GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araWsh in Photobacterium gaetbulicola Gung47

Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_044621445.1 H744_RS06410 ribose ABC transporter permease

Query= uniprot:A0KWY6
         (405 letters)



>NCBI__GCF_000940995.1:WP_044621445.1
          Length = 327

 Score =  180 bits (456), Expect = 6e-50
 Identities = 104/306 (33%), Positives = 182/306 (59%), Gaps = 14/306 (4%)

Query: 66  LLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGIDL 125
           L+AL  L++   F++ +FF +         ++++IL +++  A++++GM+LVI T GIDL
Sbjct: 29  LIALIFLIVVVSFLNPNFFTVD--------NILNILRQTSVNAIIAVGMTLVILTAGIDL 80

Query: 126 SVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVATLLL 185
           SVG+V+A+ GA  A+L+ + ++ ++  +   L+ G   G I+G +++   +Q  +ATL+ 
Sbjct: 81  SVGSVLALCGAFAASLIAM-EVPVMIAVPTALLAGAALGAISGVIIAKGKVQAFIATLVT 139

Query: 186 MVAGRGVAQLINQGQII----TFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRKT 241
           M   RGV  +   G+ I    T     FA  G G  +G+P+P+W+++ +      LL  T
Sbjct: 140 MTLLRGVTMVYTDGRPISTGFTDVADSFAWFGTGYAMGIPVPIWLMVIVFAAVWYLLNHT 199

Query: 242 ALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGLW 301
             G +I A+G N  A+R  GIN   +K+  Y I GL AALAG+I T+ +  +    AG+ 
Sbjct: 200 RFGRYIYALGGNESAARLSGINVDRVKIGVYAICGLLAALAGIIVTSRLSSAQP-TAGMG 258

Query: 302 LELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVILT 361
            ELDA+ AVV+GG +L GG+  ++ +++GALII  L   + +  + + + ++ KA+VIL 
Sbjct: 259 YELDAIAAVVLGGTSLAGGKGRIMGTLIGALIIGFLNNALNLLDVSSYYQMIAKAVVILL 318

Query: 362 VLLLQS 367
            +L+ +
Sbjct: 319 AVLVDN 324


Lambda     K      H
   0.323    0.136    0.379 

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: 300
Number of extensions: 18
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: 405
Length of database: 327
Length adjustment: 29
Effective length of query: 376
Effective length of database: 298
Effective search space:   112048
Effective search space used:   112048
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 (22.0 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