Align Immunogenic protein (characterized, see rationale)
to candidate WP_086511836.1 BZY95_RS20985 C4-dicarboxylate ABC transporter substrate-binding protein
Query= uniprot:E4PQE3 (325 letters) >NCBI__GCF_002151265.1:WP_086511836.1 Length = 327 Score = 369 bits (946), Expect = e-107 Identities = 181/317 (57%), Positives = 224/317 (70%), Gaps = 2/317 (0%) Query: 6 VMAVAFASTFAVATPATAQDRSDWPSNFTVGTASQGGTYFAYGSGWANFVAENLGVSGGA 65 ++A + VA A AQDRSDWP + TVGTASQGGTY+ YGSGWAN V + LGVS GA Sbjct: 8 LIATSVLGAALVAAGAQAQDRSDWPRSLTVGTASQGGTYYIYGSGWANMVGDALGVSFGA 67 Query: 66 EITGGPVQNMALVHTGDLKFGLTTMGPARESMDGNSPLAPGMKMDNVCAMFPMYETPFSV 125 E+TGGPVQN LV G+ FG+ TMGPA E+ GNS LAPG++ ++ A+FPMY+T + Sbjct: 68 EVTGGPVQNATLVQMGEHDFGMVTMGPAYEAWTGNSELAPGVEHTDIRAVFPMYQTTLQI 127 Query: 126 TALSSSGITSIADIPDGATIGFGPAGSTSDTYFPRMMETLGVNFERRNGSWSDLGGQLQD 185 ALS SGI+S+AD+ DG T+G GPAG TSD Y+P++ E LG+N RNG +D GQLQD Sbjct: 128 VALSGSGISSVADL-DGKTVGVGPAGGTSDMYYPQLFEKLGLNVSTRNGGAADQAGQLQD 186 Query: 186 GLIDVVAFAAGIPIPAVSQLEVQTDVNIIGMNDAEAETIISNFP-VSEFIIPASTYQSLD 244 GLID AFAAG+PI A +QLE Q +VNI ++ E E + +FP +S IPAS Y SLD Sbjct: 187 GLIDAFAFAAGVPISAFNQLEAQANVNIFSFSEEEMEQFLGDFPELSPASIPASVYNSLD 246 Query: 245 APSRVVSMWNFAMVNCDVSESFVYEITKLTMENNDKMVSIHKAARNSVPENYTKNNVLPW 304 VS+WNFA+ + D+ ES VYE+TK MENND+MV IH AA +VPEN+ N LPW Sbjct: 247 EDLPAVSIWNFAITHKDMPESLVYEVTKTVMENNDRMVQIHGAASETVPENFEYNTFLPW 306 Query: 305 HPGAARWFNENGYPIED 321 HPGA RWF ENGY I + Sbjct: 307 HPGAVRWFEENGYEIPE 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: 393 Number of extensions: 18 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: 327 Length adjustment: 28 Effective length of query: 297 Effective length of database: 299 Effective search space: 88803 Effective search space used: 88803 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