Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate WP_012977543.1 AZL_RS26820 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >NCBI__GCF_000010725.1:WP_012977543.1 Length = 369 Score = 387 bits (994), Expect = e-112 Identities = 191/361 (52%), Positives = 246/361 (68%), Gaps = 3/361 (0%) Query: 4 KLSLLVAVAATAMTAS--VAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGV 61 +L++L V+ATA+ A A+ADI + TG A GEQ G +QAVADINA GGV Sbjct: 2 RLTVLSFVSATALLAGFGTAQADILIGLGTATTGPVAALGEQSVYGAKQAVADINAKGGV 61 Query: 62 LGQKLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISP 121 LGQKL L+VGDDACDP+QAVAVANQ + V V GH CSG+SIPA+ VY EEGV+ ++P Sbjct: 62 LGQKLVLKVGDDACDPRQAVAVANQFVRDQVTAVVGHLCSGASIPAADVYQEEGVVMVTP 121 Query: 122 ASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQ 181 +TNP LT + N+FRVCGRDDQQG +AG YL + +KGKN+A+L DK AYGKGLAD Sbjct: 122 TATNPLLTAKGHPNIFRVCGRDDQQGVVAGNYLAQTFKGKNIAVLDDKQAYGKGLADVVV 181 Query: 182 KALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLN 241 + + G K + TAGEKD+SAL++ LK + +D VY GGYH E GL+ RQ ++QGL Sbjct: 182 ETVEKAGGKVAYRTSITAGEKDFSALITSLKDKGIDAVYYGGYHPELGLIVRQAQEQGLK 241 Query: 242 APIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGY-EPEGYTLY 300 ++GD L EYW+ITGPAGE T+ T P P+A++ + F+KAG EP + Y Sbjct: 242 PQFIAGDGLNNQEYWSITGPAGEGTLYTDSPSAASDPKAQDLIASFKKAGLPEPGNFAFY 301 Query: 301 TYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNG 360 +YAA+Q+ AE ++A S D K+A L SY+TV+G + FD KGD+T P YV Y WNNG Sbjct: 302 SYAAVQVIAEGLQKAGSADGGKLAKALHTGSYDTVVGSVEFDKKGDITKPNYVMYVWNNG 361 Query: 361 Q 361 Q Sbjct: 362 Q 362 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: 447 Number of extensions: 15 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: 366 Length of database: 369 Length adjustment: 30 Effective length of query: 336 Effective length of database: 339 Effective search space: 113904 Effective search space used: 113904 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 24 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