GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Sphingomonas koreensis DSMZ 15582

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Ga0059261_1870 Ga0059261_1870 ABC-type transport system involved in resistance to organic solvents, ATPase component

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__Korea:Ga0059261_1870
          Length = 273

 Score =  118 bits (295), Expect = 2e-31
 Identities = 76/228 (33%), Positives = 126/228 (55%), Gaps = 20/228 (8%)

Query: 34  DGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLNDKEMKPYR 93
           +G+ +++++GE LG+VG SG GKS L R+I+ L  PD G I   G+D+ +LN +E    R
Sbjct: 32  EGLDLDVRQGEILGVVGGSGTGKSVLMRSIIGLQEPDAGSIEVFGEDVQHLNTEEAIELR 91

Query: 94  KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEE-LLD--------MVG 144
           K+  ++FQ   G+L   +TV   ++ PL        KE     ++ LLD        M G
Sbjct: 92  KRWGVLFQG--GALFSTLTVAENVQVPL--------KEFYPAFDQALLDEIAAYKVVMTG 141

Query: 145 IGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQ 204
           +  +    +P E SGG ++R G+AR+LAL+P+ +  DEP + LD    A   +L   +Q+
Sbjct: 142 LPSDAGPKYPAELSGGMKKRAGLARSLALDPELLFLDEPTAGLDPIGAAAFDELTLALQR 201

Query: 205 KMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPY 252
            +G++   I H+L  +  I  +VAV+    ++  G +D++ L   HP+
Sbjct: 202 TLGLTVFLITHDLDTLYAICDRVAVLADKHVIAVGTIDEL-LALDHPW 248


Lambda     K      H
   0.321    0.142    0.417 

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: 238
Number of extensions: 13
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: 328
Length of database: 273
Length adjustment: 27
Effective length of query: 301
Effective length of database: 246
Effective search space:    74046
Effective search space used:    74046
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: 48 (23.1 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