~~~~~a~~ViwsridqkSc~k-ai~~AGl~~~vV~~~~~~d~l~td~~~ie~ 146 (389)
T PF05889_consen 68 IAGLRSCKSCFVVPMATGMSLTLCLLALRKRPKADYVIWSRIDQKSCFK-AIERAGLEPVVVPTVLEGDELITDEEAIEK 146 (389)
T ss_dssp H---CCHC-EECHSS----HHHHHHHHHHHHCC--EEEEEEEETHHHHH-HHHH---EEEEE-BEETTT-EE-HHHHHHH
T ss_pred HCCCCCCCEEEEEECCCCCHHHHHHHHHHCCCCCCEEEEECCCCCCHHH-HHHHCCCEEEEEECCCCCCCCCCCHHHHHH
T ss_conf 7498510306884033423299999997435788679995036520689-999669727996535678700585899999
Q ss_pred HCCH-----HHHHHHCCCCCCCCCCC-HHHHHHHHHHCC-CCCCCCCCCCCCCCCCCHHHH---CCCH-HHHHHHHHHHC
Q ss_conf 0002-----43133036633222223-799999997378-720252100258866200332---4520-01202346523
Q T0636 132 VSRD-----DCVVLANPSNPTGQALS-AGELDQLRQRAG-KLLIDETYVDYSSFRARGLAY---GENE-LVFRSFSKSYG 200 (336)
Q Consensus 132 ~~~~-----~~i~l~nPnNPTG~~~~-~~~l~~l~~~~~-~~IvDeaY~~f~~~~~~~l~~---~~n~-iv~~S~SK~~g 200 (336)
..+. .+++++.+.---+..-+ .++|.++|++.+ ..|+..||.==.......+.. ..++ +++.|.-|.|=
T Consensus 147 ~ie~~g~~~ilcvltttscfapr~~D~i~~Iaklc~~~~IPhlvNnAYgvQ~~~~~~~l~~a~~~GRvD~~vqStDKNFl 226 (389)
T PF05889_consen 147 AIEELGADNILCVLTTTSCFAPRNPDDIEEIAKLCKEYDIPHLVNNAYGVQSSYIMHLLEKAWRVGRVDAVVQSTDKNFL 226 (389)
T ss_dssp HHHHCH-TCEEEEEEESS--TTB----HHHHHHHHHHHT--EEEE---TTT-HHHHHHHHHHTTS---SEEECTHHHHHC
T ss_pred HHHHHCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCCEEECCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEE
T ss_conf 99972888768999804765888874199999999981997697251111259899999876441322237873598868
Q ss_pred CCCCCCE--EEC-CCHHHHHHHHHCCCCCCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHCCCEE
Q ss_conf 3434531--311-78899999973378778777789999--9997459999999999999999999999----8589786
Q T0636 201 LAGLRLG--ALF-GPSELIAAMKRKQWFCNVGTLDLHAL--EAALDNDRAREAHIAKTLAQRRRVADAL----RGLGYRV 271 (336)
Q Consensus 201 l~GlRiG--~~i-~~~~~i~~l~~~~~~~~~~~~~~~aa--~~~l~~~~~~~~~~~~~~~~r~~l~~~l----~~lg~~~ 271 (336)
.| +| -+. .++..++.+.+....=-..++..... +-.|.... +...+....+...++.+.| ++.|.++
T Consensus 227 Vp---vGgai~as~~~~~v~~is~~YpgRas~s~~ld~fitLlsLG~tg-~~~ll~~r~~~f~~l~erl~~~a~e~~e~l 302 (389)
T PF05889_consen 227 VP---VGGAIMASSDPSGVLAISKEYPGRASRSPILDLFITLLSLGCTG-YGALLKERMASFPYLKERLKKWAEEVGERL 302 (389)
T ss_dssp ---------CEEES-HHHHHHHCCCGHHHHTSHHHHHHHHHHHH---HH-HHHHHHHHHHHHHHHHHHHHHHHHHCCEEB
T ss_pred EE---CCCCEEEECCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCHH
T ss_conf 20---49838882587899999866799541565079999999860556-778999999999999999999999860314
Q ss_pred ECCCCCEEEEE--CC--------CHHHHHHHHHHCCCE----EEECCCCC---C----CCEEEE-E-EC-CHHHHHHHHH
Q ss_conf 16986478865--69--------889999999876938----96077888---8----874788-7-47-9899999999
Q T0636 272 ASSEANFVLVE--NA--------AGERTLRFLRERGIQ----VKDAGQFG---L----HHHIRI-S-IG-REEDNDRLLA 327 (336)
Q Consensus 272 ~~s~~~Fi~~~--~~--------~~~~~~~~L~~~gi~----vr~~~~fg---~----~~~iRi-s-~~-~~ee~~~l~~ 327 (336)
...--|.+.+. ++ +...+...|..+||. |.+...+. . -.|+-+ | +| +.||++.+++
T Consensus 303 ~~~p~N~is~aitl~~l~~~~~k~~~~lgs~L~~RgVsG~RvV~~~~~~~ts~~~~~~~~Yl~~asaiG~t~eevd~~~~ 382 (389)
T PF05889_consen 303 LETPRNHISIAITLPTLDEISQKDITFLGSMLFSRGVSGIRVVTPTWKKQTSHLDEYPVPYLTAASAIGLTREEVDYFVD 382 (389)
T ss_dssp ---TT-SSEEEEE-CCCHHHCCSHHHHHHHHHHHTTEE--E-EETT---EESSSS--SSSEEEEEE-----HHHHHHHHH
T ss_pred HCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHH
T ss_conf 31578972689965654323211088999999748875551104688855346777773166888880898999999999
