GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Dinoroseobacter shibae DFL-12

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate 3607592 Dshi_1001 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)

Query= BRENDA::P9WNX3
         (528 letters)



>FitnessBrowser__Dino:3607592
          Length = 316

 Score =  186 bits (472), Expect = 1e-51
 Identities = 109/304 (35%), Positives = 164/304 (53%), Gaps = 6/304 (1%)

Query: 6   VLIADKLAPSTVAALGDQVEVRWVDG--PDRDKLLAAVPEADALLVRSATTVDAEVLAAA 63
           V+I + +    ++  G +V+V +      DR   L AV  AD ++VR+ T VD   L AA
Sbjct: 5   VVITETIDTRALSRFGPEVDVIYAPELVEDRAACLVAVARADGVIVRNRTQVDRPFLDAA 64

Query: 64  PKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADAS 123
            +L+++   G GLDN+D+ A  ARG+ V  A  +N  S AE+ +   L  +R+   +   
Sbjct: 65  SRLRVIGLLGTGLDNIDMAACAARGISVHPATGANTRSVAEYVITAALMLTRRAFMSTPE 124

Query: 124 LREHTWKRSSFS-GTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQL 182
           ++E  W R     G EI G+ +G+ G G + Q VA+        ++ +DP++ P      
Sbjct: 125 MQEGAWPRGPLGEGGEIAGRKLGLYGCGAVAQAVARLAKPLSMTILGHDPHLGPGHPLWT 184

Query: 183 GIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALA 242
            +  +S  +LLARAD +S+HLP TPET G ID  AL   KPG I++N A G +VD  A+ 
Sbjct: 185 EVTRVSDAELLARADVLSLHLPLTPETRGRIDATALTAMKPGAILINTAHGEIVDARAVC 244

Query: 243 DAITGGHVRAAGLDVFATEP--CTDSPLFE-LAQVVVTPHLGASTAEAQDRAGTDVAESV 299
           DA+  GH+  A LDVF  EP    D+  F  +  +++TPH+   T EA  R      ++V
Sbjct: 245 DALRRGHLGGAALDVFEPEPLGTQDAARFRGVPNLILTPHVAGVTVEADRRVSALTVDNV 304

Query: 300 RLAL 303
           R AL
Sbjct: 305 RAAL 308


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: 388
Number of extensions: 29
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: 528
Length of database: 316
Length adjustment: 31
Effective length of query: 497
Effective length of database: 285
Effective search space:   141645
Effective search space used:   141645
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: 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