GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Klebsiella michiganensis M5al

Align D-3-phosphoglycerate dehydrogenase; 3-PGDH; EC 1.1.1.95 (characterized)
to candidate BWI76_RS07875 BWI76_RS07875 dihydrofolate reductase

Query= SwissProt::O08651
         (533 letters)



>FitnessBrowser__Koxy:BWI76_RS07875
          Length = 342

 Score =  167 bits (424), Expect = 4e-46
 Identities = 110/308 (35%), Positives = 163/308 (52%), Gaps = 29/308 (9%)

Query: 33  KQNLSKEELIAELQDCEGLIVRSATKVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKG 92
           K  LS  +LI    D E ++V S  +VT  VI A  +LQV+        N+D +AA  +G
Sbjct: 31  KPKLSAGQLIELAHDAE-VLVTSYDEVTEAVIAACPRLQVIACTRANPVNIDTKAAQARG 89

Query: 93  VLVMNTPNGNSLSAAELTCGMLMCLARQIPQATASMKDGK-------------------- 132
           + V+ TP  N+ +AAELT G+++ LAR IPQ+ A++K G+                    
Sbjct: 90  IRVLYTPGRNADAAAELTLGLMLSLARHIPQSHAALKRGEFTHAENAAQATQSGLRRDVV 149

Query: 133 WD------RKKFMGTELNGKTLGILGLGRIGREVAARMQAFGMKTVGYDPIISPEVAASF 186
           WD       + F G+EL  KTLG++G G IGR VA   +AFGM  +  DP ++ E     
Sbjct: 150 WDVSPQSPYEVFKGSELRNKTLGLIGYGNIGRRVARIARAFGMAVLVVDPFVAAEDINEP 209

Query: 187 GVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDSTFAQCKKGVRVVNCARGGIVDEGALL 246
           G+Q+  LE ++   D +++H    P + GL+N       K G  ++N +R  +VDE AL+
Sbjct: 210 GLQKTTLEGLFREADIVSLHLSSGPHSDGLVNAQLLNSMKPGALLINTSRAAVVDEEALI 269

Query: 247 RALQSGQCAGAALDVFTEEPP-RDRALV-DHENVISCPHLGASTKEAQSRCGEEIAVQFV 304
            AL+ G   GAALDV+  EP  RD   V + +NVI  PH+  +T+E+ ++    IA    
Sbjct: 270 HALRHGPLGGAALDVYHREPLWRDHPFVTEFDNVIITPHIAGATRESIAKHTAMIAADLQ 329

Query: 305 DMVKGKSL 312
             V G+ L
Sbjct: 330 RYVAGEPL 337


Lambda     K      H
   0.318    0.134    0.394 

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: 366
Number of extensions: 21
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: 533
Length of database: 342
Length adjustment: 32
Effective length of query: 501
Effective length of database: 310
Effective search space:   155310
Effective search space used:   155310
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: 51 (24.3 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