Align Alpha-ketoglutarate permease (characterized)
to candidate HSERO_RS07330 HSERO_RS07330 major facilitator transporter
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__HerbieS:HSERO_RS07330 Length = 432 Score = 228 bits (581), Expect = 3e-64 Identities = 135/422 (31%), Positives = 227/422 (53%), Gaps = 15/422 (3%) Query: 13 TSSDTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAAG 72 T++ ++ ++ +SGN +E FDF++Y F + Y + FFPS N L+ T G F AG Sbjct: 5 TTNAKHSKLSTVLRVTSGNFLEMFDFFLYGFYASYISKTFFPSDNEFVSLILTFGTFGAG 64 Query: 73 FLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLARL 132 FLMRP+G + G D+ GR++ +++++ +M G+L+IA +PGY TIG AP L+L RL Sbjct: 65 FLMRPLGAIILGSYIDRVGRRQGLIVTLAIMAIGTLLIAFVPGYATIGVAAPILVLTGRL 124 Query: 133 FQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVLQHTMEDAAL 192 QG S G E G + Y++E+A G KGFY S+Q + + + L+ ++ ++ + Sbjct: 125 LQGFSAGVELGGVSVYLAEMATPGNKGFYVSWQSASQQAAIMASALIGYLVSQSLSPVQI 184 Query: 193 REWGWRIPFALGAVLAVVALWLRRQLDETSQQETRALKEA-----GSLKGLWRNRRAFIM 247 +WGWRIPF +G ++ +RR L ET + R + S+ W+ A +M Sbjct: 185 SDWGWRIPFFIGCMIVPAIFIIRRSLQETDEFLARKRHPSFGEIMSSIAQNWKIVVAGMM 244 Query: 248 VLGFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGALSDKIG 307 ++ T ++ FY T Y + N + A+ + + P++GALSD++G Sbjct: 245 MVVMT---TVSFYLITVYTPTFGKNVLKLSASDSLIVTFCVGLSNFCWLPIMGALSDRVG 301 Query: 308 RRTSMLCFGSLAAIFTVPILSALQNVSSPYAAFGLVMCALLIVSFYTSISG---ILKAEM 364 RR ++ F L + P++S L S + L++ L + Y S +G + E+ Sbjct: 302 RRPVLVAFTLLTLLTAYPVMSWL---VSDISFKNLLITELWLSFLYASYNGAAVVALTEV 358 Query: 365 FPAQVRALGVGLSYAVANAIFGGSAEYVALSL-KSIGMETAFFWYVTLMAVVAFLVSLML 423 PA VR +G L+Y++A AIFGG V+ L ++ G + A ++++ AV L +L+L Sbjct: 359 MPAHVRTVGFSLAYSLATAIFGGFTPLVSTWLIETSGDKAAPGYWMSFAAVCGLLATLVL 418 Query: 424 HR 425 +R Sbjct: 419 YR 420 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: 493 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 432 Length of database: 432 Length adjustment: 32 Effective length of query: 400 Effective length of database: 400 Effective search space: 160000 Effective search space used: 160000 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