GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16935 in Klebsiella michiganensis M5al

Align L-arabinose-binding periplasmic protein; Short=ABP (characterized, see rationale)
to candidate BWI76_RS18250 BWI76_RS18250 arabinose ABC transporter substrate-binding protein

Query= uniprot:A0A161H4E4
         (334 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS18250 BWI76_RS18250 arabinose ABC
           transporter substrate-binding protein
          Length = 326

 Score =  379 bits (974), Expect = e-110
 Identities = 194/322 (60%), Positives = 240/322 (74%), Gaps = 2/322 (0%)

Query: 12  RAALAVTAVSLSSHLLAADAVKIGFLVKQAEEPWFQTEWAFAEKAAKDKGFQLIKIAVPD 71
           +A  A+   ++ S    A+ +K+GFLVKQ EEPWFQTEW FA+KA KD GF +IKIAVPD
Sbjct: 6   KALAAIGLAAVMSQSAMAETLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFDVIKIAVPD 65

Query: 72  GEKTLSAIDSLAANGAKGFVICPPDVSLGPAIVAKAKLNDMKVIAVDDRFVGSDGKFMED 131
           GEKTL+AIDSLAA+GAKGFVIC PD  LG AIVAKA+  DMKVI VDD+FV + GK M+ 
Sbjct: 66  GEKTLNAIDSLAASGAKGFVICTPDPKLGAAIVAKARGYDMKVITVDDQFVNAKGKPMDS 125

Query: 132 VPYLGMAAFEVGQKQGGAMAAEAKKRGWDWKDTYAVINTYNELDTGKKRTDGSVDALKKA 191
           VP + MAA E+G +QG  +  E +KRGWD KDT  +  T +ELDT ++RT GS+DALK A
Sbjct: 126 VPLVMMAASEIGARQGQELYKEMQKRGWDVKDTAVMAITADELDTARRRTTGSIDALKAA 185

Query: 192 GMPADHILYSALKTLDVPGSMDSTNSALVKLPSAAKNLIIGGMNDNTVLGGVRATEAAGF 251
           G P   I     K+ D+PG+ D+ NS LV+ P+  K+ +I GMNDNTVLGGVRATE  GF
Sbjct: 186 GFPEQQIYRVPTKSNDIPGAFDAGNSMLVQHPN-VKHWLIVGMNDNTVLGGVRATEGQGF 244

Query: 252 KAANVIGIGINGTDAIGELKKPD-SGFFGSMLPSPHIEGYKTAEMMYEWITTGKEPPKYT 310
           KA +VIGIGING DA+ EL K   +GF+GS+LPSP I GYKT+EM+Y W+T   EPPK+T
Sbjct: 245 KAPDVIGIGINGVDAVNELSKAQATGFYGSLLPSPDIHGYKTSEMLYNWVTKDVEPPKFT 304

Query: 311 AMDEVTLITRENFKQELEKIGL 332
           A+ +V LITR+NFK+EL K GL
Sbjct: 305 AVTDVVLITRDNFKEELAKKGL 326


Lambda     K      H
   0.316    0.133    0.388 

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: 372
Number of extensions: 11
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: 334
Length of database: 326
Length adjustment: 28
Effective length of query: 306
Effective length of database: 298
Effective search space:    91188
Effective search space used:    91188
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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