Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate WP_012401215.1 BPHY_RS09275 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >NCBI__GCF_000020045.1:WP_012401215.1 Length = 448 Score = 253 bits (645), Expect = 1e-71 Identities = 145/422 (34%), Positives = 229/422 (54%), Gaps = 16/422 (3%) Query: 22 ASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRP 81 AS K+I + ++GN +E++D+ +Y+ F+ K +FP AQL+ F VGF+MRP Sbjct: 24 ASHAKAIAAITLGNGLEFFDFTIYSFFATIIGKLYFPVEGQLAQLMLAVGTFGVGFIMRP 83 Query: 82 IGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLS 141 +GG ++G YADRAGRKAA+ +++LM GS +IA +P Y +IG+ AP L++ ARL+QG + Sbjct: 84 VGGVVLGAYADRAGRKAAMSLTLWLMTLGSAMIAFAPTYASIGLAAPALVILARLIQGFA 143 Query: 142 VGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGW 201 +GGE G S + L E + RGF+ S+Q+V+ ++ + + L L+ L WGW Sbjct: 144 LGGEIGASTSLLMEYGSDRTRGFYGSWQFVSQGLNTVVGSLLGVALAAMLSPHALESWGW 203 Query: 202 RIPFAIGALCAIVALYLRRGMEETESFAKKEKSKESAMRTLLRHPKELMTVVG------- 254 R+PF IG + +Y+RR ++ET S ++++R K + + G Sbjct: 204 RVPFVIGMAMGPIGVYIRRHLDET--LPLPASSDDASVREAAAVAKPVREIFGTHLGSIA 261 Query: 255 ----LTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKV 310 T+GGT A Y Y+ Y + + M +S + S F+ + P G LSD+ Sbjct: 262 KGVVTTIGGTAANYIVLFYLSTYAIRILHMPMSLALWASWTAAFVTVICSPFAGTLSDRY 321 Query: 311 GRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSI-NAVVKAELF 369 GR+ +L +L L P ++ + T ++A L ++ T++ N V+ E+F Sbjct: 322 GRKRVLWVSRVLLILAVYPAFMVINAVPT-VPVLLAVVAVLGVLVALTAVPNIVMLPEMF 380 Query: 370 PTEIRALGVGLPYALTVSIFGGTAEYIALWFKSI-GMETGYYWYVTACIAVSLLVYVTMK 428 P EIRA G+ + Y L VSIFGG A++ A W + G WY+ C VSLL +K Sbjct: 381 PREIRATGMSIVYCLGVSIFGGFAQFFATWLIQLSGNSLAPAWYLIGCGVVSLLALPFVK 440 Query: 429 DT 430 +T Sbjct: 441 ET 442 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: 574 Number of extensions: 32 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: 448 Length adjustment: 32 Effective length of query: 407 Effective length of database: 416 Effective search space: 169312 Effective search space used: 169312 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