Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate CA265_RS15560 CA265_RS15560 glutamate/aspartate:proton symporter GltP
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Pedo557:CA265_RS15560 Length = 428 Score = 448 bits (1153), Expect = e-130 Identities = 221/405 (54%), Positives = 305/405 (75%), Gaps = 2/405 (0%) Query: 5 LFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGM 64 +F +L FQVL AI IGI +G ++P K + GF+ LI M+IAP+IF T+V GIA M Sbjct: 10 VFSNLTFQVLLAIIIGIYVGAYFPGFAPTAKLISQGFINLISMLIAPIIFFTIVLGIAHM 69 Query: 65 ESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQA 124 MK VGR G ALLYFEIVST+A+ IGL++ NV++PGAGM DA +A YA+QA Sbjct: 70 GDMKKVGRVGGKALLYFEIVSTVAIAIGLLVANVLKPGAGMIAKAG--DATKIAGYAEQA 127 Query: 125 KDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184 KD F + +IP ++I +FA GNILQ+LLFA+LFG+ L++LG +G + N + S+V Sbjct: 128 KDMNWAEFFLHIIPHNIIASFAEGNILQILLFAILFGYGLNKLGGEGTTVLNAFDKISKV 187 Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244 +F I+ +IMRLAPIGAFG MAF+IG +G+ ++V + +L+ Y+TC LF+ ++L I + Sbjct: 188 LFKIMKLIMRLAPIGAFGGMAFSIGTHGLESIVGMAKLMGSVYLTCFLFIFVILNGICRY 247 Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304 FS++ +++YIR+E+LIVLGTSSSESALP M+ KME +GC KSVVGLVIPTGYSFNLDG Sbjct: 248 YNFSLWAYLKYIRQEILIVLGTSSSESALPSMMQKMEAIGCDKSVVGLVIPTGYSFNLDG 307 Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364 T+IYL MA +F+ Q + + + QIT+L VL+++SKGAAGVTGSGFIVL +TL+A+ + Sbjct: 308 TAIYLAMAVIFLCQVFHVDLTLGQQITVLGVLMITSKGAAGVTGSGFIVLVSTLTALKIM 367 Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKK 409 P+ +++++G+DRFMSEARA+TN++GNGVATIV+AK K+ D +K Sbjct: 368 PIEHISILIGVDRFMSEARAITNVIGNGVATIVIAKSEKQFDEQK 412 Lambda K H 0.327 0.142 0.401 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: 558 Number of extensions: 23 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: 428 Length of database: 428 Length adjustment: 32 Effective length of query: 396 Effective length of database: 396 Effective search space: 156816 Effective search space used: 156816 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 (21.7 bits) S2: 51 (24.3 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