Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate PP_1141 PP_1141 branched-chain amino acids ABC transporter - periplasmic leucine binding subunit
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__Putida:PP_1141 Length = 371 Score = 282 bits (722), Expect = 9e-81 Identities = 147/361 (40%), Positives = 217/361 (60%), Gaps = 3/361 (0%) Query: 4 KLSLLVAVAATAMTAS--VAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGV 61 K+S L A A AS A I + AGP TG +G+ G +QA+ DINAAGGV Sbjct: 3 KISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVTQYGDMQFIGAKQAIKDINAAGGV 62 Query: 62 LGQKLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISP 121 G+ L+ + DDACDPKQAVAVAN++ GVKFV GH CS S+ PAS +Y +EGV+ I+P Sbjct: 63 DGKMLEAKEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEGVIMITP 122 Query: 122 ASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQ 181 A+T+P++T + K +FR G D QG AG Y+ ++ K K VA+LHDK YG+G+A + Sbjct: 123 AATSPEITARGYKLIFRTIGLDSAQGPAAGNYIADHVKPKVVAVLHDKQQYGEGIATAVK 182 Query: 182 KALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLN 241 + L + G K ++E AG+KD+S+++ KLKQ VD VY GGYH E GL+ RQ +++GL Sbjct: 183 QTLESKGTKVAVFEGLNAGDKDFSSIIQKLKQNNVDFVYYGGYHPELGLILRQAQEKGLK 242 Query: 242 APIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEG-YTLY 300 A + + + + I A E ++T P K+ V+ + G +P G + Sbjct: 243 AKFMGPEGVGNDSISQIAQNASEGLLVTLPKSFDADPANKKIVDAIKADGKDPSGPFVFP 302 Query: 301 TYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNG 360 Y+A+++ A+ K+A S D+ K+A+ + K ++ T G + FD KGD+ +V Y W+ G Sbjct: 303 AYSAVELIAQGIKKAGSDDTDKVAEAIHKGTFKTPTGDLSFDDKGDLKDFKFVVYEWHFG 362 Query: 361 Q 361 + Sbjct: 363 K 363 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: 415 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: 366 Length of database: 371 Length adjustment: 30 Effective length of query: 336 Effective length of database: 341 Effective search space: 114576 Effective search space used: 114576 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