Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 202604 SO3503 glucose/galactose transporter (NCBI ptt file)
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__MR1:202604 Length = 435 Score = 194 bits (492), Expect = 6e-54 Identities = 139/428 (32%), Positives = 224/428 (52%), Gaps = 29/428 (6%) Query: 27 MAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLV 86 + M ++ ++FF+ GF T LN L+P+LK + +LN +A L+ F+F+ A +LP+ ++ Sbjct: 13 LPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVI 72 Query: 87 ARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALL 146 ++GYK G+ G+ V + F PAA + FL A V+ G T+LQ A N YV L Sbjct: 73 RKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNPYVVRL 132 Query: 147 GPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSA--EQIAKLSPAEQVAYRVQE 204 GPE+SA++R+++ LN +AP L+ SA +L + ++I Q+ + Sbjct: 133 GPEESAAARVSVMGILNKGAGVIAP-----LVFSALILDSFKDRIGTTLTQVQID---EM 184 Query: 205 AQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLV-SPLRHPHVLFGVLA 263 A + PYLG+A+ + +LA+ V LP L+ + E A S + + L HP++ GVLA Sbjct: 185 ANGLVLPYLGMAVFIGILALAVKKSPLPELSNEDEVADHTDKSQIKAALSHPNLALGVLA 244 Query: 264 IFFYVGGEV----AIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLG-AMIGRFIGSALLA 318 +F YV EV IG+F ++ L + G M+ V Y LG +I R I Sbjct: 245 LFVYVAVEVIAGDTIGTFALS-LGIDHYGVMTSYTMVCMVLGYILGILLIPRVISQPTAL 303 Query: 319 KLSPRKLLAIFAAI------NMALVLTTMMTKGTVA----MYSVVSIGLFNSIMFPTIFS 368 +S L + I + A+ ++ G VA + + +GL N+I++P ++ Sbjct: 304 MISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANAIVWPAVWP 363 Query: 369 LGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLF--ADHIGVQHAFFLPLLCYAYIVFYG 426 L + MG +T S+LLIM I GGA P GL A +G Q + + L CY +I+FY Sbjct: 364 LALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPCYLFILFYA 423 Query: 427 LYGSRIKS 434 + G +++S Sbjct: 424 VKGHKMRS 431 Lambda K H 0.327 0.140 0.414 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: 502 Number of extensions: 28 Number of successful extensions: 5 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: 442 Length of database: 435 Length adjustment: 32 Effective length of query: 410 Effective length of database: 403 Effective search space: 165230 Effective search space used: 165230 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