GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nbaE in Sphingomonas koreensis DSMZ 15582

Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases

Query= metacyc::MONOMER-13361
         (500 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1680 Ga0059261_1680
           NAD-dependent aldehyde dehydrogenases
          Length = 469

 Score =  254 bits (648), Expect = 6e-72
 Identities = 159/479 (33%), Positives = 236/479 (49%), Gaps = 28/479 (5%)

Query: 24  IDGNFVTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRAAL 83
           +DG  +  A +F  I+P  G+  +D   A    ++ AV AA+ A  G W    ++DRAA 
Sbjct: 8   VDGKPLAMAETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPG-WAATPIEDRAAA 66

Query: 84  IHKIADGIQARFEEFVAAEVADTGRPVHQA-----RTLDIPRAIANFRTFADLAKTSHTD 138
           I  IAD I+A  +E      A+ G+PV  A       L   RA A  R   D+ K   + 
Sbjct: 67  ILAIADSIEAAKDELARLLSAEQGKPVPNAVGEIMGALAWARATAGLRPAVDVLKDDDSV 126

Query: 139 LFEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESP 198
             E+             RKPLGV+  ISPWN P+++  W + P L  GNTVV KPS  +P
Sbjct: 127 RVEVH------------RKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTP 174

Query: 199 SSATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAV 258
            +A  + E+ + A +PPGV N + G  +   G  +  HPGI  + FTG + TG +IM   
Sbjct: 175 LAALRMVEIAN-AHLPPGVLNSVTG--EVEIGRAIASHPGIDKIVFTGSTPTGRSIMADG 231

Query: 259 ADGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEF 318
           A  +K ++ ELGG +AA+V  DAD+D     +   +F NSGQ+C   +RVYVH SI D  
Sbjct: 232 AANLKRLTLELGGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDAL 291

Query: 319 VSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFND 378
              L   A   VVG         GP+ +    D V +    A   G   + GG      +
Sbjct: 292 AEKLAEMARTAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGG------E 345

Query: 379 ERDQGAYVQP-TIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIW 437
            R+   Y  P ++   ++D  R V EE FGP+  +  + D ++ + R N +  GL  ++W
Sbjct: 346 AREGDGYFFPLSVVVDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVW 405

Query: 438 TTNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANI 496
           + + + A   ++++  G VWVN         PFGG K SG+G E G + ++ Y  +  +
Sbjct: 406 SADPAAALAFAQRLEAGTVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTV 464


Lambda     K      H
   0.318    0.135    0.405 

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: 549
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: 500
Length of database: 469
Length adjustment: 34
Effective length of query: 466
Effective length of database: 435
Effective search space:   202710
Effective search space used:   202710
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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