GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Sphingomonas koreensis DSMZ 15582

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases

Query= reanno::pseudo13_GW456_L13:PfGW456L13_805
         (497 letters)



>FitnessBrowser__Korea:Ga0059261_3374
          Length = 474

 Score =  280 bits (716), Expect = 8e-80
 Identities = 179/475 (37%), Positives = 265/475 (55%), Gaps = 19/475 (4%)

Query: 23  YINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSRLAPTK 82
           YI GE+ ++  G   + I+P     + +I     ADA +AV  A+A F+S  +SR +  +
Sbjct: 8   YIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDS--FSRTSVDE 65

Query: 83  RKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQALSWSGEAIDKIYDEV 142
           R + +       K  A +LA     +MG PIS      +   AQ  S  G  +  I    
Sbjct: 66  RIALLEAILAEYKNRAGDLADAIAAEMGAPIS------LAKTAQVGSGIGHLMSTINALK 119

Query: 143 AATPHDQLG--LVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTA 200
           A    +Q+G  LV  EP+GVV  I PWN+PL     K+ PAL+ GN+++LKPSE++P +A
Sbjct: 120 AFEFSEQIGQSLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSA 179

Query: 201 IRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYSGESN 260
              AE+  +AG+P GV N++ G G  VG AL+ H DVD + FTGST+   Q+   + E+ 
Sbjct: 180 AIFAEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAET- 238

Query: 261 MKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIKDKFLP 320
           +KRV  E GGKSPN++   A +L  A +    ++  N G+ C A +R+LV  S   +   
Sbjct: 239 VKRVHQELGGKSPNVILPGA-DLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQ 297

Query: 321 LVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARLVAGGK-RTLQETG 379
           +    +KA + G+P     ++G +V+  Q   +   I  G  +GA+L  GG  R      
Sbjct: 298 IASGLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDGIET 357

Query: 380 GTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAVWTADIS 439
           G +V+PT+F GV N M IA+EEIFGPV+++I +   EEA+ IANDT YGL+A ++ +   
Sbjct: 358 GYFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLSAVLFGSP-E 416

Query: 440 KAHLTARALRAGSVWVNQYDGG--DMTAPFGGFKQSGNGRDKSLHAFDKYTELKA 492
           +    A  LRAG V++N   GG  D + PFGG+KQSGNGR+       ++ E+KA
Sbjct: 417 EVKRVAPRLRAGMVYIN---GGQPDPSLPFGGYKQSGNGREHGKFGLAEFMEVKA 468


Lambda     K      H
   0.316    0.132    0.390 

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: 613
Number of extensions: 33
Number of successful extensions: 7
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: 497
Length of database: 474
Length adjustment: 34
Effective length of query: 463
Effective length of database: 440
Effective search space:   203720
Effective search space used:   203720
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 (21.6 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