Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate PP_0545 PP_0545 aldehyde dehydrogenase
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__Putida:PP_0545 Length = 506 Score = 350 bits (897), Expect = e-101 Identities = 192/491 (39%), Positives = 291/491 (59%), Gaps = 17/491 (3%) Query: 3 QYRNYINGEWVESARR--FDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60 +Y NYI GE+V + F++ +PV+G ++A+ + E +D A+ A HAA AWGRT+ Sbjct: 18 RYGNYIGGEFVTPVKGQYFENTSPVNGKLIAEFPRSTAEDIDKALDAAHAAA-DAWGRTS 76 Query: 61 VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120 V +R+ +L +IAD I++ + E D GKP+ DIP +FR FA ++ Sbjct: 77 VQDRSNVLLKIADRIEQNLELLAITETWDNGKPIRETLNADIPLAVDHFRYFAGCIRAQ- 135 Query: 121 LDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEE 180 + ++ +G A Y + +PLGVVG I PWN P+L+ WK+APALA GN VV KP+E+ Sbjct: 136 -EGGAAEINEGTVA--YHIHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQ 192 Query: 181 TPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMR 240 TP T+L EV+ + +PPGV N+V G+G + AGE + T+ I I FTG + GS IM+ Sbjct: 193 TPLGITVLLEVIGDL-LPPGVLNVVQGYGRE-AGEALATSKRIAKIAFTGSTPVGSHIMK 250 Query: 241 AAATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVYV 294 AA ++ P + ELGGK+ + F D EK +GM+ A F + G+VC C R V Sbjct: 251 CAAENIIPSTVELGGKSPNVYFEDIMQAEPSFIEKAAEGMVLA-FFNQGEVCTCPSRALV 309 Query: 295 ERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVG 354 + IY +F++ +++V +K G P D T +G S + +K+LSY ++A+EEGA++L G Sbjct: 310 QESIYPQFMEVVMKKVLQIKRGDPLDTDTMVGAQASQQQFEKILSYLQIAQEEGAELLTG 369 Query: 355 GGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKY 414 G V K + G++++PT++ G R +EE+FGP+ V+ F EAEA+A+ANDT++ Sbjct: 370 GKVEKLEGSLATGYYIQPTLLKG-NNKMRVFQEEIFGPVVSVTTFKDEAEALAIANDTEF 428 Query: 415 GLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFY 474 GL A WT ++NR +R+ ++ G W N + L FGG SG+GRE L+ Y Sbjct: 429 GLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHY 488 Query: 475 SELTNVCVRID 485 + N+ V D Sbjct: 489 QQTKNLLVSYD 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: 580 Number of extensions: 23 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: 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 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