Align ABC transporter permease (characterized, see rationale)
to candidate 3609311 Dshi_2696 inner-membrane translocator (RefSeq)
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Dino:3609311 Length = 554 Score = 130 bits (326), Expect = 9e-35 Identities = 94/299 (31%), Positives = 151/299 (50%), Gaps = 14/299 (4%) Query: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63 + Q + GL LGS+ L A+G + +G++ +IN AHGE++MIGA T++ +++ + P Sbjct: 258 MAQNVWFGLSLGSVLLLAAIGLAITFGVMGVINMAHGELVMIGAYTTFFVQEIIRTSFPH 317 Query: 64 APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIW 123 W LL+A +A VA + IE+ R L P L L+ G+S++LQ I+ Sbjct: 318 LFDWS-LLIAAPLAFAVAGAVGVAIERGCVRFLYGRP-LETLLATWGISLILQQTVRSIF 375 Query: 124 KPNYKPY--PTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATA 181 PN + P+ + S FE+G IT ++ IL A L++++ T +G MRA Sbjct: 376 GPNNREVGNPSWM-SGAFEVGQMTITYNRLWILLFALAVFAVLLFVLKKTAIGLQMRAVT 434 Query: 182 ENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVF 241 +N +A+ MG++ V + TF +GA +A +AG+ S +G + +F VF Sbjct: 435 QNRAMAANMGIRTGWVDAMTFGLGAGIAGLAGVA-LSQIDNVSPNLGQSYIVDSFMVVVF 493 Query: 242 GGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GG GN+ G + LG+ Y G + +L + FI+L I RP GL Sbjct: 494 GGAGNIWGTLAAAFSLGIANKFLEPYAGAVLAKIL------VLVFIILFI--QKRPRGL 544 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: 302 Number of extensions: 8 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: 554 Length adjustment: 31 Effective length of query: 278 Effective length of database: 523 Effective search space: 145394 Effective search space used: 145394 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: 50 (23.9 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