GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsC in Pseudovibrio axinellae Ad2

Align ABC transporter permease (characterized, see rationale)
to candidate WP_068000560.1 PsAD2_RS00560 ABC transporter permease

Query= uniprot:A0A166R405
         (325 letters)



>NCBI__GCF_001623255.1:WP_068000560.1
          Length = 332

 Score =  270 bits (691), Expect = 3e-77
 Identities = 154/331 (46%), Positives = 216/331 (65%), Gaps = 9/331 (2%)

Query: 1   MNTASLAGKRSGNFYGLGTYLGLAG---ALLAMVALFSVLSSHFLSYDTFSTLANQIPDL 57
           + T     + SGNF  + T L  AG   ALLA++  FS+ + HFL+ +  + +  Q+   
Sbjct: 3   IQTGDEVAQASGNF-SIRTVLHNAGIGLALLALILFFSIFTEHFLTANNITNILTQVTIN 61

Query: 58  MVLAVGMTFVLIIGGIDLSVGSVLA----LAASAVSVAILGWGWSVLPAALLGMAVAALA 113
           ++LAVGMTFV++IGGIDLSVGSV+A    +A  A+++A LG   +++ A +   AV  + 
Sbjct: 62  LILAVGMTFVILIGGIDLSVGSVMAFASVIAGKAITLAGLGPFEAIVLAVIAATAVGVVC 121

Query: 114 GTITGSITVAWRIPSFIVSLGVLEMARGLAYQMTGSRTAYIGD-AFAWLSNPIAFGISPS 172
           G I G+IT  W +PSFI++LG+L +ARG A Q + ++T Y    AF    + + +G+   
Sbjct: 122 GAINGTITARWSLPSFIITLGMLNIARGAALQASNAQTIYSFPLAFEDFGSAMFYGVPVV 181

Query: 173 FIIALLIIFIAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAA 232
           F++AL ++FIA  +L  TVFGR L GIG NEEAVRLAG +   YKI  F++ GL AGIAA
Sbjct: 182 FMVALALVFIAWFILNFTVFGRLLYGIGNNEEAVRLAGHSVYRYKIAAFTICGLTAGIAA 241

Query: 233 LFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQI 292
           +  ++RL  + P AG G EL  IAAV+IGGTSL GGRGSVI T  G  II VLA GL  I
Sbjct: 242 VVYMARLNISSPIAGIGFELNAIAAVIIGGTSLNGGRGSVIGTLIGAFIIGVLANGLILI 301

Query: 293 GATEPTKRIITGAVIVVAVVLDTYRSQRASR 323
           G ++  +++ITG VI++AV+LD YR++   R
Sbjct: 302 GLSDFMRQMITGVVIIIAVILDYYRAKYTRR 332


Lambda     K      H
   0.325    0.139    0.393 

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: 277
Number of extensions: 17
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: 325
Length of database: 332
Length adjustment: 28
Effective length of query: 297
Effective length of database: 304
Effective search space:    90288
Effective search space used:    90288
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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