Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate WP_057507667.1 ABB28_RS05485 proline/glycine betaine transporter ProP
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >NCBI__GCF_001431535.1:WP_057507667.1 Length = 495 Score = 236 bits (602), Expect = 1e-66 Identities = 139/412 (33%), Positives = 218/412 (52%), Gaps = 15/412 (3%) Query: 26 KSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPIGGW 85 +++ + ++GN +EW+D+ VY ++ + FFP + TAQL+ T A F V FL+RP+GG Sbjct: 35 RAVGAAALGNAMEWFDFGVYGYLAVTLGQVFFPASNPTAQLIATFATFTVAFLVRPLGGL 94 Query: 86 LMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSVGGE 145 + G DR GR+ L ++ LM G+ I L P YE IG+ AP+LL+ ARL+QG S GGE Sbjct: 95 VFGPLGDRYGRQKVLAFTMILMALGTFSIGLIPSYERIGIWAPVLLLLARLVQGFSTGGE 154 Query: 146 YGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWRIPF 205 YG +AT+++E AT RG S+ + G + + L L+ Q+ DWGWRIPF Sbjct: 155 YGGAATFIAEYATDRNRGLMGSWLEFGTLGGYIAGAATVTTLHLLLSGAQMLDWGWRIPF 214 Query: 206 AIGALCAIVALYLRRGMEETESF-------AKKEKSKESAMRTLLRHPKELMTVVGLTMG 258 + ++ LY+R +EET +F AK++ + L H ++L+ +GL + Sbjct: 215 LVAGPLGLLGLYMRMRLEETPAFRAYAEEAAKRDHERPGLGELLRVHGRQLLICMGLVLV 274 Query: 259 GTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGL-SDKVGRRPILI 317 + Y TYM YL T+G + S + + + M L I+GGL SD++GRRP++I Sbjct: 275 FNVTDYMLLTYMPSYLTVTLGYAESKGLLLIIIVMLVMMPLN-IVGGLFSDRLGRRPMII 333 Query: 318 AFGILGTLFTVPILTTLHTIQTWWGAFFL-IMAALIIVSGYTSINAVVKAELFPTEIRAL 376 I L +P L + + + G FL +M I + +TS LF T +R Sbjct: 334 GACIALLLLAIPCLLLVRSGED--GLIFLGLMLLGIALVCFTSSMPSTLPALFYTPVRYS 391 Query: 377 GVGLPYALTVSIFGGTAEYIALWF---KSIGMETGYYWYVTACIAVSLLVYV 425 + + + ++VS+FGGT + W M YY A I + +++V Sbjct: 392 ALSIAFNVSVSLFGGTTPLVTAWLVERSGDPMVPAYYLMGAAVIGLVTMLFV 443 Lambda K H 0.325 0.138 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: 613 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: 439 Length of database: 495 Length adjustment: 33 Effective length of query: 406 Effective length of database: 462 Effective search space: 187572 Effective search space used: 187572 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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