Align Rhizopine-binding protein (characterized, see rationale)
to candidate Pf6N2E2_1005 Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)
Query= uniprot:A0A0N9WNI6 (308 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1005 Length = 317 Score = 133 bits (335), Expect = 5e-36 Identities = 98/313 (31%), Positives = 158/313 (50%), Gaps = 15/313 (4%) Query: 4 KIRFASLALSLMLASG-------AALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDG 56 K + L S +LA+G A A +I ++ + Y+ E ++AK + Sbjct: 2 KAQKGGLLCSAVLAAGLTFQLSPAFAAGEKILINFQTLSIPYFIYMHEQASQEAKVL--N 59 Query: 57 VKLQFEDARSDVVKQLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRR 116 V+L +DA+S KQ S VE+ ++Q VDA+VV P D A + +PLV V+RR Sbjct: 60 VELLVQDAQSSSTKQSSDVENALTQGVDAMVVAPNDVTALAPALNEVLSEKVPLVTVDRR 119 Query: 117 PDDLKLPKGVITVASNDLEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEV 176 + P V V ++ + G++ + + MK + + G +++ +R KGV E Sbjct: 120 VEGTDTP--VPYVTADSVAGGRLMAELVTSNMKNGARVAFIGGTPGSSTAIDRAKGVHEG 177 Query: 177 LAKYPG-IKIDQEQTGTWSRDKGMTLVNDWLT--QGRKFDAIVSNNDEMAIGAAMALKQA 233 L G ++ EQ+G W R K M++ + LT DAI+ + +MA+GAA A++ Sbjct: 178 LKAGGGKFQLVAEQSGEWERAKAMSVAENILTSLSANPPDAIICASGDMALGAAEAVRAT 237 Query: 234 GVEKGSVLIAGVDGTPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAKNEPVEQAVW 293 G+ KG V + G D P+ LRA++ GD+A V Q + Q ++ AVK + E + V Sbjct: 238 GL-KGKVKVIGFDAYPEVLRAIRDGDIAGIVEQSPSKQIRTALRMAVKKVRGEGELETVI 296 Query: 294 VPYRLITPENVDQ 306 V +ITPEN+ Q Sbjct: 297 VQPFMITPENLSQ 309 Lambda K H 0.315 0.130 0.360 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: 206 Number of extensions: 6 Number of successful extensions: 4 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: 308 Length of database: 317 Length adjustment: 27 Effective length of query: 281 Effective length of database: 290 Effective search space: 81490 Effective search space used: 81490 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 (21.5 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