GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21219 in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate HSERO_RS02200 HSERO_RS02200 mannitol ABC transporter permease

Query= reanno::Smeli:SM_b21219
         (281 letters)



>FitnessBrowser__HerbieS:HSERO_RS02200
          Length = 271

 Score =  129 bits (325), Expect = 5e-35
 Identities = 82/263 (31%), Positives = 144/263 (54%), Gaps = 12/263 (4%)

Query: 20  AVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAFIASLLN 79
           A+V+  P+ W+ + +    +      L + P+   L  +R + S       + ++  + N
Sbjct: 19  AIVLFFPIFWVAVTAFKTESQAYTPSLVFLPT---LETFREVFSR------SHYLGYVQN 69

Query: 80  SIKVAGMATLAAVVVAVPAAWAVSRTPAVAWS--LYAVIATYMLPPVALAVPLYMGLAYF 137
           S+ V+  +TL ++++AVPAA++++  P       L  +++T M+P V + +P+Y+     
Sbjct: 70  SLIVSLGSTLLSLLLAVPAAYSMAFFPTGRTQKLLLWMLSTKMMPAVGVLIPIYLMAKNT 129

Query: 138 GLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARLDQILRILTLPLAA 197
           GLL++V GL ++Y  I  P   W+  + F+ +P+EI  AA IDGA   Q +  L LP A 
Sbjct: 130 GLLDTVTGLTIIYTLINLPIAVWMAFTYFNDVPKEILEAARIDGANAWQEMIYLLLPTAM 189

Query: 198 PVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSDYGLIATAGVLAAL 257
           P +A++AL   +L+W+E F++L  TS   A  LTV IA  +      +  ++ A +LA  
Sbjct: 190 PGLASTALLLVILSWNEAFWSLNLTS-VNAAPLTVFIASYSNPEGLFWAKLSAASLLAIA 248

Query: 258 PPVLIGLIMQRALISGLTSGGVK 280
           P + +G + Q+ L+ GLT G VK
Sbjct: 249 PIMALGWLAQKQLVRGLTFGAVK 271


Lambda     K      H
   0.325    0.136    0.402 

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: 202
Number of extensions: 11
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: 281
Length of database: 271
Length adjustment: 25
Effective length of query: 256
Effective length of database: 246
Effective search space:    62976
Effective search space used:    62976
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 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