GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Alistipes indistinctus YIT 12060

Align Glucose/galactose porter (characterized)
to candidate WP_009133853.1 HMPREF9450_RS05320 sugar MFS transporter

Query= TCDB::P0C105
         (412 letters)



>NCBI__GCF_000231275.1:WP_009133853.1
          Length = 445

 Score =  206 bits (525), Expect = 9e-58
 Identities = 127/419 (30%), Positives = 219/419 (52%), Gaps = 36/419 (8%)

Query: 24  ALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVK 83
           A+  L L+FF++GF + +N IL+P+ K   +LN+ QS LI F  + AY I+++P+  ++K
Sbjct: 19  AMAILGLMFFIFGFTSWVNSILVPYFKIGCELNHFQSYLIVFALYSAYLIMAIPSSAILK 78

Query: 84  RISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILG 143
           R+ +KRGI+ G    A+G  +FIPAA +R Y +FL   FV+ +G  +LQ AANPYVT++G
Sbjct: 79  RVGFKRGIMYGFFCTALGALIFIPAAWWRSYPVFLAGSFVIGAGSAMLQAAANPYVTMIG 138

Query: 144 KPETAASRLTLTQAFNSLGTTVAPVFGAVLILS-----------------AATDATVNAE 186
              T   R+ +    N     VAP+  A ++L                  AA  A +++ 
Sbjct: 139 PINTTVKRMAIMGICNKFAGLVAPLIFAAVVLKVTDSDLFVQLESATLDPAARSAMLDSL 198

Query: 187 ADAVRFPYLLLALAFTVLAII--FAILKPPDVQE---DEPALSDKKEGSAWQYRHLVLGA 241
              V  PY + A    V+ +   F++L   +++E    E A   + + S +Q+ +L+LG 
Sbjct: 199 VHRVMVPYAIFAAFLIVIGVFIRFSMLPELNLEEKNKQEVAPGGEGKTSVFQFPYLILGV 258

Query: 242 IGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIG-------S 294
           + +F+++G +V     ++++       G+   +A    +Y     ++G  +G        
Sbjct: 259 VAMFLHIGTQVVTIDTIISYAQ---TMGMDLLEAKTFPSYTLSLVILGNVLGVLLIPKII 315

Query: 295 AAMRYIDDGKALAFNAFVAIILLFITVATTGH---IAMWSVLAIGLFNSIMFPTIFSLAL 351
           +  R       L F   + ++     V   GH   I++W ++ IGL NS+++  I+ LA+
Sbjct: 316 SQTRVFQICCTLGFLLSLGVVWGNTQVDFLGHHANISIWFLVGIGLANSLVYGGIWPLAI 375

Query: 352 HGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPII-CYAYIAFYGLIG 409
            GLG  T  GS +L +A+ G A+VPLI G +AD   + +A+   ++  +AY+ FY   G
Sbjct: 376 RGLGRFTKTGSSMLIMALFGNAVVPLIYGYIADTASLRIAYFWILLPGFAYLMFYAFCG 434


Lambda     K      H
   0.328    0.141    0.420 

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: 532
Number of extensions: 32
Number of successful extensions: 4
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: 412
Length of database: 445
Length adjustment: 32
Effective length of query: 380
Effective length of database: 413
Effective search space:   156940
Effective search space used:   156940
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: 51 (24.3 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