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.
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:
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