Align Glucose/galactose porter (characterized)
to candidate WP_057509309.1 ABB28_RS14540 glucose/galactose MFS transporter
Query= TCDB::P0C105 (412 letters) >NCBI__GCF_001431535.1:WP_057509309.1 Length = 429 Score = 206 bits (523), Expect = 1e-57 Identities = 135/409 (33%), Positives = 208/409 (50%), Gaps = 34/409 (8%) Query: 30 LLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISYKR 89 +LFF+ GF T LN LI +K F+L+ + L+ F+ +YF ++LP+ +++R K+ Sbjct: 22 VLFFLIGFFTWLNGPLITFVKLAFELDEVGAFLVLMVFYLSYFFLALPSSWILRRTGMKK 81 Query: 90 GIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPETAA 149 G+ + L+V A G A F A+ R Y LG LF++ SG+ +LQ A NPY++ILG ETAA Sbjct: 82 GLSLSLLVMAAGAATFGEFATQRWYPGALGGLFIIGSGLALLQTAINPYISILGPIETAA 141 Query: 150 SRLTLTQAFNSLGTTVAPVFGAVLILSAATD--------------ATVNAEADAVRFPYL 195 R+ L N + +APV L+L D A +N A + PYL Sbjct: 142 RRIALMGICNKVAGMLAPVLIGTLVLHGVGDLSTAVEQADVATRAALLNDFAAKIHAPYL 201 Query: 196 LLALAFTVLAIIFAILKPPDVQEDEPALSDKKEG-----SAWQYRHLVLGAIGIFVYVGA 250 +A VL++ P+++ E + +G S +Q+ HL LG + +FVYVG Sbjct: 202 GMAALLVVLSVAVLFSPLPELKSSEANAAPAGKGGIERSSIFQFPHLWLGVLCLFVYVGV 261 Query: 251 EVSVGSFL------VNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDGK 304 EV G + + D T S T A V Y G ++ RF+ + RY Sbjct: 262 EVMAGDAIGTYGHGFDLPLDQTKMFTSLTLGAMLVGYVVGLLLIPRFVSQS--RY----- 314 Query: 305 ALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGI 364 L+ +A + ++ T G++++ V +G N++M+P IF LA+ GLG T GS + Sbjct: 315 -LSISASLGVLFCVGAYFTHGYVSVAFVALLGFANAMMWPAIFPLAIRGLGRFTETGSAL 373 Query: 365 LCLAIVGGAIVPLIQGALADAIGIHLAFLMPII-CYAYIAFYGLIGSKS 412 L + I GGAI+P L + L FL+ ++ CY YI FY IG ++ Sbjct: 374 LVMGIAGGAIIPQAFAVLKQHVDFQLVFLLLMVPCYLYILFYSTIGHRA 422 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: 497 Number of extensions: 31 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: 429 Length adjustment: 32 Effective length of query: 380 Effective length of database: 397 Effective search space: 150860 Effective search space used: 150860 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: 50 (23.9 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