GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Sphingomonas koreensis DSMZ 15582

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__Korea:Ga0059261_3374
          Length = 474

 Score =  236 bits (602), Expect = 1e-66
 Identities = 159/471 (33%), Positives = 236/471 (50%), Gaps = 15/471 (3%)

Query: 4   KLLINGELVSGEG-EKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKV 62
           K  I GE V  EG  +  V NPAT   + EI   S    D AV AA AAF  + +T+   
Sbjct: 6   KHYIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDSFSRTSVDE 65

Query: 63  RAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLA 122
           R   L  +    +      A+  +   G P+  A   ++ + +            +N L 
Sbjct: 66  RIALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGI------GHLMSTINALK 119

Query: 123 AGEYLEG-HTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTA 181
           A E+ E    S++  +P+GVVA I PWN+PL     K+APALAAGN +VLKPSE  P +A
Sbjct: 120 AFEFSEQIGQSLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSA 179

Query: 182 LKLAELA-KDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSI 240
              AE+  K   PAGV N++ G G  VG  L+ H  V MVS TGS   G  +  + A ++
Sbjct: 180 AIFAEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAETV 239

Query: 241 KRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKL 300
           KR H ELGGK+P ++   AD+   V+        N+GQ C A  R+   +       +  
Sbjct: 240 KRVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQIA 299

Query: 301 GAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKG---NG 357
              +  +++G P  E   +GP+ + A  E++   + +    G  K+ TGG  R      G
Sbjct: 300 SGLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEG-AKLETGGPGRPDGIETG 358

Query: 358 YYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGR 417
           Y+  PTL +G   D  I ++E+FGPV+++ P+ +EE+ V  AND+ YGL S+V       
Sbjct: 359 YFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGL-SAVLFGSPEE 417

Query: 418 AHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVR 468
             RV+ RL+ G  ++N        +P GG K SG G++   +GL ++  V+
Sbjct: 418 VKRVAPRLRAGMVYINGG-QPDPSLPFGGYKQSGNGREHGKFGLAEFMEVK 467


Lambda     K      H
   0.317    0.134    0.397 

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: 525
Number of extensions: 22
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: 474
Length of database: 474
Length adjustment: 33
Effective length of query: 441
Effective length of database: 441
Effective search space:   194481
Effective search space used:   194481
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: 51 (24.3 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