GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Lactobacillus delbrueckii ZN7a-9

Align Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized)
to candidate WP_002880378.1 B506_RS08415 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

Query= SwissProt::P94358
         (485 letters)



>NCBI__GCF_000387565.1:WP_002880378.1
          Length = 476

 Score =  254 bits (649), Expect = 5e-72
 Identities = 161/470 (34%), Positives = 255/470 (54%), Gaps = 14/470 (2%)

Query: 9   SFINGKWTGGESGRTEDILNPYDQSVITTASLATGKQLEDAFDIAQKAQKEWAKSTTEDR 68
           +++NG+W   +S    +I  P     + T    + + ++   D A+KA   W   +  +R
Sbjct: 7   NYVNGEWR--DSADAIEIFEPATGKSLGTVPAMSHEDVDYVMDSAKKALPAWRALSYVER 64

Query: 69  KAVLQKARGYLHENRDDIIMMIARETGGTIIKSTIELEQTIAILDEA----MTYTGEL-- 122
            A LQKA   L+ + + I   +++E    +  S  E+ +T  I++      +T  GE+  
Sbjct: 65  AAYLQKAADILYRDAEKIGSTLSKEIAKGLKSSIGEVTRTAEIVEYTAKVGVTLDGEVME 124

Query: 123 GGVKEVPSDIEGKTNKIYRLPLGVISSISPFNFPMNLSMRSIAPAIALGNSVVHKPDIQT 182
           GG  E  S  + K   + R P+G++ +ISPFN+P+NL+   IAPA+  GN V  KP  Q 
Sbjct: 125 GGNFEAAS--KNKLAVVRREPVGLVLAISPFNYPVNLAGSKIAPALMGGNVVAFKPPTQG 182

Query: 183 AISGGTIIAKAFEHAGLPAGVLNVMLTDVKEIGDGMLTNPIPRLISFTGSTAVGRHIGEI 242
           AISG  ++AKAF  AGLPAGV N +    + IGD ++ +P    I+FTGS+AVG++IG++
Sbjct: 183 AISG-LLLAKAFAEAGLPAGVFNTITGRGRVIGDYIVEHPAVNFINFTGSSAVGKNIGKL 241

Query: 243 AGRAFKRMALELGGNNPFAVLSDADVDRAVDAAIFGKFIHQGQICMIINRIIVHQDVYDE 302
           AG   + + LELGG +   VL DAD+D      + G F + GQ C  + R++V   V DE
Sbjct: 242 AG--MRPIMLELGGKDAAIVLEDADLDLTAKNIVAGAFGYSGQRCTAVKRVLVMDSVADE 299

Query: 303 FVEKFTARVKQLPYGDQTDPKTVVGPLINERQIEKALEIIEQAKTDGIELAVEGKRVGNV 362
            VEK TA VK L  G   +   +  PLI+ +  +    +IE+A   G +   + KR GN+
Sbjct: 300 LVEKVTALVKDLTVGMPEEDADIT-PLIDTKSADYVQGLIEEAAEKGAKPLFDFKREGNL 358

Query: 363 LTPYVFVGADNNSKIAQTELFAPIATIIKAGSDQEAIDMANDTEYGLSSAVFTSDLEKGE 422
           + P V      + ++A  E F P+   I+  S  EA+ +AN++EYGL S+VF+ + EK  
Sbjct: 359 IYPMVMDQVTTDMRLAWEEPFGPVLPFIRVKSADEAVKIANESEYGLQSSVFSRNFEKAF 418

Query: 423 KFALQIDSGMTHVNDQSVNDSPNIAFGGNKASGVGRFGNPWVVEEFTVTK 472
             + +++ G  H+N+++     N  F G K+SG G  G  + ++  T  K
Sbjct: 419 AISGKLEVGTVHINNKTQRGPDNFPFLGVKSSGAGVQGVKYSIQAMTRVK 468


Lambda     K      H
   0.316    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: 523
Number of extensions: 22
Number of successful extensions: 4
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: 485
Length of database: 476
Length adjustment: 34
Effective length of query: 451
Effective length of database: 442
Effective search space:   199342
Effective search space used:   199342
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 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