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 6939496 Sama_3588 putative ABC-type multidrug transport system, ATPase component (RefSeq)
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__SB2B:6939496 Length = 322 Score = 98.6 bits (244), Expect = 1e-25 Identities = 70/214 (32%), Positives = 111/214 (51%), Gaps = 8/214 (3%) Query: 20 GYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGL 79 G +K VD GV+ + G + +GPNG GKST + + GLL P +G+I G+ + G Sbjct: 27 GALKAVD---GVDLAIPRGSIYGFLGPNGCGKSTSIRMLTGLLKPTSGEIRVLGEPLKGA 83 Query: 80 KSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFP--RLSDRR 137 + R+G Y+ Q +++ +L+V ENL A I KD+I + L R Sbjct: 84 EEKLRRRIG--YMTQKFSLYENLTVLENLRFVARIYGLQGNKAKDRIEQLLSLYSLEGRE 141 Query: 138 RQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTAII 197 Q AG++SGG++Q LA+ A + EP LL LDEP++A+ P + +E++ ++ +G I Sbjct: 142 SQMAGSMSGGQKQRLALAAATIHEPELLFLDEPTSAVDPENRREFWERLFDLSAKG-CTI 200 Query: 198 LVEQNARKALEMADRGYVLESGRDAISGPGQELL 231 LV + E +LE G G + L+ Sbjct: 201 LVSTHYMDEAERCHGLAILERGIKRADGSPKALM 234 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: 173 Number of extensions: 11 Number of successful extensions: 2 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: 322 Length adjustment: 26 Effective length of query: 221 Effective length of database: 296 Effective search space: 65416 Effective search space used: 65416 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 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