GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Phaeobacter inhibens BS107

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF3174 PGA1_c32250 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__Phaeo:GFF3174
          Length = 494

 Score =  471 bits (1213), Expect = e-137
 Identities = 239/474 (50%), Positives = 318/474 (67%)

Query: 24  INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83
           I+G+   A  G T + LSP+DGR L ++A   + D  RA+ +ARA F    W+   PA R
Sbjct: 21  IDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAIASARAAFEDRRWAGQPPAAR 80

Query: 84  KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVA 143
           K  L+++A+L+  +   LA+L   D G  I  +   +   AA  I + AEA+DK+Y E+A
Sbjct: 81  KKVLMKWAELIEADALNLAVLGVRDNGTEITMALKAEPGSAAATIRYYAEALDKIYGEIA 140

Query: 144 PTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRI 203
           PT  D LG+V +EPVGVVGAI+PWNFP+++  WKL PALA GNSVVLKPSE + L+ +R+
Sbjct: 141 PTSSDVLGMVHKEPVGVVGAIIPWNFPMMIGAWKLAPALAMGNSVVLKPSETASLSLMRM 200

Query: 204 AQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKR 263
            +LA+EAG+P GVLN + G G  VG+AL L MDVD LVFTGS +  ++LM YA  SN+KR
Sbjct: 201 VELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFTGSGQTGRRLMEYAARSNLKR 260

Query: 264 IWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVV 323
           ++LE GGKSPNIVFADAPDL  AA+  A+ I  N G+VC AGSRLLVE SI D F+  V 
Sbjct: 261 VYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCVAGSRLLVEASIHDAFVEEVA 320

Query: 324 EALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYV 383
           +A +  + G+PL   T +GA+    Q+   L ++     +G +++ GG+R L ETGG+Y+
Sbjct: 321 KAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVEGGQIITGGQRLLSETGGSYM 380

Query: 384 EPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHK 443
            PTI  GVT    +AQEE+FGPVL+V  F+T  EA+ IAN T YGLA  +WTS +++AH+
Sbjct: 381 APTIVTGVTPDATLAQEEVFGPVLAVTPFETDAEALRIANATVYGLAGAVWTSGLTRAHR 440

Query: 444 TARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497
             + VR G + VN Y G D T P GG  QSGNG DKSLHA++KY  LK  W+KL
Sbjct: 441 MVQGVRTGVMHVNTYGGADGTVPLGGVGQSGNGADKSLHAIDKYINLKTAWMKL 494


Lambda     K      H
   0.316    0.132    0.390 

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: 666
Number of extensions: 32
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: 497
Length of database: 494
Length adjustment: 34
Effective length of query: 463
Effective length of database: 460
Effective search space:   212980
Effective search space used:   212980
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 (21.6 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