Align ABC transporter (characterized, see rationale)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 145 bits (366), Expect = 1e-39 Identities = 93/242 (38%), Positives = 139/242 (57%), Gaps = 18/242 (7%) Query: 4 LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDS------ICG 57 + + V K GG LR+VSL++A GE +V GPSG GKSTL+R I GL++ G Sbjct: 2 IHMAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIG 61 Query: 58 GDLLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFG----LKLAKTDKTSLRER 113 D + RRV L+ VGMVFQ + L+PH+++ +N + LA+ +L Sbjct: 62 EDEVRPDRRV--LQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARE 119 Query: 114 VLKTAQIL-QLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQM 172 +L+ +I Q DK P +LSGGQ+QR A+ RA+A +P+I+LFDEP S LDA + V+ Sbjct: 120 LLERVRIADQADKY----PAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEM-VKE 174 Query: 173 RNEIARLHDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAG 232 +I + G TM+ VTH+ A +AD+I+ ++ G++ + GSPR+ + P Sbjct: 175 VLDIMKALATEGITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRA 234 Query: 233 FL 234 FL Sbjct: 235 FL 236 Lambda K H 0.320 0.137 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: 209 Number of extensions: 6 Number of successful extensions: 4 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: 381 Length of database: 241 Length adjustment: 27 Effective length of query: 354 Effective length of database: 214 Effective search space: 75756 Effective search space used: 75756 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 (21.8 bits) S2: 48 (23.1 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