GapMind for catabolism of small carbon sources

 

Aligments for a candidate for N515DRAFT_2924 in Pedobacter sp. GW460-11-11-14-LB5

Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate CA265_RS15000 CA265_RS15000 amino acid permease

Query= uniprot:A0A1I1Y8J0
         (492 letters)



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

 Score =  395 bits (1015), Expect = e-114
 Identities = 212/473 (44%), Positives = 295/473 (62%), Gaps = 20/473 (4%)

Query: 29  LKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCYAEF 88
           LKR L+A  LV LG+GAIIGAG+FV T  AAA++AGP++ + F+ A I CALA LCYAE 
Sbjct: 23  LKRTLSAGALVALGVGAIIGAGLFVRTAAAAAQNAGPSVTIGFIIAAIGCALAGLCYAEL 82

Query: 89  AAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALISGWI 148
           ++ +P+SGSAY+Y+YAT+GE +AW +GW LVLEY    ATV   WS Y NKLL  +    
Sbjct: 83  SSSIPISGSAYTYTYATMGELMAWVIGWDLVLEYAVGAATVGIAWSEYLNKLLVEVL--- 139

Query: 149 GHDVSLPQTLAAAPF-TVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSIIV 207
            H   +P     +PF +  DG +      +NLPA+ I+  ++ L   G ++SAFVN +IV
Sbjct: 140 -HTSPIPYEWCHSPFQSHPDGTVNG---IMNLPALFIVGLLSLLLIKGTSESAFVNGLIV 195

Query: 208 AIKVTVILLFIAFATKYINPDNWHPFIPASE--------GASKYGWAGVGRAAAIVFFSY 259
             KV +++L I     +IN  N HP+IPA+           S  G+ GV  AA  VFF++
Sbjct: 196 ITKVGIVILIIVLGWGFINESNHHPYIPAATTYVDHAGISHSFGGFWGVIGAAGTVFFAF 255

Query: 260 IGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIAD---FRLLGTPEPV 316
           IGFDAVSTAA E KNP+  MPIGI+GSL +CT+LYI+ A +LTGIA    FR  G    V
Sbjct: 256 IGFDAVSTAAQETKNPKTAMPIGILGSLAVCTVLYILFAHVLTGIAPVEFFRTKGGEASV 315

Query: 317 STALDNY-PSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQK 375
             A+  Y     WL  +V +  + G SSV+LVML+GQ R+FYSM++DGL+P +F  +H K
Sbjct: 316 VAAISEYMTGYSWLSKLVTVAILAGFSSVILVMLLGQSRVFYSMSKDGLLPKMFSDLHPK 375

Query: 376 FRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAF 435
           F+TP+   +V+ ++           V+G+M ++GTL AF  VC+ V++LR T P+LPR F
Sbjct: 376 FKTPYKANLVILIIVGLFAAFIPGDVVGDMTSIGTLFAFMLVCVAVIILRKTDPDLPRQF 435

Query: 436 RVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKLR 488
           + P   ++  LG +AC  + L     +W  +  W+A+G  IYF Y   +S L+
Sbjct: 436 KTPWVPLIPILGVVACGLMILGLGWTNWLRLFGWLALGFIIYFGYSKKNSHLK 488


Lambda     K      H
   0.328    0.141    0.441 

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: 764
Number of extensions: 42
Number of successful extensions: 5
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: 492
Length of database: 491
Length adjustment: 34
Effective length of query: 458
Effective length of database: 457
Effective search space:   209306
Effective search space used:   209306
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, 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