Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 5210736 Shew_3164 ABC transporter-related protein (RefSeq)
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__PV4:5210736 Length = 241 Score = 147 bits (370), Expect = 4e-40 Identities = 82/227 (36%), Positives = 130/227 (57%), Gaps = 6/227 (2%) Query: 20 LQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQID 79 +++ + K FG ++VLKGID + GE V +GPSG GKST LR I LE T G + ID Sbjct: 2 IKISNLHKYFGDNQVLKGIDESIARGEVVSVIGPSGSGKSTFLRCINLLEQPTQGEIVID 61 Query: 80 GVEV----GHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAG-VPKAEIEEKVAKAA 134 G + + ++ + MVFQ++ L+PH TV+ N+ L + G + +AE + + + Sbjct: 62 GQSITAPDACIDKLRQKVGMVFQNFNLFPHKTVQQNITLAPVKLGLMTQAEADSEAMRLL 121 Query: 135 GMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIAR 194 + L + PA LSGGQ+QRVAI RA+ +P+L LFDEP S LD + V L++ + Sbjct: 122 DQVGLSDKASAYPASLSGGQKQRVAIARALAMKPELMLFDEPTSALDPEM-VGDVLDVMK 180 Query: 195 LHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRP 241 TM+ VTH+ A ++D+++ ++ G + + P L+ +P Sbjct: 181 QLAQAGMTMVIVTHEMGFAKDVSDRVIFMDGGYVVESNVPALLFGQP 227 Lambda K H 0.320 0.137 0.393 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: 211 Number of extensions: 9 Number of successful extensions: 4 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: 352 Length of database: 241 Length adjustment: 26 Effective length of query: 326 Effective length of database: 215 Effective search space: 70090 Effective search space used: 70090 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