Align KguT (characterized, see rationale)
to candidate BWI76_RS27095 BWI76_RS27095 MFS transporter
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__Koxy:BWI76_RS27095 Length = 439 Score = 273 bits (699), Expect = 6e-78 Identities = 161/412 (39%), Positives = 238/412 (57%), Gaps = 11/412 (2%) Query: 9 RRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVP 68 +RW I+P + IT ++Y+DR N FA GM DL I+ ++ L G +FF+GY F QVP Sbjct: 15 QRWLRIIPPILITCIISYMDRVNIAFAMPGGMDADLGISATMAGLAGGIFFIGYLFLQVP 74 Query: 69 GAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLC 128 G A S KK I SL+ W ++ LTG++ + L+A+RFLLGV E ++P +L + Sbjct: 75 GGKIAVHGSGKKFIGWSLVAWAVISVLTGLITNQYQLLALRFLLGVAEGGMLPVVLTMIS 134 Query: 129 HWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAFIWWRL 188 +WF AER RAN +I+ P+ + + +SG+++ DWRW+FIIEGL +++ +W Sbjct: 135 NWFPDAERGRANAIVIMFVPIAGIITAPLSGWIITVLDWRWLFIIEGLLSLVVLVLWAYT 194 Query: 189 VDDRPEQASWLKAQEKTALREALAAEQQGI--KPVKNYR-EAFRSPKVI--ILSLQYFCW 243 + DRP++A W+ EK L E LAAEQ+ I VKN A S K + +++L +F + Sbjct: 195 IYDRPQEARWISEAEKRYLVETLAAEQKAIAGTEVKNASLSAVLSDKTMWQLIALNFF-Y 253 Query: 244 SIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWP 303 G+YG+ LWLP+ILK+ + G L+ +PY+GA+ M S SDR KRK FV Sbjct: 254 QTGIYGYTLWLPTILKELTHSSMGQVGMLAILPYVGAIAGMFLFSSLSDRTGKRKLFVCL 313 Query: 304 PLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMAL 363 PL+ AL + S L + W SY LV G + + G F+ I L + +AGGA + Sbjct: 314 PLIGFALCMFLSVALKNQ-IWLSYAALVGCGFFLQSAAGVFWTIPARLFSAEMAGGARGV 372 Query: 364 INSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAV-ALTAVLNPSQ 414 IN++G LG F G + VG L + Y C A+ +A+ AL A+L P++ Sbjct: 373 INALGNLGGFCGPYAVGVLITLYSKDAGVY---CLAISLALAALMALLLPAK 421 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: 595 Number of extensions: 25 Number of successful extensions: 3 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