GapMind for Amino acid biosynthesis

 

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

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate H281DRAFT_01534 H281DRAFT_01534 tartrate dehydrogenase/decarboxylase / D-malate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>FitnessBrowser__Burk376:H281DRAFT_01534
          Length = 364

 Score =  204 bits (520), Expect = 2e-57
 Identities = 135/346 (39%), Positives = 190/346 (54%), Gaps = 21/346 (6%)

Query: 3   YRICLIEGDGIGHEVIPAARRVLEATG-----LPLEFVEAEAGWETFERRGTSVPEETVE 57
           YRI  I GDGIG EV+PA  +VLEA          EF   + G + + + G  +P + ++
Sbjct: 4   YRIATIPGDGIGKEVVPAGAQVLEALARTTKSFAFEFENFDWGGDYYRKHGVMMPADGLD 63

Query: 58  KILSCHATLFGAATSPTRKVPGFFGAIRY-LRRRLDLYANVRPAK-----SRPVPGSRP- 110
            I    A LFG+A  P          +R  + +  D YANVRP +       P+   +P 
Sbjct: 64  AIRGKDAILFGSAGDPDIADHITLWGLRLKICQGFDQYANVRPTRILPGIDAPLKRCKPE 123

Query: 111 GVDLVIVRENTEGLYVEQERRY-----LDVAIADAVISKKASERIGRAALRIAEGRPRKT 165
            ++ VIVREN+EG Y     R      ++ A   +++++   ERI R A R+A+ RPRK 
Sbjct: 124 DLNWVIVRENSEGEYSGVGGRVHQGHPIEAATDVSIMTRAGVERIMRFAFRLAQSRPRKL 183

Query: 166 LHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTNL 225
           L +  K+N       ++ +   +V+K+FP V     +VD    +++ RP   D IV TNL
Sbjct: 184 LTVITKSNAQRHAMVMWDEIALQVSKEFPDVTWDKELVDASTARMINRPASLDTIVATNL 243

Query: 226 LGDILSDLAAGLVGGLGLAPSGNIGDT---TAVFEPVHGSAPDIAGKGIANPTAAILSAA 282
             DILSDLAA L G LG+AP+GNI       ++FEP+HGSA DI GKG+ANP     S  
Sbjct: 244 HADILSDLAAALAGSLGIAPTGNIDPERRFPSMFEPIHGSAFDIMGKGLANPVGTFWSVV 303

Query: 283 MMLDYLGEKEAAKRVEKAVDLV-LERGPRTPDLGGDATTEAFTEAV 327
           M+L++LGE +AA RV +AV+ V  ++   T DLGG ATT   T AV
Sbjct: 304 MLLEHLGELDAANRVMQAVEAVTADKSLHTGDLGGTATTAQVTAAV 349


Lambda     K      H
   0.319    0.137    0.391 

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: 308
Number of extensions: 20
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: 334
Length of database: 364
Length adjustment: 29
Effective length of query: 305
Effective length of database: 335
Effective search space:   102175
Effective search space used:   102175
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 (21.7 bits)
S2: 49 (23.5 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