Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS29450 RR42_RS29450 ABC transporter
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Cup4G11:RR42_RS29450 Length = 265 Score = 207 bits (527), Expect = 2e-58 Identities = 115/264 (43%), Positives = 161/264 (60%), Gaps = 9/264 (3%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 DTLL V LS++FGG++A+ SF+ +RG++ LIGPNGAGKTTVFN I+ Y PT G I Sbjct: 3 DTLLSVRDLSVRFGGVLALGGVSFDVRRGEVFTLIGPNGAGKTTVFNLISRIYPPTSGEI 62 Query: 72 TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131 + S L RLP I + +ARTFQNI LF TVL+NLL+ H +ASG+ Sbjct: 63 LWQGSS-----LTRLPPHAIAAQG-IARTFQNIELFEHATVLQNLLIGHHTH--RASGFW 114 Query: 132 ILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPE 191 L+ +R A A +E DL D LPYG ++ +E+ARA+C+ P Sbjct: 115 A-DLLFTPAARRSELAARHKAEEMIELLDLQAHRDALVAGLPYGVRKVVELARALCSSPR 173 Query: 192 LLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKI 251 LL LDEP++GLN E+ + ++ I++E G ++L++EHDMS+V +SD V+ + GQ + Sbjct: 174 LLLLDEPSSGLNVEETEDMAWWIRDIQSELGITVLMVEHDMSLVSRVSDRVLAMNQGQVL 233 Query: 252 SDGTPDHVKNDPRVIAAYLGVEDE 275 + GTP V+ P VI AYLG D+ Sbjct: 234 AQGTPAEVQEHPGVIEAYLGTVDD 257 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: 184 Number of extensions: 6 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