Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate HSERO_RS00870 HSERO_RS00870 ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__HerbieS:HSERO_RS00870 Length = 378 Score = 191 bits (486), Expect = 2e-53 Identities = 122/364 (33%), Positives = 194/364 (53%), Gaps = 11/364 (3%) Query: 7 LLVAVAATAMTASVAKAD----IAVATAGPITGQYATFGEQMKKGIEQAVADINAAG-GV 61 L + A+ A+ + A A + + + P+TG A+ G+ + G+ A+ +NA V Sbjct: 8 LNIIAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITV 67 Query: 62 LGQKLKLEV--GDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQI 119 G+K+K +V DD DPK VAVA +LA GVK + G + SG +IPAS+VY + G++ + Sbjct: 68 GGKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIV-V 126 Query: 120 SPASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADE 179 + ++NPK+T+Q +FRV D Q G Y + K K VA++ D++AYG+GLA E Sbjct: 127 ATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQE 186 Query: 180 TQKALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQG 239 K A G + D++A+++ +K + D V++GGY + G + RQMK G Sbjct: 187 FIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLG 246 Query: 240 LNAPIVSGDALVTNEYWAITGPA-GENTMMTFGPDPRE-MPEAKEAVEKFRKAGYEP-EG 296 ++ P++ GD + + E + G A GE+ T G + E K ++++K P E Sbjct: 247 VDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAET 306 Query: 297 YTLYTYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYR 356 Y + Y + + A+A KQANS D + L K SY V G+ FDA D+ YR Sbjct: 307 YAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYR 366 Query: 357 WNNG 360 + +G Sbjct: 367 FKDG 370 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: 391 Number of extensions: 22 Number of successful extensions: 6 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: 378 Length adjustment: 30 Effective length of query: 336 Effective length of database: 348 Effective search space: 116928 Effective search space used: 116928 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