Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate WP_106712861.1 CU102_RS19525 ABC transporter substrate-binding protein
Query= uniprot:A0KWY4 (313 letters) >NCBI__GCF_003010955.1:WP_106712861.1 Length = 318 Score = 350 bits (899), Expect = e-101 Identities = 178/314 (56%), Positives = 231/314 (73%), Gaps = 3/314 (0%) Query: 1 MKHNKIITALGLWAVSATCAYATTVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADA 60 MK + + + + A A TVGFSQ+GSESGWR + + K EAK+R IDLK ADA Sbjct: 1 MKRILLASTVAMSFAGAASASDLTVGFSQIGSESGWRAAETSVSKIEAKKRSIDLKIADA 60 Query: 61 QQKQENQIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSL 120 QQKQENQIKA+R F+AQGVDAI +APVV TGW VL EAK A+IPV+++DR I+ ++ L Sbjct: 61 QQKQENQIKAIRGFVAQGVDAIFVAPVVATGWDTVLAEAKEAEIPVILLDRTIETANNDL 120 Query: 121 FLTRIASDFSEEGRKIGQWLMDKTQGN-CDIAELQGTVGATAAIDRAAGFNQVIANYPNA 179 +LT + SD EG+ G WL+ T G C++ ELQGTVG++ AI+R GF + IA+ N Sbjct: 121 YLTAVTSDTVHEGKVAGDWLVKTTAGKPCNVVELQGTVGSSPAINRKKGFEEGIASASNI 180 Query: 180 KIVRSQTGEFTRAKGKEVMEGFLKAQN-GQPLCAVWSHNDEMALGAVQAIKEAGLKPGKD 238 KI RSQTG+FTRAKGKEVMEGFLKA+N G+ +CA+++HND+MA+GA+QAIKEAGLKPGKD Sbjct: 181 KITRSQTGDFTRAKGKEVMEGFLKAENGGKNICALYAHNDDMAVGAIQAIKEAGLKPGKD 240 Query: 239 ILIVSVDGVPDYFKAMADGDVNATVELSPYLGGPAFDAIDAYLKGNKDQAKLISTTGDVF 298 IL+VS+D VPD FKAM++G+ NATVEL+P + GPAFDA+ AY K K I T ++ Sbjct: 241 ILVVSIDAVPDIFKAMSEGEANATVELTPNMAGPAFDALKAYKDSGKAPPKWIQTESKLY 300 Query: 299 TQ-ETAAAEYEKRR 311 TQ + YE+++ Sbjct: 301 TQADDPKKVYEEKK 314 Lambda K H 0.316 0.131 0.376 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: 324 Number of extensions: 12 Number of successful extensions: 3 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: 313 Length of database: 318 Length adjustment: 27 Effective length of query: 286 Effective length of database: 291 Effective search space: 83226 Effective search space used: 83226 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 (21.6 bits) S2: 48 (23.1 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