GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Acidovorax sp. GW101-3H11

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Ac3H11_1480 Aldehyde dehydrogenase B (EC 1.2.1.22)

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1480
          Length = 486

 Score =  530 bits (1366), Expect = e-155
 Identities = 255/480 (53%), Positives = 360/480 (75%), Gaps = 6/480 (1%)

Query: 46  LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           LL+   ++ G+W+     AT  V +PA+GA +GT+ + G  + + A+ AA  AF  WK+ 
Sbjct: 11  LLKARCYIDGQWVDADNGATLAVNNPANGALIGTIPNAGAAQTQTAIAAADRAFGPWKDR 70

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           + ++R+ +LR+W++LM+Q++++LA I+T+E GKPL EA+GEI Y+A ++EWF+EEARR+Y
Sbjct: 71  TAEDRARILRRWFELMLQHQEDLALIMTSEQGKPLAEARGEIAYAASYIEWFAEEARRIY 130

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           G++I +   DKR +V ++PVGV + ITPWNFP+AMITRKV  ALAAGCT++VKPA  TP 
Sbjct: 131 GEVIPSPWLDKRIVVTREPVGVCAAITPWNFPAAMITRKVAPALAAGCTIIVKPATQTPL 190

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           SALA+A+LA +AG+P GV++VI      A+ +G  L   P+V K++FTGST  G++L   
Sbjct: 191 SALAMAELAARAGVPAGVFSVI---TGDARPIGAELTASPVVRKLTFTGSTEIGRVLAAQ 247

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
            A ++K++S+ELGG APFIVF+ A++D AVAGAMASK+RN GQTCVC+NR LVQ G++D+
Sbjct: 248 CAPTLKKMSLELGGNAPFIVFEDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGVYDA 307

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  K A  +  +L+VG+G EEG  QGPLI+E ++ KVE  V DA A+GA VVTGG+RH  
Sbjct: 308 FAEKLARTV-AALKVGHGLEEGVEQGPLIDEASLTKVEALVADAKARGARVVTGGRRHAL 366

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
           GG F+EPT+L+++T DM    EE FGPVAP+ +F  E EA+ +AN  + GLA YFYS+D 
Sbjct: 367 GGTFYEPTILADITPDMRMAREEIFGPVAPLFRFHTEAEAIQMANDTEFGLAAYFYSRDV 426

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
            ++WRV+  L+ GMVG+N G+IS+   PFGGVKQSG+GREGS +GI+EY++ KY+C GG+
Sbjct: 427 GRVWRVSGALQYGMVGINAGVISTAVAPFGGVKQSGMGREGSVHGIEEYVDTKYLCMGGV 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: 654
Number of extensions: 21
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