Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_000009985.1:WP_011385763.1 Length = 363 Score = 136 bits (342), Expect = 9e-37 Identities = 76/214 (35%), Positives = 122/214 (57%), Gaps = 9/214 (4%) Query: 21 DINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIGGQTVTTT------PPAK 74 D+ L+ G ++ G SG GK++++ +++GL G IS+ G+ + + PP Sbjct: 16 DVRLSAGPGVTALY-GRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLPPEA 74 Query: 75 RGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSLEDYLDRRPSEL 134 R + VFQ + L+PHLSVR N+ Q+ P E + + +L +E LDRRP++L Sbjct: 75 RRLGYVFQEHRLFPHLSVRGNLEFG--QKLLPSAERTQSLDKVVELLGIESLLDRRPAKL 132 Query: 135 SGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSASMIYVTHDQ 194 SGG++QRVAIGRA++ P++ L DEPL+ LD A + IA+L R+ S ++YV+H Sbjct: 133 SGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVSHSM 192 Query: 195 IEAMTLADKIVVLRDGRIEQVGTPMELYNNPANR 228 E + LAD + ++ G++ G L +P R Sbjct: 193 DEVLRLADTLALMDGGKVAASGPLESLMGDPGLR 226 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: 295 Number of extensions: 14 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: 331 Length of database: 363 Length adjustment: 29 Effective length of query: 302 Effective length of database: 334 Effective search space: 100868 Effective search space used: 100868 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