Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_023430731.1 N177_RS02905 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000496075.1:WP_023430731.1 Length = 375 Score = 150 bits (378), Expect = 7e-41 Identities = 115/370 (31%), Positives = 180/370 (48%), Gaps = 21/370 (5%) Query: 10 VAAIAAAA----GVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIG 65 VAAIA AA G A AQE VKIG + P+SG + G NG ++AI++ NA+ +G Sbjct: 13 VAAIALAAVVATGAADAQE-TVKIGFIGPLSGGNSQQGLTARNGFQLAIDQANARE-DLG 70 Query: 66 GKKIKFELVAEDDAADPKQGTAAAQKLC-DAKVAGVVGHLNSGTTIPASKVYNDCGIPHV 124 K E V +DDA++P+ G +AA KL D V V GH NS + + V GIP V Sbjct: 71 ---FKIEGVIQDDASNPQTGVSAALKLTNDPAVIAVTGHWNSPVALATAPVITRAGIPFV 127 Query: 125 TGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADV 184 A +P +T+ R++ LA +A + + + +AI+ D + YG Sbjct: 128 IWGAISPKITETNNPLLARVVPTLVNTNEPLAAWAAEEIG-QNIAIVSDTSDYGMANVAA 186 Query: 185 FKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLG 244 F+K G + + TDF A LT IK+ NPDAI++GG+ + G + +QM+++G Sbjct: 187 FRKPFEEAGGTITSVETAPVGTTDFRATLTKIKSDNPDAIYFGGVVTEAGLVRQQMKEVG 246 Query: 245 MGNVKYFGGDGICTSEIAKLAAGAK--TLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPN 302 + +V G DG E K+A A T+ ++ L +M +A A + Sbjct: 247 L-DVPMIGVDGFHDPEFIKIAGDAAEGTISGIMKETENEKLVEMN-----EAYAAAGFAE 300 Query: 303 QFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPA- 361 Y+ YDA +I+ A++ A + D + + G +F+ NG+ K P Sbjct: 301 PVGTYTKNAYDAANIIIAAIEEAGT-DRAAVGEAIRAMEYDGAMGHTSFDENGQTKLPVD 359 Query: 362 ITLYVYKDGK 371 + L V ++G+ Sbjct: 360 LELRVVRNGQ 369 Lambda K H 0.315 0.131 0.375 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: 326 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 375 Length of database: 375 Length adjustment: 30 Effective length of query: 345 Effective length of database: 345 Effective search space: 119025 Effective search space used: 119025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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