Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_011385946.1 AMB_RS18160 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_000009985.1:WP_011385946.1 Length = 265 Score = 193 bits (490), Expect = 4e-54 Identities = 101/269 (37%), Positives = 170/269 (63%), Gaps = 8/269 (2%) Query: 8 TMSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPT 67 +++D+ +L+V +S+ FGG+ A+ + SF+ +G++ ++IGPNGAGKT++ NC++G YKPT Sbjct: 2 SVTDNPVLEVRDVSLAFGGVRALTEVSFQVNKGELFSIIGPNGAGKTSMLNCVSGRYKPT 61 Query: 68 MGMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKA 127 G + + + + P+ R T + RTFQN+ LF ++VL+N++V +H+ L Sbjct: 62 SGRVFMDGRD----VTGLSPNVRAT--LGLGRTFQNLALFGHMSVLDNIMVGRHHLLGNN 115 Query: 128 SGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMC 187 + L + G K E A ++ ++ ++ AG LPYG ++R+E+ARAM Sbjct: 116 AATGALYWLS-GARKEELAHRRKVEDI-IDFLEIAHIRKAVAGTLPYGLRKRVELARAMA 173 Query: 188 TGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEY 247 P+++ LDEP AG+N E + + + E G ++++IEHDM VVM+IS V+VLE+ Sbjct: 174 VEPKVILLDEPMAGMNLEEKEDMARYIVDLNEEWGMTVIMIEHDMGVVMDISHRVMVLEF 233 Query: 248 GQKISDGTPDHVKNDPRVIAAYLGVEDEE 276 G+KI++G PD V N+ RV AYLG++++E Sbjct: 234 GRKIAEGLPDEVMNNERVKVAYLGIDEDE 262 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: 186 Number of extensions: 9 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: 265 Length adjustment: 25 Effective length of query: 267 Effective length of database: 240 Effective search space: 64080 Effective search space used: 64080 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 17 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