GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Methylocystis bryophila S285

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_245300279.1 B1812_RS18275 sulfate/molybdate ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_002117405.1:WP_245300279.1
          Length = 353

 Score =  114 bits (286), Expect = 2e-30
 Identities = 77/232 (33%), Positives = 116/232 (50%), Gaps = 15/232 (6%)

Query: 15  FGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFELDGKPYSPSAP 74
           FG   AL  V + I  G++  L+GP+G+GKTT   VI GL  P  G    D    +  + 
Sbjct: 8   FGSYPALRDVSLDIAGGELVALLGPSGSGKTTLLRVIAGLNSPHRGAVFFDALNATSLS- 66

Query: 75  HEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAREEEAAIREKS 134
             V +  +   FQN  LF  M+V +NV            FG   R +A+R  +  I  + 
Sbjct: 67  --VQERRVGFVFQNYALFKHMSVADNV-----------AFGLKARPRASRPPKREIAARV 113

Query: 135 QKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMNATEKLGLRE 194
            +LL+ V +    +R    LS G ++R+ +ARALA +P++L LDEP   ++A  +  LR 
Sbjct: 114 AELLELVQLEGLGQRYPAQLSGGQRQRVALARALAIEPRVLLLDEPFGALDARVRKDLRR 173

Query: 195 LLVKI-QAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKNPA 245
            L +I +  G T + + HD    M L +R+ VL+ G+    G PA +   PA
Sbjct: 174 WLREIHKRTGLTTVFVTHDQDEAMELADRVVVLNQGRIEQAGSPAALYDRPA 225


Lambda     K      H
   0.320    0.138    0.394 

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: 196
Number of extensions: 6
Number of successful extensions: 4
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: 255
Length of database: 353
Length adjustment: 27
Effective length of query: 228
Effective length of database: 326
Effective search space:    74328
Effective search space used:    74328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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