Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate N515DRAFT_4292 N515DRAFT_4292 maleylacetoacetate isomerase
Query= reanno::psRCH2:GFF3446 (219 letters) >FitnessBrowser__Dyella79:N515DRAFT_4292 Length = 221 Score = 242 bits (618), Expect = 4e-69 Identities = 123/220 (55%), Positives = 151/220 (68%), Gaps = 5/220 (2%) Query: 1 MGTELTLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPL 60 M ++L LYGYWRSSAAYRVRIALNLKGLAY PVHLV+DGG+Q YRALNPQ+LVP Sbjct: 1 MTSDLVLYGYWRSSAAYRVRIALNLKGLAYESRPVHLVRDGGEQHQQAYRALNPQELVPC 60 Query: 61 LVDEGNGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRV 120 LVD G ++QS+AI+EYLDE P PALLP D RA+VRSLA +AC++HPL NLRV Sbjct: 61 LVD---GAQVLTQSMAIMEYLDETHPAPALLPPDAAGRARVRSLAQLLACDVHPLGNLRV 117 Query: 121 LQYLSAELGVDDEAKNAWYRHWVSQGLAAVEQGL--ETFGDKLSLNDRPGYLEACLVPQV 178 LQYL EL D+ + +W RHW+ +G A+E L + D+P +ACLVPQ Sbjct: 118 LQYLGNELHADEAVRGSWSRHWIGEGFRALEAMLAGNAATGRFCHGDQPTLADACLVPQH 177 Query: 179 YNARRFACDLAAYPRILEIVARCETLPAFQQAAPEVQPDA 218 YNA R+ + +P I IV C+ L AF++A PE QPDA Sbjct: 178 YNALRWKLPMEEFPTIRRIVEACQALDAFKRAVPEAQPDA 217 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: 201 Number of extensions: 7 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: 219 Length of database: 221 Length adjustment: 22 Effective length of query: 197 Effective length of database: 199 Effective search space: 39203 Effective search space used: 39203 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 N515DRAFT_4292 N515DRAFT_4292 (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.29481.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-93 297.1 0.0 3.8e-93 297.0 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_4292 N515DRAFT_4292 maleylacetoacetat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_4292 N515DRAFT_4292 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 297.0 0.0 3.8e-93 3.8e-93 2 210 .. 7 217 .. 6 218 .. 0.99 Alignments for each domain: == domain 1 score: 297.0 bits; conditional E-value: 3.8e-93 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkidegevltqS 66 lY+y+rSsa+yRvRiaL+Lkg++yes+pv+L++d Geq++++++alNPqelvP L+++ ++vltqS lcl|FitnessBrowser__Dyella79:N515DRAFT_4292 7 LYGYWRSSAAYRVRIALNLKGLAYESRPVHLVRDgGEQHQQAYRALNPQELVPCLVDG-AQVLTQS 71 9********************************************************9.6****** PP TIGR01262 67 lAiieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlk 132 +Ai+eyL+et+p paLlp d+a rarvr+la+l+acd+hPl Nlrvlq+l ++l++de+ + +w++ lcl|FitnessBrowser__Dyella79:N515DRAFT_4292 72 MAIMEYLDETHPAPALLPPDAAGRARVRSLAQLLACDVHPLGNLRVLQYLGNELHADEAVRGSWSR 137 ****************************************************************** PP TIGR01262 133 hwiekGlaalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealael 196 hwi +G++alE++l+ +++g+fc+Gd++tlad cLvpq ynA r+++ ++++Pt++ri ea+++l lcl|FitnessBrowser__Dyella79:N515DRAFT_4292 138 HWIGEGFRALEAMLAgnAATGRFCHGDQPTLADACLVPQHYNALRWKLPMEEFPTIRRIVEACQAL 203 **************988899********************************************** PP TIGR01262 197 pafqeahpenqpdt 210 +af++a pe qpd+ lcl|FitnessBrowser__Dyella79:N515DRAFT_4292 204 DAFKRAVPEAQPDA 217 *************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (221 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: 00:00:00.00 # Mc/sec: 6.78 // [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