Align NatE, 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 AO353_02425 AO353_02425 spermidine/putrescine ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__pseudo3_N2E3:AO353_02425 Length = 334 Score = 111 bits (278), Expect = 2e-29 Identities = 69/211 (32%), Positives = 117/211 (55%), Gaps = 6/211 (2%) Query: 27 ILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQIVR 86 + +N ++ GE VT++GP+G GKSTL + I GL GKI G ++ L S Q Sbjct: 23 VFSDINCEIQKGEFVTLLGPSGCGKSTLLRCIAGLTAVDGGKILLDGHDLVPL-SPQKRG 81 Query: 87 LGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFP--RLSDRRRQRAGTL 144 +GM + Q +FP+++VE+N+ G ++ + + ++ + L+D + L Sbjct: 82 IGMVF--QSYALFPNMTVEQNVAFGLRMQKVNADDSRKRVLQVLQLVELTDFASRYPHQL 139 Query: 145 SGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQE-GTAIILVEQNA 203 SGG+ Q +A+ ++L+ P LL+LDEP +AL + + EQ++QI +E G I V + Sbjct: 140 SGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRQIQRELGLTTIFVTHDQ 199 Query: 204 RKALEMADRGYVLESGRDAISGPGQELLTDP 234 +AL M+DR +++ G+ SG + L T P Sbjct: 200 EEALTMSDRIFLMNQGKIVQSGDAETLYTAP 230 Lambda K H 0.317 0.136 0.377 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: 170 Number of extensions: 5 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: 247 Length of database: 334 Length adjustment: 26 Effective length of query: 221 Effective length of database: 308 Effective search space: 68068 Effective search space used: 68068 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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