Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate AO353_25100 AO353_25100 glucose transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25100 Length = 425 Score = 323 bits (827), Expect = 8e-93 Identities = 176/395 (44%), Positives = 244/395 (61%), Gaps = 3/395 (0%) Query: 34 SIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVARLGYKK 93 S+FF+ G +T LND+L+P LK +F L+Y EAMLVQ +FF AYF+ ++PAGLL++R+GY + Sbjct: 28 SLFFILGSITSLNDVLVPKLKHLFSLSYTEAMLVQSSFFFAYFIFAIPAGLLISRIGYMR 87 Query: 94 GIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALLGPEKSAS 153 V GL + G F PA +PAFLGALFVLA G+T +QV AN ++LLG +A Sbjct: 88 AAVLGLLLMAGGCLLFIPATQSALFPAFLGALFVLAIGVTTVQVVANPLLSLLGTAATAP 147 Query: 154 SRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEAQTVQGPYL 213 SRLTL A NSLGT +AP G +LIL + L+A + LSPAE ++ QEA + Y Sbjct: 148 SRLTLGHAFNSLGTTVAPYLGAILILGS--LNAVDTSALSPAELTSFLSQEASVISNTYA 205 Query: 214 GLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVA 273 + + + ++A+ V+L R L T + + ++ L+ P G +IF YVG EV Sbjct: 206 SITLFICMVALIVWLKR-NELQPSTRPERLNPLAALNLLKQPRFALGTASIFLYVGAEVT 264 Query: 274 IGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRKLLAIFAAIN 333 IGS + +YL +P + +AA VA+YW GA++GRFIGSAL+ +P KLLA A Sbjct: 265 IGSLITDYLMLPTTLALPAEAAGKHVAFYWGGALVGRFIGSALMRTFAPGKLLAFAATAV 324 Query: 334 MALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLIMAIVGGA 393 + L+ + T+G VA +S++++GLFNSIMFPTIF+L +G E S L AIVGGA Sbjct: 325 IVLLTISATTQGVVAGWSLLAVGLFNSIMFPTIFTLATAGLGHRAAEGSGLFCCAIVGGA 384 Query: 394 IVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLY 428 +P + G AD + A +P CYA I YG Y Sbjct: 385 FIPPLTGYAADLSTLAMALSVPATCYACIAIYGWY 419 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: 510 Number of extensions: 26 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: 442 Length of database: 425 Length adjustment: 32 Effective length of query: 410 Effective length of database: 393 Effective search space: 161130 Effective search space used: 161130 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