GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Marivita geojedonensis DPG-138

Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate WP_085634732.1 MGEO_RS00455 sugar ABC transporter permease

Query= reanno::WCS417:GFF4323
         (302 letters)



>NCBI__GCF_002115805.1:WP_085634732.1
          Length = 305

 Score =  351 bits (901), Expect = e-101
 Identities = 165/293 (56%), Positives = 222/293 (75%), Gaps = 8/293 (2%)

Query: 16  LQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLP--------TYKWAGLAQYAR 67
           LQ WLPKLVL+PS+ +VL+  YG+IL+T  +SFT+S  LP        T +  G + Y +
Sbjct: 13  LQNWLPKLVLSPSLAMVLIFVYGFILFTVYVSFTDSRILPFVNNDGQRTLELIGFSNYEK 72

Query: 68  LFDNDRWWVASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIV 127
           LF    W ++  N+A F G++IGI   +G+ LAIFLDQKIR EG +RTIYLYPMALS IV
Sbjct: 73  LFSLSHWEISLWNMATFAGLYIGICTCLGLGLAIFLDQKIRAEGALRTIYLYPMALSFIV 132

Query: 128 TGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLA 187
           TGTAWKW L+PG+GL+ +++ WGW  F  DW+ + D  +Y +V+AAVWQ SGF+MAMFLA
Sbjct: 133 TGTAWKWFLDPGIGLENVMQSWGWTSFEFDWIKNRDYAIYTVVLAAVWQTSGFVMAMFLA 192

Query: 188 GLRGVDQSIVRAAQIDGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAG 247
           GLRG+D  I++AAQ+DGAS   +Y  +++P LRP F SA +IL+H+AIK+FDLV A+T G
Sbjct: 193 GLRGIDNEILKAAQMDGASNWNLYRRIIIPQLRPAFLSAFVILSHLAIKTFDLVIALTGG 252

Query: 248 GPGYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELRTKR 300
           GPG +++LPA FMYS+TFSR QMG+G++SA++ML  I AI++PYLY+ELR K+
Sbjct: 253 GPGRATELPATFMYSYTFSRNQMGIGASSAVIMLMTIAAIMIPYLYAELREKK 305


Lambda     K      H
   0.330    0.141    0.455 

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: 385
Number of extensions: 14
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: 302
Length of database: 305
Length adjustment: 27
Effective length of query: 275
Effective length of database: 278
Effective search space:    76450
Effective search space used:    76450
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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