Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate AO353_26710 AO353_26710 citrate-proton symporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26710 Length = 434 Score = 241 bits (616), Expect = 2e-68 Identities = 134/413 (32%), Positives = 215/413 (52%), Gaps = 5/413 (1%) Query: 23 SRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPI 82 S++ +IF + GN +E +D++++ ++ Y A AFFP A L+ T A+F GFLMRP+ Sbjct: 14 SKVSAIFRVTSGNFLEQFDFFLFGFYATYIAAAFFPASSEFASLMMTFAVFGAGFLMRPL 73 Query: 83 GGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSV 142 G ++G Y D GR+ L+ ++ +M G+++I L PGYETIG+ AP L++ RLLQG S Sbjct: 74 GAVILGAYIDDVGRRKGLIVTLSIMASGTILIVLVPGYETIGLFAPALVLIGRLLQGFSA 133 Query: 143 GGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWR 202 G E G + YL+E+AT R+GFF+S+Q + ++A + L Q + + DWGWR Sbjct: 134 GAELGGVSVYLAEIATPGRKGFFTSWQSASQQVAIVVAAALGYALNQWMPATVVADWGWR 193 Query: 203 IPFAIGALCAIVALYLRRGMEETESFA--KKEKSKESAMRTLLRHPKELMTVVGLTMGGT 260 IPF +G + LRR +EET F + S TLL++ + ++ + + T Sbjct: 194 IPFFVGCMIVPFIFLLRRSLEETAEFTARRHRPSMRQVFGTLLQNWQIVIAGMLMVALTT 253 Query: 261 LAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPILIAFG 320 AFY T Y + + +S SD+ ++ C P+ G LSD++GRRP+L+A Sbjct: 254 TAFYLITVYAPTFGKTVLHLSTSDALLVTLLVGVSNFCWLPLGGALSDRIGRRPVLVAMT 313 Query: 321 ILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGVGL 380 +L P LT L ++ +++ I Y E+ P E+R G L Sbjct: 314 LLTLATAYPALTYLVQAPSFINMLLVLLWLSFIYGLYNGAMVAALTEIMPVEVRVAGFSL 373 Query: 381 PYALTVSIFGGTAEYIA---LWFKSIGMETGYYWYVTACIAVSLLVYVTMKDT 430 Y+L ++FGG I+ + + GY+ A A+ +Y+ + T Sbjct: 374 AYSLATAVFGGFTPAISTFLIQYSGDKAAPGYWMSFAALCALCATLYLYRRST 426 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: 545 Number of extensions: 34 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: 434 Length adjustment: 32 Effective length of query: 407 Effective length of database: 402 Effective search space: 163614 Effective search space used: 163614 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