Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate RR42_RS21375 RR42_RS21375 succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__Cup4G11:RR42_RS21375 Length = 488 Score = 566 bits (1458), Expect = e-166 Identities = 277/480 (57%), Positives = 362/480 (75%), Gaps = 3/480 (0%) Query: 46 LLRGDSFVGGRW--LPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 LLR +F+GG+W + ATFPV +PA G+ +GTV G E A+ AA A ++W+ Sbjct: 8 LLRSQAFIGGQWQSADSGATFPVTNPADGSLIGTVPLMGAAETTRAIEAARVAQAAWRRK 67 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + +ER+ +LR WYDLM+ N D+LA ++T E GKPL EA+GE +Y+A FLEWF+E+A+RV+ Sbjct: 68 TARERAQVLRAWYDLMLANADDLAVLMTTEQGKPLAEARGEAVYAASFLEWFAEQAKRVH 127 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD++ T A DKR LV+K+PVGV + ITPWNFP AMITRK G ALAAGC +V+KPAEDTP Sbjct: 128 GDVLATPASDKRLLVVKEPVGVCAAITPWNFPLAMITRKAGPALAAGCAMVLKPAEDTPL 187 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALALA LA +AG+P G+ +V+ + E+G L P+V K+SFTGST G+IL+ Sbjct: 188 SALALALLAERAGLPAGLLSVVTGDAASSIEIGAELTGSPVVRKLSFTGSTEVGRILMRQ 247 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 +A ++K++S+ELGG APFIVFD A++D AV GAMASK+RNAGQTCVC+NR V ++D+ Sbjct: 248 SAPTIKKLSLELGGNAPFIVFDDADLDAAVEGAMASKYRNAGQTCVCANRLYVHDKVYDA 307 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F K A+ K+L+VG+G E G QGPLINE AV KVE+H+ DA+ KGA ++TGGKRH Sbjct: 308 FAQKLVAAV-KTLKVGHGLEPGVQQGPLINEDAVAKVEQHIADALGKGARLLTGGKRHDL 366 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 GG FFEPT+L+NVT DM+ +ETFGP+AP+ +F +EE V +AN + GLA YF+S+D Sbjct: 367 GGTFFEPTVLANVTPDMVVAKQETFGPLAPLFRFTSDEEVVNMANDTEFGLASYFFSRDI 426 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 +IWRVAE LE GMVG+N GLIS+ PFGGVKQSGLGREG+ YGI+EYLEVKY+C GG+ Sbjct: 427 GRIWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGASYGIEEYLEVKYLCMGGV 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: 690 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: 523 Length of database: 488 Length adjustment: 34 Effective length of query: 489 Effective length of database: 454 Effective search space: 222006 Effective search space used: 222006 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