Q ss_pred HHHHHHH
Q ss_conf 9999984
Q T0636 328 ALAEYSD 334 (336)
Q Consensus 328 aL~~~~e 334 (336)
.|++..+
T Consensus 383 ~l~k~~~ 389 (389)
T PF05889_consen 383 RLDKILK 389 (389)
T ss_dssp HHHHHHH
T ss_pred HHHHHHC
T ss_conf 9988649
No 14
>PF03841 SelA: L-seryl-tRNA selenium transferase; InterPro: IPR004534 In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This family describes SelA. A close homolog of SelA is found in Helicobacter pylori, but all other required elements are missing and the protein is shorter at the N-terminus than SelA from other species. The trusted cut-off is set above the score generated for Helicobacter pyloriputative SelA.; GO: 0004125 L-seryl-tRNASec selenium transferase activity, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2aeu_A 2aev_A.
Probab=97.46 E-value=1.7e-05 Score=52.06 Aligned_cols=203 Identities=23% Similarity=0.251 Sum_probs=113.9
Q ss_pred CCHHHHHHHHHHHHHHHCCCC---------CC--HHHHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHHC-CCCEEECC
Q ss_conf 768999999999875005889---------86--1899999999848885438860778899999999846-99257638
Q T0636 29 VEPRVQAAIAAAAARINRYPF---------DA--EPRVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEFS-SMRFVTAW 96 (336)
Q Consensus 29 p~~~v~~al~~~~~~~~~Ypd---------~~--~~~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~~-~~~vii~~ 96 (336)
.++.+.+++.+.... |.+ .| +..+.+.++...|. +..+++|....++.+++.++. +.+|++.-
T Consensus 18 ls~~a~~a~~~~~~~---y~nLE~dL~~G~RG~R~~~v~~ll~~ltgA--EaA~VVNNNAAAV~L~L~~la~~kEVIVSR 92 (367)
T PF03841_consen 18 LSEEAIDAVKEVASG---YSNLEYDLETGKRGSRYSHVEELLCELTGA--EAALVVNNNAAAVLLALNTLAAGKEVIVSR 92 (367)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 222222222222222---222222222222222222222222222222--222222222222222222222222222222
Q ss_pred C---CCH---HHHHHHHHHCCCEEEECCCCCCCCCHHHHHH--HCCHHHHHHHCCCCCCCC----CCCHHHHHHHHHHCC
Q ss_conf 8---735---6999999818803641554356778899973--000243133036633222----223799999997378
Q T0636 97 P---GFD---GYRARIAVSGLRHFEIGLTDDLLLDPNDLAQ--VSRDDCVVLANPSNPTGQ----ALSAGELDQLRQRAG 164 (336)
Q Consensus 97 P---~y~---~y~~~~~~~g~~~~~vp~~~~~~~d~~~l~~--~~~~~~i~l~nPnNPTG~----~~~~~~l~~l~~~~~ 164 (336)
= .+. ......+..|.++++|-.++.- .+.+++. .++|.+++-..+.|-.-. -.+.+++.+++++++
T Consensus 93 GelVeiGg~FRIpdvm~~sGa~LvEVGtTN~T--~~~Dye~AI~e~Ta~llkVh~Sn~~i~GFt~~~~~~el~~la~~~~ 170 (367)
T PF03841_consen 93 GELVEIGGSFRIPDVMRQSGAKLVEVGTTNRT--HLRDYENAINENTAALLKVHTSNFRIQGFTEEVSLEELAELAKEHG 170 (367)
T ss_dssp ----------------------------------------------------------------------HHHHHHHHHT
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf 22222222222222222222222222222222--2222222222222222222222222222234447999999986659
Q ss_pred -CCCCCCCC---CCCC-----CCCCC--HHHHCCCHHHHHHHHHHHCCCCCCCEEECCCHHHHHHHHHCCC--CCCCCHH
Q ss_conf -72025210---0258-----86620--0332452001202346523343453131178899999973378--7787777
Q T0636 165 -KLLIDETY---VDYS-----SFRAR--GLAYGENELVFRSFSKSYGLAGLRLGALFGPSELIAAMKRKQW--FCNVGTL 231 (336)
Q Consensus 165 -~~IvDeaY---~~f~-----~~~~~--~l~~~~n~iv~~S~SK~~gl~GlRiG~~i~~~~~i~~l~~~~~--~~~~~~~ 231 (336)
.+++|-.- .|+. +++.. .+....+ +|+.|=.|.+| |-..|.+++.+++|+++++-.. .+-+..+
T Consensus 171 ip~i~DlgSG~l~dl~~~gl~~Ep~v~~~l~~GaD-lV~fSGdKlLg--GPQAGiI~Gkk~lI~~lk~~~l~RalrvdK~ 247 (367)
