Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate PP_2680 PP_2680 aldehyde dehydrogenase
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__Putida:PP_2680 Length = 506 Score = 333 bits (854), Expect = 8e-96 Identities = 185/485 (38%), Positives = 276/485 (56%), Gaps = 17/485 (3%) Query: 22 NYIDGNFVTSASS--FANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQD 79 N+I G FV + F N +PVNG+ I++ + A+ V A+ AA A + WGK SVQD Sbjct: 21 NFIGGEFVQPLAGQYFINSSPVNGQPIAEFPRSTAQDVERALDAAHAAAEA-WGKTSVQD 79 Query: 80 RAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDL 139 RA ++ KIAD I+ E E D G+ + + D+P A +FR FA + + Sbjct: 80 RARVLLKIADRIEQNLEVLAVTESWDNGKAIRETLNADVPLAADHFRYFAGCIRAQEGGV 139 Query: 140 FEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPS 199 E++ G + Y + +PLGV+G I PWN PLL+ WK+APALA GN VV KP+E++P Sbjct: 140 GEIN----EGTVAYHIHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCVVLKPAEQTPL 195 Query: 200 SATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVA 259 S T+ AE++ D +P GV N++ GFG++ AGE L I+ + FTG + GS IMK A Sbjct: 196 SITVFAELIADL-LPAGVLNIVQGFGRE-AGEALATSKRIAKIAFTGSTPVGSHIMKCAA 253 Query: 260 DGVKEVSFELGGKNAAVVFAD------ADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRS 313 + + + ELGGK+ + F D A ++ A EG++ + F N G+VC C R + S Sbjct: 254 ENIIPSTVELGGKSPNIFFEDIMQAEPAFIEKAAEGLVLAFF-NQGEVCTCPSRALIQES 312 Query: 314 IFDEFVSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGV 373 I++ F++ + + ++ G P +G S DK+LSY +A +EGA ++TGGG Sbjct: 313 IYEPFMAEVMKKIAKITRGNPLDTETMVGAQASEQQYDKILSYLEIAREEGAQLLTGGGA 372 Query: 374 PKFNDERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLA 433 + + G Y+QPT+ G ++K R EEIFGPV ++ F DE E + NDS +GL Sbjct: 373 ERLQGDLASGYYIQPTLLKG-NNKMRVFQEEIFGPVVGVTTFKDEAEALAIANDSEFGLG 431 Query: 434 CAIWTTNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDI 493 +WT +++RA+R+ R I G VW N ++L FGG K SG+GRE + +D Y Sbjct: 432 AGLWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQQT 491 Query: 494 ANICI 498 N+ + Sbjct: 492 KNLLV 496 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: 553 Number of extensions: 20 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: 500 Length of database: 506 Length adjustment: 34 Effective length of query: 466 Effective length of database: 472 Effective search space: 219952 Effective search space used: 219952 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