Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= reanno::psRCH2:GFF2388 (503 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 823 bits (2125), Expect = 0.0 Identities = 400/496 (80%), Positives = 450/496 (90%) Query: 8 PTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKTWRKTP 67 P ++LLIDG+FIES+T W+DVVNPATQ+VLA+VPFAT E+D AVA+ ++AFKTWRKTP Sbjct: 6 PRIRLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFKTWRKTP 65 Query: 68 IGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIGNLQLG 127 IG RARIFLKYQQLIRENM ELA L+AEQGKT+ DAEGDVFRGLEVVEHAA IGNLQLG Sbjct: 66 IGTRARIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEHAAAIGNLQLG 125 Query: 128 ELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 187 ELANNVA GVDTYTL+QPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV Sbjct: 126 ELANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 185 Query: 188 TMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNRASQAG 247 TMRL ELALEAG+P GVLNVVHGG +VVNAICDHPDIKAVSFVGST+VGTHVYNRAS AG Sbjct: 186 TMRLVELALEAGIPKGVLNVVHGGEEVVNAICDHPDIKAVSFVGSTRVGTHVYNRASLAG 245 Query: 248 KRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQAWIPDLV 307 KRVQCMMGAKNHA+VLPDA+KEQTLN + GAAFGAAGQRCMA S +VLVGEA++W+PDLV Sbjct: 246 KRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEARSWVPDLV 305 Query: 308 AKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGYENGN 367 AKA+TLKV+AG AGTDVGP++SC+A +RV GLI G+ +GA L+LDGRNP V G+E GN Sbjct: 306 AKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDGFEKGN 365 Query: 368 FVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTRSGAAA 427 FVGPTIFSGVT +M +YQEEIFGPVL ++ A T+++AI L+N+NPNGNGTA+FT+SGAAA Sbjct: 366 FVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQSGAAA 425 Query: 428 RHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTKTITERWF 487 R FQE+IDVGQVGINVPIPVPVP+FSFTGSRASKLGDLGPYGKQVV FYTQTKTIT RWF Sbjct: 426 RKFQEDIDVGQVGINVPIPVPVPLFSFTGSRASKLGDLGPYGKQVVMFYTQTKTITARWF 485 Query: 488 DENEVGGPVNTTINLK 503 D+ +G VNTTI+LK Sbjct: 486 DDETLGHGVNTTISLK 501 Lambda K H 0.318 0.134 0.394 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: 794 Number of extensions: 22 Number of successful extensions: 2 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: 503 Length of database: 501 Length adjustment: 34 Effective length of query: 469 Effective length of database: 467 Effective search space: 219023 Effective search space used: 219023 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 WP_057507564.1 ABB28_RS04920 (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.559803.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-226 737.5 2.6 3.5e-226 737.3 2.6 1.0 1 NCBI__GCF_001431535.1:WP_057507564.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001431535.1:WP_057507564.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 737.3 2.6 3.5e-226 3.5e-226 1 477 [] 8 484 .. 8 484 .. 1.00 Alignments for each domain: == domain 1 score: 737.3 bits; conditional E-value: 3.5e-226 TIGR01722 1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 +++lidG+f+e+ ++++ +v npat++vla+v++a++ evd ava+a+e+f +w++t++ rar++l+yq+l+ NCBI__GCF_001431535.1:WP_057507564.1 8 IRLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFKTWRKTPIGTRARIFLKYQQLI 80 5899********************************************************************* PP TIGR01722 74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146 +e+ e+a+ +saeqGkt+ da+Gdv+rGlevveha ++ l lGe+ ++va+ vd+y++ qplGv+aGitpf NCBI__GCF_001431535.1:WP_057507564.1 81 RENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEHAAAIGNLQLGELANNVANGVDTYTLMQPLGVCAGITPF 153 ************************************************************************* PP TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219 nfpamiplwmfp+aia Gntfvlkpse++p +++l el +eaG+p+GvlnvvhG++e v+ +++hpd+kavs NCBI__GCF_001431535.1:WP_057507564.1 154 NFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVTMRLVELALEAGIPKGVLNVVHGGEEVVNAICDHPDIKAVS 226 ************************************************************************* PP TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaake 292 fvGs++vg ++y+++s gkrvq+++Gaknh+vvlpda+ke++l+a+vgaa+GaaGqrcma s+ vlvG+a+ NCBI__GCF_001431535.1:WP_057507564.1 227 FVGSTRVGTHVYNRASLAGKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEARS 299 ************************************************************************* PP TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365 +v++++ +a+ ++v+ag+ +g+++Gp+i+ +a+erv+ liasg ++Ga + ldGr+ +v+G+e+GnfvG+t++ NCBI__GCF_001431535.1:WP_057507564.1 300 WVPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDGFEKGNFVGPTIF 372 ************************************************************************* PP TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438 ++v +dm+iy+eeifGpvlv+lea+tle+ai+l+n +p GnGta+ft++Gaaarkfq +i+vGqvG+nvpipv NCBI__GCF_001431535.1:WP_057507564.1 373 SGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQSGAAARKFQEDIDVGQVGINVPIPV 445 ************************************************************************* PP TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477 p+p+fsftG+++s Gdl yGkq v fyt++kt+tarw NCBI__GCF_001431535.1:WP_057507564.1 446 PVPLFSFTGSRASKLGDLGPYGKQVVMFYTQTKTITARW 484 *************************************** 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 30.43 // [ok]
This GapMind analysis is from Apr 09 2024. 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