Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Echvi_1096 Echvi_1096 nitrate transport ATP-binding subunits C and D
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Cola:Echvi_1096 Length = 294 Score = 151 bits (382), Expect = 2e-41 Identities = 91/216 (42%), Positives = 133/216 (61%), Gaps = 9/216 (4%) Query: 1 MTALQLTNVCKSFGP----VEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDAT 56 M ++L NV KSFG V+VL DINL V +GEFV VG SG GK+TL+ +++GL Sbjct: 1 MAIIELNNVSKSFGMGASRVDVLSDINLQVAEGEFVAIVGFSGSGKTTLINLLNGLAFPD 60 Query: 57 AGEISIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQ--ERQPKEEIAARV 114 GE+ + GQ VT P RG+ +FQ+Y+L P LSV N+ LA+ + + +E A+ + Sbjct: 61 QGEVLLHGQPVTGPGP-DRGV--IFQNYSLLPWLSVYNNVKLAVDEVFPQLSSKEKASHI 117 Query: 115 AEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRL 174 + M++L +D+ P ELSGG RQRV++ RA+ P++ L DEPLS LDA R + + Sbjct: 118 KKYIGMVNLTPAMDKLPKELSGGMRQRVSVARALAMNPEILLMDEPLSALDALTRGSLQE 177 Query: 175 EIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDG 210 EI R+ Q + I +T+D E + +AD+I+ L G Sbjct: 178 EIIRIWSQDKKTAILITNDVDEGILMADRIIPLTPG 213 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: 205 Number of extensions: 9 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: 294 Length adjustment: 27 Effective length of query: 304 Effective length of database: 267 Effective search space: 81168 Effective search space used: 81168 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: 48 (23.1 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