Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_050654861.1 C1M55_RS10170 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_002893965.1:WP_050654861.1 Length = 501 Score = 556 bits (1433), Expect = e-163 Identities = 280/497 (56%), Positives = 359/497 (72%), Gaps = 4/497 (0%) Query: 3 LIKHLIGGELIADTGR-TADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPP 61 +I H + G+ A T TA V NP+TG+ ++ LA+ E + IDAA AAFPAWR+T Sbjct: 8 VIAHWLDGKPFAGTSEDTAPVTNPATGQITGRLALANLEDARAVIDAAAAAFPAWRDTSL 67 Query: 62 AKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGE 121 A+R QVLF F++LL A + + ++I+ EHGK + DA GE+ RG E VE+A P +LKG Sbjct: 68 ARRTQVLFSFRELLNARKGELAEIITAEHGKVLSDALGEISRGQEVVEFACGIPHLLKGG 127 Query: 122 YSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSST 181 Y+ N +D +S QP+G V I+PFNFPAMVP+W +P+AIA GNT ILKPSE+DP++ Sbjct: 128 YTENASTKVDVYSIRQPLGPVGIISPFNFPAMVPMWFFPVAIAAGNTVILKPSEKDPTAA 187 Query: 182 LLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGK 241 + +AEL+ EAGLP GV NV+ GDK AVD L+E VKA+SFVGSTPIA+Y+Y+ GT GK Sbjct: 188 IWLAELWAEAGLPPGVFNVLQGDKLAVDELLENKAVKAISFVGSTPIAQYVYATGTANGK 247 Query: 242 RVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKL 301 RVQALGGAKNHA+++PDADLD A A++ A +GS GERCMAIS V VGD IAD LV K+ Sbjct: 248 RVQALGGAKNHAIVLPDADLDLAADAMVNAGFGSAGERCMAISALVAVGD-IADELVAKI 306 Query: 302 VPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENG 361 V + L G GT DMGPLVT A RDKV Y+D G GA +VVDGR + G +G Sbjct: 307 VERTTPLVTGDGTK-NSDMGPLVTKAHRDKVASYVDAGEKDGATIVVDGRTVQADGGPDG 365 Query: 362 FFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEA 421 F+LG TL D VT +M+IY +EIFGPVL +VRV++ ++A++LIN++ YGNGT IFT DG A Sbjct: 366 FWLGPTLIDHVTTDMSIYTDEIFGPVLSVVRVDTYDQALELINNNPYGNGTAIFTNDGGA 425 Query: 422 ARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRW 481 AR F +E+EVGM+G+NVP+PVP+AY+SFGGWK SLFGD HA+G +GV F+T+ KA+T RW Sbjct: 426 ARRFQNEVEVGMIGINVPIPVPMAYYSFGGWKNSLFGDTHAHGTEGVHFFTRGKAVTSRW 485 Query: 482 PQRKSHEAAQFAFPSNS 498 SH FP NS Sbjct: 486 LD-PSHGGINLGFPENS 501 Lambda K H 0.319 0.137 0.411 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: 732 Number of extensions: 28 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: 501 Length adjustment: 34 Effective length of query: 464 Effective length of database: 467 Effective search space: 216688 Effective search space used: 216688 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_050654861.1 C1M55_RS10170 (CoA-acylating methylmalonate-semialdehyde dehydrogenase)
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.1201628.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-210 686.4 0.4 1.2e-210 686.2 0.4 1.0 1 NCBI__GCF_002893965.1:WP_050654861.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_050654861.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 686.2 0.4 1.2e-210 1.2e-210 2 477 .] 10 485 .. 9 485 .. 0.99 Alignments for each domain: == domain 1 score: 686.2 bits; conditional E-value: 1.2e-210 TIGR01722 2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallk 74 h++dGk g+s+ pv+npat+++++++a a e+ a + +a +f+aw++ts+a+r++vl+ +++ll+ NCBI__GCF_002893965.1:WP_050654861.1 10 AHWLDGKPFAGTSEDTAPVTNPATGQITGRLALANLEDARAVIDAAAAAFPAWRDTSLARRTQVLFSFRELLN 82 79*********************************************************************** PP TIGR01722 75 ehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfn 147 +++ e+a++i+ae+Gk+l+da G++ rG evve+ac+++ ll+G +e+ +++vdvysirqplG v i+pfn NCBI__GCF_002893965.1:WP_050654861.1 83 ARKGELAEIITAEHGKVLSDALGEISRGQEVVEFACGIPHLLKGGYTENASTKVDVYSIRQPLGPVGIISPFN 155 ************************************************************************* PP TIGR01722 148 fpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220 fpam+p+w fp+aia Gnt +lkpsek+p+aa+ lael+ eaG+p Gv+nv+ Gdk avd+lle vka+sf NCBI__GCF_002893965.1:WP_050654861.1 156 FPAMVPMWFFPVAIAAGNTVILKPSEKDPTAAIWLAELWAEAGLPPGVFNVLQGDKLAVDELLENKAVKAISF 228 ************************************************************************* PP TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.ke 292 vGs+++++y+y tg+a+gkrvqal+Gaknh++vlpdad++ a+da+v+a +G+aG+rcmaisa v+vG++ +e NCBI__GCF_002893965.1:WP_050654861.1 229 VGSTPIAQYVYATGTANGKRVQALGGAKNHAIVLPDADLDLAADAMVNAGFGSAGERCMAISALVAVGDIaDE 301 ********************************************************************988** PP TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365 lv +i+er + g g++ ++++Gpl+tk+++++vas++++g k+Ga +++dGr+++ +G ++G ++G+tl+ NCBI__GCF_002893965.1:WP_050654861.1 302 LVAKIVERTTPLVTGDGTK-NSDMGPLVTKAHRDKVASYVDAGEKDGATIVVDGRTVQADGGPDGFWLGPTLI 373 ***************9997.579************************************************** PP TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438 ++v +dm+iy +eifGpvl v+++dt+++a++lin++pyGnGtaift+dG+aar+fq e+evG++G+nvpipv NCBI__GCF_002893965.1:WP_050654861.1 374 DHVTTDMSIYTDEIFGPVLSVVRVDTYDQALELINNNPYGNGTAIFTNDGGAARRFQNEVEVGMIGINVPIPV 446 ************************************************************************* PP TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477 p++++sf+Gwk+slfGd+h++G +Gv+f+tr+k+vt+rw NCBI__GCF_002893965.1:WP_050654861.1 447 PMAYYSFGGWKNSLFGDTHAHGTEGVHFFTRGKAVTSRW 485 *************************************** PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (501 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: 00:00:00.21 # Mc/sec: 1.09 // [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