Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Pf6N2E2_1381 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1381 Length = 506 Score = 339 bits (870), Expect = 1e-97 Identities = 188/496 (37%), Positives = 285/496 (57%), Gaps = 27/496 (5%) Query: 3 QYRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60 +Y N+I GE+V + F + +PV+G V+A+ + +D A+ A HAA AWG+T+ Sbjct: 18 RYGNFIGGEFVAPVNGEYFTNTSPVNGEVIAEFPRSSAADIDKALDAAHAAA-DAWGKTS 76 Query: 61 VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120 V +R+ +L +IAD I++ + +E D GK V D+P A +FR FA ++ Sbjct: 77 VQDRSLVLLKIADRIEQNLEILAVSETWDNGKAVRETLNADVPLAADHFRYFAGCIRAQE 136 Query: 121 LDTFQTDLPDGARALN-----YAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVA 175 GA +N Y +PLGVVG I PWN PLL+ WK+APALA GN +V Sbjct: 137 ---------GGAAEINELTTAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVL 187 Query: 176 KPSEETPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTG 235 KP+E+TP + + E++ + +PPGV N+VHGFG + AGE + T+ I I FTG + G Sbjct: 188 KPAEQTPLSIMVFIELVADL-LPPGVLNIVHGFGRE-AGEALATSKRIAKIAFTGSTPIG 245 Query: 236 SAIMRAAATHVKPVSFELGGKNAAIIFAD------CDFEKMIDGMMRAVFLHSGQVCLCA 289 S IM+ AA ++ P + ELGGK+ I F D EK +G++ A F + G+VC C Sbjct: 246 SHIMKCAAENIIPSTVELGGKSPNIFFEDIMQAEPAFIEKAAEGLVLA-FFNQGEVCTCP 304 Query: 290 ERVYVERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGA 349 R V+ IY F+ ++++ +K G P D T +G S + DK+LSY ++A++EGA Sbjct: 305 SRALVQESIYAPFMAEVMKKIAKIKRGNPLDTETMVGAQASEQQFDKILSYLEIAQQEGA 364 Query: 350 QVLVGGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALA 409 ++L GG + +G++++PT++ G R +EE+FGP+ V+ F EAEA+A+A Sbjct: 365 ELLTGGAAERLEGDLSSGYYIQPTLLKG-HNKMRVFQEEIFGPVVGVTTFKDEAEALAIA 423 Query: 410 NDTKYGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMH 469 NDT++GL A WT ++NR +R+ A++ G W N + L FGG SG+GRE Sbjct: 424 NDTEFGLGAGLWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKM 483 Query: 470 SLNFYSELTNVCVRID 485 L+ Y + N+ V D Sbjct: 484 MLDHYQQTKNLLVSYD 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: 611 Number of extensions: 29 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