GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araF in Klebsiella michiganensis M5al

Align L-arabinose-binding periplasmic protein; ABP (characterized)
to candidate BWI76_RS18250 BWI76_RS18250 arabinose ABC transporter substrate-binding protein

Query= SwissProt::P02924
         (329 letters)



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

 Score =  609 bits (1571), Expect = e-179
 Identities = 301/326 (92%), Positives = 317/326 (97%)

Query: 1   MHKFTKALAAIGLAAVMSQSAMAENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIK 60
           MHKFTKALAAIGLAAVMSQSAMAE LKLGFLVKQPEEPWFQTEWKFADKAGKDLGF+VIK
Sbjct: 1   MHKFTKALAAIGLAAVMSQSAMAETLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFDVIK 60

Query: 61  IAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKG 120
           IAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLG+AIVAKARGYDMKVI VDDQFVNAKG
Sbjct: 61  IAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGAAIVAKARGYDMKVITVDDQFVNAKG 120

Query: 121 KPMDTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMD 180
           KPMD+VPLVMMAA++IG RQGQELYKEMQKRGWDVK++AVMAITA+ELDTARRRTTGS+D
Sbjct: 121 KPMDSVPLVMMAASEIGARQGQELYKEMQKRGWDVKDTAVMAITADELDTARRRTTGSID 180

Query: 181 ALKAAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATE 240
           ALKAAGFPE+QIY+VPTKSNDIPGAFDA NSMLVQHP VKHWLIVGMND+TVLGGVRATE
Sbjct: 181 ALKAAGFPEQQIYRVPTKSNDIPGAFDAGNSMLVQHPNVKHWLIVGMNDNTVLGGVRATE 240

Query: 241 GQGFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEP 300
           GQGFKA D+IGIGINGVDAV+ELSKAQATGFYGSLLPSPD+HGYK+SEMLYNWV KDVEP
Sbjct: 241 GQGFKAPDVIGIGINGVDAVNELSKAQATGFYGSLLPSPDIHGYKTSEMLYNWVTKDVEP 300

Query: 301 PKFTEVTDVVLITRDNFKEELEKKGL 326
           PKFT VTDVVLITRDNFKEEL KKGL
Sbjct: 301 PKFTAVTDVVLITRDNFKEELAKKGL 326


Lambda     K      H
   0.315    0.132    0.381 

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: 504
Number of extensions: 19
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: 329
Length of database: 326
Length adjustment: 28
Effective length of query: 301
Effective length of database: 298
Effective search space:    89698
Effective search space used:    89698
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: 48 (23.1 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