Align Immunogenic protein (characterized, see rationale)
to candidate WP_086510300.1 BZY95_RS12735 C4-dicarboxylate ABC transporter substrate-binding protein
Query= uniprot:E4PQE3 (325 letters) >NCBI__GCF_002151265.1:WP_086510300.1 Length = 324 Score = 342 bits (878), Expect = 6e-99 Identities = 160/298 (53%), Positives = 209/298 (70%), Gaps = 2/298 (0%) Query: 25 DRSDWPSNFTVGTASQGGTYFAYGSGWANFVAENLGVSGGAEITGGPVQNMALVHTGDLK 84 DR WPS+ T+GT SQG TY+ YGSGW N +E G S GAE+TGGPVQN+ LV G+ + Sbjct: 24 DRDSWPSSLTIGTGSQGATYYIYGSGWGNLASEATGASFGAEVTGGPVQNVTLVQMGEHE 83 Query: 85 FGLTTMGPARESMDGNSPLAPGMKMDNVCAMFPMYETPFSVTALSSSGITSIADIPDGAT 144 FG+ T GPA E+ GNS LAPG++ ++ A+FPMY+T V ALS SGI+SI+D+ DG T Sbjct: 84 FGMVTTGPAYEAWRGNSELAPGVEHTDIRAVFPMYQTALQVIALSGSGISSISDL-DGKT 142 Query: 145 IGFGPAGSTSDTYFPRMMETLGVNFERRNGSWSDLGGQLQDGLIDVVAFAAGIPIPAVSQ 204 +G GPAG T D Y+P++ E LG+N RN +D Q+QDGL+D AFAAGIP+ A SQ Sbjct: 143 VGIGPAGGTGDMYYPQLFEKLGLNVRTRNAGAADQASQVQDGLLDAFAFAAGIPVSAFSQ 202 Query: 205 LEVQTDVNIIGMNDAEAETIISNFP-VSEFIIPASTYQSLDAPSRVVSMWNFAMVNCDVS 263 LE Q DVNI ++ E E + +FP S IPAS Y SLDA + +S+WNFA+ + D+ Sbjct: 203 LEAQVDVNIFSFSEEEMEVFLEDFPEFSPATIPASAYSSLDADTSAISLWNFAITHKDMP 262 Query: 264 ESFVYEITKLTMENNDKMVSIHKAARNSVPENYTKNNVLPWHPGAARWFNENGYPIED 321 ES VYE+TK MEN+++MV +H +A +VPEN+ +N +PWHPGA RWF ENGY I + Sbjct: 263 ESLVYEVTKAVMENHERMVQVHGSASETVPENFVENTFIPWHPGAVRWFEENGYDIPE 320 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: 371 Number of extensions: 17 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: 324 Length adjustment: 28 Effective length of query: 297 Effective length of database: 296 Effective search space: 87912 Effective search space used: 87912 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