Align Glucose/galactose transporter (characterized, see rationale)
to candidate WP_057509309.1 ABB28_RS14540 glucose/galactose MFS transporter
Query= uniprot:A0KXM0 (423 letters) >NCBI__GCF_001431535.1:WP_057509309.1 Length = 429 Score = 209 bits (531), Expect = 2e-58 Identities = 132/402 (32%), Positives = 210/402 (52%), Gaps = 14/402 (3%) Query: 32 LFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYFLVSIPAGQLVKRLGYQKG 91 LFF+ GF T LN LI +K F L+ A L+ F+ +YF +++P+ +++R G +KG Sbjct: 23 LFFLIGFFTWLNGPLITFVKLAFELDEVGAFLVLMVFYLSYFFLALPSSWILRRTGMKKG 82 Query: 92 IVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQVAANPYVNALGSSETASS 151 + L++ + G F A+ Y LG LF++ SG+ +LQ A NPY++ LG ETA+ Sbjct: 83 LSLSLLVMAAGAATFGEFATQRWYPGALGGLFIIGSGLALLQTAINPYISILGPIETAAR 142 Query: 152 RLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQA---------NAEAEVVKLPYLL 202 R+ L N + +AP L+L +S+ + QA N A + PYL Sbjct: 143 RIALMGICNKVAGMLAPVLIGTLVLHGVGDLSTAVEQADVATRAALLNDFAAKIHAPYLG 202 Query: 203 LAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSALQSMHLVLGAVGIFVYVGAE 262 +AA L VL++ LP ++ AA + + ++S Q HL LG + +FVYVG E Sbjct: 203 MAALLVVLSVAVLFSPLPELKSSEANAAPAGKGGIERSSIFQFPHLWLGVLCLFVYVGVE 262 Query: 263 VSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFIGSAVMQK-IPAGTVLAFNA 321 V G + + H +P +Q + + G +VG +G ++ + + L+ +A Sbjct: 263 VMAGDAIGTY---GHGFDLPLDQTKMFTSLTLGAMLVGYVVGLLLIPRFVSQSRYLSISA 319 Query: 322 FMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALRDLGPHTSQGSGILCLAIV 381 + L + A T G V++ + +G N++M+P IF LA+R LG T GS +L + I Sbjct: 320 SLGVLFCVGAYFTHGYVSVAFVALLGFANAMMWPAIFPLAIRGLGRFTETGSALLVMGIA 379 Query: 382 GGAIVPLLQGVLADNLGIQLAFILPVV-CYGFILFYGAKGSK 422 GGAI+P VL ++ QL F+L +V CY +ILFY G + Sbjct: 380 GGAIIPQAFAVLKQHVDFQLVFLLLMVPCYLYILFYSTIGHR 421 Lambda K H 0.326 0.138 0.402 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: 462 Number of extensions: 32 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: 423 Length of database: 429 Length adjustment: 32 Effective length of query: 391 Effective length of database: 397 Effective search space: 155227 Effective search space used: 155227 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