GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligU in Acidovorax sp. GW101-3H11

Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate Ac3H11_2325 2-methylaconitate cis-trans isomerase

Query= SwissProt::Q88JY0
         (361 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2325
          Length = 396

 Score =  213 bits (542), Expect = 7e-60
 Identities = 149/389 (38%), Positives = 206/389 (52%), Gaps = 48/389 (12%)

Query: 3   QTRIPCLLMRGGTSKGAYFLHDDLPAP----GPLRDRVLLAVMGSPD--ARQIDGIGGAD 56
           Q ++P   +RGGTSKG +FL +DLPAP    GP RD +LL V+GSPD   +QIDG+G A 
Sbjct: 7   QIKVPATYLRGGTSKGVFFLLEDLPAPAQQPGPARDALLLRVLGSPDPYGKQIDGMGNAS 66

Query: 57  SLTSKVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAAS- 115
           S TSK  I+  S R   DVDYLF QV +++  VD+  NCGN+ A VGP A+  GL+ A+ 
Sbjct: 67  SSTSKAVILSRSTRPGHDVDYLFGQVSINQPFVDWSGNCGNLSAAVGPCAIHMGLIDAAR 126

Query: 116 ---GASTPVRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVA--G 170
                + PVRI+  N G+  VA VP   GQV+  GD  +DGV   AA + + F D A  G
Sbjct: 127 IPQNGTIPVRIWQANIGKTIVAHVPITHGQVQETGDFELDGVTFAAAEVALEFMDPADDG 186

Query: 171 ASCGALLPTGNSRDCVE-----GVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSAL 225
              G + PTGN  D +E         T I+ G+P + L A++LG TG E    +  D+  
Sbjct: 187 DEGGGMFPTGNVVDTLEVPGVGSFAATLINAGIPTIFLNAQELGYTGTELQGAINGDAVA 246

Query: 226 KTRLEAIR----LQLGPRMNLGDVSQR-NVPKMCLLSAPRNGGTVNTRSFIPHR------ 274
             R EAIR    L++G   +LG+ + R + PK+  + APR   T ++   I  +      
Sbjct: 247 LARFEAIRAHGALRMGLIQHLGEATTRQHTPKIAFV-APRASYTASSGKAIDAKDIDLLV 305

Query: 275 --------CHASIGVFGAVSVATACLIEGSVAQGLASTSGGDRQRLAVEHPSGEFTVEIS 326
                    HA +G   AV++ TA  I G++     +  GG R  +   HPSG  T+ + 
Sbjct: 306 RAISMGQLHHAMMGT-AAVAIGTAAAIPGTLVN--LAAGGGVRSSVRFGHPSG--TLRVG 360

Query: 327 LEHGVIKGCGLV------RTARLLFDGVV 349
            E   I G   V      R+AR+L +G V
Sbjct: 361 AEAAQINGQWKVTKALMSRSARILMEGWV 389


Lambda     K      H
   0.320    0.138    0.412 

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: 422
Number of extensions: 32
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: 361
Length of database: 396
Length adjustment: 30
Effective length of query: 331
Effective length of database: 366
Effective search space:   121146
Effective search space used:   121146
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 (21.8 bits)
S2: 50 (23.9 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