Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate BPHYT_RS28825 BPHYT_RS28825 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >lcl|FitnessBrowser__BFirm:BPHYT_RS28825 BPHYT_RS28825 methylmalonate-semialdehyde dehydrogenase Length = 507 Score = 609 bits (1570), Expect = e-179 Identities = 306/491 (62%), Positives = 374/491 (76%), Gaps = 4/491 (0%) Query: 6 HLIGGELIADT-GRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKR 64 H IGG A T GR DVFNP+TG+ V LA E + A+ AA+AAFPAW T P KR Sbjct: 17 HYIGGAPAAPTSGRFKDVFNPATGKVTGSVALASVEEVDAAVQAARAAFPAWSETAPLKR 76 Query: 65 AQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSR 124 A++LFRFK+LL + + + LI+ EHGK DA GE+ RGIE VE+A P +LK +++ Sbjct: 77 ARILFRFKELLNQHHDELAMLITREHGKVFTDAQGEVVRGIEVVEFACGIPNLLKTDFTD 136 Query: 125 NVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLI 184 +G ID W+ Q +GVVAGITPFNFP MVP+WM+P+A+ACGNTF+LKPSERDPS++L + Sbjct: 137 QIGGGIDNWNLRQALGVVAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSASLRL 196 Query: 185 AELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQ 244 AEL EAGLP GV NVV+GDK AVDALI+ P+V ALSFVGSTPIAEYI++E +KRGKRVQ Sbjct: 197 AELLKEAGLPDGVFNVVNGDKVAVDALIDHPDVAALSFVGSTPIAEYIHTEASKRGKRVQ 256 Query: 245 ALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQ 304 ALGGAKNH V+MPDADLD AV AL+GAAYGS GERCMAISVAV VG+ +AD L++KLVP+ Sbjct: 257 ALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGN-VADKLIEKLVPR 315 Query: 305 IKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFL 364 +K L I G +MGPLVT + KVTGYI +G A+GA+L+VDGR + V +E GFF+ Sbjct: 316 VKSLVIKNGEHLDAEMGPLVTAEHKAKVTGYIASGEAEGAKLIVDGRAHPVT-NEEGFFV 374 Query: 365 GGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARL 424 GGTLFD V EM IYKEEIFGPVL +VRV A+ LIN HE+GNG +FT DG AR Sbjct: 375 GGTLFDHVGTEMKIYKEEIFGPVLAVVRVPDFASAVDLINAHEFGNGVSLFTSDGGVARA 434 Query: 425 FCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRWPQR 484 F +I+VGMVG+NVP+PVP+A+HSFGGWKRSLFGD HAYG +GVRFYT+ K+I QRWP Sbjct: 435 FGRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGVRFYTRYKSIMQRWPDS 494 Query: 485 KSHEAAQFAFP 495 + + A+F P Sbjct: 495 IA-KGAEFTMP 504 Lambda K H 0.319 0.137 0.411 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: 783 Number of extensions: 26 Number of successful extensions: 3 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: 498 Length of database: 507 Length adjustment: 34 Effective length of query: 464 Effective length of database: 473 Effective search space: 219472 Effective search space used: 219472 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
Align candidate BPHYT_RS28825 BPHYT_RS28825 (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.17346.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-214 697.0 1.0 6.8e-214 696.8 1.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS28825 BPHYT_RS28825 methylmalonate-sem Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS28825 BPHYT_RS28825 methylmalonate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 696.8 1.0 6.8e-214 6.8e-214 3 477 .] 17 491 .. 15 491 .. 0.99 Alignments for each domain: == domain 1 score: 696.8 bits; conditional E-value: 6.8e-214 TIGR01722 3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqal 72 h+i+G+ + +s+++ +v npat++v++ va as+eevdaav +ar +f+aw+et+ ++rar+l+r+++l lcl|FitnessBrowser__BFirm:BPHYT_RS28825 17 HYIGGAPAAPTSGRFKDVFNPATGKVTGSVALASVEEVDAAVQAARAAFPAWSETAPLKRARILFRFKEL 86 9********************************************************************* PP TIGR01722 73 lkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaG 142 l++h+de+a li+ e+Gk+++da+G+v+rG+evve+ac+++ ll+ + ++++ +d + +rq lGvvaG lcl|FitnessBrowser__BFirm:BPHYT_RS28825 87 LNQHHDELAMLITREHGKVFTDAQGEVVRGIEVVEFACGIPNLLKTDFTDQIGGGIDNWNLRQALGVVAG 156 ********************************************************************** PP TIGR01722 143 itpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrlleh 212 itpfnfp m+p+wmfp+a+acGntfvlkpse++psa+++laell+eaG+pdGv+nvv Gdk+avd l++h lcl|FitnessBrowser__BFirm:BPHYT_RS28825 157 ITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSASLRLAELLKEAGLPDGVFNVVNGDKVAVDALIDH 226 ********************************************************************** PP TIGR01722 213 pdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmais 282 pdv a+sfvGs++++eyi++ +s++gkrvqal+Gaknh vv+pdad+++a+dal+gaa+G+aG+rcmais lcl|FitnessBrowser__BFirm:BPHYT_RS28825 227 PDVAALSFVGSTPIAEYIHTEASKRGKRVQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAIS 296 ********************************************************************** PP TIGR01722 283 aavlvGaa.kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykv 351 +av+vG++ ++l+e+++ r++ + + g++ ae+Gpl+t ++k++v+ +iasg +eGa++++dGr+ v lcl|FitnessBrowser__BFirm:BPHYT_RS28825 297 VAVAVGNVaDKLIEKLVPRVKSLVIKNGEHLDAEMGPLVTAEHKAKVTGYIASGEAEGAKLIVDGRAHPV 366 *******989***********************************************************9 PP TIGR01722 352 eGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkf 421 eeG fvG tl+++v ++mkiykeeifGpvl+v+++ + a+ lin+ +GnG ++ftsdG+ ar f lcl|FitnessBrowser__BFirm:BPHYT_RS28825 367 T-NEEGFFVGGTLFDHVGTEMKIYKEEIFGPVLAVVRVPDFASAVDLINAHEFGNGVSLFTSDGGVARAF 435 7.699***************************************************************** PP TIGR01722 422 qheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477 +i+vG+vG+nvpipvp++++sf+Gwk slfGd+h+yG++Gvrfytr k + rw lcl|FitnessBrowser__BFirm:BPHYT_RS28825 436 GRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGVRFYTRYKSIMQRW 491 *******************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (507 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10.01 // [ok]
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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