Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_011777945.1 MVAN_RS03390 class II fructose-bisphosphate aldolase
Query= BRENDA::P9WQA3 (344 letters) >NCBI__GCF_000015305.1:WP_011777945.1 Length = 345 Score = 606 bits (1563), Expect = e-178 Identities = 297/343 (86%), Positives = 325/343 (94%) Query: 1 MPIATPEVYAEMLGQAKQNSYAFPAINCTSSETVNAAIKGFADAGSDGIIQFSTGGAEFG 60 MPIATPEVYAEMLG+AK++S+AFPAINC SE+VNAAIKGFADAGSDGIIQFSTGGAEF Sbjct: 1 MPIATPEVYAEMLGRAKEHSFAFPAINCVGSESVNAAIKGFADAGSDGIIQFSTGGAEFA 60 Query: 61 SGLGVKDMVTGAVALAEFTHVIAAKYPVNVALHTDHCPKDKLDSYVRPLLAISAQRVSKG 120 SGLGVK+MVTGAVALAEF HVIAAKY + VALHTDHCPKDKLD+YVRPLLAISA+RV++G Sbjct: 61 SGLGVKEMVTGAVALAEFAHVIAAKYDITVALHTDHCPKDKLDTYVRPLLAISAERVARG 120 Query: 121 GNPLFQSHMWDGSAVPIDENLAIAQELLKAAAAAKIILEIEIGVVGGEEDGVANEINEKL 180 NPLFQSHMWDGSAVPIDENL+IAQELLK AAAAKIILEIEIGVVGGEEDGV EIN+KL Sbjct: 121 QNPLFQSHMWDGSAVPIDENLSIAQELLKQAAAAKIILEIEIGVVGGEEDGVEAEINDKL 180 Query: 181 YTSPEDFEKTIEALGAGEHGKYLLAATFGNVHGVYKPGNVKLRPDILAQGQQVAAAKLGL 240 YT+PEDFEKTIEALGAGEHGKYLLAATFGNVHGVYKPGNV L+P++LA+GQ+VA+AKLGL Sbjct: 181 YTTPEDFEKTIEALGAGEHGKYLLAATFGNVHGVYKPGNVVLKPEVLAEGQRVASAKLGL 240 Query: 241 PADAKPFDFVFHGGSGSLKSEIEEALRYGVVKMNVDTDTQYAFTRPIAGHMFTNYDGVLK 300 PA +KPFDFVFHGGSGSLKSEIE++LRYGVVKMNVDTDTQYAFTRPI GHMFTNYDGVLK Sbjct: 241 PAGSKPFDFVFHGGSGSLKSEIEDSLRYGVVKMNVDTDTQYAFTRPIVGHMFTNYDGVLK 300 Query: 301 VDGEVGVKKVYDPRSYLKKAEASMSQRVVQACNDLHCAGKSLT 343 VDGEVG KKVYDPRSY KKAEA MS+RVV+AC DLH AG+S++ Sbjct: 301 VDGEVGNKKVYDPRSYFKKAEAGMSERVVEACKDLHSAGRSVS 343 Lambda K H 0.316 0.133 0.384 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: 470 Number of extensions: 10 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: 344 Length of database: 345 Length adjustment: 29 Effective length of query: 315 Effective length of database: 316 Effective search space: 99540 Effective search space used: 99540 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_011777945.1 MVAN_RS03390 (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.aa/TIGR01520.hmm # target sequence database: /tmp/gapView.10849.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-155 500.9 0.3 1e-154 500.8 0.3 1.0 1 lcl|NCBI__GCF_000015305.1:WP_011777945.1 MVAN_RS03390 class II fructose-b Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011777945.1 MVAN_RS03390 class II fructose-bisphosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 500.8 0.3 1e-154 1e-154 9 356 .. 3 340 .. 1 341 [. 0.99 Alignments for each domain: == domain 1 score: 500.8 bits; conditional E-value: 1e-154 TIGR01520 9 vilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkdeaek 77 ++++e++a++++ ake++fa+Pain+v+se+vnaa+++++da+s++i+qfs+gga+f +G+Gvk+ lcl|NCBI__GCF_000015305.1:WP_011777945.1 3 IATPEVYAEMLGRAKEHSFAFPAINCVGSESVNAAIKGFADAGSDGIIQFSTGGAEFASGLGVKE---- 67 789**************************************************************.... PP TIGR01520 78 aasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllp.yvdglleadekyfkkegkPlfsshmldlse 145 +++Ga+a+ae+ ++ia+ky + v+lhtdhC+k++l+ yv++ll++++++++++++Plf+shm+d+s+ lcl|NCBI__GCF_000015305.1:WP_011777945.1 68 --MVTGAVALAEFAHVIAAKYDITVALHTDHCPKDKLDtYVRPLLAISAERVARGQNPLFQSHMWDGSA 134 ..9****************************************************************** PP TIGR01520 146 epieenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelsk.ispk 213 +pi+en++ia+++lk++a++k+ileieiG++GGeedGv+ e + ++lyt+Ped+ek++e+l + +++k lcl|NCBI__GCF_000015305.1:WP_011777945.1 135 VPIDENLSIAQELLKQAAAAKIILEIEIGVVGGEEDGVEAEIN--DKLYTTPEDFEKTIEALGAgEHGK 201 *****************************************99..79****************99**** PP TIGR01520 214 fsiaaafGnvhGvykpGnvklrPdiladgqeyvaeklglke.akplsfvfhGGsGstkeeikealsyGv 281 + +aa+fGnvhGvykpGnv+l+P++la+gq+++++klgl++ +kp++fvfhGGsGs+k+ei+++l+yGv lcl|NCBI__GCF_000015305.1:WP_011777945.1 202 YLLAATFGNVHGVYKPGNVVLKPEVLAEGQRVASAKLGLPAgSKPFDFVFHGGSGSLKSEIEDSLRYGV 270 ****************************************99*************************** PP TIGR01520 282 vkvnvdtdtqyaalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekalee 350 vk+nvdtdtqya++++i +++++n+d +++++G e++nkkvydPr++ ++ae+ m++rv++a+++ lcl|NCBI__GCF_000015305.1:WP_011777945.1 271 VKMNVDTDTQYAFTRPIVGHMFTNYDGVLKVDG-----EVGNKKVYDPRSYFKKAEAGMSERVVEACKD 334 *********************************.....9****************************** PP TIGR01520 351 lnaink 356 l+++++ lcl|NCBI__GCF_000015305.1:WP_011777945.1 335 LHSAGR 340 *99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (357 nodes) Target sequences: 1 (345 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.96 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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