GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Limnohabitans curvus MWH-C5

Align Aconitate isomerase; AI; EC 5.3.3.7 (uncharacterized)
to candidate WP_108401383.1 B9Z44_RS00285 molybdate ABC transporter substrate-binding protein

Query= curated2:A0A0A1H8I4
         (262 letters)



>NCBI__GCF_003063475.1:WP_108401383.1
          Length = 263

 Score =  190 bits (483), Expect = 2e-53
 Identities = 104/258 (40%), Positives = 157/258 (60%), Gaps = 4/258 (1%)

Query: 4   RLPTLALGALLLASTPLLAAQPVTTLTVLSSGGIMGTIREVAPAYEKATGVKLDIAAAPS 63
           RL  + +G  L A+    AA+    + V++SG      +++ P +EK TG K+  A   S
Sbjct: 10  RLLLVGVGLFLAAAQIAQAAE----IRVITSGAFTEAYKQLVPEFEKQTGHKVISAFGAS 65

Query: 64  MGDTPQAIPNRLARNEPADVVLMVGSALDKLVASGQVAKDSRVDLGQSFIAMAVRQGAPK 123
           +G+ P AIP R +R E  D++++    L+ ++  G V + SRVDL +S I  AVR+G PK
Sbjct: 66  VGNAPDAIPTRFSRGEKFDLIILSDGGLEAMIKKGNVIQGSRVDLVRSQIGAAVRKGTPK 125

Query: 124 PDISNMDAFKQTLEKAQSVAYSDSASGVYLSRILFPRMQLDKSFMAKARMIPAEPVGAVV 183
           PDIS + A KQTL  A+S+AYS SASG YLS  LFP++ + +     A+ I +E VGAVV
Sbjct: 126 PDISTVAALKQTLLNAKSIAYSASASGTYLSTELFPKLGVAEQLKDTAKKIMSERVGAVV 185

Query: 184 ARGEAQLGFQQLSELKAVPGIDIVGLIPDQAQKMTLYSGAMVSKSQHPEAARALLQYLAS 243
           ARG+A+LGFQQ+SEL     +D +G +P+  Q+   +S  +V  S   + A+ L+++  S
Sbjct: 186 ARGDAELGFQQVSELIYFKELDFIGTLPESVQQTIFFSAGLVEGSTEQDTAKQLIKFFQS 245

Query: 244 KDAAKAIEDSGLKPVPAQ 261
            + A+ I  +GL PV A+
Sbjct: 246 PEVAETIRQTGLDPVAAR 263


Lambda     K      H
   0.316    0.130    0.354 

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: 159
Number of extensions: 8
Number of successful extensions: 1
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: 262
Length of database: 263
Length adjustment: 25
Effective length of query: 237
Effective length of database: 238
Effective search space:    56406
Effective search space used:    56406
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. 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