Align Rhizopine-binding protein (characterized, see rationale)
to candidate 16259 b2150 methyl-galactoside transporter subunit (NCBI)
Query= uniprot:A0A0N9WNI6 (308 letters) >FitnessBrowser__Keio:16259 Length = 332 Score = 135 bits (339), Expect = 2e-36 Identities = 99/332 (29%), Positives = 169/332 (50%), Gaps = 31/332 (9%) Query: 2 KTKIRFASLALSLMLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQF 61 K + +++ S++ + A AD RIGV++ ++DD +++ +R+++++ AK+ PD V+L Sbjct: 3 KKVLTLSAVMASMLFGAAAHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPD-VQLLM 61 Query: 62 EDARSDVVKQLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLK 121 D+++D KQ Q++ +++ V A+ +N VD AA + E A +P+V+ N+ P Sbjct: 62 NDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKA 121 Query: 122 LPK--GVITVASNDLEAGQMQMQYLAE----------KMKGKGDIVILLGDLANNSTTNR 169 L V ++ E+G +Q +A+ G+ V+L G+ + R Sbjct: 122 LDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEAR 181 Query: 170 TKGV-KEVLAKYPGIKIDQEQ--TGTWSRDKGMTLVNDWLT--QGRKFDAIVSNNDEMAI 224 T V KE+ K GIK +Q Q T W + ++ WL+ K + +++NND MA+ Sbjct: 182 TTYVIKELNDK--GIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAM 239 Query: 225 GAAMALKQAGVEKGSVLIAGVDGTPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAK 284 GA ALK K S+ + GVD P+ L VK G LA +V DAN QA + D A +A Sbjct: 240 GAVEALK--AHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLAD 297 Query: 285 NEPV---------EQAVWVPYRLITPENVDQF 307 + + V VPY + +N+ +F Sbjct: 298 GKGAADGTNWKIDNKVVRVPYVGVDKDNLAEF 329 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: 264 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: 308 Length of database: 332 Length adjustment: 28 Effective length of query: 280 Effective length of database: 304 Effective search space: 85120 Effective search space used: 85120 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