Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate Ga0059261_0507 Ga0059261_0507 maleylacetoacetate isomerase
Query= reanno::MR1:200836 (216 letters) >FitnessBrowser__Korea:Ga0059261_0507 Length = 212 Score = 213 bits (542), Expect = 2e-60 Identities = 115/215 (53%), Positives = 149/215 (69%), Gaps = 7/215 (3%) Query: 1 MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60 M L+GY+RS+A+YRVRIALNLKG+ E +S HL + GEQ Y+A+NPQ LVP L + Sbjct: 4 MRLHGYFRSTASYRVRIALNLKGMGYEPVSHHLRK--GEQRAPGYLAVNPQGLVPALELG 61 Query: 61 DEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQY 120 D G LTQSLAI EYLDE+ P LLPA + RAHVRA A IAC+IHP+ NL+VL Sbjct: 62 D---GAVLTQSLAICEYLDEIAPDPALLPADPVARAHVRAFAQAIACDIHPVQNLKVLDR 118 Query: 121 LTQKLTVNEEAKSAWYHHWVATGFTALETQLVRHSGRYCFGDKVTIADLCLVPQVYNAQR 180 L + L ++E+A + W + G A + + H+G +CFGD VT+AD+CLVPQ+ NA+R Sbjct: 119 L-RGLGLDEDAVNGWARATIEDGLDAWDRLIAEHAGAFCFGDAVTLADICLVPQLVNARR 177 Query: 181 FNVDLTPYPNIMRVWAECNQLPAFADAAPERQADA 215 F DL +P ++ + A C LPAF+DAAPERQADA Sbjct: 178 FGADLR-WPRLLAIEAACLALPAFSDAAPERQADA 211 Lambda K H 0.321 0.134 0.408 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: 167 Number of extensions: 6 Number of successful extensions: 5 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: 216 Length of database: 212 Length adjustment: 22 Effective length of query: 194 Effective length of database: 190 Effective search space: 36860 Effective search space used: 36860 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 (21.9 bits) S2: 45 (21.9 bits)
Align candidate Ga0059261_0507 Ga0059261_0507 (maleylacetoacetate isomerase)
to HMM TIGR01262 (maiA: maleylacetoacetate isomerase (EC 5.2.1.2))
# 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/TIGR01262.hmm # target sequence database: /tmp/gapView.23735.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01262 [M=211] Accession: TIGR01262 Description: maiA: maleylacetoacetate isomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-83 264.1 0.0 4.9e-83 263.9 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0507 Ga0059261_0507 maleylacetoacetat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0507 Ga0059261_0507 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.9 0.0 4.9e-83 4.9e-83 2 210 .. 6 211 .. 5 212 .] 0.98 Alignments for each domain: == domain 1 score: 263.9 bits; conditional E-value: 4.9e-83 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAii 70 l++yfrS+asyRvRiaL+Lkg+ ye v+ +L+k Geq+++ + a+NPq+lvP+L+ ++g+vltqSlAi lcl|FitnessBrowser__Korea:Ga0059261_0507 6 LHGYFRSTASYRVRIALNLKGMGYEPVSHHLRK-GEQRAPGYLAVNPQGLVPALELGDGAVLTQSLAIC 73 889******************************.9********************************** PP TIGR01262 71 eyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGl 139 eyL+e p+paLlp+dp +ra+vra+a++iacdihP+qNl+vl +l+ lg de++ + w++ ie+Gl lcl|FitnessBrowser__Korea:Ga0059261_0507 74 EYLDEIAPDPALLPADPVARAHVRAFAQAIACDIHPVQNLKVLDRLR-GLGLDEDAVNGWARATIEDGL 141 ***********************************************.779****************** PP TIGR01262 140 aalEellkekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqp 208 +a ++l++e+agafc+Gd+vtlad+cLvpq+ nA+rf+ dl ++P+l +ie+a+ +lpaf++a+pe+q lcl|FitnessBrowser__Korea:Ga0059261_0507 142 DAWDRLIAEHAGAFCFGDAVTLADICLVPQLVNARRFGADL-RWPRLLAIEAACLALPAFSDAAPERQA 209 *****************************************.69************************9 PP TIGR01262 209 dt 210 d+ lcl|FitnessBrowser__Korea:Ga0059261_0507 210 DA 211 97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (212 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: 5.41 // [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