Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate AZOBR_RS27130 AZOBR_RS27130 polyamine ABC transporter substrate-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__azobra:AZOBR_RS27130 Length = 259 Score = 97.8 bits (242), Expect = 2e-25 Identities = 71/251 (28%), Positives = 114/251 (45%), Gaps = 13/251 (5%) Query: 3 LRRNLLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFVE-NGKRTGFDIELVEAIAK 61 L L + A AA T ++A LR+ T+ +PP +G G ++EL A+ + Sbjct: 4 LALGLAMGLCALAAAVPTASRADGPPLRIATEGAYPPFNMTSPDGTLGGLEVELANALCE 63 Query: 62 TMGKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKAD 121 + ++ V D+ G+IPGL+S+R+D ++ + IT ER K + F+ Y + Sbjct: 64 RIKRRCTLVAQDWDGIIPGLLSRRYDAIMATMNITPERAKAIAFSAPYMVVPAYFVAATG 123 Query: 122 NKAINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNL---VDIGRADAA 178 A L GK V Q T Y+ + F K V ++ NL + GR DAA Sbjct: 124 GGIDGTEATLAGKSVGAQTSTTHYRYVEKHFGKT--VSLKNYDTASNLLADLKSGRIDAA 181 Query: 179 VTGKPAAFQYVRTRP-------GLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKA 231 +T A +V+ G ++D ++ G+ LRK+ +L A + AI + Sbjct: 182 ITTGATASDWVKADASKSLQLVGKPLVDAEVFGPGVGVGLRKEDADLKAAFDAAIASVVQ 241 Query: 232 DGTYAAIVKKW 242 DGT A I K+ Sbjct: 242 DGTLARIAAKY 252 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: 157 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: 259 Length adjustment: 24 Effective length of query: 225 Effective length of database: 235 Effective search space: 52875 Effective search space used: 52875 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