Align Alpha-ketoglutarate permease (characterized)
to candidate RR42_RS27250 RR42_RS27250 citrate-proton symporter
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__Cup4G11:RR42_RS27250 Length = 428 Score = 235 bits (599), Expect = 2e-66 Identities = 141/419 (33%), Positives = 224/419 (53%), Gaps = 17/419 (4%) Query: 20 RIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAAGFLMRPIG 79 ++ A++ +SGN +E FDF+++ F + Y AH FFPS + L+ T VF AGFLMRP+G Sbjct: 11 KLGAVLRVTSGNFLEQFDFFLFGFYATYIAHTFFPSNSEFASLMLTFAVFGAGFLMRPLG 70 Query: 80 GWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLARLFQGLSVG 139 L G D+ GR+K +++++ +M G+++IA +PGY +IG AP L+L+ RL QG S G Sbjct: 71 AILLGAYIDEVGRRKGLIVTLSLMASGTILIALVPGYASIGVLAPVLVLIGRLLQGFSAG 130 Query: 140 GEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVLQHTMEDAALREWGWRI 199 E G + Y++E+A G KGFY ++Q + ++A + L + + L WGWRI Sbjct: 131 AELGGVSVYLAEMATPGHKGFYTAWQSASQQIAIVVAAGLGFGLNYWLTTDELGAWGWRI 190 Query: 200 PFALGAVLAVVALWLRRQLDETSQQETR----ALKEA-GSLKGLWRNRRAFIMVLGFTAA 254 PF +G ++ LRR L ET TR + +E S+ G WR A ++++ T Sbjct: 191 PFFIGCLIVPFLFVLRRSLQETEAFRTRRHHPSTREVFDSMLGNWRTVLAGMLLVAMT-- 248 Query: 255 GSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGALSDKIGRRTSMLC 314 + FY T Y + + + G+ + P+ GALSD+IGRR +L Sbjct: 249 -TTTFYLITVYTPTFGKTVLKLSTADSLGVTLCVGISNFIWLPIGGALSDRIGRRPILLA 307 Query: 315 FGSLAAIFTVPILSALQNVSSPYAAFGLVMCALLIVSF----YTSISGILKAEMFPAQVR 370 ++A + P LS L S FG ++ LL +SF Y + E+ P +VR Sbjct: 308 ISAIALVTAYPALSWLAGAPS----FGRMLIVLLWLSFLFGMYNGAMVVALTEVMPVEVR 363 Query: 371 ALGVGLSYAVANAIFGGSAEYVALSLKSI-GMETAFFWYVTLMAVVAFLVSLMLHRKGK 428 G L+Y++A A+FGG V+ L + G + A ++++ A L +L+L+RK + Sbjct: 364 VAGFSLAYSLATAVFGGFTPAVSTYLIEVTGDKAAPGYWMSFAAACGLLATLILYRKAR 422 Lambda K H 0.328 0.138 0.419 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: 511 Number of extensions: 26 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: 432 Length of database: 428 Length adjustment: 32 Effective length of query: 400 Effective length of database: 396 Effective search space: 158400 Effective search space used: 158400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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