Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_110804069.1 C8J30_RS02175 fructose-bisphosphate aldolase class II
Query= BRENDA::Q55664 (359 letters) >NCBI__GCF_003217355.1:WP_110804069.1 Length = 354 Score = 481 bits (1238), Expect = e-140 Identities = 236/349 (67%), Positives = 284/349 (81%) Query: 1 MALVPMRLLLDHAAENGYGIPAFNVNNMEQIISIMQAADETDSPVILQASRGARSYAGEN 60 MAL+ +R LLDHAAE YG+PAFN+NNMEQ ++IM+AA D+PVI+QASRGARSYA + Sbjct: 1 MALITLRQLLDHAAEYSYGVPAFNINNMEQGLAIMEAAKAVDAPVIIQASRGARSYANDI 60 Query: 61 FLRHLVLGAVETYPHIPIAMHQDHGNSPATCYSAIRNGFTSVMMDGSLEADAKTPASFEY 120 L ++ YP IP+ MHQDHGN+ ATC +AIR+GFTSVMMDGSLE DAKTPAS+EY Sbjct: 61 MLAKMIEALAAIYPDIPLCMHQDHGNNEATCMTAIRHGFTSVMMDGSLEGDAKTPASYEY 120 Query: 121 NVNVTAEVVKVAHSVGASVEGELGCLGSLETGQGEAEDGHGFEGKLDHSQLLTDPEEAVE 180 NV++T V ++AH VGASVEGELG LGSLETGQGEAEDGHG EG LDHSQLLTDP++AV+ Sbjct: 121 NVDITERVSRMAHWVGASVEGELGVLGSLETGQGEAEDGHGAEGVLDHSQLLTDPDQAVD 180 Query: 181 FVNKTQVDALAVAIGTSHGAYKFTRKPTGEVLAISRIEEIHRLLPNTHLVMHGSSSVPQE 240 FV KTQVDALA+A GTSHGAYKF+RKP GE+LA+S IE IH+ LPNTHLVMHGSSSVPQ+ Sbjct: 181 FVKKTQVDALAIACGTSHGAYKFSRKPDGEILAMSVIEAIHKKLPNTHLVMHGSSSVPQD 240 Query: 241 WIDMINEFGGAIPETYGVPVEEIQKGIKSGVRKVNIDTDNRLAITAAFREAAAKDPKNFD 300 D+INEFGGA+P+T+GVPVEEI +GIK GVRKVNIDTD R+A+T FR A ++ FD Sbjct: 241 LQDIINEFGGAMPQTFGVPVEEIVRGIKMGVRKVNIDTDCRMAMTGQFRRIAEQNKAEFD 300 Query: 301 PRHFLKPSIKYMKQVCADRYQQFWTAGNASKIKQLTLDDYAAKYAKGEL 349 PR FLKP++ M+ +C R + F TAG+ASKIK + +DD A +YA G L Sbjct: 301 PRKFLKPAMDAMRDLCRARLEAFGTAGHASKIKVIPMDDMAKRYASGSL 349 Lambda K H 0.315 0.131 0.377 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: 447 Number of extensions: 13 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: 354 Length adjustment: 29 Effective length of query: 330 Effective length of database: 325 Effective search space: 107250 Effective search space used: 107250 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_110804069.1 C8J30_RS02175 (fructose-bisphosphate aldolase class II)
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.1068811.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-200 650.0 1.1 4.8e-200 649.8 1.1 1.0 1 NCBI__GCF_003217355.1:WP_110804069.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003217355.1:WP_110804069.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 649.8 1.1 4.8e-200 4.8e-200 1 347 [] 3 349 .. 3 349 .. 1.00 Alignments for each domain: == domain 1 score: 649.8 bits; conditional E-value: 4.8e-200 TIGR01521 1 lislrqlldhaaergygvpafnvnnleqilaimeaadktdspvilqasrgarsyagevllrklvlaaveeypd 73 li+lrqlldhaae +ygvpafn+nn+eq laimeaa++ d+pvi+qasrgarsya++ +l+k+++a+ ypd NCBI__GCF_003217355.1:WP_110804069.1 3 LITLRQLLDHAAEYSYGVPAFNINNMEQGLAIMEAAKAVDAPVIIQASRGARSYANDIMLAKMIEALAAIYPD 75 69*********************************************************************** PP TIGR01521 74 ipvvlhqdhgnspatclsaiqlgftsvmmdgslkedaktpadydynvsvtaevvklahavgasvegelgclgs 146 ip+++hqdhgn+ atc++ai++gftsvmmdgsl+ daktpa+y+ynv++t++v+++ah vgasvegelg lgs NCBI__GCF_003217355.1:WP_110804069.1 76 IPLCMHQDHGNNEATCMTAIRHGFTSVMMDGSLEGDAKTPASYEYNVDITERVSRMAHWVGASVEGELGVLGS 148 ************************************************************************* PP TIGR01521 147 letgkgeaedghgfegaldrsqlltdpeeaaefvkktkvdalavaigtshgaykftrkptgevlaidrieeih 219 letg+geaedghg+eg+ld+sqlltdp++a++fvkkt+vdala+a gtshgaykf+rkp ge+la+++ie ih NCBI__GCF_003217355.1:WP_110804069.1 149 LETGQGEAEDGHGAEGVLDHSQLLTDPDQAVDFVKKTQVDALAIACGTSHGAYKFSRKPDGEILAMSVIEAIH 221 ************************************************************************* PP TIGR01521 220 erlpdthlvmhgsssvpqewldvineyggeiketygvpveeivkgikfgvrkvnidtdlrlaataalrrvaak 292 ++lp+thlvmhgsssvpq+ +d+ine+gg++++t+gvpveeiv+gik+gvrkvnidtd r+a+t+ +rr+a++ NCBI__GCF_003217355.1:WP_110804069.1 222 KKLPNTHLVMHGSSSVPQDLQDIINEFGGAMPQTFGVPVEEIVRGIKMGVRKVNIDTDCRMAMTGQFRRIAEQ 294 ************************************************************************* PP TIGR01521 293 dpsefdprkflkkaveamkdvckaryeafgtagnaskikvvsleemarryakgel 347 ++ efdprkflk+a++am+d+c ar eafgtag askikv+++++ma+rya+g+l NCBI__GCF_003217355.1:WP_110804069.1 295 NKAEFDPRKFLKPAMDAMRDLCRARLEAFGTAGHASKIKVIPMDDMAKRYASGSL 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: 20.76 // [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