Align Methylisocitrate lyase (EC 4.1.3.30) (characterized)
to candidate AO356_20865 AO356_20865 2-methylisocitrate lyase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6061 (294 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20865 Length = 294 Score = 570 bits (1468), Expect = e-167 Identities = 293/294 (99%), Positives = 294/294 (100%) Query: 1 MSNSTPGQRFRDAVANEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG 60 MSNSTPGQRFRDAVA+EHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG Sbjct: 1 MSNSTPGQRFRDAVASEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAGSLGVPDLG 60 Query: 61 ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120 ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA Sbjct: 61 ITGLDDVLTDVRRITDVCDLPLLVDVDTGFGSSAFNVARTVKSMIKFGAAAIHIEDQVGA 120 Query: 121 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEA 180 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEA Sbjct: 121 KRCGHRPNKEIVSQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEA 180 Query: 181 GADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF 240 GADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF Sbjct: 181 GADMIFPEAITELEMYKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAF 240 Query: 241 RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294 RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK Sbjct: 241 RAMNKAAENVYTAIRRDGTQQNVIDTMQTRMELYDRIDYHTFEQKLDALFAAKK 294 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: 383 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: 294 Length adjustment: 26 Effective length of query: 268 Effective length of database: 268 Effective search space: 71824 Effective search space used: 71824 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 AO356_20865 AO356_20865 (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.22110.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-135 435.5 1.7 4.8e-135 435.2 1.7 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865 AO356_20865 2-methylisocitrate l Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865 AO356_20865 2-methylisocitrate lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.2 1.7 4.8e-135 4.8e-135 2 284 .. 7 291 .. 6 292 .. 0.99 Alignments for each domain: == domain 1 score: 435.2 bits; conditional E-value: 4.8e-135 TIGR02317 2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaa.slglPDlglttleevae 63 g+++r+++++e++lq++G+ina++alla++aGf+a+YlsG+++aa slg+PDlg+t l++v++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865 7 GQRFRDAVASEHPLQVVGTINANHALLAKRAGFKAIYLSGGGVAAgSLGVPDLGITGLDDVLT 69 789****************************************999***************** PP TIGR02317 64 earritrvtklpllvDaDtGfGe.alnvartvkeleeagvaavhieDqvapkkCGhldgkelv 125 ++rrit+v++lpllvD+DtGfG+ a+nvartvk++++ g+aa+hieDqv +k+CGh+++ke+v lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865 70 DVRRITDVCDLPLLVDVDTGFGSsAFNVARTVKSMIKFGAAAIHIEDQVGAKRCGHRPNKEIV 132 **********************889************************************** PP TIGR02317 126 skeemvkkikaavkakkdedfvliaRtDaraveGldaaieRakaYveaGadaiftealeseee 188 s++emv++ikaav+a++d++fv++aRtDa aveGl++a++Ra a +eaGad+if+ea++++e+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865 133 SQQEMVDRIKAAVDARTDDSFVIMARTDALAVEGLESALDRAAACIEAGADMIFPEAITELEM 195 *************************************************************** PP TIGR02317 189 frefakavkvpllanmtefGktplltadeleelgykiviyPvtalRaalkaaekvyeelkkkG 251 ++ fa++vk+p+lan+tefG tpl+t+++l+ + +++v+yP++a+Ra++kaae+vy+ ++++G lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865 196 YKLFASRVKAPILANITEFGATPLYTTEQLAGADVSLVLYPLSAFRAMNKAAENVYTAIRRDG 258 *************************************************************** PP TIGR02317 252 tqkelldklqtRkelYellgyedyekkdkelfk 284 tq++++d++qtR elY+ ++y+++e+k++ lf+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20865 259 TQQNVIDTMQTRMELYDRIDYHTFEQKLDALFA 291 ****************************99985 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: 00:00:00.01 # Mc/sec: 6.88 // [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