Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate HSERO_RS05710 HSERO_RS05710 aldehyde dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__HerbieS:HSERO_RS05710 Length = 486 Score = 236 bits (602), Expect = 1e-66 Identities = 163/474 (34%), Positives = 238/474 (50%), Gaps = 12/474 (2%) Query: 10 YIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLRRS 69 YIDG+ Q + + V PAT +AL + VD AV +A A PAW+ S L R+ Sbjct: 19 YIDGKWQPPQGSERAAVVAPATEERVCEIALGNAADVDQAVQAARRAIPAWAATSPLERA 78 Query: 70 RVMFKFKELLDRHHDELAQIISREHGKVLSDAH-GEVTRGIEIVEYACGAPNLLKTDFSD 128 ++ + LL + AQ ++ E G +S A V E + A NL F Sbjct: 79 ALLGRVHALLLERSELFAQALTLEMGAPISYARTAHVPLAAEHLRVA--RDNLADYPFIR 136 Query: 129 NIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLM 188 G +R+P+GVCA +TP+N+P+ + AL AG +LKPSE P ++LL Sbjct: 137 PRG---TTAIVREPIGVCALITPWNWPIYQITAKVGPALAAGCTVVLKPSELSPLSALLF 193 Query: 189 ARLLTEAGLPDGVFNVVQGDKVAVDALLQ-HPDIEAISFVGSTPIAEYIHQQGTAQGKRV 247 A ++ EAG+P GVFN+V G V A L HP ++ IS GST + Q KRV Sbjct: 194 AEIVHEAGVPAGVFNLVNGSGAEVGAALSAHPQVDMISITGSTRAGVLVAQAAAVTVKRV 253 Query: 248 QALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPR 307 G K+ +V+PDADL++A + AA + G+ C A + + + L Sbjct: 254 AQELGGKSPNLVLPDADLERAIPPGVAAALRNMGQSCSAPTRLIVPRAALARVHELALAT 313 Query: 308 IDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFFV 367 + Q+K+G+ T GPL +V+ I+AG+ +GARL+ G G + G QG++ Sbjct: 314 LAQMKVGDPNDAATTHGPLANRAQFLRVQQMIEAGLQDGARLLAGGPG-RPDGLAQGYYA 372 Query: 368 GATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARA 427 T+F +V +M I Q+EIFGPVL I+ A+A+ N +G G RD RA Sbjct: 373 RPTIFSEVHTDMVIAQEEIFGPVLAILPYDTVEEAIAIANDTVYGLGAHVQGRDKDQVRA 432 Query: 428 FARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVM 481 A I+ G V +N P P A FGG+K+S G+ YG EG+ Y K+++ Sbjct: 433 VAARIQSGQVHLNYPAWDPQA--PFGGYKQS--GNGREYGVEGMEEYMEVKAIL 482 Lambda K H 0.320 0.137 0.412 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: 556 Number of extensions: 29 Number of successful extensions: 6 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