GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Lutibaculum baratangense AMV1

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_023433101.1 N177_RS14415 aldehyde dehydrogenase

Query= BRENDA::Q1XGK8
         (486 letters)



>NCBI__GCF_000496075.1:WP_023433101.1
          Length = 492

 Score =  287 bits (735), Expect = 5e-82
 Identities = 174/484 (35%), Positives = 256/484 (52%), Gaps = 12/484 (2%)

Query: 5   KHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGP-WGKLSV 63
           +++I+GAF    +G +FE ++P+ G+   ++  A  A+VD AV+AA  A   P W +L+ 
Sbjct: 7   RNYIDGAFCEGGAG-SFESVDPATGEAWANMPAANAADVDRAVRAADRAFHDPSWSRLTA 65

Query: 64  AERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVAN 123
            +R ++L+R+AD +        E E  DTGK     S   I   A  ++ +A L   +  
Sbjct: 66  TQRGKLLYRLADLVAENAQALAELETRDTGKIIRETS-AQIAYVADYYRYYAGLADKIEG 124

Query: 124 EAFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEET 183
               +  PD      Y  R P GV+  + PWN  L L   K+GPALA G TVV+K SE+ 
Sbjct: 125 AHLPIDKPDME---TYLRREPIGVVAAVVPWNSQLFLSAVKLGPALAAGCTVVLKASEDG 181

Query: 184 PLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRA 243
           P        ++  AG P GV N++ GFG D  G+ L  HP V    FTG   T   I+R 
Sbjct: 182 PAPLLAFARLVDQAGFPPGVVNILTGFG-DQCGSALASHPLVARIAFTGGPATARHIVRH 240

Query: 244 AAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDE 303
           +A+ +  V+LELGGK+  +VF D D+D      +   FA  GQ C+   R+ V+R I D 
Sbjct: 241 SAENLAAVTLELGGKSPVVVFEDADLDSVANAVVAGIFAATGQSCVAGSRLIVQRGIKDA 300

Query: 304 FVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPD-M 362
            + RL   A ++ IG P    +  GPL + +    +     +++  GG ++TGGG PD  
Sbjct: 301 LLERLVQKARAIRIGDPQAQETEMGPLATARQLRHIEDVIARSLAAGGRLVTGGGRPDGF 360

Query: 363 PAHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAI 422
           PA    G + +PTI    +     V EE+FGP   +  F+ E EA+E AN  PYGLAS +
Sbjct: 361 PA----GHYFEPTIIDCDATTIPSVEEELFGPVLSVLGFEEETEAVEFANRTPYGLASGV 416

Query: 423 WTENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNI 482
           +T + +RAHR+   I AG+VWVN++        FGG   SG GREGG+ +   YT  K +
Sbjct: 417 FTASLTRAHRMIRAIRAGVVWVNTYRAVSPIMPFGGYGLSGSGREGGLDAALDYTRTKAV 476

Query: 483 CVKL 486
            +++
Sbjct: 477 WIRV 480


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: 666
Number of extensions: 30
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 24 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