GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Shewanella loihica PV-4

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate 5210291 Shew_2734 4-carboxymuconolactone decarboxylase (RefSeq)

Query= BRENDA::Q0SH24
         (400 letters)



>FitnessBrowser__PV4:5210291
          Length = 127

 Score =  115 bits (287), Expect = 9e-31
 Identities = 51/120 (42%), Positives = 78/120 (65%)

Query: 266 RAAHAQGMTVRRSILGDAHVDRSVAGTTDFTAPFQDFITRTAWGDIWSRPGLDHELRRLL 325
           +A + QG+ +RR ++GD+ VDR+++  +DFT P Q+ +TR AWG++W+R GLD   R L+
Sbjct: 3   KAKYDQGLAIRREVMGDSFVDRALSSASDFTQPLQELVTRNAWGEVWAREGLDRRTRSLI 62

Query: 326 TIAVLTAVGNEHELDMHIRAALRAGVDADTIGEVLLHTSVYAGVPNSNLGFALGKQALAD 385
           TIA L A+    EL  H+R ALR G   + I EVLLH++VY G+P     F    + +++
Sbjct: 63  TIATLAALKASTELKGHVRGALRNGCTVEEIQEVLLHSTVYCGMPAGVEAFRAANEVISE 122


Lambda     K      H
   0.318    0.132    0.392 

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: 127
Number of extensions: 2
Number of successful extensions: 1
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: 400
Length of database: 127
Length adjustment: 22
Effective length of query: 378
Effective length of database: 105
Effective search space:    39690
Effective search space used:    39690
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 (21.7 bits)
S2: 45 (21.9 bits)

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate 5209389 Shew_1860 alpha/beta hydrolase fold (RefSeq)

Query= BRENDA::Q0SH24
         (400 letters)



>FitnessBrowser__PV4:5209389
          Length = 277

 Score =  104 bits (260), Expect = 3e-27
 Identities = 75/241 (31%), Positives = 121/241 (50%), Gaps = 20/241 (8%)

Query: 20  PVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPA-PDGPYSVRDLSEDVLAL 78
           PV++L  S   + +MW PQ+A LS   R +  D   HG S   P G  S++ L+E  LAL
Sbjct: 26  PVLLLGHSYLWDSAMWAPQLAHLSQHYRCIVPDLWAHGHSDVLPSGCRSLKHLAEHYLAL 85

Query: 79  LDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQAWIERA------ 132
           +DSL +D    +GLS+GG     L   APRRV +L ++     F EP+  + RA      
Sbjct: 86  MDSLEIDEFSILGLSVGGMWGTELTLMAPRRVKTLVMMGCFLGF-EPE--VSRAKYYAML 142

Query: 133 ----AASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCD---- 184
               AA R   PE L + +   +FS+ + ++ PE +  ++  +AS +PE   +       
Sbjct: 143 DAMTAAGRL--PEPLIEQIAPLFFSDNVEQKQPELIASFKASLASIAPERLESISRLGRI 200

Query: 185 ALADWDFTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQ 244
                D   D+ +++ PTL++ G +D  +P     ++ D I  + F  +  A H++ LEQ
Sbjct: 201 IFGRRDIMEDIEQLTLPTLIMTGTQDKPSPVLEAYLMHDAIDGSEFLHIPEAGHISTLEQ 260

Query: 245 A 245
           +
Sbjct: 261 S 261


Lambda     K      H
   0.318    0.132    0.392 

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: 269
Number of extensions: 14
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: 400
Length of database: 277
Length adjustment: 28
Effective length of query: 372
Effective length of database: 249
Effective search space:    92628
Effective search space used:    92628
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 (21.7 bits)
S2: 49 (23.5 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