Align ABC transporter for L-Histidine, periplasmic substrate-binding component 2 (characterized)
to candidate YP_004142525.1 Mesci_3352 family 3 extracellular solute-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2562 (321 letters) >NCBI__GCF_000185905.1:YP_004142525.1 Length = 316 Score = 360 bits (925), Expect = e-104 Identities = 181/310 (58%), Positives = 228/310 (73%), Gaps = 2/310 (0%) Query: 11 LAAAAACVMALAAPAQAQDTKIVLGMSGWTGFAPLTLADKAGIFKKNGLDVEIKMIPQKD 70 L A L+APA A T + +G+SGWTGFAPLTLA +AGIF+K+GLDV +K +PQ Sbjct: 7 LTATLTLAAGLSAPAMAA-TSVTIGISGWTGFAPLTLAKQAGIFEKHGLDVTLKKVPQAS 65 Query: 71 RHLALASKSIQCAATTVETHVAWNANGVPIVQIFQMDKSYGADGIAVRGDIKSFADLKGK 130 R LA+AS +QCAATTVET + WNA+GV QIFQ+DKSYGADGI R +IK+ ADLKGK Sbjct: 66 RPLAIASGDLQCAATTVETWLVWNASGVTTKQIFQLDKSYGADGIVARNNIKTVADLKGK 125 Query: 131 TIGVDAPGTAPYFGLAWMLSKNGMSLKDVKTTTLSPQAAAQAFVAGQNDAAMTYEPYLST 190 + APGT+PYF LAW+L+KNG+S KDV L P AAAQAF+AGQNDAA+TYEP++S Sbjct: 126 NVASSAPGTSPYFMLAWVLNKNGISTKDVTVVNLEPDAAAQAFLAGQNDAAVTYEPFISA 185 Query: 191 VRDNPAAGKILATTLDYPMVMDTVGCDPTWLKANGKAAQALANSYFQALDMIKADPAKSN 250 VRD G ILATTLDYPMV+DTVGC P +LK N AA+ALA+SYF ALD+IK+DP KS Sbjct: 186 VRDKSDQGHILATTLDYPMVLDTVGCTPEFLKTNPDAAKALADSYFDALDLIKSDPQKSY 245 Query: 251 EIMGAAVKQTGEQFAKSSSFLRWQDKAANQKFFAGELTTFMKDATAILLEAGIIRKANED 310 E MGA VKQ+ ++F S+ +L+W D+A N++FF E F K A +LL+ G+I++A D Sbjct: 246 ETMGADVKQSAKEFEDSAKYLKWADRAENKQFFTKEFQDFSKTAGELLLQMGLIKEA-PD 304 Query: 311 LAVTFDASFI 320 + D S + Sbjct: 305 VTTLADTSAV 314 Lambda K H 0.317 0.129 0.374 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: 342 Number of extensions: 11 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: 321 Length of database: 316 Length adjustment: 27 Effective length of query: 294 Effective length of database: 289 Effective search space: 84966 Effective search space used: 84966 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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