GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Bacteroides thetaiotaomicron VPI-5482

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 350735 BT1207 glycerate dehydrogenase (NADH-dependent) (NCBI ptt file)

Query= curated2:Q58424
         (524 letters)



>FitnessBrowser__Btheta:350735
          Length = 318

 Score =  161 bits (408), Expect = 3e-44
 Identities = 101/306 (33%), Positives = 157/306 (51%), Gaps = 20/306 (6%)

Query: 18  LEEVGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEKAEKLKVIGRAGVGVDNI 77
           L+ +GE  +      EE+LE+   A+V++      +  D +    +LK IG    G + +
Sbjct: 21  LKALGECTIYDRTAPEEVLERAAGAEVILTNK-VIINADHMTALPELKYIGVLATGYNVV 79

Query: 78  DVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATASLKRGEWDRKR------ 131
           D   A E+GIIV N P  S+ SVA++    +L   + +   +  + +G W   +      
Sbjct: 80  DTAVAKERGIIVTNIPAYSTASVAQMVFAHILNICQQVQHHSEEVHKGRWTNNKDFCFWD 139

Query: 132 FKGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDP----YIPKEVAESMGVELVDD 187
              IEL  K +G++GLG  G    + A  FGM +          +P E+ +        D
Sbjct: 140 TPLIELRDKKIGLVGLGNTGYTTARVAIGFGMQVYALTSKSHFQLPPEIKKM-------D 192

Query: 188 INELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEG 247
           +++L    D I+LH PLTP+T  ++   ++ALMK NAI++N  RG L++E+ L +AL  G
Sbjct: 193 LDQLFSECDIISLHCPLTPETHELVNARRLALMKPNAILINTGRGPLVNEQDLADALNSG 252

Query: 248 KIRAAALDVFEEEPPK-DNPLLTLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVLRGEL 306
           KI AA +DV   EPP+ DNPLLT  N   TPH   ++ EA++    I    ++  + G  
Sbjct: 253 KIYAAGVDVLSSEPPRADNPLLTAKNCYITPHIAWASTEARERLMNIAISNLQAYISG-T 311

Query: 307 AENVVN 312
            ENVVN
Sbjct: 312 PENVVN 317


Lambda     K      H
   0.316    0.137    0.372 

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: 369
Number of extensions: 16
Number of successful extensions: 5
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: 524
Length of database: 318
Length adjustment: 31
Effective length of query: 493
Effective length of database: 287
Effective search space:   141491
Effective search space used:   141491
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 (21.5 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