GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc7a1 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)



>FitnessBrowser__Pedo557:CA265_RS15000
          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 (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