Align 2-methylcitrate lyase (EC 4.1.3.30) (characterized)
to candidate WP_013136520.1 ARNIT_RS13710 methylisocitrate lyase
Query= metacyc::MONOMER-13636 (302 letters) >NCBI__GCF_000092245.1:WP_013136520.1 Length = 294 Score = 382 bits (981), Expect = e-111 Identities = 193/294 (65%), Positives = 234/294 (79%), Gaps = 3/294 (1%) Query: 11 SAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGISNL 70 SAG RFR+AL +E PLQ+VGTINA AL A + G++AIYLSGGG+A S GLPDLG++ + Sbjct: 2 SAGKRFREALKEERPLQIVGTINAYQALQATKVGFKAIYLSGGGIANASYGLPDLGMTMI 61 Query: 71 DDVLTDIRRITDVCDTPLLVDVDTGFGASAFNVARTTKSLIKFGAAAMHIEDQVGAKRCG 130 +DV DIRR+T +CDTPL+VD DTG+G AFNVART K I+ GAA +HIEDQV AKRCG Sbjct: 62 EDVCIDIRRVTSICDTPLIVDADTGWG-HAFNVARTVKEFIRSGAAGLHIEDQVAAKRCG 120 Query: 131 HRPNKEIVTQGEMVDRIRAAVDART--DENFVIMARTDALAVEGLDKAIERAVACAEAGA 188 HRPNKE+V+ EM DRIRAAVDA+ D +F I+ARTDA A EG + A+ RA A EAGA Sbjct: 121 HRPNKELVSTEEMCDRIRAAVDAKMELDPDFYIIARTDAHASEGQEAAVARAKAYVEAGA 180 Query: 189 DAIFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFRA 248 DAIF EA+ L Y++F D + VPVLANITEFGATP+FTTEELG G+ MVLYPLSAFRA Sbjct: 181 DAIFAEAVHTLKEYKEFCDQMSVPVLANITEFGATPMFTTEELGSVGIEMVLYPLSAFRA 240 Query: 249 MNKAAENVYAAIRRDGTQKNVVDTMQTRAELYESIGYHDFEQKLDALFAQGKGK 302 MNKAA +VY +R GTQ++ +DTMQTR ELYE +GYH++EQK+D+LFA+GK K Sbjct: 241 MNKAALHVYQELRDKGTQESTLDTMQTRMELYEMLGYHEYEQKMDSLFAKGKAK 294 Lambda K H 0.320 0.134 0.376 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: 267 Number of extensions: 10 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: 302 Length of database: 294 Length adjustment: 26 Effective length of query: 276 Effective length of database: 268 Effective search space: 73968 Effective search space used: 73968 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: 48 (23.1 bits)
Align candidate WP_013136520.1 ARNIT_RS13710 (methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))
# 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.carbon/TIGR02317.hmm # target sequence database: /tmp/gapView.458114.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02317 [M=285] Accession: TIGR02317 Description: prpB: methylisocitrate lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-134 433.8 2.0 1.5e-134 433.6 2.0 1.0 1 NCBI__GCF_000092245.1:WP_013136520.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000092245.1:WP_013136520.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 433.6 2.0 1.5e-134 1.5e-134 2 284 .. 4 289 .. 3 290 .. 0.98 Alignments for each domain: == domain 1 score: 433.6 bits; conditional E-value: 1.5e-134 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearritrvtk 73 gk++re+lk+e +lqi+G+ina+ al+a k+Gf+a+YlsG+++a+ s glPDlg+t +e+v+ ++rr+t++++ NCBI__GCF_000092245.1:WP_013136520.1 4 GKRFREALKEERPLQIVGTINAYQALQATKVGFKAIYLSGGGIANaSYGLPDLGMTMIEDVCIDIRRVTSICD 76 799*****************************************989************************** PP TIGR02317 74 lpllvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkak..kde 144 pl+vDaDtG+G a+nvartvke++++g+a++hieDqva+k+CGh+++kelvs+eem+++i+aav+ak d+ NCBI__GCF_000092245.1:WP_013136520.1 77 TPLIVDADTGWGHAFNVARTVKEFIRSGAAGLHIEDQVAAKRCGHRPNKELVSTEEMCDRIRAAVDAKmeLDP 149 ********************************************************************54589 PP TIGR02317 145 dfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltade 217 df++iaRtDa+a+eG++aa++RakaYveaGadaif+ea+++++e++ef++++ vp+lan+tefG tp++t++e NCBI__GCF_000092245.1:WP_013136520.1 150 DFYIIARTDAHASEGQEAAVARAKAYVEAGADAIFAEAVHTLKEYKEFCDQMSVPVLANITEFGATPMFTTEE 222 ************************************************************************* PP TIGR02317 218 leelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284 l ++g+++v+yP++a+Ra++kaa +vy+el++kGtq+++ld++qtR elYe+lgy++ye+k ++lf+ NCBI__GCF_000092245.1:WP_013136520.1 223 LGSVGIEMVLYPLSAFRAMNKAALHVYQELRDKGTQESTLDTMQTRMELYEMLGYHEYEQKMDSLFA 289 ***************************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (294 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 12.21 // [ok]
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