GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Paraburkholderia bryophila 376MFSha3.1

Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate H281DRAFT_05213 H281DRAFT_05213 gluconate 2-dehydrogenase

Query= uniprot:Q5JGC4
         (304 letters)



>FitnessBrowser__Burk376:H281DRAFT_05213
          Length = 321

 Score =  200 bits (509), Expect = 3e-56
 Identities = 122/287 (42%), Positives = 164/287 (57%), Gaps = 7/287 (2%)

Query: 23  EVVYEEYPDEDRLVELVKDVDAIIVRSKPKVTRKVIEAAPKLKVIGRAGVGLDNIDLKAA 82
           EVV  +    D  V  ++D D  I  S  K+T  ++E A +LK +    VG D  D+   
Sbjct: 23  EVVQVDPAQHDAFVAALRDADGGIGASV-KITPAMLEGATRLKALSTISVGFDQFDVADL 81

Query: 83  EERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADRKMREGVWAKK---QCMGIELEG 139
             RGI + ++P   + S A+    LI A AR++      ++ G W +       G++++G
Sbjct: 82  TRRGIVLAHTPDVLTESTADTVFSLILASARRVVELAAWVKAGQWQQSIGPAQFGVDVQG 141

Query: 140 KTIGVVGFGRIGYQVAKIANALG--MKVLFYDPYPNEERAKEVGGKFADLETLLKESDVV 197
           KT+G+VG GRIG  VA+ A ALG  MKVL+ +   N E  +  G +  +L  LL  +D V
Sbjct: 142 KTLGIVGLGRIGGAVARRA-ALGFNMKVLYTNRSANREAEEAYGARRVELPELLANADFV 200

Query: 198 TLHVPLVDATYHLINEERLKLMKPTAILINAARGAVVDTDALVKALQEGWIAGAGLDVFE 257
            L VPL   T H+I  + L  MK +AILINA+RGA VD  AL++ALQ G I GAGLDVFE
Sbjct: 201 CLQVPLTPQTRHMIGAKELSSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFE 260

Query: 258 EEPLPADHPLTKLDNVVLTPHIGASTVEAQMRAGVEVAEKIVEALKG 304
            EPLPAD PL KL NVV  PHIG++T E +       AE +V AL G
Sbjct: 261 TEPLPADSPLLKLANVVALPHIGSATRETRHAMARNAAENLVAALNG 307


Lambda     K      H
   0.317    0.136    0.378 

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: 249
Number of extensions: 8
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: 304
Length of database: 321
Length adjustment: 27
Effective length of query: 277
Effective length of database: 294
Effective search space:    81438
Effective search space used:    81438
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: 48 (23.1 bits)

This GapMind analysis is from Jul 25 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