Align L-arabinose-binding periplasmic protein; Short=ABP (characterized, see rationale)
to candidate BWI76_RS18250 BWI76_RS18250 arabinose ABC transporter substrate-binding protein
Query= uniprot:A0A161H4E4 (334 letters) >FitnessBrowser__Koxy:BWI76_RS18250 Length = 326 Score = 379 bits (974), Expect = e-110 Identities = 194/322 (60%), Positives = 240/322 (74%), Gaps = 2/322 (0%) Query: 12 RAALAVTAVSLSSHLLAADAVKIGFLVKQAEEPWFQTEWAFAEKAAKDKGFQLIKIAVPD 71 +A A+ ++ S A+ +K+GFLVKQ EEPWFQTEW FA+KA KD GF +IKIAVPD Sbjct: 6 KALAAIGLAAVMSQSAMAETLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFDVIKIAVPD 65 Query: 72 GEKTLSAIDSLAANGAKGFVICPPDVSLGPAIVAKAKLNDMKVIAVDDRFVGSDGKFMED 131 GEKTL+AIDSLAA+GAKGFVIC PD LG AIVAKA+ DMKVI VDD+FV + GK M+ Sbjct: 66 GEKTLNAIDSLAASGAKGFVICTPDPKLGAAIVAKARGYDMKVITVDDQFVNAKGKPMDS 125 Query: 132 VPYLGMAAFEVGQKQGGAMAAEAKKRGWDWKDTYAVINTYNELDTGKKRTDGSVDALKKA 191 VP + MAA E+G +QG + E +KRGWD KDT + T +ELDT ++RT GS+DALK A Sbjct: 126 VPLVMMAASEIGARQGQELYKEMQKRGWDVKDTAVMAITADELDTARRRTTGSIDALKAA 185 Query: 192 GMPADHILYSALKTLDVPGSMDSTNSALVKLPSAAKNLIIGGMNDNTVLGGVRATEAAGF 251 G P I K+ D+PG+ D+ NS LV+ P+ K+ +I GMNDNTVLGGVRATE GF Sbjct: 186 GFPEQQIYRVPTKSNDIPGAFDAGNSMLVQHPN-VKHWLIVGMNDNTVLGGVRATEGQGF 244 Query: 252 KAANVIGIGINGTDAIGELKKPD-SGFFGSMLPSPHIEGYKTAEMMYEWITTGKEPPKYT 310 KA +VIGIGING DA+ EL K +GF+GS+LPSP I GYKT+EM+Y W+T EPPK+T Sbjct: 245 KAPDVIGIGINGVDAVNELSKAQATGFYGSLLPSPDIHGYKTSEMLYNWVTKDVEPPKFT 304 Query: 311 AMDEVTLITRENFKQELEKIGL 332 A+ +V LITR+NFK+EL K GL Sbjct: 305 AVTDVVLITRDNFKEELAKKGL 326 Lambda K H 0.316 0.133 0.388 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: 11 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: 334 Length of database: 326 Length adjustment: 28 Effective length of query: 306 Effective length of database: 298 Effective search space: 91188 Effective search space used: 91188 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: 49 (23.5 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