Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_013010475.1 DACET_RS05940 C4-dicarboxylate ABC transporter permease
Query= reanno::psRCH2:GFF84 (674 letters) >NCBI__GCF_000025725.1:WP_013010475.1 Length = 632 Score = 342 bits (878), Expect = 2e-98 Identities = 212/620 (34%), Positives = 340/620 (54%), Gaps = 18/620 (2%) Query: 7 LHASPSEWPRALFYVALLFSI-YQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYPARGNG 65 ++A ++ + +F +A +F + + A PVS++ + +V L+FL Y ++ Sbjct: 1 MYADLKKFEKIIFDIAAVFLVLFYSYAALIKPVSTEYHKGIYVFITYFLIFLVYKSKN-- 58 Query: 66 KPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGI 125 K + + ++L LA Y F DL R+G T D + + +++ E ARR +G Sbjct: 59 KWLRIIDYILILAACVPVLYFMIFFVDLNYRAGAETIMDQWMSVVGVLMGIEVARRAVGS 118 Query: 126 ALPIICALFLAYGLLGEYLPGDLAHRG-YYLDQIVNQLSFGTEGLYGTPTYVSATYIFLF 184 ++ + YG+ G+ +P H G +LD I + +G++G V ATY+ LF Sbjct: 119 VFVLLGGAMILYGVFGDKVPDLFQHSGGNFLDTISVAIFLTNDGVFGIMADVLATYVLLF 178 Query: 185 ILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFT 244 +LFG+FLE++G K F D + GHK GGPAKV+V++SA+ G+I+GS +AN V+TG FT Sbjct: 179 VLFGAFLEKSGAQKFFIDLPLAAVGHKTGGPAKVAVIASAIFGSISGSAIANTVSTGAFT 238 Query: 245 IPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALL 304 IPLMK+ G++P AG VE +S+G MPP+MGA FIMAE VP+ I A+ PAL+ Sbjct: 239 IPLMKKAGFKPHVAGAVEPAASIGGMFMPPIMGAGGFIMAELTEVPYQTIMLVAIFPALM 298 Query: 305 YFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPMFAG 364 YF SVF MVH EAK ++G + S KE W+ ++PLV++ L+ G++P ++ Sbjct: 299 YFFSVFVMVHYEAKLHNIRG--EKSAVSPKQIFKEGWHYVMPLVLITILMIMGKSPGYSA 356 Query: 365 TIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALVAVCW 424 +G+ L+ ++I + VS F + + LG+L A + G + + A L + Sbjct: 357 VVGM-LSCVIITWTRGSKYVSIFTI-----VLLGVLFADSVK-GFDSVNEMSAGLSTLVT 409 Query: 425 F-IKGGRDTLVICLHALVEGARH----AVPVGIACALVGVIIGVVSLTGVASTFAGYILA 479 F R L I L +E +R+ ++ +G ++G+II +++ +G+ TF+ I+ Sbjct: 410 FGFAALRGELRINLKEFIEASRNGTESSLKIGATVGVIGIIISMLTYSGLTLTFSSIIIH 469 Query: 480 VGENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGI 539 + L+L++LL L LVLGMG+P Y+IT+ +A PAL +LGV I +HM V++ Sbjct: 470 LAAGKLWLTILLIALASLVLGMGVPVTAAYLITAVVAVPALTELGVSPIAAHMVVYWLSQ 529 Query: 540 MADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGAT 599 +++TPPV +A FA A IAK + A + A ++ PF+ Y PA M+ G+ Sbjct: 530 DSNITPPVCIAAFAGATIAKANMWLTAFNAFKFAKFLYLGPFLFAYVPAFSMRHYLPGSD 589 Query: 600 LYMLFKAAFAVGLWGAVFTG 619 Y F + AV G Sbjct: 590 SYEWFSPTTITLTFIAVIIG 609 Lambda K H 0.330 0.143 0.445 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: 1155 Number of extensions: 66 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: 674 Length of database: 632 Length adjustment: 38 Effective length of query: 636 Effective length of database: 594 Effective search space: 377784 Effective search space used: 377784 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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