Align Glucose/galactose porter (characterized)
to candidate WP_009133853.1 HMPREF9450_RS05320 sugar MFS transporter
Query= TCDB::P0C105 (412 letters) >NCBI__GCF_000231275.1:WP_009133853.1 Length = 445 Score = 206 bits (525), Expect = 9e-58 Identities = 127/419 (30%), Positives = 219/419 (52%), Gaps = 36/419 (8%) Query: 24 ALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVK 83 A+ L L+FF++GF + +N IL+P+ K +LN+ QS LI F + AY I+++P+ ++K Sbjct: 19 AMAILGLMFFIFGFTSWVNSILVPYFKIGCELNHFQSYLIVFALYSAYLIMAIPSSAILK 78 Query: 84 RISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILG 143 R+ +KRGI+ G A+G +FIPAA +R Y +FL FV+ +G +LQ AANPYVT++G Sbjct: 79 RVGFKRGIMYGFFCTALGALIFIPAAWWRSYPVFLAGSFVIGAGSAMLQAAANPYVTMIG 138 Query: 144 KPETAASRLTLTQAFNSLGTTVAPVFGAVLILS-----------------AATDATVNAE 186 T R+ + N VAP+ A ++L AA A +++ Sbjct: 139 PINTTVKRMAIMGICNKFAGLVAPLIFAAVVLKVTDSDLFVQLESATLDPAARSAMLDSL 198 Query: 187 ADAVRFPYLLLALAFTVLAII--FAILKPPDVQE---DEPALSDKKEGSAWQYRHLVLGA 241 V PY + A V+ + F++L +++E E A + + S +Q+ +L+LG Sbjct: 199 VHRVMVPYAIFAAFLIVIGVFIRFSMLPELNLEEKNKQEVAPGGEGKTSVFQFPYLILGV 258 Query: 242 IGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIG-------S 294 + +F+++G +V ++++ G+ +A +Y ++G +G Sbjct: 259 VAMFLHIGTQVVTIDTIISYAQ---TMGMDLLEAKTFPSYTLSLVILGNVLGVLLIPKII 315 Query: 295 AAMRYIDDGKALAFNAFVAIILLFITVATTGH---IAMWSVLAIGLFNSIMFPTIFSLAL 351 + R L F + ++ V GH I++W ++ IGL NS+++ I+ LA+ Sbjct: 316 SQTRVFQICCTLGFLLSLGVVWGNTQVDFLGHHANISIWFLVGIGLANSLVYGGIWPLAI 375 Query: 352 HGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPII-CYAYIAFYGLIG 409 GLG T GS +L +A+ G A+VPLI G +AD + +A+ ++ +AY+ FY G Sbjct: 376 RGLGRFTKTGSSMLIMALFGNAVVPLIYGYIADTASLRIAYFWILLPGFAYLMFYAFCG 434 Lambda K H 0.328 0.141 0.420 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: 532 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: 412 Length of database: 445 Length adjustment: 32 Effective length of query: 380 Effective length of database: 413 Effective search space: 156940 Effective search space used: 156940 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