Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__psRCH2:GFF3786 Length = 295 Score = 145 bits (365), Expect = 1e-39 Identities = 99/299 (33%), Positives = 166/299 (55%), Gaps = 18/299 (6%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 ++ FL QL+ GL G+ Y ++++G +++G++ +INFAHG YMIGAF +L + +L Sbjct: 9 IQAFLGQLLIGLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAG---YLLLATL 65 Query: 61 GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQI 120 GI + P +L ++ L +AV +ER+A L + L L+ G+++ L+ + Sbjct: 66 GIGYWPALILAPIIVG-LCSAV----IERLALSRLYNLDHLYSLLFTFGLALALEGAFRY 120 Query: 121 LQGARSKP--LQPILPG--NLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRA 176 G+ +P + L G NL M ++V LA++VI IA LI +T LG Sbjct: 121 FYGSSGQPYAVPKELAGGYNLGFMFLPKYRAWVVLASLVICIASWL----LIEKTKLGAY 176 Query: 177 QRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAF 236 RA ++ + G+NV +++ T+ MGAALA +AGM+ IY V +G + F Sbjct: 177 LRAATENPTLVRTFGINVPLLLTFTYGMGAALAGLAGMLAAPIYQVSPL-MGSNLIIVVF 235 Query: 237 TAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGR 295 V+GG+GS+ GA++ G ++G++E + E ++ F I+ +VL+ RP GL+GR Sbjct: 236 AVVVVGGMGSILGAIITGYMLGILEGLTKVFY-PEASNIVIFVIMAIVLLVRPAGLMGR 293 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: 320 Number of extensions: 15 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: 295 Length adjustment: 26 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 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