Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate WP_086509183.1 BZY95_RS06635 maleylacetoacetate isomerase
Query= reanno::psRCH2:GFF3446 (219 letters) >NCBI__GCF_002151265.1:WP_086509183.1 Length = 214 Score = 244 bits (623), Expect = 9e-70 Identities = 130/215 (60%), Positives = 154/215 (71%), Gaps = 6/215 (2%) Query: 6 TLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPLLVDEG 65 TLYGY+RSSAAYRVRIALNLKGLAY QV V+LVK G+QRA + A NPQ LVP+L E Sbjct: 3 TLYGYFRSSAAYRVRIALNLKGLAYEQVAVNLVK--GEQRAEENLARNPQGLVPVL--ET 58 Query: 66 NGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRVLQYLS 125 + G R++QSLAI EYL+E P PALLP DP RA+VRSLA +ACEIHPLNNL+VL+YL Sbjct: 59 DDGTRLTQSLAICEYLEERHPEPALLPGDPAGRARVRSLAQLVACEIHPLNNLKVLKYLV 118 Query: 126 AELGVDDEAKNAWYRHWVSQGLAAVEQGL--ETFGDKLSLNDRPGYLEACLVPQVYNARR 183 EL +D+ AK AWYRHW+++G A+E L E D P + CLVPQV+NA R Sbjct: 119 HELKLDEAAKLAWYRHWIAEGFTALEARLSGEAATGAFCHGDSPSLADVCLVPQVFNAER 178 Query: 184 FACDLAAYPRILEIVARCETLPAFQQAAPEVQPDA 218 F CDL+AYP I I RC + AF +AAP QPDA Sbjct: 179 FECDLSAYPTIRRIAERCRAMEAFAKAAPGAQPDA 213 Lambda K H 0.321 0.137 0.412 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: 199 Number of extensions: 9 Number of successful extensions: 4 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: 219 Length of database: 214 Length adjustment: 22 Effective length of query: 197 Effective length of database: 192 Effective search space: 37824 Effective search space used: 37824 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: 45 (21.9 bits)
Align candidate WP_086509183.1 BZY95_RS06635 (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.24646.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-95 305.0 0.0 1.4e-95 304.9 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086509183.1 BZY95_RS06635 maleylacetoacetate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086509183.1 BZY95_RS06635 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 304.9 0.0 1.4e-95 1.4e-95 1 210 [. 3 213 .. 3 214 .] 0.99 Alignments for each domain: == domain 1 score: 304.9 bits; conditional E-value: 1.4e-95 TIGR01262 1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeefkalNPqelvPtLkidegevltqSlAi 69 +lY+yfrSsa+yRvRiaL+Lkg++ye v+vnL+k Geq++ee+ a+NPq+lvP+L++d+g++ltqSlAi lcl|NCBI__GCF_002151265.1:WP_086509183.1 3 TLYGYFRSSAAYRVRIALNLKGLAYEQVAVNLVK-GEQRAEENLARNPQGLVPVLETDDGTRLTQSLAI 70 59********************************.9********************************* PP TIGR01262 70 ieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekG 138 eyLee++pepaLlp dpa rarvr+la+l+ac+ihPl+Nl+vl++l ++l+ de++k +w++hwi++G lcl|NCBI__GCF_002151265.1:WP_086509183.1 71 CEYLEERHPEPALLPGDPAGRARVRSLAQLVACEIHPLNNLKVLKYLVHELKLDEAAKLAWYRHWIAEG 139 ********************************************************************* PP TIGR01262 139 laalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpe 205 ++alE+ l+ +++gafc+Gd+++ladvcLvpqv nAerfe+dl++yPt++ri+e++++++af++a+p lcl|NCBI__GCF_002151265.1:WP_086509183.1 140 FTALEARLSgeAATGAFCHGDSPSLADVCLVPQVFNAERFECDLSAYPTIRRIAERCRAMEAFAKAAPG 208 ********988899******************************************************* PP TIGR01262 206 nqpdt 210 qpd+ lcl|NCBI__GCF_002151265.1:WP_086509183.1 209 AQPDA 213 ***96 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.11 // [ok]
This GapMind analysis is from Sep 24 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