Align Fructose import permease protein FrcC (characterized)
to candidate WP_068000560.1 PsAD2_RS00560 ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >NCBI__GCF_001623255.1:WP_068000560.1 Length = 332 Score = 194 bits (492), Expect = 4e-54 Identities = 123/310 (39%), Positives = 175/310 (56%), Gaps = 20/310 (6%) Query: 56 VLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSSV 115 +L+LI F I F +A +T IL QV I I+ T VIL GIDLSVG++M +SV Sbjct: 31 LLALILFFSIFTEHFLTANNITNILTQVTINLILAVGMTFVILIGGIDLSVGSVMAFASV 90 Query: 116 IMGQFTFRYGFPP----ALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLAS 171 I G+ G P L+VI VG +CG INGT+ AR LP FI+TLGM I + Sbjct: 91 IAGKAITLAGLGPFEAIVLAVIAATAVGVVCGAINGTITARWSLPSFIITLGMLNIARGA 150 Query: 172 NFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVL----LVCLLWYVLNR 227 S +TI + ++ G+A+F YGV V+ + LV + W++LN Sbjct: 151 ALQASNAQTIYSFPLAFED-----------FGSAMF-YGVPVVFMVALALVFIAWFILNF 198 Query: 228 TAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQF 287 T +GR +Y +G++ EA +LAG +V R I+ +T+ GL +A + R+ SP AG Sbjct: 199 TVFGRLLYGIGNNEEAVRLAGHSVYRYKIAAFTICGLTAGIAAVVYMARLNISSPIAGIG 258 Query: 288 ANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIII 347 + +I AV+IGG SL GGRGS++G L GA I+GV + GL L+G ++ G++III Sbjct: 259 FELNAIAAVIIGGTSLNGGRGSVIGTLIGAFIIGVLANGLILIGLSDFMRQMITGVVIII 318 Query: 348 AVAIDQWIRK 357 AV +D + K Sbjct: 319 AVILDYYRAK 328 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: 371 Number of extensions: 20 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: 332 Length adjustment: 29 Effective length of query: 331 Effective length of database: 303 Effective search space: 100293 Effective search space used: 100293 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 Sep 24 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