T PF03841_consen 171 IPVIVDLGSGSLVDLSKYGLPDEPTVQEALAAGAD-LVTFSGDKLLG--GPQAGIIVGKKELIEKLKKHPLGRALRVDKE 247 (367)
T ss_dssp --EEEE------HHHHTT----------CCC-----EEE--TTSS----------EE--HHHHHHHHH----------HH
T ss_pred CCEEEECCCCCCCCCCCCCCCCHHHHHHHHHCCCC-EEEEECCEECC--CCCCEEEEEHHHHHHHHHHCCCCEEEECCHH
T ss_conf 98899899986547751246302559999977999-89988998178--9983699513999999977787640047999
Q ss_pred HHHHHHHHHH
Q ss_conf 8999999974
Q T0636 232 DLHALEAALD 241 (336)
Q Consensus 232 ~~~aa~~~l~ 241 (336)
+..+..+.|+
T Consensus 248 tlaaL~atL~ 257 (367)
T PF03841_consen 248 TLAALEATLR 257 (367)
T ss_dssp HH---HHHHH
T ss_pred HHHHHHHHHH
T ss_conf 9999999999
No 15
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1ywx_A 1xn9_A 2v94_B 2g1d_A.
Probab=57.14 E-value=3.2 Score=17.87 Aligned_cols=24 Identities=17% Similarity=0.303 Sum_probs=17.3
Q ss_pred CCHHHHHHHHHHHHCCCHHHEEEE
Q ss_conf 861899999999848885438860
Q T0636 50 DAEPRVMRKLAEHFSCPEDNLMLV 73 (336)
Q Consensus 50 ~~~~~Lr~aia~~~~v~~d~I~~t 73 (336)
+.-.++|+.||+.|++++|.|++.
T Consensus 13 psr~eirekLA~~~~~~~~~vvv~ 36 (84)
T PF01282_consen 13 PSRKEIREKLAAMYKVDPDLVVVF 36 (84)
T ss_dssp --HHHHHHHHHHHHTS-STTEEEE
T ss_pred CCHHHHHHHHHHHHCCCCCEEEEE
T ss_conf 899999999999978995859983
No 16
>PF03786 UxuA: D-mannonate dehydratase (UxuA); InterPro: IPR004628 This Fe2+-requiring enzyme plays a role in D-glucuronate catabolism in Escherichia coli. Mannonate dehydratase converts D-mannonate to 2-dehydro-3-deoxy-D-gluconate. An apparent equivalog is found in a glucuronate utilization operon in Bacillus stearothermophilus T-6.; GO: 0008927 mannonate dehydratase activity, 0006064 glucuronate catabolic process; PDB: 3dbn_A 3bdk_B 3ban_A 1tz9_A.
Probab=42.36 E-value=5.8 Score=16.19 Aligned_cols=14 Identities=7% Similarity=0.003 Sum_probs=6.5
Q ss_pred ECCCHHHHHHHHHC
Q ss_conf 11788999999733
Q T0636 209 LFGPSELIAAMKRK 222 (336)
Q Consensus 209 ~i~~~~~i~~l~~~ 222 (336)
++++.+-++++-+.
T Consensus 219 Iv~~~ed~~~~l~~ 232 (351)
T PF03786_consen 219 IVSTEEDYQRLLDL 232 (351)
T ss_dssp -TTSHHHHHHHHHC
T ss_pred EECCHHHHHHHHHH
T ss_conf 40799999999974
No 17
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue . Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Sinorhizobium meliloti protein mosA , which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry . Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3e96_B 3d0c_A 3dz1_A 3eb2_C 2r8w_A 2v9d_C 2v8z_B 1nal_3 1fdy_B 1fdz_B ....
Probab=35.97 E-value=9.3 Score=14.89 Aligned_cols=22 Identities=32% Similarity=0.442 Sum_probs=17.1
Q ss_pred CCC--CCCCCCHHHHHHHHHHCCCC
Q ss_conf 633--22222379999999737872
Q T0636 144 SNP--TGQALSAGELDQLRQRAGKL 166 (336)
Q Consensus 144 nNP--TG~~~~~~~l~~l~~~~~~~ 166 (336)
||| ||..++.+.+.+|++ ++-+
T Consensus 134 n~P~~~g~~ls~~~~~~L~~-~p~v 157 (289)
T PF00701_consen 134 NIPSRTGVDLSPETLARLAE-HPNV 157 (289)
T ss_dssp E-TTTHSSTS-HHHHHHHHT-STTB
T ss_pred ECCCCCCCCCCHHHHHHHHC-CCCE
T ss_conf 78866542788999999718-8988
No 18
>PF07021 MetW: Methionine biosynthesis protein MetW; InterPro: IPR010743 This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, Gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In Pseudomonas putida, as in Gram-positive bacteria and certain fungi, the second and third steps are a direct sulphydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells .
