Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_004846864.1 M988_RS16965 class II fructose-bisphosphate aldolase
Query= BRENDA::P0AB71 (359 letters) >NCBI__GCF_001655005.1:WP_004846864.1 Length = 359 Score = 677 bits (1747), Expect = 0.0 Identities = 328/359 (91%), Positives = 344/359 (95%) Query: 1 MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQ 60 MSKIFDFVKPGVITGDDVQKVFQ+AKENNFALPAVNCVGTDSINAV+E AAKV+APVIVQ Sbjct: 1 MSKIFDFVKPGVITGDDVQKVFQIAKENNFALPAVNCVGTDSINAVMEAAAKVRAPVIVQ 60 Query: 61 FSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI 120 FSNGGA+FIAGKGVK+DVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPW+ Sbjct: 61 FSNGGAAFIAGKGVKTDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWL 120 Query: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTG 180 DGLLDAGEKHFAATGKPLFSSHMIDLSEESL+ENIEICSKYL RMSKIGMTLEIELGCTG Sbjct: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLEENIEICSKYLTRMSKIGMTLEIELGCTG 180 Query: 181 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240 GEEDGVDNSHMD+SALYTQPEDVDYAYT+L+ ISPRFTIAASFGNVHGVYKPGNV LTP Sbjct: 181 GEEDGVDNSHMDSSALYTQPEDVDYAYTKLNAISPRFTIAASFGNVHGVYKPGNVQLTPK 240 Query: 241 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGV 300 IL +SQEYVSKKHNLPHNSLNFVFHGGSGSTA EIK++VSYGVVKMNIDTDTQWATWEG+ Sbjct: 241 ILHNSQEYVSKKHNLPHNSLNFVFHGGSGSTAAEIKEAVSYGVVKMNIDTDTQWATWEGI 300 Query: 301 LNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL 359 LNYYK NE YLQGQLGNP+G D+PNKKYYDPRVWLRA QTSMIARLE AF ELN DVL Sbjct: 301 LNYYKKNEGYLQGQLGNPEGADKPNKKYYDPRVWLRAAQTSMIARLELAFDELNCKDVL 359 Lambda K H 0.316 0.133 0.392 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: 582 Number of extensions: 8 Number of successful extensions: 1 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: 359 Length of database: 359 Length adjustment: 29 Effective length of query: 330 Effective length of database: 330 Effective search space: 108900 Effective search space used: 108900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_004846864.1 M988_RS16965 (class II fructose-bisphosphate aldolase)
to HMM TIGR01520 (fbaA: fructose-bisphosphate aldolase, class II (EC 4.1.2.13))
# 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/TIGR01520.hmm # target sequence database: /tmp/gapView.1528989.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01520 [M=357] Accession: TIGR01520 Description: FruBisAldo_II_A: fructose-bisphosphate aldolase, class II 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-193 628.7 0.4 1.5e-193 628.6 0.4 1.0 1 NCBI__GCF_001655005.1:WP_004846864.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001655005.1:WP_004846864.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 628.6 0.4 1.5e-193 1.5e-193 1 356 [. 4 358 .. 4 359 .] 0.99 Alignments for each domain: == domain 1 score: 628.6 bits; conditional E-value: 1.5e-193 TIGR01520 1 vldklktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkd 73 ++d++k+gvi+g+dv+k+f++ake++fa+Pa+n+v+++++na++eaa+++++p+i+qfsnggaafiaGkGvk+ NCBI__GCF_001655005.1:WP_004846864.1 4 IFDFVKPGVITGDDVQKVFQIAKENNFALPAVNCVGTDSINAVMEAAAKVRAPVIVQFSNGGAAFIAGKGVKT 76 6899********************************************************************* PP TIGR01520 74 eaekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmldlsee 146 +++++a+i Gai++a++v+++ae+ygvpv+lhtdhCakkllp++dgll+a+ek+f+++gkPlfsshm+dlsee NCBI__GCF_001655005.1:WP_004846864.1 77 DVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWLDGLLDAGEKHFAATGKPLFSSHMIDLSEE 149 ************************************************************************* PP TIGR01520 147 pieenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispkfsiaaa 219 ++eeniei++kyl rm+ki ++leie+G+tGGeedGvdn+++d+++lyt+Pedv+++y++l++isp+f+iaa+ NCBI__GCF_001655005.1:WP_004846864.1 150 SLEENIEICSKYLTRMSKIGMTLEIELGCTGGEEDGVDNSHMDSSALYTQPEDVDYAYTKLNAISPRFTIAAS 222 ************************************************************************* PP TIGR01520 220 fGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkvnvdtdtqy 292 fGnvhGvykpGnv+l+P+il+++qeyv++k++l+ +++l+fvfhGGsGst+ eikea+syGvvk+n+dtdtq+ NCBI__GCF_001655005.1:WP_004846864.1 223 FGNVHGVYKPGNVQLTPKILHNSQEYVSKKHNLP-HNSLNFVFHGGSGSTAAEIKEAVSYGVVKMNIDTDTQW 294 **********************************.9************************************* PP TIGR01520 293 aalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleelnaink 356 a++egil+y++kne ylq+q+Gnp+g +kpnkk+ydPrvwlr+a++sm+ar+e a++eln+ ++ NCBI__GCF_001655005.1:WP_004846864.1 295 ATWEGILNYYKKNEGYLQGQLGNPEGADKPNKKYYDPRVWLRAAQTSMIARLELAFDELNCKDV 358 ************************************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (357 nodes) Target sequences: 1 (359 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: 25.68 // [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