GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Marinobacter adhaerens HP15

Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate GFF3190 HP15_3132 fumarate hydratase class II

Query= curated2:P26899
         (475 letters)



>FitnessBrowser__Marino:GFF3190
          Length = 458

 Score =  355 bits (910), Expect = e-102
 Identities = 200/463 (43%), Positives = 279/463 (60%), Gaps = 8/463 (1%)

Query: 7   EYRVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDV 66
           E+R E D LG+ Q+ AD  +G QT RA ENFP++G  + +  I A+A +K+AAA AN  +
Sbjct: 3   EFRTETDSLGDVQVPADALWGAQTQRAVENFPVSGQPMPQPFIAAVAQIKRAAAEANTSL 62

Query: 67  KRLYEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIGNRALEIMGHKK 126
             L   +  AI QA +++++G++ DQF VD  Q G+GTS NMN NEVI + A        
Sbjct: 63  GLLDNDLRDAISQACEDLVKGEYADQFPVDRYQTGSGTSTNMNVNEVIASIA-----RNA 117

Query: 127 GDYIHLSPNTHVNMSQSTNDVFPTAIHIST-LKLLEKLLKTMEDMHSVFKQKAQEFDSVI 185
           G  +H  PN HVNMSQS+NDV PTAIH+S  +   EKLL  +  +  V  ++   F S +
Sbjct: 118 GFEVH--PNDHVNMSQSSNDVIPTAIHVSAVIAAKEKLLPALSHLCGVIYEQEAAFSSQV 175

Query: 186 KMGRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHLYEVNMGATAVGTGLNADPEY 245
           K GRTHL DA+P+ LGQE + +   L    KR++ +   L  V  G TAVGTG+NA PE+
Sbjct: 176 KTGRTHLMDAMPVTLGQELKTWREQLLAVEKRVEAAADELLAVPQGGTAVGTGINALPEF 235

Query: 246 IKQVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLKVCMMNMSKIANDLRLMASGP 305
             Q VK L   +G P    DH        DA   +SA L+   + ++KIANDLR M SGP
Sbjct: 236 PGQFVKFLRANTGYPFTSLDHKFTGQSAVDAPVALSAQLRGAAIVLTKIANDLRWMNSGP 295

Query: 306 RAGLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIGNDNTICLASEAGQLELNVME 365
             GLAEISLPA QPGSSIMPGKVNPV+ E +  +  QV+G D+ + +A ++G  +LNVM 
Sbjct: 296 IHGLAEISLPALQPGSSIMPGKVNPVIPESVAMVGAQVMGLDSAVAIAGQSGNFQLNVML 355

Query: 366 PVLVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYVEKSAGVITAVNPHLGYEAAA 425
           P++  NLL    ++ N      D  +K    N   +   V K+  ++TA+NP +GY  AA
Sbjct: 356 PLVGGNLLDMTDLLANAAIMLADKAIKDFTVNADNLNAGVGKNPVLVTALNPEIGYSLAA 415

Query: 426 RIAREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEMTKPGIA 468
            IA+EA  TG+ V D+  +   L+ E L+ +++P ++T+ GIA
Sbjct: 416 DIAKEAYKTGRPVIDVAEERSGLSRERLEELMDPLKLTRGGIA 458


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: 502
Number of extensions: 28
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: 475
Length of database: 458
Length adjustment: 33
Effective length of query: 442
Effective length of database: 425
Effective search space:   187850
Effective search space used:   187850
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 (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