Align candidate WP_055436038.1 ASC41_RS07585 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))
# 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.aa/TIGR00657.hmm # target sequence database: /tmp/gapView.288079.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00657 [M=442] Accession: TIGR00657 Description: asp_kinases: aspartate kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-84 269.5 0.3 3.4e-84 269.4 0.3 1.0 1 NCBI__GCF_001418085.1:WP_055436038.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001418085.1:WP_055436038.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 269.4 0.3 3.4e-84 3.4e-84 5 384 .. 3 384 .. 1 415 [. 0.88 Alignments for each domain: == domain 1 score: 269.4 bits; conditional E-value: 3.4e-84 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhle 75 V KFGG Sv++++ +k+v+k ++k +++ ++VvSAm+++T+aL +++k +e++ ++++++++ h + NCBI__GCF_001418085.1:WP_055436038.1 3 VFKFGGASVKDANGVKNVVKVLEKVGHEN--TLIVVSAMGKTTNALEVVIDKYLNEKNtfIAELDTVKNYHRT 73 89******************999988555..999******************999998787888899999999 PP TIGR00657 76 aleela.sqalkeklkallekeleevkk..........ereldlilsvGEklSaallaaaleelgvkavsllg 137 ++ l + + ++ +++ ++e+ + + +d ++ +GE +S+++++ +l++l + ++l+ NCBI__GCF_001418085.1:WP_055436038.1 74 IMMDLFnN--QQDQVFITVQALFNELLQffksnkspnyNFIYDQVIGYGELVSTTIISHYLNSLH-INNTWLD 143 88887744..4555555556666555555667999999999************************.677899* PP TIGR00657 138 aeagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdev 210 ++ i td+ ++rA+v ei+++ + + ++e ++++++GFi++++++ +ttLGR GSD+tAa+ A +l+A+ v NCBI__GCF_001418085.1:WP_055436038.1 144 VRQCIKTDDYYRRANVNWEITQNSIISKVKESTLYITQGFIASDSNNFTTTLGREGSDYTAAIFAYCLNAQSV 216 ************************************************************************* PP TIGR00657 211 eiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTliv 283 i++DV+G++ DPr+ +++++l++isy Ea ELa +Ga v+hp+tl+p+ r++ip++vks npe+ GT + NCBI__GCF_001418085.1:WP_055436038.1 217 TIWKDVPGVLNGDPRYFNNTQLLNTISYTEAIELAFYGASVIHPKTLQPLQRKEIPLHVKSFINPENAGTTVN 289 ************************************************************************9 PP TIGR00657 284 akskseeepavkalsldknqalvsvsgttmk...pgilaevfgalaeakvnvdlilqsssetsisfvvdked. 352 +++ ep+v l++nq+l+s+s + ++e+f+ la k +vd+i +s isf v e+ NCBI__GCF_001418085.1:WP_055436038.1 290 KSQG--IEPKVPCFILKQNQVLLSLSTLDFSyvvEENISEIFNLLALYKMKVDVIQ-NS---AISFSVCFENt 356 9955..669*******************999888888999**************98.33...48898887773 PP TIGR00657 353 adkakellkkkvkeekaleevevekklalvsl 384 ++ ++l ++++ka +ve++++++l ++ NCBI__GCF_001418085.1:WP_055436038.1 357 FNNLEKL----LLHLKAKFKVECHENVSLFTI 384 4555555....466666678999999998777 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (416 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: 24.40 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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