GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Sphingomonas koreensis DSMZ 15582

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate Ga0059261_0484 Ga0059261_0484 ABC-type multidrug transport system, ATPase component

Query= uniprot:A0A159ZWL6
         (233 letters)



>FitnessBrowser__Korea:Ga0059261_0484
          Length = 245

 Score =  102 bits (254), Expect = 7e-27
 Identities = 75/211 (35%), Positives = 105/211 (49%), Gaps = 10/211 (4%)

Query: 5   ENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRYMGEE 64
           ++VS  YG  + L  + + V  G I  L+G NGAGKST L  L G  +A SG+I   G +
Sbjct: 11  QDVSLAYGAQEVLRGLTLSVPAGSITALLGGNGAGKSTTLAALLGFVRAQSGTILVCGVD 70

Query: 65  LVGQDSSHIMRKSIAVVPEGRRVFARLTVEEN----LAMGGFFTDKGDYQEQMDKVLHLF 120
             G D     R+ IA +PE   ++  L+  EN    LA+ G    + D  E         
Sbjct: 71  -PGSDPDGARRR-IAYLPENVALYEHLSATENAEYLLALSGEQHARRDITEAFAAA---- 124

Query: 121 PRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR 180
              +E + QR G  S G +Q +AI  AL+ +  +LLLDEP+ GL P        ++ Q+R
Sbjct: 125 GLQEEAWDQRLGGFSKGMRQKVAIAVALLRRVPVLLLDEPTSGLDPRATADFNALVAQVR 184

Query: 181 KDGVTVFLVEQNANQALKIADRAYVLENGRV 211
             G  V +V  +   A  +ADR   LENGRV
Sbjct: 185 DRGTAVLMVTHDLLSAADVADRIAFLENGRV 215


Lambda     K      H
   0.320    0.137    0.381 

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: 139
Number of extensions: 7
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: 233
Length of database: 245
Length adjustment: 23
Effective length of query: 210
Effective length of database: 222
Effective search space:    46620
Effective search space used:    46620
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: 46 (22.3 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