GapMind for catabolism of small carbon sources

 

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

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Ac3H11_1480 Aldehyde dehydrogenase B (EC 1.2.1.22)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_805
         (497 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1480
          Length = 486

 Score =  313 bits (803), Expect = 7e-90
 Identities = 184/478 (38%), Positives = 271/478 (56%), Gaps = 14/478 (2%)

Query: 18  IEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSR 77
           ++ R YI+G++ DA +G T    +P +G L+G I +  AA  Q A+  A   F  G W  
Sbjct: 12  LKARCYIDGQWVDADNGATLAVNNPANGALIGTIPNAGAAQTQTAIAAADRAF--GPWKD 69

Query: 78  LAPTKRKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQALSWSGEAIDK 137
                R   + R+  L+ QH E+LAL+ T + GKP++++   ++  AA  + W  E   +
Sbjct: 70  RTAEDRARILRRWFELMLQHQEDLALIMTSEQGKPLAEARG-EIAYAASYIEWFAEEARR 128

Query: 138 IYDEVAATPH-DQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKS 196
           IY EV  +P  D+  +VTREPVGV  AI PWNFP  M   K+ PAL+ G ++I+KP+ ++
Sbjct: 129 IYGEVIPSPWLDKRIVVTREPVGVCAAITPWNFPAAMITRKVAPALAAGCTIIVKPATQT 188

Query: 197 PLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYS 256
           PL+A+ +AELA  AG+P GV +V+ G    +G  L     V  L FTGST+I + L    
Sbjct: 189 PLSALAMAELAARAGVPAGVFSVITGDARPIGAELTASPVVRKLTFTGSTEIGRVLAAQC 248

Query: 257 GESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAF---NQGEVCTAGSRLLVERS 313
             + +K++ LE GG +P IVF DA    D   A AGA+A    N G+ C   +RLLV+  
Sbjct: 249 APT-LKKMSLELGGNAPFIVFEDA----DLDAAVAGAMASKYRNTGQTCVCANRLLVQDG 303

Query: 314 IKDKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARLVAGGKR 373
           + D F   +   + A K G+ L+     G L+D   +  V + +    A GAR+V GG+R
Sbjct: 304 VYDAFAEKLARTVAALKVGHGLEEGVEQGPLIDEASLTKVEALVADAKARGARVVTGGRR 363

Query: 374 TLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAV 433
                GGT+ EPTI   ++  M++A+EEIFGPV  +  F +  EAI +ANDT +GLAA  
Sbjct: 364 --HALGGTFYEPTILADITPDMRMAREEIFGPVAPLFRFHTEAEAIQMANDTEFGLAAYF 421

Query: 434 WTADISKAHLTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELK 491
           ++ D+ +    + AL+ G V +N        APFGG KQSG GR+ S+H  ++Y + K
Sbjct: 422 YSRDVGRVWRVSGALQYGMVGINAGVISTAVAPFGGVKQSGMGREGSVHGIEEYVDTK 479


Lambda     K      H
   0.316    0.132    0.390 

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: 29
Number of successful extensions: 7
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: 497
Length of database: 486
Length adjustment: 34
Effective length of query: 463
Effective length of database: 452
Effective search space:   209276
Effective search space used:   209276
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 (21.6 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