Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate 16034 b1920 cystine transporter subunit (NCBI)
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__Keio:16034 Length = 266 Score = 138 bits (348), Expect = 1e-37 Identities = 84/248 (33%), Positives = 131/248 (52%), Gaps = 6/248 (2%) Query: 8 LLASLAAAAFCTTGAQ---AQDNVLRVGTDATFPPMEFV-ENGKRTGFDIELVEAIAKTM 63 L+A ++ +F G + L VG + T+PP F ++GK TGF++E + +AK + Sbjct: 19 LVAGMSVKSFADEGLLNKVKERGTLLVGLEGTYPPFSFQGDDGKLTGFEVEFAQQLAKHL 78 Query: 64 GKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNK 123 G + + G++ L SKR D+ ++ + I+DERKK DF+ Y G+ +VK N+ Sbjct: 79 GVEASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALVKKGNE 138 Query: 124 AINKLA-DLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAVTGK 182 K A DL GKKV V +GT +L + V + + + + +GR DA + + Sbjct: 139 GTIKTADDLKGKKVGVGLGTNYEEWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVDR 198 Query: 183 PAAFQYV-RTRPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKK 241 AA V +T L V E + +E G+ALRK +L KAVN AI +++ DGT A+ +K Sbjct: 199 LAALDLVKKTNDTLAVTGEAFSRQESGVALRKGNEDLLKAVNDAIAEMQKDGTLQALSEK 258 Query: 242 WFSNSAAK 249 WF K Sbjct: 259 WFGADVTK 266 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: 147 Number of extensions: 6 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: 249 Length of database: 266 Length adjustment: 24 Effective length of query: 225 Effective length of database: 242 Effective search space: 54450 Effective search space used: 54450 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 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