Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate BWI76_RS21985 BWI76_RS21985 aldehyde dehydrogenase
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__Koxy:BWI76_RS21985 Length = 506 Score = 333 bits (854), Expect = 8e-96 Identities = 186/487 (38%), Positives = 274/487 (56%), Gaps = 17/487 (3%) Query: 4 YRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTTV 61 Y N+I+G++VE F + +PVDG+ + Q +D + +D A+ A H A AWG+T+ Sbjct: 19 YGNFIDGKFVEPIGGEFFMNTSPVDGSNIGQFPRSDAKDIDFALDAAHRAA-DAWGKTSA 77 Query: 62 AERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAPL 121 RA +L ++AD I+ + AE D GKP+ D+P +FR FA L+ Sbjct: 78 QHRANLLLQVADRIEANLEYLAVAESWDNGKPIRETLNADLPLAVDHFRYFAGCLRAQEG 137 Query: 122 DTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEET 181 T + D + Y +PLGVVG I PWN PLL+ WK+APALA GN VV KP+E+T Sbjct: 138 STAEID----ETTVAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCVVLKPAEQT 193 Query: 182 PGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRA 241 P + TLL E++ + P GV N+V GFG + AGE + T+ I I FTG + G IM Sbjct: 194 PLSITLLLEIIGDL-FPAGVLNVVQGFGKE-AGEALATSKRIAKIAFTGSTPVGRHIMAC 251 Query: 242 AATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVYVE 295 AA ++ P + ELGGK+ I FAD EK ++G++ F + G+VC C R ++ Sbjct: 252 AAENIIPCTVELGGKSPNIYFADVMEGEEEYIEKAVEGLVLG-FFNQGEVCTCPSRALIQ 310 Query: 296 RPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGG 355 IY F+ +++V ++ G P D T +G S + DK+LSY K+AR+EG ++L GG Sbjct: 311 ESIYEPFMARVMDKVAQIRRGDPFDTDTMIGAQASRQQFDKILSYIKIARDEGGKILTGG 370 Query: 356 GVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKYG 415 D GF+++PT+I G R +EE+FGP+ V+ F EAEA+++AN T++G Sbjct: 371 ERASISAELDNGFYIQPTLIQGR-NDMRSFQEEIFGPVIGVTTFKDEAEALSIANQTQFG 429 Query: 416 LSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFYS 475 L A WT + N +R+ ++ G W N + + FGG SG+GRE +LN Y Sbjct: 430 LGAGVWTRDTNLAYRMGRGIKAGRVWTNCYHIYPAHAAFGGYKQSGVGRETHKMALNAYQ 489 Query: 476 ELTNVCV 482 + N+ V Sbjct: 490 QTKNLLV 496 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: 638 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