GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aspA in Pseudomonas stutzeri RCH2

Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate GFF2631 Psest_2682 fumarate hydratase, class II

Query= curated2:P26899
         (475 letters)



>lcl|FitnessBrowser__psRCH2:GFF2631 Psest_2682 fumarate hydratase,
           class II
          Length = 464

 Score =  363 bits (933), Expect = e-105
 Identities = 192/459 (41%), Positives = 283/459 (61%), Gaps = 1/459 (0%)

Query: 9   RVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDVKR 68
           R E D LG  ++    Y+G QT R+  NF I   ++  E+++ALA++KKAAA  N  +  
Sbjct: 3   RTETDSLGPVEVPDQAYWGAQTQRSLSNFEIGTERMPIEVLHALALIKKAAARVNDRIGD 62

Query: 69  LYEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIGNRALEIMGHKKGD 128
           L   + + I QAADEIL G+  DQF +   Q G+GT  NMN NEVI  RA E+ G  +G 
Sbjct: 63  LPPDVARLIEQAADEILHGQHDDQFPLVVWQTGSGTQSNMNVNEVIAGRANELAGGTRGG 122

Query: 129 YIHLSPNTHVNMSQSTNDVFPTAIHISTLKLLE-KLLKTMEDMHSVFKQKAQEFDSVIKM 187
              + PN HVN +QS+ND FPTA+HI+  K +  KLL  + ++     + +     +IK 
Sbjct: 123 KSPVHPNDHVNRAQSSNDCFPTAMHIAAAKAVHAKLLPALAELSGGLAELSVRHGKLIKT 182

Query: 188 GRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHLYEVNMGATAVGTGLNADPEYIK 247
           GRTH+ DA PI  GQE  A+   L+   + I+ +   +YE+  G TAVGTGLN+   + +
Sbjct: 183 GRTHMMDATPITFGQEMSAFVAQLDIAERTIRHTLPAVYELAQGGTAVGTGLNSPHGFAE 242

Query: 248 QVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLKVCMMNMSKIANDLRLMASGPRA 307
            +   LA +SGLP V A +   A    +    +S +LK   + + K+ANDLRL+ SGPR 
Sbjct: 243 AIAAELAALSGLPFVSAPNKFAALAGHEPLVALSGALKTLAVALMKLANDLRLLGSGPRG 302

Query: 308 GLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIGNDNTICLASEAGQLELNVMEPV 367
           G AE+ LPA +PGSSIMPGKVNP   E ++ +A QV+GND TI  A+  G L+LNV +PV
Sbjct: 303 GFAEVRLPANEPGSSIMPGKVNPTQCEALSMLACQVMGNDMTISFAASQGHLQLNVFKPV 362

Query: 368 LVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYVEKSAGVITAVNPHLGYEAAARI 427
           ++ NLLQSI ++++G R+F  +C+ G+E +  RM +++E+   ++TA+NPH+GY+ AA I
Sbjct: 363 IIHNLLQSIQLLSDGCRNFNTHCIAGLEPDPARMAEHLERGLMLVTALNPHIGYDRAAEI 422

Query: 428 AREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEMTKPG 466
           A++A   G ++R+  ++   L+ EE D  + P  M + G
Sbjct: 423 AKKAYAQGTTLREASMELGYLSSEEFDQWVRPETMLESG 461


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: 477
Number of extensions: 18
Number of successful extensions: 2
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: 464
Length adjustment: 33
Effective length of query: 442
Effective length of database: 431
Effective search space:   190502
Effective search space used:   190502
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 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