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 AO353_06080 AO353_06080 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 AO353_06080 methylmalonate-semialdehyde dehydrogenase Length = 497 Score = 903 bits (2334), Expect = 0.0 Identities = 442/496 (89%), Positives = 465/496 (93%) Query: 1 MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60 M+LI HLI GEL+ D RTADVFNPSTG+ + KVPLA RET+Q+AID+AKAAFPAWRNTP Sbjct: 1 MSLIPHLINGELVTDNARTADVFNPSTGQPIHKVPLASRETIQKAIDSAKAAFPAWRNTP 60 Query: 61 PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120 PAKRAQV+FRFKQLLE NE RI +LISEEHGKT+EDAAGELKRGIENVE+A AAPEILKG Sbjct: 61 PAKRAQVMFRFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKG 120 Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180 EYSRNVGPNIDAWSDFQP+GVVAGITPFNFPAMVPLWMYPLAI CGN FILKPSERDPSS Sbjct: 121 EYSRNVGPNIDAWSDFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDPSS 180 Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240 TLLIA+L EAGLPKGVL+VVHGDK AVDALIEAPEVKALSFVGSTPIAEYIY+EGTKRG Sbjct: 181 TLLIAQLLLEAGLPKGVLSVVHGDKAAVDALIEAPEVKALSFVGSTPIAEYIYAEGTKRG 240 Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQ+ADALV K Sbjct: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQVADALVTK 300 Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360 LVPQIK LKIGAGTSCGLDMGPLV+G ARDKV+GYI+ GV+ GA L+VDGRG VAGHE Sbjct: 301 LVPQIKALKIGAGTSCGLDMGPLVSGQARDKVSGYIEDGVSAGASLIVDGRGLSVAGHEE 360 Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420 GFFLGG LFD VTPEM IYKEEIFGPVLCIVRVNSLE AMQLINDHEYGNGTCIFTRDGE Sbjct: 361 GFFLGGCLFDNVTPEMRIYKEEIFGPVLCIVRVNSLEAAMQLINDHEYGNGTCIFTRDGE 420 Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYT+RKAITQR Sbjct: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTRRKAITQR 480 Query: 481 WPQRKSHEAAQFAFPS 496 WPQR SHEA+QFAFPS Sbjct: 481 WPQRASHEASQFAFPS 496 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: 903 Number of extensions: 17 Number of successful extensions: 1 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: 497 Length adjustment: 34 Effective length of query: 464 Effective length of database: 463 Effective search space: 214832 Effective search space used: 214832 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 AO353_06080 AO353_06080 (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.17132.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-210 685.1 0.0 2.8e-210 684.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 AO353_06080 methylmalonate-semia Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 AO353_06080 methylmalonate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 684.9 0.0 2.8e-210 2.8e-210 3 477 .] 6 481 .. 4 481 .. 0.99 Alignments for each domain: == domain 1 score: 684.9 bits; conditional E-value: 2.8e-210 TIGR01722 3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvll 67 hli+G++v +++ +v np t++ + kv+ as e +++a+ sa+ +f+aw++t+ a+ra+v++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 6 HLINGELVTD-NARTADVFNPSTGQPIHKVPLASRETIQKAIDSAKAAFPAWRNTPPAKRAQVMF 69 8999999976.56789************************************************* PP TIGR01722 68 ryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvys 132 r+++ll++++ ia+lis e+Gktleda G++ rG+e ve+ac+ + +l+Ge + +v ++d +s lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 70 RFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKGEYSRNVGPNIDAWS 134 ***************************************************************** PP TIGR01722 133 irqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvln 197 qplGvvaGitpfnfpam+plwm+plai+cGn+f+lkpse++ps+++ +a+ll+eaG+p+Gvl lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 135 DFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDPSSTLLIAQLLLEAGLPKGVLS 199 ***************************************************************** PP TIGR01722 198 vvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaa 262 vvhGdk avd l+e p+vka+sfvGs++++eyiy g+++gkrvqal+Gaknh+v++pdad+++a lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 200 VVHGDKAAVDALIEAPEVKALSFVGSTPIAEYIYAEGTKRGKRVQALGGAKNHAVLMPDADLDNA 264 ***************************************************************** PP TIGR01722 263 ldalvgaavGaaGqrcmaisaavlvGaa..kelveeireraekvrvgagddpgaelGplitkqak 325 ++al+gaa+G+ G+rcmais+av vG+ + lv +++ +++ +++gag+ g ++Gpl++ qa+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 265 VSALMGAAYGSCGERCMAISVAVCVGDQvaDALVTKLVPQIKALKIGAGTSCGLDMGPLVSGQAR 329 **************************855699********************************* PP TIGR01722 326 ervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvlead 390 ++v+ +i++g+ Ga++++dGrg+ v G+eeG f+G +l+++v p+m+iykeeifGpvl++++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 330 DKVSGYIEDGVSAGASLIVDGRGLSVAGHEEGFFLGGCLFDNVTPEMRIYKEEIFGPVLCIVRVN 394 ***************************************************************** PP TIGR01722 391 tleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGd 455 +le a++lin+ yGnGt+ift+dG aar f eievG+vGvnvp+pvp++++sf+Gwk slfGd lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 395 SLEAAMQLINDHEYGNGTCIFTRDGEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGD 459 ***************************************************************** PP TIGR01722 456 lhiyGkqGvrfytrlktvtarw 477 lh+yG +Gvrfytr k++t rw lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 460 LHAYGPDGVRFYTRRKAITQRW 481 ********************** PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (497 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: 00:00:00.03 # Mc/sec: 7.90 // [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