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 Synpcc7942_1861 Synpcc7942_1861 periplasmic binding protein of ABC transporter for natural amino acids
Query= TCDB::Q8YVY4 (441 letters) >FitnessBrowser__SynE:Synpcc7942_1861 Length = 421 Score = 387 bits (993), Expect = e-112 Identities = 189/382 (49%), Positives = 262/382 (68%), Gaps = 1/382 (0%) Query: 55 GLKIGSLLPATGDLASIGQQMAAAVPLVVETVNACGGVNGQPVSLVAVDDQTDPKAGAAG 114 GLK+GSLLP TGDLA G+ M L+V+TVNACGGV G PV L+ DD+T P G A Sbjct: 34 GLKLGSLLPLTGDLAQYGRPMQDTAELLVQTVNACGGVQGLPVRLIPADDETKPDRGVAA 93 Query: 115 MTKLATVDKVAGVVGSFASSVSTAAVSIAAQNKVLLISPGSTSPVFTEKAQKGDFNGFWA 174 MTKLA VD+VAGVVG+ AS+VS AA+++A N+V++ISP STSP FTE+A++GDF G+W Sbjct: 94 MTKLAEVDRVAGVVGAAASNVSDAALTLAVNNRVVMISPSSTSPRFTERARRGDFKGYWF 153 Query: 175 RTVPPDSYQGPALAELANKKGFKRVSTIVINNDYGVGFEKAFVQAFEKLGGTVVNKNNPV 234 RT P D+ QGPALA+LA +G++ VS I INNDYG G ++F+ AFE+ GG V N++ PV Sbjct: 154 RTAPSDALQGPALAKLALDQGWRSVSVIAINNDYGNGLLRSFIPAFEQAGGVVFNRDQPV 213 Query: 235 RYDPKATTFETEAAAAFAGKPDAVLGVFYVETGSLLLKSAYQQG-VAQGVQIMLTDGMKS 293 Y P A++F++E F +PDAV+ + Y ++G+L+LKSAY++G + Q Q++LTDG+K+ Sbjct: 214 LYTPDASSFDSEVEQVFRDRPDAVVLIGYPDSGALILKSAYEKGLLGQSTQMLLTDGLKT 273 Query: 294 DEFPAQVGKTADGKFIASGIIGTVPGSDGKGLEALTKLWQSKKGSAPGEFAPQAWDATAL 353 D+ VG+ G++I ++G P S G G EA K +Q + +P F WDA AL Sbjct: 274 DQLAELVGRNPQGRYIVQDLVGVAPSSGGPGREAFLKRYQERFQRSPQVFDANTWDAAAL 333 Query: 354 LVLAAQAAKENTGVGIAGKIRDVSSAPGVEVTDVCEGLKLLQEGKDINYQGASGNVDIDA 413 LVLAA+ +K G + + +++ PG V+D+C+ L L++ GK INYQGAS + +D Sbjct: 334 LVLAAEKSKSLEGEKLKDSVAAIANGPGEPVSDICQALALVRAGKPINYQGASSELKLDN 393 Query: 414 NGDVIGVYDVWTVGDDGKIKTI 435 NGDV G YD W DGK+K + Sbjct: 394 NGDVSGRYDFWQFDADGKVKIL 415 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: 419 Number of extensions: 12 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: 441 Length of database: 421 Length adjustment: 32 Effective length of query: 409 Effective length of database: 389 Effective search space: 159101 Effective search space used: 159101 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 17 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