GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacC in Amantichitinum ursilacus IGB-41

Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate WP_053939460.1 WG78_RS19225 SMP-30/gluconolactonase/LRE family protein

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



>NCBI__GCF_001294205.1:WP_053939460.1
          Length = 301

 Score =  278 bits (712), Expect = 8e-80
 Identities = 135/286 (47%), Positives = 188/286 (65%), Gaps = 2/286 (0%)

Query: 3   VQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAFTA 62
           +Q L  G + L EG++   +S  ++WT+IHA  LW  D +TG  R W  P+R+CC+AFT 
Sbjct: 10  LQSLSAGQYNLAEGIIQHPQSGLLWWTNIHAKELWQLDLRTGQHRYWSTPQRVCCFAFTQ 69

Query: 63  DPQQLLIGLESRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDAGR 122
           D   LL+  ++ LA FN ++G I  +  +E + P TR NDGR DR G  VFGT++E +  
Sbjct: 70  DDDVLLVAFDAGLALFNTASGAIKRLTPVEPETPGTRCNDGRVDRAGNLVFGTMHERSAE 129

Query: 123 APIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTASGAV 182
           A    FYR +T+  L++L+LP+IAISNS+ FS DG  +Y CDS+  KIM C YD+ +GA+
Sbjct: 130 AK-GHFYRFDTESRLQQLALPAIAISNSLAFSPDGGTLYWCDSLQHKIMQCAYDSVTGAI 188

Query: 183 GGQRVFADVAQPG-GPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQPSCV 241
               VF D+      PDGST+DA GYLWNA+W G  V RYAPDG IDR + +P +QP+CV
Sbjct: 189 AEISVFHDLGDTVIEPDGSTVDAAGYLWNAEWAGHCVTRYAPDGSIDRKIHLPVAQPTCV 248

Query: 242 AFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPE 287
            FGG + +TL++T+A  G+     A  P+AG++FA+ +  VRGLPE
Sbjct: 249 TFGGPEQNTLFITSARAGLDDAALAQQPEAGSVFALEIPGVRGLPE 294


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: 373
Number of extensions: 24
Number of successful extensions: 3
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: 301
Length adjustment: 26
Effective length of query: 266
Effective length of database: 275
Effective search space:    73150
Effective search space used:    73150
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 24 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