Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate WP_012385103.1 BIND_RS10755 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >NCBI__GCF_000019845.1:WP_012385103.1 Length = 444 Score = 447 bits (1149), Expect = e-130 Identities = 231/428 (53%), Positives = 300/428 (70%), Gaps = 3/428 (0%) Query: 12 AAVPARERTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAA 71 AA P R K+I GSVGN++EWYD Y Y+AF+LYF FFP + AQ L A+ Sbjct: 13 AADPYDRADVRRRTKAILIGSVGNLIEWYDVYAYSAFALYFGGAFFPSANLVAQQLAAAS 72 Query: 72 IFAVGFLMRPIGGWLMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILL 131 +FA FLMRPIG L G ADR GR+ AL S+ LMCFGSL+IA++P+Y TIG+GAPILL Sbjct: 73 LFAAAFLMRPIGSLLFGYLADRYGRRMALTFSILLMCFGSLLIAVAPTYSTIGIGAPILL 132 Query: 132 VFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQF- 190 FAR+LQGLS GGEYGTSATYL+E++ RRGF+S Y TLI GQL A+ VL++LQ+ Sbjct: 133 AFARILQGLSQGGEYGTSATYLAEVSHPARRGFYSGIWYTTLIGGQLAAIIVLLILQKLV 192 Query: 191 LTTEQLYAWGWRIPFAIGALCAVVALYLRRGMEETESFTKKE--KSKESAMRTLLRHPKE 248 LT EQLYA+GWRIPF IGA A+ ++RR + ET+ F K + K TL R+ K Sbjct: 193 LTPEQLYAFGWRIPFFIGAALALYCFFMRRDLHETDLFKKSQALAEKVGTWTTLRRNWKT 252 Query: 249 LMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSD 308 ++ V+G T GGT AFYTYTTYMQK++ +VG++ ++T I + L + LQP+ G LSD Sbjct: 253 ILYVIGFTAGGTSAFYTYTTYMQKFVKLSVGLTEDETTLIIFGSSTLAVALQPLYGALSD 312 Query: 309 KIGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAEL 368 KIGR+P+L+AFGI+GTLFT P+LTTL T ++ AF LI A I++ YTS +VKAEL Sbjct: 313 KIGRKPMLLAFGIMGTLFTYPLLTTLQTTKSPLVAFLLICAGWGIITPYTSTAVIVKAEL 372 Query: 369 FPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYITMK 428 FPT IRA+GVG PYA+ ++FGGT + +AL FK+ G E ++ Y TACI +SL+ Y + Sbjct: 373 FPTSIRAIGVGFPYAIAAAVFGGTIDSVALSFKNQGHEEWFFLYATACIFMSLIFYCFLP 432 Query: 429 DTRKHSRI 436 D +K SR+ Sbjct: 433 DLKKKSRM 440 Lambda K H 0.326 0.138 0.416 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: 651 Number of extensions: 38 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: 444 Length adjustment: 32 Effective length of query: 407 Effective length of database: 412 Effective search space: 167684 Effective search space used: 167684 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 (21.7 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