Align MFS transporter (characterized, see rationale)
to candidate H281DRAFT_03828 H281DRAFT_03828 MFS transporter, ACS family, hexuronate transporter
Query= uniprot:A0A166QG26 (467 letters) >FitnessBrowser__Burk376:H281DRAFT_03828 Length = 429 Score = 388 bits (997), Expect = e-112 Identities = 202/454 (44%), Positives = 274/454 (60%), Gaps = 45/454 (9%) Query: 12 IGQAVGNYRWTICALLFFATTVNYLDRQVLSLLAPDLSTQFGWSNSDYANIASVFQFVYA 71 + + YRWT+CALLFFAT +NY+DRQ+L LLAP L GWS Y I F YA Sbjct: 8 LARTASRYRWTVCALLFFATVINYMDRQILGLLAPLLQHDIGWSQVQYGRIVIAFSAFYA 67 Query: 72 ISMLFAGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGIGAVSSALGIAMIPVSIA 131 + +L GR+VD +GT+ +Y +A+ IWS A++HA AV S G AM+ Sbjct: 68 VGLLCFGRIVDWLGTRISYALAMLIWSIAAMLHA----------AVGSVTGFAMV----- 112 Query: 132 GFMVSRAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSGANVGAILAPICVPLIAS 191 RA+L IGE GNFP AIK TAE+FP++ER+ ATGIFNSGAN+GA+ AP +P +A Sbjct: 113 -----RALLGIGEGGNFPAAIKTTAEWFPRRERALATGIFNSGANIGAVFAPAIIPPLAL 167 Query: 192 LWGWEAAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYIRSDQVVPVVTRPVPGVA 251 +GW +AF++IG LG VW+ VW A Y E R +L R + V Sbjct: 168 AFGWRSAFVIIGALGIVWLAVWFAFYRSAE--PRSHDDDLEEARDE----VEALDAANAN 221 Query: 252 DKKVSWFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQYGMKGQAIVMPLAVLYS 311 + W L+ RQTWAF GKF+TD VWWF+LFWLP +L+ GM Q I +PL +Y+ Sbjct: 222 ARAPGWGVLIRKRQTWAFLIGKFLTDPVWWFYLFWLPKWLNESRGMDMQHIGLPLVCIYA 281 Query: 312 MTMIGSIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPLLVLLAQPLGYIS----FWVPV 367 MT +GSIGGGW S + G + R AM + A L P+ ++S W V Sbjct: 282 MTTVGSIGGGWLSSALLRAGWSVNAARKTAMFICACCVL------PIAFVSQVDNLWGAV 335 Query: 368 LLIGVGASAHQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGLGGVVMTKIGGWVIDHYK 427 ++G+ A+AHQ WS N+FTT SD+FP++++ +VVGIGG+AG +GGV+ +++ G V+ Sbjct: 336 AIVGLAAAAHQGWSANLFTTASDLFPKRALGAVVGIGGMAGSIGGVLFSEVIGQVLQ--- 392 Query: 428 LIGDIHTG-YMIMFAICALAYLVAWSVMKALVPR 460 TG Y ++FAI ALAYL+A++VM L PR Sbjct: 393 -----RTGHYWVLFAIGALAYLIAFAVMHMLTPR 421 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: 778 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: 429 Length adjustment: 33 Effective length of query: 434 Effective length of database: 396 Effective search space: 171864 Effective search space used: 171864 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