Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate WP_110804794.1 C8J30_RS05895 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21715 (220 letters) >NCBI__GCF_003217355.1:WP_110804794.1 Length = 434 Score = 91.7 bits (226), Expect = 2e-23 Identities = 50/155 (32%), Positives = 87/155 (56%), Gaps = 5/155 (3%) Query: 20 GLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTVIRNTPILVLI----LL 75 G L L + + +I + +G+L+A S ++ L+ + IR P++ L+ LL Sbjct: 226 GFLLALVIGVTAIVVSLPLGILLALGRQSDMVMVKALSVGMIEFIRGVPLITLLFTASLL 285 Query: 76 IYFALPSLGIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLREAGLAIGLGEWQVK 135 + + LP G D + +I ++L+A AY+ EV RGGL ++P+G EA A+GL WQ + Sbjct: 286 LQYFLPP-GTTFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQ 344 Query: 136 AYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAV 170 + +P L+ +P + ++FI LFKDT+L + + Sbjct: 345 RLIIMPQALKISIPGIVSSFIGLFKDTTLVTFVGL 379 Lambda K H 0.329 0.143 0.416 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: 238 Number of extensions: 17 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: 220 Length of database: 434 Length adjustment: 27 Effective length of query: 193 Effective length of database: 407 Effective search space: 78551 Effective search space used: 78551 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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