Align Galactofuranose-binding protein YtfQ (characterized)
to candidate Pf6N2E2_1005 Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)
Query= SwissProt::P39325 (318 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1005 Length = 317 Score = 106 bits (265), Expect = 6e-28 Identities = 71/229 (31%), Positives = 120/229 (52%), Gaps = 9/229 (3%) Query: 45 AKSEAEKRGITLKIADGQQKQENQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAE 104 A EA+ + L + D Q Q V + + QGVDA+ +AP T P L E + Sbjct: 51 ASQEAKVLNVELLVQDAQSSSTKQSSDVENALTQGVDAMVVAPNDVTALAPALNEVLSEK 110 Query: 105 IPVFLLDRSIDVKDKSLYMTTVTADNILEGKLIGDWLVKEV-NGKPCNVVELQGTVGASV 163 +P+ +DR ++ D + VTAD++ G+L+ + + + NG V + GT G+S Sbjct: 111 VPLVTVDRRVEGTDTP--VPYVTADSVAGGRLMAELVTSNMKNG--ARVAFIGGTPGSST 166 Query: 164 AIDRKKGFAEAIK-NAPNIKIIRSQSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDD 222 AIDR KG E +K +++ QSG++ R+K V E+ + + + ++ A + D Sbjct: 167 AIDRAKGVHEGLKAGGGKFQLVAEQSGEWERAKAMSVAENILTSLSANPPDAIICA-SGD 225 Query: 223 MVIGAIQAIKEAGLKPGKDILTGSIDGVPDIYKAMMDGEANASVELTPN 271 M +GA +A++ GLK GK + G D P++ +A+ DG+ VE +P+ Sbjct: 226 MALGAAEAVRATGLK-GKVKVIG-FDAYPEVLRAIRDGDIAGIVEQSPS 272 Lambda K H 0.313 0.130 0.363 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: 207 Number of extensions: 14 Number of successful extensions: 5 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: 318 Length of database: 317 Length adjustment: 27 Effective length of query: 291 Effective length of database: 290 Effective search space: 84390 Effective search space used: 84390 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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