Align Alpha-ketoglutarate permease (characterized)
to candidate PP_4461 PP_4461 Major facilitator family transporter
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__Putida:PP_4461 Length = 430 Score = 236 bits (603), Expect = 8e-67 Identities = 154/423 (36%), Positives = 230/423 (54%), Gaps = 22/423 (5%) Query: 12 LTSSDTRRRIW-AIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFA 70 +T + + R+ W A+ + SGNL+E +DF VY+F + A +FFP+ + TT LLQT + Sbjct: 1 MTKTISTRKTWFAVATSGSGNLLEVYDFAVYAFFATTIAKLFFPNVDETTSLLQTFAAYG 60 Query: 71 AGFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLA 130 AGF+ RP+G ++ GRI DK GRK +MLL++ M GS+ I +P YETIG AP LL++ Sbjct: 61 AGFIARPLGSYVIGRIGDKRGRKPAMLLTIICMAIGSIGIGLIPTYETIGVGAPILLVML 120 Query: 131 RLFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVV-VVLQHTMED 189 R QG + GGE+GTSA+Y+ E + GRKGF+ SFQ V+ GG LLA LV +L ED Sbjct: 121 RCLQGFAAGGEWGTSASYIVEWSPAGRKGFFGSFQSVSSSGGALLASLVASALLLIPAED 180 Query: 190 AALREWGWRIPF-ALGAVLAVVALWLRRQLDETSQQETRALKEAGSLKGLWRNRRAFIMV 248 L +WGWR+PF A G + +L+LR +ET + + + + +++ Sbjct: 181 --LLDWGWRVPFIAGGLAIFAFSLFLRAHAEETPEYVNSKAEVVNP-----TDSKPYVLG 233 Query: 249 L---GFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGALSDK 305 L GFT + Y + YM Y N AG+ A AL + + + P+ GALSD+ Sbjct: 234 LQAFGFTIFWTTLSYLVSAYMVTYTQNHAGLTRTEALISSNIALLLQITLIPVAGALSDR 293 Query: 306 IGRRTSML--CFGSLAAIFTVPILSALQNVSSPYAAFGLVMCALLIVSFYTSISGILKAE 363 GR+ +L C G+ A PIL+ + +S + L C + + Y+ E Sbjct: 294 FGRKPLLLLACLGT--ATLAYPILNLMSGGASFHQVVMLQCCLSALFAMYSGPGPATICE 351 Query: 364 MFPAQVRALGVGLSYAVANAIFGGSAEYVA---LSLKSIGMETAFFWYVTLMAVVAFLVS 420 +FP ++R + + Y +A FGG A ++ +S+ I AF + AVV+ LV Sbjct: 352 IFPTRLRNTWMTVGYTLAVCCFGGFAPLISTWLISVTKIAASPAFL--LIPAAVVSALVI 409 Query: 421 LML 423 L L Sbjct: 410 LKL 412 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: 486 Number of extensions: 29 Number of successful extensions: 5 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: 430 Length adjustment: 32 Effective length of query: 400 Effective length of database: 398 Effective search space: 159200 Effective search space used: 159200 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