Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate 8502037 DvMF_2750 Extracellular ligand-binding receptor (RefSeq)
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__Miya:8502037 Length = 375 Score = 151 bits (381), Expect = 3e-41 Identities = 111/368 (30%), Positives = 166/368 (45%), Gaps = 8/368 (2%) Query: 1 MQLKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQ 60 M+ +K +A A+ A+A VKIG + P++G A G+D N + +ELN Sbjct: 1 MKHVVKALTLALAASLLMAATAFAAPVKIGLMCPLTGKWASEGQDMRNIVTLLADELNKA 60 Query: 61 GVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCG 120 G I G K+ ELV EDD DP+ AAQKL + V +G S T + +Y++ G Sbjct: 61 G-GINGNKV--ELVVEDDGGDPRTAALAAQKLTTSGVIAAIGTYGSAVTEASQSIYDEAG 117 Query: 121 IPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQG 180 + + +T LT+ G K R D+ G +A + K VA++ D ++Y +G Sbjct: 118 VVQIATGSTAVRLTEKGLKRFLRTAPRDDEQGM-VAAKLIKAKGYKAVALLHDNSSYAKG 176 Query: 181 VADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQM 240 +AD K G K+V T D+ AILT +KA NPD IF G P+ G +LRQ Sbjct: 177 LADETKALLDKAGTKIVFYDALTPGERDYTAILTKLKAANPDIIFCTGYYPEVGMLLRQK 236 Query: 241 EQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKY 300 ++ NV GGD +++ K++ G + G P + Y AKY Sbjct: 237 MEM-KWNVPMMGGDAANHADLVKISGKEAAKGYFFLSPPGPQDLDAPAAKSMLTAYKAKY 295 Query: 301 PN-QFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAK--SSFKGVTSTIAFEPNGEM 357 V+S DA +IV+A+K D L ++ G T I+F G+ Sbjct: 296 NGVPGSVWSVLAGDAFNVIVEAVKSTGKADSGAIAEYLKTKLKNYPGFTGQISFNEKGDR 355 Query: 358 KNPAITLY 365 +Y Sbjct: 356 VGDLYRVY 363 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: 336 Number of extensions: 15 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: 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 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