Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate WP_013089044.1 BC1002_RS05340 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >NCBI__GCF_000092885.1:WP_013089044.1 Length = 463 Score = 253 bits (645), Expect = 1e-71 Identities = 147/421 (34%), Positives = 229/421 (54%), Gaps = 17/421 (4%) Query: 26 KSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPIGGW 85 K+I + ++GN +E++D+ +Y+ F+ K +FP QL+ F VGF+MRP+GG Sbjct: 38 KAIAAITLGNGLEFFDFTIYSFFATIIGKLYFPVEGQLVQLMLAVGTFGVGFIMRPVGGI 97 Query: 86 LMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSVGGE 145 ++G YADRAGRKAA+ +++LM GS IIA +P Y IGV AP+L++ ARL+QG ++GGE Sbjct: 98 VLGGYADRAGRKAAMSLTLWLMTLGSAIIAFAPTYAAIGVAAPLLVILARLIQGFALGGE 157 Query: 146 YGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWRIPF 205 G S L E + RGF+ S+Q+V+ ++ + + L TL+ L WGWR+PF Sbjct: 158 VGASTALLLEYGSDRTRGFYGSWQFVSQGMNTVVGSLLGVALAATLSPAALESWGWRVPF 217 Query: 206 AIGALCAIVALYLRRGMEET------------ESFAKKEKSKES-AMRTLLR-HPKELMT 251 IG + +Y+RR ++ET E A++ S +R L R H + + T Sbjct: 218 VIGMAMGPIGIYIRRHLDETLPGVEDGAAAAGEMGAQRASQPPSLPVRDLFRDHARSITT 277 Query: 252 VVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVG 311 V T+GGT A Y Y+ Y + + + ++ + + + + P G LSD+VG Sbjct: 278 GVLTTIGGTAANYIVLFYLSTYAIRILHLPMATALWAAWTGAVVTVICSPFAGALSDRVG 337 Query: 312 RRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSI-NAVVKAELFP 370 R+ +L +L P T++ T ++A L ++ +T++ N V+ ELFP Sbjct: 338 RKRVLWVSRVLLIFAVYPAFMTINASPT-VPVLLAVVAGLALLVTFTAVPNIVMLPELFP 396 Query: 371 TEIRALGVGLPYALTVSIFGGTAEYIALWFKSI-GMETGYYWYVTACIAVSLLVYVTMKD 429 IRA G+ + Y L VSIFGG A++ A W + G WY+ C VSLL M++ Sbjct: 397 RAIRATGMSIVYCLGVSIFGGFAQFFATWLIQVSGSNLAPAWYLIGCGVVSLLPLPLMRE 456 Query: 430 T 430 T Sbjct: 457 T 457 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: 572 Number of extensions: 31 Number of successful extensions: 5 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: 463 Length adjustment: 33 Effective length of query: 406 Effective length of database: 430 Effective search space: 174580 Effective search space used: 174580 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