Align L-arabinose-binding periplasmic protein; ABP (characterized)
to candidate BWI76_RS18250 BWI76_RS18250 arabinose ABC transporter substrate-binding protein
Query= SwissProt::P02924 (329 letters) >FitnessBrowser__Koxy:BWI76_RS18250 Length = 326 Score = 609 bits (1571), Expect = e-179 Identities = 301/326 (92%), Positives = 317/326 (97%) Query: 1 MHKFTKALAAIGLAAVMSQSAMAENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIK 60 MHKFTKALAAIGLAAVMSQSAMAE LKLGFLVKQPEEPWFQTEWKFADKAGKDLGF+VIK Sbjct: 1 MHKFTKALAAIGLAAVMSQSAMAETLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFDVIK 60 Query: 61 IAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKG 120 IAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLG+AIVAKARGYDMKVI VDDQFVNAKG Sbjct: 61 IAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGAAIVAKARGYDMKVITVDDQFVNAKG 120 Query: 121 KPMDTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMD 180 KPMD+VPLVMMAA++IG RQGQELYKEMQKRGWDVK++AVMAITA+ELDTARRRTTGS+D Sbjct: 121 KPMDSVPLVMMAASEIGARQGQELYKEMQKRGWDVKDTAVMAITADELDTARRRTTGSID 180 Query: 181 ALKAAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATE 240 ALKAAGFPE+QIY+VPTKSNDIPGAFDA NSMLVQHP VKHWLIVGMND+TVLGGVRATE Sbjct: 181 ALKAAGFPEQQIYRVPTKSNDIPGAFDAGNSMLVQHPNVKHWLIVGMNDNTVLGGVRATE 240 Query: 241 GQGFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEP 300 GQGFKA D+IGIGINGVDAV+ELSKAQATGFYGSLLPSPD+HGYK+SEMLYNWV KDVEP Sbjct: 241 GQGFKAPDVIGIGINGVDAVNELSKAQATGFYGSLLPSPDIHGYKTSEMLYNWVTKDVEP 300 Query: 301 PKFTEVTDVVLITRDNFKEELEKKGL 326 PKFT VTDVVLITRDNFKEEL KKGL Sbjct: 301 PKFTAVTDVVLITRDNFKEELAKKGL 326 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: 504 Number of extensions: 19 Number of successful extensions: 1 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