Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate WP_004109547.1 RHSP_RS04195 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= reanno::Caulo:CCNA_01360 (500 letters) >NCBI__GCF_000359745.1:WP_004109547.1 Length = 498 Score = 673 bits (1737), Expect = 0.0 Identities = 332/500 (66%), Positives = 392/500 (78%), Gaps = 3/500 (0%) Query: 2 MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61 MR+I HFIGG++V G SGR V++P TG+VQA VALAS EL A+ANAK AQ W AT Sbjct: 1 MREIGHFIGGKRVAGTSGRTSNVYNPATGEVQATVALASVDELRAAVANAKAAQPKWGAT 60 Query: 62 NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121 NPQRRARV F F LL +MDELA LLSSEHGK + DSKGDI RGLEV EF CG+PHL K Sbjct: 61 NPQRRARVFFRFVELLNQNMDELATLLSSEHGKTVEDSKGDIIRGLEVCEFVCGIPHLQK 120 Query: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181 GE+T+GAGP ID+YS+RQP+GV AGITPFNFP MIPMWMF PAIA GNAFILKPSERDPS Sbjct: 121 GEFTEGAGPAIDMYSIRQPVGVGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180 Query: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241 +P+RLAELMIEAGLP G+LNVV+GDK V+AIL PDI AVSFVGS+ IA+ V+ A Sbjct: 181 LPIRLAELMIEAGLPAGILNVVNGDKTAVDAILTDPDIAAVSFVGSTPIARYVYGTAAMN 240 Query: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301 GKR Q GGAKNH ++MPDAD+DQAV ++GA YGSAGERCMA+ V VPVGE TA L E Sbjct: 241 GKRAQCFGGAKNHMIIMPDADMDQAVNALMGAGYGSAGERCMAVSVAVPVGEDTANRLVE 300 Query: 302 KLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHE 361 KLV I LR+G TD A GP+V+ R+ I GV+EGA+LVVDGRGF LQG+E Sbjct: 301 KLVPKIESLRIGPYTDDKADMGPLVTKEAYNRVNGLIDRGVEEGAKLVVDGRGFKLQGYE 360 Query: 362 EGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNG 421 EG+FVG TLFDHVKP Y EIFGPVL +VRA++ EE + L +H+YGNGVAI+TR+G Sbjct: 361 EGYFVGGTLFDHVKPDMDIYKTEIFGPVLSVVRAKNYEEALELPMKHEYGNGVAIYTRDG 420 Query: 422 DAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQ 481 DAAR+FA ++ +GM+G+NVPIPVP+AYHSFGGWK S FGDLNQ+G D ++F+TRTKT+T Sbjct: 421 DAARDFASRINIGMIGVNVPIPVPLAYHSFGGWKASSFGDLNQHGTDSIKFWTRTKTITA 480 Query: 482 RWPKGGAVLD-QSFVIPTMR 500 RWP G + D FV+PTM+ Sbjct: 481 RWPSG--IKDGAEFVMPTMK 498 Lambda K H 0.320 0.137 0.409 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: 844 Number of extensions: 27 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: 500 Length of database: 498 Length adjustment: 34 Effective length of query: 466 Effective length of database: 464 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 (21.8 bits) S2: 52 (24.6 bits)
Align candidate WP_004109547.1 RHSP_RS04195 (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.1929838.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-203 662.5 0.2 1.9e-203 662.4 0.2 1.0 1 NCBI__GCF_000359745.1:WP_004109547.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000359745.1:WP_004109547.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 662.4 0.2 1.9e-203 1.9e-203 2 477 .] 5 482 .. 4 482 .. 0.99 Alignments for each domain: == domain 1 score: 662.4 bits; conditional E-value: 1.9e-203 TIGR01722 2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallk 74 h+i+Gk v g+s++ +v npat+ev a va as++e+ aava a+ + + w+ t+ +rarv++r+ +ll+ NCBI__GCF_000359745.1:WP_004109547.1 5 GHFIGGKRVAGTSGRTSNVYNPATGEVQATVALASVDELRAAVANAKAAQPKWGATNPQRRARVFFRFVELLN 77 59*********************************************************************** PP TIGR01722 75 ehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfn 147 ++ de+a l+s+e+Gkt+ed+kGd++rGlev e+ c+++ l +Ge +e +d+ysirqp+Gv aGitpfn NCBI__GCF_000359745.1:WP_004109547.1 78 QNMDELATLLSSEHGKTVEDSKGDIIRGLEVCEFVCGIPHLQKGEFTEGAGPAIDMYSIRQPVGVGAGITPFN 150 ************************************************************************* PP TIGR01722 148 fpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220 fp mip+wmf aiacGn+f+lkpse++ps ++lael+ eaG+p G+lnvv Gdk avd +l pd+ avsf NCBI__GCF_000359745.1:WP_004109547.1 151 FPGMIPMWMFAPAIACGNAFILKPSERDPSLPIRLAELMIEAGLPAGILNVVNGDKTAVDAILTDPDIAAVSF 223 ************************************************************************* PP TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..k 291 vGs+++++y+y t++ +gkr q+++Gaknhm+++pdad ++a++al+ga +G+aG+rcma+s+av vG+ + NCBI__GCF_000359745.1:WP_004109547.1 224 VGSTPIARYVYGTAAMNGKRAQCFGGAKNHMIIMPDADMDQAVNALMGAGYGSAGERCMAVSVAVPVGEDtaN 296 ********************************************************************85449 PP TIGR01722 292 elveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitl 364 +lve+++ ++e +r+g+++d a++Gpl+tk+a +rv+ li+ g++eGa++++dGrg+k++GyeeG fvG tl NCBI__GCF_000359745.1:WP_004109547.1 297 RLVEKLVPKIESLRIGPYTDDKADMGPLVTKEAYNRVNGLIDRGVEEGAKLVVDGRGFKLQGYEEGYFVGGTL 369 9************************************************************************ PP TIGR01722 365 lervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpip 437 +++vkpdm iyk eifGpvl v++a +eea++l + yGnG ai+t+dG aar f +i++G++Gvnvpip NCBI__GCF_000359745.1:WP_004109547.1 370 FDHVKPDMDIYKTEIFGPVLSVVRAKNYEEALELPMKHEYGNGVAIYTRDGDAARDFASRINIGMIGVNVPIP 442 ************************************************************************* PP TIGR01722 438 vplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477 vpl+++sf+Gwk+s fGdl+ +G + ++f+tr+kt+tarw NCBI__GCF_000359745.1:WP_004109547.1 443 VPLAYHSFGGWKASSFGDLNQHGTDSIKFWTRTKTITARW 482 **************************************** PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (498 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: 00:00:00.01 # Mc/sec: 13.44 // [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