Align Immunogenic protein (characterized, see rationale)
to candidate WP_086511838.1 BZY95_RS20995 C4-dicarboxylate ABC transporter substrate-binding protein
Query= uniprot:E4PQE3 (325 letters) >NCBI__GCF_002151265.1:WP_086511838.1 Length = 348 Score = 276 bits (707), Expect = 4e-79 Identities = 144/314 (45%), Positives = 195/314 (62%), Gaps = 3/314 (0%) Query: 7 MAVAFASTFAVATPATAQDRSDWPSNFTVGTASQGGTYFAYGSGWANFVAENLGVSGGAE 66 +A A A FA A P A +R+DWP +GTAS GGTY YG G + + LG+ ++ Sbjct: 12 LAAACALLFASA-PTLADERADWPEEVLLGTASLGGTYQVYGDGLVTRLIDELGIDAVSQ 70 Query: 67 ITGGPVQNMALVHTGDLKFGLTTMGPARESMDGNSPLAPGMKMDNVCAMFPMYETPFSVT 126 TGGP NM LVHTG+ + GL T+GPARE DG + APG +M +V A+FPMY+TPF V Sbjct: 71 ATGGPYHNMTLVHTGEAELGLVTLGPARELWDGEAEFAPGEEMRDVRALFPMYQTPFHVV 130 Query: 127 ALSSSGITSIADIPDGATIGFGPAGSTSDTYFPRMMETLGV-NFERRNGSWSDLGGQLQD 185 L+ SGI SIAD+ G +G GP G T Y+P+ +E LGV + + + L L Sbjct: 131 TLAGSGIESIADL-SGKRVGVGPMGGTCAAYWPQFLEALGVEDVHLQYADANHLADYLTS 189 Query: 186 GLIDVVAFAAGIPIPAVSQLEVQTDVNIIGMNDAEAETIISNFPVSEFIIPASTYQSLDA 245 L D AF AG+PI A +LE + DV++ G+ + E T++ FPVS F IPA TY S+DA Sbjct: 190 RLSDAFAFCAGLPIRAFERLERRRDVHMFGLTEQEQSTLLDTFPVSAFEIPADTYASMDA 249 Query: 246 PSRVVSMWNFAMVNCDVSESFVYEITKLTMENNDKMVSIHKAARNSVPENYTKNNVLPWH 305 P VS WNFA+ + D+ ESFVYE+ KL +++ D M+ IH AA + E+ KN V+ +H Sbjct: 250 PHASVSFWNFAIGHKDLPESFVYELMKLVLDHPDAMMEIHPAAIETRAEHLDKNGVIWFH 309 Query: 306 PGAARWFNENGYPI 319 PGA R++ E G + Sbjct: 310 PGAVRYYEEQGLEV 323 Lambda K H 0.315 0.130 0.390 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: 319 Number of extensions: 20 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: 325 Length of database: 348 Length adjustment: 28 Effective length of query: 297 Effective length of database: 320 Effective search space: 95040 Effective search space used: 95040 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: 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