Align ABC transporter permease (characterized, see rationale)
to candidate YP_004139781.1 Mesci_0559 inner-membrane translocator
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000185905.1:YP_004139781.1 Length = 300 Score = 202 bits (514), Expect = 8e-57 Identities = 115/305 (37%), Positives = 183/305 (60%), Gaps = 20/305 (6%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 +D +LQQI+N + LGS+YAL+A+G ++V+G+++L NFAHG+V+M+GA +G+ Sbjct: 4 LDYILQQIVNAVSLGSLYALVAVGLSIVFGVLKLTNFAHGDVMMVGAFGVALLVGI---- 59 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 G P +A I AA F+IE++AYRP+R +P +A L+T++ ++ +++ + + Sbjct: 60 --GVP----FPVAVICGIAAAAVAGFLIERIAYRPIRDAPDVARLLTSLAVTYIIENVGI 113 Query: 121 IIW--KPNYKPYPTMLPSSPFEIGGAFITPTQI--LILGVTAVALASLVYLVNHTNLGRA 176 +++ P P P +L +S +E+ IT T I L + +T V+L L + + T G Sbjct: 114 LVFTSSPRNFPLPDILNTS-WEMSNGAITFTSINLLTIALTFVSLLLLGWFITRTTTGLG 172 Query: 177 MRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAF 236 MRA AE+ A L+G+ + +I FI+ + A +AGI++A+ G Q MGF P LKAF Sbjct: 173 MRAAAEDMSAAHLVGLNVNRLIIVAFIVASAYAGLAGILWAAQAGVVQPQMGFTPLLKAF 232 Query: 237 TAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLR 296 AA+ GG G++AGA+VGG +LG +E ++ + S Y D F VLI L +R Sbjct: 233 VAAIIGGFGSIAGALVGGYILGALEIFIVAFLPSSV-----SSYRDAIVFAVLIAFLLVR 287 Query: 297 PSGLL 301 P GLL Sbjct: 288 PGGLL 292 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: 233 Number of extensions: 14 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: 309 Length of database: 300 Length adjustment: 27 Effective length of query: 282 Effective length of database: 273 Effective search space: 76986 Effective search space used: 76986 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