Align NatB, 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_043531481.1 JH15_RS14375 ABC transporter substrate-binding protein
Query= TCDB::Q8YVY4 (441 letters) >NCBI__GCF_000759345.1:WP_043531481.1 Length = 399 Score = 176 bits (446), Expect = 1e-48 Identities = 133/398 (33%), Positives = 202/398 (50%), Gaps = 22/398 (5%) Query: 44 ATDTTATSGGSGLKIGSLLPATGDLASIGQQMAAAVPLVVETVNACGGV-NGQPVSLVAV 102 A T A+ + +KIG L TG + S+ + A L V +N GG+ +G+ + + Sbjct: 11 AAATVASVAQADVKIGFLGGFTGPIESLTPPIYAGAQLAVSQINEQGGILDGETLVMPNA 70 Query: 103 DDQ-TDPKAGAAGMTKLATVDKVAGVVGSFASSVSTAAVSIAA-QNKVLLISPGSTSPVF 160 D D A + ++ +KV +VG+ + + AA + AA V+++SP ST+P Sbjct: 71 DTTCADASAASNAADRMVNSEKVTAIVGALCTGATVAAANNAAIPGGVVMVSPASTAPAV 130 Query: 161 TEKAQKGDFNGFWARTVPPDSYQGPALAELANKKGFKRVSTIVINNDYGVGFEKAFVQAF 220 TE D N RTVP D++QG LA+L +KG V+ +NNDYG G AF F Sbjct: 131 TEL----DDNDLVFRTVPSDAFQGEMLAKLLLEKGIDNVAVTYVNNDYGQGLADAFTTTF 186 Query: 221 EKLGGTVVNKNNPVRYDPKATTFETEAAAAFAGKPDAVLGVFYVET-GSLLLKSAYQQGV 279 E GGT+ N D +A + +E + + + ++ + Y +T G LL+ AY+ GV Sbjct: 187 EDEGGTIA--ANQAHEDNRA-DYRSELGSLSSSGAETLVVLAYADTSGQTLLRQAYESGV 243 Query: 280 AQGVQIMLTDGMKSDEFPAQVGKTADGKFIASGIIGTVPGS-DGKGLEALTKLWQSKKGS 338 Q + DGM + VG AD + G+I T PGS D G E ++ + Sbjct: 244 F--TQYVGADGMVGNSLVGAVG--AD---VLEGMIATRPGSPDLPGAEVFAEMANAADVD 296 Query: 339 APGEFAPQAWDATALLVLAAQAAKENTGVGIAGKIRDVSSAPGVEVT--DVCEGLKLLQE 396 FA QA+DAT LL LA + ++ G++ +RDV+ APG + + + +LL + Sbjct: 297 PSAVFAAQAYDATFLLALAIEKNGSDSREGLSQALRDVAMAPGETILPGEWKKAKQLLAD 356 Query: 397 GKDINYQGASGNVDIDANGDVIGVYDVWTVGDDGKIKT 434 G++INY+GASG + D NGDV GV V +DG T Sbjct: 357 GQEINYEGASGTHEFDDNGDVPGVVVEMAV-EDGSFVT 393 Lambda K H 0.312 0.130 0.367 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: 379 Number of extensions: 21 Number of successful extensions: 4 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: 441 Length of database: 399 Length adjustment: 32 Effective length of query: 409 Effective length of database: 367 Effective search space: 150103 Effective search space used: 150103 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 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