Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011911728.1 PST_RS02550 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Query= BRENDA::G5CZI2 (498 letters) >NCBI__GCF_000013785.1:WP_011911728.1 Length = 500 Score = 636 bits (1641), Expect = 0.0 Identities = 311/501 (62%), Positives = 384/501 (76%), Gaps = 4/501 (0%) Query: 1 MTTIGHLINGQLVT-ENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNT 59 M T+G+LIN + V + R V+NPATGE + L+S +AI+AAQ AF W T Sbjct: 1 MLTLGNLINNEAVAGRSERHATVYNPATGEPRLYVSLSSADETREAIAAAQAAFEAWSKT 60 Query: 60 PPLKRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLK 119 PPL RARVMFRFKELLE+ D++ RLI EHGK+ DA GE+ RG+E VE+ACG P LLK Sbjct: 61 PPLVRARVMFRFKELLEKRRDDVARLITSEHGKVFSDAQGEVTRGLEVVEFACGIPHLLK 120 Query: 120 GEHSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPS 179 GE S NVG IDS S QP+GV AGITPFNFP MVPLWM P+AI CGN FVLKPSE+DPS Sbjct: 121 GEFSSNVGRDIDSNSLMQPLGVCAGITPFNFPAMVPLWMLPVAIACGNTFVLKPSEKDPS 180 Query: 180 STLYIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASAN 239 +T+ I +LL EAGLP GV+N+VNGDKEAVD LL D+RV++VSFVGSTPIAEYIY TASA+ Sbjct: 181 ATMLIGELLAEAGLPAGVLNIVNGDKEAVDVLLTDERVQSVSFVGSTPIAEYIYATASAH 240 Query: 240 GKRCQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVS 299 GKRCQALGGAKNH +VMPDAD V+ L+GAA+GS+GERCMA+SVAV VGD D LV Sbjct: 241 GKRCQALGGAKNHMVVMPDADPQQVVSSLMGAAYGSAGERCMAISVAVCVGDEVADKLVE 300 Query: 300 KMTQAMQKLKVGP--STDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPN 357 + + +++ GP + GP++TR+HQ+KV GYI+ + GAT+V DGR KV Sbjct: 301 MLKGEISQMRTGPGLGVEPEPHMGPLVTREHQQKVSGYIDLGVEDGATLVCDGRGIKVEG 360 Query: 358 HENGFFVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTR 417 +ENGF+VG TL D VTP M Y+EEIFGPVL VVRVA+ +A+ LI+ HE+GNGT IFTR Sbjct: 361 YENGFYVGPTLFDRVTPSMRIYREEIFGPVLAVVRVASFDEALQLINDHEFGNGTSIFTR 420 Query: 418 DGEAARYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTV 477 DG+ AR F +N++VGMVG+N+P+PVP+A+H FGGWKRS+FG L+ +GPD VRF+T+ KTV Sbjct: 421 DGDTARQFEENVKVGMVGVNVPIPVPMAFHCFGGWKRSVFGPLNMHGPDGVRFFTRMKTV 480 Query: 478 TQRWPSAGVREGAEFSMPTMK 498 T+RWP+ G+R G EF+MPTMK Sbjct: 481 TRRWPT-GIRAGTEFAMPTMK 500 Lambda K H 0.319 0.135 0.405 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: 740 Number of extensions: 33 Number of successful extensions: 3 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: 498 Length of database: 500 Length adjustment: 34 Effective length of query: 464 Effective length of database: 466 Effective search space: 216224 Effective search space used: 216224 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 (21.7 bits) S2: 52 (24.6 bits)
Align candidate WP_011911728.1 PST_RS02550 (methylmalonate-semialdehyde dehydrogenase (CoA acylating))
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))
# 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/TIGR01722.hmm # target sequence database: /tmp/gapView.28245.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01722 [M=477] Accession: TIGR01722 Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-211 686.8 0.0 8.5e-211 686.6 0.0 1.0 1 lcl|NCBI__GCF_000013785.1:WP_011911728.1 PST_RS02550 methylmalonate-semia Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013785.1:WP_011911728.1 PST_RS02550 methylmalonate-semialdehyde dehydrogenase (CoA acylating) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 686.6 0.0 8.5e-211 8.5e-211 4 477 .] 7 484 .. 4 484 .. 0.99 Alignments for each domain: == domain 1 score: 686.6 bits; conditional E-value: 8.5e-211 TIGR01722 4 lidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqal 72 li+ + v g+s+++ v npat+e v+ +sa+e +a+a+a+ +f aw++t+ + rarv++r+++l lcl|NCBI__GCF_000013785.1:WP_011911728.1 7 LINNEAVAGRSERHATVYNPATGEPRLYVSLSSADETREAIAAAQAAFEAWSKTPPLVRARVMFRFKEL 75 789999*************************************************************** PP TIGR01722 73 lkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvva 141 l+++rd++a+li++e+Gk+++da+G+v rGlevve+ac+++ ll+Ge +++v +d+d s+ qplGv+a lcl|NCBI__GCF_000013785.1:WP_011911728.1 76 LEKRRDDVARLITSEHGKVFSDAQGEVTRGLEVVEFACGIPHLLKGEFSSNVGRDIDSNSLMQPLGVCA 144 ********************************************************************* PP TIGR01722 142 GitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrll 210 Gitpfnfpam+plwm+p+aiacGntfvlkpsek+psa++ + ell eaG+p Gvln+v Gdkeavd ll lcl|NCBI__GCF_000013785.1:WP_011911728.1 145 GITPFNFPAMVPLWMLPVAIACGNTFVLKPSEKDPSATMLIGELLAEAGLPAGVLNIVNGDKEAVDVLL 213 ********************************************************************* PP TIGR01722 211 ehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcm 279 v++vsfvGs++++eyiy t+sahgkr qal+Gaknhmvv+pdad ++++++l+gaa+G+aG+rcm lcl|NCBI__GCF_000013785.1:WP_011911728.1 214 TDERVQSVSFVGSTPIAEYIYATASAHGKRCQALGGAKNHMVVMPDADPQQVVSSLMGAAYGSAGERCM 282 ********************************************************************* PP TIGR01722 280 aisaavlvGaa..kelveeireraekvrvgag..ddpgaelGplitkqakervasliasgakeGaevll 344 ais+av vG+ ++lve ++ + ++r g+g +p ++Gpl+t++++++v+ +i+ g+++Ga ++ lcl|NCBI__GCF_000013785.1:WP_011911728.1 283 AISVAVCVGDEvaDKLVEMLKGEISQMRTGPGlgVEPEPHMGPLVTREHQQKVSGYIDLGVEDGATLVC 351 *********7446***************9996337999******************************* PP TIGR01722 345 dGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaifts 413 dGrg+kveGye+G +vG+tl++rv p+m+iy+eeifGpvl+v+++ +++ea++lin+ +GnGt+ift+ lcl|NCBI__GCF_000013785.1:WP_011911728.1 352 DGRGIKVEGYENGFYVGPTLFDRVTPSMRIYREEIFGPVLAVVRVASFDEALQLINDHEFGNGTSIFTR 420 ********************************************************************* PP TIGR01722 414 dGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477 dG +ar+f+ +++vG+vGvnvpipvp++f+ f+Gwk s+fG l+++G +Gvrf+tr+ktvt rw lcl|NCBI__GCF_000013785.1:WP_011911728.1 421 DGDTARQFEENVKVGMVGVNVPIPVPMAFHCFGGWKRSVFGPLNMHGPDGVRFFTRMKTVTRRW 484 **************************************************************** PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (500 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.23 // [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