GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Phyllobacterium brassicacearum STM 196

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_106710100.1 CU102_RS05900 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase family protein

Query= curated2:B6IPH8
         (386 letters)



>NCBI__GCF_003010955.1:WP_106710100.1
          Length = 423

 Score =  103 bits (257), Expect = 9e-27
 Identities = 113/418 (27%), Positives = 175/418 (41%), Gaps = 49/418 (11%)

Query: 4   DPIALARDLIRCPSVTP---ADAGALDRVQSVLEGLGFTCHRLPFQ-EPG-TERVD--NL 56
           D IAL R+LIR P++ P   A     + +   L+ +GF    +  +  PG T+R    N+
Sbjct: 15  DLIALTRELIRFPTINPPGEAYTPCAEYLAHRLQKIGFETQLIRGEGTPGDTDRYPRTNV 74

Query: 57  YARLGDK--GPNFCFAGHTDVVPAGDAAAWTVDPFGGEIIDGRLYGRGAADMKGGVAAFI 114
            AR   +  G    F  H DVV  G+   WTVDPF G + DG++YGRGA DMKGG+AA I
Sbjct: 75  VARFDGRRHGQTVHFNSHIDVVDTGEG--WTVDPFEGVVKDGKIYGRGACDMKGGLAASI 132

Query: 115 AAVGSFLERNGPPAGSISLLITGDEEGPAVNGTRKVLDWMAAAGERIDACLVGEPTNPRA 174
            A  +FLE      G+I +  T DEE     G   +      +  R+D  ++ EP N   
Sbjct: 133 IAAEAFLEVYPDFTGAIEISGTVDEESGGFGGVAYLASKGFFSKPRVDHVIIPEPLNK-- 190

Query: 175 LGDMIKVGRRGSLTATLTALGAQGHTAYPHLADNPLPRLAEALHLL----------ASSP 224
             D I +G RG   A +   G   H + P L D  +  +   L               + 
Sbjct: 191 --DRICLGHRGVWWAEIETKGEIAHGSMPFLGDCAVRHMGAVLDAFEKELFPLLDRKQTR 248

Query: 225 LDMGTPHFQPSTLALTSIDVGN-------PASNVIPARGTARFNIRFNDLHTPESLEAHI 277
           + +     + ST+ + SI  G        P+ NV P       + RF        ++  +
Sbjct: 249 MPVVPEGARRSTMNINSIHGGQTDDYSGLPSPNV-PDSCRLTIDRRFLLEEDVTEVKREV 307

Query: 278 RDVLEEVGGAWE---LALQTSGVAFLTP-----PGALSDIVAAAVEAHTGRTPELSTSGG 329
             +L+ +   WE          +  + P        +   VA  + +  GR PE   S G
Sbjct: 308 TSILDRL--QWERPKFHYNIRDIMEVQPLMTERDAPVVTAVAQGIRSVFGREPEYVISPG 365

Query: 330 TSDARFIK-----DHCPVVEFGLVGASMHKVDENVAVADLLELTAIYRTVLERWFAGA 382
           + D + I        C     G++  + H+ DE V + D++E   +    L+   +G+
Sbjct: 366 SYDQKHIARIGLLHDCIAYGPGILDLA-HRPDEYVGIEDMIESAKVMALGLKVLLSGS 422


Lambda     K      H
   0.318    0.136    0.413 

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: 452
Number of extensions: 31
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: 386
Length of database: 423
Length adjustment: 31
Effective length of query: 355
Effective length of database: 392
Effective search space:   139160
Effective search space used:   139160
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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