GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Phaeobacter inhibens BS107

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate GFF1354 PGA1_c13710 diaminopimelate decarboxylase-like protein

Query= curated2:O27390
         (428 letters)



>FitnessBrowser__Phaeo:GFF1354
          Length = 828

 Score =  159 bits (402), Expect = 3e-43
 Identities = 128/418 (30%), Positives = 204/418 (48%), Gaps = 33/418 (7%)

Query: 22  ELADEYGTPLYVIDEMRIRENYRRLYRAFSGEYSRFQVFYACKANTNLAVMRILEEEGSG 81
           E+A   GTP Y+ D   +R   RRL  A      +   FY+ K+N NL+V R+L   G+G
Sbjct: 15  EIATTAGTPFYLYDASVLR---RRL-DALRAALPQVDFFYSLKSNPNLSVTRVLHGHGAG 70

Query: 82  IDAVSPGEIYTALMAGFDPDRILYTGNNVRDDELQFALDSGVR-INVDSRSQLLRLSEIA 140
            +  S  E+ T+L AG  P+RIL  G    + EL  A++ G++ I V+S  +L ++  +A
Sbjct: 71  CEVSSLLELETSLQAGATPERILMVGPGKSETELTRAIELGIKAIVVESAYELTQIDALA 130

Query: 141 PEGLR---ISFRVNPLVGAGHHEHCITGGEMSKFGVMEREAPEVYRMAMDLG-FEPVGIH 196
            +  R   I+ RVNP   AG  +  ++G   ++FG+ + E P+V + A         G+H
Sbjct: 131 RQQGRVQNIALRVNPDFHAGGAKLNMSG-RPTQFGIDQSELPDVLKQAEGCAQLRLCGLH 189

Query: 197 AHIGSGILDPEPFMLAVETLMDIAGRVHEATGVEFEFIDFGGGLGIPYTPEEEPLDIDEF 256
           A++G+ IL  E  +  V  ++++A  V  +  V  +F+D GGG GIPY   E  LD+D  
Sbjct: 190 AYMGTRILTHETVVANVGNILNLATEVVSSLKVPLDFVDVGGGFGIPYYDGETELDLDAL 249

Query: 257 ASKITGLFKDKLSEYGLGRP--MMCLEPGRYIVGDASYLLTRVNTIKESY-RKFAGVDAG 313
              +T L    +  +G   P   + +E GRY+ G +   +TRV   K S    FA  D G
Sbjct: 250 GQAVTPL----VQSFGTTHPKTRVVIELGRYLSGPSGQFVTRVQQTKSSKGEHFAVCDGG 305

Query: 314 FNTLLRPAMYGSYHHILVAERPL-----------DEPSEKMDVAGNVCESGDLFARDRQL 362
            N  +  A  G     L    P+           DE ++   + G +C   D+  +   +
Sbjct: 306 SNVHVAAAGQG----FLRKNFPIRLLRDGKAEIDDEAAQPWTLTGPLCTPQDVIGKSVLM 361

Query: 363 PEINEGDVLAIMNAGAYSFSMSS-QYNSRPRPAEVLVREGKVDVVRERETFSDLLRGQ 419
                GD+++I  +GAY  + S   +     PAEV++   ++ +VR R+T    L GQ
Sbjct: 362 ATPQVGDLISIGQSGAYGPTASPVNFLGFGAPAEVMIDGTELRLVRSRDTVEARLAGQ 419


Lambda     K      H
   0.320    0.140    0.408 

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: 802
Number of extensions: 37
Number of successful extensions: 7
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: 428
Length of database: 828
Length adjustment: 37
Effective length of query: 391
Effective length of database: 791
Effective search space:   309281
Effective search space used:   309281
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 (21.8 bits)
S2: 53 (25.0 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