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 AO356_07950 AO356_07950 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07950 Length = 497 Score = 905 bits (2339), Expect = 0.0 Identities = 444/496 (89%), Positives = 466/496 (93%) Query: 1 MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60 M+LI HLI GE ++D+ RTADVFNPSTG+A+ KVPLADR T+QQAIDAAKAAFPAWRNTP Sbjct: 1 MSLIPHLINGERLSDSARTADVFNPSTGQAIHKVPLADRATIQQAIDAAKAAFPAWRNTP 60 Query: 61 PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120 AKRAQV+FRFKQLLE NE RI +LISEEHGKT+EDAAGELKRGIENVE+A AAPEILKG Sbjct: 61 AAKRAQVMFRFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKG 120 Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180 EYSRNVGPNIDAWSDFQP+GVVAGITPFNFPAMVPLWMYPLAI CGN FILKPSERDPSS Sbjct: 121 EYSRNVGPNIDAWSDFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDPSS 180 Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240 TLLIA+L EAGLPKGVL+VVHGDK AVDALIEAPEVKALSFVGSTPIAEYIY+EGT+RG Sbjct: 181 TLLIAQLLLEAGLPKGVLSVVHGDKAAVDALIEAPEVKALSFVGSTPIAEYIYAEGTRRG 240 Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQ+ADALV K Sbjct: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQVADALVSK 300 Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360 LVPQIK LKIGAGTSCGLDMGPLVTG RDKV+GYI+ GV GA L+VDGRG VAGHE Sbjct: 301 LVPQIKALKIGAGTSCGLDMGPLVTGQHRDKVSGYIEEGVTAGASLIVDGRGLSVAGHEE 360 Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420 GFFLGG LFDRVTPEM IYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE Sbjct: 361 GFFLGGCLFDRVTPEMRIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420 Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYT+RKAITQR Sbjct: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTRRKAITQR 480 Query: 481 WPQRKSHEAAQFAFPS 496 WPQR SHEA+QFAFPS Sbjct: 481 WPQRASHEASQFAFPS 496 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: 908 Number of extensions: 17 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: 498 Length of database: 497 Length adjustment: 34 Effective length of query: 464 Effective length of database: 463 Effective search space: 214832 Effective search space used: 214832 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 AO356_07950 AO356_07950 (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.454.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-212 690.1 0.0 8.7e-212 689.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 AO356_07950 methylmalonate-semia Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 AO356_07950 methylmalonate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 689.9 0.0 8.7e-212 8.7e-212 3 477 .] 6 481 .. 4 481 .. 0.99 Alignments for each domain: == domain 1 score: 689.9 bits; conditional E-value: 8.7e-212 TIGR01722 3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarv 65 hli+G+ + + s++ +v np t++ + kv+ a + +++a+ +a+ +f+aw++t+ a+ra+v lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 6 HLINGERL-SDSARTADVFNPSTGQAIHKVPLADRATIQQAIDAAKAAFPAWRNTPAAKRAQV 67 78888876.678999************************************************ PP TIGR01722 66 llryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdv 128 ++r+++ll++++ ia+lis e+Gktleda G++ rG+e ve+ac+ + +l+Ge + +v ++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 68 MFRFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKGEYSRNVGPNI 130 *************************************************************** PP TIGR01722 129 dvysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGa 191 d +s qplGvvaGitpfnfpam+plwm+plai+cGn+f+lkpse++ps+++ +a+ll+eaG+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 131 DAWSDFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDPSSTLLIAQLLLEAGL 193 *************************************************************** PP TIGR01722 192 pdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvl 254 p+Gvl vvhGdk avd l+e p+vka+sfvGs++++eyiy g+++gkrvqal+Gaknh+v++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 194 PKGVLSVVHGDKAAVDALIEAPEVKALSFVGSTPIAEYIYAEGTRRGKRVQALGGAKNHAVLM 256 *************************************************************** PP TIGR01722 255 pdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..kelveeireraekvrvgagddpgae 315 pdad+++a++al+gaa+G+ G+rcmais+av vG+ + lv +++ +++ +++gag+ g + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 257 PDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQvaDALVSKLVPQIKALKIGAGTSCGLD 319 **********************************855699*********************** PP TIGR01722 316 lGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykee 378 +Gpl+t q++++v+ +i++g+ Ga++++dGrg+ v G+eeG f+G +l++rv p+m+iykee lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 320 MGPLVTGQHRDKVSGYIEEGVTAGASLIVDGRGLSVAGHEEGFFLGGCLFDRVTPEMRIYKEE 382 *************************************************************** PP TIGR01722 379 ifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplp 441 ifGpvl+++++++leea++lin+ yGnGt+ift+dG aar f eievG+vGvnvp+pvp++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 383 IFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARLFCDEIEVGMVGVNVPLPVPVA 445 *************************************************************** PP TIGR01722 442 ffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477 ++sf+Gwk slfGdlh+yG +Gvrfytr k++t rw lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07950 446 YHSFGGWKRSLFGDLHAYGPDGVRFYTRRKAITQRW 481 ************************************ PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (497 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11.68 // [ok]
This GapMind analysis is from Sep 17 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