Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Miya:8500849 Length = 366 Score = 214 bits (544), Expect = 3e-60 Identities = 129/317 (40%), Positives = 178/317 (56%), Gaps = 29/317 (9%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M + L + K++G VL ++LTV GE +GPSGCGK+ LLR+I+G E AG I Sbjct: 1 MADITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTI 60 Query: 61 SIGGQTVTTT------PPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARV 114 SIGG+ V+ PP R + +VFQ YA++PH+SV +N+ LK P E +V Sbjct: 61 SIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQV 120 Query: 115 AEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRL 174 E M++L +R PS+LSGGQ+QRVA+ RA+V P L L DEPL NLDA LR R Sbjct: 121 LETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRF 180 Query: 175 EIARLHRQLSASMIYVTHDQIEAMTLADKIVVL-RDGRIEQVGTPMELYNNPANRFVAEF 233 EI L R L +++YVTHDQ A+ ++D++ ++ G I QVGTP E++ PA+ FV F Sbjct: 181 EIKELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFRF 240 Query: 234 IGAPAMNFVPAQRLG--------------GNPG-----QFIGIRPEYARISPVGP-LAGE 273 +G NF+PA+R G G P G RP R++ G L G Sbjct: 241 MG--VANFLPARRRGMAMLAAGGEQPVPWGLPDGDAEHWMAGFRPSDVRLARQGDGLRGT 298 Query: 274 VIHVEKLGGDTNILVDM 290 V LG T+ L+++ Sbjct: 299 VRRASFLGAMTDYLIEV 315 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: 293 Number of extensions: 13 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: 366 Length adjustment: 29 Effective length of query: 302 Effective length of database: 337 Effective search space: 101774 Effective search space used: 101774 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 Apr 09 2024. 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