Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_084056873.1 B9A12_RS05490 DUF3394 domain-containing protein
Query= reanno::psRCH2:GFF84 (674 letters) >NCBI__GCF_900176285.1:WP_084056873.1 Length = 688 Score = 363 bits (932), Expect = e-104 Identities = 223/657 (33%), Positives = 349/657 (53%), Gaps = 54/657 (8%) Query: 12 SEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP----------A 61 S W A+ V + +S++Q+ A++ + + +RA H+ F LL+V+L +P A Sbjct: 33 SRW--AVPVVGVCWSLFQLSIASWLILDTWFVRAIHLAFGLLIVYLSFPMFKKPRLGIRA 90 Query: 62 RGNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARR 121 + W+LG+ Y + QR G D+VVG TL +L+ EA+RR Sbjct: 91 LSAKDRIPLIDWVLGIVAALAALYVIIDYQGITQRYGAPIPRDIVVGFTLFILLLEASRR 150 Query: 122 VMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYI 181 V+G AL +I +F Y G Y+P +A +G L++ V Q++ TEG+YG P VSAT + Sbjct: 151 VIGPALSLIAVVFTVYAFFGPYMPDVIAFKGVSLNRFVGQMTMSTEGIYGIPLDVSATIV 210 Query: 182 FLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTG 241 FLF+LFG+ LE+AG F A+ L G GGPAK +V++S L G ++GS +AN+VTTG Sbjct: 211 FLFVLFGAMLEKAGAGSFFIQMALSLLGGFKGGPAKAAVLASGLTGLVSGSSIANIVTTG 270 Query: 242 QFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIP 301 FTIPLMKR GY A +E +S Q+ PP+MGA AFI+AE +NVP++++ KAA IP Sbjct: 271 TFTIPLMKRVGYPARKAAAIEVAASTDGQLAPPIMGAAAFIIAEYVNVPYIDVVKAAAIP 330 Query: 302 ALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPM 361 A + ++ ++ H+EA + GL+GLP++E P + +IPLV+L++ L R Sbjct: 331 AFASYAALLYITHIEASKLGLRGLPRNELPPFFRTFVSGLHYIIPLVMLLYELVVLRHSP 390 Query: 362 FAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALVA 421 A A AI ++ ++L+ + ++A L F Q G+ IF +AA Sbjct: 391 EAS----AFNAIWVIALVMLLQHP-----VKAYLAKEPLGPAFKQ-GLADIFSSLAA--- 437 Query: 422 VCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVG 481 GAR+ V V +A A G+I+GVV++ G+ + + Sbjct: 438 ---------------------GARNMVSVAMATAAAGIIVGVVAM-GLGGLINQIVDQLS 475 Query: 482 ENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLG------VPLIVSHMFVF 535 N++L L++T L++GMG+PT YI+ +S+ APA++ +G VPL+ +H+F F Sbjct: 476 GGNIYLLLIITAFASLIIGMGLPTTATYIVMASLTAPAIVTVGGYYGFEVPLMAAHLFCF 535 Query: 536 YFGIMADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQG-G 594 +FGI+AD TPPV LA +AAA IA+ + + I I+PFM ++N L++ G Sbjct: 536 FFGILADDTPPVGLAAYAAAAIARSEPIPTGIQGFMYDIRTAILPFMFIFNHDLILHGIN 595 Query: 595 DWGATLYMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIG 651 W L + A + + G+ +E L M+ ++ +G Sbjct: 596 SWTQGLLIFAMACLGNFAFASATQGWFITRNRFYEVPLLLGVTVIMMRPDAVAGWVG 652 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: 1340 Number of extensions: 72 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: 674 Length of database: 688 Length adjustment: 39 Effective length of query: 635 Effective length of database: 649 Effective search space: 412115 Effective search space used: 412115 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