Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate HSERO_RS17350 HSERO_RS17350 ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__HerbieS:HSERO_RS17350 Length = 380 Score = 207 bits (526), Expect = 5e-58 Identities = 130/372 (34%), Positives = 194/372 (52%), Gaps = 22/372 (5%) Query: 5 LSLLVAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLG- 63 + L A+ A+ ++ + +A GP++G A G+ + G AV ++NA G +G Sbjct: 8 IPLTAAIGLAFAGAAYSQEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGFTIGG 67 Query: 64 QKLKLEV--GDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISP 121 +K+K E+ DDA DPKQA AVA +L V V GH SG++IPAS++Y++ G+ Q+SP Sbjct: 68 KKVKFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDAGIPQVSP 127 Query: 122 ASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQ 181 ++TNPK T+Q K FRV D Q G GKY ++ K +A++ D++AYG+G+ADE Sbjct: 128 SATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQGVADEFA 187 Query: 182 KALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLN 241 K A G + D++A+++ LK + DVV+ GG G + RQMK G++ Sbjct: 188 KGAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQMKQLGIS 247 Query: 242 APIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEA-------KEAVEKFR-----K 289 A + GD + T ++ G AG+ G D EA K+ ++ FR K Sbjct: 248 AKFMGGDGICTG---SLPGLAGDG----LGDDQVICAEAGGVDEAGKKGMDDFRAAYKKK 300 Query: 290 AGYEPEGYTLYTYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTS 349 G + Y Y A A+A +A S D K L K S+ V G I FDAKGD+ Sbjct: 301 FGIDVVYNAAYAYDATMTVADAMAKAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIKD 360 Query: 350 PAYVWYRWNNGQ 361 + Y + GQ Sbjct: 361 GSLTLYTYKGGQ 372 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: 410 Number of extensions: 26 Number of successful extensions: 4 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: 380 Length adjustment: 30 Effective length of query: 336 Effective length of database: 350 Effective search space: 117600 Effective search space used: 117600 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