Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate GFF38 PGA1_c00380 putative maleylacetoacetate isomerase
Query= reanno::MR1:200836 (216 letters) >FitnessBrowser__Phaeo:GFF38 Length = 228 Score = 162 bits (410), Expect = 5e-45 Identities = 96/219 (43%), Positives = 132/219 (60%), Gaps = 16/219 (7%) Query: 1 MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60 +ILY YWRSSA+YRVRIALNL G+S ++V LV+ GEQ D++A NPQ LVP L Sbjct: 4 VILYDYWRSSASYRVRIALNLAGISYRAVTVDLVK--GEQVSPDHLARNPQGLVPVL--- 58 Query: 61 DEQDGDALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQY 120 E DG LTQSLAI++YLD+ LLP + ERA +A+A IA ++HP+ NL+V ++ Sbjct: 59 -EIDGLRLTQSLAILDYLDQTR-HLDLLPRTPAERALAQALAHAIAVDLHPVCNLKVARH 116 Query: 121 LTQKLTVNEEAKSA--------WYHHWVATGFTALETQLVRHS-GRYCFGDKVTIADLCL 171 + T + + +A W H++ G A T L H YC GD +ADLCL Sbjct: 117 ASDLCTGSAASPAAQPVDMPADWMRHFIRPGLVAFNTLLEEHPVAPYCTGDHPGLADLCL 176 Query: 172 VPQVYNAQRFNVDLTPYPNIMRVWAECNQLPAFADAAPE 210 +PQ+YNA+R+ V+ P ++ + C PAFA A P+ Sbjct: 177 IPQLYNARRWGVNFDDLPRLVTIETTCAGNPAFAMAHPD 215 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: 166 Number of extensions: 9 Number of successful extensions: 6 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: 228 Length adjustment: 22 Effective length of query: 194 Effective length of database: 206 Effective search space: 39964 Effective search space used: 39964 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 GFF38 PGA1_c00380 (putative 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.28274.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-71 226.0 0.0 2.6e-71 225.6 0.0 1.1 1 lcl|FitnessBrowser__Phaeo:GFF38 PGA1_c00380 putative maleylaceto Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF38 PGA1_c00380 putative maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 225.6 0.0 2.6e-71 2.6e-71 1 206 [. 5 216 .. 5 220 .. 0.90 Alignments for each domain: == domain 1 score: 225.6 bits; conditional E-value: 2.6e-71 TIGR01262 1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAiieyLeetyp 78 +lY+y+rSsasyRvRiaL+L gi+y++v+v+L+k Geq ++++ a+NPq+lvP+L+id g +ltqSlAi++yL++t+ lcl|FitnessBrowser__Phaeo:GFF38 5 ILYDYWRSSASYRVRIALNLAGISYRAVTVDLVK-GEQVSPDHLARNPQGLVPVLEID-GLRLTQSLAILDYLDQTRH 80 59********************************.9**********************.6**************9987 PP TIGR01262 79 epaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklg...vde.....eekkewlkhwiekGlaalEellk. 147 Llp+ pa+ra ++ala++ia d+hP++Nl+v + ++ + +++ ++ ++w++h+i+ Gl a+ +ll+ lcl|FitnessBrowser__Phaeo:GFF38 81 -LDLLPRTPAERALAQALAHAIAVDLHPVCNLKVARHASDLCTgsaASPaaqpvDMPADWMRHFIRPGLVAFNTLLEe 157 .89*******************************9987654431112331111134579******************6 PP TIGR01262 148 ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpen 206 + +c+Gd+++lad+cL+pq+ynA+r++v++++ P+l +ie+++a paf+ ahp+ lcl|FitnessBrowser__Phaeo:GFF38 158 HPVAPYCTGDHPGLADLCLIPQLYNARRWGVNFDDLPRLVTIETTCAGNPAFAMAHPDA 216 67889****************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (228 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.45 // [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