Align ABC transporter substrate-binding protein (characterized, see rationale)
to candidate Ac3H11_161 TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein
Query= uniprot:A0A165IVH1 (339 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_161 Length = 323 Score = 218 bits (555), Expect = 2e-61 Identities = 119/291 (40%), Positives = 174/291 (59%), Gaps = 2/291 (0%) Query: 33 IRFGYGLNEVSNQGRATKLFAEEVEKASGGKMKVRAIGAAALGSDVQMQQALIGGAQEMM 92 +R + S+QG A FA+EVEK + G+ KV+ ALG + + +A+ G QE+ Sbjct: 26 MRISISTAQNSHQGIAIDTFAKEVEKRTSGRYKVQTFYNGALGGERESIEAVQLGTQELA 85 Query: 93 VGSTATLVGITKEMAIWDTPFLFNNAKEADVVLDGPVGQKVMDKLQEKGLVGLVYWENGF 152 ST + E I D PFLF + A VLDGP+GQ+++ K KG L + ENGF Sbjct: 86 FSSTGPIPNFVPETKILDVPFLFRDKAHARAVLDGPIGQEMLTKFDSKGFKALAWAENGF 145 Query: 153 RNLTNSKRPVNKLEDMDGIKLRVMQNNVFLDSFKTLGANAVPLPFSELFTALETKTVDGQ 212 R++TNSKR VN ED+ G+K+R M+N V + ++K G P+ F E+FTAL+ TVDGQ Sbjct: 146 RHMTNSKRSVNTPEDLKGLKMRTMENPVHIAAYKGFGIITTPMAFPEVFTALQQGTVDGQ 205 Query: 213 ENPYNTILSSKFYEVQKYLTVTNHVYSPWIVLVSKKYWDGLSKAEQKVLLDAAKKSRDFE 272 ENP I+S+KF +VQK+LT+T HVYSP I +++K +D LS A+++ +DAAK+ Sbjct: 206 ENPLPVIISAKFDQVQKHLTLTGHVYSPAIFVMNKGSFDKLSAADKQAFIDAAKEGTKAN 265 Query: 273 RQDTRAEADKALADLKGKGMQVNELPAAEANRMREKLSAVNASIAANVGES 323 R + K +ADL+ KGM V + P + ++ L+ VNA G++ Sbjct: 266 RARVDEDDAKGVADLRAKGMTVVDNP--DKSKFVAALAPVNAEFEKQFGKA 314 Lambda K H 0.316 0.130 0.364 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: 258 Number of extensions: 6 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: 339 Length of database: 323 Length adjustment: 28 Effective length of query: 311 Effective length of database: 295 Effective search space: 91745 Effective search space used: 91745 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