Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate WP_092482462.1 BM299_RS05460 amino acid ABC transporter substrate-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >NCBI__GCF_900115975.1:WP_092482462.1 Length = 285 Score = 128 bits (322), Expect = 1e-34 Identities = 79/241 (32%), Positives = 129/241 (53%), Gaps = 8/241 (3%) Query: 11 SLAAAAFCTTGAQAQDN-VLRVGTDATFPPMEFV-ENGKRTGFDIELVEAIAKTMGKQVE 68 +++A A TT Q+ V+ +G D TF PM F ENG+ GFDI++ + K +G ++E Sbjct: 35 AVSADAEKTTWELIQEKGVMTIGLDDTFRPMGFRDENGQLVGFDIDMGKEFEKRLGVKME 94 Query: 69 WVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKAINKL 128 W+ D+ G+ L SK+FD+ ++ + IT+ERKKV+DF+ Y + + V+ DN I Sbjct: 95 WIPTDWSGVTGALNSKKFDVVINGMSITEERKKVIDFSIPYVNASIGMAVQKDNNDIKTR 154 Query: 129 ADLDGKKVSVQVGT---KSVSYLTEK--FPKVQRVEVEKNQEMFNLVDIGRADAAVTGKP 183 DL GK V+ Q G+ ++ L E + + + E F + GR D V Sbjct: 155 DDLKGKTVATQAGSSGYEACKKLVEDGIIDETNLKQYNQYPEAFQDLAFGRVDVVVVDVT 214 Query: 184 AAFQYVRTRPG-LRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKKW 242 A +V RP +V++E L + Y + LRK+ +L + ++ + ++ DGT I K+W Sbjct: 215 TAQDFVNKRPDTYKVVEEPLVEDFYAIGLRKEDKDLKEVLDKTLREMMEDGTLVEISKRW 274 Query: 243 F 243 F Sbjct: 275 F 275 Lambda K H 0.317 0.133 0.369 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: 198 Number of extensions: 12 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: 249 Length of database: 285 Length adjustment: 25 Effective length of query: 224 Effective length of database: 260 Effective search space: 58240 Effective search space used: 58240 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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