GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxD in Marinobacter adhaerens HP15

Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate GFF2758 HP15_2702 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase

Query= BRENDA::Q13WK4
         (531 letters)



>FitnessBrowser__Marino:GFF2758
          Length = 685

 Score =  408 bits (1049), Expect = e-118
 Identities = 224/523 (42%), Positives = 313/523 (59%), Gaps = 12/523 (2%)

Query: 4   LLKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYA 63
           +LK+ +AGQW+ G      L   V G  +     + LD   A  + R+ GG  L A+ + 
Sbjct: 7   VLKSFIAGQWV-GEKPAKALPSAVNGEIVAHTHDDTLDFKNAVEYGRKVGGKNLMAMDFQ 65

Query: 64  QRAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGEV 122
           +RA  L  +   LQ  + + YA++  ++G+T+ D+ +DIDGG  TL  YA +G   L   
Sbjct: 66  ERALALKAMALYLQEHKKELYALSM-HTGSTKGDNGIDIDGGFGTLFSYASMGRRELPSG 124

Query: 123 HALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVK 182
           + + +G    L K+  F+  H+L P  GVA+ I+A+NFP WG+ EK AP  L+G+P IVK
Sbjct: 125 NVVHEGPVTPLGKNNHFAGTHILVPRGGVAVHIDAYNFPVWGMLEKFAPTFLAGMPSIVK 184

Query: 183 PATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLR 242
           PAT+T ++T+  V  + ++G LP G+L +I GS+  L D +   DVV+FTGSA TA  LR
Sbjct: 185 PATSTCYVTELAVRLMQESGALPEGSLQLIIGSTGDLFDHLEEQDVVTFTGSAATARKLR 244

Query: 243 AHPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRA 302
            HP  + R    N EADSLNSAIL  D TP+   FD+F+KE+ REMT K+GQKCTAIRR 
Sbjct: 245 NHPNIINRSIPFNAEADSLNSAILAPDVTPEHEEFDVFVKEIRREMTAKAGQKCTAIRRI 304

Query: 303 FVPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVLAY 362
           FVP+  +  V + LK +L+KITVG+P  + VRMG+L S +Q E+V A I  L + + L  
Sbjct: 305 FVPKDQVNAVCDKLKEQLSKITVGDPSVEGVRMGALASIDQLEDVKANIQELLKTSELVV 364

Query: 363 DSSAVPLIDAD-ANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNALP 421
                     D     A + PHL +  +P+N    HD+E FGPVA+V PY    D     
Sbjct: 365 GGEGNFKATGDGTEKGAFIEPHLLLCRNPENGCGAHDIEAFGPVATVIPYETIDD----- 419

Query: 422 EAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVMP 481
              AV L  RG+GSLV ++ + D A  GR+A  LA  HGR+H +        TGHG+ +P
Sbjct: 420 ---AVELCSRGRGSLVTTLTTRDPAIAGRIAPLLAAFHGRLHLLDAEAAKESTGHGSPLP 476

Query: 482 MSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLTQ 524
           M  HGGPGRAGGGEELGG+RA+  Y +R+AIQ + + +  +T+
Sbjct: 477 MLKHGGPGRAGGGEELGGIRAVHHYLQRTAIQGSPSMLAAVTR 519


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: 750
Number of extensions: 39
Number of successful extensions: 6
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: 685
Length adjustment: 37
Effective length of query: 494
Effective length of database: 648
Effective search space:   320112
Effective search space used:   320112
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