Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_157123969.1 B9N75_RS12890 phosphate ABC transporter ATP-binding protein
Query= TCDB::P48243 (242 letters) >NCBI__GCF_900177405.1:WP_157123969.1 Length = 267 Score = 149 bits (375), Expect = 7e-41 Identities = 95/245 (38%), Positives = 139/245 (56%), Gaps = 12/245 (4%) Query: 2 IKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRL-ETIE----EG 56 I+ V ++G+ A+ D+ ++I + V +GPSG GKST RT+NR+ +TI EG Sbjct: 20 IRAENVSVFYGNKKAIDDVSIDIDQDNVTAFIGPSGCGKSTFLRTLNRMNDTIASARVEG 79 Query: 57 TIEIDGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAP-IKVRKMKKSEAEK 115 I +DG+ + G + LRA VGMVFQ N FP +I DNV P I KSE E Sbjct: 80 RITLDGEDIYSSGMDVVQLRARVGMVFQKPNPFPK-SIFDNVAYGPRIHGLATSKSELEG 138 Query: 116 LAMSLLERVGIANQADKYPAQ----LSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEM 171 + L+R G+ ++ A LSGGQQQR+ IARA+A++P+++L DEP SALDP Sbjct: 139 IVERSLKRAGLWDEVKDRLADSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIA 198 Query: 172 VNEVLDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDR 231 ++ +++ L + +V VTH M A + + R F G +VE + + FTNP R Sbjct: 199 TAKIEELIHEL-RGRYAIVIVTHNMQQAARVSQRTAFFHLGHLVEYGDTSAIFTNPTETR 257 Query: 232 AKDFL 236 KD++ Sbjct: 258 TKDYI 262 Lambda K H 0.319 0.135 0.379 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: 160 Number of extensions: 10 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: 242 Length of database: 267 Length adjustment: 24 Effective length of query: 218 Effective length of database: 243 Effective search space: 52974 Effective search space used: 52974 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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