Align ABC transporter permease (characterized, see rationale)
to candidate RR42_RS00195 RR42_RS00195 ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Cup4G11:RR42_RS00195 Length = 309 Score = 189 bits (479), Expect = 9e-53 Identities = 98/313 (31%), Positives = 176/313 (56%), Gaps = 10/313 (3%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGA---LTSWSCIGMM 57 M ++ Q + NGL+LG +YA++A+G+T+ +G++ +I F+HG+ LM+GA L + + + M+ Sbjct: 1 MSVIGQYVFNGLMLGMIYAMVAVGFTLFFGVLDVIKFSHGDTLMVGAFAGLAASTGVLML 60 Query: 58 QGAMPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQT 117 P W+ LL + A V L I K PLR + L L+ + + +++ Sbjct: 61 DIQSP----WIRLLAVVLCAICVTGLLGAAIAKFLILPLRKAAPLNTLLATLMLGTVMRE 116 Query: 118 LAMIIWKP--NYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGR 175 + + N KP+P +LP++ E+G + +++L + + L+ T G Sbjct: 117 SVRLFYPDGSNPKPFPALLPTASIELGSLSLRADNLILLATGIAIIVGVHLLITRTRFGM 176 Query: 176 AMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKA 235 A+RA A++ A LMG+ + V+ TF +G+ +AA+AG+M Y +G L G+ Sbjct: 177 AIRAVAQDGETARLMGINFEAVVLLTFALGSGMAALAGVMNGLYYNEINFNVGLLLGVIG 236 Query: 236 FTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTL 295 F AA+ GG+GN+ GA++GG L ++ +GS + L + S Y D+FAF V+I+++ Sbjct: 237 FAAAILGGLGNIYGAILGGFLFAALQVLGSATLPALIPD-IPSAYKDVFAFAVVIVLMAW 295 Query: 296 RPSGLLGERVADR 308 +P+GL+ E+ ++R Sbjct: 296 KPTGLIAEKSSER 308 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: 246 Number of extensions: 11 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: 309 Length adjustment: 27 Effective length of query: 282 Effective length of database: 282 Effective search space: 79524 Effective search space used: 79524 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 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