GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Dinoroseobacter shibae DFL-12

Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate 3607560 Dshi_0972 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= reanno::Phaeo:GFF1303
         (276 letters)



>FitnessBrowser__Dino:3607560
          Length = 276

 Score =  489 bits (1259), Expect = e-143
 Identities = 243/276 (88%), Positives = 262/276 (94%)

Query: 1   MARAVTPRRKAINTALAWAVGLLIFFPILWTILTSFKTEAQAISDPPVFLFFDWTLENYS 60
           MARAVT +RK INT LAW +GLLIFFPILWTILTSFKTEA AI+DPPVFL FDWTLENY+
Sbjct: 1   MARAVTQQRKLINTTLAWGIGLLIFFPILWTILTSFKTEATAIADPPVFLAFDWTLENYT 60

Query: 61  VVQERSDYMRFLWNSVIIAGGSTILGIIIAVPAAWSMAFVPSKRTKDILLWMLSTKMLPA 120
            V ERS+Y +FLWNS+IIAGGSTILGI+IAVPAAWSMAFVPS+RTKDILLWMLSTKMLPA
Sbjct: 61  AVLERSNYAKFLWNSIIIAGGSTILGIMIAVPAAWSMAFVPSRRTKDILLWMLSTKMLPA 120

Query: 121 VGVLYPIYILFIKMGLLDNRFGLVVVLMLINLPIIVWMLYTYFKEIPGEILEAARMDGAT 180
           VGVLYPIY++ I++G+LD+R  LVV+LML+NLPIIVWMLYTYFKEIPGEILEAARMDGA+
Sbjct: 121 VGVLYPIYLICIELGILDSRVALVVILMLMNLPIIVWMLYTYFKEIPGEILEAARMDGAS 180

Query: 181 LKEEILYVLTPMAIPGIASTLLLNIILAWNEAFWTLNLTAAKAAPLTAFIASYSSPEGLF 240
           LKEEILYVLTPMAIPGIASTLLLN ILAWNEAFWTLNLTAA AAPLTAFIASYSSPEGLF
Sbjct: 181 LKEEILYVLTPMAIPGIASTLLLNFILAWNEAFWTLNLTAANAAPLTAFIASYSSPEGLF 240

Query: 241 YAKLSAASTMAIAPILILGWFSQKQLVSGLTFGAVK 276
           +AKLSAASTMAIAPILILGWFSQKQLVSGLTFGAVK
Sbjct: 241 FAKLSAASTMAIAPILILGWFSQKQLVSGLTFGAVK 276


Lambda     K      H
   0.327    0.139    0.428 

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: 469
Number of extensions: 13
Number of successful extensions: 1
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: 276
Length adjustment: 25
Effective length of query: 251
Effective length of database: 251
Effective search space:    63001
Effective search space used:    63001
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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