Align N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized)
to candidate GFF725 PGA1_c07400 binding protein dependent transport system permease
Query= reanno::Phaeo:GFF2752 (280 letters) >FitnessBrowser__Phaeo:GFF725 Length = 282 Score = 132 bits (333), Expect = 6e-36 Identities = 80/265 (30%), Positives = 138/265 (52%), Gaps = 3/265 (1%) Query: 18 ALITYTLIA-LFPVFVILVNSFKTRKAIFRDPL-GLPTSDTFSLVGYQTVLKQGDFFLYF 75 AL+ L+ L P+ + + S K G+P+S L Y V D Y Sbjct: 19 ALVPAALVMWLLPLIAVAIFSIKPEADFTTGNYWGVPSSFE-GLSNYGRVFFGSDMPRYL 77 Query: 76 QNSMIVTVVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIGTVAILELMV 135 NS+++TV ++ + M FAL Y+F+GN+LL G +P +I V + +L + Sbjct: 78 LNSVLITVPTVIGAVALSCMTGFALGVYKFRGNLLLFFMFVAGNFVPFQILMVPVRDLTL 137 Query: 136 DTGLVNTLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIFFRLVLPL 195 D GL NT T L+L + A + F++ + +L A R++G++E+ IF+ +VLPL Sbjct: 138 DMGLYNTKTGLVLFHIAFQTGFCTLFMRNFIRALPFELIEAARVEGVAEWRIFWFVVLPL 197 Query: 196 VRPAMATVAVFNMIPIWNDLWFPLILAPAEETKTLTLGSQVFIGQFVTDWNAVLSALSMA 255 ++PA+A ++V IWND ++ ++L E++ +T G F Q+ ++ + + +A Sbjct: 198 MKPAIAALSVLIFTFIWNDYFWAVVLTQGAESQPVTAGITSFNAQYRAAYHLMSAGSIVA 257 Query: 256 ILPVMVLYVIFSRQLIRGITSGAVK 280 LP + ++ + R I G+T GAVK Sbjct: 258 ALPPVAMFFLMQRHFIAGLTLGAVK 282 Lambda K H 0.330 0.143 0.414 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: 214 Number of extensions: 12 Number of successful extensions: 1 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: 280 Length of database: 282 Length adjustment: 26 Effective length of query: 254 Effective length of database: 256 Effective search space: 65024 Effective search space used: 65024 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 (21.8 bits) S2: 47 (22.7 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