Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Ga0059261_0341 Ga0059261_0341 ABC-type antimicrobial peptide transport system, ATPase component
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Korea:Ga0059261_0341 Length = 224 Score = 117 bits (292), Expect = 4e-31 Identities = 78/216 (36%), Positives = 113/216 (52%), Gaps = 13/216 (6%) Query: 23 KTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVE 82 +T + VL+GIDL V GE V +GPSG GKSTLL+ + LE GS++I GVE Sbjct: 13 RTFSQGGADIHVLRGIDLTVGQGEIVALLGPSGSGKSTLLQAVGLLEGGFEGSIRISGVE 72 Query: 83 VGHVAPAKRGI------AMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136 VG + R + V+Q + L P +N+ L + A + + A++ G+ Sbjct: 73 VGKLESHARTVTRRDKLGFVYQFHHLLPDFNALENVEL---PQLIQNATLADARARSEGL 129 Query: 137 LS---LEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIA 193 L+ L L RP++LSGG++QRVA+ RA+ P L L DEP NLD E Sbjct: 130 LTALGLGARLTHRPSQLSGGEQQRVAVARALANRPALVLADEPTGNLDEHTADIVLAEFL 189 Query: 194 RLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIE 229 RL R A + TH++ A + D++V L+ G +E Sbjct: 190 RLVRGEGAAALIATHNERLAAKM-DRVVRLHEGVLE 224 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: 181 Number of extensions: 5 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: 224 Length adjustment: 26 Effective length of query: 326 Effective length of database: 198 Effective search space: 64548 Effective search space used: 64548 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: 47 (22.7 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