GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Klebsiella michiganensis M5al

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BWI76_RS15205 BWI76_RS15205 succinate-semialdehyde dehydrogenase

Query= BRENDA::A6T8Z5
         (462 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS15205 BWI76_RS15205
           succinate-semialdehyde dehydrogenase
          Length = 461

 Score =  819 bits (2116), Expect = 0.0
 Identities = 403/461 (87%), Positives = 436/461 (94%)

Query: 2   MNLSATHAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIG 61
           MNLSATHAVSVNPTTGE +SSLPWASE++VD+AI LA  GYRQWR+  +A RA  LR +G
Sbjct: 1   MNLSATHAVSVNPTTGETLSSLPWASEQQVDSAIALAEQGYRQWRKVSVAQRATTLRNVG 60

Query: 62  AALRARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAV 121
           AA+RAR E +AQMI+LEMGKPIAQARGEVAKSANLCDWYAEHGPAML TEATLVE+N+AV
Sbjct: 61  AAMRARSEALAQMISLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLNTEATLVEDNKAV 120

Query: 122 IEYRPLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGL 181
           IEYRP+GAILA+MPWNFPVWQV+RGAVPILLAGNSYLLKHAPNV+GSA ++GEIFAAAG+
Sbjct: 121 IEYRPMGAILAIMPWNFPVWQVLRGAVPILLAGNSYLLKHAPNVLGSAAMIGEIFAAAGV 180

Query: 182 PDGVFGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPF 241
           P+GVFGWVNATNDGVSQ+IND RIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPF
Sbjct: 181 PEGVFGWVNATNDGVSQMINDPRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPF 240

Query: 242 IVLNDADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPR 301
           IVLNDADLDEAVKAAV GRYQN+GQVCAA+KRFI+EAGIAEAFT+KFV AVAALKMGDPR
Sbjct: 241 IVLNDADLDEAVKAAVIGRYQNTGQVCAAAKRFIVEAGIAEAFTQKFVAAVAALKMGDPR 300

Query: 302 DEQNYVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTG 361
           DEQNY+GPMARFDLRDELH+QV ATL EGATLLLGAEKIEGAGNYYAPTVLGNVTA MTG
Sbjct: 301 DEQNYIGPMARFDLRDELHEQVRATLKEGATLLLGAEKIEGAGNYYAPTVLGNVTAEMTG 360

Query: 362 FRQELFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNG 421
           FR+ELFGPVAT+T ARDADHALALAN+SEFGLSATVYTT E QA+RFA ELECGGVF+NG
Sbjct: 361 FREELFGPVATITEARDADHALALANESEFGLSATVYTTSETQARRFADELECGGVFING 420

Query: 422 YCASDARVAFGGVKKSGFGRELSHFGLHEFCNAQTVWKDRR 462
           YCASDARVAFGGVKKSGFGRELSHFGLHEFCN QTVW+DRR
Sbjct: 421 YCASDARVAFGGVKKSGFGRELSHFGLHEFCNVQTVWRDRR 461


Lambda     K      H
   0.319    0.133    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: 716
Number of extensions: 11
Number of successful extensions: 1
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: 462
Length of database: 461
Length adjustment: 33
Effective length of query: 429
Effective length of database: 428
Effective search space:   183612
Effective search space used:   183612
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, 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