Probab=32.47 E-value=11 Score=14.53 Aligned_cols=158 Identities=13% Similarity=0.175 Sum_probs=80.0
Q ss_pred HHHHHHHCCCCCCEECCCCCCCCCCCHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHCC-----C------HH---H
Q ss_conf 57897503665535735765488876899999999987500588-98618999999998488-----8------54---3
Q T0636 5 EAMDTEVRAAAQAVCLAFNENPEAVEPRVQAAIAAAAARINRYP-FDAEPRVMRKLAEHFSC-----P------ED---N 69 (336)
Q Consensus 5 ~~~~~~~~~~~~~i~L~~Nenp~~p~~~v~~al~~~~~~~~~Yp-d~~~~~Lr~aia~~~~v-----~------~d---~ 69 (336)
..+.+..+++++++||.-+. | ...+.+++. .....|. +-.......++++-+.| + +| .
T Consensus 5 ~~I~~~I~pgsrVLDlGCG~---G---~LL~~L~~~-k~~~~~GIEid~~~v~~~~~~Gl~Vi~~die~~l~~f~d~~FD 77 (193)
T PF07021_consen 5 EIIAEWIPPGSRVLDLGCGD---G---ELLAYLKEE-KGVRGYGIEIDEENVAACIARGLNVIQGDIEEGLSDFPDQSFD 77 (193)
T ss_pred HHHHHHCCCCCEEEEECCCC---C---HHHHHHHHH-CCCCEEEEECCHHHHHHHHHCCCEEEEECHHHHHHHCCCCCCC
T ss_conf 99998638999478748999---7---899999984-5982899963999999999869959992577878648888888
Q ss_pred EEEECCHHHHHHH---HHHH-H-CCCCEEECCCCCHHHHHHHHHH--CCCEEEECCCCCCCCCHHHHHHHCCHHHHHHHC
Q ss_conf 8860778899999---9998-4-6992576388735699999981--880364155435677889997300024313303
Q T0636 70 LMLVRGIDECFDR---ISAE-F-SSMRFVTAWPGFDGYRARIAVS--GLRHFEIGLTDDLLLDPNDLAQVSRDDCVVLAN 142 (336)
Q Consensus 70 I~~t~Gs~~~i~~---~~~~-~-~~~~vii~~P~y~~y~~~~~~~--g~~~~~vp~~~~~~~d~~~l~~~~~~~~i~l~n 142 (336)
.++-+-+-|.+.. ++.. + .|.++++..|.|..+.....+. |.-.+.--+...| ..+
T Consensus 78 ~VIlsqtLqh~~~P~~vL~emLrvg~~~IVsfPNf~~w~~r~~l~~~GrmP~t~~lp~~W-----------------ydT 140 (193)
T PF07021_consen 78 YVILSQTLQHLRNPDKVLREMLRVGREAIVSFPNFGHWRVRLQLLFRGRMPVTEFLPYEW-----------------YDT 140 (193)
T ss_pred EEEEHHHHHHHHHHHHHHHHHHHHCCEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCC-----------------CCC
T ss_conf 997367888365689999999873897999747737899999999669999788888743-----------------489
Q ss_pred CCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCH
Q ss_conf 66332222237999999973787202521002588662003324520
Q T0636 143 PSNPTGQALSAGELDQLRQRAGKLLIDETYVDYSSFRARGLAYGENE 189 (336)
Q Consensus 143 PnNPTG~~~~~~~l~~l~~~~~~~IvDeaY~~f~~~~~~~l~~~~n~ 189 (336)
| -=+.++..+.++|+++.++-|++..+.+-...........||+
T Consensus 141 p---nIh~~T~~DF~~lc~~~~~~i~~~~~~~~~~~~~~~~~~~pNl 184 (193)
T PF07021_consen 141 P---NIHFCTIKDFEELCRELGIRILERVALDGDHRPSWLVRLWPNL 184 (193)
T ss_pred C---CCCCEEHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCCCHH
T ss_conf 9---8030209999999998799899999974888755533236424
No 19
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF)
Probab=29.89 E-value=12 Score=14.25 Aligned_cols=16 Identities=19% Similarity=0.439 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 8999999999999984
Q T0636 319 EEDNDRLLAALAEYSD 334 (336)
Q Consensus 319 ~ee~~~l~~aL~~~~e 334 (336)
.++.+++.+.|.++.+
T Consensus 163 ~~~~~~i~~~la~~~~ 178 (188)
T PF09581_consen 163 SEEEEEIKNFLADFYG 178 (188)
T ss_pred HHHHHHHHHHHHHHHC
T ss_conf 0789999999999959
No 20
>PF05728 UPF0227: Uncharacterised protein family (UPF0227); InterPro: IPR008886 Despite being classed as uncharacterised proteins, the members of this family are almost certainly enzymes in that they contain a domain distantly related to IPR000073 from INTERPRO.
