GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0028 in Sphingomonas koreensis DSMZ 15582

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate Ga0059261_1870 Ga0059261_1870 ABC-type transport system involved in resistance to organic solvents, ATPase component

Query= TCDB::Q9WXN5
         (330 letters)



>FitnessBrowser__Korea:Ga0059261_1870
          Length = 273

 Score = 90.5 bits (223), Expect = 4e-23
 Identities = 74/237 (31%), Positives = 123/237 (51%), Gaps = 16/237 (6%)

Query: 26  DGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVELSSMT 85
           +GL  ++ + E++GVVG SG GK+ L   I + + +P     G I   V GE V+  +  
Sbjct: 32  EGLDLDVRQGEILGVVGGSGTGKSVLMRSI-IGLQEPDA---GSI--EVFGEDVQHLNTE 85

Query: 86  RDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVR-HLAESHGIDEEELLDK-ARRRFEE 143
                RK WG    ++ Q    AL  T+ + + V+  L E +   ++ LLD+ A  +   
Sbjct: 86  EAIELRKRWG----VLFQGG--ALFSTLTVAENVQVPLKEFYPAFDQALLDEIAAYKVVM 139

Query: 144 VGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKVLMQM 203
            GL      +YP ELSGGM++RA +A +  L+P LL  DEPT+ LD +      ++ + +
Sbjct: 140 TGLPSDAGPKYPAELSGGMKKRAGLARSLALDPELLFLDEPTAGLDPIGAAAFDELTLAL 199

Query: 204 KRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGLFN 260
           +R  +  ++  ITHD+ T+  I DR+ ++    ++    ++ LL    HP+ Q  FN
Sbjct: 200 QRT-LGLTVFLITHDLDTLYAICDRVAVLADKHVIAVGTIDELLALD-HPWIQEYFN 254


Lambda     K      H
   0.321    0.138    0.405 

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: 210
Number of extensions: 16
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: 330
Length of database: 273
Length adjustment: 27
Effective length of query: 303
Effective length of database: 246
Effective search space:    74538
Effective search space used:    74538
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