Align L-arabinose-binding periplasmic protein; ABP (characterized)
to candidate GFF2161 PS417_11025 sugar ABC transporter substrate-binding protein
Query= SwissProt::P02924 (329 letters) >FitnessBrowser__WCS417:GFF2161 Length = 334 Score = 363 bits (931), Expect = e-105 Identities = 188/322 (58%), Positives = 242/322 (75%), Gaps = 6/322 (1%) Query: 9 AAIGLAAVMSQSAM---AENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPD 65 AA+ ++A MS S + AE +K+GFLVKQ EEPWFQTEW FA+KAGK+ GF VIKIAVPD Sbjct: 13 AAVAVSA-MSLSGLLLAAEEVKIGFLVKQAEEPWFQTEWAFAEKAGKEHGFTVIKIAVPD 71 Query: 66 GEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPMDT 125 GEKTL+AIDSLAA+GAKGFVIC PD LG AIVAKA+ +KVIAVDD+FV+AKG M+ Sbjct: 72 GEKTLSAIDSLAANGAKGFVICPPDVSLGPAIVAKAKANGLKVIAVDDRFVDAKGNFMED 131 Query: 126 VPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAA 185 VP + MAA ++G++QG + E +KRGWD K++ + T NELDT ++RT GS+ +L+ A Sbjct: 132 VPYLGMAAFEVGQKQGAAMAAEAKKRGWDWKDTYAVINTFNELDTGKKRTDGSVKSLEEA 191 Query: 186 GFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPE-VKHWLIVGMNDSTVLGGVRATEGQGF 244 G P+ I K+ D+PG+ DA NS LV+ P K+ +I GMND+TVLGGVRATE GF Sbjct: 192 GIPKDHILFTAAKTLDVPGSMDATNSALVKLPSGAKNLIIGGMNDNTVLGGVRATESAGF 251 Query: 245 KAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFT 304 KAA++IGIGING DA+ EL K ++GF+GS+LPSP + GY ++ M+Y WV K EP K+T Sbjct: 252 KAANVIGIGINGTDAIGELKK-PSSGFFGSMLPSPHIEGYNTALMMYEWVTKGTEPAKYT 310 Query: 305 EVTDVVLITRDNFKEELEKKGL 326 + +V LITR+NF+ EL K GL Sbjct: 311 AMDEVTLITRENFQAELTKIGL 332 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: 355 Number of extensions: 14 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: 334 Length adjustment: 28 Effective length of query: 301 Effective length of database: 306 Effective search space: 92106 Effective search space used: 92106 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