GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacC in Pseudomonas fluorescens FW300-N1B4

Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate Pf1N1B4_4510 Gluconolactonase (EC 3.1.1.17)

Query= reanno::HerbieS:HSERO_RS05225
         (292 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4510
          Length = 297

 Score =  155 bits (391), Expect = 1e-42
 Identities = 105/305 (34%), Positives = 153/305 (50%), Gaps = 27/305 (8%)

Query: 1   MNVQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAF 60
           M V+L+VD  + +GE  +W     +++W DI    L   +  +G   +W  P+ L C A 
Sbjct: 1   MQVELIVDARNAVGESPVWVPEENALYWVDIPTGGLQRWNADSGHVHAWKAPQMLACIA- 59

Query: 61  TADPQQLLIGLESRLAFFNL---STGTIAP--ICRIEDDLPSTRLNDGRCDRQGRFVFGT 115
                  + G+ES   FF+L   + G++    +  ++   P  RLNDGRCDRQGRF  G+
Sbjct: 60  RHSAGGWVAGMES--GFFHLHPHNDGSLDSELLAHVDHARPDMRLNDGRCDRQGRFWAGS 117

Query: 116 LNEDAG-RAPIASFYRLNT------DLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAG 168
           +  + G  A   + YR +       D  L    +P     N + FS DGK MY  DS   
Sbjct: 118 MVLNMGANAADGTLYRYSARQPGPLDARLSGFIVP-----NGLGFSPDGKTMYLSDSHPN 172

Query: 169 --KIMVCDYDTASGAVGGQRVFADVAQ-PGGPDGSTIDAEGYLWNAQWGGARVVRYAPDG 225
             +I   DYD  SG    +R+F D+    G PDG+ +DAEG  W        + R+ PDG
Sbjct: 173 VQQIWAFDYDIDSGTPSNRRLFVDMHHFLGRPDGAAVDAEGCYWICANDAGLIHRFTPDG 232

Query: 226 RIDRVVAIPTSQPSCVAFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGL 285
           R+DR + +P  +P+  AFGG+Q DTL+VT+      A+       AG +FA+    V+GL
Sbjct: 233 RLDRSLPVPVKKPTMCAFGGSQLDTLFVTSIR---PADDHDEQSLAGGVFALN-PGVKGL 288

Query: 286 PEVRF 290
           PE  F
Sbjct: 289 PEPAF 293


Lambda     K      H
   0.322    0.138    0.437 

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: 321
Number of extensions: 27
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: 292
Length of database: 297
Length adjustment: 26
Effective length of query: 266
Effective length of database: 271
Effective search space:    72086
Effective search space used:    72086
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 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