GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutG' in Dinoroseobacter shibae DFL-12

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate 3606958 Dshi_0386 N-formylglutamate amidohydrolase (RefSeq)

Query= reanno::acidovorax_3H11:Ac3H11_2548
         (270 letters)



>FitnessBrowser__Dino:3606958
          Length = 287

 Score = 85.1 bits (209), Expect = 2e-21
 Identities = 76/242 (31%), Positives = 107/242 (44%), Gaps = 25/242 (10%)

Query: 14  TAPLLVSMPHAG-TYVPPVLAARFTDEARQVPDTDWHMERLYAFAKDMGASILVATHSRY 72
           T  ++ + PH+G  Y    L +   D        D  ++ L A A   GA  + AT  R 
Sbjct: 15  TTSVIFASPHSGRAYSKDFLRSTVLDTQTIRSSEDAFVDELIACAPRYGAQTIAATAPRA 74

Query: 73  VVDLNRPPDGASLYPG--------------QSVTGLCPVDTFDDTPIYAQGDVPDDAEVA 118
            +DLNR  D   L P                S  G+ P    +   IY +G +  + E  
Sbjct: 75  YIDLNRNAD--ELDPAVVSGLRRVTHNPRISSGLGVVPRVVANGRAIY-RGKMHLN-EAK 130

Query: 119 ARRDAVWAPYHAQLRAELSRIRAQHGVAVLWDAHSIR----SVLPRFFEGKLPDLNLGTA 174
           AR DA W PYH QLR  L   R   G A+L D HS+       L +  E + PD+ LG  
Sbjct: 131 ARLDAYWHPYHDQLRRMLDVTRNAFGQAILVDCHSMPHEAIDALHQHSEAR-PDVVLGDR 189

Query: 175 DGASCDPALAQALLAIAQSAPGYTGVLNGRFKGGHITRHYGQPAQNIHAVQLEMTQCSYM 234
            GA+    +   + A  ++A G     N  F G  I +HYG+P++N H VQ+E+ +  YM
Sbjct: 190 FGAASAAHIVDQVEAAFKNA-GLRVARNAPFAGAFIAQHYGRPSRNQHVVQIEIDRALYM 248

Query: 235 QE 236
            E
Sbjct: 249 DE 250


Lambda     K      H
   0.321    0.135    0.416 

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: 175
Number of extensions: 13
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: 270
Length of database: 287
Length adjustment: 25
Effective length of query: 245
Effective length of database: 262
Effective search space:    64190
Effective search space used:    64190
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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