Align ATPase (characterized, see rationale)
to candidate 3608829 Dshi_2221 ABC transporter related (RefSeq)
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Dino:3608829 Length = 259 Score = 232 bits (592), Expect = 5e-66 Identities = 125/248 (50%), Positives = 165/248 (66%), Gaps = 11/248 (4%) Query: 21 MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80 +I + K YG + L GVS+ +RG+VV ++G SGSGKST LR N LE QRG++ Sbjct: 8 VIEIRDLHKAYG-ALEVLKGVSIRAERGDVVSLIGSSGSGKSTLLRCCNLLEDSQRGDVL 66 Query: 81 IEGH----------RLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWP 130 G R D++ + IR + MVFQQFNL+ H+T+L+N+M APV V P Sbjct: 67 FCGEPVTWTGSGLDRRPADKKQVIRIRTNLSMVFQQFNLWAHMTILENVMEAPVTVLGEP 126 Query: 131 VAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDP 190 + EA AR LL++V I ++ D YP QLSGGQQQR AIAR LAM+P+ LLFDEPTSALDP Sbjct: 127 PKEVEARARALLDKVGIGDKCDAYPAQLSGGQQQRAAIARGLAMEPKALLFDEPTSALDP 186 Query: 191 EMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQS 250 E+ +EV+ V++DLA+EG TML+ TH++ A +V+D VV + G I EE PPD F P+S Sbjct: 187 ELEQEVVKVIKDLAAEGRTMLIVTHDMRLAADVSDHVVFLHQGLIEEEGPPDILFGQPKS 246 Query: 251 DRAKQFLA 258 R KQFL+ Sbjct: 247 ARLKQFLS 254 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: 197 Number of extensions: 5 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: 259 Length adjustment: 24 Effective length of query: 237 Effective length of database: 235 Effective search space: 55695 Effective search space used: 55695 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: 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