Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BPHYT_RS22430 BPHYT_RS22430 succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__BFirm:BPHYT_RS22430 Length = 486 Score = 549 bits (1414), Expect = e-160 Identities = 270/480 (56%), Positives = 356/480 (74%), Gaps = 6/480 (1%) Query: 46 LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 LL+ +++ G W TF V +PA+G + TV G E R A+ A A+ +W+ Sbjct: 11 LLKSHAYIAGEWQGADDGTTFEVKNPATGETIATVPRMGTAETRRAIDTANAAWPAWRAT 70 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + K+R+ +LRKW+DLM++N D+LAKI+T E GKPL EA+GEI Y+A FLEWF+EE +RV Sbjct: 71 TAKQRAVILRKWHDLMMENADDLAKILTTEQGKPLAEAKGEIQYAASFLEWFAEEGKRVN 130 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD I T A DKR +V K+P+GV + ITPWNFP+AMITRKVG ALAAGC ++VKPAE TP Sbjct: 131 GDTIPTPASDKRIVVTKEPIGVCAAITPWNFPAAMITRKVGPALAAGCPIIVKPAEATPL 190 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALALA LA +AG+P GV+NV+ + K +G + +P+V K+SFTGST G++L+ Sbjct: 191 SALALAVLAERAGVPRGVFNVV---TGEPKAIGAEMTGNPIVRKLSFTGSTPVGRLLMAQ 247 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 A +VK+VS+ELGG APFIVFD A++D AVAGA+ASK+RN+GQTCVC+NRF V ++D+ Sbjct: 248 CAPTVKKVSLELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYVHDKVYDA 307 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F K A+++ L+VG G E+G TQGPLIN+ AV KVE H+ DA+AKGA +VTGGKRH Sbjct: 308 FAEKLRVAVEQ-LKVGRGTEDGVTQGPLINDAAVLKVESHIEDALAKGARIVTGGKRHAL 366 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 G FFEPT+L++VT M +ETFGP+AP+ +F +EE + +AN + GLA YFYS+D Sbjct: 367 GHGFFEPTVLADVTPAMKVARDETFGPLAPLFRFSSDEEVIRLANDTEFGLASYFYSRDI 426 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 ++WRVAE LE GMVG+N GLIS+ PFGGVKQSGLGREGS YGID+Y+ +KY+C GG+ Sbjct: 427 GRVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYVVIKYLCVGGI 486 Lambda K H 0.318 0.135 0.400 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: 695 Number of extensions: 26 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: 523 Length of database: 486 Length adjustment: 34 Effective length of query: 489 Effective length of database: 452 Effective search space: 221028 Effective search space used: 221028 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: 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