GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctP in Bacteroides thetaiotaomicron VPI-5482

Align L-lactate permease (characterized, see rationale)
to candidate 350981 BT1453 L-lactate permease (NCBI ptt file)

Query= uniprot:Q8EIL2
         (545 letters)



>lcl|FitnessBrowser__Btheta:350981 BT1453 L-lactate permease (NCBI
           ptt file)
          Length = 499

 Score =  267 bits (683), Expect = 6e-76
 Identities = 162/520 (31%), Positives = 283/520 (54%), Gaps = 26/520 (5%)

Query: 15  LTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVSIALASAIYGFSY 74
           +T I+A++P++   + +   K+ G  +  ++L++ + +A+  +   V     S +YG   
Sbjct: 1   MTLILAIIPVLLLIVLMAFFKMSGDKSSIISLIVTMLIALFGFAFSVDNLFYSFLYGALK 60

Query: 75  GLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGFSFGAFLEGAAGF 134
            + PI  II+ A+F Y + +KT + EII+    S++ D+ +Q+LL+ + FG  LE  AGF
Sbjct: 61  AVSPILIIILMAIFSYNVLLKTEKMEIIKQQFASISTDKSIQVLLLTWGFGGLLEAMAGF 120

Query: 135 GAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQVSSLDPFHIGQLA 194
           G  VAI AA+L+ LGF P+++A + LIAN+   AFGA+G P++V  + ++LD   +    
Sbjct: 121 GTAVAIPAAILISLGFKPIFSATVSLIANSVATAFGAIGTPVLVLAKETNLDVLQLSTNV 180

Query: 195 GRQLPILSIIVPFWLIAMMD-GIRGI-RQTWPATLVAGVSFAVTQFLTSNFIGPELPDIT 252
             QL +L  ++P  L+ + +  ++ + +  + A LV GVS  V Q+L + ++G E P I 
Sbjct: 181 VLQLSVLMFLIPLVLLFLTNPKLKALPKNIFLALLVGGVSL-VGQYLAARYMGAESPAII 239

Query: 253 SALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPKSTFSNGQIFKAWSPFIILTAIVTLW 312
            +++S+I + L+ K+   KE       K R    KST     I  AWS ++++  ++ L 
Sbjct: 240 GSILSIIVIVLYGKLTASKE------EKAR----KSTLKTKDILNAWSIYLLILFLIILT 289

Query: 313 SIKDVQLALSFATISIEVPYLHNLVIKTAPIVAKETPYAAIYKLNLLGAVGTAILIAAMI 372
           S     L  +           +N V + +  V   T     Y ++ L   G  + +   I
Sbjct: 290 SPLFPSLRSTLE---------NNWVTRISLPVNATT---VNYTISWLTHAGVLLFLGTFI 337

Query: 373 SIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFAFVANYSGLSSTLALVLA-GTGVA 431
             ++    +        +T+ +L+   +++  ++  + + + SG+ + +A  LA  TG  
Sbjct: 338 GGLIQGAKVKELFIVLWNTVKQLKKTFITVICLVGLSTIMDTSGMIAVIATALATATGSL 397

Query: 432 FPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPELLVAANTTGGVTGKMISP 491
           +P F+P +G LG F+TGSDTSSN LFG LQA+ A QI V+P+ L AANT G   GK+ISP
Sbjct: 398 YPLFAPVIGCLGTFITGSDTSSNILFGKLQASVAGQIHVSPDWLSAANTVGATGGKIISP 457

Query: 492 QSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVL 531
           QSIA+A +A    GKE ++ +  + ++L +    G++  +
Sbjct: 458 QSIAIATSAGNQQGKEGEILKAAIPYALAYVVITGIIVYI 497


Lambda     K      H
   0.327    0.140    0.419 

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: 727
Number of extensions: 32
Number of successful extensions: 4
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: 545
Length of database: 499
Length adjustment: 35
Effective length of query: 510
Effective length of database: 464
Effective search space:   236640
Effective search space used:   236640
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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