Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122 Length = 323 Score = 152 bits (385), Expect = 9e-42 Identities = 93/299 (31%), Positives = 157/299 (52%), Gaps = 15/299 (5%) Query: 47 LALLIVIGAFISPSFLTKANL-ISVLGASAALALVVLAESLIVLTGKFDLSLESTVGIAP 105 +A ++I F+SP + L IS G +A L LA +G FDLS+ S + A Sbjct: 36 VACTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLA------SGHFDLSVGSVIACAG 89 Query: 106 AVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFIVTLAMLIV 165 V A+++ S G+ A +V+G ++G ING ++ +LR+NA I TLA + + Sbjct: 90 VVAAVVMRDTNSVFLGV--------CAALVMGLIVGLINGIVIAKLRVNALITTLATMQI 141 Query: 166 LRGMLVGATKGGTLFDMPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLRYHRLGRALY 225 +RG+ G + SFF + G+P+ + + F ++L Y GR Sbjct: 142 VRGLAYIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNTM 201 Query: 226 AIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGNGMIFTVFAA 285 AIGGN EAA AG+ V+R +F + ++ ++ G+I+ + + G G TV +A Sbjct: 202 AIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISA 261 Query: 286 AVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIILGSLMVARL 344 V+GG+SL GG G + + GVL+L +++N + L + +F+ I G+I+L ++++ RL Sbjct: 262 CVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRL 320 Lambda K H 0.326 0.140 0.397 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: 242 Number of extensions: 7 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: 1 Length of query: 351 Length of database: 323 Length adjustment: 28 Effective length of query: 323 Effective length of database: 295 Effective search space: 95285 Effective search space used: 95285 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 (21.6 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