Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate PP_5168 PP_5168 sulfate/thiosulfate import ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Putida:PP_5168 Length = 329 Score = 224 bits (571), Expect = 2e-63 Identities = 132/324 (40%), Positives = 185/324 (57%), Gaps = 19/324 (5%) Query: 3 ALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISI 62 ++++ NV K F + L INL + GE V +GPSGCGK+TLLR+I+GLE G I Sbjct: 2 SIEVRNVSKRFNSFQALNAINLDINSGELVALLGPSGCGKTTLLRIIAGLETPDQGNIVF 61 Query: 63 GGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALAL----KQERQPKEEIAARVAEAS 118 G+ V+ R + VFQ YAL+ H+SV +N+A L K ER + +IA +V E Sbjct: 62 HGEDVSGHDVRDRNVGFVFQHYALFRHMSVFDNVAFGLRMKPKGERPSESKIAEKVHELL 121 Query: 119 RMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIAR 178 M+ L+ DR P +LSGGQRQR+A+ RA+ EPK+ L DEP LDA +R R +AR Sbjct: 122 NMVQLDWLSDRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLAR 181 Query: 179 LHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPA 238 LH ++ + ++VTHDQ EAM +AD+IVV+ G IEQ+G+P E+Y+ PAN FV F+G Sbjct: 182 LHEDINLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGSPGEVYDQPANDFVYHFLG--- 238 Query: 239 MNFVPAQRLGGNPGQFIGIRPEYARIS---PVGPLAGEVIHVEKLGGDTNILVDM-GEDL 294 + RL + G + RP +S G A EV + LG T + + + G+ Sbjct: 239 ----DSNRLALSEGHHVLFRPHEVSLSRHETEGHHAAEVRDIRPLGATTRVTLKVEGQSE 294 Query: 295 TFTARLFGQHDTNV----GETLQF 314 A + HD+ GETL F Sbjct: 295 LIEAEVVKDHDSLTGLARGETLFF 318 Lambda K H 0.320 0.137 0.391 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: 286 Number of extensions: 14 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: 331 Length of database: 329 Length adjustment: 28 Effective length of query: 303 Effective length of database: 301 Effective search space: 91203 Effective search space used: 91203 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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