Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_042445631.1 AZL_RS25715 C4-dicarboxylate ABC transporter
Query= reanno::psRCH2:GFF85 (317 letters) >NCBI__GCF_000010725.1:WP_042445631.1 Length = 320 Score = 385 bits (988), Expect = e-112 Identities = 194/315 (61%), Positives = 237/315 (75%), Gaps = 1/315 (0%) Query: 3 LTKRLGLLAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNK-IDGAKTSV 61 +T+R+ L AA + A TFI +LTGGTSGVYYP+GVALS Y K + GAK + Sbjct: 6 VTRRILTLCMAAGIGLAALPARAETFITVLTGGTSGVYYPLGVALSNVYGKALPGAKVTA 65 Query: 62 QATKASVENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQI 121 QATKASVENLNLLQAGRGE+ F+LGDS+ DAW G E+ GFK L +LR IA Y NYIQ+ Sbjct: 66 QATKASVENLNLLQAGRGEIGFTLGDSLSDAWKGNEEVGFKQKLDKLRTIAAIYPNYIQV 125 Query: 122 VASAESGIKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVEL 181 VA+ ESGI+TL DLKGKR+SVGAPKSGTELNARAIF AAGL YKD + E+LP+ ESV+L Sbjct: 126 VAAKESGIRTLADLKGKRVSVGAPKSGTELNARAIFGAAGLTYKDFAKTEYLPFGESVDL 185 Query: 182 IKNRQLDATLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIESDAYLAGVIPAGTYDGQ 241 IKNRQLDATL S+GLG+AAI+DL+S+ +T V IPA++V K+ AY+ IPAGTY GQ Sbjct: 186 IKNRQLDATLISAGLGVAAIKDLSSSQEITVVSIPADIVRKVGDPAYITETIPAGTYPGQ 245 Query: 242 DADVPTVAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIP 301 VPT A+ N+LV+H VSD+ AY MTK +F+NL AL AH AAK IKL+ P+P Sbjct: 246 TEAVPTAAVRNLLVSHSGVSDDAAYAMTKTLFENLDALAAAHVAAKQIKLDQTATQSPVP 305 Query: 302 LHPGAERFYKEAGVL 316 LHPGA ++YKE G++ Sbjct: 306 LHPGAVKYYKEKGLM 320 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: 313 Number of extensions: 6 Number of successful extensions: 2 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: 320 Length adjustment: 27 Effective length of query: 290 Effective length of database: 293 Effective search space: 84970 Effective search space used: 84970 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: 48 (23.1 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