GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CCNA_00435 in Methylocystis bryophila S285

Align Amino acid transporter (characterized, see rationale)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease

Query= uniprot:A0A0H3C3Q5
         (483 letters)



>NCBI__GCF_002117405.1:WP_085770386.1
          Length = 488

 Score =  315 bits (807), Expect = 2e-90
 Identities = 180/472 (38%), Positives = 270/472 (57%), Gaps = 20/472 (4%)

Query: 13  RRKAIDTITAGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGL-AGPGVILSF 71
           R K+I+++ A   +   L++ L    LV +G+G ++G GI+ LTGV A   AGPGV LSF
Sbjct: 8   RAKSIESLQAEALERGALRRALGLWQLVGIGLGGLIGVGIFVLTGVVAATQAGPGVALSF 67

Query: 72  LIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAV 131
           LIAG     AALCYAE ++M+P +GSAYTY+YA +GE  AW +GW L+LEY LV A V++
Sbjct: 68  LIAGVASGAAALCYAEFASMLPVAGSAYTYAYAVLGELPAWIIGWDLLLEYALVVAVVSI 127

Query: 132 GWSAHAHGLFKMIGFPDALLA----GPHQGGLINMPAVFISMAVAGLLALGTRESATVNM 187
           GWS +   L  + G      A    G   G ++++ A+  +  VA LL L     A  N 
Sbjct: 128 GWSGYLRALLALFGVAPPEWAAGAPGTGDGHILDLFAMLGAFGVALLLTLRVEWGARFNT 187

Query: 188 VLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFF 247
            +V +KI A+IV ++   P  N A++ PFMP GF               GV+  A+++FF
Sbjct: 188 AMVLLKIAAVIVVILAAAPHINPANWRPFMPFGFG--------------GVVEGAAVVFF 233

Query: 248 AFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPL 307
           A +G+D ++TA EE   P+RDL   ++ S+ V   +Y++++    G +R +    + AP+
Sbjct: 234 AVFGYDTLTTAGEEALEPQRDLPRAVLLSLVVSLTLYILMSLALTGIARYDTLDNA-APV 292

Query: 308 VFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTG 367
                +L  G    +V+ AAV+ + +V+LAF+ G +RI+F M+RDGLLP   ++ + +  
Sbjct: 293 ASAFAALGMGWATLVVSAAAVVGILSVMLAFLLGCARIWFAMSRDGLLPAWFARPHPQFA 352

Query: 368 TPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFST 427
           TP   TL+ G L A++S    ++++AEL N GTL AF+ +  +VI LR   P+ PR F  
Sbjct: 353 TPYRPTLIAGGLCALVSAFFPIREVAELVNIGTLSAFVVICLAVIALRHTRPDVPRGFRA 412

Query: 428 PLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVLAQ 479
           PL P +   G+   L+L   LP      F+   +IG  VY  YG R S LA+
Sbjct: 413 PLSPYLPLIGVGFSLWLLSKLPAIAWERFVVWLIIGLAVYFLYGRRHSRLAK 464


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: 661
Number of extensions: 37
Number of successful extensions: 7
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: 488
Length adjustment: 34
Effective length of query: 449
Effective length of database: 454
Effective search space:   203846
Effective search space used:   203846
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 Apr 09 2024. 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