Align 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 3, chloroplastic; Cobalamin-independent methionine synthase 3; AtMS3; EC 2.1.1.14 (characterized)
to candidate WP_039652020.1 PN53_RS03355 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= SwissProt::Q0WNZ5 (812 letters) >NCBI__GCF_000816635.1:WP_039652020.1 Length = 776 Score = 644 bits (1660), Expect = 0.0 Identities = 346/781 (44%), Positives = 476/781 (60%), Gaps = 29/781 (3%) Query: 51 SHIVGYPRIGPKRELKFALESFWDGKTNVDDLQNVAANLRKSIWKHMAHAGIKYIPSNTF 110 S IVGYPRIG RELKFA+ES++ G + ++L + LR W +G+ IPSN F Sbjct: 4 STIVGYPRIGVNRELKFAVESYFKGNIDSNELFSTGKKLRDEYWSKQKESGLDIIPSNDF 63 Query: 111 SYYDQMLDTTAMLGAVPSRYGWESGEIGFDVYFSMARG----NASAHAMEMTKWFDTNYH 166 SYYD MLD +L +P +Y + G D YF+MARG + A+ M KWF+TNYH Sbjct: 64 SYYDNMLDMAFLLNIIPQKYK-DLGLSPLDTYFAMARGYQNNSKDIRALPMKKWFNTNYH 122 Query: 167 YIVPELGPDVNFSYASHKAVVEFKEAKALGIDTVPVLIGPMTYLLLSKPAKGVEKSFCLL 226 YIVPE+ + FS K ++E+K L I+T PV+IG T+L LS CL Sbjct: 123 YIVPEIDQNTIFSINDTKPFDLYRESKELNIETKPVIIGIFTFLKLSNLKGNTTFEHCL- 181 Query: 227 SLIDKILPVYKEVLADLKSAGARWIQFDEPILVMDLDTSQLQAFSDAYSHMESSLAGLNV 286 +K+ +Y ++L + G +++Q DEPILV DL +++ F + Y + + Sbjct: 182 ---NKLANIYIDILDKFQQEGIKYLQIDEPILVTDLTEYEIELFKNVYDKILNKKYSFKT 238 Query: 287 LIATYFADVPAEAYKTLMSLKCVTGFGFDLVRGLETLDLI-KMNFPRGKLLFAGVVDGRN 345 L+ TYF D+ + Y+ L +LK G G D V G + L L+ K FP K+L AG+V+G+N Sbjct: 239 LLQTYFGDI-RDIYENLQNLK-FNGIGLDFVEGKKNLTLLQKYGFPDNKILIAGIVNGKN 296 Query: 346 IWANDLSASLKTLQTLEDIVGKEKVVVSTSCSLLHTAVDLVNEMKLD------------- 392 IW ND S++ + + + K+ +STSCSLLH + E +D Sbjct: 297 IWRNDYKHSIQLMNNIGKYIDTNKIYISTSCSLLHVPYTVKPEGHIDDKNIGKVDNLINM 356 Query: 393 KELKSWLAFAAQKVVEVNALAKSFSGA--KDEALFSSNSMRQASRRSSPRVTNAAVQQDV 450 E L+FA +K+ E++ + + + ++ + N +R +P N ++ ++ Sbjct: 357 SEYIESLSFAEEKLNELSEIKELLKCKYYEKQSKYIKNQDILKRKRQNPLCYNKEIRTNI 416 Query: 451 DAVKKSDHHRSTEVSVRLQAQQKKLNLPALPTTTIGSFPQTTDLRRIRREFKAKKISEVD 510 + +K D R + R + Q LP LPTTTIGSFPQT +++++R++ + I++ + Sbjct: 417 NNLKPEDFTRKDSLEFRKKVQNNTFKLPLLPTTTIGSFPQTHEIKKLRKDLRGNTITKEN 476 Query: 511 YVQTIKEEYEKVIKLQEELGIDVLVHGEAERNDMVEFFGEQLSGFAFTSNGWVQSYGSRC 570 Y I E+ ++V+KLQE++G+DVLVHGE ER DMVE+FG L GF FT NGWVQSYG+R Sbjct: 477 YENQIMEKIKEVLKLQEDIGLDVLVHGEYERADMVEYFGRLLDGFLFTKNGWVQSYGTRA 536 Query: 571 VKPPIIYGDITRPKAMTVFWSSMAQKMTQRPMKGMLTGPVTILNWSFVRNDQPRHETCFQ 630 VKPPIIYGD+ R MT+ W AQ T +P+KGMLTGP+TILNWSF R D + +Q Sbjct: 537 VKPPIIYGDVKRTAPMTLDWIKFAQDQTDKPVKGMLTGPITILNWSFPREDLDLKQIAYQ 596 Query: 631 IALAIKDEVEDLEKAGVTVIQIDEAALREGLPLR-KSEQKFYLDWAVHAFRITNSGVQDS 689 I LAI +EV DLE G+ +IQIDEAALRE LPLR K K YLDWA+ AFR+TNS V+ Sbjct: 597 IGLAIGEEVLDLESEGIKIIQIDEAALREKLPLRTKDWHKKYLDWAIPAFRLTNSKVKSE 656 Query: 690 TQIHTHMCYSNFNDIIHSIIDMDADVITIENSRSDEKLLSVFHEGVKYGAGIGPGVYDIH 749 TQIHTHMCYS F+ I+ I DMDADV +IE +RSD +L F + + + IGPG+YDIH Sbjct: 657 TQIHTHMCYSEFSSIVQEIKDMDADVYSIEAARSDFSILD-FLKNNNFKSQIGPGIYDIH 715 Query: 750 SPRIPSTEEIAERINKMLAVLDSKVLWVNPDCGLKTRNYSEVKSALSNMVAAAKLIRSQL 809 SPRIPS EE+ + I ML +D LW+NPDCGLKTR+ EVK +L NMV A K IR +L Sbjct: 716 SPRIPSIEELEKSIKIMLDKIDCDKLWINPDCGLKTRDIDEVKKSLINMVLATKNIRKKL 775 Query: 810 N 810 N Sbjct: 776 N 776 Lambda K H 0.318 0.133 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1415 Number of extensions: 73 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 812 Length of database: 776 Length adjustment: 41 Effective length of query: 771 Effective length of database: 735 Effective search space: 566685 Effective search space used: 566685 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 bits)
Align candidate WP_039652020.1 PN53_RS03355 (5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase)
to HMM TIGR01371 (metE: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase (EC 2.1.1.14))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01371.hmm # target sequence database: /tmp/gapView.60410.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01371 [M=754] Accession: TIGR01371 Description: met_syn_B12ind: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1036.8 3.0 0 1036.5 3.0 1.1 1 NCBI__GCF_000816635.1:WP_039652020.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000816635.1:WP_039652020.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1036.5 3.0 0 0 1 754 [] 7 774 .. 7 774 .. 0.96 Alignments for each domain: == domain 1 score: 1036.5 bits; conditional E-value: 0 TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgai 73 +g+Prig +Relk+a+e+y+kg+i+++el ++ k+lr + ++kqke+g+d+ip+ndfs+YD++Ld+a ll++i NCBI__GCF_000816635.1:WP_039652020.1 7 VGYPRIGVNRELKFAVESYFKGNIDSNELFSTGKKLRDEYWSKQKESGLDIIPSNDFSYYDNMLDMAFLLNII 79 69*********************************************************************** PP TIGR01371 74 perfkeladdesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeake 144 p+++k+l + s ldtyFa+aRG+++ kd+ al m+kwfntnYhY+vPe+++++ f+++ +k+++ y+e ke NCBI__GCF_000816635.1:WP_039652020.1 80 PQKYKDL--GLSPLDTYFAMARGYQNnsKDIRALPMKKWFNTNYHYIVPEIDQNTIFSINDTKPFDLYRESKE 150 ******9..4557**********998789******************************************** PP TIGR01371 145 lgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaa 217 l++etkPv++G++tflkL+ k +++ ++ l+kl ++Y ++l+k++++g++++qideP+lv+dl++ e+++ NCBI__GCF_000816635.1:WP_039652020.1 151 LNIETKPVIIGIFTFLKLSNLKG--NTTFEHCLNKLANIYIDILDKFQQEGIKYLQIDEPILVTDLTEYEIEL 221 *******************9886..57899******************************************* PP TIGR01371 218 vkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakee.lelakakfeedkvLvaGvidG 289 +k++y+++ +++ + k llqtYf+++++ +e+l++l+++++glD+ve+k++ + l+k++f+++k+L+aG+++G