GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Sphingomonas koreensis DSMZ 15582

Align Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::S0ENH1
         (461 letters)



>FitnessBrowser__Korea:Ga0059261_1680
          Length = 469

 Score =  323 bits (828), Expect = 7e-93
 Identities = 169/462 (36%), Positives = 264/462 (57%), Gaps = 9/462 (1%)

Query: 9   IITGQPRSARETTSGVNPLDRSSLWPAPVATGNDVEEAVRSAQEAFPAWSEKTYKQRTEL 68
           I+ G+P +  ET   ++P        AP+A+  D++ AV +A+ AFP W+    + R   
Sbjct: 7   IVDGKPLAMAETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIEDRAAA 66

Query: 69  LEKFADLYLVHANEFCQLIATECGRTAGNAAIEVYVAAQWLRYPSKYEIPEEVTEDEKKT 128
           +   AD      +E  +L++ E G+   NA  E+  A  W R  +      +V +D+   
Sbjct: 67  ILAIADSIEAAKDELARLLSAEQGKPVPNAVGEIMGALAWARATAGLRPAVDVLKDDDSV 126

Query: 129 SIVTH-EPLGVVAAICPWNFPLMLALGKIAPALATGNCVILKPSPFTPYSSLKLVELAQQ 187
            +  H +PLGVVA+I PWNFP+M+A+  I P L  GN V++KPS FTP ++L++VE+A  
Sbjct: 127 RVEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRMVEIANA 186

Query: 188 VFPPSVLQVLHGHDDLGPMLVKHPRIQKITFTGSTTTGKQILRDAAETMKRVTLETAGNN 247
             PP VL  + G  ++G  +  HP I KI FTGST TG+ I+ D A  +KR+TLE  GN+
Sbjct: 187 HLPPGVLNSVTGEVEIGRAIASHPGIDKIVFTGSTPTGRSIMADGAANLKRLTLELGGND 246

Query: 248 ASIILPDVNIEAVIPQLAGGLWFNAGQVCIATRRMYIHQDIFDEAVAQLAEASK------ 301
           A+I+LPD +++ V  ++    + N+GQ+C A +R+Y+H+ I D    +LAE ++      
Sbjct: 247 AAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAEMARTAVVGP 306

Query: 302 --DLASGMEPIQNEMQLVRLQQALSDANAAGCELLSLGKTEAAEGFFIQPTILKSPPPDA 359
             D AS   P+QN  Q   ++    DA A G   L+ G+    +G+F   +++       
Sbjct: 307 GSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGDGYFFPLSVVVDVTDGM 366

Query: 360 DVVQQENFGPIVSCIKFSSLDEAISLANNSDTGLAASVWSSDVSAARRVAAKLEVGNVYI 419
            +V +E FGPI+  I++S  ++A++ AN ++ GL  SVWS+D +AA   A +LE G V++
Sbjct: 367 RIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLEAGTVWV 426

Query: 420 NGPPQPDPYVPFGGHKQSGLGVEYGLPGLLSFCQTKSTYLYK 461
           N      P VPFGG KQSG+G E+GL GL  + Q ++  + K
Sbjct: 427 NDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTVRVAK 468


Lambda     K      H
   0.316    0.132    0.392 

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: 501
Number of extensions: 14
Number of successful extensions: 3
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: 461
Length of database: 469
Length adjustment: 33
Effective length of query: 428
Effective length of database: 436
Effective search space:   186608
Effective search space used:   186608
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: 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