GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24010 in Lutibaculum baratangense AMV1

Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate WP_081718345.1 N177_RS02595 ABC transporter permease

Query= uniprot:B2TBJ8
         (250 letters)



>NCBI__GCF_000496075.1:WP_081718345.1
          Length = 248

 Score =  152 bits (385), Expect = 5e-42
 Identities = 84/226 (37%), Positives = 135/226 (59%), Gaps = 2/226 (0%)

Query: 3   FDFDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVF 62
           F  DF      ++L+   TT+ L   SL++G  +SL +   R+SP+ +    A  Y+  F
Sbjct: 19  FSTDFAQRYGFRMLSGFWTTIELVTLSLLIGAAISLPVAAGRLSPNPVIGALAYGYVYFF 78

Query: 63  RGSPLLIQMFLVYYGMGQFGVIRESF-LWPVLREPYMCAVLSLALCTAGYTAEIIRGGLM 121
           RG+PLL Q FLVYYG G F    ++  LW   R+ + CAV + +L T+ Y AEI+ G + 
Sbjct: 79  RGTPLLAQTFLVYYGAGSFRAELDAVGLWTFFRDAWFCAVFTFSLNTSAYQAEILAGAIR 138

Query: 122 AVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVT 181
            VP  QIEAG ++GLS + +  R++ P AL   L  Y  E VL++K +A+AS++T++++ 
Sbjct: 139 TVPRSQIEAGQALGLSRYVIATRIVLPQALVVALRPYGNEVVLMIKGSAIASIITIYDLM 198

Query: 182 GVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRHL 227
           G  ++   +++   + +I AA++YL L   + RL  ++E RL+RHL
Sbjct: 199 GETRRAFSRSF-DFQTYIWAAILYLVLVETLRRLWDVMERRLTRHL 243


Lambda     K      H
   0.331    0.143    0.431 

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: 164
Number of extensions: 9
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: 250
Length of database: 248
Length adjustment: 24
Effective length of query: 226
Effective length of database: 224
Effective search space:    50624
Effective search space used:    50624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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