Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate GFF1646 PGA1_c16690 binding protein-dependent transport system, inner membrane component
Query= reanno::Koxy:BWI76_RS01820 (296 letters) >FitnessBrowser__Phaeo:GFF1646 Length = 283 Score = 126 bits (316), Expect = 6e-34 Identities = 89/287 (31%), Positives = 148/287 (51%), Gaps = 23/287 (8%) Query: 14 FTTHLLLLVFIAAIMFPL--LMVIAISLREGNFATGS-LIPESISWEHWRLALGFSVEHA 70 F + + ++ +FPL LM IAI+ F+ G+ ++P ++++E++ L F E Sbjct: 16 FGKYAAIAFYLGFALFPLYWLMKIAITPDALIFSEGTRMLPSAVTFENFATVL-FETEF- 73 Query: 71 DGRVTPPPFPVLLWLWNSIKVAGITAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQM 130 L + NS+ V+ TA ++ YAF+R F GK ++ MLI QM Sbjct: 74 -----------LAYFRNSLTVSLGTAFFTTLIAAGAGYAFSRFVFAGKRIIIAVMLITQM 122 Query: 131 FPAVLSLVALYALFDRLGQYVPFVGLNTHGGVIFAYMG-GIALHVWTIKGYFETIDGSLE 189 FP ++ + +Y + LG LN+ +I Y I + ++ +F+ I LE Sbjct: 123 FPLLMIIAPIYKIVADLGL------LNSLTSLIVVYTAFNIPFATFLMQSFFDGIPKDLE 176 Query: 190 EAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGM 249 EAA +DG + +QA R V+ PL++P L F AA +E+ A +L+ ++ T VG+ Sbjct: 177 EAAMMDGCSRFQALRTVVFPLTLPGLGATLGFVFTAAWSELLFALMLISKNDAMTFPVGL 236 Query: 250 QQYLNPQNYLWGDFAAAAVLSAIPITVVFLLAQRWLVNGLTAGGVKG 296 +++ + WG AA VL+ +P + F+ QR+LV GLT+G VKG Sbjct: 237 LTFVSKFSVDWGQMMAAGVLALVPSCLFFIFIQRYLVQGLTSGAVKG 283 Lambda K H 0.328 0.141 0.438 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: 229 Number of extensions: 8 Number of successful extensions: 3 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: 296 Length of database: 283 Length adjustment: 26 Effective length of query: 270 Effective length of database: 257 Effective search space: 69390 Effective search space used: 69390 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 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