Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_090271761.1 BLU11_RS01725 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_900105005.1:WP_090271761.1 Length = 236 Score = 91.3 bits (225), Expect = 2e-23 Identities = 76/252 (30%), Positives = 124/252 (49%), Gaps = 27/252 (10%) Query: 9 MSDDTLLKVEHLSMKFGG-----LMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGF 63 MSDD +L++E + F ++D RG++TALIGP+G+GK+T+ N I Sbjct: 1 MSDD-VLRLERIGKIFNQGTPLESTVLHDIDLRLGRGELTALIGPSGSGKSTLLNLIGLL 59 Query: 64 YKPTMGMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNK 123 P+ G + + + + + +A + FQ L S +VLEN+L+ Sbjct: 60 DVPSAGELYLQGQPTRDS--DDATRTHLRNQA-LGFVFQFHHLISAFSVLENVLMP---- 112 Query: 124 LMKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIA 183 L+ SG R + EAI+LAR L + L AD ++ G Q+R+ IA Sbjct: 113 LIIRSG-------------RPSTEAIDLARGLLREVGLEKMADKKPTEISGGQQQRVAIA 159 Query: 184 RAMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVV 243 RA+ T P LL DEP L+ + + ++ L + I ++ G SIL++ HD + V Sbjct: 160 RALITRPPLLLADEPTGNLDTKTAESVFDLFRRINSQFGCSILVVTHDPRLAASCPRTVQ 219 Query: 244 VLEYGQKISDGT 255 +++ G+ +SD T Sbjct: 220 LVD-GRIVSDET 230 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: 162 Number of extensions: 9 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: 292 Length of database: 236 Length adjustment: 25 Effective length of query: 267 Effective length of database: 211 Effective search space: 56337 Effective search space used: 56337 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 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