Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_156966509.1 U743_RS02115 iron-containing alcohol dehydrogenase
Query= BRENDA::P0DJA2 (383 letters) >NCBI__GCF_000733765.1:WP_156966509.1 Length = 410 Score = 244 bits (622), Expect = 4e-69 Identities = 135/347 (38%), Positives = 203/347 (58%), Gaps = 2/347 (0%) Query: 15 GEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINSAVYDGVMPNPTV 74 G G+ + + +G K L+V+DA + + G+VK + + L++ G+ YDGV P+PT+ Sbjct: 41 GAGAAMQLCDAIAATGAKKVLLVTDAMLVELGLVKPIQEKLESLGVGVVTYDGVKPDPTI 100 Query: 75 TAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEGIDKSKKPALPLM 134 + G+ I K + +I++GGGS D AK IA A N V+ G+ + + PL Sbjct: 101 EQIETGVDIYKGQGCEAIIAVGGGSSIDAAKVIAARARNPHGVRWMAGLFRLLRSPAPLY 160 Query: 135 SINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVGMPKGLTAATGMD 194 ++ TTAGT SE+T +++D + K AI+D + P ++ D LM G+P +TAATGMD Sbjct: 161 AVPTTAGTGSEVTIAAVVSDPEKVRKFAIMDFRLVPRMAALDGSLMTGVPAAITAATGMD 220 Query: 195 ALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAREAMAYAQFLAGMAF 254 ALTHA EA+ S AT TDA A +A ++I ++L +GKD+ +R MA A + AG+AF Sbjct: 221 ALTHAVEAFISRNATKETDAEAREAVALIMEHLPRVMADGKDLESRSQMAVASYKAGLAF 280 Query: 255 NNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKDVGVAMGLDIANL 314 A +GYVHA AH G Y++PHG NA+LLP+VL Y+ RL ++ G+ + Sbjct: 281 TKAGVGYVHAFAHNFGARYHIPHGKANAILLPYVLEYSKHASRSRLAELARIAGVGEQSA 340 Query: 315 GDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDA 361 + A+A I +RDL GIPA + EL A D+P +A +A +A Sbjct: 341 SEAALADAFIAHIRDLNQRFGIPARVDELDA--ADIPTIATNARSEA 385 Lambda K H 0.316 0.132 0.373 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: 342 Number of extensions: 11 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: 383 Length of database: 410 Length adjustment: 31 Effective length of query: 352 Effective length of database: 379 Effective search space: 133408 Effective search space used: 133408 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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