GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Phaeacidiphilus oryzae TH49

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  223 bits (567), Expect = 9e-63
 Identities = 128/322 (39%), Positives = 184/322 (57%), Gaps = 23/322 (7%)

Query: 25  NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84
           +L IA G F  L+G SGCGK+TTLRM++GLE  T G I +GD+DVT   P  R +  VFQ
Sbjct: 38  DLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLGDQDVTDRKPYRRPVNTVFQ 97

Query: 85  NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144
           NYAL+PH+ + EN+ F L+  G     + K V++    + L     RKP  LSGGQ+QR+
Sbjct: 98  NYALFPHLDIFENVAFGLRRRGIRS--VKKPVEDMLDLVELGHLARRKPTQLSGGQQQRI 155

Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204
           A+ RA++  PQV L+DEPL  LD KLR Q + ++  +Q ++G+T V+VTHDQ EA+TM D
Sbjct: 156 ALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEVGLTFVHVTHDQEEAMTMAD 215

Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDA--TSGHARIKL 262
            IAV+  G ++Q+G+P ELY+ P   FVA F+G   +  GT     GD    + H R   
Sbjct: 216 TIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQSNLIAGTVESVSGDVVQVAAHGRSLA 275

Query: 263 SPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFLYGKLVG 322
            P   AA     +G + +G RPE + I      T+  +P            + L GK+  
Sbjct: 276 LP---AARCRTTSGPVILGVRPEKVRI----AKTEAEVP---------SGANHLTGKVTD 319

Query: 323 EGDLGSSSE---DVPESGQIVV 341
              +G S++   ++P   ++ V
Sbjct: 320 ASFIGVSTQYLVELPSGEELAV 341


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: 366
Number of extensions: 14
Number of successful extensions: 2
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: 376
Length of database: 386
Length adjustment: 30
Effective length of query: 346
Effective length of database: 356
Effective search space:   123176
Effective search space used:   123176
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: 50 (23.9 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