Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate Pf1N1B4_5977 Transporter, MFS superfamily
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5977 Length = 465 Score = 205 bits (522), Expect = 2e-57 Identities = 138/428 (32%), Positives = 220/428 (51%), Gaps = 25/428 (5%) Query: 4 TTQASTPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFC-AIYFAPAFFPKGD-PTSQL 61 T A+TP KR+ A A +G + EW++F++Y A+ F FF + D P + Sbjct: 7 TQSATTPSGL----KRVVA--AAMAGTVAEWYEFFLYGTASALVFGQLFFRQTDSPIDGI 60 Query: 62 LNTAGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAW 121 + ++A GFL RP+GG +FG DK GRK + +S++++ + + +P + IG Sbjct: 61 IAAFALYAVGFLARPLGGLVFGHYGDKFGRKRLLQLSLVVVGITTFLMGCLPGFDQIGYA 120 Query: 122 APALLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFG 181 AP LL+L RL QG + GGE+G + +SE P+ RRGF+AS+ + G L+A + L Sbjct: 121 APVLLVLLRLIQGFAFGGEWGGAILLVSEHCPDNRRGFWASWPQAGVPAGNLVATVALLL 180 Query: 182 MQQWLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAET---SSAGAR----KKKDAGTL 234 + L++ + +AWGWRV F AV L+ ++R+S+ + A AR K++ G + Sbjct: 181 LSSNLSEEQFLAWGWRVAFWFSAVVVLIGYWIRTSVDDAPIFKEAQARQAQIKQQQLGVV 240 Query: 235 KGLLQHKRAFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMIL 294 + L H RA L +G ++++YT T+ YL D +M GA V+ L Sbjct: 241 EVLRHHWRAVLVGIGARFAENILYYTVVTFSITYLKLVVHKDTSEILLLMFGAHLVHFFL 300 Query: 295 QPIFGAISDKIGRR----NSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVS 350 P+ G +SD +GR+ + AF+G VG FP++ D + + MA IL L I S Sbjct: 301 IPLMGYLSDIVGRKPVYLTGAVLTAFWGFVG-FPMM----DTGNNWLIMAAIILGLGIES 355 Query: 351 FYTSISGLIKAEMFPPEVRALGVGLSYAVGNAIFGGSAEFVALSLKSAGIESA-FYWYVS 409 + + AEMFP VR + L Y V G A +A++L + S WY+ Sbjct: 356 MTYAPYSALMAEMFPTHVRYTALSLCYQVAPIFAGSLAPLIAITLLNKYHSSTPIAWYLV 415 Query: 410 ALCLVALI 417 L++++ Sbjct: 416 GAALISIV 423 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: 565 Number of extensions: 36 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: 465 Length adjustment: 33 Effective length of query: 424 Effective length of database: 432 Effective search space: 183168 Effective search space used: 183168 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