Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__azobra:AZOBR_RS22315 Length = 497 Score = 274 bits (700), Expect = 6e-78 Identities = 164/469 (34%), Positives = 247/469 (52%), Gaps = 11/469 (2%) Query: 22 NYIDGNF--VTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQD 79 ++ G F +S F +NP G+ +++ +A V+ AV AA A K W K V++ Sbjct: 22 HFFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAAVAAQK-EWAKRPVRE 80 Query: 80 RAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDL 139 R L+ + + A EE +TG+ + ++ F F LA + Sbjct: 81 RGKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFGGLAPELKGET 140 Query: 140 FEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPS 199 + S L TVR+P+GV+G I PWN+PLLL K+APA+ GN VV K +EE+P Sbjct: 141 IPFNPS----MLTMTVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVKSAEEAPL 196 Query: 200 SATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVA 259 + + ++++ +P GV N++ G+G + G L H + +TFTG +TG + K A Sbjct: 197 AVLRVVQLINTV-IPAGVVNILSGYGPE-CGAPLVAHKDVKKVTFTGSVETGKIVYKTAA 254 Query: 260 DGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSS-FTNSGQVCLCSERVYVHRSIFDEF 318 + + V+ ELGGK+ +V DADLD AI G + FT GQ C S R++VH SI D F Sbjct: 255 EKLIPVTLELGGKSPMIVCGDADLDQAIAGAIAGMRFTRQGQSCTASSRIFVHDSIHDAF 314 Query: 319 VSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFND 378 V LK + + +G P + ++G ++S D+V SY + + GAT +P + Sbjct: 315 VEKLKEKVNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCSAMPS-DP 373 Query: 379 ERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWT 438 + +G YVQP I+TG+ + R EEIFGPVC + + D +EVI + ND+ YGLA IWT Sbjct: 374 KLTKGLYVQPHIFTGVKNSDRIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGLAATIWT 433 Query: 439 TNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSM 487 +L A ++ G V VN + +GGVK SGLG+E +M Sbjct: 434 RDLKVAMDAVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEASLEAM 482 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: 529 Number of extensions: 29 Number of successful extensions: 6 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: 497 Length adjustment: 34 Effective length of query: 466 Effective length of database: 463 Effective search space: 215758 Effective search space used: 215758 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