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_009546487.1 CCE_RS01915 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q8YVY4 (441 letters) >NCBI__GCF_000017845.1:WP_009546487.1 Length = 440 Score = 540 bits (1390), Expect = e-158 Identities = 268/438 (61%), Positives = 332/438 (75%), Gaps = 8/438 (1%) Query: 3 RISAALSLGLATFTAGFLLAACETSNTTPNGAANNGATSTPATDTTATSGGSGLKIGSLL 62 R+ + L+ GLA + LL C +N TP + + +TP T+ G GLK+G+LL Sbjct: 9 RLKSPLAWGLALAFSSSLLVGC--NNPTPTDTGTSPSPNTP------TASGEGLKLGALL 60 Query: 63 PATGDLASIGQQMAAAVPLVVETVNACGGVNGQPVSLVAVDDQTDPKAGAAGMTKLATVD 122 P TGDL+SIG M AV L V+ +NACGGVNGQPV+LV D QTDP AG A MTKLA VD Sbjct: 61 PVTGDLSSIGANMPEAVKLAVDEINACGGVNGQPVTLVTEDTQTDPTAGGAAMTKLAEVD 120 Query: 123 KVAGVVGSFASSVSTAAVSIAAQNKVLLISPGSTSPVFTEKAQKGDFNGFWARTVPPDSY 182 +VAGVVG+FASSVS AAV IAAQNKV+LISPGSTSPVFT++A+ G+FNG+WART PPD+Y Sbjct: 121 RVAGVVGAFASSVSGAAVGIAAQNKVMLISPGSTSPVFTDQAKNGEFNGYWARTAPPDTY 180 Query: 183 QGPALAELANKKGFKRVSTIVINNDYGVGFEKAFVQAFEKLGGTVVNKNNPVRYDPKATT 242 Q ALA LA K+GF+ VST+VINNDYGVGFE+ FV +FEK GG + NK PVRYDPKA T Sbjct: 181 QAQALAALAQKQGFENVSTVVINNDYGVGFEQQFVGSFEKAGGKLTNKEQPVRYDPKAAT 240 Query: 243 FETEAAAAFAGKPDAVLGVFYVETGSLLLKSAYQQGVAQGVQIMLTDGMKSDEFPAQVGK 302 ++EAAAAFA PDAV V Y ETGS+LL++AY+QG+++GV ++LTDG+ S++F QVGK Sbjct: 241 LDSEAAAAFANNPDAVAAVLYAETGSILLQAAYKQGLSEGVTVLLTDGVYSEDFVEQVGK 300 Query: 303 TADGKFIASGIIGTVPGSDGKGLEALTKLWQSKKGSAPGEFAPQAWDATALLVLAAQAAK 362 T DGK+I G +GTVPG+DG+ L+A T W K G F P +WDAT LL+LAA+AAK Sbjct: 301 TPDGKYILEGALGTVPGADGQALDAFTTKWNEKTGKDVTAFVPHSWDATILLMLAAEAAK 360 Query: 363 ENTGVGIAGKIRDVSSAPGVEVTDVCEGLKLLQEGKDINYQGASGNVDIDANGDVIGVYD 422 NTG I KIR+V++APG EV+D CE + L+++G+DINYQGASGNVDID NGDV+G YD Sbjct: 361 ANTGEAIQSKIREVANAPGTEVSDPCEAIALVRDGEDINYQGASGNVDIDENGDVVGSYD 420 Query: 423 VWTVGDDGKIKTIDKVTP 440 VWTV DG + IDKV+P Sbjct: 421 VWTVKADGTTEVIDKVSP 438 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: 541 Number of extensions: 16 Number of successful extensions: 1 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: 440 Length adjustment: 32 Effective length of query: 409 Effective length of database: 408 Effective search space: 166872 Effective search space used: 166872 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: 51 (24.3 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