GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acaP in Lactobacillus shenzhenensis LY-73

Align Aspartate/glutamate permease AcaP (characterized)
to candidate WP_022529769.1 L248_RS08515 amino acid permease

Query= SwissProt::A2RL65
         (489 letters)



>NCBI__GCF_000469325.1:WP_022529769.1
          Length = 480

 Score =  590 bits (1522), Expect = e-173
 Identities = 274/473 (57%), Positives = 358/473 (75%), Gaps = 1/473 (0%)

Query: 2   DTKKIRWFTVAFIAFNMVWGMGNVVNNFAQQGITVVTSWLLILALYFIPYALIVGQLCST 61
           + K++RW+ +A +AF  VWG+GNVVNNF  QG+TVV SW+LI+ LYF+PY L+VGQL +T
Sbjct: 4   EQKQLRWYNIALLAFVAVWGLGNVVNNFYNQGLTVVVSWILIMILYFVPYTLMVGQLGAT 63

Query: 62  FKDSKGGVSSWVENTSTKRLAYYAAWTYWVVHIPYLAQKPQAILIAFGWVGQGNGNLVSQ 121
           F    GGVSSW++N S KRLAY+AAWTYWVVH+PYLAQKPQAI+IAF W+ Q NG  +++
Sbjct: 64  FATEGGGVSSWIQNLSGKRLAYFAAWTYWVVHVPYLAQKPQAIMIAFSWLFQSNGKFINE 123

Query: 122 MSMTAVALISLAIFLAFLWLSTKGLNTLKVIGGLAGTAMFVMSLLFIVMAIGAPFIAKDF 181
            +   V  + L +FL F+W+S++G+ TL  +G +AG+AMFV+S+LFI++ + AP +    
Sbjct: 124 SNPLIVQTLCLVLFLLFMWMSSRGITTLNRLGSIAGSAMFVLSILFIILGVSAPMMTGS- 182

Query: 182 HIATPDMGNIKTYIPKFDFSYFTTISMLVFAVGGAEKISPYVNQTKNPAKEFPRGMFLLA 241
            IAT  M  + +YIPKFDF+Y TTI+MLVFAVGGAEKISPYVN+T NPAKEFP+GM  LA
Sbjct: 183 SIATAHMDQLSSYIPKFDFNYLTTIAMLVFAVGGAEKISPYVNKTHNPAKEFPKGMIALA 242

Query: 242 GMVGICAVLGSIAMGMIFSSGNLPKDLMANGAYAAFQILGQHFGVGNFLMIVYALTNGVG 301
            MV + A+LGS AMGMIF + ++P DL ANGAY AFQ LG  + VGN  M +YA+TN + 
Sbjct: 243 IMVAVSAILGSFAMGMIFDAHHMPADLYANGAYMAFQRLGDFYHVGNIFMWIYAVTNAMA 302

Query: 302 QIAALAFSIDAPLRILLADADPEYVPAWLRKKTNKGTLKNGYTLTGILVSIIILLPLLGI 361
            +AALA SIDAPLR+LLADAD  ++P  + K  ++G   NGY +T +LV +II++P LGI
Sbjct: 303 SMAALAVSIDAPLRMLLADADTHFIPKAMTKTNSRGVYINGYKMTAVLVGLIIMIPALGI 362

Query: 362 GDMNELVKWLTNLNSVVMPMRYLWVFFAFIMLNRAVKHFQSEYKFIKQKRLAMIAGAWCF 421
             MN L  WL NLN++VMPMRYLWVF A+++L+R +  F S+Y F+K K +A I G WCF
Sbjct: 363 HGMNGLYGWLLNLNAIVMPMRYLWVFLAYMLLSRQMDKFHSDYMFVKNKSVAFIFGLWCF 422

Query: 422 LFTLIACVLGMVPKLDYAANPSAWWFQLASNILTPIVLILLGMLLPFIARREQ 474
           LFT  AC+LGM PK  +A +   WWFQLA N+LTPIVL+LLG++LP IARR +
Sbjct: 423 LFTAFACILGMTPKAAFAGDTKTWWFQLALNVLTPIVLLLLGLILPIIARRHE 475


Lambda     K      H
   0.328    0.140    0.438 

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: 795
Number of extensions: 31
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: 489
Length of database: 480
Length adjustment: 34
Effective length of query: 455
Effective length of database: 446
Effective search space:   202930
Effective search space used:   202930
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: 52 (24.6 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