Align MFS transporter (characterized, see rationale)
to candidate PP_2604 PP_2604 major facilitator family transporter
Query= uniprot:A0A166QG26 (467 letters) >FitnessBrowser__Putida:PP_2604 Length = 441 Score = 308 bits (788), Expect = 3e-88 Identities = 167/450 (37%), Positives = 242/450 (53%), Gaps = 40/450 (8%) Query: 16 VGNYRWTICALLFFATTVNYLDRQVLSLLAPDLSTQFGWSNSDYANIASVFQFVYAISML 75 VG RW + AL+FFATT+NY+DR L ++ P L+ + W+ DYANI FQ YAI L Sbjct: 28 VGKTRWGMLALVFFATTLNYIDRAALGIMQPVLAKEMSWTAMDYANINFWFQVGYAIGFL 87 Query: 76 FAGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGIGAVSSALGIAMIPVSIAGFMV 135 GR++DK+G K A+ A+ +WS H A S AGFMV Sbjct: 88 LQGRLIDKVGVKRAFFFAVLLWSLATGAHGLAT--------------------SAAGFMV 127 Query: 136 SRAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSGANVGAILAPICVPLIASLWGW 195 R +L + EA N+P +K +FP ER+ ATG+FN+G NVGA++ P +PLI ++WGW Sbjct: 128 CRFILGLTEAANYPACVKTVRLWFPAGERAIATGLFNAGTNVGAMVTPALLPLILAVWGW 187 Query: 196 EAAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYIRSDQVVPVVTRPVPGVADKKV 255 +AAFI +G LG VWV W+ Y PE R+ E+ YI+ D P P +V Sbjct: 188 QAAFIAMGSLGLVWVVFWVLKYYNPEDHPRVRQSEVQYIQQDD------EPEP----TRV 237 Query: 256 SWFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQY--GMKGQAIVMPLAVLYSMT 313 + ++L R TWAFA +T V+WF+L+WLP +L+ QY G+ + +PL +++ Sbjct: 238 PFSRILRLRGTWAFAVAYAITAPVFWFYLYWLPPFLNQQYSLGINVTQMGIPLIIIWLTA 297 Query: 314 MIGSIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPLLVLLAQPLGYISFWVPVLLIGVG 373 GSIGGG S+ + RG R+ +ML+ A L V+ A WV V I + Sbjct: 298 DFGSIGGGILSSWLIGRGVRATTARLVSMLIFACTMLSVIFAANAS--GLWVAVAAISIA 355 Query: 374 ASAHQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGLGGVVMTKIGGWVIDHYKLIGDIH 433 AHQAW+ NI++ V D P+ +++V G G + +GG+ MT+I G V+ + Sbjct: 356 VGAHQAWTANIWSLVMDYTPKHLVSTVFGFGSMCAAIGGMFMTQIVGSVLT------ATN 409 Query: 434 TGYMIMFAICALAYLVAWSVMKALVPRHKE 463 Y ++F + Y +A M + PR E Sbjct: 410 NNYAVLFTMIPAMYFLALVWMYFMAPRKVE 439 Lambda K H 0.327 0.140 0.449 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: 727 Number of extensions: 33 Number of successful extensions: 5 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: 467 Length of database: 441 Length adjustment: 33 Effective length of query: 434 Effective length of database: 408 Effective search space: 177072 Effective search space used: 177072 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 (21.7 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