GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Azospirillum brasilense Sp245

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate AZOBR_RS29185 AZOBR_RS29185 aldehyde dehydrogenase

Query= BRENDA::Q97UA1
         (478 letters)



>FitnessBrowser__azobra:AZOBR_RS29185
          Length = 478

 Score =  350 bits (899), Expect = e-101
 Identities = 194/454 (42%), Positives = 267/454 (58%), Gaps = 6/454 (1%)

Query: 23  NPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEF 82
           NPA    V+      + +  +EA+  A A    W+ +    R  +L + G+ +   A+E 
Sbjct: 23  NPARPGEVIGHYAWASVEQAEEALGAAHAALPGWAASNPQTRSDVLRRVGDELNARAEEL 82

Query: 83  ALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGVV 142
             L+T EEGKTL++ + EV RS  +  +      +  G+ LP     T     +EP+GVV
Sbjct: 83  GALLTREEGKTLREGIGEVRRSAQIFHYAAGEPLRQGGEALPGLRDGTTAMVSREPVGVV 142

Query: 143 ALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLVV 202
            LITPWNFP+++P WK A ALA GNT V+KP+  TP    +L ++L +AGLP G  NLVV
Sbjct: 143 VLITPWNFPMAVPAWKTAYALAFGNTVVLKPSEVTPACAWELADILHRAGLPAGAFNLVV 202

Query: 203 GKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSA 262
           G G  +G  +V  D   AVSFTGS  VG+ I  L  +  RMTR+QLELGGKN L V   A
Sbjct: 203 GDGRTLGPALV--DGADAVSFTGSPGVGRAI--LERSVARMTRVQLELGGKNPLVVHDDA 258

Query: 263 DLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVG-PGTEDVDM 321
           DL LA ++A++G F  TGQ CTATSR+I+++ V+  F +RL+ R+   RVG P     DM
Sbjct: 259 DLELAVDIALQGAFHSTGQRCTATSRIIVDRRVHDAFVERLVTRIAALRVGDPMDAATDM 318

Query: 322 GPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPGKGYFLEPTIFEGVTSDMRLFKEEIF 381
           GPVV E Q  KDL  I   ++ GA+L +GG  + G GYFLEPT+F G  + MR+ ++E+F
Sbjct: 319 GPVVSEAQLAKDLHCIADARSEGAELAFGGGRMDGDGYFLEPTLFVGTDNAMRINRDEVF 378

Query: 382 GPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVGLE 441
           GPV  V  A  LD AI + N  D+  ++GIV   + +   F  R  AG++ VN PT G++
Sbjct: 379 GPVACVIPADGLDHAIAIANDSDHALSSGIVTRGLASAETFRRRSRAGLVMVNAPTAGID 438

Query: 442 LQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475
              PFGG   SG    +E G  A+EF+ + KT Y
Sbjct: 439 YHVPFGGRGPSG-YGGREQGSAAVEFFTEGKTAY 471


Lambda     K      H
   0.316    0.135    0.389 

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: 578
Number of extensions: 18
Number of successful extensions: 5
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: 478
Length of database: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
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: 51 (24.3 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