Align L-arabinose-binding periplasmic protein; ABP (characterized)
to candidate Pf1N1B4_411 L-arabinose-binding periplasmic protein precursor AraF (TC 3.A.1.2.2)
Query= SwissProt::P02924 (329 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_411 Length = 334 Score = 366 bits (940), Expect = e-106 Identities = 189/321 (58%), Positives = 240/321 (74%), Gaps = 4/321 (1%) Query: 9 AAIGLAAVMSQSAM--AENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDG 66 AA+ + AV S + AE +K+GFLVKQ EEPWFQTEW FA+KAGKD GF +IKIAVPDG Sbjct: 13 AALAVTAVSLSSTLLAAEEVKIGFLVKQAEEPWFQTEWAFAEKAGKDKGFTLIKIAVPDG 72 Query: 67 EKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPMDTV 126 EKTL+AIDSLAA+GAKGFVIC PD LG AI+AKA+ +KVIAVDD+FV+A GK M+ V Sbjct: 73 EKTLSAIDSLAANGAKGFVICPPDVSLGPAIMAKAKLNGLKVIAVDDRFVDAGGKFMEDV 132 Query: 127 PLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAG 186 P + MAA ++G++QG + E +KRGW+ K++ + T NELDT ++RT GS+ AL+ AG Sbjct: 133 PYLGMAAFEVGQKQGAAMATEAKKRGWEWKDTYAVINTYNELDTGKKRTDGSVKALEDAG 192 Query: 187 FPEKQIYQVPTKSNDIPGAFDAANSMLVQHP-EVKHWLIVGMNDSTVLGGVRATEGQGFK 245 P+ I K+ D+PG+ DA NS LV+ P K+ +I GMND+TVLGGVRATE GF Sbjct: 193 MPKDHILFSALKTLDVPGSMDATNSALVKLPGAAKNLIIGGMNDNTVLGGVRATESAGFA 252 Query: 246 AADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFTE 305 AA++IGIGING DA+ EL K +GF+GS+LPSP + GY ++ M+Y WV EPPK+T Sbjct: 253 AANVIGIGINGTDAIGELKKPN-SGFFGSMLPSPHIEGYNTASMMYEWVTTGKEPPKYTA 311 Query: 306 VTDVVLITRDNFKEELEKKGL 326 + DV LITRDNFK+ELEK GL Sbjct: 312 MDDVTLITRDNFKQELEKIGL 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: 357 Number of extensions: 15 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