Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate AO356_23175 AO356_23175 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::G5CZI2 (498 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23175 Length = 500 Score = 615 bits (1587), Expect = 0.0 Identities = 296/494 (59%), Positives = 382/494 (77%), Gaps = 3/494 (0%) Query: 4 IGHLINGQL-VTENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPPL 62 +GH I+G++ ++N R NVFNPATG + ++ LA TV+ A+++A AFP W L Sbjct: 7 VGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSL 66 Query: 63 KRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKGEH 122 +R+RVMF+FKELL++H DE+ ++I EHGK+ DA GE+ RGIE VEYACGAP LLK + Sbjct: 67 RRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDF 126 Query: 123 SRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSSTL 182 S N+G GID+W+ QP+GV AG+TPFNFPVMVPLWM P+A+V GNCF+LKPSERDPS++L Sbjct: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186 Query: 183 YIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANGKR 242 +A+LL EAGLPDGV NVV GDK AVDALL ++A+SFVGSTPIAEYI++ +A GKR Sbjct: 187 LMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKR 246 Query: 243 CQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSKMT 302 QALGGAKNH IVMPDAD+D A + L+GAA+GS+GERCMA+S+AVAVGD GD L++K+ Sbjct: 247 VQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGD-VGDELIAKLL 305 Query: 303 QAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHENGF 362 + +LK+G G D GP++T +H+ KV G+I++ +GA ++VDGR KVP E GF Sbjct: 306 PRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGF 365 Query: 363 FVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGEAA 422 FVG TL D VT EM+ YQ+EIFGPVL +VRV A+ LI+AHE+GNG FTRDG A Sbjct: 366 FVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIA 425 Query: 423 RYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQRWP 482 R F+ +I+VGMVGIN+P+PVP+A+HSFGGWKRSLFGD HAYG + +RFY++ K+V QRWP Sbjct: 426 RAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWP 485 Query: 483 SAGVREGAEFSMPT 496 + + +G EFSMPT Sbjct: 486 DS-IAKGPEFSMPT 498 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: 754 Number of extensions: 28 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: 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 AO356_23175 AO356_23175 (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.30567.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-212 692.0 0.2 2.2e-212 691.8 0.2 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23175 AO356_23175 methylmalonate-semia Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23175 AO356_23175 methylmalonate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 691.8 0.2 2.2e-212 2.2e-212 1 477 [] 7 484 .. 7 484 .. 1.00 Alignments for each domain: == domain 1 score: 691.8 bits; conditional E-value: 2.2e-212 TIGR01722 1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaera 63 v h+idG++ + +++ +v npat+ v a+va a vdaavasa +f+aw+e s ++r+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23175 7 VGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLRRS 69 679************************************************************ PP TIGR01722 64 rvllryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvak 126 rv++++++ll+ h+de+a++is e+Gk+l+da+G+v rG+e+ve+ac+ + ll+ + ++++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23175 70 RVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSDNIGG 132 *************************************************************** PP TIGR01722 127 dvdvysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellsea 189 +d + +rqplGv+aG+tpfnfp m+plwm pla++ Gn+f+lkpse++psa++ +a+ll+ea lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23175 133 GIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLMARLLTEA 195 *************************************************************** PP TIGR01722 190 GapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmv 252 G+pdGv+nvv Gdk+avd ll+hpd+ a+sfvGs++++eyi+++g+a+gkrvqal+Gaknhm+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23175 196 GLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKRVQALGGAKNHMI 258 *************************************************************** PP TIGR01722 253 vlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.kelveeireraekvrvgagddpga 314 v+pdad+++a+dal+gaa+G+aG+rcmais+av+vG++ +el+ ++ r++++++g g++pg+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23175 259 VMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVgDELIAKLLPRIDQLKIGNGQQPGT 321 **************************************9************************ PP TIGR01722 315 elGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiyke 377 ++Gpl+t ++k++v+ +i++g++eGa++++dGrg+kv G e+G fvG tl+++v ++m+iy++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23175 322 DMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFFVGATLFDQVTAEMSIYQQ 384 *************************************************************** PP TIGR01722 378 eifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvpl 440 eifGpvl ++++ + a++lin+ +GnG + ft+dG+ ar f i+vG+vG+nvpipvp+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23175 385 EIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARAFARSIKVGMVGINVPIPVPM 447 *************************************************************** PP TIGR01722 441 pffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477 +++sf+Gwk slfGd+h+yG++G+rfy+r k v rw lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23175 448 AWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRW 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.38 // [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:
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