Align Glucose/galactose porter (characterized)
to candidate WP_057508914.1 ABB28_RS12315 glucose/galactose MFS transporter
Query= TCDB::P0C105 (412 letters) >NCBI__GCF_001431535.1:WP_057508914.1 Length = 438 Score = 424 bits (1089), Expect = e-123 Identities = 216/426 (50%), Positives = 297/426 (69%), Gaps = 17/426 (3%) Query: 3 TSIPTNNPLHTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSML 62 +S P N + + N AL T +FFMWGF+TCLNDILIPHLK VF+LNY ++ML Sbjct: 4 SSTPRLNTTPGQGAPPVNTRMALGVATTIFFMWGFLTCLNDILIPHLKAVFELNYARAML 63 Query: 63 IQFCFFGAYFIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALF 122 +QF FFGAYF++SLPAG+LV + YK+GIV GL++A +G F PAA R Y+ FLGALF Sbjct: 64 VQFTFFGAYFLMSLPAGRLVAHLGYKKGIVAGLLIAGVGALGFWPAAELREYSAFLGALF 123 Query: 123 VLASGVTILQVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLI-------- 174 VLA+G+T+LQVAANPYV +LG ET++SRLTL QA NSLGT +AP+FG +LI Sbjct: 124 VLATGITVLQVAANPYVALLGPVETSSSRLTLAQALNSLGTAIAPIFGGLLILGNTVKSA 183 Query: 175 -----LSAATDATVN-AEADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSD--- 225 LS A A AEA +V+ PY+ LA+A +LA+ + + P + E + D Sbjct: 184 DEINALSVAEQAAYRAAEAQSVQGPYIGLAIALVLLALFVYLFRLPTLSESAEKVDDGPQ 243 Query: 226 KKEGSAWQYRHLVLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGG 285 + G+A ++RHL+ +GIF YVGAEVS+GSFLVN+LS PT+ G +E A H+V+ +W Sbjct: 244 QSYGAALRHRHLLFAVLGIFFYVGAEVSIGSFLVNYLSMPTIGGFTEQQATHYVSAYWTM 303 Query: 286 AMVGRFIGSAAMRYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPT 345 AM+GRF GSA + LA A + ++LL T+A++G +A++SV+AIGLFNSIMFPT Sbjct: 304 AMIGRFAGSALLTRYSPRHMLALFAGINVLLLGTTMASSGQVALYSVVAIGLFNSIMFPT 363 Query: 346 IFSLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFY 405 IF+L + LG T++ S +L +AIVGGA+VP +QG LAD IG+ +F++P++CY Y+ F+ Sbjct: 364 IFALGIERLGPLTNKASSLLIMAIVGGALVPYLQGVLADHIGLQPSFILPLLCYGYVIFF 423 Query: 406 GLIGSK 411 GL+G++ Sbjct: 424 GLVGAR 429 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: 608 Number of extensions: 29 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: 412 Length of database: 438 Length adjustment: 32 Effective length of query: 380 Effective length of database: 406 Effective search space: 154280 Effective search space used: 154280 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