Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate WP_057508727.1 ABB28_RS11315 methylisocitrate lyase
Query= reanno::Cup4G11:RR42_RS11260 (302 letters) >NCBI__GCF_001431535.1:WP_057508727.1 Length = 296 Score = 456 bits (1172), Expect = e-133 Identities = 228/290 (78%), Positives = 256/290 (88%) Query: 11 SAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGISNL 70 SAGARFRQALA E PLQV+G INANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGI+ L Sbjct: 7 SAGARFRQALAAESPLQVIGAINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGINTL 66 Query: 71 DDVLTDVRRITDVCDVPLLVDVDTGFGASAFNVARTTRSLIKFGAGAMHIEDQVGAKRCG 130 +DVL DVRRITDVCD+PL+VD+DTGFG SAFN+ART +SLIK GAGA HIEDQVGAKRCG Sbjct: 67 EDVLIDVRRITDVCDLPLMVDIDTGFGPSAFNIARTVKSLIKAGAGACHIEDQVGAKRCG 126 Query: 131 HRPGKEIVSQGEMADRIKAAVDARTDENFVIMARTDALAVEGLDKAIERAVACVEAGADA 190 HRPGKEIVSQGEM DR+KAA DA+TD F ++ARTDA+ V+G+D AIERA+ACVEAGAD Sbjct: 127 HRPGKEIVSQGEMVDRVKAAADAKTDPAFFLIARTDAIQVDGVDAAIERAIACVEAGADG 186 Query: 191 IFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFRAMN 250 IF EA DL YR+FVDAVKVPVLANITEFGATPLF+ +EL AGV++ L+PLSAFRA N Sbjct: 187 IFAEAAYDLDTYRRFVDAVKVPVLANITEFGATPLFSRDELASAGVAIQLFPLSAFRAAN 246 Query: 251 KAAENVYAAIRRDGTQQNVVDTMQTRAELYESIGYHAYEQKLDALFAQGK 300 KAAE+VY A+RRDG Q+NVVD MQTR ELY+ IGYHA+EQ+LDALFA K Sbjct: 247 KAAESVYEAVRRDGHQRNVVDAMQTRNELYDRIGYHAFEQQLDALFAARK 296 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: 338 Number of extensions: 7 Number of successful extensions: 1 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: 296 Length adjustment: 27 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 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_057508727.1 ABB28_RS11315 (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.29484.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-126 406.0 1.5 4.4e-126 405.8 1.5 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057508727.1 ABB28_RS11315 methylisocitrate l Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057508727.1 ABB28_RS11315 methylisocitrate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.8 1.5 4.4e-126 4.4e-126 2 284 .. 9 293 .. 8 294 .. 0.99 Alignments for each domain: == domain 1 score: 405.8 bits; conditional E-value: 4.4e-126 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearrit 69 g+++r++l++e++lq++Gaina++alla++aG++a+YlsG+++aa slglPDlg+ tle+v+ ++rrit lcl|NCBI__GCF_001431535.1:WP_057508727.1 9 GARFRQALAAESPLQVIGAINANHALLAKRAGYRAIYLSGGGVAAgSLGLPDLGINTLEDVLIDVRRIT 77 689****************************************999*********************** PP TIGR02317 70 rvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaa 137 +v++lpl+vD+DtGfG a+n+artvk+l++ag++a+hieDqv +k+CGh++gke+vs+ emv+++kaa lcl|NCBI__GCF_001431535.1:WP_057508727.1 78 DVCDLPLMVDIDTGFGPsAFNIARTVKSLIKAGAGACHIEDQVGAKRCGHRPGKEIVSQGEMVDRVKAA 146 ****************769************************************************** PP TIGR02317 138 vkakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmte 206 ++ak+d+ f+liaRtDa v+G+daaieRa a veaGad if+ea +++ +r+f +avkvp+lan+te lcl|NCBI__GCF_001431535.1:WP_057508727.1 147 ADAKTDPAFFLIARTDAIQVDGVDAAIERAIACVEAGADGIFAEAAYDLDTYRRFVDAVKVPVLANITE 215 ********************************************************************* PP TIGR02317 207 fGktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedy 275 fG tpl++ del+++g++i ++P++a+Raa+kaae+vye ++++G q++++d +qtR+elY+ +gy+++ lcl|NCBI__GCF_001431535.1:WP_057508727.1 216 FGATPLFSRDELASAGVAIQLFPLSAFRAANKAAESVYEAVRRDGHQRNVVDAMQTRNELYDRIGYHAF 284 ********************************************************************* PP TIGR02317 276 ekkdkelfk 284 e++++ lf+ lcl|NCBI__GCF_001431535.1:WP_057508727.1 285 EQQLDALFA 293 ****99985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (296 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 8.67 // [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