Align KguT (characterized, see rationale)
to candidate BWI76_RS06145 BWI76_RS06145 MFS transporter
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__Koxy:BWI76_RS06145 Length = 428 Score = 580 bits (1496), Expect = e-170 Identities = 276/418 (66%), Positives = 334/418 (79%) Query: 5 RLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFF 64 +L RRWWY+MPI+FITYSLAYLDRANYGFAAA+G+ DL IT +SL+GALFFLGYFF Sbjct: 6 KLPARRWWYLMPIIFITYSLAYLDRANYGFAAAAGIESDLGITKGTASLIGALFFLGYFF 65 Query: 65 FQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAML 124 FQVPGAIYA KRSV+K+IF SLILWG A TG V ++ +L+AIRF LGVVEAAVMPAML Sbjct: 66 FQVPGAIYAVKRSVRKMIFCSLILWGFCAAATGFVSNIPMLMAIRFTLGVVEAAVMPAML 125 Query: 125 IYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAFI 184 IY+ +WFT+ ERSRANTFLILGNPVT+LWMS+VSGYL++ + WR MFIIEG+PAVLWA Sbjct: 126 IYISNWFTKTERSRANTFLILGNPVTVLWMSIVSGYLIQAWGWREMFIIEGIPAVLWAVC 185 Query: 185 WWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWS 244 WW LV D+P + SWL QEK L++ + +EQ IKPV+NY EA RS VI+L + WS Sbjct: 186 WWILVRDKPSEVSWLNEQEKETLQKVMDSEQSHIKPVRNYGEALRSRNVIMLCAVHALWS 245 Query: 245 IGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPP 304 IGVYGF++W+PSILK AA +DIV GWL+AVPYL A++ ML VSW SD+ Q RK F+WP Sbjct: 246 IGVYGFMMWMPSILKNAAQMDIVAVGWLAAVPYLAAIILMLTVSWLSDKFQNRKLFIWPL 305 Query: 305 LLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALI 364 LLIAA+AF+GS+++G + FW SY LLVIA ACMYAPYGPFFA++PELLP NV+G +M LI Sbjct: 306 LLIAAIAFFGSWMVGNQAFWLSYALLVIAAACMYAPYGPFFALIPELLPRNVSGVSMGLI 365 Query: 365 NSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQARRQQLA 422 NS GALG+F G+WLVGYLNG+TGGPG SY FM ALL +V L + + Q+ +A Sbjct: 366 NSFGALGAFLGAWLVGYLNGITGGPGVSYTFMAVALLSSVVLMFNVRANPQSSSPAVA 423 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: 798 Number of extensions: 35 Number of successful extensions: 2 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: 428 Length adjustment: 32 Effective length of query: 393 Effective length of database: 396 Effective search space: 155628 Effective search space used: 155628 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