GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:16751
          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:

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