Align aldehyde dehydrogenase-like protein yneI (characterized)
to candidate CA265_RS19780 CA265_RS19780 aldehyde dehydrogenase family protein
Query= CharProtDB::CH_024181 (462 letters) >FitnessBrowser__Pedo557:CA265_RS19780 Length = 513 Score = 206 bits (523), Expect = 2e-57 Identities = 137/448 (30%), Positives = 217/448 (48%), Gaps = 21/448 (4%) Query: 11 SINPATGEQLSVLPWAGADDIENALQLAAAGFRDWRETNIDYRAEKLRDIGKALRARSEE 70 S +P G+ ++ A ADD + + A F WR R E +R G ALR + Sbjct: 38 SFSPVDGKLIASAKIATADDYDAVVLKAQEAFTAWRSVPAPKRGEIVRQFGDALRENKDA 97 Query: 71 MAQMITREMGKPINQARAEVAKSANLCDWYAE-----HGPAMLKAEPTLVENQQAVIEYR 125 + +++ EMGK + + EV + ++CD+ +G M P+ + ++ Sbjct: 98 LGTLVSYEMGKSLQEGFGEVQEMIDICDFAVGLSRQLYGLTMHSERPS----HRMYEQWH 153 Query: 126 PLGTILAIMPWNFPLWQVMRGAVPIILAGNGYLLKHAPNV----MGCAQLIAQVFKDAGI 181 PLG + I +NFP+ ++ GN + K + + C +IA+VFKD I Sbjct: 154 PLGIVGIISAFNFPVAVWSWNTALALVCGNVCIWKPSEKTPLTAIACQHIIAKVFKDNDI 213 Query: 182 PQGVYGWLNADNDGVSQMIKDSRIAAVTVTGSVRAGAAIGAQAGAALKKCVLELGGSDPF 241 +GV + D + +M D RI ++ TGS R G A+GA GA L K +LELGG++ Sbjct: 214 AEGVCNLILGDREVGERMTNDGRIPLISATGSTRMGKAVGAAVGARLGKSLLELGGNNAI 273 Query: 242 IVLNDADLELAVKAAVAGRYQNTGQVCAAAKRFIIEEGIASAFTERFVAAAAALKMGDPR 301 I+ ADL++++ AV G GQ C + +R II E + AFT + V A L++GDP Sbjct: 274 IISEHADLDMSLIGAVFGAVGTAGQRCTSTRRLIIHESVYDAFTAKLVKAYGQLRIGDPL 333 Query: 302 DEENALGPMARFDLRDELHHQVEKTLAQGARLLLGGEKMAG----AGNYYPPTVLANVTP 357 D+ N +GP+ D + K A+G ++ G ++G +G Y P + A V Sbjct: 334 DQNNHVGPLIDTDAVAAYLDSIAKCKAEGGNFVVEGGVLSGDAYTSGCYVKPCI-AEVQN 392 Query: 358 EMTAFREEMFGPVAAITIAKDAEHALELANDSEFGLSATIFTTDETQARQM--AARLECG 415 + + E F P+ + K + A+ L N GLS+ I T + +A Q A +CG Sbjct: 393 DFKIVQHETFAPILYLIKYKTLDEAIALQNGVPQGLSSAIMTLNLREAEQFLSAKGSDCG 452 Query: 416 GVFIN-GYCASDARVAFGGVKKSGFGRE 442 +N G ++ AFGG K++G GRE Sbjct: 453 IANVNIGTSGAEIGGAFGGEKETGGGRE 480 Lambda K H 0.319 0.134 0.397 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: 490 Number of extensions: 23 Number of successful extensions: 5 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: 462 Length of database: 513 Length adjustment: 34 Effective length of query: 428 Effective length of database: 479 Effective search space: 205012 Effective search space used: 205012 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