Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF3990 Psest_4063 sulfate ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__psRCH2:GFF3990 Length = 334 Score = 219 bits (557), Expect = 1e-61 Identities = 124/294 (42%), Positives = 178/294 (60%), Gaps = 13/294 (4%) Query: 19 SLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQI 78 S+++ I K FG + L I+L ++ GE V +GPSGCGK++LLR IAGLE SGS+ Sbjct: 2 SIEISHINKRFGQFQALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSIVF 61 Query: 79 DGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGL----KQAGVPKAEIEEKVAKAA 134 G +V R + VFQ YAL+ H+TV +N+ GL K+ +A I EKV + Sbjct: 62 HGEDVSSRDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHELL 121 Query: 135 GMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIAR 194 G++ L+ R P +LSGGQRQR+A+ RA+ EPK+ L DEP LDA +R R +AR Sbjct: 122 GLVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLAR 181 Query: 195 LHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQ 254 LH + T ++VTHDQ EAM +AD+IVV+N G IEQ+G+P E+Y PA+ FV F+G Sbjct: 182 LHEDVHLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFLG--- 238 Query: 255 MNFIEAAKLGDGEAKTIGIRPEHIGLSRE--SGDWKGKVIHVEHLGADTIIYIE 306 +A +L + +++ RP + LSRE + G+V + LGA T + ++ Sbjct: 239 ----DANRLQLDDQRSVLFRPHEVALSREAVAEHLAGEVRDIRPLGALTRVTLK 288 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: 316 Number of extensions: 18 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: 352 Length of database: 334 Length adjustment: 29 Effective length of query: 323 Effective length of database: 305 Effective search space: 98515 Effective search space used: 98515 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