Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate WP_011385357.1 AMB_RS15010 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:Q1MDE9 (367 letters) >NCBI__GCF_000009985.1:WP_011385357.1 Length = 366 Score = 313 bits (803), Expect = 4e-90 Identities = 162/354 (45%), Positives = 222/354 (62%), Gaps = 2/354 (0%) Query: 9 TLVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGILGEKVVLE 68 TL A+L A A ADITIG+ PL+G AA+G+Q K GA AV++IN KGG+LG+K+ L Sbjct: 10 TLAAALLMAGAARADITIGVAGPLSGSEAAFGEQFKRGAMKAVEDINAKGGVLGQKLALT 69 Query: 69 LADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPTATAPDLT 128 L DDA +PKQ V+ AN++ + FV G SG +IP S+V AE G+L ++P +T P T Sbjct: 70 LGDDACDPKQAVAVANEMAAKKVPFVAGHFCSGSSIPASEVYAETGILQISPASTNPKFT 129 Query: 129 KRGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKATLNAGGI 188 +RGL N+ RTCGRDDQQ +AA Y+ K+ KDK VAIV+DK AYGKGLAD + L GI Sbjct: 130 ERGLPNIFRTCGRDDQQGVIAADYIAKHQKDKVVAIVHDKSAYGKGLADQTRDALGKAGI 189 Query: 189 TEVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAANATIIGGDG 248 + +AI+ G+KD+SAL T++K+ KVD++YFGGY E GL+ RQL D ++GGD Sbjct: 190 KAALYEAISAGEKDYSALVTKLKASKVDLLYFGGYKTEAGLIVRQLRDQGMQTRLMGGDA 249 Query: 249 LSNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAADALAAKNIPAEAFTLNAYAAVEVLK 308 L E+WAI A GT+ T + D K+P + A+ EA+TL Y ++ Sbjct: 250 LVTEEYWAITGAAGEGTMMTFSPDPRKNPANADLVKYYRAQKYEPEAYTLYTYGTIQAWA 309 Query: 309 AGIEKAGSAEDAEAVATALKDGKEIPTAIGKVTYGETGDLTSQSFSLYKWEAGK 362 EKA D + VA LK ++ TAIGK+ + GD+ + + +Y W+ GK Sbjct: 310 QAAEKA-KTTDWKKVAAVLK-AEKFDTAIGKIGFDAKGDVAAPGYVMYVWKGGK 361 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: 389 Number of extensions: 11 Number of successful extensions: 2 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: 367 Length of database: 366 Length adjustment: 30 Effective length of query: 337 Effective length of database: 336 Effective search space: 113232 Effective search space used: 113232 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: 49 (23.5 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