Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate AO356_07870 AO356_07870 methylmalonate-semialdehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_5146 (508 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07870 Length = 508 Score = 957 bits (2474), Expect = 0.0 Identities = 475/508 (93%), Positives = 501/508 (98%) Query: 1 MNVSLTPNDTTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISA 60 MNVSLTP+DT +Q V+LLIDG+WVES+++EWHDI+NPATQQVLAKVPFATA EVDAAI+A Sbjct: 1 MNVSLTPSDTALQTVRLLIDGEWVESQSSEWHDIVNPATQQVLAKVPFATASEVDAAIAA 60 Query: 61 AHRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV 120 A RAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV Sbjct: 61 AQRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV 120 Query: 121 EHACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT 180 EHACSIG+LQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT Sbjct: 121 EHACSIGTLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT 180 Query: 181 FVLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAV 240 FVLKPSEQDP+STMLLVELAIEAG+PAGVLNVVHGGKDVVD LCTHKDIKAVSFVGSTAV Sbjct: 181 FVLKPSEQDPLSTMLLVELAIEAGVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAV 240 Query: 241 GTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL 300 GTHVYDLAG+HGKRVQSMMGAKNHAVVLPDANREQ LNALVGAGFGAAGQRCMATSVVVL Sbjct: 241 GTHVYDLAGRHGKRVQSMMGAKNHAVVLPDANREQTLNALVGAGFGAAGQRCMATSVVVL 300 Query: 301 VGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDG 360 VGAAKQWLP+LKALAQKLKVNAGSEPGTDVGPVISK+AKARIL+LIESG+KEGAKLELDG Sbjct: 301 VGAAKQWLPELKALAQKLKVNAGSEPGTDVGPVISKRAKARILELIESGVKEGAKLELDG 360 Query: 361 REISVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFGN 420 R ISVPG+E+GNFVGPTLFSGVTT+M+IYT+EIFGPVLVVLEV+TLD+AIALVNANPFGN Sbjct: 361 RGISVPGFEQGNFVGPTLFSGVTTEMRIYTEEIFGPVLVVLEVDTLDQAIALVNANPFGN 420 Query: 421 GTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 480 GTGLFTQSGAAARKFQ+EIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF Sbjct: 421 GTGLFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 480 Query: 481 YTQTKTVTSRWFDDDSVNDGVNTTINLR 508 YTQTKTVT+RWFDDDSVNDGVNTTINLR Sbjct: 481 YTQTKTVTARWFDDDSVNDGVNTTINLR 508 Lambda K H 0.318 0.135 0.395 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: 915 Number of extensions: 25 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: 508 Length of database: 508 Length adjustment: 34 Effective length of query: 474 Effective length of database: 474 Effective search space: 224676 Effective search space used: 224676 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 (21.7 bits) S2: 52 (24.6 bits)
Align candidate AO356_07870 AO356_07870 (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.22857.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-234 762.8 2.1 7.4e-234 762.7 2.1 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 AO356_07870 methylmalonate-semia Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 AO356_07870 methylmalonate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 762.7 2.1 7.4e-234 7.4e-234 1 477 [] 15 491 .. 15 491 .. 1.00 Alignments for each domain: == domain 1 score: 762.7 bits; conditional E-value: 7.4e-234 TIGR01722 1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaera 63 v++lidG+ ve++s+++ ++ npat++vlakv++a+a evdaa+a+a+++f++w+ t++ r lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 15 VRLLIDGEWVESQSSEWHDIVNPATQQVLAKVPFATASEVDAAIAAAQRAFQTWKLTPIGARM 77 799************************************************************ PP TIGR01722 64 rvllryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvak 126 r++l+ qal++eh + ia ++saeqGkt++da+Gd++rGlevvehacs+ +l +Ge e+va lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 78 RIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVVEHACSIGTLQMGEFAENVAG 140 *************************************************************** PP TIGR01722 127 dvdvysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellsea 189 vd+y++rqp+Gv+aGitpfnfpamiplwmfp+aiacGntfvlkpse++p++++ l el ea lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 141 GVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPLSTMLLVELAIEA 203 *************************************************************** PP TIGR01722 190 GapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmv 252 G+p GvlnvvhG+k+ vd l+ h d+kavsfvGs+avg ++y+ + +hgkrvq+++Gaknh+v lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 204 GVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGRHGKRVQSMMGAKNHAV 266 *************************************************************** PP TIGR01722 253 vlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagddpgae 315 vlpda++e++l+alvga +GaaGqrcma s++vlvGaak++++e++ a+k++v+ag++pg++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 267 VLPDANREQTLNALVGAGFGAAGQRCMATSVVVLVGAAKQWLPELKALAQKLKVNAGSEPGTD 329 *************************************************************** PP TIGR01722 316 lGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykee 378 +Gp+i+k+ak+r+ +li+sg+keGa++ ldGrg+ v G+e+GnfvG+tl+++v ++m+iy ee lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 330 VGPVISKRAKARILELIESGVKEGAKLELDGRGISVPGFEQGNFVGPTLFSGVTTEMRIYTEE 392 *************************************************************** PP TIGR01722 379 ifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplp 441 ifGpvlvvle+dtl++ai+l+n++p+GnGt +ft++Gaaarkfq ei+vGqvG+n+pipvp+p lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 393 IFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAARKFQSEIDVGQVGINIPIPVPVP 455 *************************************************************** PP TIGR01722 442 ffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477 ffsftG+++s Gdl yGkq v+fyt++ktvtarw lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07870 456 FFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARW 491 ************************************ PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (477 nodes) Target sequences: 1 (508 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.83 // [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