Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate GFF950 HP15_929 branched-chain amino acid ABC transporter, permease protein
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Marino:GFF950 Length = 315 Score = 138 bits (348), Expect = 1e-37 Identities = 90/292 (30%), Positives = 152/292 (52%), Gaps = 16/292 (5%) Query: 7 QLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGIT-WV 65 QL+ G+ GA Y L+++G +++G++ +INFAHG +YM+G A+ T L LG+ WV Sbjct: 35 QLLIGIINGAFYALLSLGLAVIFGLLKIINFAHGAMYMLG---AMTTVLMFDYLGVNYWV 91 Query: 66 PLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGAR 125 L L +LV + +G +E R + + L+ G+++ + + G Sbjct: 92 ALLLAPLLVGA------FGVAIEYFLLRRIAGQDHIYSLLLTFGVALIISGVLVNWFGVS 145 Query: 126 S--KPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQD 183 + + G + L G + + Y R IV + + + +I +T LG RA +D Sbjct: 146 GLRYTMPDMFKGGVNL--GFMFMPYYRAWVIVAALVVCFATWFVIEKTKLGAYLRAGTED 203 Query: 184 KKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGG 243 ++ G+NV +ISLT+ G ALAA AG++ IY V +G + F V+GG Sbjct: 204 SQLMQGFGINVPLLISLTYGFGVALAAFAGVLAAPIYSVTP-VMGSATLITVFAVVVIGG 262 Query: 244 IGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGR 295 +GS+ GA++ G+++G+IE + F ++VLVL+FRP+GL G+ Sbjct: 263 MGSIGGAIITGILMGVIEGLTKTFYPPA-SSAIIFLVMVLVLMFRPSGLFGK 313 Lambda K H 0.329 0.144 0.425 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: 339 Number of extensions: 24 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: 301 Length of database: 315 Length adjustment: 27 Effective length of query: 274 Effective length of database: 288 Effective search space: 78912 Effective search space used: 78912 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 (21.8 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