Align ABC transporter permease (characterized, see rationale)
to candidate GFF561 Psest_0566 urea ABC transporter, permease protein UrtB
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__psRCH2:GFF561 Length = 523 Score = 114 bits (286), Expect = 4e-30 Identities = 94/308 (30%), Positives = 148/308 (48%), Gaps = 15/308 (4%) Query: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63 LL Q +GL LGS+ L ALG + +G++ +IN AHGE+LM+GA T++ +M P Sbjct: 227 LLGQAFSGLSLGSILLLAALGLAITFGLLGVINMAHGEMLMLGAYTTYMVQVLMARLAPE 286 Query: 64 APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMS-ILLQTLAMII 122 A + L+A +A V A + +E+ R L P L L+ G+S IL+Q + ++ Sbjct: 287 ALAF-YPLVALPVAFFVTAAIGMALERTVIRHLYGRP-LETLLATWGISLILIQLVRVLF 344 Query: 123 WKPNYKPYPTMLPSSPFEIGGAFITP-TQILILGVTAVALASLVYLVNHTNLGRAMRATA 181 N + S ++ + P +++I+G + L+N T LG +RA Sbjct: 345 GAQNVEVANPAWLSGGLQVLPNLVLPYNRMVIIGFALFVVLLTWLLLNKTRLGLNVRAVT 404 Query: 182 ENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVF 241 +N +A+ GV + F +G+ +A + G+ S G +G + +F V Sbjct: 405 QNRNMAACCGVPTGRIDMLAFGLGSGIAGLGGVA-LSQIGNVGPDLGQSYIIDSFLVVVL 463 Query: 242 GGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL- 300 GG+G LAG++ LG+ I IG + G +L I A I+L I RP GL Sbjct: 464 GGVGQLAGSIFAAFGLGIANKILEPQIGAVLGKIL------ILALIILFI--QKRPQGLF 515 Query: 301 -LGERVAD 307 L RV D Sbjct: 516 ALKGRVID 523 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: 294 Number of extensions: 11 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: 523 Length adjustment: 31 Effective length of query: 278 Effective length of database: 492 Effective search space: 136776 Effective search space used: 136776 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