Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF3742 PGA1_262p01460 aldehyde dehydrogenase
Query= BRENDA::Q97YT9 (492 letters) >FitnessBrowser__Phaeo:GFF3742 Length = 497 Score = 246 bits (629), Expect = 1e-69 Identities = 147/474 (31%), Positives = 253/474 (53%), Gaps = 9/474 (1%) Query: 16 KLYINGEFIDSKTDTIGKAYNPAK-DEIIAEVPFSAKDEVEEAIQSAQEAFEKWREVPIT 74 K I GE++ +++ + NP+ +++ ++ D++E + AQ A +W + Sbjct: 21 KNLIAGEWLAGESEVENR--NPSDLSDLVGIFAQASADQLEATLDQAQVAQREWAAYGLE 78 Query: 75 TRIQYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEAAISAAYTLYK-G 133 + L A+ N + +E + ++ + GK + E +G++ R + AA L + G Sbjct: 79 RKQAVLNAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFF--TYYAAECLRQIG 136 Query: 134 EHLDQVSQEVDETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITPVP 193 E+ D V +++ V RE +G II+P+NFPT W + A+ GN VV KP+ ITP Sbjct: 137 ENADSVRPDIEVDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANITPAS 196 Query: 194 MDFIIRIFDEIKLPRGVVNVVHGA-KDVVDEFLTNKLVQGVTFVGSTRVGKYIYENAGKN 252 + I + +P+G+ ++V G+ + + + + V ++F GS VGK I A +N Sbjct: 197 AVALAEIIERQDIPKGLFSLVMGSGRSIGQRLVESPKVNAISFTGSVPVGKGIASAAIQN 256 Query: 253 GKKAIVQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLAAANLVAVGNIYDEVKRK 312 K ++ G+KN + VM DADL+ A+ + FG GQ+C A++ LV I+D K Sbjct: 257 LTKVQMEMGSKNALAVMDDADLDLAVTLALGGAFGGTGQKCTASSRLVVHAGIHDAFVEK 316 Query: 313 FIEASKQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKVPEYPN 372 + +K +K+G+ L+ V MGPVV++ + Y++ G EGA+L G+ +++P Sbjct: 317 LVTGAKAMKVGHALEAGVQMGPVVSEQQLNENLAYVDLGKTEGAELACGGQRLEMPH--Q 374 Query: 373 GYFLGPTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGNASSIFTTSGY 432 G+++ P VF T +M I +EE+F P+ S+I V + DEA++++N +N+G S I T S Sbjct: 375 GFYMSPGVFLNTTNDMRINREEMFAPLTSVIKVGSYDEALSVVNDTNFGLTSGIVTQSLA 434 Query: 433 YARKFRREVNTGNIGINIGVAAPMAFFPFGGRKESFFGILHGQIDSVDFFTDKK 486 A FRR TG + +N+ A PFGGR +S +G + +F+T K Sbjct: 435 RATHFRRNARTGVVTVNLPTAGTDYHVPFGGRGDSSYGPREQGKAAAEFYTTVK 488 Lambda K H 0.319 0.139 0.398 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: 516 Number of extensions: 21 Number of successful extensions: 4 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: 492 Length of database: 497 Length adjustment: 34 Effective length of query: 458 Effective length of database: 463 Effective search space: 212054 Effective search space used: 212054 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 (21.7 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