Align KguT (characterized, see rationale)
to candidate BPHYT_RS05360 BPHYT_RS05360 MFS transporter
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__BFirm:BPHYT_RS05360 Length = 439 Score = 224 bits (572), Expect = 3e-63 Identities = 136/420 (32%), Positives = 225/420 (53%), Gaps = 23/420 (5%) Query: 12 WYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAI 71 W + P++ + Y +AYLDR N GFA M DL ++ A+ +FF+GYF F++P + Sbjct: 30 WRLAPLLMLCYVVAYLDRVNVGFAKLQ-MTSDLGLSDAVYGFGAGIFFVGYFIFEIPSNV 88 Query: 72 YAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWF 131 K + I ++ WG ++ LT V + ++ +RFLLG+ EA P +++YL +W+ Sbjct: 89 ILHKVGARVWIARIMVSWGVISMLTMFVTTPTMFYVMRFLLGLAEAGFFPGIILYLTYWY 148 Query: 132 TRAERSRANTFLILGNPVTILWMSVVSGYLVKHFD-------WRWMFIIEGLPAVLWAFI 184 R R T+ + ++ + VSGY++K F+ W+W+F++EG+P+V+ + Sbjct: 149 PAHRRGRMTTWFMTAIALSGVIGGPVSGYILKTFNGMNGWHGWQWLFLLEGIPSVIVGIM 208 Query: 185 WWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWS 244 + ++DDR +A WL +E+ L ++AE + K R+ S +V++LSL YF + Sbjct: 209 VFTMLDDRISKAKWLTKEEQQLLERHVSAE-EATKHDMPIRQVLTSGRVLMLSLTYFSFV 267 Query: 245 IGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPP 304 +G+YG WLP+I+K D G LSA+P+ GAV+AM+ VS ++DR ++R+ W Sbjct: 268 MGLYGVSFWLPTIIKATGVTDAFMIGLLSAIPFAGAVVAMVFVSRSADRKRERR---WH- 323 Query: 305 LLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYG-----PFFAIVP-ELLPSNVAG 358 IA AF G+ L W T+L +A + A G P F +P +L A Sbjct: 324 --IALPAFAGAVGLVLSVVWAHNTVLAMASLTL-ATMGILTTLPLFWSLPTAILAGTGAA 380 Query: 359 GAMALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQARR 418 +A+INS+G L F + VG+L T S ++M A +V L A+ P++ + Sbjct: 381 AGIAMINSIGNLAGFLSPYAVGWLKQATAA-NDSGMYMLAAFMVLGGLLAISVPAKMVNK 439 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: 609 Number of extensions: 31 Number of successful extensions: 7 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: 425 Length of database: 439 Length adjustment: 32 Effective length of query: 393 Effective length of database: 407 Effective search space: 159951 Effective search space used: 159951 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