GapMind for catabolism of small carbon sources

 

Aligments for a candidate for boxD in Phaeobacter inhibens BS107

Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate GFF2643 PGA1_c26830 phenylacetic acid degradation protein PaaZ

Query= BRENDA::Q13WK4
         (531 letters)



>lcl|FitnessBrowser__Phaeo:GFF2643 PGA1_c26830 phenylacetic acid
           degradation protein PaaZ
          Length = 676

 Score =  418 bits (1075), Expect = e-121
 Identities = 228/513 (44%), Positives = 313/513 (61%), Gaps = 11/513 (2%)

Query: 5   LKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYAQ 64
           + +  AGQWIA      ++   +TG  L +  ++ LD+     +AR  GG +LR LT+  
Sbjct: 6   VSSFAAGQWIAPGAGARSIASAITGAPLAQAGNDALDVQGMLDYARTVGGPSLRKLTFHD 65

Query: 65  RAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGEVH 123
           RA  L  +   L   +   Y ++  N+G T++D  +DIDGGI T+  +A  G   + + H
Sbjct: 66  RARMLKALAGHLNQHKQALYDLSF-NTGATQSDHMIDIDGGIGTMFVFASKGRREMPDAH 124

Query: 124 ALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVKP 183
              DG  E LS++ +F  QH+ +P +GVA+ INAFNFP WG+ EK AP LL+GVP IVKP
Sbjct: 125 VYLDGDIEQLSRNGTFLGQHICTPLQGVAVHINAFNFPVWGMLEKLAPTLLAGVPAIVKP 184

Query: 184 ATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLRA 243
           ATAT ++T+  V  ++++GILP GAL ++ G    +LD +   DVVSFTGSA TA  LRA
Sbjct: 185 ATATCYVTELAVRLMLESGILPEGALQLVSGGLGDMLDHLTMQDVVSFTGSAQTALKLRA 244

Query: 244 HPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRAF 303
           +P  ++   R   E DSLN++IL  DA P TP FDLF+KEV REMT K+GQKCTAIRR  
Sbjct: 245 NPVILENSIRFVAEQDSLNASILGPDAGPGTPEFDLFVKEVSREMTTKAGQKCTAIRRII 304

Query: 304 VPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVLAY- 362
            P+A +E V+EAL A+LAK  +G+PR +  RMG+LVS  Q  +VL   A + +EA   + 
Sbjct: 305 APDAQVEAVIEALSARLAKTRIGDPRLETTRMGALVSNSQKRDVLEKAAIIGQEAERVFG 364

Query: 363 DSSAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNALPE 422
           D     +  ADA   A V P LF   DPD A  +HD E FGPV+++  Y           
Sbjct: 365 DPENFSVDGADAEKGAFVPPMLFHCADPDKAQRVHDTEAFGPVSTIMGYHDLD------- 417

Query: 423 AHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVMPM 482
            HA+ LA RG+GSLVAS+ ++D      +AL     HGR++  +       TGHG+ +P 
Sbjct: 418 -HAITLANRGEGSLVASVITHDTEVAREVALGAGAYHGRLYFNNRDSMKESTGHGSPLPH 476

Query: 483 SLHGGPGRAGGGEELGGLRALAFYHRRSAIQAA 515
            +HGGPGRAGGGEELGG+R +  Y +R+AIQ +
Sbjct: 477 MVHGGPGRAGGGEELGGVRGVKHYMQRTAIQGS 509


Lambda     K      H
   0.318    0.132    0.379 

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: 805
Number of extensions: 34
Number of successful extensions: 5
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: 531
Length of database: 676
Length adjustment: 37
Effective length of query: 494
Effective length of database: 639
Effective search space:   315666
Effective search space used:   315666
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: 53 (25.0 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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