Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate H281DRAFT_02373 H281DRAFT_02373 methylmalonate-semialdehyde dehydrogenase [acylating]
Query= reanno::pseudo6_N2E2:Pf6N2E2_515 (500 letters) >FitnessBrowser__Burk376:H281DRAFT_02373 Length = 512 Score = 767 bits (1980), Expect = 0.0 Identities = 364/492 (73%), Positives = 423/492 (85%) Query: 9 HYLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWSEQSSLRR 68 H++NG D S RF +VFNPA G V ARV LA VDAAVA+A AAFPAWSE + ++R Sbjct: 21 HFINGKAIDGTSGRFGDVFNPALGDVAARVPLASVAEVDAAVAAAYAAFPAWSETAPIKR 80 Query: 69 SRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSD 128 +RV+FKFKELLDRHHDELA++I+REHGKV SDA GEV RGIE+VE+ACG PNLLKTDF+D Sbjct: 81 ARVLFKFKELLDRHHDELAELITREHGKVFSDAKGEVMRGIEVVEFACGIPNLLKTDFTD 140 Query: 129 NIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLM 188 IGGGIDNWNLRQPLGV G+TPFNFP+MVP WM P+A+ GN F+LKPSERDPSAS + Sbjct: 141 QIGGGIDNWNLRQPLGVVVGITPFNFPMMVPCWMFPVAIACGNTFVLKPSERDPSASNRL 200 Query: 189 ARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAHGKRVQ 248 A LL EAGLPDGVFNVV GDKVAVDALL HPD+ A+SFVGSTPIAEYIH +GT HGKRVQ Sbjct: 201 AELLKEAGLPDGVFNVVHGDKVAVDALLVHPDVSAVSFVGSTPIAEYIHTEGTKHGKRVQ 260 Query: 249 ALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPRI 308 ALGGAKNH++VMPDADLDQA DALIGAAYGSAGERCMAIS+AVAVG + DELI +L PR+ Sbjct: 261 ALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGHIADELIERLTPRV 320 Query: 309 DQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQGFFVG 368 + LKI NG + +MGPLVTA H+ KV G+I+AG+AEGA+L+VDGR +V G E+GFF+G Sbjct: 321 ESLKIMNGMESAAEMGPLVTAVHREKVVGYIEAGIAEGAKLVVDGRGHRVDGHEKGFFLG 380 Query: 369 ATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARAF 428 TLFD V+ +M IY++EIFGPVL +VRVPDFA+AV LINA++F NGVS FT DGGIARAF Sbjct: 381 GTLFDDVSTDMKIYREEIFGPVLCVVRVPDFASAVELINANDFANGVSLFTSDGGIARAF 440 Query: 429 ARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPDSI 488 +R I++GMVGINVPIPVPMAWHSFGGWK+SLFGDHHAYGEEG+RFY+RYKS+MQRWPDSI Sbjct: 441 SRQIQIGMVGINVPIPVPMAWHSFGGWKKSLFGDHHAYGEEGVRFYTRYKSIMQRWPDSI 500 Query: 489 AKGPEFSMPTAQ 500 AKG EF+MP A+ Sbjct: 501 AKGAEFTMPVAK 512 Lambda K H 0.321 0.137 0.415 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: 849 Number of extensions: 32 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: 512 Length adjustment: 34 Effective length of query: 466 Effective length of database: 478 Effective search space: 222748 Effective search space used: 222748 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)
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