GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Dechlorosoma suillum PS

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_2058 Dsui_2058 ABC-type branched-chain amino acid transport systems, ATPase component

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__PS:Dsui_2058
          Length = 260

 Score =  201 bits (511), Expect = 1e-56
 Identities = 122/270 (45%), Positives = 157/270 (58%), Gaps = 12/270 (4%)

Query: 7   NTMSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKP 66
           N      LL + ++   FGGL  + D SFE   G I  LIGPNGAGKTTVFN ITG   P
Sbjct: 2   NAPQQPNLLSIRNVGKHFGGLHVLQDVSFEVPAGSIYGLIGPNGAGKTTVFNLITGLLTP 61

Query: 67  TMGMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMK 126
           + G I F  ++     L  L   RIT +  +ARTFQNIR+F  + +LEN++V  H+ L  
Sbjct: 62  SAGQIDFQGQT-----LIGLEPHRITHQG-IARTFQNIRIFKEMDLLENVMVGMHDHL-- 113

Query: 127 ASGYTILGLIGVGPYKREA-AEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARA 185
              Y   G+    P  R A  +A E A   L    L  +AD  A +L YG QR+LE ARA
Sbjct: 114 --NYGGFGIFLNSPACRAAEKKARERALELLSWVGLDHKADMLADNLSYGDQRKLEFARA 171

Query: 186 MCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVL 245
           + T P+LL LDEP AG+NP E   L   + +IR   G  + +IEHDM  VM + D + VL
Sbjct: 172 LATEPKLLLLDEPVAGMNPSEKTILMEEINNIR-NRGYGVFMIEHDMRFVMGLCDRIAVL 230

Query: 246 EYGQKISDGTPDHVKNDPRVIAAYLGVEDE 275
            +G+ I++GTPD V+N+P VI AYLG EDE
Sbjct: 231 NFGRIIAEGTPDEVRNNPDVIEAYLGKEDE 260


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: 225
Number of extensions: 13
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: 292
Length of database: 260
Length adjustment: 25
Effective length of query: 267
Effective length of database: 235
Effective search space:    62745
Effective search space used:    62745
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