Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate 6936584 Sama_0772 ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__SB2B:6936584 Length = 319 Score = 95.5 bits (236), Expect = 1e-24 Identities = 68/228 (29%), Positives = 121/228 (53%), Gaps = 21/228 (9%) Query: 12 LAASGLCKSF-GGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRV-I 69 L GL K++ GG++AV+ +EVA+G L+GPNGAGK+T ++S+ ++ G+V + Sbjct: 10 LRIEGLKKTYKGGVEAVKGISLEVAKGDFFALLGPNGAGKSTTIGIISSLVQKSSGKVEV 69 Query: 70 FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129 F + +QL+ ++ + + F + E +L Q G ++ V +P+ + Sbjct: 70 FGHDIDRQLEAAKLCIGLVPQEF-------NFNQFETVLQIVVNQAG--YYGVP-RPEAL 119 Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189 ++ EK L ++ L K + LSGG ++ L + RALM PKL++LDEP AG Sbjct: 120 LRAEK--------YLSALDLWDKRNSPSRQLSGGMKRRLMIARALMHEPKLLILDEPTAG 171 Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQ 237 V+ L + + NRQ G+T ++ H ++ LC + ++ +G+ Sbjct: 172 VDIELRRSMWSFLTELNRQ-GVTIILTTHYLEEAEMLCRNIGIIDKGE 218 Lambda K H 0.319 0.136 0.391 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: 151 Number of extensions: 8 Number of successful extensions: 3 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: 319 Length adjustment: 26 Effective length of query: 234 Effective length of database: 293 Effective search space: 68562 Effective search space used: 68562 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 (21.7 bits) S2: 47 (22.7 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