Align KguT (characterized, see rationale)
to candidate PP_3391 PP_3391 putative Tartrate MFS transporter
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__Putida:PP_3391 Length = 438 Score = 179 bits (453), Expect = 2e-49 Identities = 126/413 (30%), Positives = 199/413 (48%), Gaps = 16/413 (3%) Query: 12 WYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAI 71 W IMP+ I + +Y DR N FA M +L ++ A L ++FF+GY F+VP ++ Sbjct: 28 WRIMPLAIICFLFSYFDRINISFAKTQ-MQQELGLSDAAYGLAASMFFVGYVLFEVPSSL 86 Query: 72 YAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWF 131 ++ I ++ WG + L +RFL+GV+EA PA+L YL WF Sbjct: 87 GLKRYGAPAWICRIMVSWGLATAALVFAYTQYTLYFLRFLIGVMEAGFGPAILFYLACWF 146 Query: 132 TRAERSRANTFLILGNPVTILWMSVVSGYLVKHFD-------WRWMFIIEGLPAVLWAF- 183 R ++ N L P+ +G+L+ D W W+F++ GLP VL Sbjct: 147 PRKHLAKMNGLWFLAVPLAGAVGGPAAGFLLGTMDGVLGLAGWHWLFLMSGLPCVLLGLL 206 Query: 184 IWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVK-NYREAFRSPKVIILSLQYFC 242 + W+L D E A WL +EK L E LA +++ KP+ + + +V I++ Y+ Sbjct: 207 VLWKL-DRDIEAAKWLSREEKDLLAENLAQDKRTAKPILGSIWRVLLTREVAIMAFIYYV 265 Query: 243 WSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVW 302 YG W+P ++K + D++ G LSA+PY A + M+ ++ SDR +RKR++ Sbjct: 266 VKTASYGLNFWMPHLIKSSGVQDMLWVGVLSALPYAVACIGMVLLTRHSDRTGERKRYLV 325 Query: 303 PPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVA-GGAM 361 LL AA+ + + + F T LV+A A + P F +P+ S +A Sbjct: 326 YCLLAAAVGYLLACLFSDSPF-AMMTALVLATAGTFIAI-PIFWTIPQSTFSGLAIATGT 383 Query: 362 ALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVA--VALTAVLNP 412 A INS+G L +VG +N +T L + +LVA V + V NP Sbjct: 384 AAINSVGQLSGIVAPVMVGKINDLTDSTYMGMLSIAPLILVACLVVMRYVRNP 436 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: 603 Number of extensions: 49 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: 438 Length adjustment: 32 Effective length of query: 393 Effective length of database: 406 Effective search space: 159558 Effective search space used: 159558 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