Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate PfGW456L13_3039 Various polyols ABC transporter, ATP-binding component
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3039 Length = 367 Score = 360 bits (923), Expect = e-104 Identities = 192/359 (53%), Positives = 253/359 (70%), Gaps = 33/359 (9%) Query: 17 VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76 + +L++K ++K F ++KGIDL+V D EFV+FVGPSGCGKSTLLR IAGLE+ + G++ Sbjct: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60 Query: 77 QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136 ++DG ++ V+PAKR +AMVFQ+YALYPH++V+ NM L AGV KAE+E+KV++AA + Sbjct: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARI 120 Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196 L L P L R+P +LSGGQRQRVAIGRAIVR PK+FLFDEPLSNLDAALRV RLE+ RLH Sbjct: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180 Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256 + L+ATMIYVTHDQVEAMT+ADK+VVLN G+IEQVGSP++LY++PANLFVAGF+G+P+M Sbjct: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240 Query: 257 FIE--------------------------AAKLGDGEAKTIGIRPEHIGLSRESGDWKGK 290 F++ L G A T+GIRPEH+ L++ GD + Sbjct: 241 FLKGKITRVDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELAK-PGDCALQ 299 Query: 291 VIH--VEHLGADTIIYIESETVGLLTVRLFGE--HRYATDDIVHATPVIGSMHRFDADG 345 V E LG+DT ++ + + LT+R+ G+ RY +H H FDADG Sbjct: 300 VTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLD--AQHCHLFDADG 356 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: 375 Number of extensions: 14 Number of successful extensions: 3 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: 367 Length adjustment: 29 Effective length of query: 323 Effective length of database: 338 Effective search space: 109174 Effective search space used: 109174 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