GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC 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)



>FitnessBrowser__Keio:15507
          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 (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