GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aspA in Desulfovibrio vulgaris Miyazaki F

Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate 8501342 DvMF_2075 fumarate hydratase, class II (RefSeq)

Query= curated2:P26899
         (475 letters)



>lcl|FitnessBrowser__Miya:8501342 DvMF_2075 fumarate hydratase,
           class II (RefSeq)
          Length = 528

 Score =  321 bits (823), Expect = 3e-92
 Identities = 178/480 (37%), Positives = 278/480 (57%), Gaps = 22/480 (4%)

Query: 8   YRVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDVK 67
           +R+E+D +G  ++E    +G QT R+ +NF I   ++   +++ALA +KKAAAL N D+ 
Sbjct: 43  HRLERDSMGLVEVEQGRLWGAQTQRSLDNFRIGTDRMPLAVVHALARIKKAAALVNRDLG 102

Query: 68  RL------------YEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIG 115
            L               + +AI +AADE+L G+  D F +   Q G+GT  NMN NEV+ 
Sbjct: 103 LLPPPPPGQPDQPGLPHMAEAIARAADEVLAGQHDDHFPLSVWQTGSGTQTNMNVNEVLA 162

Query: 116 NRALEIMGHK-----KGDYIHLSP----NTHVNMSQSTNDVFPTAIHIST-LKLLEKLLK 165
           NRA +++         G + H+ P    N HVN  QS+ND FP A+H++  L L + LL 
Sbjct: 163 NRATQLLAEAAHAAASGGHPHIHPPIHPNDHVNRCQSSNDAFPAAMHLAAALALRDDLLP 222

Query: 166 TMEDMHSVFKQKAQEFDSVIKMGRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHL 225
            +  +    + KA     ++K+GRTHLQDAVP+ LG E   ++  L+  ++ +  +  HL
Sbjct: 223 GVRHLRDALRAKAAACADIVKIGRTHLQDAVPLTLGDEMSGWAAQLDACLEGLDAAMPHL 282

Query: 226 YEVNMGATAVGTGLNADPEYIKQVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLK 285
             + +G TAVGTGLNA P +  + +  LAD++GLPLV A +   A    D     S +L+
Sbjct: 283 CRLALGGTAVGTGLNAHPAFAPRAIALLADMTGLPLVPAPNPFAALAAHDGLVLTSGALR 342

Query: 286 VCMMNMSKIANDLRLMASGPRAGLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIG 345
                + KIAND+R +ASGPR G+ E+ LP  +PGSSIMPGKVNP   E +  +A QV+G
Sbjct: 343 ALATALLKIANDVRWLASGPRCGIGELRLPENEPGSSIMPGKVNPTQCEALTMVAVQVMG 402

Query: 346 NDNTICLASEAGQLELNVMEPVLVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYV 405
            D  + +A   G  ELNV +P+++ N+L S+ ++ +G RSF D+ + G++ +   +  +V
Sbjct: 403 LDVAVGMAGSQGNFELNVFKPLIIHNVLTSMRLLADGCRSFADHAVAGMQPDRAGIAAHV 462

Query: 406 EKSAGVITAVNPHLGYEAAARIAREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEMTKP 465
            +S  ++TA+ P +GY+ AA+ A  A   G ++R+ CL+  +L     D  ++P  M +P
Sbjct: 463 GRSLMLVTALAPVVGYDRAAQAAHRAHAQGITLREACLEMQLLDGAAFDAAVDPLRMARP 522


Lambda     K      H
   0.317    0.133    0.370 

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: 573
Number of extensions: 25
Number of successful extensions: 6
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: 528
Length adjustment: 34
Effective length of query: 441
Effective length of database: 494
Effective search space:   217854
Effective search space used:   217854
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: 52 (24.6 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