GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxD in Magnetospirillum magneticum AMB-1

Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; EC 1.2.1.77 (characterized)
to candidate WP_011382620.1 AMB_RS00880 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase

Query= SwissProt::Q84HH8
         (515 letters)



>NCBI__GCF_000009985.1:WP_011382620.1
          Length = 515

 Score =  508 bits (1309), Expect = e-148
 Identities = 263/479 (54%), Positives = 331/479 (69%), Gaps = 8/479 (1%)

Query: 1   MKLANYVYGQWIEGAGEGAALTDPVTGEALVRVSSDGIDVARALEFARTAGGAALKALTY 60
           ++L +Y+ G+W +GAG GA L DPV+GE L   S DG+D+A AL FAR  GG AL+AL++
Sbjct: 2   IRLQSYLAGRWQDGAGSGAQLKDPVSGEVLATASGDGLDIAEALAFARDRGGPALRALSF 61

Query: 61  EERAAKLAAIAELLQAKRAEYFDISLRNSGATEGDASFDVDGAIFTVKSYARAGKALGAG 120
             RA  + A+A +L   R  Y  ++L NSG T  DA  DVDG I T+K YA  G+ LG  
Sbjct: 62  AGRAGLINALAGVLAENRERYNTVALANSGNTAVDAGLDVDGGIGTLKYYASIGRKLGEA 121

Query: 121 RHLKEGGRVALAKTDVFQGQHFLMPLTGVAVFINAFNFPAWGLWEKAAPALLAGVPVFAK 180
           R L E     L K + F+G+H      GVAV INAFNFP+WGLWEKAA +LLAGVP  AK
Sbjct: 122 RLLAEATDDQLTKDEAFRGRHIWTSNRGVAVHINAFNFPSWGLWEKAAVSLLAGVPFLAK 181

Query: 181 PATPTAWLAQRMVADVVEAGILPPGAISIVCGGARDLLDHVTECDVVSFTGSADTAARMR 240
           PAT T+WLA  MV DVV AG+LP GA+S++CGG RDL+DH+   DVV+FTGSA+TAA++R
Sbjct: 182 PATATSWLAYEMVKDVVAAGVLPEGAMSLLCGGGRDLMDHLKPGDVVAFTGSAETAAQLR 241

Query: 241 THPNVVARSVRINIEADSVNSAILGPDAQPGTPEFDLAVKEIVREMTVKTGQKCTAIRRI 300
           ++PNV+A +VR  +EADS+N   LGPDA P  PEF   +KE+ REMTVK GQKCTAIRR+
Sbjct: 242 SNPNVIAANVRFAVEADSLNLCALGPDAAPDAPEFAAFIKEVSREMTVKAGQKCTAIRRV 301

Query: 301 LAPAGVSRALADAVSGKLAGCKVGNPRSEGVRVGPLVSKAQQAAAFEGLAKLRQECEVVF 360
           L P      +  A+   LA   +G+PR+EGVR+GPLVS+AQ  AA+ GL  L+ E +VV 
Sbjct: 302 LVPRSRVDDVVAALKPALAKALMGDPRTEGVRMGPLVSRAQTVAAWAGLEALKAETQVVA 361

Query: 361 GGDPDFEPVDADAAVSAFVQPTLLYCDKGLAARHVHDVEVFGPVATMVPYADTRDAVAIA 420
           GG  D            FV  TLL C+  LAAR VH++EVFGPVAT++PY     AV +A
Sbjct: 362 GGGND--------DGGCFVPATLLLCNDPLAARAVHEIEVFGPVATLMPYDSVEQAVDLA 413

Query: 421 RRGHGSLVASVYSGDAAFLGELVPGIADLHGRVMVVDAAVGANHTGHGNVMPTCLHGGP 479
            +G GSL ASV+SGDAAFL   VP IA  HGRV+VVD++V A+H+GHG VMP C+HGGP
Sbjct: 414 HKGGGSLAASVFSGDAAFLAGFVPAIATSHGRVLVVDSSVAASHSGHGVVMPHCIHGGP 472


Lambda     K      H
   0.319    0.135    0.399 

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: 724
Number of extensions: 36
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: 515
Length of database: 515
Length adjustment: 35
Effective length of query: 480
Effective length of database: 480
Effective search space:   230400
Effective search space used:   230400
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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