Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate AZOBR_RS08260 AZOBR_RS08260 ABC transporter
Query= uniprot:Q1MDE9 (367 letters) >FitnessBrowser__azobra:AZOBR_RS08260 Length = 366 Score = 313 bits (802), Expect = 5e-90 Identities = 157/358 (43%), Positives = 223/358 (62%), Gaps = 2/358 (0%) Query: 5 TLTATLVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGILGEK 64 +L + A+ A +A ADI + P+TG A +G+Q+K G + AV +IN GG+LG+K Sbjct: 6 SLLVAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQK 65 Query: 65 VVLELADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPTATA 124 + LE+ DDA +PKQ V+ AN++ G++FV G SG +IP S V AE GVL ++P +T Sbjct: 66 LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTN 125 Query: 125 PDLTKRGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKATLN 184 P LT++ L NV R CGRDDQQ ++A KY+L+N+K K VAI++DK AYGKGLAD + LN Sbjct: 126 PKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALN 185 Query: 185 AGGITEVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAANATII 244 AGG E + +A T G+KD+SAL +++K E VDVVY GGYH E GLLARQ+ D NA I+ Sbjct: 186 AGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPIV 245 Query: 245 GGDGLSNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAADALAAKNIPAEAFTLNAYAAV 304 GD L E+WAI A T+ T D + P++K A + E +TL YAA+ Sbjct: 246 SGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEGYTLYTYAAL 305 Query: 305 EVLKAGIEKAGSAEDAEAVATALKDGKEIPTAIGKVTYGETGDLTSQSFSLYKWEAGK 362 ++ ++A S + A+ K+ T IGK+ + GD+TS ++ Y+W G+ Sbjct: 306 QIWAEAAKQANSTDSAKIADVLRKNSYN--TVIGKIGFDAKGDVTSPAYVWYRWNNGQ 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: 405 Number of extensions: 20 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