Align leucine-specific-binding protein LivK (characterized)
to candidate YP_427258.1 Rru_A2171 extracellular ligand-binding receptor
Query= CharProtDB::CH_107418 (369 letters) >NCBI__GCF_000013085.1:YP_427258.1 Length = 370 Score = 284 bits (727), Expect = 2e-81 Identities = 152/355 (42%), Positives = 206/355 (58%) Query: 14 ALAISHTAMADDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKGGIKGDKLVGVEYD 73 ALAIS DI V + ++G IA G+ GA AI N GG+KG+ + D Sbjct: 15 ALAISPLPALADIPVGLALGLTGQIAAIGEQSRRGAEAAIAAFNKAGGLKGETITLQVED 74 Query: 74 DACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMISPGATNPELTQRG 133 DACDPKQ VAVANK V+ G++ VIGH+C+ T AS +Y +E I M++ AT P+LT+RG Sbjct: 75 DACDPKQGVAVANKFVSAGVEAVIGHMCTGPTMAASTVYSEEEIPMVTASATGPDLTERG 134 Query: 134 YQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQDGLKAANANVV 193 ++ R G D QG A K I E Q AI+HDKQ YG GLA + + AA Sbjct: 135 LTNVFRATGRDDQQGTIAGKMIAERFADQTTAIVHDKQAYGRGLAEEAKKAMNAAGKEEA 194 Query: 194 FFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSVGLKTQFMGPEGVGN 253 F I GE+DFSALI+RLK+ + VYYGGYY ++GQ++RQ+R+ GL F+G +G+ + Sbjct: 195 LFAAIVPGEQDFSALISRLKQAGVKVVYYGGYYNDLGQIVRQSRAQGLDAVFVGGDGLSS 254 Query: 254 ASLSNIAGDAAEGMLVTMPKRYDQDPANQGIVDALKADKKDPSGPYVWITYAAVQSLATA 313 + I G+A EG L T +PA + V+A KAD K + + + YAA Q L A Sbjct: 255 SEFWAITGEAGEGTLFTFTPDASTNPAAKEAVEAFKADGKGDADNFAYYYYAAAQVLTQA 314 Query: 314 LERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDLKGFDFGVFQWHADGSSTAA 368 + + GS +P A+ K L+ N TV GP+++D KGDL F +QW A AA Sbjct: 315 MAKAGSADPEAVTKALRDNTFETVAGPMDFDAKGDLTAPAFVFYQWSAGKPKPAA 369 Lambda K H 0.315 0.133 0.386 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: 381 Number of extensions: 19 Number of successful extensions: 1 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: 369 Length of database: 370 Length adjustment: 30 Effective length of query: 339 Effective length of database: 340 Effective search space: 115260 Effective search space used: 115260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 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