Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF882 Psest_0905 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__psRCH2:GFF882 Length = 499 Score = 345 bits (886), Expect = 2e-99 Identities = 192/480 (40%), Positives = 280/480 (58%), Gaps = 10/480 (2%) Query: 23 YIDGNFVTS--ASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDR 80 +ID +V+ + INP NGK+++++ A A V+ AV AAQ A W S +R Sbjct: 20 FIDNQWVSDEYGETLDIINPANGKILTNIPNATAADVDRAVQAAQRAFM-TWRTTSPAER 78 Query: 81 AALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLF 140 A + KIAD ++A + F E D G+P+ ++R++DIP AI +FR FA + ++ + Sbjct: 79 ANALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFAGVIRSQSDEAV 138 Query: 141 EMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSS 200 + S AL+ +PLGV+G + PWN PLL+ WK+APA+A GNTVV KPSE +P + Sbjct: 139 MLDEQTLSIALS----EPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSELTPVT 194 Query: 201 ATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVAD 260 LA++ +P GV N++ G G + G+ L HP + L FTG ++ G + A A Sbjct: 195 ILELAKIFAKV-LPAGVVNIVTGLGT-TVGQALLDHPDLRKLAFTGSTRVGELVANAAAK 252 Query: 261 GVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVS 320 + + ELGGK+A +VF DA+ D A+EG + + N GQVC R++VH SI++ F++ Sbjct: 253 KIIPATLELGGKSANIVFPDANWDKAVEGAVLAILWNQGQVCESGARLFVHESIYERFLA 312 Query: 321 GLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDER 380 LK + E + VG P MG +S +++L Y +A EGA V+ GGG Sbjct: 313 ELKHKFEAVRVGDPLNPDTMMGAQVSKSQMERILGYVDIAKQEGAEVLIGGG-RLTGANY 371 Query: 381 DQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTN 440 D G ++QPTI G+ + R EEIFGPV + PF DE EVI NDS YGLA A+WT + Sbjct: 372 DAGFFIQPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVWTQD 431 Query: 441 LSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICIKI 500 ++RA RV+R + G +WVNT++ PFGG K SGLGRE + ++ YS NI + + Sbjct: 432 INRALRVARAVETGRMWVNTYHEIPAHAPFGGYKKSGLGRETHKSMLEAYSQKKNIYVSL 491 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: 573 Number of extensions: 27 Number of successful extensions: 5 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