Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate AZOBR_RS08570 AZOBR_RS08570 C4-dicarboxylate ABC transporter
Query= reanno::psRCH2:GFF85 (317 letters) >FitnessBrowser__azobra:AZOBR_RS08570 Length = 312 Score = 387 bits (995), Expect = e-112 Identities = 196/308 (63%), Positives = 237/308 (76%), Gaps = 1/308 (0%) Query: 10 LAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNK-IDGAKTSVQATKASV 68 LAA + A F+ +LTGGTSGVYYP+GVALS Y K I GAK +VQATKASV Sbjct: 5 LAAVGVCMLTALPAQAEQFVTVLTGGTSGVYYPLGVALSGIYGKAIPGAKVTVQATKASV 64 Query: 69 ENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASAESG 128 ENLNLLQ+ RGE+AFSLGDS+ AW G E+AGFK L +LR +A Y NYIQIVAS +SG Sbjct: 65 ENLNLLQSERGEIAFSLGDSLSGAWKGDEEAGFKTKLTKLRTVAAIYPNYIQIVASKDSG 124 Query: 129 IKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNRQLD 188 +KTL DLKGKR+SVGAPKSGTELNARAIF AAGL YKD + E+LP+AESV+LIKNRQLD Sbjct: 125 VKTLADLKGKRVSVGAPKSGTELNARAIFAAAGLGYKDFAKTEYLPFAESVDLIKNRQLD 184 Query: 189 ATLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIESDAYLAGVIPAGTYDGQDADVPTV 248 ATL S+GLG+AAI+DLA++ +T V IPA+V++K+ AY+A IPA +Y GQ VPT Sbjct: 185 ATLISAGLGVAAIKDLATSQDITIVSIPADVIQKVGDPAYIAETIPANSYSGQSEPVPTA 244 Query: 249 AITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIPLHPGAER 308 A+ N+LVTH VSD+ Y MTK MF+NL A+G AH+AAK IKL+ T P+PLHPGAE+ Sbjct: 245 AVRNLLVTHAGVSDDAVYAMTKAMFENLDAMGAAHAAAKQIKLDATTIQSPVPLHPGAEK 304 Query: 309 FYKEAGVL 316 FYKE G++ Sbjct: 305 FYKEKGLM 312 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: 334 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: 312 Length adjustment: 27 Effective length of query: 290 Effective length of database: 285 Effective search space: 82650 Effective search space used: 82650 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 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