Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate CA265_RS22390 CA265_RS22390 alpha-ketoglutarate transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Pedo557:CA265_RS22390 Length = 428 Score = 206 bits (524), Expect = 1e-57 Identities = 134/426 (31%), Positives = 218/426 (51%), Gaps = 27/426 (6%) Query: 15 KVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAI 74 K IF S G ++EWYD+Y + A A + F+ P ++ G FAVGFL+RP G Sbjct: 14 KSIFGGSVGNLVEWYDWYTYSAFALYFSPAFFPNSNPTAQLLDTAGIFAVGFLMRPIGGW 73 Query: 75 VFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQ 134 +FG I D +GRK + +++ IM + +IGL P +G A ++LI R++QGL+ GG+ Sbjct: 74 LFGSIADKLGRKRSMTLSVLIMAIGSLIIGLTPGYKQIGIAAPLLLIFARLIQGLSTGGE 133 Query: 135 YGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGV-ILITRISLGEADFNEWGWRLP 193 YG +AT+++E A + RGFY+S+ T G L++LG+ +++ L A+ +EWGWR+P Sbjct: 134 YGTSATYLSEMATKKHRGFYSSFQYVTLIGGQLLALGIQLILQNWLLTPAELHEWGWRIP 193 Query: 194 FMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATM 253 F +L ++L++RR + E+ F+ K+T A K + P + + G T+ Sbjct: 194 FFIGAILSFIALYLRRHIDETSAFKS-KNT-ADKKGGIAVLMKYPKE----VFTVVGLTL 247 Query: 254 GQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRKKVML 313 G + +YT Y +L + S + +LL+ + FG LSD+IGRK +++ Sbjct: 248 GGTIAFYTFSTYMQKFLVNTVHLSKETSTTLSFISLLVFVVLQPLFGLLSDKIGRKPLLI 307 Query: 314 SGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYGPIA 373 +L L YPI +A + N I+ LL+ +I V+ A Sbjct: 308 GFGVLGTLCTYPILTGLAGES---------------NTTIIFLLMIGALIIVSGYTSINA 352 Query: 374 AFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIAGICL 433 ELFP +IR + LPY + +FGG L N G++ W+ + G C+ Sbjct: 353 VVKAELFPAEIRALGVGLPYALTVAIFGGTAEYFALWFKN-IGHENYFYWY---VTG-CI 407 Query: 434 VVGFLL 439 ++ +L Sbjct: 408 LISLIL 413 Score = 42.4 bits (98), Expect = 3e-08 Identities = 51/183 (27%), Positives = 84/183 (45%), Gaps = 26/183 (14%) Query: 240 NLRWVLIALFGATMGQGVV---WYTGQFYALFYLQKIF-----NTPLIDSNLIVGAALLL 291 ++ + L ++FG ++G V WYT +AL++ F L+D+ I L+ Sbjct: 8 DVEYRLKSIFGGSVGNLVEWYDWYTYSAFALYFSPAFFPNSNPTAQLLDTAGIFAVGFLM 67 Query: 292 SMPFFVFFGSLSDRIGRKKVM-LSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGY- 349 FGS++D++GRK+ M LS +++A+ + I GL PG + IG Sbjct: 68 RPIGGWLFGSIADKLGRKRSMTLSVLIMAIGSL--IIGL-------TPG----YKQIGIA 114 Query: 350 NPVILGLLVFIQVIYVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGL 409 P++L IQ + YG A +L E+ K R S Y + GG + +G+ Sbjct: 115 APLLLIFARLIQGLSTGGEYGTSATYLSEMATKKHRGFYSSFQYVT---LIGGQLLALGI 171 Query: 410 ILI 412 LI Sbjct: 172 QLI 174 Lambda K H 0.328 0.144 0.450 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: 616 Number of extensions: 43 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 468 Length of database: 428 Length adjustment: 33 Effective length of query: 435 Effective length of database: 395 Effective search space: 171825 Effective search space used: 171825 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 (21.7 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