Align Fructose import permease protein FrcC (characterized)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 166 bits (419), Expect = 1e-45 Identities = 108/310 (34%), Positives = 166/310 (53%), Gaps = 12/310 (3%) Query: 49 AVPLIVLVLSLIAFGVI--LGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSV 106 ++ L +L L+L+ V+ L F + + IL Q ++GI+ T VILT GIDLSV Sbjct: 31 SLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVILTGGIDLSV 90 Query: 107 GAIMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQ 166 G++ LS +++G Y P A ++ G+ GA G ++G L+ +L F+VTLGM Sbjct: 91 GSVAGLSGIVLGLALKDYPIPVA--ILLGVLTGAGVGLVSGILIGYFRLAAFVVTLGMMA 148 Query: 167 IVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLN 226 I + +++S I ++ + + F I V G + L W L Sbjct: 149 IGRSLAYIFSGQTAISGFPSDLSSIV---YTDVFGIPTNVLFLGFAYL-----LAWGYLT 200 Query: 227 RTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQ 286 T GR +YA+G + EAA+ AG+ V I Y +SG + A+A + +I SV P G Sbjct: 201 YTKGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPLTGN 260 Query: 287 FANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLII 346 +++I AVVIGG SL+GGRGSI+G L G LI+ + GL L+G P W IG +II Sbjct: 261 GMELDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIII 320 Query: 347 IAVAIDQWIR 356 +A+ +++ +R Sbjct: 321 MALLVERLVR 330 Lambda K H 0.327 0.141 0.420 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: 372 Number of extensions: 25 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: 360 Length of database: 335 Length adjustment: 29 Effective length of query: 331 Effective length of database: 306 Effective search space: 101286 Effective search space used: 101286 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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