Probab=29.19 E-value=12 Score=14.18 Aligned_cols=112 Identities=17% Similarity=0.195 Sum_probs=53.4
Q ss_pred CCEECC-CCCCCCCCCHHHHHHHHHHHHHH---HCCCCC--C-HHH-HHHHHHHHH-CCCHHHEEEECCHHHHHHHHHHH
Q ss_conf 535735-76548887689999999998750---058898--6-189-999999984-88854388607788999999998
Q T0636 16 QAVCLA-FNENPEAVEPRVQAAIAAAAARI---NRYPFD--A-EPR-VMRKLAEHF-SCPEDNLMLVRGIDECFDRISAE 86 (336)
Q Consensus 16 ~~i~L~-~Nenp~~p~~~v~~al~~~~~~~---~~Ypd~--~-~~~-Lr~aia~~~-~v~~d~I~~t~Gs~~~i~~~~~~ 86 (336)
+++.|+ ||.+|...-. +++.+...+. ..|+++ . .++ ..+.+.+.. ...++++++.-.|-.++.....+
T Consensus 1 ~ilylHGF~Ssp~s~Ka---~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~i~~~~~~~~~LiGSSLGG~~A~~LA 77 (187)
T PF05728_consen 1 MILYLHGFNSSPQSHKA---QALAEYFAEHGPDIEYPDPNLPHFPQQALARLEQLIEQLKDENVVLIGSSLGGYYATYLA 77 (187)
T ss_pred CEEEECCCCCCCCCHHH---HHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHH
T ss_conf 97994587889875789---999999997598628867999978999999999999853778718999786999999999
Q ss_pred H-CCCCEEECCCCCHHHHHHHHHHCCCEEEECCCCCCCCCHHHHHH
Q ss_conf 4-69925763887356999999818803641554356778899973
Q T0636 87 F-SSMRFVTAWPGFDGYRARIAVSGLRHFEIGLTDDLLLDPNDLAQ 131 (336)
Q Consensus 87 ~-~~~~vii~~P~y~~y~~~~~~~g~~~~~vp~~~~~~~d~~~l~~ 131 (336)
. .+-..++.+|.+..+.......|-+... ...++|.++...+.+
T Consensus 78 ~~~~~~aVLinPAv~p~~~l~~~lG~~~~~-~~~e~~~l~~~h~~~ 122 (187)
T PF05728_consen 78 ERYGIKAVLINPAVRPYELLRDYLGEQTNP-YTGEEYELEEYHYAE 122 (187)
T ss_pred HHHCCCEEEECCCCCHHHHHHHHCCCCCCC-CCCCEEEEEHHHHHH
T ss_conf 984999799958878789987741876456-778425774789874
No 21
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon .
Probab=28.96 E-value=12 Score=14.15 Aligned_cols=11 Identities=36% Similarity=0.836 Sum_probs=3.7
Q ss_pred HHHHHCCCHHH
Q ss_conf 99984888543
Q T0636 59 LAEHFSCPEDN 69 (336)
Q Consensus 59 ia~~~~v~~d~ 69 (336)
+|+.++|-|.+
T Consensus 31 LA~~F~CvPSQ 41 (152)
T PF05848_consen 31 LADRFDCVPSQ 41 (152)
T ss_pred HHHHHCCCHHH
T ss_conf 88871867466
No 22
>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 2qh8_A.
Probab=28.42 E-value=12 Score=14.09 Aligned_cols=114 Identities=16% Similarity=0.170 Sum_probs=51.8
Q ss_pred CHHHHHHHHHHHH-CCCHHHEEEECCHHHHHHHHHHHHCC-CCEE---ECCCCCHHHHHHHHHHCCCEEEECCCCCCCCC
Q ss_conf 6189999999984-88854388607788999999998469-9257---63887356999999818803641554356778
Q T0636 51 AEPRVMRKLAEHF-SCPEDNLMLVRGIDECFDRISAEFSS-MRFV---TAWPGFDGYRARIAVSGLRHFEIGLTDDLLLD 125 (336)
Q Consensus 51 ~~~~Lr~aia~~~-~v~~d~I~~t~Gs~~~i~~~~~~~~~-~~vi---i~~P~y~~y~~~~~~~g~~~~~vp~~~~~~~d 125 (336)
+..+...++++.+ .-.+ +++++.|+..+..+. +...+ -.|+ +.+|...++......-|..+..+.....+.-.
