Align ATPase (characterized, see rationale)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3200 Length = 604 Score = 248 bits (634), Expect = 2e-70 Identities = 140/276 (50%), Positives = 181/276 (65%), Gaps = 23/276 (8%) Query: 8 PEPVTAIASAPETM------------IYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMG 55 P PV A AP + + GV K YG + L V+LTV G V V++G Sbjct: 330 PGPVVPAAPAPVAVPRWTGALNRGGEVTIHGVSKRYG-ALEVLKDVTLTVLPGSVTVILG 388 Query: 56 PSGSGKSTFLRTLNALESHQRGEIWIEGHRLSHDR----------RDIATIRQEVGMVFQ 105 PSGSGKST LR++N LE G I I+G + + + DI R +VGMVFQ Sbjct: 389 PSGSGKSTLLRSINHLERVDGGFIAIDGELIGYRQDADALYELGENDILKRRVDVGMVFQ 448 Query: 106 QFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQR 165 FNLFPHLTVL+N++ APV VR+ A+AEA A +LL RV ++++A YP QLSGGQQQR Sbjct: 449 NFNLFPHLTVLENIVEAPVTVRKLARAEAEALALELLARVGLSDKAHSYPRQLSGGQQQR 508 Query: 166 VAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLASEGMTMLVATHEVGFAREVAD 225 VAIARALA++P++LLFDEPTSALDPE+V EVLDV+++LA G T+++ THE+GFAREVAD Sbjct: 509 VAIARALALKPKVLLFDEPTSALDPELVGEVLDVIKELARTGTTLVIVTHEIGFAREVAD 568 Query: 226 RVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQIL 261 VV M G++VE P + F+ P R FLA++L Sbjct: 569 TVVFMEQGRVVETGTPAKVFSQPDHPRTAAFLAKVL 604 Lambda K H 0.321 0.134 0.387 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: 369 Number of extensions: 19 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: 261 Length of database: 604 Length adjustment: 31 Effective length of query: 230 Effective length of database: 573 Effective search space: 131790 Effective search space used: 131790 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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