GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Sphingomonas koreensis DSMZ 15582

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Ga0059261_1870 Ga0059261_1870 ABC-type transport system involved in resistance to organic solvents, ATPase component

Query= reanno::pseudo5_N2C3_1:AO356_09610
         (276 letters)



>FitnessBrowser__Korea:Ga0059261_1870
          Length = 273

 Score =  127 bits (318), Expect = 3e-34
 Identities = 81/210 (38%), Positives = 120/210 (57%), Gaps = 4/210 (1%)

Query: 51  LSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRH 110
           L L +  GEI  ++G SG+GKS L+R    L +P +G+I V GED+  L+ +   E R+ 
Sbjct: 34  LDLDVRQGEILGVVGGSGTGKSVLMRSIIGLQEPDAGSIEVFGEDVQHLNTEEAIELRK- 92

Query: 111 KISMVFQSFGLLPHKSVLDNVAYGLK--VRGESKQVCAERALHWINTVGLKGYEN-KYPH 167
           +  ++FQ   L    +V +NV   LK       + +  E A + +   GL      KYP 
Sbjct: 93  RWGVLFQGGALFSTLTVAENVQVPLKEFYPAFDQALLDEIAAYKVVMTGLPSDAGPKYPA 152

Query: 168 QLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITH 227
           +LSGGM++R GLAR+LA D +++ +DE  + LDP+  A   +  L LQ+TL  T+  ITH
Sbjct: 153 ELSGGMKKRAGLARSLALDPELLFLDEPTAGLDPIGAAAFDELTLALQRTLGLTVFLITH 212

Query: 228 DLDEAVRIGNRIAILKDGKLIQVGTPREIL 257
           DLD    I +R+A+L D  +I VGT  E+L
Sbjct: 213 DLDTLYAICDRVAVLADKHVIAVGTIDELL 242


Lambda     K      H
   0.321    0.138    0.387 

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: 197
Number of extensions: 14
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: 276
Length of database: 273
Length adjustment: 25
Effective length of query: 251
Effective length of database: 248
Effective search space:    62248
Effective search space used:    62248
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 (21.9 bits)
S2: 47 (22.7 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