GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bgtA in Azospirillum brasilense Sp245

Align ATPase (characterized, see rationale)
to candidate AZOBR_RS23525 AZOBR_RS23525 ABC transporter ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS23525 AZOBR_RS23525 ABC
           transporter ATP-binding protein
          Length = 269

 Score =  245 bits (625), Expect = 8e-70
 Identities = 131/246 (53%), Positives = 170/246 (69%), Gaps = 6/246 (2%)

Query: 21  MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80
           +I    V K +G+  + L  VSLTV      V++GPSGSGKST LR  N LE+  RGEI 
Sbjct: 1   VIEIRNVYKSFGST-EVLKDVSLTVPPSRTTVVIGPSGSGKSTLLRCCNCLETADRGEIR 59

Query: 81  IEGHRLSHDRR-----DIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAE 135
           I    +  D +     ++  +R E GMVFQ FNLFPH+T ++N+M APV VR    A+A 
Sbjct: 60  INHRTIIADGKPLPDKELNALRAETGMVFQSFNLFPHMTTVENVMRAPVVVRGMAKAEAR 119

Query: 136 ATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVRE 195
             A +LL +V + ++AD YP  LSGGQ+QR AIARALAM+P+++LFDEPTSALDPE+V E
Sbjct: 120 ELAMELLRKVGLGDKADVYPSTLSGGQKQRAAIARALAMKPKVMLFDEPTSALDPELVGE 179

Query: 196 VLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQ 255
           VL VM+ LA EGMTM+V THE+GFAREVAD VV+MADG+IVE   P++ FT P  +R + 
Sbjct: 180 VLQVMKTLAEEGMTMMVVTHEMGFAREVADTVVVMADGRIVESGSPEQIFTNPTQERTRG 239

Query: 256 FLAQIL 261
           FL  ++
Sbjct: 240 FLRALV 245


Lambda     K      H
   0.321    0.134    0.387 

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: 217
Number of extensions: 7
Number of successful extensions: 2
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: 261
Length of database: 269
Length adjustment: 25
Effective length of query: 236
Effective length of database: 244
Effective search space:    57584
Effective search space used:    57584
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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