Align LacF, component of Lactose porter (characterized)
to candidate AZOBR_RS25585 AZOBR_RS25585 ABC transporter permease
Query= TCDB::P29823 (298 letters) >FitnessBrowser__azobra:AZOBR_RS25585 Length = 301 Score = 144 bits (363), Expect = 2e-39 Identities = 94/294 (31%), Positives = 154/294 (52%), Gaps = 10/294 (3%) Query: 8 SLKRYYDVNGWLFVAPAIALISVFMLYPILRSLVLSLYTGRGMMLK-FSGTG--NLVRLW 64 SL R WLF+ P + +++ +P+ R++ S L+ F G G N + L Sbjct: 9 SLMRQRRRAAWLFLLPMLIVLAGVAGWPLFRTVFFSFTDATLATLEGFQGVGLDNYLWLM 68 Query: 65 NDPVFWQALQNTVIFFVVQVPIMITMALILAAMLNNPKLRYSGLFRTMIFLPCVSSLVAY 124 DPV+W+A+ NT++F VV V I + L +A +LN L GL R + +P V Sbjct: 69 RDPVWWRAVWNTLVFTVVSVGIETALGLGIALILN-AHLPGRGLLRAAVLIPWAIPTVVS 127 Query: 125 SILFKSMF-SLDGVVNNTLLAIGIIGEPIGWLTDPFWAKVLIIIAITWRWTGYNMIFYLA 183 + ++ MF L GVVN L+ +G+I EP W DP A ++I W+ T + + LA Sbjct: 128 AQMWGWMFHDLYGVVNAILMGLGLIAEPRAWTADPDLALPVVIAVDVWKSTPFMALLILA 187 Query: 184 ALQNIDRSIYEAAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTLQLFDEVYNFTEG 243 ALQ + R +YEAA++DGV F +T+P+++P ++ + T+ L++FD +Y T Sbjct: 188 ALQMLPRDLYEAARVDGVHPVKVFVRITLPLIRPALMVAVLFRTLDALRVFDLMYVLT-- 245 Query: 244 TGGPANSTLTLSLYIYNLTFRFMPSFSYAATVSYVIVLMVAVLSFLQFYAARER 297 G + ST+++S+Y F Y + + ++VL++AV + L R R Sbjct: 246 --GNSRSTMSMSVYARQYLIDFQ-DVGYGSAAATLLVLVLAVATVLAVTLGRVR 296 Lambda K H 0.329 0.141 0.435 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: 261 Number of extensions: 22 Number of successful extensions: 4 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: 298 Length of database: 301 Length adjustment: 27 Effective length of query: 271 Effective length of database: 274 Effective search space: 74254 Effective search space used: 74254 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