Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_013528159.1 MESCI_RS01435 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_000185905.1:WP_013528159.1 Length = 311 Score = 195 bits (495), Expect = 1e-54 Identities = 107/262 (40%), Positives = 158/262 (60%), Gaps = 9/262 (3%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 LL ++ +S+ FGG++A+ D ++G+I A+IGPNGAGK+++ N I+G Y+P G + Sbjct: 52 LLSLQGISLSFGGVVALADIDLSVRQGEIRAIIGPNGAGKSSLINVISGVYRPDRGHVQL 111 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 + S Q +RL VARTFQN+ LF GL+VL+N+ K+ +L Sbjct: 112 DGTSYAQVPTQRLAHLG------VARTFQNLALFKGLSVLDNVASGLAYKVRSNFAGQVL 165 Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193 G +G + E ++ A LE L D G LPYG Q+R+E+ARA+ P LL Sbjct: 166 G---IGRSRGEQRDSRSRAEQILEFLHLTAIRDRLVGTLPYGLQKRVELARALVAEPRLL 222 Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253 LDEP AG+ E + + + +++ R T+++LIEHD+ VVM +SD + VL+YG+KI+D Sbjct: 223 LLDEPMAGMTASEKSEMASFVRAARDRFATTVVLIEHDVGVVMGLSDRIAVLDYGRKIAD 282 Query: 254 GTPDHVKNDPRVIAAYLGVEDE 275 TPD V+ND RVI AYLGV + Sbjct: 283 ATPDEVRNDQRVIDAYLGVASD 304 Lambda K H 0.318 0.136 0.386 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: 228 Number of extensions: 12 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: 292 Length of database: 311 Length adjustment: 27 Effective length of query: 265 Effective length of database: 284 Effective search space: 75260 Effective search space used: 75260 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 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