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 WP_014819569.1 BLS63_RS10600 ABC transporter ATP-binding protein
Query= TCDB::Q8YT15 (247 letters) >NCBI__GCF_900100495.1:WP_014819569.1 Length = 590 Score = 119 bits (297), Expect = 2e-31 Identities = 73/231 (31%), Positives = 122/231 (52%), Gaps = 8/231 (3%) Query: 2 SGSAQNFTPLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGL 61 +G+ ++ ++E + H G DV L+G++ R+ G L ++GP+GAGK+TL + + GL Sbjct: 12 AGAGEDAAIVIEDVDKHFG---DVKALRGLSARIHYGRLTGLVGPDGAGKTTLMRILTGL 68 Query: 62 LTPHTGKITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQP 121 L P+ G +T G ++ +K N + + Y+PQ ++ LSV EN+ + A +R Sbjct: 69 LVPNAGHVTLAGYDV--VKDNDAIHVASGYMPQRFGLYEDLSVMENMRLYAQLRGMDADR 126 Query: 122 LKDKIFAM--FPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILV 179 D + F RL ++ AG LSGG +Q L + ALM P +L+LDEP + P+ Sbjct: 127 NADLFAELLDFTRLGPFTKRLAGKLSGGMKQKLGLACALMARPKVLLLDEPGVGVDPVSR 186 Query: 180 TQVFEQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQEL 230 ++ V+ + EG A++ +A E + +L G+ GP QEL Sbjct: 187 QDLWRMVQALTDEGMAVVWSTAYLDEA-ERCESVLLLNQGQLLFDGPPQEL 236 Score = 84.3 bits (207), Expect = 5e-21 Identities = 58/184 (31%), Positives = 94/184 (51%), Gaps = 5/184 (2%) Query: 31 VNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQIVRLGMC 90 V+F V+ GE+ ++GPNGAGKST K + GLL P G+ G ++ RLG Sbjct: 359 VSFEVQKGEIFGLLGPNGAGKSTTFKMLCGLLKPTAGEAHVVGHDLRRATGAAKSRLG-- 416 Query: 91 YVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFPR--LSDRRRQRAGTLSGGE 148 Y+ Q +++ LSV++NLE A + +++I M L D +L G Sbjct: 417 YMAQKFSLYGLLSVQQNLEFSAGVYGLEGNTRRERIAEMIETFDLGDWLSATPDSLPLGH 476 Query: 149 RQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTAIILVEQNARKALE 208 +Q LA+ +LM P +L LDEP++ + PI + + + + ++G I++ +A E Sbjct: 477 KQRLALACSLMHRPPVLFLDEPTSGVDPITRREFWTHINGLARKGVTIMVTTHFMDEA-E 535 Query: 209 MADR 212 DR Sbjct: 536 YCDR 539 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: 343 Number of extensions: 22 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 247 Length of database: 590 Length adjustment: 30 Effective length of query: 217 Effective length of database: 560 Effective search space: 121520 Effective search space used: 121520 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: 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