Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >NCBI__GCF_000526715.1:WP_024852149.1 Length = 263 Score = 160 bits (404), Expect = 3e-44 Identities = 90/247 (36%), Positives = 145/247 (58%), Gaps = 4/247 (1%) Query: 9 VSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLD 68 ++ + + K Q L ++ + ++G SGCGKSTLL+++AGL + G V ++ Sbjct: 10 IAELSHSYKKQLPPVLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVRIN 69 Query: 69 GAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGF 128 G V P A+ M+FQ +L+PW+++ +N GL G + Q+++R + VGL Sbjct: 70 GKTVVKPSAKWNMMFQKPSLYPWMSVRENAALGLVFAGTYK-QKQDRVEELLDMVGLSEH 128 Query: 129 EQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKT 188 + ++LSGG QQR A+AR+LA +P+ILL+DEPF ALD TR +Q + I + T Sbjct: 129 KDKNVQELSGGQQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICHEQGIT 188 Query: 189 VLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMDLKARLTEE 248 ++ VTHDI+EAI MA++V + S PG I +L V L +PR +++ +F++LK L + Sbjct: 189 MIMVTHDIEEAIAMADKVVIMSHNPGEIVGDLDVPLTYPRD---RSAADFIELKETLFNQ 245 Query: 249 IRAESMA 255 +A Sbjct: 246 FEQIDLA 252 Lambda K H 0.322 0.136 0.394 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: 145 Number of extensions: 4 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: 259 Length of database: 263 Length adjustment: 25 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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