Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate N515DRAFT_0481 N515DRAFT_0481 2-oxoisovalerate dehydrogenase E1 component
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Dyella79:N515DRAFT_0481 Length = 755 Score = 135 bits (339), Expect = 4e-36 Identities = 110/333 (33%), Positives = 153/333 (45%), Gaps = 25/333 (7%) Query: 6 MAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAILG 65 +A + AL + + P ++LFGED+ GGV+ +T GL F R F+T L E+ ILG Sbjct: 422 LAIQIGQALHEVMAKYPESLLFGEDVALKGGVYTVTKGLFKTFKGNRVFNTLLDETVILG 481 Query: 66 TAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIP---YGGG 122 A G A G P+ E+Q+ A+ + A +Q+ L+ + PL +R+ Y G Sbjct: 482 LAQGYANMGMLPMPEIQYLAYFHNACDQIRGEACSLQFFSNDQYRNPLVMRVAALGYQKG 541 Query: 123 IGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLR--RSIASPDPVV--FLEPKRLYW 178 GG H+D+S PGL V P+ DA ++LR ++A D V FLEP LY Sbjct: 542 FGG-HFHNDNSIAALRDIPGLVVGCPSRGDDAAAMLRTLMALAKVDGRVCAFLEPIALYM 600 Query: 179 RKE-----------ALGLPVDTGPLGSA-VIRRHGTHATLIAYGPAVTTALEAA-EAAAE 225 K+ A P + PLG V + + +G V AL AA E + Sbjct: 601 TKDLYEAGDGQWQFAYPAPGEALPLGEGRVYEQDADDLVVFTFGNGVPMALRAAREIEKK 660 Query: 226 HGWDLEVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITE-RCFYHL 284 HGW V+DLR L PL+D + R R +V+ E AG G I I E C Sbjct: 661 HGWRTRVVDLRWLAPLNDKFIAGQARNARRILVLDEGRRSAGVGEGIITAIVEGGCG--- 717 Query: 285 EAPVRRVTGFDVPYPPPLLERHYLPGVDRILDA 317 P++RV G D P LPG I+ A Sbjct: 718 ATPLQRVVGADTYTPLAGAALLVLPGEAEIVAA 750 Lambda K H 0.322 0.138 0.418 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: 594 Number of extensions: 27 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: 328 Length of database: 755 Length adjustment: 34 Effective length of query: 294 Effective length of database: 721 Effective search space: 211974 Effective search space used: 211974 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 (21.9 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