GapMind for catabolism of small carbon sources

 

Alignments for a candidate for boxD in Kocuria flava HO-9041

Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; EC 1.2.1.77 (characterized)
to candidate WP_058857816.1 AS188_RS04315 aldehyde dehydrogenase family protein

Query= SwissProt::Q84HH8
         (515 letters)



>NCBI__GCF_001482365.1:WP_058857816.1
          Length = 491

 Score =  112 bits (281), Expect = 2e-29
 Identities = 124/438 (28%), Positives = 181/438 (41%), Gaps = 37/438 (8%)

Query: 5   NYVYGQWIEGAG-EGAALTDPVTGEALVRV-SSDGIDVARALEFARTAGGAALKALTYEE 62
           +++ G ++   G +   + DP T E    V ++   D+ RA+  A  A  A   A T  E
Sbjct: 23  HFIDGAYLASTGAQRNDVVDPATEEVWASVPNATEEDLDRAVGAAERAF-AGWAARTPAE 81

Query: 63  RAAKLAAIAELLQAKRAEYFDISLRNSGATEGDASFDVDGAIFTVKSYARAGKALGAGRH 122
           RA  L   AE ++ +R      + R +G    +       A    + +A   +A      
Sbjct: 82  RAQVLLRAAEEIETRREPMALTNTRENGTPLAETRGAAANAAGIFRYFAPWLEAEDVRPF 141

Query: 123 LKEGGRVALAKTDVFQGQHFLMPLTGVAVFINAFNFPAWGLWEKAAPALLAGVPVFAKPA 182
               G   + +  V           GV   I  +NFP   +  K APALLAG  V  KPA
Sbjct: 142 PNGAGETVVHENPV-----------GVCALIAPWNFPINLVVAKLAPALLAGCTVVIKPA 190

Query: 183 TPTAWLAQRMVADVVEAGILPPGAISIVCGGAR--DLLDHVTECDVVSFTGSADTAARMR 240
           +PT  L+ R V D + A  +P G +++V G  R  D L        V+FTG      R+ 
Sbjct: 191 SPTP-LSVRFVVDALTAAGVPAGVVNLVTGNGRMGDRLVRHPAVRKVAFTGCTPVGRRIA 249

Query: 241 THPNVVARSVRINIEADSVNSAILGPDAQPGTPEFDLAVKEIVREMTVKTGQKCTAIRRI 300
                  + V   +E    +SAI+ PDA     + +     ++R     TGQ C    RI
Sbjct: 250 AACGEQLKPV--TLELGGKSSAIVLPDA-----DLEHMSSVLLRSCLRNTGQTCYISTRI 302

Query: 301 LAPAGVSRALADAVSGKLAGCKVGNPRSEGVRVGPLVSKAQQAAAFEGLAKLRQE-CEVV 359
           L P      + + V   +A    G+P  EG   GP+ ++AQ       L   R E   VV
Sbjct: 303 LDPESRYDEVVEMVGATVAAAPQGDPLEEGTVFGPMANRAQYDVVMGYLETARAEGARVV 362

Query: 360 FGGDPDFEPVDADAAVSAFVQPTLL--YCDKGLAARHVHDVEVFGPVATMVPYADTRDAV 417
            GG        AD     +V PT+L     +   AR     E+FGPV T++ Y D  +AV
Sbjct: 363 TGGG------RADRETGFYVAPTVLADVTPEMTVARE----EIFGPVITVLRYRDVDEAV 412

Query: 418 AIARRGHGSLVASVYSGD 435
           A+A      L   V+S D
Sbjct: 413 ALANNTPFGLGGIVFSAD 430


Lambda     K      H
   0.319    0.135    0.399 

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: 604
Number of extensions: 31
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: 515
Length of database: 491
Length adjustment: 34
Effective length of query: 481
Effective length of database: 457
Effective search space:   219817
Effective search space used:   219817
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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