Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate AO353_13340 AO353_13340 amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__pseudo3_N2E3:AO353_13340 Length = 377 Score = 337 bits (863), Expect = 4e-97 Identities = 174/362 (48%), Positives = 241/362 (66%), Gaps = 4/362 (1%) Query: 9 VAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQKLKL 68 +AVAA +S +AD+ + AGP+TG A+FG Q KG + A INA GG+ G+K+ L Sbjct: 13 LAVAAALGVSSFVQADVKLGVAGPMTGPSASFGLQYMKGAQAAADAINAKGGINGEKIVL 72 Query: 69 EVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTNPKL 128 GDDAC+PKQAVAVAN++ + V V GHFCS S+IPAS+VY++ G++ I+P STNP + Sbjct: 73 VQGDDACEPKQAVAVANKMVQDKVIGVVGHFCSSSTIPASEVYSDAGIIAITPGSTNPTV 132 Query: 129 TEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALNAGG 188 TE+ L + R+CGRDDQQG +AG Y+++ KGK VA+++DK YGKGLAD T K L A G Sbjct: 133 TERGLPAMMRMCGRDDQQGIVAGNYIVDVLKGKKVAVINDKDTYGKGLADATAKQLTARG 192 Query: 189 QKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGL-NAPIVSG 247 K + E T GEKD+SAL++K++ DV+Y GG H EAG L Q+++QGL + +S Sbjct: 193 VKPVLEEGLTRGEKDFSALITKVRSVGADVLYFGGLHPEAGPLVHQLREQGLKDVKFMSD 252 Query: 248 DALVTNEYWAITG--PAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEGYTLYTYAAL 305 D +VT+E G P + MTFG DPR +P++K V+ FRK+GYEPEGYTLY YA++ Sbjct: 253 DGIVTDEMVTTAGGAPYVDGVYMTFGADPRLIPDSKAVVDTFRKSGYEPEGYTLYAYASV 312 Query: 306 QIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWN-NGQYAQ 364 Q A A S + A L+ + TV+GK +D+KGD+ YV Y+W+ G+Y Q Sbjct: 313 QALAAGFNGAKSNKGEEAAKWLKAHPVETVMGKKEWDSKGDLKISDYVVYQWDAAGKYHQ 372 Query: 365 VK 366 ++ Sbjct: 373 LE 374 Lambda K H 0.312 0.129 0.366 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: 417 Number of extensions: 17 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: 366 Length of database: 377 Length adjustment: 30 Effective length of query: 336 Effective length of database: 347 Effective search space: 116592 Effective search space used: 116592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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