GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruP in Alistipes indistinctus YIT 12060

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate WP_009133853.1 HMPREF9450_RS05320 sugar MFS transporter

Query= uniprot:A0A1I2JXG1
         (442 letters)



>NCBI__GCF_000231275.1:WP_009133853.1
          Length = 445

 Score =  201 bits (511), Expect = 4e-56
 Identities = 138/447 (30%), Positives = 223/447 (49%), Gaps = 31/447 (6%)

Query: 10  SKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQF 69
           S  +LP AA  R T    AM +L  +FF++GF + +N IL+P+ K   +LN+ ++ L+ F
Sbjct: 2   STGNLPAAAPARKTSVA-AMAILGLMFFIFGFTSWVNSILVPYFKIGCELNHFQSYLIVF 60

Query: 70  TFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLA 129
             + AY +M++P+  ++ R+G+K+GI+ G     +GA  F PAA    YP FL   FV+ 
Sbjct: 61  ALYSAYLIMAIPSSAILKRVGFKRGIMYGFFCTALGALIFIPAAWWRSYPVFLAGSFVIG 120

Query: 130 TGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAE-- 187
            G  +LQ AAN YV ++GP  +   R+ +    N     +AP     LI +A VL     
Sbjct: 121 AGSAMLQAAANPYVTMIGPINTTVKRMAIMGICNKFAGLVAP-----LIFAAVVLKVTDS 175

Query: 188 ------QIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALT--EKTE 239
                 + A L PA + A        V  PY   A  L ++ VF+    LP L   EK +
Sbjct: 176 DLFVQLESATLDPAARSAMLDSLVHRVMVPYAIFAAFLIVIGVFIRFSMLPELNLEEKNK 235

Query: 240 Q-ASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANW 298
           Q  +       S  + P+++ GV+A+F ++G +V     +++Y        M    A  +
Sbjct: 236 QEVAPGGEGKTSVFQFPYLILGVVAMFLHIGTQVVTIDTIISYAQTM---GMDLLEAKTF 292

Query: 299 VAYYWLGAMIGRFIGSALLAK-LSPRKLLAIFAAINMALVLTTMMTK---------GTVA 348
            +Y     ++G  +G  L+ K +S  ++  I   +   L L  +              ++
Sbjct: 293 PSYTLSLVILGNVLGVLLIPKIISQTRVFQICCTLGFLLSLGVVWGNTQVDFLGHHANIS 352

Query: 349 MYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGV 408
           ++ +V IGL NS+++  I+ L I  +G  T   SS+LIMA+ G A+VP + G  AD   +
Sbjct: 353 IWFLVGIGLANSLVYGGIWPLAIRGLGRFTKTGSSMLIMALFGNAVVPLIYGYIADTASL 412

Query: 409 QHAFFLPLL-CYAYIVFYGLYGSRIKS 434
           + A+F  LL  +AY++FY   G RI S
Sbjct: 413 RIAYFWILLPGFAYLMFYAFCGYRITS 439


Lambda     K      H
   0.327    0.140    0.414 

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: 501
Number of extensions: 22
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: 442
Length of database: 445
Length adjustment: 32
Effective length of query: 410
Effective length of database: 413
Effective search space:   169330
Effective search space used:   169330
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