Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_057507532.1 ABB28_RS04725 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_001431535.1:WP_057507532.1 Length = 298 Score = 83.2 bits (204), Expect = 7e-21 Identities = 75/241 (31%), Positives = 110/241 (45%), Gaps = 34/241 (14%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 L + + +++ +A+ S + + G++ AL+G NGAGKTT + G P G +T Sbjct: 8 LAALHDVQVRYRNAIALAGVSLQVRPGEVLALLGRNGAGKTTAIAVLLGLRLPDAGQVT- 66 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 LL P R +E +V Q+ L L V E LV Q + Y Sbjct: 67 --------LLGGDPQCRSQRE-QVGVMLQDTALPPKLRVGE--LVEQFR-----ASY--- 107 Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193 P R A+ + +A DL RA G L G QRR++ A A+C GP LL Sbjct: 108 ------PRPRPLADCLAIAGV----QDLQQRA---YGQLSGGQQRRVQFAIALCGGPRLL 154 Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253 LDEP GL+ + + +RAE G I+L H + ++ VVVLE G+ ++D Sbjct: 155 FLDEPTTGLDIEARQAMWHAIAQLRAE-GCGIVLTTHYLEEAEALASRVVVLEQGRVLAD 213 Query: 254 G 254 G Sbjct: 214 G 214 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: 187 Number of extensions: 13 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: 298 Length adjustment: 26 Effective length of query: 266 Effective length of database: 272 Effective search space: 72352 Effective search space used: 72352 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 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