Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate BPHYT_RS02805 BPHYT_RS02805 maleylacetoacetate isomerase
Query= reanno::MR1:200836 (216 letters) >FitnessBrowser__BFirm:BPHYT_RS02805 Length = 214 Score = 238 bits (608), Expect = 5e-68 Identities = 124/218 (56%), Positives = 153/218 (70%), Gaps = 8/218 (3%) Query: 1 MILYGYWRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVD 60 M LY Y+RSSA+YRVRIALN+K + + + VHLVRDGGEQ K +Y +N +VPT V Sbjct: 1 MKLYSYFRSSASYRVRIALNVKNLPYDYVPVHLVRDGGEQLKPEYRKVNADGIVPTFV-- 58 Query: 61 DEQDG-DALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLRVLQ 119 DG D + QSLAIIEYL+E++P+ LLP + +RA+VRA+AL +ACEIHPLNNLRVL+ Sbjct: 59 ---DGNDVMPQSLAIIEYLEEVHPEPALLPKAPADRAYVRALALQVACEIHPLNNLRVLK 115 Query: 120 YLTQKLTVNEEAKSAWYHHWVATGFTALETQLV--RHSGRYCFGDKVTIADLCLVPQVYN 177 YL L V++ AK AWY HWV GF ET L +G+ CFGD TIAD CL+PQV+N Sbjct: 116 YLKHTLGVDDYAKDAWYRHWVEAGFATFETHLAGDPRTGKLCFGDTPTIADTCLIPQVFN 175 Query: 178 AQRFNVDLTPYPNIMRVWAECNQLPAFADAAPERQADA 215 AQRF VD T +P I R++ QL AFA AAP Q DA Sbjct: 176 AQRFKVDTTKFPTIQRIYDHAMQLDAFARAAPGAQPDA 213 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: 174 Number of extensions: 6 Number of successful extensions: 3 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: 214 Length adjustment: 22 Effective length of query: 194 Effective length of database: 192 Effective search space: 37248 Effective search space used: 37248 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 BPHYT_RS02805 BPHYT_RS02805 (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.7266.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-90 286.6 0.0 6.1e-90 286.5 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS02805 BPHYT_RS02805 maleylacetoacetate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS02805 BPHYT_RS02805 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 286.5 0.0 6.1e-90 6.1e-90 1 210 [. 2 213 .. 2 214 .] 0.99 Alignments for each domain: == domain 1 score: 286.5 bits; conditional E-value: 6.1e-90 TIGR01262 1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkidegevltqSlAi 69 klYsyfrSsasyRvRiaL++k++ y +vpv+L++d Geq k+e++++N + vPt++++ ++v+ qSlAi lcl|FitnessBrowser__BFirm:BPHYT_RS02805 2 KLYSYFRSSASYRVRIALNVKNLPYDYVPVHLVRDgGEQLKPEYRKVNADGIVPTFVDG-NDVMPQSLAI 70 69********************************************************9.5********* PP TIGR01262 70 ieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGl 139 ieyLee +pepaLlpk pa+ra vralal +ac+ihPl+Nlrvl++l+++lgvd+ +k++w++hw+e+G+ lcl|FitnessBrowser__BFirm:BPHYT_RS02805 71 IEYLEEVHPEPALLPKAPADRAYVRALALQVACEIHPLNNLRVLKYLKHTLGVDDYAKDAWYRHWVEAGF 140 ********************************************************************** PP TIGR01262 140 aalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenq 207 a++E++l+ +++g+ c+Gd++t+ad cL+pqv nA+rf+vd +++Pt++ri +++ +l+af++a+p q lcl|FitnessBrowser__BFirm:BPHYT_RS02805 141 ATFETHLAgdPRTGKLCFGDTPTIADTCLIPQVFNAQRFKVDTTKFPTIQRIYDHAMQLDAFARAAPGAQ 210 *******99999********************************************************** PP TIGR01262 208 pdt 210 pd+ lcl|FitnessBrowser__BFirm:BPHYT_RS02805 211 PDA 213 **7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (214 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: 6.03 // [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