Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate Pf1N1B4_409 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_409 Length = 322 Score = 151 bits (381), Expect = 3e-41 Identities = 93/313 (29%), Positives = 160/313 (51%), Gaps = 20/313 (6%) Query: 38 LRELALLPALALLIVIGAFISPSFLTKANL------ISVLGASAALALVVLAESLIVLTG 91 L + +L A + V+ + +FL+ N+ IS G +A L LA +G Sbjct: 21 LDDWVMLLAAVGIFVLCTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLA------SG 74 Query: 92 KFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRL 151 FDLS+ S + A V A+++ S G+ A +V+G ++G ING ++ +L Sbjct: 75 HFDLSVGSVIACAGVVAAVVMRDTDSVFLGVS--------AALVMGLIVGLINGIVIAKL 126 Query: 152 RLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIVLGLPLSVWLAAAAFAIA 211 R+NA I TLA + ++RG+ G + FF + G+P+ + + F Sbjct: 127 RVNALITTLATMQIVRGLAYIFANGKAVGVSQEQFFVFGNGQLFGVPVPILITIVCFLFF 186 Query: 212 AFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAIN 271 ++L Y GR AIGGN EAA AG+ V+R +F + ++ ++ G+I+ + + Sbjct: 187 GWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKTLIFAVHGVIGALAGVILASRMTSGQ 246 Query: 272 ANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIY 331 G G TV +A V+GG+SL GG G + + GVL+L +++N + L + +F+ I Sbjct: 247 PMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIR 306 Query: 332 GAIILGSLMVARL 344 G+I+L ++++ RL Sbjct: 307 GSILLLAVVIDRL 319 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: 1 Number of HSP's successfully gapped: 1 Length of query: 351 Length of database: 322 Length adjustment: 28 Effective length of query: 323 Effective length of database: 294 Effective search space: 94962 Effective search space used: 94962 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