Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate H281DRAFT_03644 H281DRAFT_03644 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__Burk376:H281DRAFT_03644 Length = 499 Score = 333 bits (853), Expect = 1e-95 Identities = 187/457 (40%), Positives = 263/457 (57%), Gaps = 8/457 (1%) Query: 35 FANINPVNGKLISDVFEADAKQVNEAVVAAQNAL-KGPWGKLSVQDRAALIHKIADGIQA 93 + ++ P + + ++ A+A EAV AA A K W L RA ++++IAD I A Sbjct: 31 YKSLYPADQSVNMEISTANADDAREAVEAADIAWRKSDWSGLKPHQRALILYRIADLIMA 90 Query: 94 RFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDGSGALNY 153 R E + D G+P+ + R L + A FR FA +T L E T L Sbjct: 91 RHEALAQLQRRDNGKPIGETRVL-VASAANTFRYFAACLET----LDEEVTPSRGDYLTM 145 Query: 154 TVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGV 213 +V +P+GVI I+PWN P+ K+APALA GN VV KP+E +P + LA + +AGV Sbjct: 146 SVYEPIGVIAAITPWNSPIASDAQKLAPALAGGNAVVLKPAEVTPLVSLALARICEEAGV 205 Query: 214 PPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKN 273 P GV +++ G G G+ L +HP + ++FTG ++ G I + AD + VS ELGGK+ Sbjct: 206 PKGVISVLPGKGS-VIGDVLVRHPLVKKVSFTGGTEVGRGIARIAADKLMPVSLELGGKS 264 Query: 274 AAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGY 333 VVF DADLD A+ GVL F++SG+ C+ R++V RS++D F+ L A +L VG Sbjct: 265 PTVVFDDADLDHAVNGVLYGIFSSSGEACIAGSRLFVQRSVYDAFMKRLVEGARKLRVGD 324 Query: 334 PDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERDQGAYVQPTIWTG 393 P + MGPLI+ HR+ V Y L ++EG ++ GG P D R+QG Y QPTI G Sbjct: 325 PSRVETQMGPLITQAHRETVERYVALGLEEGGRLLCGGERP-VGDGREQGTYFQPTILEG 383 Query: 394 LSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHV 453 LS+ AR EEIFGPV PFDDE ++ N+S +GLA IWT + RA+R +R + Sbjct: 384 LSNNARICQEEIFGPVLVAMPFDDEASLLKEANNSVFGLAAGIWTRDYKRAYRTARALEA 443 Query: 454 GLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFY 490 G +W+NT+ L + TPF G K SG+GRE GR + Y Sbjct: 444 GTIWINTYKLFSISTPFSGWKESGMGREKGRLGIREY 480 Lambda K H 0.318 0.135 0.405 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: 547 Number of extensions: 24 Number of successful extensions: 4 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: 500 Length of database: 499 Length adjustment: 34 Effective length of query: 466 Effective length of database: 465 Effective search space: 216690 Effective search space used: 216690 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 (21.7 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