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_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases

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



>FitnessBrowser__Korea:Ga0059261_3374
          Length = 474

 Score =  270 bits (689), Expect = 1e-76
 Identities = 171/481 (35%), Positives = 259/481 (53%), Gaps = 22/481 (4%)

Query: 18  SQLLNYIDGNFVTSASSFAN--INPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKL 75
           S L +YI G +V S     +  INP     ++++        ++AV AA+ A    + + 
Sbjct: 3   SYLKHYIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDS-FSRT 61

Query: 76  SVQDRAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTS 135
           SV +R AL+  I    + R  +   A  A+ G P+  A+T  +   I +  +  +  K  
Sbjct: 62  SVDERIALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLMSTINALKA- 120

Query: 136 HTDLFEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSE 195
               FE S   G   +   V +P+GV+ +I+PWN PL     KVAPALA GNT+V KPSE
Sbjct: 121 ----FEFSEQIGQSLV---VHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSE 173

Query: 196 ESPSSATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIM 255
           E+P SA + AE+M  AGVP GVFNL+ G G    G  L++H  +  ++FTG ++ G  + 
Sbjct: 174 EAPGSAAIFAEIMDKAGVPAGVFNLVQGDG-PIVGTALSRHRDVDMVSFTGSTRAGIQVA 232

Query: 256 KAVADGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIF 315
           K  A+ VK V  ELGGK+  V+   ADL  A++  L S   NSGQ C+   R+ VH S  
Sbjct: 233 KNAAETVKRVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQA 292

Query: 316 DE---FVSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGG 372
            E     SGL    E    G P Q+G ++GP+++    +K+    R  ++EGA + TGG 
Sbjct: 293 AEAAQIASGLMKAVE---TGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGG- 348

Query: 373 VPKFNDERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGL 432
            P   D  + G +V+PT+++G+ +      EEIFGPV  I P+ DE+E +   ND++YGL
Sbjct: 349 -PGRPDGIETGYFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGL 407

Query: 433 ACAIWTTNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSD 492
           +  ++ +      RV+ ++  G+V++N     D   PFGG K SG GRE G+F +  + +
Sbjct: 408 SAVLFGSP-EEVKRVAPRLRAGMVYINGGQ-PDPSLPFGGYKQSGNGREHGKFGLAEFME 465

Query: 493 I 493
           +
Sbjct: 466 V 466


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: 551
Number of extensions: 23
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: 500
Length of database: 474
Length adjustment: 34
Effective length of query: 466
Effective length of database: 440
Effective search space:   205040
Effective search space used:   205040
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