Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate SMc01869 SMc01869 transport transmembrane protein
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >FitnessBrowser__Smeli:SMc01869 Length = 436 Score = 206 bits (523), Expect = 2e-57 Identities = 136/415 (32%), Positives = 214/415 (51%), Gaps = 23/415 (5%) Query: 23 SRIKSIFSGSVGNMVEWYDWYVYA-AFSLYFAKVFFPKGDTTAQLLNTAAIFAVGFLMRP 81 S + +F+ VG +E++D+YVYA A + F +FFP D T+ +L + A F++ F RP Sbjct: 22 SPARVLFASLVGTTIEFFDFYVYATAAVIIFPHLFFPAADPTSAMLQSLATFSIAFFARP 81 Query: 82 IGGWLMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLLQGLS 141 +G + G + DR GRK L+A++ M +++I L P+Y TIGV AP+LL R QGL Sbjct: 82 LGAVIFGHFGDRIGRKATLVAALMTMGISTVVIGLLPTYSTIGVVAPLLLALCRFGQGLG 141 Query: 142 VGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQFLTTEQLYAWGW 201 +GGE+G + +E A + +R +++ F + G +++ G ++L + ++ E AWGW Sbjct: 142 LGGEWGGAVLLATENAPEGKRSWYAMFPQLGAPIGFILSAGTFLILGEVMSEEAFLAWGW 201 Query: 202 RIPFAIGALCAVVALYLRRGMEETESFTK---KEKSKESAMRTLLR-HPKELMTVVGLTM 257 R+PF L +V LY+R + ET F K K + E + + R H + L+ + + Sbjct: 202 RVPFIASVLLVIVGLYVRLKITETPEFQKAIDKHERVEVPVAAIFRSHKRSLVLGTFVAL 261 Query: 258 GGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSDKIGRRPIL- 316 + FY T + + +G S + + F + PV G LSD+ GRR +L Sbjct: 262 ATFVLFYLMTVFSLSWGTTKLGYSREQFLLVQMTGVVFFGLMIPVSGILSDRFGRRLVLV 321 Query: 317 ---IAFGILGTLFTVPILTTLHTIQTWWGAF-FLIMAALIIVSGYTSINAVVKAELFPTE 372 I G+ G LF P+L++ GAF F I+ ++ Y I A + A FPT Sbjct: 322 LTTIGIGVFG-LFMAPLLSS-----GLGGAFVFSIVGLGLMGLTYGPIGAALAAP-FPTA 374 Query: 373 IRALGVGLPYALTVSIFGGT-AEYIALWFK---SIGMETGYYWYVTACIAVSLLV 423 +R G + + L IFG + A YIA W S+G GYY A I + L+ Sbjct: 375 VRYTGASMTFNL-AGIFGASLAPYIATWLATNYSLG-HVGYYLLAAASITLVCLL 427 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: 553 Number of extensions: 25 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: 436 Length adjustment: 32 Effective length of query: 407 Effective length of database: 404 Effective search space: 164428 Effective search space used: 164428 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 17 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