Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate PP_2680 PP_2680 aldehyde dehydrogenase
Query= reanno::psRCH2:GFF2231 (506 letters) >FitnessBrowser__Putida:PP_2680 Length = 506 Score = 917 bits (2370), Expect = 0.0 Identities = 443/506 (87%), Positives = 478/506 (94%) Query: 1 MIYAQPGTPGAVVSFKPRYGNYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEK 60 MIYAQPGTPGAVVSFKPRYGN+IGGEFV P+ G+YF+N+SPVNG+ IAEFPRS A+D+E+ Sbjct: 1 MIYAQPGTPGAVVSFKPRYGNFIGGEFVQPLAGQYFINSSPVNGQPIAEFPRSTAQDVER 60 Query: 61 ALDAAHAAADAWGKTSVQDRALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPL 120 ALDAAHAAA+AWGKTSVQDRA +LLKIADRIE NLE LAV E+WDNGKA+RETLNADVPL Sbjct: 61 ALDAAHAAAEAWGKTSVQDRARVLLKIADRIEQNLEVLAVTESWDNGKAIRETLNADVPL 120 Query: 121 AADHFRYFAGCIRAQEGSAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALA 180 AADHFRYFAGCIRAQEG EINE T AYH HEPLGVVGQIIPWNFPLLMAAWKLAPALA Sbjct: 121 AADHFRYFAGCIRAQEGGVGEINEGTVAYHIHEPLGVVGQIIPWNFPLLMAAWKLAPALA 180 Query: 181 AGNCIVLKPAEQTPLSIMVFIEVVGDLLPPGVLNIVQGFGREAGQALATSTRIAKIAFTG 240 AGNC+VLKPAEQTPLSI VF E++ DLLP GVLNIVQGFGREAG+ALATS RIAKIAFTG Sbjct: 181 AGNCVVLKPAEQTPLSITVFAELIADLLPAGVLNIVQGFGREAGEALATSKRIAKIAFTG 240 Query: 241 STPVGSHIMRCAAENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEV 300 STPVGSHIM+CAAENIIPSTVELGGKSPNIFFEDIM AEPAFIEKAAEGLVLAFFNQGEV Sbjct: 241 STPVGSHIMKCAAENIIPSTVELGGKSPNIFFEDIMQAEPAFIEKAAEGLVLAFFNQGEV 300 Query: 301 CTCPSRALIQESIFEPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQ 360 CTCPSRALIQESI+EPFM VMKKI I RGNPLDT+TMVGAQASEQQ+DKILSY+EIA+ Sbjct: 301 CTCPSRALIQESIYEPFMAEVMKKIAKITRGNPLDTETMVGAQASEQQYDKILSYLEIAR 360 Query: 361 QEGAQILTGGAAEKLEGSLSTGYYVQPTLIKGHNKMRVFQEEIFGPVVGVATFKDEAEAL 420 +EGAQ+LTGG AE+L+G L++GYY+QPTL+KG+NKMRVFQEEIFGPVVGV TFKDEAEAL Sbjct: 361 EEGAQLLTGGGAERLQGDLASGYYIQPTLLKGNNKMRVFQEEIFGPVVGVTTFKDEAEAL 420 Query: 421 AIANDTEFGLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET 480 AIAND+EFGLGAG+WTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET Sbjct: 421 AIANDSEFGLGAGLWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET 480 Query: 481 HKMMLDHYQQTKNLLISYDINPLGFF 506 HKMMLDHYQQTKNLL+SYDINPLGFF Sbjct: 481 HKMMLDHYQQTKNLLVSYDINPLGFF 506 Lambda K H 0.319 0.136 0.406 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: 884 Number of extensions: 25 Number of successful extensions: 1 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: 506 Length of database: 506 Length adjustment: 34 Effective length of query: 472 Effective length of database: 472 Effective search space: 222784 Effective search space used: 222784 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