GapMind for catabolism of small carbon sources

 

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

Align aconitate DELTA-isomerase (EC 5.3.3.7) (characterized)
to candidate Ac3H11_2325 2-methylaconitate cis-trans isomerase

Query= BRENDA::Q8EJW4
         (397 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2325
          Length = 396

 Score =  609 bits (1570), Expect = e-179
 Identities = 304/389 (78%), Positives = 340/389 (87%), Gaps = 1/389 (0%)

Query: 7   PPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGG 66
           P QIKV ATY+RGGTSKGVFF L+DLP  AQ PGPARDALLLRV+GSPDPY KQIDGMG 
Sbjct: 5   PHQIKVPATYLRGGTSKGVFFLLEDLPAPAQQPGPARDALLLRVLGSPDPYGKQIDGMGN 64

Query: 67  ATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDA 126
           A+SSTSK VILS S++  HDVDYLFGQVSI++PFVDWSGNCGNL+AAVG  AI  GLIDA
Sbjct: 65  ASSSTSKAVILSRSTRPGHDVDYLFGQVSINQPFVDWSGNCGNLSAAVGPCAIHMGLIDA 124

Query: 127 ARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAA 186
           ARIP+NG   VRIWQANIGKTI+AHVPIT G VQETGDFELDGVTF AAEV +EFM+PA 
Sbjct: 125 ARIPQNGTIPVRIWQANIGKTIVAHVPITHGQVQETGDFELDGVTFAAAEVALEFMDPA- 183

Query: 187 DDDGEGGCMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSD 246
           DD  EGG MFPTGN+VD LEVPG+G F AT+INAGIPTIF+NA++LGYTGTELQ  IN D
Sbjct: 184 DDGDEGGGMFPTGNVVDTLEVPGVGSFAATLINAGIPTIFLNAQELGYTGTELQGAINGD 243

Query: 247 NAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDL 306
             ALA+FE IRAHGALRMGLI+H+ EA +RQHTPKIAFVAP  SY +SSGK + A+D+DL
Sbjct: 244 AVALARFEAIRAHGALRMGLIQHLGEATTRQHTPKIAFVAPRASYTASSGKAIDAKDIDL 303

Query: 307 LVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQA 366
           LVRA+SMG+LHHAMMGTAAVAIGTAAAIPGTLVNLAAGGG + +VRFGHPSGTLRVGA+A
Sbjct: 304 LVRAISMGQLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGVRSSVRFGHPSGTLRVGAEA 363

Query: 367 VQENGEWTVIKAIMSRSARVLMEGFVRVP 395
            Q NG+W V KA+MSRSAR+LMEG+VRVP
Sbjct: 364 AQINGQWKVTKALMSRSARILMEGWVRVP 392


Lambda     K      H
   0.318    0.134    0.393 

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: 596
Number of extensions: 18
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: 397
Length of database: 396
Length adjustment: 31
Effective length of query: 366
Effective length of database: 365
Effective search space:   133590
Effective search space used:   133590
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: 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