NCBI__GCF_000816635.1:WP_039652020.1 222 FKNVYDKILNKKYSFKTLLQTYFGDIRDIYENLQNLKFNGIGLDFVEGKKNlTLLQKYGFPDNKILIAGIVNG 294 *************************************************99777899**************** PP TIGR01371 290 rniwkadlekslkllkkleakag.dklvvstscsllhvpvdleleekldk.............elkellafak 348 +niw++d+++s++l++++ ++ + +k+ +stscsllhvp++++ e ++d+ e+ e l+fa+ NCBI__GCF_000816635.1:WP_039652020.1 295 KNIWRNDYKHSIQLMNNIGKYIDtNKIYISTSCSLLHVPYTVKPEGHIDDknigkvdnlinmsEYIESLSFAE 367 ********************9999**********************9986333322222222245678***** PP TIGR01371 349 ekleelkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekk 420 ekl+el+ +ke+l+ +++++ ++++ ++++++++ ++++++++++lk ++++r+ s+e R++ q+++ NCBI__GCF_000816635.1:WP_039652020.1 368 EKLNELSEIKELLKCkYYEKQSKYIKNQDILKRKRQNPLCYNKEIRTNINNLKPEDFTRKDSLEFRKKVQNNT 440 **************9666666677777788888889999********************************** PP TIGR01371 421 lnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmvey 493 ++lPllPtttiGsfPqt+e++k R+++r ++i++e+Ye+ i e+ik+v+klqe++glDvLvhGe eR Dmvey NCBI__GCF_000816635.1:WP_039652020.1 441 FKLPLLPTTTIGSFPQTHEIKKLRKDLRGNTITKENYENQIMEKIKEVLKLQEDIGLDVLVHGEYERADMVEY 513 ************************************************************************* PP TIGR01371 494 FgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvRe 566 Fg l+Gf+ft+ngWvqsYG+R+vkPpiiygdv+r++pmt++++k+aq t+kpvkGmLtGP+tilnWsf+Re NCBI__GCF_000816635.1:WP_039652020.1 514 FGRLLDGFLFTKNGWVQSYGTRAVKPPIIYGDVKRTAPMTLDWIKFAQDQTDKPVKGMLTGPITILNWSFPRE 586 ************************************************************************* PP TIGR01371 567 DlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdk.eeYldwaveaFrlaasgvkdetqi 638 Dl++k+ia+qi+la+ +ev dLe++gikiiqiDe+alRe+lPlr++d+ ++Yldwa+ aFrl++s+vk etqi NCBI__GCF_000816635.1:WP_039652020.1 587 DLDLKQIAYQIGLAIGEEVLDLESEGIKIIQIDEAALREKLPLRTKDWhKKYLDWAIPAFRLTNSKVKSETQI 659 ***********************************************9679********************** PP TIGR01371 639 hthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaellek 711 hthmCYsef+ i+++i+++daDv siea+rsd ++ld lk+ ++++++iG+G+yDihspr+Ps eel+++++ NCBI__GCF_000816635.1:WP_039652020.1 660 HTHMCYSEFSSIVQEIKDMDADVYSIEAARSDFSILDFLKN-NNFKSQIGPGIYDIHSPRIPSIEELEKSIKI 731 *****************************************.77***************************** PP TIGR01371 712 alkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754 +l+k++ ++lW+nPDCGLktR+ +evk++l n+v a+k++R+k NCBI__GCF_000816635.1:WP_039652020.1 732 MLDKIDCDKLWINPDCGLKTRDIDEVKKSLINMVLATKNIRKK 774 *****************************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (754 nodes) Target sequences: 1 (776 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 31.92 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory