GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Phaeobacter inhibens BS107

Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate GFF442 PGA1_c04530 ureidoglycolate lyase

Query= reanno::Smeli:SM_b21112
         (281 letters)



>FitnessBrowser__Phaeo:GFF442
          Length = 282

 Score =  355 bits (912), Expect = e-103
 Identities = 168/282 (59%), Positives = 207/282 (73%), Gaps = 1/282 (0%)

Query: 1   MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGN 60
           MKLLRY      +PGL   DG +RDL  +++DL    L      +LA+L +  LP + G 
Sbjct: 1   MKLLRYHSASGIRPGLKADDGTLRDLGEYIADLTGAELGRDTQAKLASLPLADLPIIRGE 60

Query: 61  PRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEK 120
           PRL PCV   GKF+CIGLNY DHA E    +P  PI+F+KA SAI GPND +VLPRG+EK
Sbjct: 61  PRLAPCVGNVGKFLCIGLNYRDHAEEAELAIPKHPILFLKANSAISGPNDPVVLPRGAEK 120

Query: 121 TDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGP 180
            DWEVELG+VIGKTAKYV   +ALD+VAGYC V+DVSER+FQ +  GQWTKGKSCD+FGP
Sbjct: 121 VDWEVELGVVIGKTAKYVGAEDALDHVAGYCVVNDVSERSFQMDLSGQWTKGKSCDSFGP 180

Query: 181 TGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIIS 240
            GPWLVT DEV DPQ LA++  VNG+ MQ G + TM++  A ++S+LSQ M+L PGD+I+
Sbjct: 181 IGPWLVTPDEVPDPQQLALYCDVNGKRMQQGHSGTMIFSVAEIISHLSQLMTLHPGDLIA 240

Query: 241 TGTPPGVGMGMKP-PRYLKAGDVVELGIEGLGSQKQRVRADA 281
           TGTPPGVGMG KP P YLKAGD + LGI+GLG Q+Q +  D+
Sbjct: 241 TGTPPGVGMGQKPVPVYLKAGDTLRLGIDGLGEQRQHIVEDS 282


Lambda     K      H
   0.315    0.136    0.408 

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: 351
Number of extensions: 8
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: 281
Length of database: 282
Length adjustment: 26
Effective length of query: 255
Effective length of database: 256
Effective search space:    65280
Effective search space used:    65280
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: 42 (22.0 bits)
S2: 47 (22.7 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