Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF3406 PS417_17430 aldehyde dehydrogenase
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__WCS417:GFF3406 Length = 506 Score = 341 bits (874), Expect = 4e-98 Identities = 189/497 (38%), Positives = 286/497 (57%), Gaps = 27/497 (5%) Query: 2 KQYRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRT 59 ++Y NYI GE+V S F + +PV G V+A+ ++ +D A+ A HAA AWG+T Sbjct: 17 QRYGNYIGGEFVAPLSGEYFTNTSPVTGEVIAEFPRSNAADIDKALDAAHAAA-DAWGKT 75 Query: 60 TVAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTA 119 + +R+ +L +IAD I++ + E D GK V D+P A +FR FA ++ Sbjct: 76 SPQDRSLVLLKIADRIEQHLEVLAVTESWDNGKAVRETLNADVPLAADHFRYFAGCIRAQ 135 Query: 120 PLDTFQTDLPDGARALN-----YAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVV 174 GA +N Y +PLGVVG I PWN PLL+ WK+APALA GN +V Sbjct: 136 E---------GGAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIV 186 Query: 175 AKPSEETPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRT 234 KP+E+TP + + AE+++ + +PPGV N+V GFG + AGE + T+ I I FTG + Sbjct: 187 LKPAEQTPLSIMVFAELINDL-LPPGVLNIVQGFGRE-AGEALATSKRIAKIAFTGSTPI 244 Query: 235 GSAIMRAAATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLC 288 G+ IM AAA ++ P + ELGGK+ I F D EK +G++ A F + G+VC C Sbjct: 245 GAHIMHAAAENLIPSTVELGGKSPNIFFEDIMQAEPQFIEKAAEGLVLA-FFNQGEVCTC 303 Query: 289 AERVYVERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEG 348 R V+ IY+ F+ ++++ +K G P D T +G S + DK+LSY K+A+EEG Sbjct: 304 PSRALVQESIYDDFMKVVMKKIVKIKRGNPLDTETMVGAQASEQQYDKILSYLKIAQEEG 363 Query: 349 AQVLVGGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIAL 408 A++L GG + +G++++PT++ G R +EE+FGP+ ++ F EAEA+A+ Sbjct: 364 AELLTGGAAERLEGDLSSGYYIQPTLLKG-HNKMRVFQEEIFGPVVGITTFKDEAEALAI 422 Query: 409 ANDTKYGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGM 468 AND+++GL A WT ++NR +R+ A++ G W N + L FGG SG+GRE Sbjct: 423 ANDSEFGLGAGLWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRENHK 482 Query: 469 HSLNFYSELTNVCVRID 485 L+ Y + N+ V D Sbjct: 483 MMLDHYQQTKNLLVSYD 499 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: 624 Number of extensions: 28 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: 506 Length adjustment: 34 Effective length of query: 456 Effective length of database: 472 Effective search space: 215232 Effective search space used: 215232 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