GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Brucella inopinata BO1

Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate WP_008509253.1 BIBO1_RS15350 D-xylose ABC transporter substrate-binding protein

Query= reanno::Phaeo:GFF3639
         (341 letters)



>NCBI__GCF_000182725.1:WP_008509253.1
          Length = 339

 Score =  235 bits (600), Expect = 1e-66
 Identities = 134/324 (41%), Positives = 190/324 (58%), Gaps = 12/324 (3%)

Query: 11  AFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSAKQLS 70
           A  AT + A  E   +G S  + + ERW  D     AA E  GA      A  +  KQ+ 
Sbjct: 20  AMGATPASASPEHPVIGFSIDDLRVERWARDRDYFIAAAEKLGAKVNVQSADGNEEKQVK 79

Query: 71  DIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYLTFDNVEV 129
            +E+LI+QGVDA++++  +++     V  A   GI V++YDRLI +     Y++FDN  V
Sbjct: 80  QVENLISQGVDAIVIVPMNSKVFDAVVADAKASGIKVLSYDRLILNADIDAYISFDNERV 139

Query: 130 GRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAYTDGW 189
           G MQA+AVL+A+P GNY ++ GSPTD NA  LR GQ++ ++ A+DSG +KIVG  +   W
Sbjct: 140 GFMQAQAVLKAKPEGNYYLLGGSPTDNNAKLLRAGQEKALKEAVDSGKVKIVGSQWVKEW 199

Query: 190 LPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQDGDHAALN 248
            P  A   ME  LTA  NK+DAVVASNDGTAGG + AL AQG+ G  AVSGQD D AA+ 
Sbjct: 200 SPTEALSIMENALTATQNKIDAVVASNDGTAGGAIQALAAQGLAGKTAVSGQDSDLAAVK 259

Query: 249 RVAKGTQTVSVWKDARDLGKAAANIAVEMA---EGAVMGDVAGGAAWTSPAGTELTARFL 305
           R+  GTQTV+V+K  + + + AA + V++    +    G +  G+        ++    L
Sbjct: 260 RLVDGTQTVTVYKPLKLIAEEAAKLTVQLVRDEKPEFNGKINNGS-------KDVDTLLL 312

Query: 306 EPIPVTADNLSVVVDAGWITKEAL 329
            P  VT DN+ + +  G+ TKE +
Sbjct: 313 TPTAVTKDNIDIYIKDGFYTKEQI 336


Lambda     K      H
   0.313    0.128    0.362 

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: 247
Number of extensions: 12
Number of successful extensions: 5
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: 341
Length of database: 339
Length adjustment: 28
Effective length of query: 313
Effective length of database: 311
Effective search space:    97343
Effective search space used:    97343
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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