GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Azospirillum brasilense Sp245

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate AZOBR_RS25630 AZOBR_RS25630 ABC transporter

Query= TCDB::Q8DQH8
         (254 letters)



>FitnessBrowser__azobra:AZOBR_RS25630
          Length = 255

 Score =  218 bits (556), Expect = 7e-62
 Identities = 121/253 (47%), Positives = 164/253 (64%), Gaps = 2/253 (0%)

Query: 3   LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62
           LL+++ +++ FGG+ AV DVT  ++EGELVGLIGPNGAGKTTLFNL++G    S GTV  
Sbjct: 4   LLDIRNVSRRFGGVLAVNDVTGHVDEGELVGLIGPNGAGKTTLFNLISGFTPLSSGTVAF 63

Query: 63  DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLI-AFGNHHKQHVFTSFLRLPAF 121
           DG  ++G    ++A LG+ RTFQN+R+F +++V DNV + A G   +  +   F  L   
Sbjct: 64  DGRTISGLKTNQVARLGISRTFQNLRVFPNMSVFDNVSVGAVGALPQGALGALFGSLAGG 123

Query: 122 YKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAG 181
                E+  +  E L+   L   A  LA NL YGQ++ LEI RALA +P+ L LDEPAAG
Sbjct: 124 GARSAEISRRTWEALEAVGLTHVAGELAANLPYGQRKYLEIARALAMQPRFLILDEPAAG 183

Query: 182 MNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKT 241
           +N  ET  L + I+R+     +TIML+EHDM LVM + +RI VL  GR IA G PD I+ 
Sbjct: 184 LNDTETRALADFIKRLHGT-GLTIMLVEHDMTLVMSICQRILVLASGRKIADGPPDAIRR 242

Query: 242 NKRVIEAYLGGEA 254
           +  V+EAYLG +A
Sbjct: 243 DPAVLEAYLGVDA 255


Lambda     K      H
   0.319    0.139    0.385 

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: 187
Number of extensions: 10
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: 254
Length of database: 255
Length adjustment: 24
Effective length of query: 230
Effective length of database: 231
Effective search space:    53130
Effective search space used:    53130
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 (21.7 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:

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