Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_011384688.1 AMB_RS11580 amino acid ABC transporter substrate-binding protein
Query= BRENDA::Q01269 (268 letters) >NCBI__GCF_000009985.1:WP_011384688.1 Length = 279 Score = 101 bits (252), Expect = 2e-26 Identities = 77/248 (31%), Positives = 116/248 (46%), Gaps = 3/248 (1%) Query: 5 FRHLVQALACLALLASASLQAQESRLDRILESGVLRVATTGDYKPFSYR-TEEGGYAGFD 63 F L+ A + L L A A +L +I ++G LRV DY SYR T G G D Sbjct: 17 FASLIAAFSLLVLGAQPLAAAPGGKLAKIRQAGELRVCIWPDYYSISYRNTRTGNLEGID 76 Query: 64 VDMAQRLAESLGAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRD 123 +DMAQ L + LG ++ V +S+ ++ D D+ DI+M ++I RQ + F+ P+LR Sbjct: 77 IDMAQELGKDLGVQVRFVDSSFKTMIDDLLSDKCDISMHAVAITPARQEKLAFTRPHLRS 136 Query: 124 GKTPITLCSEEARFQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQ 183 G IT + + ID+ GV G + LKKAR+L Q+ Sbjct: 137 GIFAITSKTNPV-VKEWSDIDRDGVVVAAASGTFMVGVMKEELKKARLLEVATPEAREQE 195 Query: 184 IVDGKADLMMTDAIEARLQSRLHPELCAVHPQQPFDFAEKAY-LLPRDEAFKRYVDQWLH 242 ++ G+ADL +TD +R H + P P + AY + P D + VD ++ Sbjct: 196 VMSGRADLFVTDYPFSRKMLARHDWAKLLTPPTPLAPSPYAYAMAPGDGEWLDAVDSFVA 255 Query: 243 IAEQSGLL 250 A+ G L Sbjct: 256 RAKTDGRL 263 Lambda K H 0.322 0.135 0.406 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: 168 Number of extensions: 9 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: 268 Length of database: 279 Length adjustment: 25 Effective length of query: 243 Effective length of database: 254 Effective search space: 61722 Effective search space used: 61722 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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