Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_010442657.1 G7G_RS0117040 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >NCBI__GCF_000192475.1:WP_010442657.1 Length = 349 Score = 305 bits (781), Expect = 9e-88 Identities = 151/262 (57%), Positives = 203/262 (77%), Gaps = 1/262 (0%) Query: 9 IEVKNVFKIFGNRSKEALELIR-QNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMGLS 67 I+ K V+K+FG RS+EAL+ I + +K +VL CVVGV D S I GE+F +MGLS Sbjct: 7 IDAKGVWKVFGARSQEALQAIHSEGLSKTEVLEHFDCVVGVADASFEIERGELFCVMGLS 66 Query: 68 GSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLLPHKSV 127 GSGKSTLVRH NRL++PT G I +DGED++ L+ ++LR+ R +++MVFQ+FGL+PH++V Sbjct: 67 GSGKSTLVRHVNRLLEPTDGHIYLDGEDVMGLNDESLRDLRNRRVAMVFQNFGLMPHRTV 126 Query: 128 LDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARALAADT 187 DNVA L++RG K E A + V L G+E+KY H+LSGGM+QRVGLARA+AAD Sbjct: 127 RDNVAMPLEIRGTGKARRWEEADRVLELVELNGWEDKYAHELSGGMQQRVGLARAIAADP 186 Query: 188 DIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDGKL 247 +I+LMDE FSALDPLIR ++QDQ ++L L+KT +FITHDLDEA+RIG+RIAI+KDG++ Sbjct: 187 EILLMDEPFSALDPLIRKQLQDQFMDLSHKLNKTTMFITHDLDEAIRIGHRIAIMKDGRI 246 Query: 248 IQVGTPREILHSPADEYVDRFV 269 +Q+GTP EI+ +PAD+YV FV Sbjct: 247 VQIGTPEEIILNPADDYVADFV 268 Lambda K H 0.321 0.138 0.387 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: 311 Number of extensions: 10 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: 276 Length of database: 349 Length adjustment: 27 Effective length of query: 249 Effective length of database: 322 Effective search space: 80178 Effective search space used: 80178 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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