GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CCNA_00435 in Dyella japonica UNC79MFTsu3.2

Align Amino acid transporter (characterized, see rationale)
to candidate N515DRAFT_2924 N515DRAFT_2924 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Query= uniprot:A0A0H3C3Q5
         (483 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2924
          Length = 492

 Score =  336 bits (861), Expect = 1e-96
 Identities = 196/469 (41%), Positives = 273/469 (58%), Gaps = 31/469 (6%)

Query: 30  LKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGL-AGPGVILSFLIAGAVCACAALCYAEL 88
           LK+ L+  HLV LG+GAI+G GI+ +TG  A   AGP ++LSF+ AG  CA AALCYAE 
Sbjct: 29  LKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCYAEF 88

Query: 89  STMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVGWSAHAHGLFKMI---- 144
           + M+P SGSAY+YSYA +GE VAWFVGWSL+LEY    A VA GWS + + L  +I    
Sbjct: 89  AAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALISGWI 148

Query: 145 ----GFPDALLAGPH---------QGGLINMPAVFISMAVAGLLALGTRESATVNMVLVF 191
                 P  L A P           G  IN+PAV I  A+ GL  +G  +SA VN ++V 
Sbjct: 149 GHDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSIIVA 208

Query: 192 VKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFFAFYG 251
           +K+  +++F+       N  ++ PF+P        EG A+     GV  AA+++FF++ G
Sbjct: 209 IKVTVILLFIAFATKYINPDNWHPFIP------ASEG-ASKYGWAGVGRAAAIVFFSYIG 261

Query: 252 FDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPLVFIL 311
           FDAVSTAA E KNP+RD+ IGI+GS+ +CT +Y+IVA +  G +   +    E P+   L
Sbjct: 262 FDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPE-PVSTAL 320

Query: 312 E---SLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGT 368
           +   SL+  +I  +V + AV  L +V+L  + GQ RIF+ MARDGL+P    +++ K  T
Sbjct: 321 DNYPSLHWLQI--IVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRT 378

Query: 369 PVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFSTP 428
           P + T++ GVLAA + GL ++  + E+   GTL AF  V   V++LR   P  PR F  P
Sbjct: 379 PHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVP 438

Query: 429 LWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVL 477
           +  IV P G L C+ LFL    +   + L    IG  +Y  YG   S L
Sbjct: 439 VPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKL 487


Lambda     K      H
   0.326    0.138    0.415 

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: 675
Number of extensions: 43
Number of successful extensions: 6
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: 483
Length of database: 492
Length adjustment: 34
Effective length of query: 449
Effective length of database: 458
Effective search space:   205642
Effective search space used:   205642
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 (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