Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate H281DRAFT_02405 H281DRAFT_02405 amino acid/amide ABC transporter substrate-binding protein, HAAT family
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__Burk376:H281DRAFT_02405 Length = 382 Score = 332 bits (851), Expect = 1e-95 Identities = 178/380 (46%), Positives = 241/380 (63%), Gaps = 9/380 (2%) Query: 1 MQLKLKLTVVAAIAAA---AGVASAQE-QVVKIGHVAPVSGAQAHYGKDNENGARMAIEE 56 MQ K+ AA+ AA AG A+AQ VKIG P++GAQAHYGKD +NG +A+E+ Sbjct: 1 MQHKMTQLAGAALVAAMSLAGTANAQSTDDVKIGFAGPMTGAQAHYGKDFQNGITLAVED 60 Query: 57 LNAQGVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVY 116 +NA IGGK ++F L + DD ADP+ GT AQKL D + G++GH NSGTTIPAS++Y Sbjct: 61 INATKPVIGGKPVRFVLDSADDQADPRTGTTVAQKLVDDGIKGMLGHFNSGTTIPASRIY 120 Query: 117 NDCGIPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTA 176 + GIP + AT P T+ G+KTTFR++ +D G+ +AV TL +K + I+DDRTA Sbjct: 121 ANAGIPEIA-MATAPEYTQQGFKTTFRMMTSDTQQGSVAGTFAVKTLGVKKIVIVDDRTA 179 Query: 177 YGQGVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPM 236 YGQG+AD F+K A A G +VD ++T DKA DF +ILT +KA NPD I+YGG D Q PM Sbjct: 180 YGQGLADQFEKAAKAAGGTIVDREYTNDKAVDFKSILTKLKAANPDLIYYGGADSQAAPM 239 Query: 237 LRQMEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKY 296 ++QM+ LG+ GG+ + T ++A A + + G L +MPGG + AKY Sbjct: 240 VKQMKALGI-KAPLMGGEMVHTPTFIQIAGDA--ANGTVASLAGLPLEEMPGGKDYVAKY 296 Query: 297 DAKYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTST-IAFEPNG 355 ++ Q YSPY YD + AMK+ANS DP Y P LAK+S VTS+ ++++ G Sbjct: 297 KKRFNEDVQTYSPYAYDGAMAMFAAMKKANSTDPAKYLPVLAKTSMPAVTSSNLSYDAKG 356 Query: 356 EMKNPAITLYVYKDGKKTPL 375 ++KN ITLY DGK T L Sbjct: 357 DLKNGGITLYKVVDGKWTTL 376 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: 499 Number of extensions: 25 Number of successful extensions: 4 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: 382 Length adjustment: 30 Effective length of query: 345 Effective length of database: 352 Effective search space: 121440 Effective search space used: 121440 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