Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_068462410.1 APY04_RS10560 branched-chain amino acid transporter permease subunit LivH
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_001541235.1:WP_068462410.1 Length = 304 Score = 371 bits (953), Expect = e-107 Identities = 186/304 (61%), Positives = 240/304 (78%), Gaps = 3/304 (0%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGS- 59 MEYF+QQLINGL+LG+IYGLIAIGYTMV+GIIGM+NFAHG+++MI AF+ALI + + Sbjct: 1 MEYFVQQLINGLTLGSIYGLIAIGYTMVFGIIGMVNFAHGDVFMISAFIALILLILLTQF 60 Query: 60 LGITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQ 119 LG+T + LALL++LVA M TA++ W +ERIAYRPL S RLAPLISAIGM+IFL N+VQ Sbjct: 61 LGVTSIGLALLIVLVAGMFLTALWSWVIERIAYRPLAGSFRLAPLISAIGMAIFLLNFVQ 120 Query: 120 ILQGARSKPLQPILPGNLTLM--DGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQ 177 + QG R+K IL +T+ +G+V++S + ++T L+ F ++ +T LGRAQ Sbjct: 121 VTQGPRNKASPSILNNVMTIPMGNGSVTISERQALIFIVTAILLLAFWAIVQKTKLGRAQ 180 Query: 178 RACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFT 237 RACEQD++MA LLG+NVDR ISLTFV+G ALA+VAG+M + YGV+ F GF GVKAFT Sbjct: 181 RACEQDRRMAALLGINVDRTISLTFVIGGALASVAGLMFMSYYGVVSFSDGFTPGVKAFT 240 Query: 238 AAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPE 297 AAVLGGIGSLPGA++GG++IGLIE WS Y ++KDVA F+IL +VLIF P+GLLGRP+ Sbjct: 241 AAVLGGIGSLPGAVIGGLLIGLIETMWSAYFSIDYKDVAAFSILAIVLIFMPSGLLGRPD 300 Query: 298 IEKV 301 +EKV Sbjct: 301 VEKV 304 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: 410 Number of extensions: 19 Number of successful extensions: 3 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: 304 Length adjustment: 27 Effective length of query: 274 Effective length of database: 277 Effective search space: 75898 Effective search space used: 75898 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 24 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