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 Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__Cola:Echvi_3653 Length = 290 Score = 92.8 bits (229), Expect = 7e-24 Identities = 65/225 (28%), Positives = 112/225 (49%), Gaps = 31/225 (13%) Query: 29 EARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQLQPHQIAQQGM 88 + ++ ++QG L GP+G+GKT+ ++S + PDKG + +GE Q Sbjct: 20 DIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGE------------QWF 67 Query: 89 VRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEE-----KQLQEQA--M 141 +F + +S +++ G F L P + VKE K +++A M Sbjct: 68 DASF--GKNVS----------PGRRKLGYLFQDYSLFPNMTVKENIAFALKNAKDKAYLM 115 Query: 142 FLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDICDR 201 LLES+GL LSGGQ++ + + RAL P ++LLDEP + ++P + + + + Sbjct: 116 ELLESMGLLHLQDTLPKHLSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEY 175 Query: 202 ILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAE 246 IL +R+ +T +++ H+ I+ L DR+ L G+ L TP E Sbjct: 176 ILAIHRKYALTTILVSHDAGEIIKLSDRIIELDHGKVLRQCTPKE 220 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: 159 Number of extensions: 4 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 260 Length of database: 290 Length adjustment: 25 Effective length of query: 235 Effective length of database: 265 Effective search space: 62275 Effective search space used: 62275 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