GapMind for catabolism of small carbon sources

 

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

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Ac3H11_4805 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)

Query= BRENDA::Q83XU8
         (485 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4805
          Length = 491

 Score =  313 bits (801), Expect = 1e-89
 Identities = 184/460 (40%), Positives = 254/460 (55%), Gaps = 14/460 (3%)

Query: 24  SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83
           SP++ A++ ++ E   A VDAAV+AA  A   AW  ++ A+R   L   A  I +R + F
Sbjct: 34  SPIDQALLGRISEGSPAHVDAAVSAAARAFP-AWSALTAAERKPYLDRFAAEIGKRAEAF 92

Query: 84  LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143
              E  D G  +S  +H  +PR   N   FA+   ++     E        A +     P
Sbjct: 93  CTLESNDAGVLLSRMKHGVVPRAMLNITWFAEHALSLQDRPIETEQ-----ATHLVRHDP 147

Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203
            GVV +I PWN PL+L TWK+GPALA GN V+VKP E  P T++LL +  + AG+PPGV+
Sbjct: 148 AGVVAIITPWNAPLMLATWKLGPALAAGNCVIVKPPEWAPLTSSLLADCAHAAGLPPGVF 207

Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263
           N+V G G  STG  L S P +  I+FTG   T + I ++A     P SLELGGK+A IV 
Sbjct: 208 NIVQGAGV-STGARLVSDPRLARISFTGSVPTAKWIAQSAGANLVPCSLELGGKSAFIVL 266

Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323
            D D+D A   T    + N GQVCL   R  V R + D FV+ L+   E + +G P D A
Sbjct: 267 EDADIDNA-AATGALMYRNAGQVCLAGTRFLVHRKVHDAFVAALRGYVEKLTVGDPRDGA 325

Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383
           T +GP+I     E+V  + ++AV  GAT++ GG          G  + QPT+ T +  DS
Sbjct: 326 TEVGPIIHPRQVERVHGFVQRAVADGATLLWGGAQHPF-----GAQYYQPTLLTDVRQDS 380

Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443
            + + E+FGP   +  FDS+EE I  AN  DYGL    +      A  VA  +  G  WV
Sbjct: 381 EIVQNEVFGPVLTLQTFDSDEEAIALANGTDYGLGGVCYGAT-EHASAVAQQVRTGFIWV 439

Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCI 483
           NS+ +RDL   FGG K+SG+GREGG  S EF+ ++K+V +
Sbjct: 440 NSFGIRDLAAPFGGIKRSGVGREGGDWSFEFFCDVKDVVV 479


Lambda     K      H
   0.318    0.135    0.406 

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: 566
Number of extensions: 19
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: 485
Length of database: 491
Length adjustment: 34
Effective length of query: 451
Effective length of database: 457
Effective search space:   206107
Effective search space used:   206107
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