Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Ac3H11_4393 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4393 Length = 507 Score = 325 bits (834), Expect = 2e-93 Identities = 187/488 (38%), Positives = 272/488 (55%), Gaps = 17/488 (3%) Query: 3 QYRNYINGEWVESARR--FDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60 QY N+I G++V + FD + PV G V + + E ++ A+ A HAA +WG+T Sbjct: 19 QYDNFIGGKFVPPVKGQYFDVITPVSGKVYTRAARSTAEDIELALDAAHAAA-DSWGKTD 77 Query: 61 VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120 A RA IL +IA+ I+ + AE D GK + DIP +FR FA ++ Sbjct: 78 AATRANILLKIANRIEENLERLAYAETVDNGKAIRETLNADIPLTVDHFRYFAGCVRAQE 137 Query: 121 LDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEE 180 D + Y +++PLGVVG I PWN P+L+ WK+APAL GN VV KP+E Sbjct: 138 GALSNID----ENTVAYHIQEPLGVVGQIIPWNFPILMAAWKLAPALGAGNCVVLKPAES 193 Query: 181 TPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMR 240 TP + +L E++ + +PPGV N+V+GFG + AG + + I I FTG + TG I + Sbjct: 194 TPISILILVELIADL-LPPGVLNIVNGFGRE-AGMPLAQSKRIAKIAFTGSTSTGRVIAQ 251 Query: 241 AAATHVKPVSFELGGKNAAIIFAD------CDFEKMIDGMMRAVFLHSGQVCLCAERVYV 294 AAA ++ P + ELGGK+ I FAD +K I+G++ F + G+VC C R + Sbjct: 252 AAANNLIPATLELGGKSPNIFFADIMDKDDAFLDKAIEGLVLFAF-NQGEVCTCPSRAII 310 Query: 295 ERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVG 354 + IY++F++ ++RV A+K P D + MG S E K+LSY L ++EGA+VL G Sbjct: 311 QESIYDQFMERVLKRVAAIKHQNPLDTDSMMGAQASKEQLTKILSYLDLGKQEGAEVLAG 370 Query: 355 GGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKY 414 GG G + G++V+PT+ G R +EE+FGP+ V+ F EAEA+A+ANDT Y Sbjct: 371 GGQAHLGGDLEGGYYVQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALAIANDTLY 429 Query: 415 GLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFY 474 GL A W+ N N +R+ A++ G W N + FGG SGIGRE L+ Y Sbjct: 430 GLGAGVWSRNGNVAYRMGRAIKAGRVWTNCYHAYPAHAAFGGYKESGIGRETHKMMLDHY 489 Query: 475 SELTNVCV 482 + N+ V Sbjct: 490 QQTKNLLV 497 Lambda K H 0.321 0.137 0.420 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: 566 Number of extensions: 26 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: 490 Length of database: 507 Length adjustment: 34 Effective length of query: 456 Effective length of database: 473 Effective search space: 215688 Effective search space used: 215688 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