GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Burkholderia phytofirmans PsJN

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BPHYT_RS22430 BPHYT_RS22430 succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__BFirm:BPHYT_RS22430
          Length = 486

 Score =  549 bits (1414), Expect = e-160
 Identities = 270/480 (56%), Positives = 356/480 (74%), Gaps = 6/480 (1%)

Query: 46  LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           LL+  +++ G W       TF V +PA+G  + TV   G  E R A+  A  A+ +W+  
Sbjct: 11  LLKSHAYIAGEWQGADDGTTFEVKNPATGETIATVPRMGTAETRRAIDTANAAWPAWRAT 70

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           + K+R+ +LRKW+DLM++N D+LAKI+T E GKPL EA+GEI Y+A FLEWF+EE +RV 
Sbjct: 71  TAKQRAVILRKWHDLMMENADDLAKILTTEQGKPLAEAKGEIQYAASFLEWFAEEGKRVN 130

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           GD I T A DKR +V K+P+GV + ITPWNFP+AMITRKVG ALAAGC ++VKPAE TP 
Sbjct: 131 GDTIPTPASDKRIVVTKEPIGVCAAITPWNFPAAMITRKVGPALAAGCPIIVKPAEATPL 190

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           SALALA LA +AG+P GV+NV+     + K +G  +  +P+V K+SFTGST  G++L+  
Sbjct: 191 SALALAVLAERAGVPRGVFNVV---TGEPKAIGAEMTGNPIVRKLSFTGSTPVGRLLMAQ 247

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
            A +VK+VS+ELGG APFIVFD A++D AVAGA+ASK+RN+GQTCVC+NRF V   ++D+
Sbjct: 248 CAPTVKKVSLELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYVHDKVYDA 307

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  K   A+++ L+VG G E+G TQGPLIN+ AV KVE H+ DA+AKGA +VTGGKRH  
Sbjct: 308 FAEKLRVAVEQ-LKVGRGTEDGVTQGPLINDAAVLKVESHIEDALAKGARIVTGGKRHAL 366

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
           G  FFEPT+L++VT  M    +ETFGP+AP+ +F  +EE + +AN  + GLA YFYS+D 
Sbjct: 367 GHGFFEPTVLADVTPAMKVARDETFGPLAPLFRFSSDEEVIRLANDTEFGLASYFYSRDI 426

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
            ++WRVAE LE GMVG+N GLIS+   PFGGVKQSGLGREGS YGID+Y+ +KY+C GG+
Sbjct: 427 GRVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYVVIKYLCVGGI 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: 695
Number of extensions: 26
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: 486
Length adjustment: 34
Effective length of query: 489
Effective length of database: 452
Effective search space:   221028
Effective search space used:   221028
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