Align ATPase (characterized, see rationale)
to candidate WP_041670877.1 RSPH17029_RS18130 amino acid ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_000015985.1:WP_041670877.1 Length = 242 Score = 281 bits (720), Expect = 7e-81 Identities = 144/241 (59%), Positives = 180/241 (74%), Gaps = 1/241 (0%) Query: 21 MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80 MI V KWYG+ FQ L VSL V++GE VV+ GPSGSGKST +R +N LE HQ G+I+ Sbjct: 1 MIRMSHVSKWYGH-FQVLHDVSLDVRKGERVVVCGPSGSGKSTLIRCINRLEVHQSGQIF 59 Query: 81 IEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQ 140 ++G ++ + ++I TIR+ +GMVFQ FNLFPHLTVL+NL L P+ R+ + AE A Sbjct: 60 VKGLEMTDNVKNIDTIRRHIGMVFQNFNLFPHLTVLENLTLGPMLTRQMKKSAAEDLAMH 119 Query: 141 LLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVM 200 L +VRI EQ+ KYP QLSGGQQQRVAIAR+L M+P I+LFDEPTSALDPEM++EVLD M Sbjct: 120 FLRKVRIPEQSGKYPLQLSGGQQQRVAIARSLCMEPEIMLFDEPTSALDPEMIKEVLDTM 179 Query: 201 RDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260 +LA GMTM+V THE+GFAR VAD VV MADG+ VE PP+ FF P+ +R + FL QI Sbjct: 180 IELAESGMTMIVVTHEMGFARTVADNVVFMADGRKVESGPPEEFFGNPREERTRAFLDQI 239 Query: 261 L 261 L Sbjct: 240 L 240 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: 203 Number of extensions: 6 Number of successful extensions: 1 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: 242 Length adjustment: 24 Effective length of query: 237 Effective length of database: 218 Effective search space: 51666 Effective search space used: 51666 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 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