Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate WP_011842443.1 RSPH17029_RS17965 ABC transporter substrate-binding protein
Query= uniprot:Q1MDE9 (367 letters) >NCBI__GCF_000015985.1:WP_011842443.1 Length = 389 Score = 116 bits (290), Expect = 1e-30 Identities = 112/358 (31%), Positives = 160/358 (44%), Gaps = 24/358 (6%) Query: 8 ATLVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGIL--GEKV 65 A +A LA PL +I +G + P+TGP YG Q AV+EIN GG+ GE Sbjct: 10 ACALAMLA-TPLWADEIVVGDLHPITGPANFYGLPESRAIQLAVEEINAAGGLSVGGESH 68 Query: 66 V--LELADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVL-AENGVLMVTPTA 122 ++ D P GVSA K+V +RFV+GP++SGV + ++ +G+ + Sbjct: 69 TFRIQTEDTQANPTVGVSALKKLVSSDVRFVIGPLSSGVGPALFPIIDRSDGITQIIDGT 128 Query: 123 TAPDLTKRGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYG-KGLADAFKA 181 A +T N+ R Q +V+ + K V ++ D+ G G A A Sbjct: 129 IAEGVTNG--RNIFRNQATVSQY-DVSVVDLFKAKGYGSVTMMTDRFHAGFVGTQPALAA 185 Query: 182 TLNAGGITEVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAANA 241 +L G + GD DFSA TR+ S DV+ GY EG L+ +Q L Sbjct: 186 SLKELGAEIAGEEGYKLGDTDFSATLTRVASRNPDVLLIRGYPAEGALITKQARQLGFEG 245 Query: 242 TII------GGDGLSNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAA--DALAAK-NIP 292 ++ L N A + I D + KA A +A A+ N P Sbjct: 246 QVVWEMVSPPSTVLKNIS--AAEMEGVYNCIPATTEDYIALGNEKAIALEEAYRARFNEP 303 Query: 293 AEAFTLNAYAAVEVLKAGIEKAGSAEDAEAVATALKD--GKEIPTAIGKVTYGETGDL 348 A ++ +Y AV +LKA IEKAGS E+ EAV AL + +E+P I GE G L Sbjct: 304 AGELSVLSYDAVHILKAAIEKAGSLEN-EAVNAALAELTVEEVPQLISDYVPGEGGQL 360 Lambda K H 0.312 0.131 0.362 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: 322 Number of extensions: 17 Number of successful extensions: 4 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: 367 Length of database: 389 Length adjustment: 30 Effective length of query: 337 Effective length of database: 359 Effective search space: 120983 Effective search space used: 120983 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. 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