Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate WP_057507967.1 ABB28_RS07090 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >NCBI__GCF_001431535.1:WP_057507967.1 Length = 445 Score = 335 bits (859), Expect = 2e-96 Identities = 191/424 (45%), Positives = 259/424 (61%), Gaps = 10/424 (2%) Query: 11 SAAVPAKEKTTASR-IKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNT 69 +AA P E+ R + + GS GN+VEWYD YVY+ F+ YF FF D + + Sbjct: 7 TAASPVSERAALKRSVSNTLKGSAGNLVEWYDVYVYSVFAKYFESQFFSADDKNSTMY-I 65 Query: 70 AAIFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPI 129 IFA FLMRPIG W G +ADR GR+ AL SV +M S +IA++P +IG+ A + Sbjct: 66 WGIFAATFLMRPIGAWYFGRFADRYGRRLALTVSVSVMAACSFLIAIAPTAASIGIWAAV 125 Query: 130 LLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQ 189 +L+FARLLQG + GGEYG SATY+SE A RGF SSF YVTL+ G ++A VL+V+ Sbjct: 126 ILLFARLLQGFATGGEYGASATYMSEAAVPGWRGFLSSFHYVTLVGGHVLAQAVLLVMLL 185 Query: 190 TLTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETES-----FAKKEKSKES-AMRTL- 242 + T + +WGWR+ F IG + A+V +LRR M+E+ S AK K+K S +MR L Sbjct: 186 SWDTSHVSEWGWRVAFGIGGIGALVVFWLRRTMDESLSAESIEAAKDGKAKASGSMRELF 245 Query: 243 LRHPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNT-VGMSISDSTTISAATLFLFMCLQP 301 + + L+ +T GGT+AFYTYT K + G + T I+ L M LQP Sbjct: 246 VNQWRPLLLCFLITAGGTVAFYTYTINGPKMIQTAFAGDDVITGTWINLGVLTFLMLLQP 305 Query: 302 IIGGLSDKVGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSIN 361 + G LSD++GR+ +L+ FG+ G L+T ++T L + AF ++ +I++GYTSIN Sbjct: 306 LGGLLSDRIGRKSLLVFFGVGGVLYTWYLVTALPQQTSALSAFLILATGFVILTGYTSIN 365 Query: 362 AVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSL 421 AVVKAELFP IRALGVGL YAL S+FGGTA + G + Y+TA IAVSL Sbjct: 366 AVVKAELFPAHIRALGVGLGYALANSLFGGTAPLLYQGALKAGRVDEFVIYITAVIAVSL 425 Query: 422 LVYV 425 +VY+ Sbjct: 426 VVYI 429 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: 597 Number of extensions: 34 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: 445 Length adjustment: 32 Effective length of query: 407 Effective length of database: 413 Effective search space: 168091 Effective search space used: 168091 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