T Consensus 43 ~d~~~~~~i~~~l~~~~~-DlIva~gt~aa~~l~-~~~~~~iPIVf~~V~dp~~~glv~s~~~pg~nvTGv~~~~~~~~~ 120 (294)
T PF04392_consen 43 GDPERLAAIARKLVADKP-DLIVAIGTPAAQALA-KAIKDDIPIVFSGVSDPVGAGLVPSLDRPGGNVTGVSEPVPVEKQ 120 (294)
T ss_dssp --HHHHHHHHHHH------SEEE---HHHHHHHH-HH-SS-S-EEEEEES------S-S-SS-----EE-EE----HHHH
T ss_pred CCHHHHHHHHHHHHHCCC-CEEEEECCHHHHHHH-HHHCCCCCEEEEECCCHHHCCCCCCCCCCCCCEEEEEECCCHHHH
T ss_conf 899999999999975699-999991849999999-730788649999716834335665566899988999915789999
Q ss_pred HHHHHHH-CCHH-HHHHHCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf 8999730-0024-3133036633222223799999997378720
Q T0636 126 PNDLAQV-SRDD-CVVLANPSNPTGQALSAGELDQLRQRAGKLL 167 (336)
Q Consensus 126 ~~~l~~~-~~~~-~i~l~nPnNPTG~~~~~~~l~~l~~~~~~~I 167 (336)
++-+.+. ++.| +-++.||+++++. ...+++.+.++..++-+
T Consensus 121 l~ll~~l~P~~k~igvly~~~~~~~~-~~~~~~~~~a~~~gi~l 163 (294)
T PF04392_consen 121 LELLKELLPDAKRIGVLYDPSEPNSV-AQVEELKAAAKELGIEL 163 (294)
T ss_dssp HHHHHHHSTT--EE-EEE----HHHH-HHHHHHHHHHHH---EE
T ss_pred HHHHHHHCCCCCEEEEEECCCCCCHH-HHHHHHHHHHHHCCCEE
T ss_conf 99999868788689999789885469-99999999999869879
No 23
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins of unknown function.
Probab=26.99 E-value=11 Score=14.44 Aligned_cols=79 Identities=19% Similarity=0.238 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHCCCEEECCCCCEE-E---EECCCHH---HHHHHHHHCCCEEEECCCCCCCCE-------EEEEECCHH
Q ss_conf 9999999999858978616986478-8---6569889---999999876938960778888874-------788747989
Q T0636 255 AQRRRVADALRGLGYRVASSEANFV-L---VENAAGE---RTLRFLRERGIQVKDAGQFGLHHH-------IRISIGREE 320 (336)
Q Consensus 255 ~~r~~l~~~l~~lg~~~~~s~~~Fi-~---~~~~~~~---~~~~~L~~~gi~vr~~~~fg~~~~-------iRis~~~~e 320 (336)
.++..+.+.|+..|++..++....- - ...+... .++..+...|+ |+..+.-.+..| -++-..+.+
T Consensus 25 ~el~~Vl~~l~~~Gfk~~~~~~~~~~~~~~~~~~~~~KI~ALw~~l~~~~~-v~~~s~~al~~~vkr~~gv~~l~wl~~~ 103 (119)
T PF06252_consen 25 AELQKVLDHLKAKGFKPRKPAKKPGPRPGMARSAQLRKIRALWIQLGKAGA-VRDRSEAALDAFVKRQFGVDRLRWLDPE 103 (119)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCHHHHCCHH
T ss_conf 999999999997568675433466889888778899999999999775678-6562799999999999685327668999
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99999999999984
Q T0636 321 DNDRLLAALAEYSD 334 (336)
Q Consensus 321 e~~~l~~aL~~~~e 334 (336)
+..+++++|+.|..
T Consensus 104 qa~~vIeaLk~w~~ 117 (119)
T PF06252_consen 104 QASKVIEALKKWQR 117 (119)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 99999999999880
No 24
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation . These sequences contain the C-terminal region of DltD.; PDB: 3bma_C.
Probab=26.83 E-value=4.3 Score=17.04 Aligned_cols=84 Identities=20% Similarity=0.162 Sum_probs=38.6
Q ss_pred CCCCCCCCCHHHHHHHCCHHHHHHHCCCCC-----CCCCCCHHHHH-------HHHHHCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf 554356778899973000243133036633-----22222379999-------999737872025210025886620033
Q T0636 117 GLTDDLLLDPNDLAQVSRDDCVVLANPSNP-----TGQALSAGELD-------QLRQRAGKLLIDETYVDYSSFRARGLA 184 (336)
Q Consensus 117 p~~~~~~~d~~~l~~~~~~~~i~l~nPnNP-----TG~~~~~~~l~-------~l~~~~~~~IvDeaY~~f~~~~~~~l~ 184 (336)
|+-.||++-++.+.+ .+++.++|.-|-|+ || ++.+... ..++.++.=|+ ||+.....+--
T Consensus 33 pEy~DlqllL~~~~~-~~~~vlfIi~PvNgkWydytG--~~~~~r~~~y~kI~~~~~~~Gf~i~-----D~s~~~y~pYf 104 (130)
T PF04914_consen 33 PEYGDLQLLLDQFKE-LGADVLFIIPPVNGKWYDYTG--LSKEMRQQYYKKIKYQLKSQGFNIA-----DLSDDEYEPYF 104 (130)
T ss_dssp THHHHHHHHHHHHHH-TT-EEEEEE----HHHHHH----B-HHHHHHHHHHHHHHHHT----EE-----E-TT----TTS
T ss_pred CCHHHHHHHHHHHHH-CCCCCEEEECCCCCHHHHHHC--CCHHHHHHHHHHHHHHHHHCCCCEE-----ECCCCCCCCCE
T ss_conf 234789999999998-399617985578715888808--8999999999999999998799487-----32136898764
Q ss_pred HCCCHHHHHHHHHHHCCCCCCCEEECCCHHHHHHHH
Q ss_conf 245200120234652334345313117889999997
Q T0636 185 YGENELVFRSFSKSYGLAGLRLGALFGPSELIAAMK 220 (336)
Q Consensus 185 ~~~n~iv~~S~SK~~gl~GlRiG~~i~~~~~i~~l~ 220 (336)
..+ + -..||+ ||+..++.+.+.+.
