GapMind for catabolism of small carbon sources

 

Aligments for a candidate for CAT1 in Pedobacter sp. GW460-11-11-14-LB5

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate CA265_RS15000 CA265_RS15000 amino acid permease

Query= CharProtDB::CH_091324
         (622 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS15000 CA265_RS15000 amino acid
           permease
          Length = 491

 Score =  226 bits (577), Expect = 1e-63
 Identities = 135/410 (32%), Positives = 222/410 (54%), Gaps = 20/410 (4%)

Query: 28  LSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCYGEF 87
           L R L+   LVALGVG+ +GAG++V   A A +NAGP++ I F+IAA+   LAGLCY E 
Sbjct: 23  LKRTLSAGALVALGVGAIIGAGLFVRTAAAAAQNAGPSVTIGFIIAAIGCALAGLCYAEL 82

Query: 88  GARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKPIG-- 145
            + +P +GSAY Y+Y T+GEL A++ GW+L+L Y +G ++V  AWS   ++L+ + +   
Sbjct: 83  SSSIPISGSAYTYTYATMGELMAWVIGWDLVLEYAVGAATVGIAWSEYLNKLLVEVLHTS 142

Query: 146 ----EFSRQHMALNAPGVLAQTPDIFAVIIIIILTGLLTLGVKESAMVNK--IFTCINVL 199
               E+       +  G +    ++ A+ I+ +L+ LL  G  ESA VN   + T + ++
Sbjct: 143 PIPYEWCHSPFQSHPDGTVNGIMNLPALFIVGLLSLLLIKGTSESAFVNGLIVITKVGIV 202

Query: 200 VLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATCFYAF 259
           +L  ++  GF+  S  +  +       ++   +  +G       GF GV+  A T F+AF
Sbjct: 203 ILIIVLGWGFINESNHHPYIPAATTYVDHAGISHSFG-------GFWGVIGAAGTVFFAF 255

Query: 260 VGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMP---YFCLDIDSPL 316
           +GFD ++T  +E KNP+ A+P+GI+ SL +C + Y   +  LT + P   +     ++ +
Sbjct: 256 IGFDAVSTAAQETKNPKTAMPIGILGSLAVCTVLYILFAHVLTGIAPVEFFRTKGGEASV 315

Query: 317 PGAFKH--QGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNR 374
             A      G+      V +  L   S+ +L  +    RV Y+M++DGLL K  + ++ +
Sbjct: 316 VAAISEYMTGYSWLSKLVTVAILAGFSSVILVMLLGQSRVFYSMSKDGLLPKMFSDLHPK 375

Query: 375 TKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLR 424
            KTP  A +    I  + A       + D+ SIGTL A+ LV   V++LR
Sbjct: 376 FKTPYKANLVILIIVGLFAAFIPGDVVGDMTSIGTLFAFMLVCVAVIILR 425



 Score = 60.8 bits (146), Expect = 1e-13
 Identities = 48/142 (33%), Positives = 73/142 (51%), Gaps = 19/142 (13%)

Query: 455 SESQTGFLPVAEKFSLKSILSPKNVEPSKFSGLIVNISAGLLAALIITVCIVAVLGREAL 514
           S S+ G LP      + S L PK   P K + L++ I  GL AA I       V+G +  
Sbjct: 358 SMSKDGLLP-----KMFSDLHPKFKTPYK-ANLVILIIVGLFAAFIPG----DVVG-DMT 406

Query: 515 AEGTLWAVFVMTGSVLLCMLVTGIIWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQL 574
           + GTL+A       +L+C+ V  II R+ +      FK P+VP++P+L +     +++ L
Sbjct: 407 SIGTLFAF------MLVCVAV--IILRKTDPDLPRQFKTPWVPLIPILGVVACGLMILGL 458

Query: 575 DQGTWVRFAVWMLIGFTIYFGY 596
               W+R   W+ +GF IYFGY
Sbjct: 459 GWTNWLRLFGWLALGFIIYFGY 480


Lambda     K      H
   0.324    0.138    0.417 

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: 729
Number of extensions: 36
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 622
Length of database: 491
Length adjustment: 36
Effective length of query: 586
Effective length of database: 455
Effective search space:   266630
Effective search space used:   266630
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 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