Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__azobra:AZOBR_RS09720 Length = 497 Score = 546 bits (1408), Expect = e-160 Identities = 270/483 (55%), Positives = 362/483 (74%), Gaps = 7/483 (1%) Query: 44 ADLLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWK 101 A+LLR FV GRW+ + T V +PA G+ LG+V G E R A+ AA A+ +W+ Sbjct: 17 AELLRFQGFVDGRWIDADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWPAWR 76 Query: 102 EISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARR 161 ++ KER+ LR W+DLM+ N++++A+I+TAE GKPL EA+GE+ Y+A F+EWF+EE +R Sbjct: 77 ALTAKERAKTLRTWFDLMMANQEDIARIMTAEQGKPLAEARGEVAYAASFIEWFAEEGKR 136 Query: 162 VYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDT 221 VYGD I +R +V K+P+GV + ITPWNFP+AMITRK G ALAAGC +V+KPA T Sbjct: 137 VYGDTIPQHLPGRRIVVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPATAT 196 Query: 222 PYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILL 281 P +ALA+A LA +AGIP G+ +V+ S A+ +G + +P V K++FTGST GK L+ Sbjct: 197 PLTALAMAVLAERAGIPAGILSVVTGS---ARAIGGEMTGNPTVRKLTFTGSTEIGKELM 253 Query: 282 HHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIH 341 A +VK+VS+ELGG APF+VF+ A++D+AV GA+ASK+RN GQTCVC+NR LVQ G++ Sbjct: 254 AQCAGTVKKVSLELGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLLVQSGVY 313 Query: 342 DSFVTKFAEAMKKSLRVGNGFE-EGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKR 400 D+F K AEA+K +L+VG G EG QGPLI+ AVEKVE H+ DA KGA VV GGKR Sbjct: 314 DAFAAKLAEAVK-ALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVVLGGKR 372 Query: 401 HQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYS 460 H+ GG+FFEPT+L++VT M EETFGPVAP+ +F+ EEEAV +ANA + GLA YFYS Sbjct: 373 HELGGSFFEPTILADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAYFYS 432 Query: 461 QDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCY 520 +D ++WRVAE LE G+VG+NEG+IS+ PFGG+K+SG+GREGSKYGI++YLE+KY+C Sbjct: 433 RDIGRVWRVAEALEYGIVGINEGIISTEVAPFGGMKESGIGREGSKYGIEDYLEIKYLCM 492 Query: 521 GGL 523 GG+ Sbjct: 493 GGI 495 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: 676 Number of extensions: 20 Number of successful extensions: 4 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: 497 Length adjustment: 34 Effective length of query: 489 Effective length of database: 463 Effective search space: 226407 Effective search space used: 226407 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