GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_1680
          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:

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