T Consensus 105 m~D-t----------iHlgw~-GWv~~D~~i~~f~~ 128 (130)
T PF04914_consen 105 MQD-T----------IHLGWK-GWVYVDKAIYPFMK 128 (130)
T ss_dssp -SS-S----------S--------HHHHHHHHHHHH
T ss_pred EEE-C----------CCCCCH-HHHHHHHHHHHHHH
T ss_conf 744-4----------335601-69999999999973
No 25
>PF05127 DUF699: Putative ATPase (DUF699); InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase. This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO.; PDB: 1w36_D 2zpa_B.
Probab=25.21 E-value=10 Score=14.66 Aligned_cols=23 Identities=9% Similarity=-0.024 Sum_probs=16.1
Q ss_pred CC-CEEECCCCCHHHHHHHHHHCC
Q ss_conf 99-257638873569999998188
Q T0636 89 SM-RFVTAWPGFDGYRARIAVSGL 111 (336)
Q Consensus 89 ~~-~vii~~P~y~~y~~~~~~~g~ 111 (336)
+. +|++..|+........+....
T Consensus 25 ~~~~I~vtAPt~~av~~l~~~~~~ 48 (174)
T PF05127_consen 25 GKLRILVTAPTGKAVKTLFEFLIK 48 (174)
T ss_dssp ----EEEEBSS--CHHHHHHC---
T ss_pred HCCEEEEECCCHHHHHHHHHHHHH
T ss_conf 064389966866899999999875
No 26
>PF01974 tRNA_int_endo: tRNA intron endonuclease, catalytic C-terminal domain; InterPro: IPR006677 tRNA-intron endonucleases (3.1.27.9 from EC) cleave pre-tRNA producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron . This entry is for C-terminal domain of tRNA-intron endonuclease. ; GO: 0000213 tRNA-intron endonuclease activity, 0006388 tRNA splicing, 0000214 tRNA-intron endonuclease complex; PDB: 2zyz_A 1a79_A 2ohe_A 2ohc_B 1r11_A 1r0v_A 2gjw_D 1rlv_A 2cv8_B.
Probab=21.81 E-value=15 Score=13.47 Aligned_cols=20 Identities=40% Similarity=0.564 Sum_probs=10.5
Q ss_pred HHHHHHHHCCCEEEECCCCC
Q ss_conf 99999987693896077888
Q T0636 288 RTLRFLRERGIQVKDAGQFG 307 (336)
Q Consensus 288 ~~~~~L~~~gi~vr~~~~fg 307 (336)
.++..|+++|..+++|..||
T Consensus 6 ~vy~dLr~rG~~v~~G~kfG 25 (85)
T PF01974_consen 6 AVYKDLRSRGYVVKSGIKFG 25 (85)
T ss_dssp HHHHHHHH---EEEEEEE-T
T ss_pred HHHHHHHHCCCEECCCCCCC
T ss_conf 99999998888876464368
No 27
>PF05448 AXE1: Acetyl xylan esterase (AXE1); InterPro: IPR008391 This family consists of several bacterial acetyl xylan esterase proteins. Acetyl xylan esterases are enzymes that hydrolyse the ester linkages of the acetyl groups in position 2 and/or 3 of the xylose moieties of natural acetylated xylan from hardwood. These enzymes are one of the accessory enzymes which are part of the xylanolytic system, together with xylanases, beta-xylosidases, alpha-arabinofuranosidases and methylglucuronidases; these are all required for the complete hydrolysis of xylan .; PDB: 1vlq_J 1ods_A 1l7a_B 1odt_C.
