Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_011779173.1 MVAN_RS09735 C4-dicarboxylate ABC transporter substrate-binding protein
Query= reanno::psRCH2:GFF85 (317 letters) >NCBI__GCF_000015305.1:WP_011779173.1 Length = 339 Score = 172 bits (436), Expect = 1e-47 Identities = 108/300 (36%), Positives = 170/300 (56%), Gaps = 8/300 (2%) Query: 20 TAAVAAPTFINILTGGTSGVYYPIGVALSQQYNKI-DG-AKTSVQATKASVENLNLLQAG 77 T V + T ++I TG ++GVY+ +G A ++Q + DG K + T ASV+N+ L G Sbjct: 40 TCEVGSDTRVSIATGNSTGVYFSLGNAYAEQISAATDGRVKATAAETGASVQNIQQLVGG 99 Query: 78 RGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASAESGIKTLDDLKG 137 ++AFSL D+ DA G F + ++AI+ Y NY Q++A +SGI ++ D++G Sbjct: 100 SYQVAFSLADTAADAVEG--KGSFDGEKQPIQAISRIYPNYTQVIARTDSGITSIADMRG 157 Query: 138 KRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNRQLDATLQSSGLG 197 KR+S G+P SGTE+ A + ++AGL+ + + L A++V+ +K+ +DA S GL Sbjct: 158 KRVSTGSPGSGTEVIANRLLQSAGLNPESDVAAQRLDLAKTVDGVKDGSIDALFWSGGLP 217 Query: 198 MAAIRDLASTM--PVTFVEIPAEVVEKIE-SDAYLAGVIPAGTYDGQDADVPTVAITNIL 254 I DL +T V F++I ++ + E S AY GVIPA TY ADV T+ + N+L Sbjct: 218 TPGITDLLTTSRDDVVFIDITPQLPKMSEISPAYEEGVIPAATYQ-LPADVKTIVVPNML 276 Query: 255 VTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIPLHPGAERFYKEAG 314 + E + +A +TK +F+ L AAK I L+NA P+PL+ GA+ + G Sbjct: 277 LVREDLDANLACVLTKTLFEKKPELEQVVGAAKGINLDNARDTDPVPLNRGAQHALDQLG 336 Lambda K H 0.314 0.131 0.359 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: 260 Number of extensions: 20 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: 317 Length of database: 339 Length adjustment: 28 Effective length of query: 289 Effective length of database: 311 Effective search space: 89879 Effective search space used: 89879 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 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