Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 164 bits (416), Expect = 3e-45 Identities = 85/234 (36%), Positives = 138/234 (58%), Gaps = 6/234 (2%) Query: 7 TNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIGGQT 66 + + K+ G +KD NL++ +GE V +G SG GKSTLLR I+ L T+GE+ I G Sbjct: 31 SEILKATGCTVAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTD 90 Query: 67 VTTTPPA------KRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 + ++ +AMVFQ++ L PH SV N+A L+ + K E + E+ ++ Sbjct: 91 IAKVSDKELLQIRRKELAMVFQNFGLLPHRSVLHNIAFGLELQGVKKGEREQKAMESMQL 150 Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 + L+ Y ++ SELSGG +QRV + RA+ P++ L DE S LD +R+ + E+ L Sbjct: 151 VGLKGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQ 210 Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFI 234 ++ +++++THD EA+ L D+I +++DG I Q+GT E+ PAN +V F+ Sbjct: 211 SKMKKTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVERFV 264 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: 281 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: 331 Length of database: 408 Length adjustment: 30 Effective length of query: 301 Effective length of database: 378 Effective search space: 113778 Effective search space used: 113778 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