GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate HSERO_RS18950 HSERO_RS18950 glycerol-3-phosphate transporter permease

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



>FitnessBrowser__HerbieS:HSERO_RS18950
          Length = 294

 Score =  136 bits (342), Expect = 7e-37
 Identities = 83/289 (28%), Positives = 148/289 (51%), Gaps = 13/289 (4%)

Query: 18  RWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTY-----KWAGLAQYARLFDND 72
           +WLP L++AP + I L+ F+    W  V +   S  L        ++     +  LF + 
Sbjct: 10  KWLPYLLVAPQIIITLLFFF----WPAVQALYQSMLLQDAFGGYSEFVWFDNFKTLFGDP 65

Query: 73  RWWVASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAW 132
            +  + +  A+F  +     L + + LA+F D+  R     +T  ++P A+S +V G  W
Sbjct: 66  TYLESFRTTAIFSALVAFFGLALSLLLAVFADRVRRGASIYKTFLIWPYAVSPVVVGVLW 125

Query: 133 KWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGV 192
            +LL+P +G+  L     W G   D++I+    +  +VIAA+W+   +    FLAGL+ +
Sbjct: 126 MFLLSPSLGI--LSHVLSWLGLPWDYMINGTHAMILIVIAAIWKQISYNFLFFLAGLQSI 183

Query: 193 DQSIVRAAQIDGASMPRIYWSVVLPSLRP-VFFSAVMILAHIAIKSFDLVAAMTAGGPGY 251
            +S++ AA IDGA   + ++++V P + P  FF  V+ + +    +F +V A T GGPG 
Sbjct: 184 PKSLIEAAAIDGAGPVKRFFTIVFPLISPTTFFLFVVNVVYAFFDTFVIVDATTHGGPGK 243

Query: 252 SSDLPAMFMYSFTFSRGQMGMGSA-SAILMLGAILAIIVPYLYSELRTK 299
            +++    ++S  F  G +G  +A S +LM   IL  +V + Y E + +
Sbjct: 244 DTEILVYKVFSDGFKGGDLGGSAAQSVVLMALVILLTVVQFKYVEKKVQ 292


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: 273
Number of extensions: 13
Number of successful extensions: 5
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: 294
Length adjustment: 26
Effective length of query: 276
Effective length of database: 268
Effective search space:    73968
Effective search space used:    73968
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 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