GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Marinomonas arctica 328

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_111607209.1 DK187_RS09960 ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_003259225.1:WP_111607209.1
          Length = 249

 Score =  161 bits (408), Expect = 1e-44
 Identities = 89/253 (35%), Positives = 141/253 (55%), Gaps = 15/253 (5%)

Query: 1   MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60
           +S P++  SG+   +G    ++GV+    + + V ++GPNGAGKTT+F  L G   P+ G
Sbjct: 5   LSTPVITGSGIDKHYGAFQVLHGVDFSANKGEAVGIVGPNGAGKTTLFGVLAGATAPSAG 64

Query: 61  LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKT 120
            +   GE+I      +    G+ RT Q  R F  MT  ENLL A          AGL   
Sbjct: 65  SVIYQGEDITTTNAAQRCHAGIARTHQVPRPFLGMTVFENLLTAAQNG------AGL--- 115

Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180
                S  +A +YA H L++ ++   ANR    L    ++RLE+AR + T P++L+LDE 
Sbjct: 116 -----SGDDAEKYAVHALQQADIAHLANRPTSALGLLDRKRLELARALATAPKVLLLDEI 170

Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240
             GL   E   L ALI++L+++  +T++ IEH +  ++ + D +V +++G  +A+G P  
Sbjct: 171 GGGLTEGELHQLIALISELKAD-GLTIIWIEHILHALLKVIDRLVCMSEGRVIAEGAPSD 229

Query: 241 IRDNPDVIKAYLG 253
           + +NPDV+KAYLG
Sbjct: 230 VMNNPDVMKAYLG 242


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: 160
Number of extensions: 6
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: 249
Length adjustment: 24
Effective length of query: 231
Effective length of database: 225
Effective search space:    51975
Effective search space used:    51975
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: 46 (22.3 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