Align MFS transporter (characterized, see rationale)
to candidate PfGW456L13_1423 Hexuronate transporter
Query= uniprot:A0A166QG26 (467 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1423 Length = 433 Score = 300 bits (767), Expect = 8e-86 Identities = 163/452 (36%), Positives = 243/452 (53%), Gaps = 40/452 (8%) Query: 11 RIGQAVGNYRWTICALLFFATTVNYLDRQVLSLLAPDLSTQFGWSNSDYANIASVFQFVY 70 R AVG RW + AL+FFATT+NY+DR L ++ P L+ + W+ DYANI FQ Y Sbjct: 13 RGAMAVGKTRWGMLALVFFATTLNYIDRAALGVMQPILAKEMSWTAMDYANINFWFQVGY 72 Query: 71 AISMLFAGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGIGAVSSALGIAMIPVSI 130 AI + GR++D++G K + A+ +WS H A S Sbjct: 73 AIGFVLQGRLIDRVGVKRVFFCAVLLWSLATGAHGLAT--------------------SA 112 Query: 131 AGFMVSRAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSGANVGAILAPICVPLIA 190 GFMV R +L + EA N+P +K T +FP ER+ ATGIFN+G NVGA+ P+ +PLI Sbjct: 113 VGFMVCRFILGLTEAANYPACVKTTRLWFPAGERAVATGIFNAGTNVGAMFTPMLLPLIL 172 Query: 191 SLWGWEAAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYIRSDQVVPVVTRPVPGV 250 +WGW+AAF+ + LG +W+ W Y PE + EL YI+ +V P TR Sbjct: 173 HVWGWQAAFLCMASLGGIWLLFWGLKYFNPEDHPSVKQSELDYIQK-EVEPEQTR----- 226 Query: 251 ADKKVSWFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQY--GMKGQAIVMPLAV 308 V + K+L R TWAFA +T V+WF+L+WLP +L+ QY G+ + +PL + Sbjct: 227 ----VPFSKILRMRGTWAFALAYSITAPVFWFYLYWLPPFLNQQYNLGINVTQMGIPLII 282 Query: 309 LYSMTMIGSIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPLLVLLAQPLGYISFWVPVL 368 +Y GS+GGG S+ + RG P R+ +M + A + V++A G + WV V Sbjct: 283 IYLTADFGSVGGGILSSFLIGRGVNPIKARLMSMFLFACCIIGVIMA--AGSSNLWVAVA 340 Query: 369 LIGVGASAHQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGLGGVVMTKIGGWVIDHYKL 428 I + AHQAW+ NI++ V D P+ +++V G GG+ +GG+ MT++ G ++ Sbjct: 341 AISLAIGAHQAWTANIWSLVMDYTPKHMMSTVFGFGGMCAAIGGMFMTQLVGHILT---- 396 Query: 429 IGDIHTGYMIMFAICALAYLVAWSVMKALVPR 460 + Y ++F + Y +A M + PR Sbjct: 397 --ITNNNYTVLFTMIPAMYFIALIWMYFMAPR 426 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: 702 Number of extensions: 33 Number of successful extensions: 6 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: 433 Length adjustment: 33 Effective length of query: 434 Effective length of database: 400 Effective search space: 173600 Effective search space used: 173600 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