Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate AO353_00900 AO353_00900 2-methylisocitrate lyase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6061 (294 letters) >FitnessBrowser__pseudo3_N2E3:AO353_00900 Length = 297 Score = 556 bits (1434), Expect = e-163 Identities = 285/293 (97%), Positives = 289/293 (98%) Query: 2 SNSTPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI 61 + STPGQRFRDAVA+EHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI Sbjct: 4 NKSTPGQRFRDAVASEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLGI 63 Query: 62 TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK 121 TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK Sbjct: 64 TGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGAK 123 Query: 122 RCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAG 181 RCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAG Sbjct: 124 RCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAG 183 Query: 182 ADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAFR 241 ADM+FPEAITEL+MYKLFASRVKAPILANITEFGATPLYTTEQL ADVSLVLYPLSAFR Sbjct: 184 ADMVFPEAITELDMYKLFASRVKAPILANITEFGATPLYTTEQLKAADVSLVLYPLSAFR 243 Query: 242 AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294 AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFA KK Sbjct: 244 AMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAQKK 296 Lambda K H 0.320 0.134 0.375 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: 374 Number of extensions: 3 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: 294 Length of database: 297 Length adjustment: 26 Effective length of query: 268 Effective length of database: 271 Effective search space: 72628 Effective search space used: 72628 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 AO353_00900 AO353_00900 (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.24595.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-135 434.8 1.8 7.5e-135 434.6 1.8 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_00900 AO353_00900 2-methylisocitrate l Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_00900 AO353_00900 2-methylisocitrate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 434.6 1.8 7.5e-135 7.5e-135 2 284 .. 9 293 .. 8 294 .. 0.99 Alignments for each domain: == domain 1 score: 434.6 bits; conditional E-value: 7.5e-135 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevaeea 65 g+++r+++++e++lq++G+ina++alla++aGf+a+YlsG+++aa slg+PDlg+t l++v++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_00900 9 GQRFRDAVASEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAgSLGVPDLGITGLDDVLTDV 73 789****************************************999******************* PP TIGR02317 66 rritrvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelvskee 129 rrit+v++lpllvD+DtGfG+ a+nvartvk++++ g+aa+hieDqv +k+CGh+++ke+vs++e lcl|FitnessBrowser__pseudo3_N2E3:AO353_00900 74 RRITDVCDLPLLVDVDTGFGSsAFNVARTVKSMIKFGAAAIHIEDQVGAKRCGHRPNKEIVSQQE 138 ********************889****************************************** PP TIGR02317 130 mvkkikaavkakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefak 194 mv++ikaav+a++d++fv++aRtDa aveGl++a++Ra a +eaGad++f+ea++++++++ fa+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_00900 139 MVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAGADMVFPEAITELDMYKLFAS 203 ***************************************************************** PP TIGR02317 195 avkvpllanmtefGktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkGtqkelldk 259 +vk+p+lan+tefG tpl+t+++l+ + +++v+yP++a+Ra++kaae+vy+ ++++Gtq++++d+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_00900 204 RVKAPILANITEFGATPLYTTEQLKAADVSLVLYPLSAFRAMNKAAENVYTAIRRDGTQQNVIDT 268 ***************************************************************** PP TIGR02317 260 lqtRkelYellgyedyekkdkelfk 284 +qtR elY+ ++y+++e+k++ lf+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_00900 269 MQTRMELYDRIDYHTFEQKLDALFA 293 ********************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (297 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: 9.29 // [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