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 3608587 Dshi_1981 ABC transporter related (RefSeq)
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__Dino:3608587 Length = 257 Score = 226 bits (575), Expect = 5e-64 Identities = 118/250 (47%), Positives = 165/250 (66%), Gaps = 1/250 (0%) Query: 10 PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69 P+LA GL FG +A+ +EVA G++TGLIGPNGAGK+TLFN+L+ +RP G V Sbjct: 4 PILATHGLTHDFGPFRALHGVSLEVAPGTMTGLIGPNGAGKSTLFNVLTGALRPTSGTVT 63 Query: 70 FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129 G I P + + G+ R+FQ+ R +R++VLEN++LA + Q GE W L P+ + Sbjct: 64 LQGTDITGQPPDALFRAGLARSFQIPRPFARMTVLENVMLAPKAQIGERVWGAFLNPRAM 123 Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189 +E ++++AM +LE V LAK A + AG +SGGQ KLLE+ R LM +P LILLDEPAAG Sbjct: 124 AAQENAIRQKAMEVLEFVTLAKLADQAAGEISGGQMKLLELARVLMGDPTLILLDEPAAG 183 Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249 VNP L + + D+I T NR G TF+IIEH+MD +M C V L +G+ + +GTP + Sbjct: 184 VNPALTEVLIDKIETLNR-TGTTFVIIEHDMDFVMQHCTPVIALGQGRVIFEGTPEQALA 242 Query: 250 NSQVLEAYLG 259 + +L+AYLG Sbjct: 243 DPVLLDAYLG 252 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: 164 Number of extensions: 6 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: 257 Length adjustment: 24 Effective length of query: 236 Effective length of database: 233 Effective search space: 54988 Effective search space used: 54988 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 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