Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 8501918 DvMF_2633 Aldehyde Dehydrogenase (RefSeq)
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__Miya:8501918 Length = 460 Score = 122 bits (305), Expect = 3e-32 Identities = 104/351 (29%), Positives = 164/351 (46%), Gaps = 24/351 (6%) Query: 133 RALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEETPGTATLLAEVM 192 +A +Y R+PLG V + W P L +A A+ GNAVV +PS E P TA ++ ++ Sbjct: 92 KARSYVRRQPLGRVVAYAHWADPFRSLLVPLADAIGAGNAVVLRPSAEAPATAEMVTRMV 151 Query: 193 HTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRAAATHVKPVSFE 252 P V V G G ++ + T D + + G++R I AA + P + Sbjct: 152 RQYFEPEHV--AVVGGGAETDEALLATAPDF--VWYDGDARGARTIAVLAAPTLTPYAAI 207 Query: 253 LGGKNAAIIFADCDFEKMIDGMMRAVFLHSGQVCLCAERVYVERPIYNRFLDAFVERVKA 312 GG +AA++ D D ++ A FLH+GQ+ + + V+R + +R LDA R + Sbjct: 208 TGGPSAALVHGDADMAMAARRIVWAKFLHAGQLRAAPDVLLVQRTVLDRVLDAL--RTEL 265 Query: 313 LKLGWPQDGTTG-MGPLISAEHRDKVLSYFKLAREEGAQVLVGGGVP-KFGDARD----A 366 + PQ T+ G ++SA AR + ++ +G +P GDA + A Sbjct: 266 ERAFGPQPRTSADFGRMVSAA---------GFAR-QAERLAIGRALPFGPGDAANQPDRA 315 Query: 367 GFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKYGLSATTWTGNLN 426 +V PT++T +P + ++EE FGP+ V P+ EA A + +T Sbjct: 316 SLYVPPTLLTDVPDDSPVLREEGFGPVLVVRPYTRLDEATAFLAGLPALTALYAFTTAHA 375 Query: 427 RGHRVSEAMRVGLSWVN--SWFLRDLRTPFGGVGLSGIGREGGMHSLNFYS 475 RG R+ E R G +N + L + R P GGVG +G G G L +S Sbjct: 376 RGERLMENTRAGAVLINDAATHLANPRLPQGGVGETGHGAMAGPAGLATFS 426 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: 542 Number of extensions: 29 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: 490 Length of database: 460 Length adjustment: 33 Effective length of query: 457 Effective length of database: 427 Effective search space: 195139 Effective search space used: 195139 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: 51 (24.3 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