Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_011383782.1 AMB_RS06945 phosphate ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >NCBI__GCF_000009985.1:WP_011383782.1 Length = 259 Score = 153 bits (387), Expect = 3e-42 Identities = 94/246 (38%), Positives = 138/246 (56%), Gaps = 9/246 (3%) Query: 9 ISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVA 68 IS L ++G Q L + +I +V ++IGPSGCGKSTFLRC+NR+ + G Sbjct: 12 ISARGLNVHYGEKQALHDIDLDIPAGEVTALIGPSGCGKSTFLRCINRMNDMVDGAKVTG 71 Query: 69 GVDLSGAKIDQKHLR--QLRVRVGMVFQHFNLFPHLTVLQNLLLAPR-KVLRIPMAEAKD 125 + L G+ + + L QLR RVGMVFQ N FP ++ N+ PR L AE + Sbjct: 72 SLTLDGSDVYDRSLDVVQLRARVGMVFQKPNPFPK-SIYDNVAYGPRIHGLARDQAELDE 130 Query: 126 RALTYLDKVGLGTKADNYPDQ----LSGGQKQRVAIARGLCMKPEILLFDEPTSALDPEL 181 + L+K GL + ++ + LSGGQ+QR+ IAR + + PE++L DEP SALDP Sbjct: 131 IVMNSLEKAGLLAEVESRLSESGTGLSGGQQQRLCIARAIAVAPEVILMDEPCSALDPIA 190 Query: 182 VGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDR 241 +V ++ +L + T+ +VTH MQ A VS R FF+ G + E G E+F NPK Sbjct: 191 TAKVEELIDEL-RDNYTIVIVTHSMQQAARVSQRTAFFHLGKLIEVGGTEEIFTNPKEPL 249 Query: 242 LRAFLS 247 + +++ Sbjct: 250 TQGYIT 255 Lambda K H 0.321 0.139 0.397 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: 180 Number of extensions: 6 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: 252 Length of database: 259 Length adjustment: 24 Effective length of query: 228 Effective length of database: 235 Effective search space: 53580 Effective search space used: 53580 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