Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate 349840 BT0312 2-oxoisovalerate dehydrogenase beta subunit (NCBI ptt file)
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Btheta:349840 Length = 678 Score = 195 bits (496), Expect = 2e-54 Identities = 128/325 (39%), Positives = 179/325 (55%), Gaps = 10/325 (3%) Query: 6 MAKALNTALRDALRDDPRTILFGEDIG--ALGGVFRITDGLAAEFGDERCFDTPLAESAI 63 + A+N L+ R +P T ++G+D+ GGVF +T G+ EFG+ R F P+AE I Sbjct: 352 LVNAINETLKAEFRHNPDTFIWGQDVANREKGGVFNVTKGMQQEFGEARVFSAPIAEDYI 411 Query: 64 LGTAVGMAMYGYRPVVEMQFDAFA---YPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 +GTA GM+ + + V ++ FA +PA EQ V + R+ G +T+R+ G Sbjct: 412 VGTANGMSRFDPKIHVVIEGAEFADYFWPAVEQYVECTHEYW-RSNGKFAPNITLRLASG 470 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180 G IGG +HS + E PG +V P+ A DA LLR S+ S +FLEPK LY Sbjct: 471 GYIGGGLYHSQNIEGALTTLPGARIVCPSFADDAAGLLRTSMRSKGFTLFLEPKALYNSV 530 Query: 181 EALGL-PVDTG-PLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAA-EHGWDLEVIDLRT 237 EA + P D P G A IRR GT ++I YG L AE E GW +EVID+R+ Sbjct: 531 EAAAVVPEDFEVPFGKARIRREGTDLSIITYGNTTHFCLHVAEQLEKESGWKVEVIDIRS 590 Query: 238 LMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVP 297 L+PLD + SV++T +A+VVHE F+G GAE+AA I F +L+ PV+RV P Sbjct: 591 LIPLDKEAIFESVKKTSKALVVHEDKVFSGFGAELAAMIGTDMFRYLDGPVQRVGSTFTP 650 Query: 298 YP-PPLLERHYLPGVDRILDAVASL 321 P+LE+ LP +I +A L Sbjct: 651 VGFNPILEKEILPDEAKIYEAAKKL 675 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: 471 Number of extensions: 15 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: 328 Length of database: 678 Length adjustment: 33 Effective length of query: 295 Effective length of database: 645 Effective search space: 190275 Effective search space used: 190275 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: 51 (24.3 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