GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Erythrobacter gangjinensis K7-2

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_047006707.1 AAW01_RS07015 ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_001010925.1:WP_047006707.1
          Length = 317

 Score = 97.4 bits (241), Expect = 3e-25
 Identities = 76/241 (31%), Positives = 118/241 (48%), Gaps = 26/241 (10%)

Query: 1   MSRPILEVSGLTMRFGGL------LAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGF 54
           M+   +E+  L   + G       LA+ GV+  V +  V  ++GPNGAGK+T+ N + G 
Sbjct: 1   MADAAIEIRDLRKEYAGSAKAPPKLALKGVSFDVPQGSVFGLLGPNGAGKSTLINIMAGL 60

Query: 55  YQPTGGLIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFL 114
              TGG +R+ G +I     H+ A+  +    Q +      T  E L        N +  
Sbjct: 61  VNKTGGTVRIWGRDID--EDHRNAKLNIGIVPQEIVFDPFFTPYEVL-------ENQSGF 111

Query: 115 AGLFKTPAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRI 174
            G+ K  A RRSE          L  V L +  +  A TL+ G +RRL IA+ M+  P I
Sbjct: 112 YGIAK--ALRRSE--------ELLRAVRLEDKRDAYARTLSGGMKRRLLIAKAMVHSPPI 161

Query: 175 LMLDEPAAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLA 234
           L+LDEP AG++ +    L  L+ +L +E  VTV+L  H ++    + + I +IN G  +A
Sbjct: 162 LVLDEPTAGVDVELRKQLWELVGELNAE-GVTVVLTTHYLEEAEELCEQIAIINHGELIA 220

Query: 235 D 235
           +
Sbjct: 221 N 221


Lambda     K      H
   0.320    0.137    0.391 

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: 179
Number of extensions: 12
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: 255
Length of database: 317
Length adjustment: 26
Effective length of query: 229
Effective length of database: 291
Effective search space:    66639
Effective search space used:    66639
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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