Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate BWI76_RS08975 BWI76_RS08975 amino acid ABC transporter substrate-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__Koxy:BWI76_RS08975 Length = 248 Score = 160 bits (406), Expect = 2e-44 Identities = 91/242 (37%), Positives = 130/242 (53%), Gaps = 3/242 (1%) Query: 5 RNLLLASLAAAAFC-TTGAQAQDNVLRVGTDATFPPMEFVENGKRTGFDIELVEAIAKTM 63 +++ SLAA + A D L V TD F P EF + K GFD++L AIAK + Sbjct: 2 KSVFKVSLAALTLAFAVSSHAADKKLVVATDTAFVPFEFKQGDKYVGFDVDLWAAIAKEL 61 Query: 64 GKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNK 123 +DF G+IP L +K D+A++ I ITDERKK +DF+D YY GL+VMV A+N Sbjct: 62 KLDYTLKPMDFSGIIPALQTKNIDLALAGITITDERKKAIDFSDGYYKSGLLVMVNANNN 121 Query: 124 AINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAVTGKP 183 I + DL+GK V+V+ GT SV Y + + + GRADA + P Sbjct: 122 DIKDVKDLNGKVVAVKGGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTGRADAVLHDTP 181 Query: 184 AAFQYVRTRPG--LRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKK 241 +++T + + + L + YG+A K + EL + VNGA+ L+ +GTY I KK Sbjct: 182 NILYFIKTAGNGKFKAVGDSLEAQNYGIAFPKGSDELREKVNGALKTLRENGTYNEIYKK 241 Query: 242 WF 243 WF Sbjct: 242 WF 243 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: 158 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: 248 Length adjustment: 24 Effective length of query: 225 Effective length of database: 224 Effective search space: 50400 Effective search space used: 50400 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