GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Sphingomonas koreensis DSMZ 15582

Align Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases

Query= curated2:Q49Z69
         (475 letters)



>FitnessBrowser__Korea:Ga0059261_3374
          Length = 474

 Score =  450 bits (1158), Expect = e-131
 Identities = 235/472 (49%), Positives = 306/472 (64%), Gaps = 1/472 (0%)

Query: 1   MRNFTKQYINGEWVESTSGETLEVINPATEEVAGTIAKGNKEDVEKAVEAADNVYLEFRH 60
           MR++ K YI GEWVES  G   +VINPATE     I  G++ D +KAV AA   +  F  
Sbjct: 1   MRSYLKHYIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDSFSR 60

Query: 61  TSVKERQDLLDQIVQEYKNRKEDLIQAITDELGAPLSVAENVHYQMGLDHFEAARDALND 120
           TSV ER  LL+ I+ EYKNR  DL  AI  E+GAP+S+A+      G+ H  +  +AL  
Sbjct: 61  TSVDERIALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLMSTINALKA 120

Query: 121 FQFEERRGDDLVVKEAIGVSGLITPWNFPTNQTSLKLAAAFAAGSPVVFKPSEETPFAAI 180
           F+F E+ G  LVV E IGV  LITPWN+P NQ   K+A A AAG+ +V KPSEE P +A 
Sbjct: 121 FEFSEQIGQSLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSAA 180

Query: 181 ILAEIFDKVGVPKGVFNLVNGDGQGVGNPLSEHPKVRMMSFTGSGPTGSSIMKKAAEDFK 240
           I AEI DK GVP GVFNLV GDG  VG  LS H  V M+SFTGS   G  + K AAE  K
Sbjct: 181 IFAEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAETVK 240

Query: 241 KVSLELGGKSPYIILDDADIDGAASAAANKVVFNTGQVCTAGTRTIVPASIKEDFLTAVK 300
           +V  ELGGKSP +IL  AD+  A       VV N+GQ C A  R +V  S   +      
Sbjct: 241 RVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQIAS 300

Query: 301 EKFSQVKVGNPREEGTQVGPIISKKQFDQVQAYIDKGIEEGAELLYGGPGKPEGLDKGYF 360
                V+ G+P +EG  +GP+++K Q++++Q  I KG+EEGA+L  GGPG+P+G++ GYF
Sbjct: 301 GLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDGIETGYF 360

Query: 361 ARPTIFNNVDNSMTIAQEEIFGPVMSVITYNDLDEAIKIANDTKYGLAGYVYGSDKDTLH 420
            +PT+F+ V N MTIA+EEIFGPV+++I Y D +EA++IANDT YGL+  ++GS ++ + 
Sbjct: 361 VKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLSAVLFGSPEE-VK 419

Query: 421 KVARSIEAGTVEINEAGRKPDLPFGGYKQSGLGREWGDYGIEEFLEVKSIAG 472
           +VA  + AG V IN     P LPFGGYKQSG GRE G +G+ EF+EVK++ G
Sbjct: 420 RVAPRLRAGMVYINGGQPDPSLPFGGYKQSGNGREHGKFGLAEFMEVKAMVG 471


Lambda     K      H
   0.313    0.134    0.380 

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: 609
Number of extensions: 28
Number of successful extensions: 2
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: 475
Length of database: 474
Length adjustment: 33
Effective length of query: 442
Effective length of database: 441
Effective search space:   194922
Effective search space used:   194922
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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