Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate AZOBR_RS22250 AZOBR_RS22250 pyruvate dehydrogenase E1 component beta subunit
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__azobra:AZOBR_RS22250 Length = 465 Score = 217 bits (552), Expect = 5e-61 Identities = 126/315 (40%), Positives = 176/315 (55%), Gaps = 2/315 (0%) Query: 5 TMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAIL 64 T+ +AL A+ + +R DP L GE++ G ++++ GL EFG +R DTP+ E Sbjct: 143 TVREALRDAMAEEMRRDPTVFLMGEEVAQYQGAYKVSQGLLQEFGADRVIDTPITEIGFA 202 Query: 65 GTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGIG 124 G VG A G RP+VE FA A + +V+ AK + G +G P+ R P G Sbjct: 203 GLGVGAAFRGLRPIVEFMTFNFALQAIDHIVNSAAKTLYMSGGQMGCPIVFRGPNGAAAR 262 Query: 125 GVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRKEALG 184 HS +Y + PGL VV P +A+D L++ +I P+PV+FLE + LY + + Sbjct: 263 VAAQHSQDFTPWYASIPGLKVVAPYSASDFKGLMKSAIRDPNPVIFLENEILYGQSFEVP 322 Query: 185 LPVD-TGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLMPLDD 243 D P+G A IRR GT T+ A+ V+ AL AA+ + G EVIDLRT+ PLD Sbjct: 323 ESEDFIVPIGRAKIRRAGTDVTITAHSLMVSYALAAADLLEKDGISAEVIDLRTIRPLDT 382 Query: 244 ATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP-PPL 302 T+ SV++T R V V EA G GAE++A + E+ F +L+APV RVTG DVP P Sbjct: 383 ETIVNSVKKTNRLVTVEEAWPTCGIGAELSALMMEQAFDYLDAPVIRVTGLDVPMPYAAN 442 Query: 303 LERHYLPGVDRILDA 317 LE+ LP DRI +A Sbjct: 443 LEKLVLPSPDRIAEA 457 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: 374 Number of extensions: 23 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 328 Length of database: 465 Length adjustment: 31 Effective length of query: 297 Effective length of database: 434 Effective search space: 128898 Effective search space used: 128898 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: 50 (23.9 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