GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Burkholderia phytofirmans PsJN

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate BPHYT_RS09900 BPHYT_RS09900 aldehyde dehydrogenase

Query= BRENDA::Q1XGK8
         (486 letters)



>FitnessBrowser__BFirm:BPHYT_RS09900
          Length = 492

 Score =  347 bits (891), Expect = e-100
 Identities = 195/482 (40%), Positives = 276/482 (57%), Gaps = 10/482 (2%)

Query: 7   FINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGP-WGKLSVAE 65
           FING   GSA+G+TF   NP+  + I  + +A  A++D AV+ ++AA +   W ++  A 
Sbjct: 15  FINGEKTGSAAGKTFPVFNPATAEEIAQIPDASEADIDHAVRTSKAAFESDAWRRMPPAV 74

Query: 66  RAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEA 125
           R  +L ++AD +    DE    E L+ GK    +  +++       +  A     +    
Sbjct: 75  REGLLLKLADLVERHSDELATLETLNQGKLIGFSKMLEVAGSVQWLRYMAGWATKIEGST 134

Query: 126 FEMATPDGAGA-INYAVRR-PKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEET 183
           F+++ P   G   N + +R P GV+  I PWN PLL+  WK+ PALACG TVV+KP+EET
Sbjct: 135 FDLSIPFPPGTRYNASTKRVPAGVVAAIVPWNFPLLMAVWKIAPALACGCTVVLKPAEET 194

Query: 184 PLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRA 243
           PLTA  L E+   AG PAGV+NVV G  G++AGA L  HP V   TFTG T  G +I R 
Sbjct: 195 PLTAIRLAELAHEAGFPAGVFNVVTG-RGETAGAALVRHPLVKKVTFTGSTEVGRIIGRQ 253

Query: 244 AAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDE 303
            A  +++ SLELGGK+  IV  DCD  KAIEG   + F N GQVC    R+YV R I+DE
Sbjct: 254 CADDLKRASLELGGKSPVIVLDDCDPRKAIEGAAGAIFFNHGQVCTAGSRLYVARSIYDE 313

Query: 304 FVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMP 363
            V  + A A+ + +G   DA++  GP+VS +HR+KV     Q  D+GG +++     +  
Sbjct: 314 VVQGIAAVADGITLGSGFDAATQMGPMVSARHRDKVAGMIAQGKDEGGEIVSRDARVERE 373

Query: 364 AHLAGGAWVQPTIWTGLS-DDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAI 422
                G +V+PT+    +    AVV EE+FGP     P+D  +E +  AN+  YGL +++
Sbjct: 374 -----GYFVRPTVIANRACKPLAVVKEEVFGPVLVAMPYDDLDEVLAQANASEYGLGASV 428

Query: 423 WTENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNI 482
           WT    +A R+   IEAG VWVN+  + D    FGG K SGIGRE G   +E YTE K++
Sbjct: 429 WTNQLDKALRLVDGIEAGTVWVNTHNMVDPAMPFGGFKASGIGREHGKSIIESYTESKSV 488

Query: 483 CV 484
           C+
Sbjct: 489 CI 490


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: 628
Number of extensions: 29
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: 486
Length of database: 492
Length adjustment: 34
Effective length of query: 452
Effective length of database: 458
Effective search space:   207016
Effective search space used:   207016
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