Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate BPHYT_RS34305 BPHYT_RS34305 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__BFirm:BPHYT_RS34305 Length = 479 Score = 221 bits (562), Expect = 6e-62 Identities = 140/460 (30%), Positives = 218/460 (47%), Gaps = 6/460 (1%) Query: 57 GSWGGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRK 116 G W + PA E +A V + + + I A++A+ W + A +R V++ Sbjct: 13 GEWYEGADTYAVLNPATGEVVAHVAKGGAAETAQAIAAAERAFPAWRALTAKERSARVKR 72 Query: 117 IGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSERPGH 176 G+ + E L L++LE GK L E GEV ++ A ++ G +PS P Sbjct: 73 WGELMLENRDALAELLTLEQGKPLAEARGEVGYAASFFEWFAEEAKRAYGDVIPSPNPNA 132 Query: 177 ALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKIIAK 236 ++ P+G+V IT +NFP+A+ AL G + K + T L + A+ + AK Sbjct: 133 KIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETPLSAFALAVLAAK 192 Query: 237 VLEDNLLPGAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSLLE 296 + PG ++ +G A+ + V LSFTGST+VGK +A + K LE Sbjct: 193 A---GIPPGVFNIVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSADTLKKLSLE 249 Query: 297 LGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNAYSQ 356 LGGN I F+DADL + A+ + GQ C V R ++ + I+D L A + Sbjct: 250 LGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFTSALTQAVRK 309 Query: 357 IRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMDHPGNYVEPTIVTG 416 +RVGN + GPL + A+ V +A ++G ++ GGK G + EPT++ Sbjct: 310 MRVGNALQGEVEQGPLINQAALKKVETHVADALQKGAKILTGGKPHTLGGTFYEPTVLAD 369 Query: 417 LVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPKGS 476 + I +ETF P+ F+FK E E E N+ GLS+ +T+DL R W + Sbjct: 370 ADNSMLIAGEETFGPVAACFRFKTEAEAIEAANDTPFGLSAYFYTRDLAR--AWRVGEAL 427 Query: 477 DCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQY 516 + G+V +N E+ FGG K +G GRE +Y Sbjct: 428 ESGMVGINEGIVSTEV-APFGGVKQSGLGREGSKYGLDEY 466 Lambda K H 0.319 0.137 0.417 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: 657 Number of extensions: 43 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: 539 Length of database: 479 Length adjustment: 34 Effective length of query: 505 Effective length of database: 445 Effective search space: 224725 Effective search space used: 224725 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 (21.7 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