Align Branched chain amino acid: Na+ symporter (characterized)
to candidate WP_011459557.1 DHAF_RS11265 branched-chain amino acid transport system II carrier protein
Query= TCDB::P19072 (437 letters) >NCBI__GCF_000021925.1:WP_011459557.1 Length = 437 Score = 302 bits (773), Expect = 2e-86 Identities = 172/430 (40%), Positives = 256/430 (59%), Gaps = 13/430 (3%) Query: 4 LKGFDLLALGFMTFALFLGAGNIIFPPSAGMAAGEHVWSAAFGFLLTGVGLPLLTVVALA 63 L D+L GF A+F GAGN+IFPP G+ +G+ + A GF+ TGVGLP L V A+A Sbjct: 3 LSSKDILITGFALLAMFFGAGNLIFPPMLGLQSGDQLSWALLGFIATGVGLPFLGVTAVA 62 Query: 64 RVGGGIGRLTQPIGRRAGVAFAIAVYLAIGPLFATPRTAVVSFEMGVAPFTGD--GGVPL 121 + GG + L + L IGPL A PRTA ++E+ +AP T + L Sbjct: 63 KAGGDLELLANRVHPAFSKMITTISVLCIGPLLAIPRTAATTYEVAIAPVTQSIHPQLAL 122 Query: 122 LIYTVAYFSVVLFLVLNPGRLVDRVGKVITPVLLSALLVLGGAAIFAPAGEIGSSSGEYQ 181 L+ +V +F +VLF VL P +++D VGK++TP +L L ++ + P G + SS Sbjct: 123 LLTSVVFFIIVLFFVLRPAKILDSVGKILTPFMLVFLTLIIYVGVTHPLGTMAQSS---Y 179 Query: 182 SAPLVQGFLQGYLTMDTLGALVFGIVIATAIRDRGISDSRLVTRYSMIAGVIAATGLSLV 241 + P QGFL+GY TMD + +++FG++I I+D+G++D+ + R ++IAG+IAA GL + Sbjct: 180 TNPFSQGFLEGYNTMDAIASVIFGMIIVKGIKDKGVTDNNQIARITIIAGMIAAAGLGFI 239 Query: 242 YLALFYLGATSQGIAGDAQNGVQILTAYVQQTFGVSGSLLLAVVITLACLTTAVGLITAC 301 Y+ L Y+GAT+ G N Q+L + GV G ++ VV+ LACLTTA+GL+ +C Sbjct: 240 YIGLAYIGATT-GTLFTGTNHGQMLIFVSESLLGVLGRTVIGVVMALACLTTAIGLVASC 298 Query: 302 GEFFSDLL--PVSYKTVVIVFSLFSLLVANQGLTQLISLSVPVLVGLYPLAIVLIALSLF 359 GE+FS L VSY TV I+ +L S ++AN GL ++ +SVP+L +YP+ IVLI L+L Sbjct: 299 GEYFSRLTHNRVSYNTVAIITTLVSFILANMGLANILKISVPLLEFVYPIIIVLIMLALL 358 Query: 360 DRLWVSAPRVFVPVMIVALLFGIVD---GLGAA-KLN-GWVPDVFAKLPLADQSLGWLLP 414 + V+V + +LF I+D LGA+ +N ++ D LP LGWL+P Sbjct: 359 HNFYKGKRAVYVWTTGIIVLFVILDTLYDLGASLGINLAFIRDGLNLLPFYHLGLGWLVP 418 Query: 415 VSIALVLAVV 424 + LVL+VV Sbjct: 419 AVLTLVLSVV 428 Lambda K H 0.327 0.144 0.422 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: 531 Number of extensions: 28 Number of successful extensions: 7 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: 437 Length of database: 437 Length adjustment: 32 Effective length of query: 405 Effective length of database: 405 Effective search space: 164025 Effective search space used: 164025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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