Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate SMa1848 SMa1848 GabD5 succinate semialdehyde dehdyrogenase
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__Smeli:SMa1848 Length = 484 Score = 507 bits (1305), Expect = e-148 Identities = 258/481 (53%), Positives = 340/481 (70%), Gaps = 6/481 (1%) Query: 45 DLLRGDSFVGGRWLP--TPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKE 102 +L R +GG W+ + V DPA+ A LGTV D G E RAA+ AA AF WK+ Sbjct: 7 ELFRQLGLIGGEWIAGASGVVVDVIDPANQAVLGTVPDMGTAETRAAIEAANAAFGPWKK 66 Query: 103 ISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRV 162 + ER+++L +W+ LMI+N ++LA ++T E GKPL+EA+GEI Y A F++WF+EE+RR+ Sbjct: 67 KTHAERAAVLERWHALMIENLEDLAVLVTMEQGKPLEEARGEIRYGAAFVKWFAEESRRI 126 Query: 163 YGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTP 222 G I + D+R +VLK+ VGV +I+TPWNFP+AMITRKV ALAAGCTVV+KP+E TP Sbjct: 127 GGHTIPSPTSDRRIVVLKEAVGVCAIVTPWNFPNAMITRKVAPALAAGCTVVIKPSEFTP 186 Query: 223 YSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLH 282 +SALAL LA +AGIP GV N++ T +G T+ V KISFTGST G +L+ Sbjct: 187 FSALALGVLAERAGIPAGVVNIVTGMPT---AIGNEFMTNETVRKISFTGSTRVGSLLMR 243 Query: 283 HAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHD 342 AA+SVKR+S+ELGG APFIVFD AN+D AV GA+ASKFRN GQTCVC+NR LVQ G++D Sbjct: 244 GAADSVKRLSLELGGNAPFIVFDDANLDLAVEGAIASKFRNGGQTCVCANRILVQAGVYD 303 Query: 343 SFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQ 402 +F K A +++VG G E G GP+INE A++K+++HV DA+AKGA + G+ Sbjct: 304 AFAEKLG-ARVNAMKVGPGTEPGIAIGPMINEAAIDKIDRHVEDAIAKGAKLAARGRSVP 362 Query: 403 SGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQD 462 G + P +L+ T DML +EETFGPVAP+ +F+ E+EA+AIAN GLA YFY++ Sbjct: 363 EGRQYTAPIVLTGATTDMLLASEETFGPVAPLFRFETEDEAIAIANGTPFGLAAYFYTEG 422 Query: 463 PAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGG 522 + WRVAE LE GM+G+N G IS+ PFGGVKQSGLGREG++ GI+EYLE+K GG Sbjct: 423 LKRSWRVAEALEFGMIGLNTGAISTEVAPFGGVKQSGLGREGAQVGIEEYLEMKSFHIGG 482 Query: 523 L 523 L Sbjct: 483 L 483 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: 679 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: 484 Length adjustment: 34 Effective length of query: 489 Effective length of database: 450 Effective search space: 220050 Effective search space used: 220050 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