Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate WP_013553262.1 NITSA_RS01510 chorismate mutase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000186245.1:WP_013553262.1 Length = 355 Score = 222 bits (566), Expect = 1e-62 Identities = 142/360 (39%), Positives = 206/360 (57%), Gaps = 16/360 (4%) Query: 7 LKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIME 66 L+ALR ID +D+++LDL +ER + +EV R+K ++ A YRPERE +L+ + Sbjct: 3 LEALRKEIDRIDDQLLDLYNERLKIVEEVGRLKNSTG-----APIYRPEREREILERLKR 57 Query: 67 LNK---GPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKP 123 N+ G L +E + LF E+ + E P RVA+LGPE +F+ AA K FG + P Sbjct: 58 RNRERGGLLSDEAIEALFLELFAVARNYELPERVAFLGPEASFTHQAAEKKFGATSAYLP 117 Query: 124 MAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVG 183 + I VFREV G FGVVP+ENS G V+ T++ ++D+ I EV + I HH+L Sbjct: 118 IHTIKGVFREVAEGKAKFGVVPIENSFNGIVSDTINCLSDYDLKIVAEVLIEI-HHVLAT 176 Query: 184 ETTKTDRITRIYSHAQSLAQCRKWL-DAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGD 242 + +I RIYS + QC ++L D VE++ V S A AA+ + +AAI + Sbjct: 177 KAEDVKQIKRIYSKDIAFGQCNQFLEDVGLDLVEQIPVESTAKAAQMAAKDPEAAAICSE 236 Query: 243 MAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMP 302 +AA+LY L L + IED N TRF I+ E P+G DKT+I+V + ++PGAL + L Sbjct: 237 VAARLYHLPILFKNIEDEGNNRTRFFIVSDFENRPSGRDKTTILVRLPHRPGALVDFLND 296 Query: 303 FHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPK 362 F I LT+I+ S +FFI+ GH +D I+ + EK HE ++K LGSY K Sbjct: 297 FKEAQIGLTKIK---SHIVGGVSIFFIEFDGHKEDEKIRKIFEK--HEE-SIKFLGSYVK 350 Lambda K H 0.319 0.133 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: 309 Number of extensions: 16 Number of successful extensions: 6 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: 365 Length of database: 355 Length adjustment: 29 Effective length of query: 336 Effective length of database: 326 Effective search space: 109536 Effective search space used: 109536 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_013553262.1 NITSA_RS01510 (chorismate mutase)
to HMM PF01817 (CM_2)
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/PF01817.25.hmm # target sequence database: /tmp/gapView.23374.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CM_2 [M=79] Accession: PF01817.25 Description: Chorismate mutase type II Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-26 77.7 2.0 3.6e-26 77.7 2.0 2.8 4 lcl|NCBI__GCF_000186245.1:WP_013553262.1 NITSA_RS01510 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013553262.1 NITSA_RS01510 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 77.7 2.0 3.6e-26 3.6e-26 1 78 [. 7 86 .. 7 87 .. 0.92 2 ? -0.9 0.0 0.13 0.13 51 72 .. 107 130 .. 97 135 .. 0.76 3 ? -3.6 0.0 0.84 0.84 11 27 .. 170 186 .. 168 190 .. 0.58 4 ? -2.3 0.0 0.33 0.33 40 53 .. 325 338 .. 322 351 .. 0.60 Alignments for each domain: == domain 1 score: 77.7 bits; conditional E-value: 3.6e-26 CM_2 1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlregaeel..gldpeavekifre 69 RkeId+iD++ll+L +eR+++++e++++K ++g p+++peRe+e+lerl++ +e+ l++ea+e++f e lcl|NCBI__GCF_000186245.1:WP_013553262.1 7 RKEIDRIDDQLLDLYNERLKIVEEVGRLKNSTGAPIYRPEREREILERLKRRNRERggLLSDEAIEALFLE 77 9**************************************************4444433689********** PP CM_2 70 iisesralQ 78 +++ r+++ lcl|NCBI__GCF_000186245.1:WP_013553262.1 78 LFAVARNYE 86 *****9998 PP == domain 2 score: -0.9 bits; conditional E-value: 0.13 CM_2 51 e..gaeelgldpeavekifreiis 72 + ga+++ l+ ++++ +fre+ + lcl|NCBI__GCF_000186245.1:WP_013553262.1 107 KkfGATSAYLPIHTIKGVFREVAE 130 256778888999999999999865 PP == domain 3 score: -3.6 bits; conditional E-value: 0.84 CM_2 11 lleLlaeRmelakeiae 27 + + la +e +k+i + lcl|NCBI__GCF_000186245.1:WP_013553262.1 170 IHHVLATKAEDVKQIKR 186 55556666665555544 PP == domain 4 score: -2.3 bits; conditional E-value: 0.33 CM_2 40 eReeevlerlrega 53 e+e+++++ e+ lcl|NCBI__GCF_000186245.1:WP_013553262.1 325 HKEDEKIRKIFEKH 338 56777777777633 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (79 nodes) Target sequences: 1 (355 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.31 // [ok]
This GapMind analysis is from Apr 10 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