Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate WP_058930128.1 AU252_RS07170 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >NCBI__GCF_001484605.1:WP_058930128.1 Length = 464 Score = 421 bits (1083), Expect = e-122 Identities = 221/438 (50%), Positives = 293/438 (66%), Gaps = 10/438 (2%) Query: 12 AAVPAKEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAA 71 A V ++ T + +I GS GN+VEWYD YVY F+ YF FF D L A Sbjct: 6 AEVQSEAAQTRRAVSNILKGSAGNLVEWYDLYVYTVFAAYFQSHFFNSQDDLQAGLEAMA 65 Query: 72 IFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILL 131 +F+ FLMRP+G W G YADR GRKAAL SV +M GS IA+ P + IGV A ILL Sbjct: 66 VFSTSFLMRPVGAWFFGRYADRKGRKAALTLSVTIMSAGSFAIAILPTTQQIGVWALILL 125 Query: 132 VFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTL 191 + RL+QG SVGGEYGTSATY+SE AT +RRGFFSSFQYVTLI GQ++AL VL++LQ T+ Sbjct: 126 ILVRLVQGFSVGGEYGTSATYMSEAATSKRRGFFSSFQYVTLIGGQMLALLVLVILQNTM 185 Query: 192 TTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETESFAKKEKSKESA---------MRTL 242 L +WGWRIPFAIG + A+V L+LRR MEET S + E +K A M+ L Sbjct: 186 DKGALTEWGWRIPFAIGGVAALVVLWLRRSMEETVSAEQVEAAKVPAVAGVAQPGTMKLL 245 Query: 243 L-RHPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQP 301 +H K L+ +G+T+GGT+AFYTYT ++ K++ +T G++ +D++ I+ LF+FM LQP Sbjct: 246 FTQHWKPLLICIGVTLGGTVAFYTYTNFILKFMNDTSGIAKTDTSVINFWALFIFMLLQP 305 Query: 302 IIGGLSDKVGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSIN 361 + G +SDKVGRRP+L+ FGI G LFT P+L+TL + + AF L++ L+IV GYTSIN Sbjct: 306 VYGIISDKVGRRPLLLWFGITGVLFTWPLLSTLAGTKDPFTAFLLMLGGLLIVGGYTSIN 365 Query: 362 AVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSL 421 A+VKAELFP IRALGVGL YA+ S+FGGT + F+ ++ YVT IA+SL Sbjct: 366 ALVKAELFPASIRALGVGLGYAIANSLFGGTVPLLGAAFQKAERVDLFFTYVTVAIAISL 425 Query: 422 LVYVTMKDTRKHSRIETD 439 +VY+ +K + ++ + Sbjct: 426 VVYIFALKNKKATHLDRE 443 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: 614 Number of extensions: 25 Number of successful extensions: 2 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: 464 Length adjustment: 33 Effective length of query: 406 Effective length of database: 431 Effective search space: 174986 Effective search space used: 174986 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