GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Echinicola vietnamensis KMM 6221, DSM 17526

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate Echvi_1427 Echvi_1427 amidohydrolase

Query= curated2:B7HMV1
         (376 letters)



>FitnessBrowser__Cola:Echvi_1427
          Length = 397

 Score =  202 bits (514), Expect = 1e-56
 Identities = 120/367 (32%), Positives = 196/367 (53%), Gaps = 11/367 (2%)

Query: 3   VSKFVQIRRDLHKIPEIGFKEWKTQRYILDYIGTLSNEHVEVKVWRTGVIVKVKGKNP-E 61
           +++ + IRR +H  PE+ F+E +T  ++  ++  +   +++ K   TG++  ++GKNP +
Sbjct: 14  LNQTIAIRRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRKA-NTGLVALIEGKNPSK 72

Query: 62  KVIGYRADIDGLPITEETGYEFASVHEGMMHACGHDLHTT--IGLGLLTAAVTERIDDDL 119
           KVI  RAD+D LPI E+    + S  EG+MHACGHD+HT+  +G   +  AV ++ +  +
Sbjct: 73  KVIALRADMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASILHAVKDQFEGTV 132

Query: 120 VFLFQPAEEG-PGGALPMLESEELKEWKPNIILGLHIAPEYPVGTIATKEGLLFANTSEL 178
             +FQP EE  PGGA  M++ + L+  +P+ I+G H+ P    G +  ++G+  A+  EL
Sbjct: 133 KLIFQPGEEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGFRKGMYMASADEL 192

Query: 179 YVDLKGKGGHAAYPHTANDMIVAASHLVTQLQSVISRNVNPLDSAVITIGKITGGTVQNI 238
           Y+ + GKGGH A P T  D ++ ASH++  LQ VISRN +P   +V++ G+I      N+
Sbjct: 193 YLKVIGKGGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLSFGRIEALGATNV 252

Query: 239 IAEKSRLEGTIRTLSVESMSRVKSRIEAIVAGIEASFQCEAIIDYGAMYHQVYNHEALT- 297
           I  +  ++GT RTL     +    ++  I  GI          +    Y  + N   LT 
Sbjct: 253 IPNEVNIQGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKGYPFLQNAPELTD 312

Query: 298 REFMQFVSEQTDMKVITCTEAMTGEDFGYMLQEIPGFMFWLGVNSE-----YGLHHAKLK 352
           R +    +   +  V      M  EDF Y  QE+ G  + LG+ +E      G+H     
Sbjct: 313 RAYKAAQAYLGEENVEDLDIWMAAEDFSYYTQEMDGCFYRLGIRNEEKGITSGVHTPTFD 372

Query: 353 PDEEAIE 359
            DE A+E
Sbjct: 373 IDESALE 379


Lambda     K      H
   0.319    0.136    0.400 

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: 372
Number of extensions: 22
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: 376
Length of database: 397
Length adjustment: 30
Effective length of query: 346
Effective length of database: 367
Effective search space:   126982
Effective search space used:   126982
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Aug 03 2021. The underlying query database was built on Aug 03 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