Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF3775 PGA1_262p01790 aldehyde dehydrogenase
Query= BRENDA::Q97YT9 (492 letters) >FitnessBrowser__Phaeo:GFF3775 Length = 483 Score = 242 bits (617), Expect = 2e-68 Identities = 142/468 (30%), Positives = 254/468 (54%), Gaps = 9/468 (1%) Query: 19 INGEFIDSKTDTIGKAYNPAK-DEIIAEVPFSAKDEVEEAIQSAQEAFEKWREVPITTRI 77 I G+++ T+ + NP+ +++I ++ D+++ ++ AQ A +W I + Sbjct: 9 IAGDWVAGATEIENR--NPSDLNDLIGMFAQASPDQLDATLEQAQRAQVEWAGYGIERKY 66 Query: 78 QYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEAAISAAYTLYK-GEHL 136 L A+ + +E + ++ + GK + E +G++ R + AA TL + G+ Sbjct: 67 NVLMAIGTEMMTRAEELGTLLAREEGKPLAEGKGEVYRAGQFF--TYYAAETLRQMGDTA 124 Query: 137 DQVSQEVDETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITPVPMDF 196 D V ++ V REP+GV +I+P+NFPT W + A+ GN VV KP+ +TP Sbjct: 125 DSVRDGIEIDVRREPVGVVVVISPWNFPTATASWKIAPALCYGNAVVWKPANVTPASAVA 184 Query: 197 IIRIFDEIKLPRGVVNVVHGAKDVVDEFLTNK-LVQGVTFVGSTRVGKYIYENAGKNGKK 255 ++ I +P+G+V++V GA + + L V ++F GS VGK I A +N + Sbjct: 185 LVEIIARQDIPKGLVSLVMGAGSSIGQRLVESPKVNAISFTGSVPVGKGIAACAIQNLTR 244 Query: 256 AIVQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLAAANLVAVGNIYDEVKRKFIE 315 ++ G+KN + VM DAD++ A+ + FG +GQ+C A++ LV +I+D+ K + Sbjct: 245 VQMEMGSKNALAVMDDADIDLAVSLALGGAFGGSGQKCTASSRLVVHQSIHDQFVEKLVM 304 Query: 316 ASKQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKVPEYPNGYF 375 +K +K+G+ L+ MGPVV++ + Y++ EGA+LL G+ +++ +GY+ Sbjct: 305 GAKAMKVGHALEAGTQMGPVVSEQQLNENLAYVDLAASEGAELLCGGQRLEMA--TDGYY 362 Query: 376 LGPTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGNASSIFTTSGYYAR 435 + P +F +M I +EE+F P+A +I V + DEA++++N +N+G + I TT+ A Sbjct: 363 VSPGIFVGTNNDMRINREEMFAPLACVIPVASYDEALHVVNDTNFGLTAGIVTTNLARAT 422 Query: 436 KFRREVNTGNIGINIGVAAPMAFFPFGGRKESFFGILHGQIDSVDFFT 483 FRR +G + +N+ A PFGGR +S +G + DF+T Sbjct: 423 HFRRNAQSGCVMVNLPTAGTDYHVPFGGRGDSSYGPREQGQTARDFYT 470 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: 485 Number of extensions: 28 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: 483 Length adjustment: 34 Effective length of query: 458 Effective length of database: 449 Effective search space: 205642 Effective search space used: 205642 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