Probab=21.73 E-value=16 Score=13.29 Aligned_cols=13 Identities=31% Similarity=0.261 Sum_probs=6.3
Q ss_pred HHHHHHHHHHCCC
Q ss_conf 9999999984888
Q T0636 54 RVMRKLAEHFSCP 66 (336)
Q Consensus 54 ~Lr~aia~~~~v~ 66 (336)
...+.+++--.++
T Consensus 27 FW~~~~~e~~~~p 39 (320)
T PF05448_consen 27 FWKKTLAELAAVP 39 (320)
T ss_dssp HHHHHHHHHHTS-
T ss_pred HHHHHHHHHHCCC
T ss_conf 9999999986389
No 28
>PF02679 ComA: (2R)-phospho-3-sulfolactate synthase (ComA); InterPro: IPR003830 Methanogenic archaea produce methane via the anaerobic reduction of acetate or single carbon compounds . Coenzyme M (CoM; 2-mercaptoethanesulphonic acid) serves as the terminal methyl carrier for this process. Previously thought to be unique to methanogenic archaea, CoM has also been found in methylotrophic bacteria. Biosynthesis of CoM begins with the Michael addition of sulphite to phosphoenolpyruvate, forming 2-phospho-3-sulpholactate (PSL). This reaction is catalyzed by members of this family, PSL synthase (ComA) . Subsequently, PSL is dephosphorylated by phosphosulpholactate phosphatase (ComB) to form 3-sulpholactate , which is then converted to 3-sulphopyruvate by L-sulpholactate dehydrogenase (ComC; 1.1.1.272 from EC) . Sulphopyruvate decarboxylase (ComDE; 4.1.1.79 from EC) converts 3-sulphopyruvate to sulphoacetaldehyde . Reductive thiolation of sulphoacetaldehyde is the final step.; GO: 0019295 coenzyme M biosynthetic process; PDB: 1u83_A 1qwg_A.
Probab=21.00 E-value=17 Score=13.23 Aligned_cols=51 Identities=18% Similarity=0.171 Sum_probs=34.7
Q ss_pred HHHHHHHHHHCCCHHHEEEECCHHHHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCEEEECC
Q ss_conf 99999999848885438860778899999999846992576388735699999981880364155
Q T0636 54 RVMRKLAEHFSCPEDNLMLVRGIDECFDRISAEFSSMRFVTAWPGFDGYRARIAVSGLRHFEIGL 118 (336)
Q Consensus 54 ~Lr~aia~~~~v~~d~I~~t~Gs~~~i~~~~~~~~~~~vii~~P~y~~y~~~~~~~g~~~~~vp~ 118 (336)
.|++.+.-++. ..|-+..|.+ +.-++.. .+ .+..|...++.+|...+++.-
T Consensus 55 ~l~eki~l~~~---~~V~v~~GGt--lfe~~~~--~~-------~~~~y~~~~k~lGf~~iEiSd 105 (244)
T PF02679_consen 55 ILREKIDLAHD---HGVYVYTGGT--LFEIAIS--QG-------KFDEYLRECKDLGFDAIEISD 105 (244)
T ss_dssp HHHHHHHHHHC---TT-EEE------HHHHHHH--TT--------HHHHHHHHHH----EEEE--
T ss_pred HHHHHHHHHHH---CCCEEECCCH--HHHHHHH--CC-------HHHHHHHHHHHCCCCEEEECC
T ss_conf 99999999998---6981707954--9999982--07-------499999999985997899759
No 29
>PF05913 DUF871: Bacterial protein of unknown function (DUF871); InterPro: IPR008589 This family consists of several conserved hypothetical proteins from bacteria and archaea. The function of this family is unknown though a number are annotated as outer surface proteins.; PDB: 1x7f_A 2p0o_A.
Probab=20.77 E-value=17 Score=13.16 Aligned_cols=37 Identities=19% Similarity=0.293 Sum_probs=15.7
Q ss_pred CCCCCHHHHHHHCCHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 567788999730002431330366332222237999999973
Q T0636 121 DLLLDPNDLAQVSRDDCVVLANPSNPTGQALSAGELDQLRQR 162 (336)
Q Consensus 121 ~~~~d~~~l~~~~~~~~i~l~nPnNPTG~~~~~~~l~~l~~~ 162 (336)
|++++.+++++..+..+-+.-|- ..++.+.|..|...
T Consensus 96 D~Gf~~~e~a~ls~ngl~I~LNa-----Sti~~~~l~~l~~~ 132 (357)
T PF05913_consen 96 DYGFSGEEIAELSKNGLKIELNA-----STITEEYLDNLMSY 132 (357)
T ss_dssp -----HHHHHHHTTT-S-EEEET-----TT--CCHHHHHCCT
T ss_pred CCCCCHHHHHHHHHCCCEEEEEC-----CCCCHHHHHHHHHH
T ss_conf 59999899999974797899977-----77977899999972
No 30
>PF06153 DUF970: Protein of unknown function (DUF970); InterPro: IPR010375 This is a family of uncharacterised bacterial proteins.
Probab=20.03 E-value=18 Score=13.06 Aligned_cols=17 Identities=24% Similarity=0.329 Sum_probs=7.1
Q ss_pred CCHHHHHHHHHHCCCEE
Q ss_conf 98899999998769389
Q T0636 284 AAGERTLRFLRERGIQV 300 (336)
Q Consensus 284 ~~~~~~~~~L~~~gi~v 300 (336)
.+++.+.+.|.++|+.+
T Consensus 11 ~Da~~l~~aL~~~g~~~ 27 (109)
T PF06153_consen 11 EDANRLSDALTENGFRA 27 (109)
T ss_pred CCHHHHHHHHHHCCCCE
T ss_conf 43799999999879108
Done!