Align ABC transporter permease (characterized, see rationale)
to candidate 3607448 Dshi_0861 inner-membrane translocator (RefSeq)
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Dino:3607448 Length = 305 Score = 128 bits (321), Expect = 2e-34 Identities = 94/312 (30%), Positives = 154/312 (49%), Gaps = 23/312 (7%) Query: 3 ILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMP 62 +L++Q++NGL G M L+A G T+V+G++ LIN AHG + M+GA + A+ Sbjct: 5 LLIEQVLNGLQFGVMLFLMAAGLTLVFGVMGLINLAHGSLYMVGAFAA--------AAVA 56 Query: 63 GAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMII 122 GA G +L LA +A AA +IE R L + L ++ + ++ I Sbjct: 57 GATGSFVLGLAAALAAAAAA--GALIEVTIIRRLYARDHLDQVLATFALILIFSEGTRWI 114 Query: 123 WK--PNYKPYPTMLPSSPFEIGGAFITPT-QILILGVTAVALASLVYLVNHTNLGRAMRA 179 + P + P L S P + P ++ I+G+ A+L +L+ T +G +RA Sbjct: 115 FGSFPLFLEVPAAL-SGPVTLPFGIEYPAYRLAIIGIGLAIAAALFWLIAKTRIGVQIRA 173 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 + + + +GV D + + F +GA LA +AG + + + Q MG + AF Sbjct: 174 GEADREMIAALGVDIDRLYTLVFALGAALAGLAGALVGA-LQSVQVGMGEPVLILAFVVI 232 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLL--------GSHYTDIFAFIVLII 291 V GGIG++ GA VG +LLGL + +G + G +L GS + +I++ Sbjct: 233 VIGGIGSIKGAFVGALLLGLTDTLGRTLLPVAFGTVLEPSMATAVGSALASMAIYILMAG 292 Query: 292 ILTLRPSGLLGE 303 +L RPSGL G+ Sbjct: 293 VLIFRPSGLFGQ 304 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: 197 Number of extensions: 7 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: 309 Length of database: 305 Length adjustment: 27 Effective length of query: 282 Effective length of database: 278 Effective search space: 78396 Effective search space used: 78396 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