Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate WP_011383782.1 AMB_RS06945 phosphate ABC transporter ATP-binding protein
Query= uniprot:Q88GX0 (260 letters) >NCBI__GCF_000009985.1:WP_011383782.1 Length = 259 Score = 155 bits (392), Expect = 8e-43 Identities = 97/246 (39%), Positives = 137/246 (55%), Gaps = 14/246 (5%) Query: 21 IRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLE-----VAQQG 75 I GLN HYG L DIDL + GE L GPSG GKST +RCINR+ G Sbjct: 12 ISARGLNVHYGEKQALHDIDLDIPAGEVTALIGPSGCGKSTFLRCINRMNDMVDGAKVTG 71 Query: 76 SIQVDGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAE-- 133 S+ +DG D+ + + Q+R+ +GMVFQ N FP S+ DN P + GL+R AE Sbjct: 72 SLTLDGSDVYDRSLDVVQLRARVGMVFQKPNPFP-KSIYDNVAYGP-RIHGLARDQAELD 129 Query: 134 ERARMYLSKVG----IESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPE 189 E L K G +ES+ + + LSGGQQQR+ IARA+ + P ++L DEP SALDP Sbjct: 130 EIVMNSLEKAGLLAEVESRLSESGTGLSGGQQQRLCIARAIAVAPEVILMDEPCSALDPI 189 Query: 190 MVAEVLDVLVQLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTE 249 A+V +++ +L T++ VTH M A +V++R F G++IE + F P+ Sbjct: 190 ATAKVEELIDELR-DNYTIVIVTHSMQQAARVSQRTAFFHLGKLIEVGGTEEIFTNPKEP 248 Query: 250 RAKAFL 255 + ++ Sbjct: 249 LTQGYI 254 Lambda K H 0.322 0.137 0.395 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: 171 Number of extensions: 8 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: 260 Length of database: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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