Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 214 bits (544), Expect = 3e-60 Identities = 135/350 (38%), Positives = 192/350 (54%), Gaps = 24/350 (6%) Query: 2 TALQLTNVCKSFGPVEV-LKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 T + L + K+F + L+ ++L + GE VV +GPSGCGK+T LR+I+GLE AG + Sbjct: 5 TTITLRHCGKTFADGTLALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGV 64 Query: 61 SI-GGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASR 119 + G VT P +RG+ MVFQSYAL+P+++V EN+A L+ R RV E Sbjct: 65 VMFGDNDVTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLA 124 Query: 120 MLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARL 179 M+ L + +RR +LSGGQRQRVA+ RA+ +P++ L DEPL+ LDA LR R +I +L Sbjct: 125 MMHLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQL 184 Query: 180 HRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGA--- 236 R L + +YVTHDQ EAM L D+I+V+ GRI Q GTP ++Y PAN FVA+FIG Sbjct: 185 LRSLHITAVYVTHDQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGTMNR 244 Query: 237 -PAMNFVPAQRLGG----------------NPGQFIGIRPEYARISPV--GPLAGEVIHV 277 PA+ A R+ G +P + RPE ++ L G V+ Sbjct: 245 LPAVLEADAWRVPGGLVPRHGTAASLAAAPSPRAELLFRPEDVALAQAEDAHLGGSVVTA 304 Query: 278 EKLGGDTNILVDMGEDLTFTARLFGQHDTNVGETLQFDFDPANCLSFDEA 327 LG T +LVD+G + G+ + D + ++ EA Sbjct: 305 LFLGNYTRLLVDVGAPAPLVVDTTRRDGWLAGDRVGLRLDTGHLITLPEA 354 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: 323 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: 357 Length adjustment: 29 Effective length of query: 302 Effective length of database: 328 Effective search space: 99056 Effective search space used: 99056 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