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_102938052.1 B1812_RS04230 amino acid permease

Query= uniprot:A0A0H3C3Q5
         (483 letters)



>NCBI__GCF_002117405.1:WP_102938052.1
          Length = 481

 Score =  326 bits (835), Expect = 1e-93
 Identities = 180/479 (37%), Positives = 280/479 (58%), Gaps = 23/479 (4%)

Query: 9   SFWTRRKAIDTITAGH-ADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTG-VGAGLAGPG 66
           S +  RK+I  + A + A+ + LK+ L W  L+A+G+G I+G GI+ LTG   A  AGPG
Sbjct: 7   SVYFSRKSIHLVIAENDAEENGLKRALGWASLMAMGIGGIIGAGIFVLTGQAAADYAGPG 66

Query: 67  VILSFLIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVC 126
           V +SFL++G  C   ALCYAEL+ +IPA+GS YTY+Y  +GE  AW +GW+L+LEY    
Sbjct: 67  VTISFLLSGLACTFVALCYAELAALIPAAGSTYTYTYVTLGEIFAWIIGWNLVLEYAAGA 126

Query: 127 AAVAVGWSAHAHGLFKMIGF--PDAL----------LAGPHQGGLINMPAVFISMAVAGL 174
           A VAVGW+ + + + + +G   P+AL          + G H  G+ N+PA  I + +  L
Sbjct: 127 ATVAVGWAGYFNRVMQGLGIHLPEALTSAYFANAHSIGGTH--GVFNVPAAAIILLLTAL 184

Query: 175 LALGTRESATVNMVLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAA 234
           L  GT ES+  N ++V +K++ ++V + +     + A++TP +P         G +    
Sbjct: 185 LMRGTSESSFFNNIIVVIKVMVVLVVIFVGAAHVDAANWTPLIPENTDHFGHFGWS---- 240

Query: 235 KVGVMAAASLIFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGA 294
             GV+  AS++FFA+ GFD VSTAA+E   P+RD+ IGI+GS+ +CT +Y+ VAAV+ G 
Sbjct: 241 --GVVRGASVVFFAYIGFDGVSTAAQEAHTPQRDVPIGILGSLVICTILYVAVAAVATGV 298

Query: 295 SRTEVFSKSEAPLVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGL 354
              +     + P+  +++      ++ +V L A+  L T IL  ++GQ+RIF+ MA+DGL
Sbjct: 299 VSYKELGVPD-PMALVMDRTGVAWLSWVVKLGAIAGLTTAILLLLFGQTRIFYAMAQDGL 357

Query: 355 LPRALSKVNAKTGTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILL 414
           LP+  + V+    TP +   L GV  A+ +GL  +  + E+ + GTL AF  V  +V+ L
Sbjct: 358 LPKVFAAVHPVWRTPAVSQALVGVFVALAAGLFPINILDEMVSIGTLAAFALVCGAVLHL 417

Query: 415 RLREPNRPRVFSTPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMR 473
           R  +P+  R F  P  P +   GI  CL L ++LP +T L  +    IG  +Y  YG++
Sbjct: 418 RRSQPDMHRPFRAPGIPAMPLLGIASCLALMVALPLETWLRLIVWTAIGMAIYFFYGVK 476


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: 708
Number of extensions: 42
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: 481
Length adjustment: 34
Effective length of query: 449
Effective length of database: 447
Effective search space:   200703
Effective search space used:   200703
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