Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 204 bits (518), Expect = 4e-57 Identities = 101/225 (44%), Positives = 138/225 (61%) Query: 27 KAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVEVGHV 86 + FGS+ + + LDV G F +GPSGCGK+TLLR +AG + G + I G + V Sbjct: 12 RRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIRGERMNDV 71 Query: 87 APAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSLEPYLARR 146 P +R + MVFQ AL+P +TV DN+ GLK+ +P E +++A+ + L R Sbjct: 72 PPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQVGLPDLEHRN 131 Query: 147 PAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSLKATMIYV 206 P ELSGGQRQRVA+ R +V EP L L DEPL LD LR ++E+ L + T +Y+ Sbjct: 132 PQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQKQFGTTFVYI 191 Query: 207 THDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIG 251 THDQ EAM ++D++ V+ GR +QV P ELY PA FVAGF+G Sbjct: 192 THDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVG 236 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: 325 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 352 Length of database: 362 Length adjustment: 29 Effective length of query: 323 Effective length of database: 333 Effective search space: 107559 Effective search space used: 107559 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