GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Escherichia coli BW25113

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 16751 b2661 succinate-semialdehyde dehydrogenase I, NADP-dependent (NCBI)

Query= BRENDA::P51650
         (523 letters)



>lcl|FitnessBrowser__Keio:16751 b2661 succinate-semialdehyde
           dehydrogenase I, NADP-dependent (NCBI)
          Length = 482

 Score =  538 bits (1385), Expect = e-157
 Identities = 262/480 (54%), Positives = 356/480 (74%), Gaps = 6/480 (1%)

Query: 44  ADLLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWK 101
           ++L R  + + G WL         V +PA+G KLG+V   G  E RAA+ AA  A  +W+
Sbjct: 6   SNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWR 65

Query: 102 EISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARR 161
            ++ KER+++LR W++LM++++D+LA+++T E GKPL EA+GEI Y+A F+EWF+EE +R
Sbjct: 66  ALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKR 125

Query: 162 VYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDT 221
           +YGD I     DKR +V+KQP+GV + ITPWNFP+AMITRK G ALAAGCT+V+KPA  T
Sbjct: 126 IYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQT 185

Query: 222 PYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILL 281
           P+SALALA+LA +AG+P GV+NV+  S   A  VG  L ++PLV K+SFTGST  G+ L+
Sbjct: 186 PFSALALAELAIRAGVPAGVFNVVTGS---AGAVGNELTSNPLVRKLSFTGSTEIGRQLM 242

Query: 282 HHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIH 341
              A  +K+VS+ELGG APFIVFD A++D+AV GA+ASKFRNAGQTCVC+NR  VQ G++
Sbjct: 243 EQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVY 302

Query: 342 DSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRH 401
           D F  K  +A+ K L +G+G + G T GPLI+EKAV KVE+H+ DA+ KGA VV GGK H
Sbjct: 303 DRFAEKLQQAVSK-LHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAH 361

Query: 402 QSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQ 461
           + GGNFF+PT+L +V  +     EETFGP+AP+ +F  E + +A AN  + GLA YFY++
Sbjct: 362 ERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYAR 421

Query: 462 DPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521
           D ++++RV E LE G+VG+N G+IS+   PFGG+K SGLGREGSKYGI++YLE+KY+C G
Sbjct: 422 DLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481


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: 626
Number of extensions: 23
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: 482
Length adjustment: 34
Effective length of query: 489
Effective length of database: 448
Effective search space:   219072
Effective search space used:   219072
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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