Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate BWI76_RS12820 BWI76_RS12820 NAD-dependent phenylacetaldehyde dehydrogenase
Query= reanno::Koxy:BWI76_RS03070 (501 letters) >FitnessBrowser__Koxy:BWI76_RS12820 Length = 499 Score = 248 bits (633), Expect = 4e-70 Identities = 174/496 (35%), Positives = 255/496 (51%), Gaps = 32/496 (6%) Query: 5 GNFIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAF--ESWSRTTP 62 G ++ G + S + + V++PATG+ + + A +V A+ A AF SW+ TP Sbjct: 21 GLYLDGTQQAAESEQRLTVWNPATGQAIASTADANAADVDRAVMSAWRAFVSRSWAGRTP 80 Query: 63 LRRARVMFNFKMLLEQHAEELAGIIVSEHGKVFSDAMGELTRGMEV------VEFACGIP 116 R R++ F L+EQH EELA + E GK + ++R EV + + G+ Sbjct: 81 ADRERILLRFADLVEQHGEELAQLETLEQGKSIN-----ISRAFEVGCTLNWMRYTAGLT 135 Query: 117 HLIKGEFSSDV------GTGVDSYSLMQPLGVVAGITPFNFPAMVPMWMFPLALACGNSF 170 I G + DV G +++ +P+GVVAGI P+NFP M+ MW ALA G S Sbjct: 136 TKISGR-TLDVSIPFPAGGRYQAWTKKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSI 194 Query: 171 VLKPPALAPTAAVRLAELLKEAGLPDGVFNVVHCSNED-AEQLYRDPRIAAVSFVGSSGV 229 V+KP P +R+AEL EAG+PDGVFNVV S L P +A VSF GS+ Sbjct: 195 VIKPSETTPLTLLRVAELATEAGVPDGVFNVVTGSGAGCGAALTSHPLVAKVSFTGSTAT 254 Query: 230 AEHIYKTASAYGKRVQAFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVA 289 + I + A+ RV KN AIV+ DAD + +M G+F + G+ C A + Sbjct: 255 GKQIARVAADRLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIY- 313 Query: 290 VGDETADKLIARLKPLVESLKVGPGCMRGKEENEMGPVVSDTHQKKVLGYIDKGVSEGAT 349 + D L++ + V+SL+VGPG + E +++ PVVS H KV Y+D+ + A Sbjct: 314 IEAPLFDTLVSGFEQAVKSLQVGPGML---ESSQINPVVSQAHCAKVAAYLDEARQQKAE 370 Query: 350 LVVDGRKPQVPGFEEGYYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNS 409 L+ P +GYY+ TL N + + REE+FGPV+ +VRVAD AL L N Sbjct: 371 LISGHAGPDA----QGYYIAPTLVINPDAGLRLCREEVFGPVVNLVRVADGEEALLLAND 426 Query: 410 HEFGNGSAVFTSNGHTAREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGP 469 +FG ++V+T + A + +QAG V VN + A FGG K+S G GP Sbjct: 427 SDFGLTASVWTRDLTQALSYTDRLQAGTVWVNSHTLID-ANLPFGGMKQS--GTGRDFGP 483 Query: 470 DGVRFYTRMKTATVRW 485 D + + K+ VR+ Sbjct: 484 DWLDDWCETKSVCVRY 499 Lambda K H 0.319 0.135 0.404 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: 601 Number of extensions: 28 Number of successful extensions: 7 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: 501 Length of database: 499 Length adjustment: 34 Effective length of query: 467 Effective length of database: 465 Effective search space: 217155 Effective search space used: 217155 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 Apr 09 2024. 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