GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Leptospirillum ferrooxidans C2-3

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_232502519.1 LFE_RS09120 ATP-binding cassette domain-containing protein

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_000284315.1:WP_232502519.1
          Length = 588

 Score = 96.7 bits (239), Expect = 2e-24
 Identities = 64/207 (30%), Positives = 103/207 (49%), Gaps = 3/207 (1%)

Query: 21  VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDR-DI 79
           V      +  GE   L+G +G GK+TT RMLAGL   T G + +  +DV  VA + R  I
Sbjct: 357 VNNLTFHVKKGEVFGLLGANGAGKTTTFRMLAGLLEPTAGKLIVAGEDVRKVAAQARGKI 416

Query: 80  AMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGG 139
             + Q ++LY  +TV +N+ F     G S     +++ ++     L  +       L  G
Sbjct: 417 GYMAQKFSLYSQLTVFQNLIFYSSAYGLSGTLQKEKIQDSLNFFELEPYKNVSSGILPLG 476

Query: 140 QRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEA 199
            RQR+A+  A++  P +  +DEP S +D   R +    I AL   +GV+ +  TH   EA
Sbjct: 477 FRQRLALSCALIHEPSILFLDEPTSGVDPNARREFWHIINAL-ATVGVSVLVTTHFMEEA 535

Query: 200 LTMGDRIAVLKDGYLQQVGAPRELYDR 226
               DR+ ++  G L  +G+P E+ ++
Sbjct: 536 -EYCDRLLIMAQGALLAMGSPAEIKEK 561



 Score = 78.2 bits (191), Expect = 6e-19
 Identities = 70/294 (23%), Positives = 128/294 (43%), Gaps = 12/294 (4%)

Query: 4   VTFKDASLSYPGAKE--PTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGA 61
           +T  + + ++P  +     + K +  +  G    L+GP G GK+T +R+L+GL     G 
Sbjct: 11  ITVNELTKTFPSPRGIVTALDKISFSLKKGSITGLIGPDGAGKTTLMRLLSGLLWPDGGD 70

Query: 62  IFIGDKDVTHVAPRDRDIAMVF--QNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEA 119
           I I   D +  AP     ++ +  Q + LY  ++V EN+     + G  +D   +     
Sbjct: 71  IRIMGNDPSK-APLSVQGSLGYMPQKFGLYEDLSVQENLDLYANLQGVPKDRRKELYAPL 129

Query: 120 AATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIA 179
            +  GL+ F +R    LSGG +Q++ +  ++V  P + L+DEP   +D   R +    + 
Sbjct: 130 LSMTGLSPFQKRLAGQLSGGMKQKLGVACSLVHQPPILLLDEPTVGVDPVSRRELWEILR 189

Query: 180 ALQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAP----RELYDRPANVFVAGF 235
            L  + G  T++V+    +     D I +L +G +   G P    +E+  R       G 
Sbjct: 190 KLVSESG-ATLFVSTSYLDEAERCDEILILYNGKVLGSGPPESFRKEVAGRGYRAETTGS 248

Query: 236 IGSPAMNLGTF-SVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALE 288
           + +    +     V D        RI +  +T   + PE+ G+I +   P   E
Sbjct: 249 LRTVEPQISLLPGVVDTVLEGSTVRIVMDGDT-PPIFPENLGKIILKSAPPRFE 301


Lambda     K      H
   0.316    0.135    0.380 

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: 504
Number of extensions: 30
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: 376
Length of database: 588
Length adjustment: 33
Effective length of query: 343
Effective length of database: 555
Effective search space:   190365
Effective search space used:   190365
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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