Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate HSERO_RS05615 HSERO_RS05615 maleylacetoacetate isomerase
Query= reanno::psRCH2:GFF3446 (219 letters) >FitnessBrowser__HerbieS:HSERO_RS05615 Length = 215 Score = 233 bits (593), Expect = 3e-66 Identities = 116/215 (53%), Positives = 149/215 (69%), Gaps = 5/215 (2%) Query: 6 TLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPLLVDEG 65 TLY Y+RSSA+YRVRIAL+LK L Y VPVHL+ GG+Q + +NP LVP+L +EG Sbjct: 3 TLYSYFRSSASYRVRIALHLKDLPYETVPVHLLNQGGEQLLPAFTEINPHALVPVLAEEG 62 Query: 66 NGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNNLRVLQYLS 125 + +SQSLA+LE L+E P P+LLP D +RA +R+L++ IAC+IHPLNNLRVL+YL Sbjct: 63 H---YVSQSLAMLELLEERHPTPSLLPGDAFQRAHIRALSLAIACDIHPLNNLRVLKYLK 119 Query: 126 AELGVDDEAKNAWYRHWVSQGLAAVEQGL--ETFGDKLSLNDRPGYLEACLVPQVYNARR 183 ELG+DDE KNAW HW++ G A+E+ L +T + D P + CLVPQ++NARR Sbjct: 120 RELGMDDERKNAWIAHWINLGFTALERQLAADTTRGHFCVGDAPTMADCCLVPQIFNARR 179 Query: 184 FACDLAAYPRILEIVARCETLPAFQQAAPEVQPDA 218 F D+A YP + I C LPAFQQA P QPDA Sbjct: 180 FEVDMAPYPTLCAIEQACHALPAFQQAHPAQQPDA 214 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: 200 Number of extensions: 9 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: 215 Length adjustment: 22 Effective length of query: 197 Effective length of database: 193 Effective search space: 38021 Effective search space used: 38021 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 HSERO_RS05615 HSERO_RS05615 (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.7320.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-93 297.2 0.0 3.5e-93 297.1 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS05615 HSERO_RS05615 maleylacetoacetate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS05615 HSERO_RS05615 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 297.1 0.0 3.5e-93 3.5e-93 1 210 [. 3 214 .. 3 215 .] 0.98 Alignments for each domain: == domain 1 score: 297.1 bits; conditional E-value: 3.5e-93 TIGR01262 1 klYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd.GeqkkeefkalNPqelvPtLkidegevltqSl 67 +lYsyfrSsasyRvRiaL Lk++ ye+vpv+Ll++ Geq ++f+++NP +lvP+L + g+ ++qSl lcl|FitnessBrowser__HerbieS:HSERO_RS05615 3 TLYSYFRSSASYRVRIALHLKDLPYETVPVHLLNQgGEQLLPAFTEINPHALVPVLAEE-GHYVSQSL 69 59*********************************9*********************99.6******* PP TIGR01262 68 AiieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwi 135 A++e Lee++p+p+Llp d+ +ra+ ral+l+iacdihPl+Nlrvl++l+++lg+d+e+k++w++hwi lcl|FitnessBrowser__HerbieS:HSERO_RS05615 70 AMLELLEERHPTPSLLPGDAFQRAHIRALSLAIACDIHPLNNLRVLKYLKRELGMDDERKNAWIAHWI 137 ******************************************************************** PP TIGR01262 136 ekGlaalEellk..ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqe 201 + G++alE+ l+ +++g+fcvGd++t+ad+cLvpq+ nA+rfevd+a+yPtl +ie+a+++lpafq+ lcl|FitnessBrowser__HerbieS:HSERO_RS05615 138 NLGFTALERQLAadTTRGHFCVGDAPTMADCCLVPQIFNARRFEVDMAPYPTLCAIEQACHALPAFQQ 205 *********99988899*************************************************** PP TIGR01262 202 ahpenqpdt 210 ahp++qpd+ lcl|FitnessBrowser__HerbieS:HSERO_RS05615 206 AHPAQQPDA 214 ********7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (215 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: 7.32 // [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