Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate BWI76_RS14445 BWI76_RS14445 amino acid ABC transporter substrate-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__Koxy:BWI76_RS14445 Length = 250 Score = 160 bits (404), Expect = 3e-44 Identities = 95/246 (38%), Positives = 137/246 (55%), Gaps = 7/246 (2%) Query: 3 LRRNLLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFVENGKRTGFDIELVEAIAKT 62 L + L + A + AQD +L VG D F P EF + K GFDI+L +AIAK Sbjct: 4 LLKKLKITLALVACSASFAVMAQDKIL-VGVDTAFVPFEFKQGNKYVGFDIDLWQAIAKK 62 Query: 63 MGKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADN 122 M E +DF GLIPGL S+ D+A++ I ITD RK+VVDF+D YY L++ VK+ + Sbjct: 63 MNVSYELRPMDFSGLIPGLQSRNLDVAMAGITITDARKQVVDFSDGYYDADLLMAVKSGD 122 Query: 123 KAINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAVTGK 182 +I K ++L GKKV ++ GT + ++ K+ K VE + + G DA V Sbjct: 123 DSITKFSELAGKKVGLKQGTAAAIFMKSKY-KANYVEFPNIDNAYLDLQAGNLDAVVHDS 181 Query: 183 PAAFQYVRTRPGLRVLD----EQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAI 238 P YV+T G +V + + ++YG AL+K++ LT V+ A+ L+ADGTY I Sbjct: 182 PNVLYYVKTAGGGKVKSTGETDSILPQKYGFALQKNS-SLTPKVDAALNALRADGTYDKI 240 Query: 239 VKKWFS 244 KWF+ Sbjct: 241 YFKWFN 246 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: 162 Number of extensions: 5 Number of successful extensions: 2 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: 250 Length adjustment: 24 Effective length of query: 225 Effective length of database: 226 Effective search space: 50850 Effective search space used: 50850 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: 46 (22.3 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