Align NatB aka SLR0559, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Synpcc7942_1861 Synpcc7942_1861 periplasmic binding protein of ABC transporter for natural amino acids
Query= TCDB::Q55387 (454 letters) >FitnessBrowser__SynE:Synpcc7942_1861 Length = 421 Score = 354 bits (909), Expect = e-102 Identities = 179/384 (46%), Positives = 254/384 (66%), Gaps = 2/384 (0%) Query: 63 GALKLGALLPATGDLSSIGQNMPLAVQLAVDTINACGGVNGQDVTVVIEDDQTDPTAGVS 122 G LKLG+LLP TGDL+ G+ M +L V T+NACGGV G V ++ DD+T P GV+ Sbjct: 33 GGLKLGSLLPLTGDLAQYGRPMQDTAELLVQTVNACGGVQGLPVRLIPADDETKPDRGVA 92 Query: 123 AMTKLAEADQVAGVVGSFASSVSSAAVPIAVRNNIMMISPGSTSPVFTDQAKKGEFKGFW 182 AMTKLAE D+VAGVVG+ AS+VS AA+ +AV N ++MISP STSP FT++A++G+FKG+W Sbjct: 93 AMTKLAEVDRVAGVVGAAASNVSDAALTLAVNNRVVMISPSSTSPRFTERARRGDFKGYW 152 Query: 183 ARTAPPDTYQAQALAALAKKQGFTDAATVVINNDYGVGFEKVFVESFTADGGNVTNKDNP 242 RTAP D Q ALA LA QG+ + + INNDYG G + F+ +F GG V N+D P Sbjct: 153 FRTAPSDALQGPALAKLALDQGWRSVSVIAINNDYGNGLLRSFIPAFEQAGGVVFNRDQP 212 Query: 243 VRYDPKAATLDTEAAQGFANSPDAVAAILYADTGSVLVQSAYRQGLMDGVT-LLLTDGVY 301 V Y P A++ D+E Q F + PDAV I Y D+G+++++SAY +GL+ T +LLTDG+ Sbjct: 213 VLYTPDASSFDSEVEQVFRDRPDAVVLIGYPDSGALILKSAYEKGLLGQSTQMLLTDGLK 272 Query: 302 SPDFVEKVGKDANGVSLLSGALGTVPGADGKSLEAFTAQWKDATGGKDVTAFVPHTYDAT 361 + E VG++ G ++ +G P + G EAF ++++ + F +T+DA Sbjct: 273 TDQLAELVGRNPQGRYIVQDLVGVAPSSGGPGREAFLKRYQERF-QRSPQVFDANTWDAA 331 Query: 362 VLMMLAAEAAKSNTGAGIQSKIRDVSNGPGEEVTDACEAIAMVREGKDINYQGASGNVDI 421 L++LAAE +KS G ++ + ++NGPGE V+D C+A+A+VR GK INYQGAS + + Sbjct: 332 ALLVLAAEKSKSLEGEKLKDSVAAIANGPGEPVSDICQALALVRAGKPINYQGASSELKL 391 Query: 422 DENGDVVGTYDVWTVKGDGTLEVI 445 D NGDV G YD W DG ++++ Sbjct: 392 DNNGDVSGRYDFWQFDADGKVKIL 415 Lambda K H 0.313 0.131 0.374 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: 456 Number of extensions: 20 Number of successful extensions: 3 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: 454 Length of database: 421 Length adjustment: 32 Effective length of query: 422 Effective length of database: 389 Effective search space: 164158 Effective search space used: 164158 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 (21.9 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