GapMind for catabolism of small carbon sources

 

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

Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate Pf1N1B4_413 L-arabinolactonase (EC 3.1.1.15)

Query= uniprot:B2UIY8
         (300 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_413
          Length = 314

 Score =  149 bits (376), Expect = 8e-41
 Identities = 103/291 (35%), Positives = 143/291 (49%), Gaps = 37/291 (12%)

Query: 19  VGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPLPEMAGCIAMAPNGWAMA-MET 77
           +GE P W A  QALYW DI G+   R          W +PE         +G A+  + +
Sbjct: 36  LGEGPFWDAPTQALYWVDIAGKQALR--LIGANVEIWQMPEHVSAFIPCESGDALVTLSS 93

Query: 78  GIFLAPPPSPGIELGPLQRLATVAHARPDMRFNDGRCDRQGRFWAGTM---VLDTSLGLP 134
           G++     SPG+E  P   L  VA  +P  R N+ RCD QGR W GTM   + +    LP
Sbjct: 94  GVYRLDLASPGLE--PRLTLFCVADPQPGNRPNEARCDAQGRLWLGTMQNNIGEQGEDLP 151

Query: 135 L----GKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDSHASRQTVWAF-- 188
           +    G L+R+D    R  RV  ++  L +PN L +S +G T+Y +DS  S  T++    
Sbjct: 152 VVRRSGGLFRID----RDARVTPLLRGLGIPNTLLWSDDGTTLYFADSLDS--TLYRHFI 205

Query: 189 --DYDIDTGT----PHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDAGFVHRFTPDGR 242
             D ++DT      PH R          G PDG+A+DA+G  W    D   + R  PDG 
Sbjct: 206 HTDGNLDTAYVWFGPHER----------GGPDGSAMDAEGYVWNARWDGSCLLRLNPDGY 255

Query: 243 LDRSIAIPTSKPAMCAFGGPGLDTLFVTSIRIG-DDPLSGATFAVRPGVTG 292
           +DR I +P S+P  C FGG    TL++TS     + PL GA  ++R  V G
Sbjct: 256 VDRVIELPVSRPTSCVFGGEDFKTLYITSAASPLNHPLDGALLSIRVDVPG 306


Lambda     K      H
   0.322    0.140    0.466 

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: 385
Number of extensions: 27
Number of successful extensions: 4
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: 300
Length of database: 314
Length adjustment: 27
Effective length of query: 273
Effective length of database: 287
Effective search space:    78351
Effective search space used:    78351
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