Align MFS transporter (characterized, see rationale)
to candidate WP_010632377.1 RH97_RS10790 SLC45 family MFS transporter
Query= uniprot:A0A1X9ZCC9 (458 letters) >NCBI__GCF_000246965.1:WP_010632377.1 Length = 459 Score = 233 bits (595), Expect = 8e-66 Identities = 133/450 (29%), Positives = 234/450 (52%), Gaps = 15/450 (3%) Query: 10 PKLTLVQIINMSVGFFGIQFGWDLQRANMGRIYENLGANPDQVPLLFLAAPLTGLLVQPI 69 P+L+L+ I M+ GFFG+ + LQ + MGRI++ +GA+P ++ F+ PL G++VQP+ Sbjct: 11 PRLSLMTIFAMTFGFFGVNMAFSLQFSQMGRIFQTIGADPTRLGYFFILPPLAGMIVQPL 70 Query: 70 IGYLSDRTWHPKWGRRRPYFMIGAIVSSIALIFMPHS----------SVLWMAAGLLWIL 119 +G SD TW K GRR PY +IGA ++++ +I +P+S + L A + + Sbjct: 71 VGKYSDLTWSNKLGRRMPYLLIGAPIAALVMILLPNSGSFGFGYASFAALLFGAVAILFM 130 Query: 120 DVFGNIAMEPFRAFVTDKLPDSQVNRGFIMQSMMIGLGGSVASALPWIMNNVFHLTNTAE 179 D+ N+ M+PF+ + D + + Q + + Q LGG +A+ +P+++ VF + NTA Sbjct: 131 DLSSNVCMQPFKMIIGDMVNEKQKDLAWSWQQSFSNLGGVIATIIPFVL-TVFGVANTAP 189 Query: 180 QGSIPENVKFSFYIGAFFFFAAVLWTVFTTKEYPPQDVDFKEKVKESNKGFGGGAREIFH 239 +G +P +V+ +FY+GA L+T+ + KEY P+ +K + ++H Sbjct: 190 RGEVPLSVRLAFYVGAGVLLLTSLYTIISVKEYDPKTYALYHHMKADEH---KDSPSLWH 246 Query: 240 ALRNMPKRMQIVSLVQFFTWPGLFLMWFYYTTAVAVNVFGGKDAADPVYAQGADFGSLTL 299 +R P+ VSLVQ F W +W Y T A+A NV+G D A Y ++ + Sbjct: 247 LVRKAPRAFWEVSLVQLFDWFAFQYLWTYATGAIAQNVWGTADPASAGYQAAGNWYGILT 306 Query: 300 AYYSVITFLFALVLPKIADALGRKTTHALCLICGAIGLISVAWVHDKNMLYLCMTGVGIA 359 S+ + ++ RK + L+ GA+G I V + H++ +L L +GI+ Sbjct: 307 CVSSLAAVAWGFLVLSHTSQFKRKFWLRVGLLSGALGFIWVFFTHNQYLLILPFCLIGIS 366 Query: 360 WASILSMPYAMLSGSLPKDKIGIYMGIFNFFIVLPEIIASLGFGWLMRNVLNNDRLLAVQ 419 + ++ + +++ + SL G YMG+FN I LP+IIAS+ + + ++ + Sbjct: 367 YLTMQTEAFSIFTSSLNGKNEGAYMGLFNCGICLPQIIASVA-SFALFPLIGKSMSGMIL 425 Query: 420 LGGGLMILAAVICYVFIREPKKTDEVLAAK 449 + G M+L A + + + VL K Sbjct: 426 IAGIAMLLGAAAVAAIHEDKPQRNTVLKKK 455 Lambda K H 0.327 0.142 0.448 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: 604 Number of extensions: 38 Number of successful extensions: 4 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: 458 Length of database: 459 Length adjustment: 33 Effective length of query: 425 Effective length of database: 426 Effective search space: 181050 Effective search space used: 181050 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 24 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