GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Sinorhizobium meliloti 1021

Align SmoG, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate SM_b21219 SM_b21219 sugar ABC transporter permease

Query= TCDB::O30833
         (276 letters)



>FitnessBrowser__Smeli:SM_b21219
          Length = 281

 Score =  140 bits (352), Expect = 4e-38
 Identities = 93/281 (33%), Positives = 146/281 (51%), Gaps = 11/281 (3%)

Query: 4   RTSTRRTLIVTLAAWTIAFLIFFPILWTVLMSFKSEGDAIKAPFAMLFSDWTLQSYADVQ 63
           R S   ++ +  +A  +A +I  P+ W ++MS     D    P A   SD  L  Y  + 
Sbjct: 3   RQSPLFSVFIHASALLLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLL 62

Query: 64  ER------SNYARHFMNSVVISLGSTLVALAIAIPAAWAMAFVPGRRTKDVLMWMLSTKM 117
                   + +    +NS+ ++  +TL A+ +A+PAAWA++  P       L  +++T M
Sbjct: 63  SAVENSAGAAFIASLLNSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWS--LYAVIATYM 120

Query: 118 MPAVGVLIPLYLIFRDTGLLDTRIGLVIVLTLINLPIVVWMLYTYFKEIPGEILEAARMD 177
           +P V + +PLY+     GLL++  GL +V   I  P   W+L + F  IP EI  AA +D
Sbjct: 121 LPPVALAVPLYMGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMID 180

Query: 178 GATLGSEILYILT-PMAVPGIASTLLLNVILAWNEAFWTLQLTT-SRAAPLTQFIASYSS 235
           GA L  +IL ILT P+A P +A++ L   +LAW+E F+ L  T+  RA  LT  IA  + 
Sbjct: 181 GARL-DQILRILTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAG 239

Query: 236 PEGLFYAKLSAASTMAIAPILILGWFSQKQLVRGLTFGAVK 276
                Y  ++ A  +A  P +++G   Q+ L+ GLT G VK
Sbjct: 240 GRVSDYGLIATAGVLAALPPVLIGLIMQRALISGLTSGGVK 280


Lambda     K      H
   0.327    0.137    0.416 

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: 239
Number of extensions: 15
Number of successful extensions: 2
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: 281
Length adjustment: 25
Effective length of query: 251
Effective length of database: 256
Effective search space:    64256
Effective search space used:    64256
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