Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate AO353_05990 AO353_05990 methylmalonate-semialdehyde dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_05990 (507 letters) >lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 AO353_05990 methylmalonate-semialdehyde dehydrogenase Length = 507 Score = 1004 bits (2597), Expect = 0.0 Identities = 507/507 (100%), Positives = 507/507 (100%) Query: 1 MNASLTPETTVQKVKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAA 60 MNASLTPETTVQKVKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAA Sbjct: 1 MNASLTPETTVQKVKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAA 60 Query: 61 HRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVE 120 HRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVE Sbjct: 61 HRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVE 120 Query: 121 HACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTF 180 HACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTF Sbjct: 121 HACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTF 180 Query: 181 VLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVG 240 VLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVG Sbjct: 181 VLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVG 240 Query: 241 THVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLV 300 THVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLV Sbjct: 241 THVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLV 300 Query: 301 GAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGR 360 GAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGR Sbjct: 301 GAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGR 360 Query: 361 DITVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNG 420 DITVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNG Sbjct: 361 DITVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNG 420 Query: 421 TGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFY 480 TGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFY Sbjct: 421 TGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFY 480 Query: 481 TQTKTVTSRWFDDDSVNDGVNTTINLR 507 TQTKTVTSRWFDDDSVNDGVNTTINLR Sbjct: 481 TQTKTVTSRWFDDDSVNDGVNTTINLR 507 Lambda K H 0.319 0.135 0.396 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: 981 Number of extensions: 28 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: 507 Length of database: 507 Length adjustment: 34 Effective length of query: 473 Effective length of database: 473 Effective search space: 223729 Effective search space used: 223729 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 AO353_05990 AO353_05990 (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.25784.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-232 756.7 2.4 5.4e-232 756.5 2.4 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 AO353_05990 methylmalonate-semia Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 AO353_05990 methylmalonate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 756.5 2.4 5.4e-232 5.4e-232 1 477 [] 14 490 .. 14 490 .. 1.00 Alignments for each domain: == domain 1 score: 756.5 bits; conditional E-value: 5.4e-232 TIGR01722 1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarv 65 vk+lidG+ ve++++++ ++ npat++vlakv++a+ +evdaa+++a+++f++w+ t++ r r+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 14 VKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAAHRAFQTWKLTPIGARMRI 78 899************************************************************** PP TIGR01722 66 llryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdv 130 +l+ qal++eh + ia ++saeqGkt++da+Gd++rGlevvehacs+ sl +Ge e+va vd+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 79 MLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEFAENVAGGVDT 143 ***************************************************************** PP TIGR01722 131 ysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGv 195 y++rqp+Gv+aGitpfnfpamiplwmfp+aiacGntfvlkpse++p +++ l el eaG+p Gv lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 144 YTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTMLLVELAIEAGIPAGV 208 ***************************************************************** PP TIGR01722 196 lnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadke 260 lnvvhG+k+ vd l+ h d+kavsfvGs+avg ++y+ + +hgkrvq+++Gaknh+vvlpda++e lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 209 LNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANRE 273 ***************************************************************** PP TIGR01722 261 aaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagddpgaelGplitkqak 325 +al+alvga +GaaGqrcma s++vlvGaak+++++++ a+k++v+ag++pg+++Gp+i+k+ak lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 274 QALNALVGAGFGAAGQRCMATSVVVLVGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAK 338 ***************************************************************** PP TIGR01722 326 ervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvlead 390 +r+ +li+sg+keGa++ ldGr ++v Gye+GnfvG+tl+++v +dm+iy +eifGpvlvvle+d lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 339 ARILDLIESGIKEGAKLELDGRDITVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVD 403 ***************************************************************** PP TIGR01722 391 tleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGd 455 tl++ai+l+n++p+GnGt +ft++Gaaarkfq ei+vGqvG+n+pipvp+pffsftG+++s Gd lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 404 TLDQAIALVNANPFGNGTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGD 468 ***************************************************************** PP TIGR01722 456 lhiyGkqGvrfytrlktvtarw 477 l yGkq v+fyt++ktvt+rw lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 469 LGPYGKQVVQFYTQTKTVTSRW 490 ********************** PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (507 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.60 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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