Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate RR42_RS33875 RR42_RS33875 alpha-ketoglutarate permease
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__Cup4G11:RR42_RS33875 Length = 436 Score = 601 bits (1549), Expect = e-176 Identities = 302/424 (71%), Positives = 355/424 (83%), Gaps = 3/424 (0%) Query: 10 PLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAGVFA 69 P S + RKRI+AI+ ASSGNLVEWFDFYVY+FCAIYFAP+FFPK DPT+QLLNTAGVFA Sbjct: 12 PPSPEDIRKRIYAIVAASSGNLVEWFDFYVYAFCAIYFAPSFFPKADPTAQLLNTAGVFA 71 Query: 70 AGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALLLLA 129 AGFLMRPIGGWLFGRIAD+HGRKTSMLISVLMMC GSL +A +PTY IG WAPALLLLA Sbjct: 72 AGFLMRPIGGWLFGRIADRHGRKTSMLISVLMMCFGSLLIACLPTYGAIGNWAPALLLLA 131 Query: 130 RLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWLTKA 189 RL QGLSVGGEYGT+ATYMSE+A GRRGFF+SFQYVTLIGGQLLAVLV+ +QQ L + Sbjct: 132 RLLQGLSVGGEYGTTATYMSEIALKGRRGFFSSFQYVTLIGGQLLAVLVVVVLQQLLDEG 191 Query: 190 ELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQ-HKRAFLNVV 248 +L +WGWRVPFV+GA+ A+VA+ LR +L ETSSA R+ K+AG+L L + HK AFL V+ Sbjct: 192 QLRSWGWRVPFVIGALTAVVALALRRTLRETSSAATRRNKEAGSLTALFRHHKAAFLTVL 251 Query: 249 GFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGAISDKIGRR 308 G+TAGGSL+FYTFTTYMQKYLVN+AGM K A+ VMTG LFVYM +QP+FGA+SD+IGRR Sbjct: 252 GYTAGGSLIFYTFTTYMQKYLVNSAGMSIKTASTVMTGCLFVYMCMQPLFGALSDRIGRR 311 Query: 309 NSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTSISGLIKAEMFPPEV 368 ++ML F G T P+L L+ VSSP A AL +AL IVS YTSISG++KAEMFPPEV Sbjct: 312 SNMLAFGALGTAATVPLLSALQIVSSPLAAFALISIALAIVSLYTSISGIVKAEMFPPEV 371 Query: 369 RALGVGLSYAVGNAIFGGSAEFVALSLKSAGIESAFYWYVSALCLVALIISLRMPDPQRD 428 RALGVGL+YA+ NAIFGGSAE+VAL+LKSAG +SAFYWYV+A+ +A +SLR+P R Sbjct: 372 RALGVGLAYAISNAIFGGSAEYVALALKSAGHQSAFYWYVTAMMALAFGVSLRLPRQAR- 430 Query: 429 GHLK 432 HL+ Sbjct: 431 -HLR 433 Lambda K H 0.325 0.138 0.418 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: 738 Number of extensions: 32 Number of successful extensions: 4 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: 457 Length of database: 436 Length adjustment: 33 Effective length of query: 424 Effective length of database: 403 Effective search space: 170872 Effective search space used: 170872 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 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