GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Cupriavidus basilensis 4G11

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS20240 RR42_RS20240 hypothetical protein

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Cup4G11:RR42_RS20240
          Length = 595

 Score =  209 bits (531), Expect = 1e-58
 Identities = 111/257 (43%), Positives = 158/257 (61%), Gaps = 6/257 (2%)

Query: 4   KSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63
           ++ E++L V    K FGGL A++DV   ++ G++ GLIGPNGAGK+T FN++TG+     
Sbjct: 338 QAGELILDVKAARKEFGGLVAVNDVSFQVRAGEIIGLIGPNGAGKSTTFNLVTGVLPATR 397

Query: 64  GTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTG----SGLFG 119
           G     G+        E+ K GI RTFQ++ L   MT LENV +G H+R       G+  
Sbjct: 398 GEVLYRGEQISGLPSREIVKRGIGRTFQHVHLLPTMTVLENVAIGAHLRGDFAPQGGVTA 457

Query: 120 AVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLI 179
           A+ R    K EEA +   A   L+ VG+      +A +L+ G QR LEIARAL  DP L+
Sbjct: 458 AILRMN--KNEEAKLLHEAARQLERVGLADCMYMEAGSLALGQQRILEIARALCCDPALL 515

Query: 180 ALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEG 239
            LDEPAAG+   EK  L EL+ +++ +  ++LL+EHD+  VM L DR+ V+++G +IAEG
Sbjct: 516 LLDEPAAGLRYKEKQALAELLKKLKGEGMSVLLVEHDMDFVMNLTDRLVVMEFGTRIAEG 575

Query: 240 NPAEVQKNEKVIEAYLG 256
            P +VQK+  V+EAYLG
Sbjct: 576 VPEDVQKDPAVLEAYLG 592


Lambda     K      H
   0.319    0.137    0.384 

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: 397
Number of extensions: 18
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: 260
Length of database: 595
Length adjustment: 31
Effective length of query: 229
Effective length of database: 564
Effective search space:   129156
Effective search space used:   129156
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: 50 (23.9 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