Align MFS transporter (characterized, see rationale)
to candidate WP_157198615.1 C943_RS18350 MFS transporter
Query= uniprot:A0A1X9ZCC9 (458 letters) >NCBI__GCF_000330725.2:WP_157198615.1 Length = 427 Score = 414 bits (1065), Expect = e-120 Identities = 207/427 (48%), Positives = 287/427 (67%), Gaps = 3/427 (0%) Query: 20 MSVGFFGIQFGWDLQRANMGRIYENLGANPDQVPLLFLAAPLTGLLVQPIIGYLSDRTWH 79 MS GF GIQFG+ LQ M RI++ LGA+ D +PLL++AAPLTGLLVQPI+GYLSDRTWH Sbjct: 1 MSFGFLGIQFGFALQGGFMSRIFQTLGADKDAIPLLWIAAPLTGLLVQPIVGYLSDRTWH 60 Query: 80 PKWGRRRPYFMIGAIVSSIALIFMPHSSVLWMAAGLLWILDVFGNIAMEPFRAFVTDKLP 139 ++GRRRP+F+IGA++S+IAL F P+SS LWMAAG LWILD NI+MEPFRA V DKLP Sbjct: 61 SRFGRRRPFFLIGAVMSTIALFFAPYSSALWMAAGALWILDASINISMEPFRALVADKLP 120 Query: 140 DSQVNRGFIMQSMMIGLGGSVASALPWIMNNVFHLTNTAEQGSIPENVKFSFYIGAFFFF 199 DSQ + GF++Q+++IG+G VAS LPW M + + NTAE G +P++VKF+F +GA F Sbjct: 121 DSQRSYGFVVQTLIIGIGTWVASNLPWFMTQI-GIPNTAEAGVVPDSVKFAFAVGAVVLF 179 Query: 200 AAVLWTVFTTKEYPPQDVDFKEKVKESNKGFGGGAREIFHALRNMPKRMQIVSLVQFFTW 259 ++L+T+ TT EYPP+D+D ++ E +KGF G +EIF + MP M+ + +VQFF+W Sbjct: 180 GSILYTILTTDEYPPEDLDAFKRENEESKGFINGLQEIFKNIAGMPPVMKQLGIVQFFSW 239 Query: 260 PGLFLMWFYYTTAVAVNVFGGKDAADPVYAQGADFGSLTLAYYSVITFLFALVLPKIAD- 318 F MW + T A+ +VF D VY AD L Y +++ FAL+L + Sbjct: 240 FAFFTMWSFATPAITEHVFKATDTTSQVYNDAADSVGNYLGTYGLVSMFFALILAFVTSK 299 Query: 319 -ALGRKTTHALCLICGAIGLISVAWVHDKNMLYLCMTGVGIAWASILSMPYAMLSGSLPK 377 + RK H L LI G +G IS+ +V ML+LC VG+AWASILSMPYAMLS ++ Sbjct: 300 VKINRKMVHMLSLIAGGVGFISIYFVQTPWMLHLCFALVGVAWASILSMPYAMLSSAVNP 359 Query: 378 DKIGIYMGIFNFFIVLPEIIASLGFGWLMRNVLNNDRLLAVQLGGGLMILAAVICYVFIR 437 ++G+YMGIFN FIV+P+I+A+LG +L + ++ + G ++ A + + I Sbjct: 360 KQMGVYMGIFNMFIVIPQIVAALGGINFSYKLLFGEEVIYTMVLAGTSLIIAGLANLLIT 419 Query: 438 EPKKTDE 444 + T + Sbjct: 420 DRSATHD 426 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: 663 Number of extensions: 33 Number of successful extensions: 3 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: 427 Length adjustment: 32 Effective length of query: 426 Effective length of database: 395 Effective search space: 168270 Effective search space used: 168270 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