GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS18250
          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:

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