Align 2-methylcitrate lyase (EC 4.1.3.30) (characterized)
to candidate HSERO_RS15660 HSERO_RS15660 2-methylisocitrate lyase
Query= metacyc::MONOMER-13636 (302 letters) >FitnessBrowser__HerbieS:HSERO_RS15660 Length = 296 Score = 495 bits (1274), Expect = e-145 Identities = 249/292 (85%), Positives = 270/292 (92%) Query: 11 SAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGISNL 70 SAGA FR+A+ +E PLQV+G INANHALLAKRAG+RAIYLSGGGVAAGSLGLPDLGISNL Sbjct: 5 SAGAAFRKAVQEESPLQVIGAINANHALLAKRAGFRAIYLSGGGVAAGSLGLPDLGISNL 64 Query: 71 DDVLTDIRRITDVCDTPLLVDVDTGFGASAFNVARTTKSLIKFGAAAMHIEDQVGAKRCG 130 DDVLTD+RRITDVCD PLLVDVDTGFGASAFNVART KS+IKFGAAAMHIEDQVGAKRCG Sbjct: 65 DDVLTDVRRITDVCDLPLLVDVDTGFGASAFNVARTVKSMIKFGAAAMHIEDQVGAKRCG 124 Query: 131 HRPNKEIVTQGEMVDRIRAAVDARTDENFVIMARTDALAVEGLDKAIERAVACAEAGADA 190 HRPNKEIV++ EMVDRI+AAVDARTDENFVIMARTDALAVEGLD AIERAVAC EAGAD Sbjct: 125 HRPNKEIVSKQEMVDRIKAAVDARTDENFVIMARTDALAVEGLDAAIERAVACVEAGADM 184 Query: 191 IFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFRAMN 250 IFPEA+TDLAMY++F +AVKVP+LANITEFG+TPLFT +EL GA V +VLYPLSAFRAMN Sbjct: 185 IFPEAITDLAMYKQFANAVKVPILANITEFGSTPLFTVDELKGADVGLVLYPLSAFRAMN 244 Query: 251 KAAENVYAAIRRDGTQKNVVDTMQTRAELYESIGYHDFEQKLDALFAQGKGK 302 KAAENVY AIRRDGTQKNVVDTMQTR ELY+ I YH +EQ+LDALFAQ K K Sbjct: 245 KAAENVYQAIRRDGTQKNVVDTMQTRMELYDRIDYHSYEQRLDALFAQQKNK 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: 364 Number of extensions: 6 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 HSERO_RS15660 HSERO_RS15660 (2-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.3604.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-136 438.3 3.5 6.5e-136 438.1 3.5 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS15660 HSERO_RS15660 2-methylisocitrate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS15660 HSERO_RS15660 2-methylisocitrate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.1 3.5 6.5e-136 6.5e-136 2 284 .. 7 291 .. 6 292 .. 0.99 Alignments for each domain: == domain 1 score: 438.1 bits; conditional E-value: 6.5e-136 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeearri 68 g+a+r+++++e++lq++Gaina++alla++aGf+a+YlsG+++aa slglPDlg+++l++v++++rri lcl|FitnessBrowser__HerbieS:HSERO_RS15660 7 GAAFRKAVQEESPLQVIGAINANHALLAKRAGFRAIYLSGGGVAAgSLGLPDLGISNLDDVLTDVRRI 74 679****************************************999********************** PP TIGR02317 69 trvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkik 135 t+v++lpllvD+DtGfG a+nvartvk++++ g+aa+hieDqv +k+CGh+++ke+vsk+emv++ik lcl|FitnessBrowser__HerbieS:HSERO_RS15660 75 TDVCDLPLLVDVDTGFGAsAFNVARTVKSMIKFGAAAMHIEDQVGAKRCGHRPNKEIVSKQEMVDRIK 142 *****************879************************************************ PP TIGR02317 136 aavkakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllan 203 aav+a++de+fv++aRtDa aveGldaaieRa a veaGad+if+ea+++++++++fa+avkvp+lan lcl|FitnessBrowser__HerbieS:HSERO_RS15660 143 AAVDARTDENFVIMARTDALAVEGLDAAIERAVACVEAGADMIFPEAITDLAMYKQFANAVKVPILAN 210 ******************************************************************** PP TIGR02317 204 mtefGktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellg 271 +tefG tpl+t+del+ + + +v+yP++a+Ra++kaae+vy+ ++++Gtqk+++d++qtR elY+ ++ lcl|FitnessBrowser__HerbieS:HSERO_RS15660 211 ITEFGSTPLFTVDELKGADVGLVLYPLSAFRAMNKAAENVYQAIRRDGTQKNVVDTMQTRMELYDRID 278 ******************************************************************** PP TIGR02317 272 yedyekkdkelfk 284 y++ye++++ lf+ lcl|FitnessBrowser__HerbieS:HSERO_RS15660 279 YHSYEQRLDALFA 291 ********99986 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.16 // [ok]
This GapMind analysis is from Sep 17 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