GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Phaeobacter inhibens BS107

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF3174 PGA1_c32250 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__Phaeo:GFF3174
          Length = 494

 Score =  441 bits (1134), Expect = e-128
 Identities = 234/474 (49%), Positives = 313/474 (66%), Gaps = 4/474 (0%)

Query: 24  INGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKR 83
           I+G+  AA++  T + + P+    L +IARG   D++RA+++AR  FE   W+   PA R
Sbjct: 21  IDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAIASARAAFEDRRWAGQPPAAR 80

Query: 84  KAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVA 143
           K VL K A+L+EA A  LA+L   D G  I  +L+ +   AA  IR+YAEA+DK+YGE+A
Sbjct: 81  KKVLMKWAELIEADALNLAVLGVRDNGTEITMALKAEPGSAAATIRYYAEALDKIYGEIA 140

Query: 144 TTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRL 203
            TSS  L M+ +EPVGV+ AI+PWNFP+++  WKL PALA GNSV+LKPSE + LS +R+
Sbjct: 141 PTSSDVLGMVHKEPVGVVGAIIPWNFPMMIGAWKLAPALAMGNSVVLKPSETASLSLMRM 200

Query: 204 AGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKR 263
             LA EAGLP GVLN VTG G   G+AL    D+D + FTGS +TG++L++ A  SN+KR
Sbjct: 201 VELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFTGSGQTGRRLMEYAARSNLKR 260

Query: 264 VWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLK 323
           V+LE GGKS NIVFAD PDL  AA  TAAGIF N GQVC+AG+RLL+E SI D F+  + 
Sbjct: 261 VYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCVAGSRLLVEASIHDAFVEEVA 320

Query: 324 QQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAAIG--- 380
           + AQ  + G PL   T +G +   A       F+   E +G  ++ G    L+   G   
Sbjct: 321 KAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVEGGQIITGGQRLLSETGGSYM 380

Query: 381 -PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHR 439
            PTI   V P+A+L++EE+FGPVL VT F ++ +AL++AN + YGL  AVWT  L+RAHR
Sbjct: 381 APTIVTGVTPDATLAQEEVFGPVLAVTPFETDAEALRIANATVYGLAGAVWTSGLTRAHR 440

Query: 440 MSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493
           M + ++ G + VN Y   D TVP GG  QSGNG DKSLHA++K+  LKT W+ L
Sbjct: 441 MVQGVRTGVMHVNTYGGADGTVPLGGVGQSGNGADKSLHAIDKYINLKTAWMKL 494


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: 550
Number of extensions: 27
Number of successful extensions: 2
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: 494
Length adjustment: 34
Effective length of query: 461
Effective length of database: 460
Effective search space:   212060
Effective search space used:   212060
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.

Links

Downloads

Related tools

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