GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Herbaspirillum seropedicae SmR1

Align KguT (characterized, see rationale)
to candidate HSERO_RS21145 HSERO_RS21145 MFS transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__HerbieS:HSERO_RS21145
          Length = 437

 Score =  208 bits (530), Expect = 2e-58
 Identities = 127/414 (30%), Positives = 213/414 (51%), Gaps = 12/414 (2%)

Query: 4   DRLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYF 63
           D L  + +W IMP + + Y +AYLDR N GFA    M+ DL  +  +  L   LFF+GYF
Sbjct: 19  DGLYKKVFWRIMPFLMLCYVIAYLDRVNVGFAKLQ-MSQDLGFSETVFGLGAGLFFIGYF 77

Query: 64  FFQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAM 123
            F+VP  I   K   +  I   +I WG L+     VQ+ +    +RFLLG+ EA   P +
Sbjct: 78  LFEVPSNILMHKVGARIWIARIMITWGILSAAFMFVQNATQFYILRFLLGLAEAGFYPGI 137

Query: 124 LIYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFD-------WRWMFIIEGL 176
           ++YL +WF    R++     + G PV  +  + +SG+++  F        W+WMF+IE +
Sbjct: 138 ILYLTYWFPSHRRAKVIAVFMSGIPVAGILGNPLSGWIMDAFHQNGGLEGWQWMFLIEAI 197

Query: 177 PAVLWAFIWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIIL 236
           PAVL        +D+  + A WL  +EK +L+  +  + +G +    +    +  +V ++
Sbjct: 198 PAVLIGVATVLYLDNDVKSAKWLNDEEKASLQADIDGDAKGKESKHGFGAIVKDARVWLM 257

Query: 237 SLQYFCWSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQK 296
            L YF + +G YG  LW+P+++K       +  G LSA+P+  A++AM  +  ++DRM++
Sbjct: 258 CLIYFSFVMGQYGLTLWMPTLVKATGVKGNLEIGLLSAIPFGCAIIAMNLIGRSADRMRE 317

Query: 297 RKRFVWPPLLIAALAFYGSYILGTEHFWWSYTL-LVIAGACMYAPYGPFFAIVPELLPSN 355
           R+  +  P L+  + F G+ +          +L L  AG    AP   F+++    L   
Sbjct: 318 RRWHLVIPALMGGVGFVGAALFADNTAVSIASLSLAAAGVLTCAPL--FWSLPTAFLSGA 375

Query: 356 VAGGAMALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAV 409
            A   +A INS+G L  F   +L+GYL  +T    A+ ++M   +LV  ++  +
Sbjct: 376 AAAVGIAAINSVGNLAGFVSPYLIGYLKDLTHN-NATGMYMLAVMLVVGSIATL 428


Lambda     K      H
   0.328    0.140    0.457 

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: 571
Number of extensions: 31
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 425
Length of database: 437
Length adjustment: 32
Effective length of query: 393
Effective length of database: 405
Effective search space:   159165
Effective search space used:   159165
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: 51 (24.3 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