Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate Dsui_0630 Dsui_0630 ABC-type branched-chain amino acid transport system, periplasmic component
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__PS:Dsui_0630 Length = 434 Score = 212 bits (539), Expect = 2e-59 Identities = 126/360 (35%), Positives = 192/360 (53%), Gaps = 5/360 (1%) Query: 12 AATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAG-GVLGQKLKLEV 70 A A A+ + + + A P+TG A G+ + G A+ ++NA G + G K+K E+ Sbjct: 33 APAAAPAAKPEITVKIGHASPLTGPQAHIGKDNEYGATLAIEELNAKGLEIGGAKVKFEL 92 Query: 71 --GDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTNPKL 128 DD DPKQ VA + A V V GH SG++IPAS++Y + G+ QIS ++TNP Sbjct: 93 ISDDDQADPKQGTTVAQKFVDAKVNGVIGHLNSGTTIPASKIYFDAGIPQISGSATNPTY 152 Query: 129 TEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALNAGG 188 T+Q FRV D+QQG+ ++ + K+VAI+ D++AYG+GLADE +KA A G Sbjct: 153 TKQGFATAFRVMANDEQQGKALAQFAAKTLAAKSVAIIDDRTAYGQGLADEFKKAAEAAG 212 Query: 189 QKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPIVSGD 248 K E D+ A+++K+K + D+++ GG + G +A+QMK+ GL A ++GD Sbjct: 213 LKVVASEYTNDKATDFKAILTKIKSKKPDLIFYGGMDPQGGPMAKQMKELGLKAKFLTGD 272 Query: 249 ALVTNEYWAITGPAGENTMMTFGPDPRE-MPEAKEAVEKF-RKAGYEPEGYTLYTYAALQ 306 T + + G A E + P + MP +KF K E + Y Y Y A Sbjct: 273 GGCTPNFITLAGAAAEGQYCSLPGVPLDKMPGGTVFKDKFVGKFKTEIQLYAPYVYDATM 332 Query: 307 IWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNGQYAQVK 366 + +A K+ANS + AK + K S+ V KIGFD GD+ A +Y + G+ V+ Sbjct: 333 VLVDAMKRANSVEPAKYLPEIGKTSFQGVTAKIGFDEFGDLKDGAISFYEYKGGKIEYVE 392 Lambda K H 0.312 0.129 0.366 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: 433 Number of extensions: 21 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: 366 Length of database: 434 Length adjustment: 31 Effective length of query: 335 Effective length of database: 403 Effective search space: 135005 Effective search space used: 135005 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 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