Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 6937537 Sama_1693 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__SB2B:6937537 Length = 867 Score = 170 bits (430), Expect = 2e-46 Identities = 134/391 (34%), Positives = 204/391 (52%), Gaps = 39/391 (9%) Query: 30 GAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLETGEKAVAFARDGKF 89 G K L++TD L G D+ L+ +G V+ +V +P L A + Sbjct: 476 GKKRALIVTDKFLFNNGYCDETIRILKSQGLETEVFYEVEADPTLAVVRAGAKVATSFQP 535 Query: 90 DLVIGVGGGSALDLAKLAAVLAVH-DGSVADY-LNLTGTRTLEKKGLPK-------ILIP 140 D+++ +GGGS +D AK+ V+ H D AD L R K PK + IP Sbjct: 536 DVIVALGGGSPMDAAKIIWVMYEHPDVDFADLALRFMDIRKRIYK-FPKLGAKAMMVAIP 594 Query: 141 TTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGIDALT 198 TTSGTGSEVT +V++ E T K + L ++AIVDP L + +P +TA GIDA+T Sbjct: 595 TTSGTGSEVTPFAVVTDEQTGAKYPIADYELTPNMAIVDPNLVMDMPKSLTAFGGIDAIT 654 Query: 199 HAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQ-ARIDMANGSYLAGLAFFN 257 HA+EAYVSV A+ SDG A+ A+ L+ + L + A G+ AR + NG+ +AG+AF N Sbjct: 655 HALEAYVSVMANEYSDGQALQALDLLFKYLPDSYARGAQAPLAREKVHNGATIAGIAFAN 714 Query: 258 AGVAGVHALAYPLGGQFHIAHGESNAVLLPYVM---------------GYIRQSCTKRMA 302 A + H++A+ LG +FH+ HG +NA+L+ V+ Y R R A Sbjct: 715 AFLGICHSMAHKLGAEFHLPHGLANALLISNVIRFNATDLPTKQAAFSQYDRPKALCRYA 774 Query: 303 DIFNALG--GNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPE----SALESLTK 356 I + LG GN+ ++VEA +EEL+ A +GIP ++ G+ E + L+ L + Sbjct: 775 AIASHLGLAGNND-EAKVEALIAKIEELK---AAIGIPVSIKDAGVNEADFMAKLDELAE 830 Query: 357 DAVQQKRLLARSPLPLLEADIRAIYEAAFAG 387 DA + A PL+ ++++ + +F G Sbjct: 831 DAFDDQCTGANPRYPLI-SELKQLLIDSFHG 860 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: 677 Number of extensions: 32 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: 867 Length adjustment: 36 Effective length of query: 359 Effective length of database: 831 Effective search space: 298329 Effective search space used: 298329 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 Apr 09 2024. 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