Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate GFF4092 HP15_4032 betaine aldehyde dehydrogenase
Query= reanno::Caulo:CCNA_01360 (500 letters) >FitnessBrowser__Marino:GFF4092 Length = 486 Score = 227 bits (579), Expect = 6e-64 Identities = 158/491 (32%), Positives = 246/491 (50%), Gaps = 22/491 (4%) Query: 2 MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVA-QAAWAA 60 M+DI H+I GQ V ASGR + +P GKV ++V A E++ A+ A+ A + W Sbjct: 1 MKDIKHYINGQYVGSASGRLFDNVNPANGKVISKVHEAGREEVDAAVKAARAALRGPWGK 60 Query: 61 TNPQRRARVMFEFKRLLEVHMDEL--AALLSSEHGKVIADSKGDIQRGLEVIE-FACGVP 117 ++R ++ + + DE A L + K +A S DI RG + FA + Sbjct: 61 MTLEQRTAILHKVADGINARFDEFLEAECLDTGKPKSLA-SHIDIPRGAANFKVFADMIK 119 Query: 118 HLLKGEYTQGA--GPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKP 175 ++ + G G Y++R+P GV+ I+P+N P ++ W GPA+A GN ++KP Sbjct: 120 NVPTESFEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKP 179 Query: 176 SERDPSVPVRLAELMIEAGLPPGVLNVVHG-DKDCVEAIL-DHPDIKAVSFVGSSDIAQS 233 SE P+ L E+M EAG+P GV NVVHG D A L +HP + +F G + + Sbjct: 180 SEETPTTTALLGEVMKEAGVPDGVYNVVHGFGGDSAGAYLTEHPQVDGFTFTGETGTGEV 239 Query: 234 VFQRAGAAGKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGE 293 + + A + + G KN GLV D D+++A+ + +A+ + G+ C+ V V Sbjct: 240 IMKAAAKGIRDISLELGGKNAGLVFADCDMEKAIEGTMRSAFANCGQVCLGTERVY-VER 298 Query: 294 KTATALREKLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGR 353 +L A GL++G D DA+ GP+VS H+ ++ SY Q VD+GA +V G Sbjct: 299 SIFDEFVGRLKEAAEGLKIGPPDDADANLGPLVSLKHREKVLSYYQKAVDDGATVVTGGG 358 Query: 354 GFSLQGH-EEGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGN 412 + G +V PT++ + S DEIFGP + ++ EE I LA+ YG Sbjct: 359 VPDMPAELAGGAWVEPTIWTGLPDDSAVVTDEIFGPCCHIRPFDTEEEAIELANSLPYGL 418 Query: 413 GVAIFTRNGDAAREFADQVEVGMVGINV----PIPVPVAYHSFGGWKRSGFGDLNQYGMD 468 AI++ N A A Q+E G++ +N + P FGG K+SG G + G+ Sbjct: 419 ASAIWSENITRAHRVAGQIEAGIIWVNSWFLRDLRTP-----FGGSKQSGVG--REGGVH 471 Query: 469 GVRFYTRTKTV 479 + FYT K + Sbjct: 472 SLEFYTEMKNI 482 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: 663 Number of extensions: 42 Number of successful extensions: 5 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: 486 Length adjustment: 34 Effective length of query: 466 Effective length of database: 452 Effective search space: 210632 Effective search space used: 210632 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