GapMind for catabolism of small carbon sources

 

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

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Ac3H11_4805 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)

Query= BRENDA::Q1XGK8
         (486 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4805
          Length = 491

 Score =  323 bits (827), Expect = 1e-92
 Identities = 191/479 (39%), Positives = 263/479 (54%), Gaps = 16/479 (3%)

Query: 6   HFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVAE 65
           H+I+G  V  AS   F+  +P +  ++G + E   A VDAAV AA  A    W  L+ AE
Sbjct: 17  HYIDGQRV--ASDMRFDLHSPIDQALLGRISEGSPAHVDAAVSAAARAFPA-WSALTAAE 73

Query: 66  RAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEA 125
           R   L R A  I  R + F   E  D G   S   H  +PR   N   FA+   ++ +  
Sbjct: 74  RKPYLDRFAAEIGKRAEAFCTLESNDAGVLLSRMKHGVVPRAMLNITWFAEHALSLQDRP 133

Query: 126 FEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPL 185
            E        A +     P GV+ +I+PWN PL+L TWK+GPALA GN V+VKP E  PL
Sbjct: 134 IETEQ-----ATHLVRHDPAGVVAIITPWNAPLMLATWKLGPALAAGNCVIVKPPEWAPL 188

Query: 186 TATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRAAA 245
           T++LL +   AAG+P GV+N+V G  G S GA L   P +   +FTG   T + I ++A 
Sbjct: 189 TSSLLADCAHAAGLPPGVFNIVQG-AGVSTGARLVSDPRLARISFTGSVPTAKWIAQSAG 247

Query: 246 KGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDEFV 305
             +   SLELGGK+A IV  D D+D A   T    + N GQVCL   R  V R + D FV
Sbjct: 248 ANLVPCSLELGGKSAFIVLEDADIDNA-AATGALMYRNAGQVCLAGTRFLVHRKVHDAFV 306

Query: 306 ARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMPAH 365
           A L+   E L +G P D ++  GP++  +  E+V  + Q+AV DG +++ GG       H
Sbjct: 307 AALRGYVEKLTVGDPRDGATEVGPIIHPRQVERVHGFVQRAVADGATLLWGGA-----QH 361

Query: 366 LAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWTE 425
             G  + QPT+ T +  DS +V  E+FGP   ++ FD++EEAI LAN   YGL    +  
Sbjct: 362 PFGAQYYQPTLLTDVRQDSEIVQNEVFGPVLTLQTFDSDEEAIALANGTDYGLGGVCYGA 421

Query: 426 NGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNICV 484
               A  VA Q+  G +WVNS+ +RDL   FGG K+SG+GREGG  S EF+ ++K++ V
Sbjct: 422 T-EHASAVAQQVRTGFIWVNSFGIRDLAAPFGGIKRSGVGREGGDWSFEFFCDVKDVVV 479


Lambda     K      H
   0.318    0.136    0.411 

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: 662
Number of extensions: 33
Number of successful extensions: 6
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: 486
Length of database: 491
Length adjustment: 34
Effective length of query: 452
Effective length of database: 457
Effective search space:   206564
Effective search space used:   206564
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: 52 (24.6 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