GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Brevibacterium jeotgali SJ5-8

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_101588846.1 BJEO58_RS07395 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_900169175.1:WP_101588846.1
          Length = 497

 Score =  546 bits (1407), Expect = e-160
 Identities = 281/500 (56%), Positives = 350/500 (70%), Gaps = 5/500 (1%)

Query: 1   MTLIKHLIGGELIADT--GRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRN 58
           MT I H I G  + ++   R  DV NP+TG +  +V LA  +  ++AI AA  AFPAWR+
Sbjct: 1   MTTISHWINGRTVEESHGARFGDVVNPATGVSSGRVALASADRGREAIQAAADAFPAWRD 60

Query: 59  TPPAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEIL 118
           T   KR  ++F F++LL A +E +  +I+ EHGK + DA GE+ RG+E VE       +L
Sbjct: 61  TSLTKRTSIIFTFRELLNARKEELAAIITAEHGKVLSDALGEVSRGLEVVELCCNISYLL 120

Query: 119 KGEYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDP 178
           KG +S N    ID  S  QP+GV A I+PFNFPAMVPLW +P+AIA GNT +LKPSE+DP
Sbjct: 121 KGGHSENASTGIDVHSVRQPVGVSAIISPFNFPAMVPLWFFPVAIATGNTVVLKPSEKDP 180

Query: 179 SSTLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTK 238
           S+   +AEL+ EAGLP GV NV+HGDK AVD L+  P+V ++SFVGSTPIA+YIY   + 
Sbjct: 181 STANWLAELWKEAGLPDGVFNVLHGDKEAVDTLLTDPQVDSVSFVGSTPIAKYIYETASA 240

Query: 239 RGKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALV 298
            GKRVQALGGAKNH +++PDADLD    + + A YG+ GERCMAISV V V D IAD LV
Sbjct: 241 HGKRVQALGGAKNHMLVLPDADLDITADSAVNAGYGAAGERCMAISVVVAV-DAIADELV 299

Query: 299 QKLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGH 358
            K+  + +GLK+G GT    DMGPL+T A RDKV GYID GV  GAELV+DGR       
Sbjct: 300 AKIAERTRGLKVGDGTR-DSDMGPLITVAHRDKVAGYIDAGVESGAELVLDGRTSTPDAD 358

Query: 359 ENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRD 418
            +  FL  TLFDRVTP+M+IY +EIFGPVL +VRV S +E + LIN + YGNGT IFT D
Sbjct: 359 SDAAFLNPTLFDRVTPDMSIYTDEIFGPVLVVVRVPSYDEGLDLINANPYGNGTAIFTND 418

Query: 419 GEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAIT 478
           G AAR F +E++VGMVGVNVP+PVPVA+ SFGGWK SLFGD HAYG +GV F+T+ K IT
Sbjct: 419 GGAARRFENEVQVGMVGVNVPIPVPVAHFSFGGWKNSLFGDTHAYGAEGVHFFTRGKVIT 478

Query: 479 QRWPQRKSHEAAQFAFPSNS 498
           +RW    SH      FP+NS
Sbjct: 479 KRWLD-PSHGGINLGFPTNS 497


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: 740
Number of extensions: 30
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: 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)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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