GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Pseudomonas simiae WCS417

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF3484 PS417_17840 betaine-aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__WCS417:GFF3484
          Length = 486

 Score =  343 bits (880), Expect = 8e-99
 Identities = 193/481 (40%), Positives = 291/481 (60%), Gaps = 19/481 (3%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           +ING    +   +TF   +P T   + ++A G + ++  A++AA+  F +  W+ ++PAK
Sbjct: 5   WINGREVES--KDTFINYNPATGEAIGEVASGGAEEVALAVAAAKEAFPK--WA-NTPAK 59

Query: 83  RKA-VLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE 141
            +A ++ KL +L+E +   LA LETLDTG PI  +    IP A+    ++AE   ++ G 
Sbjct: 60  ERARLMRKLGELIEQNVPHLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGH 119

Query: 142 VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAI 201
                   L   + +PVGV   + PWN P +   WK  P LA GN+ +LK SE SPL+A 
Sbjct: 120 SYPVDDQMLNYTLYQPVGVCGLVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTAN 179

Query: 202 RLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNM 261
            L  LA EAG+P+GVLNV+ G+G  AG AL RH D+ AI+FTG T TGK++++ AG   +
Sbjct: 180 ELGRLAVEAGIPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAG---L 236

Query: 262 KRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLAL 321
           K+  +E GGKS  ++F D  DL++A  +    IF   G+ C AG+R+ ++ES+  +F+A 
Sbjct: 237 KKYSMELGGKSPVLIFEDA-DLERALDSALFTIFSLNGERCTAGSRIFIQESVYPQFVAE 295

Query: 322 LKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG---RNAGLAA- 377
              +A+    G P DP T +G++I  AH D V  +I+ G  +G  LL G   R A L A 
Sbjct: 296 FAARAKRLIVGDPQDPKTQVGSMITQAHYDKVTGYIKIGIEEGATLLAGGLDRPANLPAH 355

Query: 378 -----AIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTR 432
                 I PT+F DV+    +++EEIFGPV+ +  F  E +ALQLAND++YGL + +WT+
Sbjct: 356 LSKGQFIQPTVFADVNNKMRIAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASYIWTQ 415

Query: 433 DLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWIS 492
           D+ +AHR++R ++AG VF+N+ N  D+  PFGG K SG GR+   ++ E F E+K + IS
Sbjct: 416 DIGKAHRLARGIEAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNVCIS 475

Query: 493 L 493
           +
Sbjct: 476 M 476


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: 527
Number of extensions: 18
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: 495
Length of database: 486
Length adjustment: 34
Effective length of query: 461
Effective length of database: 452
Effective search space:   208372
Effective search space used:   208372
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