Align KguT (characterized, see rationale)
to candidate BPHYT_RS10985 BPHYT_RS10985 MFS transporter
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__BFirm:BPHYT_RS10985 Length = 432 Score = 560 bits (1444), Expect = e-164 Identities = 267/420 (63%), Positives = 326/420 (77%), Gaps = 2/420 (0%) Query: 6 LAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFF 65 +AP+RWWY+MPI+FITYSLAYLDRANYGFAAA+G+ DL IT SSL+G+LFFLGY F Sbjct: 7 VAPQRWWYLMPIIFITYSLAYLDRANYGFAAAAGIDRDLGITHGTSSLIGSLFFLGYCLF 66 Query: 66 QVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLI 125 QVPGAIYA++ SVKKLIF SLILWG A TGMV ++ +L+ +RF+LGVVEAAVMP+ML+ Sbjct: 67 QVPGAIYAQRNSVKKLIFFSLILWGLCAAATGMVSNIPMLMMLRFVLGVVEAAVMPSMLM 126 Query: 126 YLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAFIW 185 Y+ WFTR+ERSRANTFLILGNPVT+LWMSVVSGYLV+ F WR MF+ EG PA++WA +W Sbjct: 127 YISRWFTRSERSRANTFLILGNPVTVLWMSVVSGYLVRSFGWREMFVFEGAPALIWAVVW 186 Query: 186 WRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWSI 245 W V DRP A W+ A EKT L L AEQ I PV++Y+ AFRS V+ + WSI Sbjct: 187 WFTVKDRPADAPWMSAAEKTELDARLKAEQAHIAPVRDYKAAFRSSIVLKFCAIHALWSI 246 Query: 246 GVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPPL 305 GVYGF++WLPSILK A+ +DIV+ GWL+AVPYL A++ ML SW SD+ + RK FVWP L Sbjct: 247 GVYGFIMWLPSILKAASTIDIVSVGWLAAVPYLAAIILMLLASWLSDKTRNRKLFVWPLL 306 Query: 306 LIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALIN 365 L+ +AF SY++G HFW S+ LLV+AGA MYAPYGPFFA+VPEL+P NV GGA+ LIN Sbjct: 307 LVGTIAFVASYLIGGSHFWISFALLVVAGATMYAPYGPFFALVPELIPGNVLGGAIGLIN 366 Query: 366 SMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVAL--TAVLNPSQQARRQQLAP 423 + GALG+F+GSW+VGYLNGVTG P ASY+FM G LL +V L T N + A+R P Sbjct: 367 ACGALGAFAGSWVVGYLNGVTGSPAASYIFMAGGLLSSVILMITVPANSDEHAKRGAALP 426 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: 777 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: 432 Length adjustment: 32 Effective length of query: 393 Effective length of database: 400 Effective search space: 157200 Effective search space used: 157200 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