Align ABC transporter permease (characterized, see rationale)
to candidate WP_028997559.1 H537_RS0108425 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000430725.1:WP_028997559.1 Length = 293 Score = 159 bits (402), Expect = 7e-44 Identities = 95/304 (31%), Positives = 170/304 (55%), Gaps = 20/304 (6%) Query: 3 ILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMP 62 +L QQ+IN L LG +YAL ALG+T+V+G++ +IN AHG + +GA + + + Q ++P Sbjct: 1 MLEQQLINALSLGCVYALFALGFTLVFGVLGVINLAHGAMFTVGAYA--ALVFVEQWSLP 58 Query: 63 GAPGWVILLLATIIACVVAATLNFVIEKVAYRPLR--SSPRLAPLITAIGMSILLQTLAM 120 L L+ ++A +++ +I+++ R LR ++P L P+IT IG+ I + + Sbjct: 59 -------LWLSALLAALLSGLFGLLIDRLVLRRLRENNAPHLIPMITTIGIGIAVTSTMQ 111 Query: 121 IIWKPNYKPYP-TMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 ++ + +P ++P + ++GG +T ++ I+ ++ +A L+ + T LGRA+RA Sbjct: 112 GLFGAENRRFPQEVVPDAALDLGGLHLTVLELGIILLSFALMAVLLLGIQRTQLGRALRA 171 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 AE+P+ A L+G+ + + T + A L +AG++ + MG K Sbjct: 172 IAESPKSAWLLGINVEGLFMLTSFVAAGLGGLAGVLIGLSSNAVFPLMGQPMLHKGIAVI 231 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299 + GG+G++ GA++GG+ LG E + YI GS D AF +L +IL +RP+G Sbjct: 232 ILGGMGDIRGALLGGLFLGFAEVMSVAYI--------GSTMRDAVAFGLLYLILLVRPTG 283 Query: 300 LLGE 303 L G+ Sbjct: 284 LFGK 287 Lambda K H 0.327 0.142 0.419 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: 206 Number of extensions: 15 Number of successful extensions: 4 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: 309 Length of database: 293 Length adjustment: 27 Effective length of query: 282 Effective length of database: 266 Effective search space: 75012 Effective search space used: 75012 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: 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