Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate CCNA_00294 CCNA_00294 phosphate transport ATP-binding protein pstB
Query= TCDB::P48243 (242 letters) >FitnessBrowser__Caulo:CCNA_00294 Length = 274 Score = 155 bits (393), Expect = 6e-43 Identities = 101/245 (41%), Positives = 143/245 (58%), Gaps = 12/245 (4%) Query: 2 IKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRL-ETIE----EG 56 IK GV+ ++GD AL D+DL+IP V +GPSG GKST R INR+ +TI EG Sbjct: 27 IKARGVKVFYGDKQALFDVDLDIPAKSVTAFIGPSGCGKSTFLRCINRMNDTIPSARVEG 86 Query: 57 TIEIDGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAP-IKVRKMKKSEAEK 115 +I IDG + + LR+ VGMVFQ N FP TI +NV P I K+E E Sbjct: 87 SILIDGADVNAKSVDPVVLRSRVGMVFQKPNPFPK-TIFENVAYGPRIHGLATGKAELEA 145 Query: 116 LAMSLLERVGIANQ-ADKY---PAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEM 171 + S L++ G+ N+ AD+ LSGGQQQR+ IARA+A++P+++L DEP SALDP Sbjct: 146 IVESSLKKAGLWNEVADRLHQPGTGLSGGQQQRLVIARAIAVSPEVILMDEPCSALDPIA 205 Query: 172 VNEVLDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDR 231 ++ +++ L + +V VTH M A + + R F G +VE + FTNP+ R Sbjct: 206 TAKIEELIDELRSQ-FCIVIVTHSMAQAARVSQRTAFFHLGKLVESGPTEEMFTNPRDSR 264 Query: 232 AKDFL 236 +D++ Sbjct: 265 TQDYI 269 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: 150 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: 242 Length of database: 274 Length adjustment: 24 Effective length of query: 218 Effective length of database: 250 Effective search space: 54500 Effective search space used: 54500 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 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