Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate AO353_21350 AO353_21350 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::G5CZI2 (498 letters) >lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 AO353_21350 methylmalonate-semialdehyde dehydrogenase Length = 500 Score = 623 bits (1606), Expect = 0.0 Identities = 304/496 (61%), Positives = 384/496 (77%), Gaps = 3/496 (0%) Query: 4 IGHLINGQLV-TENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPPL 62 IGH +NGQ+ T + R NVFNPATG I ++ LAS +TV++A+++A AFP W L Sbjct: 7 IGHYLNGQVQDTGSERFSNVFNPATGAIQARVGLASQQTVDEAVASALRAFPAWSEQSSL 66 Query: 63 KRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKGEH 122 +R+RVMF+FKELL++H +E+ +I EHGK+ DA GE+ RGIE VEYACGAP LLK E Sbjct: 67 RRSRVMFKFKELLDRHHNELAEIISREHGKVFSDAKGEVTRGIEIVEYACGAPNLLKTEF 126 Query: 123 SRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSSTL 182 S N+G GID+W+ QP+GV AG+TPFNFPVMVPLWM P+A+V GNCF+LKPSERDPS++L Sbjct: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVTGNCFILKPSERDPSASL 186 Query: 183 YIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANGKR 242 +A+LL EAGLPDGV +VV GDK AVDALL ++A+SFVGSTPIAEYI++ A+A GKR Sbjct: 187 LMARLLTEAGLPDGVFSVVQGDKSAVDALLQHPDIEAISFVGSTPIAEYIHQQATARGKR 246 Query: 243 CQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSKMT 302 QALGGAKNH IVMPDAD+D A + L+GAAFGS+GERCMA+S+AVAVGD GD L++K+ Sbjct: 247 VQALGGAKNHMIVMPDADLDQAADALIGAAFGSAGERCMAISIAVAVGD-VGDKLIAKLL 305 Query: 303 QAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHENGF 362 + +LKVG +D GP++T +H+ KV G+I+ QGA ++VDGR KVP ENGF Sbjct: 306 PRIDQLKVGNGMQGDSDMGPLVTAEHKAKVEGFIDQGVAQGAQLIVDGRGFKVPGAENGF 365 Query: 363 FVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGEAA 422 FVG TL D VT EM+ YQ+EIFGPVL +VRVA A+ LI+AHE+GNG FT DG A Sbjct: 366 FVGATLFDKVTTEMSIYQQEIFGPVLGIVRVADFASAVALINAHEFGNGVSCFTSDGGIA 425 Query: 423 RYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQRWP 482 R F+ I+VGMVGIN+P+PVP+A+HSFGGWKRSLFGD HAYG + +RFY++ K+V QRWP Sbjct: 426 RAFARTIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGIRFYSRYKSVMQRWP 485 Query: 483 SAGVREGAEFSMPTMK 498 + + +G EFSMPT K Sbjct: 486 DS-IAKGPEFSMPTAK 500 Lambda K H 0.319 0.135 0.405 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: 726 Number of extensions: 24 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: 500 Length adjustment: 34 Effective length of query: 464 Effective length of database: 466 Effective search space: 216224 Effective search space used: 216224 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_21350 AO353_21350 (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.20716.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-211 689.2 0.2 1.7e-211 689.0 0.2 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 AO353_21350 methylmalonate-semia Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 AO353_21350 methylmalonate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 689.0 0.2 1.7e-211 1.7e-211 2 477 .] 8 484 .. 7 484 .. 1.00 Alignments for each domain: == domain 1 score: 689.0 bits; conditional E-value: 1.7e-211 TIGR01722 2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvl 66 h+++G++ ++ s+++ +v npat+ + a+v as++ vd+avasa ++f+aw+e s ++r+rv+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 8 GHYLNGQVQDTGSERFSNVFNPATGAIQARVGLASQQTVDEAVASALRAFPAWSEQSSLRRSRVM 72 599************************************************************** PP TIGR01722 67 lryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvy 131 +++++ll+ h++e+a++is e+Gk+++dakG+v rG+e+ve+ac+ + ll+ e ++++ +d + lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 73 FKFKELLDRHHNELAEIISREHGKVFSDAKGEVTRGIEIVEYACGAPNLLKTEFSDNIGGGIDNW 137 ***************************************************************** PP TIGR01722 132 sirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvl 196 +rqplGv+aG+tpfnfp m+plwm pla++ Gn+f+lkpse++psa++ +a+ll+eaG+pdGv+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 138 NLRQPLGVCAGVTPFNFPVMVPLWMIPLALVTGNCFILKPSERDPSASLLMARLLTEAGLPDGVF 202 ***************************************************************** PP TIGR01722 197 nvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkea 261 vv Gdk avd ll+hpd+ a+sfvGs++++eyi+++++a+gkrvqal+Gaknhm+v+pdad+++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 203 SVVQGDKSAVDALLQHPDIEAISFVGSTPIAEYIHQQATARGKRVQALGGAKNHMIVMPDADLDQ 267 ***************************************************************** PP TIGR01722 262 aldalvgaavGaaGqrcmaisaavlvGaa.kelveeireraekvrvgagddpgaelGplitkqak 325 a+dal+gaa+G+aG+rcmais+av+vG++ ++l+ ++ r+++++vg g + +++Gpl+t ++k lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 268 AADALIGAAFGSAGERCMAISIAVAVGDVgDKLIAKLLPRIDQLKVGNGMQGDSDMGPLVTAEHK 332 *****************************9*********************************** PP TIGR01722 326 ervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvlead 390 ++v+ +i++g+++Ga++++dGrg+kv G e+G fvG tl+++v ++m+iy++eifGpvl ++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 333 AKVEGFIDQGVAQGAQLIVDGRGFKVPGAENGFFVGATLFDKVTTEMSIYQQEIFGPVLGIVRVA 397 ***************************************************************** PP TIGR01722 391 tleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGd 455 + a++lin+ +GnG + ftsdG+ ar f +i+vG+vG+nvpipvp++++sf+Gwk slfGd lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 398 DFASAVALINAHEFGNGVSCFTSDGGIARAFARTIKVGMVGINVPIPVPMAWHSFGGWKRSLFGD 462 ***************************************************************** PP TIGR01722 456 lhiyGkqGvrfytrlktvtarw 477 +h+yG++G+rfy+r k v rw lcl|FitnessBrowser__pseudo3_N2E3:AO353_21350 463 HHAYGEEGIRFYSRYKSVMQRW 484 *********************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (500 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: 00:00:00.02 # Mc/sec: 10.64 // [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