Align ABC transporter permease (characterized, see rationale)
to candidate RR42_RS16975 RR42_RS16975 ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Cup4G11:RR42_RS16975 Length = 311 Score = 412 bits (1058), Expect = e-120 Identities = 209/311 (67%), Positives = 257/311 (82%), Gaps = 2/311 (0%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 MDI +QQI+NGLVLGS+YALIALGYTMVYGI+ +INFAHG+VLMIGALT+ S I +Q Sbjct: 1 MDIFIQQIVNGLVLGSIYALIALGYTMVYGILGIINFAHGDVLMIGALTALSAILGLQKF 60 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 PG P W+ L++AT+IA V A L + IE+VAYRPLR++PRLAPLITAIG+SI+LQTLAM Sbjct: 61 FPGLPEWLTLVIATLIAMPVCAALAYTIERVAYRPLRNAPRLAPLITAIGVSIILQTLAM 120 Query: 121 IIWKPNYKPYPTMLPSSPFEIG--GAFITPTQILILGVTAVALASLVYLVNHTNLGRAMR 178 +IW N +P +LPSSP +IG GA IT +I+I+G+ + +A L+ LVN T LGRAMR Sbjct: 121 MIWSRNPLTFPQLLPSSPIDIGSTGATITGKEIVIIGMALMVMAGLLTLVNRTKLGRAMR 180 Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238 ATAEN +VA LMGV P+ VISATF+IGA LAA+AG+M A+NYG A MGF+PGLKAFTA Sbjct: 181 ATAENQKVAGLMGVNPNFVISATFMIGAALAALAGVMMATNYGNAHFYMGFIPGLKAFTA 240 Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298 AV GGIGNLAGA+VGG+LLGLIEA+G+GYIG LT G+ GS+Y D+FAFIVLII+L RPS Sbjct: 241 AVLGGIGNLAGAMVGGMLLGLIEALGAGYIGDLTNGVFGSNYQDVFAFIVLIIVLVFRPS 300 Query: 299 GLLGERVADRA 309 G++GERV++RA Sbjct: 301 GIMGERVSERA 311 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: 319 Number of extensions: 8 Number of successful extensions: 2 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: 311 Length adjustment: 27 Effective length of query: 282 Effective length of database: 284 Effective search space: 80088 Effective search space used: 80088 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