Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_019894862.1 A377_RS0103975 class II fructose-bisphosphate aldolase
Query= BRENDA::Q602L6 (354 letters) >NCBI__GCF_000384235.1:WP_019894862.1 Length = 354 Score = 525 bits (1352), Expect = e-154 Identities = 250/354 (70%), Positives = 303/354 (85%) Query: 1 MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60 MA+I+LR+L+D+AAEHG+G+PAFNVNNMEQ++AIM+AA AVD+PVILQGSAGAR YAGEP Sbjct: 1 MAMITLRELMDYAAEHGFGMPAFNVNNMEQVRAIMDAAKAVDSPVILQGSAGARKYAGEP 60 Query: 61 FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120 FLRHL+ AA EMYP IPV MHQDHG+ P VC R+IQSGF+SVMMDGSL DMKTPASY Y Sbjct: 61 FLRHLIEAATEMYPEIPVVMHQDHGSDPGVCTRAIQSGFTSVMMDGSLEADMKTPASYEY 120 Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180 NV+ TR VV++AH+ GVSVEGELGCLGSLETG G+EDGHG++ ++D LLTDP+EAAD Sbjct: 121 NVDVTRTVVDIAHSAGVSVEGELGCLGSLETGMMGEEDGHGSDEKMDMDALLTDPEEAAD 180 Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240 FV++T +DALA+A+GTSHGAYKFT KP+ VLRIDR+K IH+RIP H+VMHGSSSVPEE Sbjct: 181 FVKKTNLDALAVAVGTSHGAYKFTSKPSDDVLRIDRIKEIHERIPDTHIVMHGSSSVPEE 240 Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300 W ++IN+YGGD+GQT+GVPV+ IVEGI+HGVRKVNIDTDLR+AS GA+R+ + E+ NFD Sbjct: 241 WLEIINNYGGDMGQTFGVPVDAIVEGIKHGVRKVNIDTDLRMASTGAVRKHLAENPSNFD 300 Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDPIVR 354 PRK K+AQ AM+ IC+ R+EAFG AG A+KIK L LE+M YA G LD V+ Sbjct: 301 PRKFLKSAQEAMSDICKHRFEAFGCAGHASKIKSLGLEEMQRRYAAGDLDQRVK 354 Lambda K H 0.320 0.134 0.391 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: 504 Number of extensions: 16 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: 354 Length of database: 354 Length adjustment: 29 Effective length of query: 325 Effective length of database: 325 Effective search space: 105625 Effective search space used: 105625 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: 49 (23.5 bits)
Align candidate WP_019894862.1 A377_RS0103975 (class II fructose-bisphosphate aldolase)
to HMM TIGR01521 (fba: fructose-bisphosphate aldolase, class II, Calvin cycle subtype (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/TIGR01521.hmm # target sequence database: /tmp/gapView.3156206.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01521 [M=347] Accession: TIGR01521 Description: FruBisAldo_II_B: fructose-bisphosphate aldolase, class II, Calvin cycle subtype 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-188 609.9 1.1 7.8e-188 609.7 1.1 1.0 1 NCBI__GCF_000384235.1:WP_019894862.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000384235.1:WP_019894862.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 609.7 1.1 7.8e-188 7.8e-188 2 347 .] 4 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 609.7 bits; conditional E-value: 7.8e-188 TIGR01521 2 islrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypdi 74 i+lr l+d+aae+g+g+pafnvnn+eq++aim+aa++ dspvilq s+gar+yage++lr+l++aa e+yp+i NCBI__GCF_000384235.1:WP_019894862.1 4 ITLRELMDYAAEHGFGMPAFNVNNMEQVRAIMDAAKAVDSPVILQGSAGARKYAGEPFLRHLIEAATEMYPEI 76 99*********************************************************************** PP TIGR01521 75 pvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgsl 147 pvv+hqdhg++p +c +aiq gftsvmmdgsl++d ktpa+y+ynv+vt vv +ah+ g+svegelgclgsl NCBI__GCF_000384235.1:WP_019894862.1 77 PVVMHQDHGSDPGVCTRAIQSGFTSVMMDGSLEADMKTPASYEYNVDVTRTVVDIAHSAGVSVEGELGCLGSL 149 ************************************************************************* PP TIGR01521 148 etgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeihe 220 etg+ ++edghg + ++d lltdpeeaa+fvkkt++dalava+gtshgaykft kp+ +vl idri+eihe NCBI__GCF_000384235.1:WP_019894862.1 150 ETGMMGEEDGHGSDEKMDMDALLTDPEEAADFVKKTNLDALAVAVGTSHGAYKFTSKPSDDVLRIDRIKEIHE 222 ************************************************************************* PP TIGR01521 221 rlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaakd 293 r+pdth+vmhgsssvp+ewl++in+ygg++ +t+gvpv+ iv+gik+gvrkvnidtdlr+a+t+a+r+ +a++ NCBI__GCF_000384235.1:WP_019894862.1 223 RIPDTHIVMHGSSSVPEEWLEIINNYGGDMGQTFGVPVDAIVEGIKHGVRKVNIDTDLRMASTGAVRKHLAEN 295 ************************************************************************* PP TIGR01521 294 psefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347 ps+fdprkflk a eam+d+ck r+eafg ag askik++ leem rrya g+l NCBI__GCF_000384235.1:WP_019894862.1 296 PSNFDPRKFLKSAQEAMSDICKHRFEAFGCAGHASKIKSLGLEEMQRRYAAGDL 349 ****************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (347 nodes) Target sequences: 1 (354 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: 19.52 // [ok]
This GapMind analysis is from Apr 09 2024. 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