Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Dsui_1464 Dsui_1464 NAD-dependent aldehyde dehydrogenase
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__PS:Dsui_1464 Length = 506 Score = 335 bits (859), Expect = 2e-96 Identities = 188/495 (37%), Positives = 274/495 (55%), Gaps = 17/495 (3%) Query: 3 QYRNYINGEWVESARR--FDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60 +Y N+I G+WV + FD + P+ G Q ++ E ++ A+ A HAA WG+T+ Sbjct: 18 RYDNFIGGKWVAPVKGQYFDVITPITGKPYTQAAQSGAEDIELALDAAHAAA-DKWGKTS 76 Query: 61 VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120 ER+ IL +IAD I+ + E D GK + DIP A +FR FA L++ Sbjct: 77 ATERSNILLKIADRIEANLEMLAYVETVDNGKAIRETLNADIPLAADHFRYFAGCLRSQE 136 Query: 121 LDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEE 180 + D + Y +PLGVVG I PWN P+L+ WK+APAL GN VV KP+E Sbjct: 137 GSISEID----ENTIAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALGAGNCVVLKPAES 192 Query: 181 TPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMR 240 TP + +LAE++ + +PPGV N+V+G+G D AG + ++ I I FTG + TG I + Sbjct: 193 TPISILVLAELIADL-LPPGVLNIVNGYGRD-AGMALASSKRIAKIAFTGSTATGRVIAQ 250 Query: 241 AAATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVYV 294 AAA + P + ELGGK+ I FAD F+K I+G++ F + G+VC C R + Sbjct: 251 AAANSLIPATLELGGKSPNIFFADVAAADDDFFDKAIEGLVLFAF-NQGEVCTCPSRALI 309 Query: 295 ERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVG 354 IY+ F++ + RVKA+K G P D + MG S DK++SY + +EEGAQ LVG Sbjct: 310 HESIYDHFMERVLARVKAIKQGSPLDTDSMMGAQASQMQMDKIMSYLAIGKEEGAQCLVG 369 Query: 355 GGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKY 414 G + G G++++PT+ G R +EE+FGP+ V+ F TEAEA+ +ANDT Y Sbjct: 370 GDRARLGGELAEGYYIQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKTEAEALEIANDTPY 428 Query: 415 GLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFY 474 GL A W+ + N +R+ ++ G W N + FGG SGIGRE L+ Y Sbjct: 429 GLGAGVWSRDGNTAYRMGRGIKAGRVWTNCYHAYPAHATFGGYKESGIGRETHKMMLDHY 488 Query: 475 SELTNVCVRIDQEAV 489 + N+ V +A+ Sbjct: 489 QQTKNLLVSYSPKAL 503 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: 580 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