Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_028488290.1 Q394_RS0104930 aldehyde dehydrogenase
Query= reanno::psRCH2:GFF2231 (506 letters) >NCBI__GCF_000621325.1:WP_028488290.1 Length = 506 Score = 822 bits (2123), Expect = 0.0 Identities = 394/506 (77%), Positives = 447/506 (88%) Query: 1 MIYAQPGTPGAVVSFKPRYGNYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEK 60 M YA P T GAV++FK RYGN+IGGE++ PV GEYF N SPVNG+ + PRS AEDIE Sbjct: 1 MQYANPNTEGAVINFKERYGNFIGGEWIAPVNGEYFDNISPVNGKPFCQIPRSSAEDIEL 60 Query: 61 ALDAAHAAADAWGKTSVQDRALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPL 120 ALDAAHAA DAWG+TSV R+ ILLKIADRI+ANLE LAVAETWDNGKAVRETLNADVPL Sbjct: 61 ALDAAHAAKDAWGRTSVAARSNILLKIADRIDANLEMLAVAETWDNGKAVRETLNADVPL 120 Query: 121 AADHFRYFAGCIRAQEGSAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALA 180 ++DHFRYFAGC+RAQEG+ EI+EHT AYHFHEPLGVVGQIIPWNFPLLMA WKLAPALA Sbjct: 121 SSDHFRYFAGCLRAQEGTMGEIDEHTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALA 180 Query: 181 AGNCIVLKPAEQTPLSIMVFIEVVGDLLPPGVLNIVQGFGREAGQALATSTRIAKIAFTG 240 AGNC+VLKPAEQTP SI+V +E++ DLLP GVLNIV G+G EAG+ALATS RIAKIAFTG Sbjct: 181 AGNCVVLKPAEQTPASILVMMELIADLLPAGVLNIVNGYGVEAGKALATSKRIAKIAFTG 240 Query: 241 STPVGSHIMRCAAENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEV 300 STPVGS IM+ AAENIIPSTVELGGKSPN+FF D+++ E AF+ KA EG VLAFFNQGEV Sbjct: 241 STPVGSLIMKYAAENIIPSTVELGGKSPNVFFADVLDHEDAFVSKAVEGAVLAFFNQGEV 300 Query: 301 CTCPSRALIQESIFEPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQ 360 CTCPSR LIQESI+E F+ +V+++ IKRGNPLDT+ MVGAQAS++Q++KILSY++I + Sbjct: 301 CTCPSRLLIQESIYEKFIGMVIERAAQIKRGNPLDTEVMVGAQASQEQYEKILSYIQIGK 360 Query: 361 QEGAQILTGGAAEKLEGSLSTGYYVQPTLIKGHNKMRVFQEEIFGPVVGVATFKDEAEAL 420 +EGA+++TGG E + GYY+QPTL+KG N MRVFQEEIFGPVV VATFKDEAEAL Sbjct: 361 EEGAEVITGGEVESMAADYCEGYYIQPTLLKGTNNMRVFQEEIFGPVVSVATFKDEAEAL 420 Query: 421 AIANDTEFGLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET 480 AIANDTEFGLGAGVWTRD+NR+YRMGRGI+AGRVWTNCYHLYPAHAAFGGYKKSGVGRET Sbjct: 421 AIANDTEFGLGAGVWTRDMNRSYRMGRGIQAGRVWTNCYHLYPAHAAFGGYKKSGVGRET 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: 788 Number of extensions: 26 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 24 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