Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate 200542 SO1367 chorismate mutase/prephenate dehydratase (NCBI ptt file)
Query= CharProtDB::CH_024084 (386 letters) >FitnessBrowser__MR1:200542 Length = 671 Score = 411 bits (1056), Expect = e-119 Identities = 213/386 (55%), Positives = 277/386 (71%), Gaps = 7/386 (1%) Query: 1 MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60 M PL RE+I+ LD LL+LLAERR L++EV ++K + RP+RD RE++LL RL+ Sbjct: 1 MQKPQPLNHTREQITQLDNDLLSLLAERRRLSLEVARSKEVDVRPIRDTQREKELLARLV 60 Query: 61 TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKINPHSAR----IAFLGPKGSYS 116 T G+ LDAHY+ L+Q IIEDSVL QQA L + NP + + IA+LG +GSYS Sbjct: 61 TAGREKGLDAHYVISLYQSIIEDSVLNQQAYLH---GRANPETQKQQYCIAYLGARGSYS 117 Query: 117 HLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHT 176 +LAA +Y R + ++ GC F +I VE+G ADY +PIENTSSG+IN+VYD+LQHT Sbjct: 118 YLAASRYCQRRQVEMLDLGCQSFDEIVQAVESGHADYGFLPIENTSSGSINEVYDVLQHT 177 Query: 177 SLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSA 236 SLSIVGE T+ + HCLL + LS I TVY+HPQP QCS++L+++ ++EY S++ Sbjct: 178 SLSIVGETTIEVSHCLLGKPGSKLSEIKTVYAHPQPISQCSRYLSQHKALRLEYCSSSAE 237 Query: 237 AMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPA 296 AMEKV Q+ AA+GS GG LY L+ +E ANQ+ N +RF+V+ARKA+ V +Q+PA Sbjct: 238 AMEKVNQSPDNSAAAIGSAEGGALYQLESIESGLANQKINQSRFIVVARKAVAVPEQLPA 297 Query: 297 KTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQ 356 KTTL+MATGQ+AGALVEALLVL+ H L M++LESRPI G PWEEMFYLDI AN+ S MQ Sbjct: 298 KTTLIMATGQKAGALVEALLVLKAHQLNMSKLESRPIPGTPWEEMFYLDIDANISSEAMQ 357 Query: 357 KALKELGEITRSMKVLGCYPSENVVP 382 + LK+L ITR +KVLGCYP E V P Sbjct: 358 QGLKQLERITRFIKVLGCYPCETVTP 383 Lambda K H 0.318 0.132 0.374 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: 545 Number of extensions: 17 Number of successful extensions: 2 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: 386 Length of database: 671 Length adjustment: 34 Effective length of query: 352 Effective length of database: 637 Effective search space: 224224 Effective search space used: 224224 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 (21.8 bits) S2: 52 (24.6 bits)
Align candidate 200542 SO1367 (chorismate mutase/prephenate dehydratase (NCBI ptt file))
to HMM TIGR01797 (chorismate mutase (EC 5.4.99.5))
# 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/TIGR01797.hmm # target sequence database: /tmp/gapView.16074.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01797 [M=83] Accession: TIGR01797 Description: CM_P_1: chorismate mutase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-32 97.2 2.6 5.1e-32 96.2 2.6 1.6 1 lcl|FitnessBrowser__MR1:200542 SO1367 chorismate mutase/prephen Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200542 SO1367 chorismate mutase/prephenate dehydratase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 96.2 2.6 5.1e-32 5.1e-32 2 83 .] 8 89 .. 7 89 .. 0.98 Alignments for each domain: == domain 1 score: 96.2 bits; conditional E-value: 5.1e-32 TIGR01797 2 lalrekisaidkkllkllaerkelafevakskllsqkavrdierekkllqklitlgkkyqleaeyitrlfqliiedsvltq 82 re+i+++d+ ll llaer++l +eva+sk+++ +++rd +rek+ll +l+t g++ l+a+y+ +l+q iiedsvl q lcl|FitnessBrowser__MR1:200542 8 NHTREQITQLDNDLLSLLAERRRLSLEVARSKEVDVRPIRDTQREKELLARLVTAGREKGLDAHYVISLYQSIIEDSVLNQ 88 567*****************************************************************************9 PP TIGR01797 83 q 83 q lcl|FitnessBrowser__MR1:200542 89 Q 89 8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (83 nodes) Target sequences: 1 (671 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: 14.81 // [ok]
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