Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 7024610 Shewana3_1788 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__ANA3:7024610 Length = 866 Score = 173 bits (439), Expect = 2e-47 Identities = 134/375 (35%), Positives = 196/375 (52%), Gaps = 38/375 (10%) Query: 32 KHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLETGEKAVAFARDGKFDL 91 + LV+TD L G D+ L+ +G V+ +V +P L T + A K D+ Sbjct: 478 RRALVVTDRFLFNQGYCDETLKILKAQGLETEVFYEVEADPTLATVRQGAKVANSFKPDV 537 Query: 92 VIGVGGGSALDLAKLAAVLAVH-DGSVADY-LNLTGTRTLEKKGLPK-------ILIPTT 142 +I +GGGS +D AK+ V+ H D AD L R K PK + IPTT Sbjct: 538 IIALGGGSPMDAAKIIWVMYEHPDVDFADLALRFMDIRKRIYK-FPKMGVKATMVAIPTT 596 Query: 143 SGTGSEVTNISVLSLETT-KDVVTHDYLLA-DVAIVDPQLTVSVPPRVTAATGIDALTHA 200 SGTGSEVT +V++ E T K DY L ++AIVDP L + +P +TA GIDA+THA Sbjct: 597 SGTGSEVTPFAVVTDEQTGKKYPIADYQLTPNMAIVDPNLVMDMPKSLTAFGGIDAITHA 656 Query: 201 VEAYVSVNASPTSDGLAVAAIRLISRSLRKAV-ANGSDKQARIDMANGSYLAGLAFFNAG 259 +EAYVSV A+ SDG A+ A+ L+ + L A G+ AR + NG+ +AG+AF NA Sbjct: 657 LEAYVSVMANEYSDGQALQALDLLCKYLPDAYQLGGASPIAREKVHNGATIAGIAFANAF 716 Query: 260 VAGVHALAYPLGGQFHIAHGESNAVLLPYVM---------------GYIRQSCTKRMADI 304 + H++A+ LG +FH+AHG +NA+L+ V+ Y R R A I Sbjct: 717 LGICHSMAHKLGAEFHLAHGLANALLISNVIRFNATDLPTKQAAFSQYDRPKALCRYAAI 776 Query: 305 FN--ALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPE----SALESLTKDA 358 + AL GN S+ E + +E++E+ +GIP ++ G+ E + L+ L +DA Sbjct: 777 ADHLALDGN----SDAEKVEKLLEKIEQLKKTLGIPASIQEAGVNEADFLAKLDELAEDA 832 Query: 359 VQQKRLLARSPLPLL 373 + A PL+ Sbjct: 833 FDDQCTGANPRYPLI 847 Lambda K H 0.318 0.135 0.381 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: 690 Number of extensions: 33 Number of successful extensions: 3 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: 395 Length of database: 866 Length adjustment: 36 Effective length of query: 359 Effective length of database: 830 Effective search space: 297970 Effective search space used: 297970 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 (21.7 bits) S2: 53 (25.0 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