Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate Ac3H11_4393 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= reanno::psRCH2:GFF2231 (506 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4393 Length = 507 Score = 763 bits (1969), Expect = 0.0 Identities = 365/505 (72%), Positives = 426/505 (84%) Query: 2 IYAQPGTPGAVVSFKPRYGNYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEKA 61 +YA PG PGA +++KP+Y N+IGG+FVPPVKG+YF +PV+G+V RS AEDIE A Sbjct: 3 VYAAPGAPGAKITYKPQYDNFIGGKFVPPVKGQYFDVITPVSGKVYTRAARSTAEDIELA 62 Query: 62 LDAAHAAADAWGKTSVQDRALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPLA 121 LDAAHAAAD+WGKT RA ILLKIA+RIE NLE+LA AET DNGKA+RETLNAD+PL Sbjct: 63 LDAAHAAADSWGKTDAATRANILLKIANRIEENLERLAYAETVDNGKAIRETLNADIPLT 122 Query: 122 ADHFRYFAGCIRAQEGSAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAA 181 DHFRYFAGC+RAQEG+ + I+E+T AYH EPLGVVGQIIPWNFP+LMAAWKLAPAL A Sbjct: 123 VDHFRYFAGCVRAQEGALSNIDENTVAYHIQEPLGVVGQIIPWNFPILMAAWKLAPALGA 182 Query: 182 GNCIVLKPAEQTPLSIMVFIEVVGDLLPPGVLNIVQGFGREAGQALATSTRIAKIAFTGS 241 GNC+VLKPAE TP+SI++ +E++ DLLPPGVLNIV GFGREAG LA S RIAKIAFTGS Sbjct: 183 GNCVVLKPAESTPISILILVELIADLLPPGVLNIVNGFGREAGMPLAQSKRIAKIAFTGS 242 Query: 242 TPVGSHIMRCAAENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEVC 301 T G I + AA N+IP+T+ELGGKSPNIFF DIM+ + AF++KA EGLVL FNQGEVC Sbjct: 243 TSTGRVIAQAAANNLIPATLELGGKSPNIFFADIMDKDDAFLDKAIEGLVLFAFNQGEVC 302 Query: 302 TCPSRALIQESIFEPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQQ 361 TCPSRA+IQESI++ FME V+K++ AIK NPLDTD+M+GAQAS++Q KILSY+++ +Q Sbjct: 303 TCPSRAIIQESIYDQFMERVLKRVAAIKHQNPLDTDSMMGAQASKEQLTKILSYLDLGKQ 362 Query: 362 EGAQILTGGAAEKLEGSLSTGYYVQPTLIKGHNKMRVFQEEIFGPVVGVATFKDEAEALA 421 EGA++L GG L G L GYYVQPTL KGHNKMR+FQEEIFGPV+ V TFKDEAEALA Sbjct: 363 EGAEVLAGGGQAHLGGDLEGGYYVQPTLFKGHNKMRIFQEEIFGPVLAVTTFKDEAEALA 422 Query: 422 IANDTEFGLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETH 481 IANDT +GLGAGVW+R+ N AYRMGR IKAGRVWTNCYH YPAHAAFGGYK+SG+GRETH Sbjct: 423 IANDTLYGLGAGVWSRNGNVAYRMGRAIKAGRVWTNCYHAYPAHAAFGGYKESGIGRETH 482 Query: 482 KMMLDHYQQTKNLLISYDINPLGFF 506 KMMLDHYQQTKNLL+SY N LGFF Sbjct: 483 KMMLDHYQQTKNLLVSYSENKLGFF 507 Lambda K H 0.319 0.136 0.406 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: 760 Number of extensions: 24 Number of successful extensions: 1 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: 506 Length of database: 507 Length adjustment: 34 Effective length of query: 472 Effective length of database: 473 Effective search space: 223256 Effective search space used: 223256 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