Align L-arabinose-binding periplasmic protein; Short=ABP (characterized, see rationale)
to candidate PfGW456L13_2120 L-arabinose-binding periplasmic protein precursor AraF (TC 3.A.1.2.2)
Query= uniprot:A0A161H4E4 (334 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2120 Length = 334 Score = 593 bits (1530), Expect = e-174 Identities = 295/334 (88%), Positives = 311/334 (93%) Query: 1 MKHRRGIRSLCRAALAVTAVSLSSHLLAADAVKIGFLVKQAEEPWFQTEWAFAEKAAKDK 60 M R IRSLC AALAV+A SLS+ LLAA+ VKIGFLVKQAEEPWFQTEWAFAEKA K+K Sbjct: 1 MNRRHAIRSLCCAALAVSAFSLSNTLLAAEEVKIGFLVKQAEEPWFQTEWAFAEKAGKEK 60 Query: 61 GFQLIKIAVPDGEKTLSAIDSLAANGAKGFVICPPDVSLGPAIVAKAKLNDMKVIAVDDR 120 GF LIKIAVPDGEKTLSAIDSLAANGAKGFVICPPDVSLGPAI+AKAKLN +KVIAVDDR Sbjct: 61 GFTLIKIAVPDGEKTLSAIDSLAANGAKGFVICPPDVSLGPAIMAKAKLNGLKVIAVDDR 120 Query: 121 FVGSDGKFMEDVPYLGMAAFEVGQKQGGAMAAEAKKRGWDWKDTYAVINTYNELDTGKKR 180 FV + GKFMEDVPYLGMAAFEVGQKQG AMA EAKKRGWDWKDTYAVINTYNELDTGKKR Sbjct: 121 FVDASGKFMEDVPYLGMAAFEVGQKQGNAMATEAKKRGWDWKDTYAVINTYNELDTGKKR 180 Query: 181 TDGSVDALKKAGMPADHILYSALKTLDVPGSMDSTNSALVKLPSAAKNLIIGGMNDNTVL 240 TDGSV AL+ AGMP DHIL++ALKTLDVPGSMD+TNSALVKLP AAKNLIIGGMNDNTVL Sbjct: 181 TDGSVKALQDAGMPKDHILFAALKTLDVPGSMDATNSALVKLPGAAKNLIIGGMNDNTVL 240 Query: 241 GGVRATEAAGFKAANVIGIGINGTDAIGELKKPDSGFFGSMLPSPHIEGYKTAEMMYEWI 300 GGVRATE+AGF AANVIGIGINGTDAIGELKKPDSGF+GSMLPSPHIEGY TA MMYEW+ Sbjct: 241 GGVRATESAGFAAANVIGIGINGTDAIGELKKPDSGFYGSMLPSPHIEGYNTASMMYEWV 300 Query: 301 TTGKEPPKYTAMDEVTLITRENFKQELEKIGLWN 334 TTGKEP KYTAMD+VTLITR+NFKQELEKIGLWN Sbjct: 301 TTGKEPAKYTAMDDVTLITRDNFKQELEKIGLWN 334 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: 501 Number of extensions: 15 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: 334 Length of database: 334 Length adjustment: 28 Effective length of query: 306 Effective length of database: 306 Effective search space: 93636 Effective search space used: 93636 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