GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Escherichia coli BW25113

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 15507 b1385 phenylacetaldehyde dehydrogenase (VIMSS)

Query= BRENDA::P23883
         (495 letters)



>lcl|FitnessBrowser__Keio:15507 b1385 phenylacetaldehyde
           dehydrogenase (VIMSS)
          Length = 499

 Score =  345 bits (886), Expect = 2e-99
 Identities = 200/495 (40%), Positives = 289/495 (58%), Gaps = 10/495 (2%)

Query: 5   HLAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMS 64
           H+A        L  ++ L+I+G    A   +     DP T   +A  A     D+D A+ 
Sbjct: 5   HVAVLSQVQQFLDRQHGLYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVM 64

Query: 65  AARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGA 124
           +A   F    W+   PA+R+ +L + ADL+E H+EELA LETL+ GK I  S   ++   
Sbjct: 65  SAWRAFVSRRWAGRLPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCT 124

Query: 125 ARAIRWYAEAIDKVYGEVATTS------SHELAMIVREPVGVIAAIVPWNFPLLLTCWKL 178
              +R+ A    K+ G+    S      +   A   +EPVGV+A IVPWNFPL++  WK+
Sbjct: 125 LNWMRYTAGLTTKIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKV 184

Query: 179 GPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDID 238
            PALAAG S+++KPSE +PL+ +R+A LA EAG+PDGV NVVTG G   G AL+ H  + 
Sbjct: 185 MPALAAGCSIVIKPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVA 244

Query: 239 AIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQ 298
            I+FTGST TGK + + A D ++ RV LE GGK+  IV  D  D Q        G F NQ
Sbjct: 245 KISFTGSTATGKGIARTAAD-HLTRVTLELGGKNPAIVLKDA-DPQWVIEGLMTGSFLNQ 302

Query: 299 GQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIR 358
           GQVC A +R+ +E  + D  ++  +Q  ++ Q G  + P   +  L+  AH D V SF+ 
Sbjct: 303 GQVCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLD 362

Query: 359 EGESKGQLLLDGRN--AGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQ 416
           + +++   L+ G N  AG    + PT+ V+ D    L+REE+FGPV+ + R    E+ALQ
Sbjct: 363 DAQAQQAELIRGSNGPAGEGYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQ 422

Query: 417 LANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKS 476
           LAND++YGL A+VWT++LS+A   S RL+AG+V+VN++   D  +PFGG KQSG GRD  
Sbjct: 423 LANDTEYGLTASVWTQNLSQALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFG 482

Query: 477 LHALEKFTELKTIWI 491
              L+ + E K++ +
Sbjct: 483 PDWLDGWCETKSVCV 497


Lambda     K      H
   0.317    0.133    0.389 

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: 578
Number of extensions: 19
Number of successful extensions: 4
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: 495
Length of database: 499
Length adjustment: 34
Effective length of query: 461
Effective length of database: 465
Effective search space:   214365
Effective search space used:   214365
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: 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 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