Align MFS transporter (characterized, see rationale)
to candidate GFF4779 PS417_24450 membrane protein
Query= uniprot:A0A166QG26 (467 letters) >FitnessBrowser__WCS417:GFF4779 Length = 444 Score = 296 bits (759), Expect = 7e-85 Identities = 160/455 (35%), Positives = 242/455 (53%), Gaps = 40/455 (8%) Query: 15 AVGNYRWTICALLFFATTVNYLDRQVLSLLAPDLSTQFGWSNSDYANIASVFQFVYAISM 74 AVG RW + AL+FFATT+NY+DR L ++ P L+ + W+ DYANI FQ YAI Sbjct: 28 AVGKTRWGMLALVFFATTLNYIDRAALGVMQPILAKEMSWTAMDYANINFWFQVGYAIGF 87 Query: 75 LFAGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGIGAVSSALGIAMIPVSIAGFM 134 + GR++D++G K + A+ +WS H A S GFM Sbjct: 88 VLQGRLIDRVGVKRVFFCAVLLWSLATGAHGLAT--------------------SAVGFM 127 Query: 135 VSRAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSGANVGAILAPICVPLIASLWG 194 V R +L + EA N+P +K T +FP ER+ ATGIFN+G NVGA++ P+ +PLI +WG Sbjct: 128 VCRFILGLTEAANYPACVKTTRLWFPAGERAVATGIFNAGTNVGAMMTPMLLPLILHVWG 187 Query: 195 WEAAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYIRSDQVVPVVTRPVPGVADKK 254 W+AAF+ + LG +W+ W Y PE + EL Y+ + P + Sbjct: 188 WQAAFLCMSALGGIWLVFWGLKYFNPEDHPSVKQSELDYVLQE------AEP----EQPR 237 Query: 255 VSWFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQY--GMKGQAIVMPLAVLYSM 312 V + ++L R TWAFA MT V+WF+L+WLP +L+ QY G+ + +PL ++Y Sbjct: 238 VPFTRILRMRGTWAFALAYSMTAPVFWFYLYWLPPFLNQQYNLGINVTQMGIPLIIIYLT 297 Query: 313 TMIGSIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPLLVLLAQPLGYISFWVPVLLIGV 372 GS+GGG S+ + RG R+ +ML+ A + V++A G WV V I + Sbjct: 298 ADFGSVGGGILSSFLIGRGMNSIKARLLSMLLFACCIVGVIMA--AGSSQLWVAVFAISL 355 Query: 373 GASAHQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGLGGVVMTKIGGWVIDHYKLIGDI 432 AHQAW+ NI++ V D P+ +++V G GG+ +GG+ MT+I G ++ Sbjct: 356 AIGAHQAWTANIWSLVMDYTPKHMMSTVFGFGGMCAAIGGMFMTQIVGHILT------VT 409 Query: 433 HTGYMIMFAICALAYLVAWSVMKALVPRHKEITDL 467 + Y ++F + Y +A + M + PR D+ Sbjct: 410 NNNYTVLFTLIPAMYFIALTWMYFMAPRKIPTVDV 444 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: 708 Number of extensions: 37 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: 467 Length of database: 444 Length adjustment: 33 Effective length of query: 434 Effective length of database: 411 Effective search space: 178374 Effective search space used: 178374 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