Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_011842445.1 RSPH17029_RS17980 ATP-binding cassette domain-containing protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_000015985.1:WP_011842445.1 Length = 236 Score = 156 bits (394), Expect = 5e-43 Identities = 97/264 (36%), Positives = 139/264 (52%), Gaps = 30/264 (11%) Query: 13 TLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMIT 72 +LL++E L ++FGGL+A+ D S + G I L+GPNGAGKTT+ N I+G +PT G + Sbjct: 2 SLLQLEKLGVRFGGLVAVQDVSLAVEEGQIYGLLGPNGAGKTTLVNMISGLIRPTSGSLR 61 Query: 73 FNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTI 132 F ++G + + + RTFQ R F GL+V ENL +A A + Sbjct: 62 FAGEAGGPWPIAD------AVSRGIVRTFQQTRAFLGLSVRENLRIAAAASGRDADAAEL 115 Query: 133 LGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192 + G+GP ++DR PAGDLPY R L IA A+ P L Sbjct: 116 IEAFGLGP--------------------VLDR---PAGDLPYATLRHLGIALALTLKPRL 152 Query: 193 LCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKIS 252 L LDEPA GL E L L++ A G ++LLIEH++ +M ++D V VL+ G+ + Sbjct: 153 LLLDEPAVGLTGGEVDRLARLIRDWNAR-GVTVLLIEHNVRFLMSLADRVAVLDRGRLLF 211 Query: 253 DGTPDHVKNDPRVIAAYLGVEDEE 276 +GT + +P VI YLG E+ Sbjct: 212 EGTAADCQRNPEVIDVYLGRRKED 235 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: 189 Number of extensions: 12 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: 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 Apr 10 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