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_111608864.1 DK187_RS18825 urea ABC transporter ATP-binding protein UrtD

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_003259225.1:WP_111608864.1
          Length = 288

 Score =  146 bits (368), Expect = 5e-40
 Identities = 91/254 (35%), Positives = 139/254 (54%), Gaps = 16/254 (6%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           IL V GL + F G  A+N +NL V + ++  +IG NGAGKTT+ + +TG  Q   G +  
Sbjct: 39  ILYVEGLNLSFDGFKALNNLNLYVNDGELRCLIGANGAGKTTLMDVITGKTQCDSGTVFF 98

Query: 65  -DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENL---LVAQHRHLNTNFLAGLFKT 120
                +      +IA+ G+ R FQ   +F+E T  +NL   L    R L T         
Sbjct: 99  GQNHNLLNKDEAEIAQLGIGRKFQKPTVFEEQTVFDNLELSLKTDKRVLPT--------- 149

Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180
             F R     ++     L+ + L +     AG L++GQ++ LEI   ++  PR+L++DEP
Sbjct: 150 -LFSRLTPTQIDRIDEVLKTIGLAKHRFMLAGALSHGQKQWLEIGMLLVAEPRLLLIDEP 208

Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240
            AG+  +ET+    L+  L  E   TV+++EHDM+ V SI+  + V++QG+ LA+GT  Q
Sbjct: 209 VAGMTAQETERTAELLTSLAGER--TVIVVEHDMEFVRSIARTVTVLHQGSVLAEGTMNQ 266

Query: 241 IRDNPDVIKAYLGE 254
           I+ N DVI+ YLGE
Sbjct: 267 IQSNKDVIEVYLGE 280


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: 177
Number of extensions: 10
Number of successful extensions: 4
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: 288
Length adjustment: 25
Effective length of query: 230
Effective length of database: 263
Effective search space:    60490
Effective search space used:    60490
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