GapMind for catabolism of small carbon sources

 

Alignments for a candidate for QDPR in Azospirillum brasilense Sp245

Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate AZOBR_RS27900 AZOBR_RS27900 FAD-binding oxidoreductase

Query= CharProtDB::CH_003330
         (396 letters)



>FitnessBrowser__azobra:AZOBR_RS27900
          Length = 690

 Score =  116 bits (290), Expect = 2e-30
 Identities = 85/240 (35%), Positives = 113/240 (47%), Gaps = 20/240 (8%)

Query: 164 SALITSFELEPVDGGAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKR 223
           SA I SF L P DG  +  +  GQ+L + + P G     +R Y+L+  P    YRI+VKR
Sbjct: 345 SATIRSFHLRPNDGAGLLPHLAGQHLPIRVTPAGAEKPVVRTYTLSVAPSDGAYRISVKR 404

Query: 224 EEGGQVSNWLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAK 283
           E  G VS  LH+H  VGDV++   PAG F +      P  L++ GVG TP+LAML  +  
Sbjct: 405 E--GLVSRHLHDHVRVGDVIEARGPAGGFTIDARAARPAVLLAGGVGITPLLAMLRHVVY 462

Query: 284 AGHTAQ----VNWFHAAENGDVHAFADEVKELGQS------LPRFTAHTWYRQPSEADRA 333
            G   Q        HAA +     F  E+ +L  +      L R  +      P EA  A
Sbjct: 463 EGLRTQRIRPTILVHAARSKAERPFDREITDLVTAANGDVRLVRVLS-----DPGEA--A 515

Query: 334 KG-QFDSEGLMDLSKLEGAFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392
            G  +D+ G +D++ L          FYLCGP  F Q     L  L +    IH E FGP
Sbjct: 516 PGVDYDAVGRIDMALLTRILGFNDYDFYLCGPPAFTQALYDGLRGLNIADSRIHAEAFGP 575


Lambda     K      H
   0.318    0.135    0.404 

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: 633
Number of extensions: 30
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: 396
Length of database: 690
Length adjustment: 35
Effective length of query: 361
Effective length of database: 655
Effective search space:   236455
Effective search space used:   236455
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