Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 348 bits (894), Expect = e-101 Identities = 186/343 (54%), Positives = 233/343 (67%), Gaps = 14/343 (4%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M LQL + K FG +K I+LT++ GEF+VFVGPSGCGKSTLLR+I+GLE G + Sbjct: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 Query: 61 SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 + G+ +T P +KR +AMVFQSYALYPH+SV ENM+ ALK + K+ I +V A+R+ Sbjct: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120 Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 L+L YL R P ELSGGQRQRVAIGRA+VR PK+FLFDEPLSNLDAALR TR+EIA+LH Sbjct: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180 Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240 R L A+ IYVTHDQ+EAMTLAD++VVLRDG IEQVGTP+ELY+ PAN+FVA+FIG P MN Sbjct: 181 RDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMN 240 Query: 241 FVPAQRL------------GGNPGQFIGIRPEYARISPVG--PLAGEVIHVEKLGGDTNI 286 VP +L G IG+RPE + G P+ G+V +E LG +T I Sbjct: 241 VVPVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQVDLIEALGAETLI 300 Query: 287 LVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAGQ 329 V F +R + D VG+ + D D + FD AG+ Sbjct: 301 YVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFDTAGR 343 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: 374 Number of extensions: 12 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: 350 Length adjustment: 28 Effective length of query: 303 Effective length of database: 322 Effective search space: 97566 Effective search space used: 97566 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