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 350090 BT0562 putative ABC transporter ATP-binding protein (NCBI ptt file)
Query= TCDB::Q8YT15 (247 letters) >FitnessBrowser__Btheta:350090 Length = 489 Score = 110 bits (275), Expect = 5e-29 Identities = 63/189 (33%), Positives = 113/189 (59%), Gaps = 3/189 (1%) Query: 10 PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI 69 P++ V+ + Y K V+ L+ V+F VE GE+ +IGP+GAGKSTL + + LL G Sbjct: 6 PIVVVKEISKSYGK-VEALKEVSFAVEQGEVFGLIGPDGAGKSTLFRILTTLLLADKGTA 64 Query: 70 TFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAM 129 T G ++ + + +R + Y+P +++ LSVEENLE A + + +Q D I + Sbjct: 65 TVNGLDV--VTDYKQIRTKVGYMPGRFSLYQDLSVEENLEFFATVFHTLIQENYDLIKDI 122 Query: 130 FPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQI 189 + ++ +++RAG LSGG +Q LA+ +L+ +P +L LDEP+ + P+ + ++ ++ + Sbjct: 123 YQQIEPFKKRRAGALSGGMKQKLALSCSLIHKPDILFLDEPTTGVDPVSRKEFWQMLRNL 182 Query: 190 NQEGTAIIL 198 ++G II+ Sbjct: 183 RKQGITIIV 191 Score = 75.1 bits (183), Expect = 2e-18 Identities = 59/219 (26%), Positives = 105/219 (47%), Gaps = 10/219 (4%) Query: 6 QNFTPLLEVENVHA--GYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLT 63 Q P++EVE + G+ VD ++F+V+ GE+ +G NGAGK+T + + GL Sbjct: 242 QMAAPVIEVEQLTKSFGHFTAVD---HISFQVQRGEIFGFLGANGAGKTTAMRMLCGLSR 298 Query: 64 PHTGKITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLK 123 P +G G +I + + V+ + Y+ Q +++ L V EN+ + A I ++ Sbjct: 299 PTSGVGKVAGYDI--FREAEQVKRHIGYMSQKFSLYEDLKVWENIRLFAGIYGMKEMEIE 356 Query: 124 DKIFAMFPRL--SDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQ 181 +K + RL +D R L G +Q LA ++ EP ++ LDEP+ + P Q Sbjct: 357 EKTDELLERLGFADERDTLVKNLPLGWKQKLAFSVSIFHEPKIVFLDEPTGGVDPATRRQ 416 Query: 182 VFEQVKQINQEGTAIILVEQNARKALEMADRGYVLESGR 220 +E + Q G + + +A E +R ++ G+ Sbjct: 417 FWELIYQAADRGITVFVTTHYMDEA-EYCNRISIMVDGQ 454 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: 272 Number of extensions: 15 Number of successful extensions: 4 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: 489 Length adjustment: 29 Effective length of query: 218 Effective length of database: 460 Effective search space: 100280 Effective search space used: 100280 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: 49 (23.5 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