Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__MR1:203555 Length = 506 Score = 350 bits (898), Expect = e-101 Identities = 190/492 (38%), Positives = 287/492 (58%), Gaps = 17/492 (3%) Query: 2 KQYRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRT 59 ++Y N+I G+WV + + FD+ +PV+G ++ +D + ++ A+ A HAA + AWG+T Sbjct: 17 EKYANFIGGKWVAPVNGKYFDNRSPVNGQNFCKIPRSDAQDIELALDAAHAA-KDAWGKT 75 Query: 60 TVAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTA 119 +V ER+ IL RIAD +++ + AE + GK V D+P +FR FA ++ Sbjct: 76 SVTERSNILLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQ 135 Query: 120 PLDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSE 179 D ++Y +PLGVVG I PWN PLL+ WKIAPALA GN VV KP+E Sbjct: 136 EGSAADID----GNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAE 191 Query: 180 ETPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIM 239 +TP + +L E++ + +PPGV N+V+GFG + AG+ + T+ I + FTG + G I+ Sbjct: 192 QTPVSILVLLELIEDL-LPPGVLNVVNGFGAE-AGQALATSKRIAKLAFTGSTEVGFHIL 249 Query: 240 RAAATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVY 293 + AA + P + ELGGK+ + FAD +K ++GM+ A F + G+VC C RV Sbjct: 250 KCAAESLIPSTVELGGKSPNLYFADVMDQEDEYLDKAVEGMLLA-FFNQGEVCTCPSRVL 308 Query: 294 VERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLV 353 ++ IY+RF++ + R + +K G P D T +G S E DK+LSY + ++EGAQVL+ Sbjct: 309 IQESIYDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLL 368 Query: 354 GGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTK 413 GG + + + G+++ PTI+ G R +EE+FGP+ V+ F EAEA+A+ANDT+ Sbjct: 369 GGSLCQLEGEQSKGYYISPTIMKG-HNKMRIFQEEIFGPVISVTTFKDEAEALAIANDTE 427 Query: 414 YGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNF 473 YGL A WT ++NR R+ ++ G W+N + FGG SGIGRE LN Sbjct: 428 YGLGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLNH 487 Query: 474 YSELTNVCVRID 485 Y N+ V D Sbjct: 488 YQNTKNLLVSYD 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: 594 Number of extensions: 21 Number of successful extensions: 8 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 Apr 09 2024. 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