Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_019744147.1 BA79_RS03900 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000691145.1:WP_019744147.1 Length = 486 Score = 675 bits (1741), Expect = 0.0 Identities = 322/481 (66%), Positives = 403/481 (83%), Gaps = 2/481 (0%) Query: 3 EIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSK 62 +++ LKNYI G+WV+++T+Q E V NPAT EV+ +VP+STK D+++A Q A EAF TWSK Sbjct: 5 DVQTLKNYIGGQWVDAETNQTEAVYNPATGEVIAEVPLSTKTDVEHAVQAAQEAFTTWSK 64 Query: 63 VAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLM 122 AVPRRARILF +QQLL + +ELA L+T+ENGK+ EA GEV RGIE VEFAAGAP+LM Sbjct: 65 TAVPRRARILFKYQQLLVEKWDELAELVTLENGKSVTEAKGEVQRGIECVEFAAGAPTLM 124 Query: 123 MGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTP 182 MG L IAT +E+ YRYPIGV+GGI PFNFPMMVPCWMFP+AIA GNTF+LKPSERTP Sbjct: 125 MGKQLPDIATGLESGMYRYPIGVIGGITPFNFPMMVPCWMFPLAIACGNTFVLKPSERTP 184 Query: 183 LLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSE 242 +L +L ELFE+AGLPKGV N+V GAHDVVNG+LEH ++KAISFVGS+PV EYVYKKG+ Sbjct: 185 ILAARLAELFEEAGLPKGVLNIVNGAHDVVNGLLEHEKVKAISFVGSQPVAEYVYKKGTA 244 Query: 243 NLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMA 302 + KRVQ+L GAKNH+IVL DA+LE I+GAAFGSAGERCMA AVV VEE +AD+ + Sbjct: 245 HGKRVQALAGAKNHSIVLKDADLESATKQIIGAAFGSAGERCMAAAVVAVEEDVADDLIQ 304 Query: 303 KLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGREN--VSDD 360 +L ++ + IGNG++ VFLGPVIR+++K+RTL YI+ G+EEGA L+ DGR++ + + Sbjct: 305 QLVDESNQLVIGNGINKDVFLGPVIRKEHKERTLQYIQSGIEEGASLIRDGRQDNETNGE 364 Query: 361 GYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSN 420 GYFVGPTIFD+VT +M IW+DEIFAPVLS++RV +L EAI+++N+S+FANGACL+T +++ Sbjct: 365 GYFVGPTIFDHVTNQMKIWQDEIFAPVLSIVRVSSLAEAIDLSNQSKFANGACLYTDSAS 424 Query: 421 AIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTAR 480 +IR FRENI+AGMLGIN+GVPAPMAFFPFSGWK SF+G LHANG D V+FYTRKK+VTAR Sbjct: 425 SIREFRENIEAGMLGINIGVPAPMAFFPFSGWKDSFYGDLHANGTDGVEFYTRKKMVTAR 484 Query: 481 Y 481 Y Sbjct: 485 Y 485 Lambda K H 0.318 0.136 0.396 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: 707 Number of extensions: 23 Number of successful extensions: 2 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: 487 Length of database: 486 Length adjustment: 34 Effective length of query: 453 Effective length of database: 452 Effective search space: 204756 Effective search space used: 204756 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: 52 (24.6 bits)
Align candidate WP_019744147.1 BA79_RS03900 (CoA-acylating methylmalonate-semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))
# 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.carbon/TIGR01722.hmm # target sequence database: /tmp/gapView.1263542.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01722 [M=477] Accession: TIGR01722 Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-185 602.4 0.4 3.3e-185 602.2 0.4 1.0 1 NCBI__GCF_000691145.1:WP_019744147.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000691145.1:WP_019744147.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 602.2 0.4 3.3e-185 3.3e-185 2 477 .] 10 485 .. 9 485 .. 0.98 Alignments for each domain: == domain 1 score: 602.2 bits; conditional E-value: 3.3e-185 TIGR01722 2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallk 74 k +i+G+ v++++++ v npat+ev+a+v+ +++ +v+ av +a+e+f++w++t+v +rar+l++yq+ll NCBI__GCF_000691145.1:WP_019744147.1 10 KNYIGGQWVDAETNQTEAVYNPATGEVIAEVPLSTKTDVEHAVQAAQEAFTTWSKTAVPRRARILFKYQQLLV 82 789********************************************************************** PP TIGR01722 75 ehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfn 147 e+ de+a+l+++e+Gk +++akG+v rG+e ve+a + ++l++G+ +++a+ ++ +r p+Gv+ Gitpfn NCBI__GCF_000691145.1:WP_019744147.1 83 EKWDELAELVTLENGKSVTEAKGEVQRGIECVEFAAGAPTLMMGKQLPDIATGLESGMYRYPIGVIGGITPFN 155 ************************************************************************* PP TIGR01722 148 fpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220 fp m+p wmfplaiacGntfvlkpse+ p a +lael++eaG+p+Gvln+v G ++ v+ lleh +vka+sf NCBI__GCF_000691145.1:WP_019744147.1 156 FPMMVPCWMFPLAIACGNTFVLKPSERTPILAARLAELFEEAGLPKGVLNIVNGAHDVVNGLLEHEKVKAISF 228 ************************************************************************* PP TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.ke 292 vGs++v+ey+y++g+ahgkrvqalaGaknh +vl dad+e+a ++++gaa+G+aG+rcma +++ + ++ ++ NCBI__GCF_000691145.1:WP_019744147.1 229 VGSQPVAEYVYKKGTAHGKRVQALAGAKNHSIVLKDADLESATKQIIGAAFGSAGERCMAAAVVAVEEDVaDD 301 ************************************************************87655555545** PP TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365 l++++++ +++ +g g + lGp+i k++ker ++i+sg++eGa+++ dGr e eG fvG+t++ NCBI__GCF_000691145.1:WP_019744147.1 302 LIQQLVDESNQLVIGNGINKDVFLGPVIRKEHKERTLQYIQSGIEEGASLIRDGRQD-NETNGEGYFVGPTIF 373 *******************************************************75.578889********* PP TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438 ++v +mki+++eif pvl ++++ +l eai l n+s + nG++++t + ++ r+f+ +ie+G++G+n+ +p NCBI__GCF_000691145.1:WP_019744147.1 374 DHVTNQMKIWQDEIFAPVLSIVRVSSLAEAIDLSNQSKFANGACLYTDSASSIREFRENIEAGMLGINIGVPA 446 ************************************************************************* PP TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477 p++ff f+Gwkds++Gdlh+ G +Gv+fytr k+vtar+ NCBI__GCF_000691145.1:WP_019744147.1 447 PMAFFPFSGWKDSFYGDLHANGTDGVEFYTRKKMVTARY 485 *************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (486 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 30.72 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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