GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF2643
          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 (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