GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Marinobacter adhaerens HP15

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF4155 HP15_4095 branched-chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Marino:GFF4155
          Length = 271

 Score =  199 bits (506), Expect = 6e-56
 Identities = 110/268 (41%), Positives = 161/268 (60%), Gaps = 15/268 (5%)

Query: 13  TLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMIT 72
           ++L++ +LS+ FGG+ A+ D SF      +T +IGPNGAGKT++FNCI+GFYKP  G I 
Sbjct: 2   SILEISNLSLSFGGVKALQDVSFRVPENTVTTIIGPNGAGKTSLFNCISGFYKPQQGTI- 60

Query: 73  FNQKSGKQYLLERLP-DFRITKEARV--ARTFQNIRLFSGLTVLENLLVAQHNKLMKASG 129
                  +Y  + LP   +  K A +  ARTFQNI LF G+TVL+N+ +  H  +     
Sbjct: 61  -------RYQGQTLPGSIKPPKRAALGLARTFQNIALFRGMTVLDNIKLGAHVHMKSG-- 111

Query: 130 YTILGLIGVGPYKREA-AEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT 188
             +  L   GP +RE  A   ++    ++  ++      P   L YG Q+R+E+ARA+  
Sbjct: 112 -LLSALAYFGPARREEMAVRKDVEERIIDFLEIDHIRRQPVASLSYGLQKRVELARALAM 170

Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248
            P++L LDEP AG+N  E   +   +  IR E G ++L++EHDM +VM+ISDH+ VL +G
Sbjct: 171 QPKVLMLDEPVAGMNREEKEDMARFILDIREEWGVTVLMVEHDMGMVMDISDHIAVLNFG 230

Query: 249 QKISDGTPDHVKNDPRVIAAYLGVEDEE 276
           Q I++G P  V+N+P VI AYLG  D E
Sbjct: 231 QVITEGLPADVQNNPEVIKAYLGNSDIE 258


Lambda     K      H
   0.318    0.136    0.386 

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: 196
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: 292
Length of database: 271
Length adjustment: 26
Effective length of query: 266
Effective length of database: 245
Effective search space:    65170
Effective search space used:    65170
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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