Align L-arabinose-binding periplasmic protein; ABP (characterized)
to candidate GFF4165 PS417_21335 sugar ABC transporter substrate-binding protein
Query= SwissProt::P02924 (329 letters) >FitnessBrowser__WCS417:GFF4165 Length = 326 Score = 375 bits (963), Expect = e-109 Identities = 191/324 (58%), Positives = 241/324 (74%), Gaps = 2/324 (0%) Query: 4 FTKALAAIGLAAVMSQSAMAENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAV 63 F K L + LA S A+AE +K+GFLVKQ EEPWFQTEW FA+KAGKD GF VIKIAV Sbjct: 2 FKKTLGTLALAMAFSSVALAEEVKIGFLVKQAEEPWFQTEWAFAEKAGKDQGFTVIKIAV 61 Query: 64 PDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPM 123 PDGEKTL+AID+LAA+GAKGFVIC PD LG AI+AKA+ ++KV+AVDD+FV+AKGKPM Sbjct: 62 PDGEKTLSAIDTLAANGAKGFVICPPDVSLGPAIMAKAKLNNLKVLAVDDRFVDAKGKPM 121 Query: 124 DTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALK 183 + VP V + A KIG++QG+ + E + R WD K++ + T +EL+T ++RT GS++ LK Sbjct: 122 EDVPYVGLDAYKIGQKQGEAMATEAKHRNWDWKDTYAVINTFDELETGKKRTDGSVEGLK 181 Query: 184 AAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPE-VKHWLIVGMNDSTVLGGVRATEGQ 242 AAG P I K+ D+PG+ DA NS LV+ P K+ +I GMNDSTVLGGVRATE Sbjct: 182 AAGLPADHILFSAQKTLDVPGSMDATNSALVKLPSGAKNLIIGGMNDSTVLGGVRATESA 241 Query: 243 GFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPK 302 GFKAA++IG+GING DA+ EL K+ TGFYGS+L SPD GYK++ ++ WV + EP K Sbjct: 242 GFKAANVIGVGINGTDAIEELKKSD-TGFYGSMLLSPDASGYKTASAMFEWVTQGTEPAK 300 Query: 303 FTEVTDVVLITRDNFKEELEKKGL 326 FT + +V LITR NFKEEL K GL Sbjct: 301 FTALDNVTLITRANFKEELSKIGL 324 Lambda K H 0.315 0.132 0.381 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: 359 Number of extensions: 19 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: 329 Length of database: 326 Length adjustment: 28 Effective length of query: 301 Effective length of database: 298 Effective search space: 89698 Effective search space used: 89698 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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