GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaA in Sinorhizobium meliloti 1021

Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate SMc01576 SMc01576 oxidoreductase

Query= metacyc::G1G01-5614-MONOMER
         (432 letters)



>FitnessBrowser__Smeli:SMc01576
          Length = 429

 Score =  325 bits (834), Expect = 1e-93
 Identities = 170/415 (40%), Positives = 247/415 (59%), Gaps = 5/415 (1%)

Query: 13  LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72
           LW   +        LAG+   +V ++GGG TGLSAA+HL E G    V+EA  IG GGSG
Sbjct: 10  LWHATAPAAPRTAPLAGDLTVEVAIVGGGFTGLSAALHLAETGIRTAVIEARMIGFGGSG 69

Query: 73  RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132
           RNVGLVNAG W++PDD+ ATLG   G+RL   LG+ P+ V+ ++ + GI+C+A   GTLH
Sbjct: 70  RNVGLVNAGMWVQPDDLIATLGAAAGNRLLDELGDGPSFVYDLVAKHGIECEAVRNGTLH 129

Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192
           M+  A G+ ++  R  QW++RGA VE+L+  +     G +  + ALLDRRAGTI P+ Y 
Sbjct: 130 MSVGAEGLKEIREREAQWKKRGAPVEVLSAEKAHALSGAEGFTGALLDRRAGTIQPLAYA 189

Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAY----TEGDW 248
           +GLA A    G +IF  + +    R+GD W +KT RG V A  V+++T AY    T   W
Sbjct: 190 RGLARAALAAGAEIFTDTPLLAASRQGDLWNLKTPRGTVTARHVILATNAYGSLVTGVPW 249

Query: 249 SNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGR 308
              +++     Y+Q A+ PL    A ++LP  QG+WDT  V++S R D Q RL+ GS+GR
Sbjct: 250 KEYRQELTILPYFQFATNPLPDNVAARILPERQGAWDTGLVMTSFRMDRQNRLIFGSIGR 309

Query: 309 VDNKPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGY 368
           +D   A   R++A R     +P +G   +E  W G I  T ++L  +   AP +V+++GY
Sbjct: 310 LDAIAAGTHRAFAARSVRKLFPYIGDFRFEHWWDGRIGMTTNNLPAMHVLAPNVVSISGY 369

Query: 369 NGRGNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLYH 423
           NGRG   GTV GRA A   + G+  ++P+  +P++     +L++AFY +G    H
Sbjct: 370 NGRGIAPGTVFGRALARH-VTGDTSAIPLAETPVTPDPWRTLKSAFYHAGAQAKH 423


Lambda     K      H
   0.319    0.135    0.419 

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: 512
Number of extensions: 24
Number of successful extensions: 3
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: 432
Length of database: 429
Length adjustment: 32
Effective length of query: 400
Effective length of database: 397
Effective search space:   158800
Effective search space used:   158800
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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