GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Dyella japonica UNC79MFTsu3.2

Align Aldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate N515DRAFT_4224 N515DRAFT_4224 coniferyl-aldehyde dehydrogenase

Query= SwissProt::P12693
         (483 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4224 N515DRAFT_4224
           coniferyl-aldehyde dehydrogenase
          Length = 456

 Score =  331 bits (848), Expect = 4e-95
 Identities = 192/444 (43%), Positives = 253/444 (56%), Gaps = 8/444 (1%)

Query: 41  ERIAALNLLKETIQRREPEIIAALAADFR-KPASEVKLTEIFPVLQEINHAKRNLKDWMK 99
           ER   L  L + I     EI  A+  DF  +PA E  L E+FP L  I HA  + + WMK
Sbjct: 15  ERARRLRALNDLIGEHRGEIADAIHQDFGGRPAQETDLLEVFPSLSAIRHALAHGRRWMK 74

Query: 100 PRRVRAALSVAGTRAGLRYEPKGVCLIIAPWNYPFNLSFGPLVSALAAGNSVVIKPSELT 159
           PRR    L     R  +R +P GV  II PWNYP  L+ GP+V ALAAGN V++K SE T
Sbjct: 75  PRRSWPGLLFMPARNEIRPQPLGVVGIIVPWNYPLFLAAGPMVDALAAGNRVMVKMSEYT 134

Query: 160 PHTATLIGSIVREAFSVDLVAVVEGDAAVSQELLALPFDHIFFTGSPRVGKLVMEAASKT 219
           P  + L   +    F  + V VV GDA V+Q   ALPFDH+ FTGS  VG+ VM AAS  
Sbjct: 135 PQFSALFAQLAARYFKPEEVCVVTGDADVAQAFSALPFDHLLFTGSTAVGRHVMRAASAN 194

Query: 220 LASVTLELGGKSPTIIGPTANLPKAARNIVWGKFSNNGQTCIAPDHVFVHRCIAQKFNEI 279
           L  VTLELGGKSP I+GP A    A   I+ GK  N GQTCIAPD+V + R    +F   
Sbjct: 195 LTPVTLELGGKSPAIVGPGARFANAVERILVGKLFNAGQTCIAPDYVLLPRAQVDEFVAA 254

Query: 280 LVKEIVRVYGKDFAAQRRSADYCRIVNDQHFNRINKLLTDAKAKGAKI-LQGGQVDATE- 337
                 R+Y +      R+  Y  I++++ + R+  L  DA   GAK+ L G + D  + 
Sbjct: 255 ARDVAARLYPQPV----RNEQYASIISERQYQRLAALRDDAARDGAKLTLLGDETDDIQR 310

Query: 338 RLVVPTVLSNVTAAMDINHEEIFGPLLPIIEYDDIDSVIKRVNDGDKPLALYVFSEDKQF 397
           R + P +L+ V+ +M +  EEIFGPLLP++ YDDI+  I  V     PLALY+F ED   
Sbjct: 311 RRMTPALLTGVSESMAVMQEEIFGPLLPLVPYDDIEQAIAYVAAHPHPLALYLFEEDGAL 370

Query: 398 VNNIVARTSSGSVGVNLSVVHFLHPNLPFGGVNNSGIGSAHGVYGFRAFSHEKPVLID-K 456
           V+ ++ART++G V +N ++ H    +LPFGGV  SG G  HG  GFR FSH K V    +
Sbjct: 371 VDRVLARTTAGGVTINDTLYHIAQHDLPFGGVGPSGSGGYHGEAGFRTFSHLKSVFRQAR 430

Query: 457 FSITHWLFPPYTKKVKQLIGITVK 480
            +    L PPY ++ KQ++ I +K
Sbjct: 431 VNGAGLLNPPYGQRFKQMLAIMLK 454


Lambda     K      H
   0.320    0.136    0.395 

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: 484
Number of extensions: 16
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: 483
Length of database: 456
Length adjustment: 33
Effective length of query: 450
Effective length of database: 423
Effective search space:   190350
Effective search space used:   190350
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 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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