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 WP_048081181.1 EJ01_RS06730 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_000745485.1:WP_048081181.1 Length = 566 Score = 109 bits (272), Expect = 1e-28 Identities = 74/231 (32%), Positives = 119/231 (51%), Gaps = 8/231 (3%) Query: 22 GGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDG-EPIQQLQP 80 G IKA+ + + V +G I G+IG +G+GKT+L +L D G++ DG E P Sbjct: 17 GEIKALNDINLNVEEGEIVGIIGMSGSGKTSLLRILRGVEPFDSGKITLDGIEVSPDSSP 76 Query: 81 HQIAQQGMVRTFQVARTLSRL--SVLENMLLAAQKQTGENFWQVQLQPQVVVKEEKQLQE 138 + A+ + R+ + L+N++ +K G + LQ V + + Sbjct: 77 YYFAKLKKATAIHLQRSFGLWGETALQNVV---RKLAGAKYGDESLQD--VDDAVAEFGD 131 Query: 139 QAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDI 198 QA +LE VGL K +A LSGG+++ L M R L PK++LLDEPA PR +I Sbjct: 132 QAKEILEIVGLGHKINHFAPVLSGGEKQRLIMARQLAKKPKVLLLDEPATMSCPRTKQEI 191 Query: 199 CDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249 D I N++ G+T +++ H +V L DR+ ++ G+ + +G+ EI T Sbjct: 192 LDAIKNINKELGVTIVLVSHLPEVHRYLSDRLVLMENGEIIDEGSTEEIIT 242 Score = 69.3 bits (168), Expect = 2e-16 Identities = 54/278 (19%), Positives = 120/278 (43%), Gaps = 58/278 (20%) Query: 22 GGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQLQPH 81 G +++ ++ +G I LIGP+GAGKT L +++ PD G ++F +L + Sbjct: 280 GNTLQIKDVNFDIKKGEIVSLIGPSGAGKTVLLRMIAGLDAPDSGSILF------KLDDN 333 Query: 82 QIAQQGM-VRTFQVARTL--------------------SRLSVLENMLLAAQKQTGENFW 120 + Q + + V R L +RL V + +++ ++T E Sbjct: 334 WVDMQDLGLERMNVRRKLGFMHQEFALTHYATIKDQIAARLGVKDEHVISKARKTAEELG 393 Query: 121 -------------------------QVQLQPQVVVK-----EEKQLQEQAMFLLESVGLA 150 +++L+P ++ + ++++ A + +++ L Sbjct: 394 ISDKILDVLYQLTDLPEHEAKARLEKIELKPDILDLLFPKFPDTEVRKYAEPIFKALDLP 453 Query: 151 KKAYEYAG-GLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDICDRILTWNRQD 209 + LSGGQ+ + L + P +++LDEP ++P + + + + N++ Sbjct: 454 LDILDRCSYELSGGQKVRATLALVLTSKPDVLILDEPFGDLDPITLRIVSNSLKRINKEF 513 Query: 210 GMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEI 247 T L++ H++D I + R ++ +G+ + DG P ++ Sbjct: 514 NTTILMVSHHVDFIREVTTRAIMIEDGKLVGDGDPQKL 551 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: 269 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 260 Length of database: 566 Length adjustment: 30 Effective length of query: 230 Effective length of database: 536 Effective search space: 123280 Effective search space used: 123280 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: 50 (23.9 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