GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araH in Photobacterium gaetbulicola Gung47

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate WP_039469452.1 H744_RS03170 ABC transporter permease

Query= CharProtDB::CH_014278
         (328 letters)



>NCBI__GCF_000940995.1:WP_039469452.1
          Length = 338

 Score =  208 bits (529), Expect = 2e-58
 Identities = 115/334 (34%), Positives = 192/334 (57%), Gaps = 15/334 (4%)

Query: 5   STSGSGAPKSSFSFGRIWDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMV 64
           +TSG+ +P++   + R+  +Y + VVF  + +  +I  P F T  N+  +   ++  G++
Sbjct: 8   ATSGAKSPQN---YKRLISKYAIYVVFIAMCVVMSILSPVFLTVANLLNVVTQMASIGLL 64

Query: 65  ACGMLFCLASGDFDLSVASVIACAGVTTAVVINLTE------------SLWIGVAAGLLL 112
           A G+   + +   DLS  SV+A A V +A +    +             + + +   L +
Sbjct: 65  ALGVTIIIITRGIDLSSGSVLAVAAVASASMAQTLDWGMRMYPAMPELPVIVPILVALAV 124

Query: 113 GVLCGLVNGFVIAKLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFG 172
           G LCG +NG +IA   I   I TL  M I RG A + SDG+ V    +S+  +G     G
Sbjct: 125 GALCGFINGALIAYTGIPPFIATLGMMIIARGAALLYSDGRPVSSLIDSYQWIGQGTIAG 184

Query: 173 LPAPIWLTVACLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVS 232
           +P P+ + +   I+  +LLN T FG+   AIGGNE AA ++G+ V + KI+++  +GL++
Sbjct: 185 IPVPVIIFIVMAIVSYILLNYTRFGKYAYAIGGNETAAYVSGINVKKYKILVYTYAGLLA 244

Query: 233 AIAGIILASRMTSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENA 292
            IA +IL++R+ SGQP   + YEL  I++  +GGVS  GGIG I   + G +I+G ++N 
Sbjct: 245 GIAALILSARINSGQPGLGVMYELDAIASATVGGVSHAGGIGTIQGTIIGTMIMGVLQNG 304

Query: 293 MNLLNISPFAQYVVRGLILLAAVIFDRYKQKAKR 326
           ++LLN+S + Q VV+GL+++ AV+FD  +QK  +
Sbjct: 305 LDLLNVSAYWQQVVKGLVIVVAVVFDMKRQKKSK 338


Lambda     K      H
   0.327    0.141    0.414 

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: 318
Number of extensions: 17
Number of successful extensions: 1
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: 328
Length of database: 338
Length adjustment: 28
Effective length of query: 300
Effective length of database: 310
Effective search space:    93000
Effective search space used:    93000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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