Align MFS transporter (characterized, see rationale)
to candidate WP_109738207.1 C1634_RS08215 MFS transporter
Query= uniprot:A0A1X9ZCC9 (458 letters) >NCBI__GCF_002899945.2:WP_109738207.1 Length = 467 Score = 310 bits (793), Expect = 8e-89 Identities = 168/449 (37%), Positives = 260/449 (57%), Gaps = 31/449 (6%) Query: 10 PKLTLVQIINMSVGFFGIQFGWDLQRANMGRIYENLGANPDQVPLLFLAAPLTGLLVQPI 69 P+L+ QI NM+VGFFGIQ+ + LQ+ + +Y LGA+ DQ+P+L LA P+TGLL+QP+ Sbjct: 7 PRLSFWQIWNMNVGFFGIQYSFGLQQTAVNPLYSFLGAHADQLPILNLAGPVTGLLIQPL 66 Query: 70 IGYLSDRTWHPKWGRRRPYFMIGAIVSSIALIFMPHSSVLWMAAGLLWILDVFGNIAMEP 129 IG +SD+TW KWGRR+P+F++GAI+ S+AL P SS +WMA GLLWILD N AMEP Sbjct: 67 IGAISDKTWSVKWGRRKPFFLLGAILCSLALFVFPFSSSIWMAVGLLWILDAANNTAMEP 126 Query: 130 FRAFVTDKLPDSQVNRGFIMQSMMIGLGGSVASALPWIMNNVFHLTNTAEQGSIPENVKF 189 +RAF+ DKLP+ Q GF MQS+ +G G ++A+ +I F ++E G IP V + Sbjct: 127 YRAFIGDKLPEEQQTYGFQMQSLFVGGGITLANLSLFIFQKYF--GGSSESGGIPTWVYY 184 Query: 190 SFYIGAFFFFAAVLWTVFTTKEYPPQDVDFKE-KVKESNKGFGGGAREIFHALRNMPKRM 248 SF++G+F A+V+W+V+ T E PP D + + K ++ N +IF A+ NMPK + Sbjct: 185 SFFLGSFCSVASVVWSVYKTPEIPPTDEELIQLKAEKENDTVFTPFIDIFKAIVNMPKIL 244 Query: 249 QIVSLVQFFTWPGLFLMWFYYTTAVAVNVFGGKDAADP---------------------- 286 ++LV F W LF W + T + ++ + + Sbjct: 245 WQLALVYLFQWYALFCYWQFATPMIKQTLYHVSEIDEERANRFVELSKNGFSVPQNDLLW 304 Query: 287 ------VYAQGADFGSLTLAYYSVITFLFALVLPKIADALGRKTTHALCLICGAIGLISV 340 + Q L +Y+ IT + AL+L A K +A CL+ I L+ + Sbjct: 305 AKNILHLVEQAVGQTGLMNGFYNFITMISALLLIPFALKFSAKNVYAFCLLATGISLLVL 364 Query: 341 AWVHDKNMLYLCMTGVGIAWASILSMPYAMLSGSLPKDKIGIYMGIFNFFIVLPEIIASL 400 ++ ++ L M GI WA+++ +PY+M+S S+P +K G+YMG+ N IV+P +I +L Sbjct: 365 PLCTNEYIILLPMVLFGIGWAAMMGLPYSMVSPSIPANKRGVYMGVINMMIVIPMLIQTL 424 Query: 401 GFGWLMRNVLNNDRLLAVQLGGGLMILAA 429 FG + +L ++ A+++ G L +LA+ Sbjct: 425 TFGAFYKYILGSNPADAIRIAGILFLLAS 453 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: 655 Number of extensions: 34 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 458 Length of database: 467 Length adjustment: 33 Effective length of query: 425 Effective length of database: 434 Effective search space: 184450 Effective search space used: 184450 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