GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuB in Klebsiella michiganensis M5al

Align 3-isopropylmalate dehydrogenase; EC 1.1.1.85; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH (uncharacterized)
to candidate BWI76_RS11330 BWI76_RS11330 isocitrate dehydrogenase (NADP(+))

Query= curated2:B0RIP4
         (355 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS11330 BWI76_RS11330 isocitrate
           dehydrogenase (NADP(+))
          Length = 416

 Score =  118 bits (295), Expect = 3e-31
 Identities = 112/401 (27%), Positives = 164/401 (40%), Gaps = 63/401 (15%)

Query: 1   MPRTISLAVVPGDGIGPEVVHEALRVLREAVP----ADVSLDTTQYPFGAGHFLETGQI- 55
           +P    +  + GDGIG +V    L+V+  AV      +  +   +   G       GQ  
Sbjct: 23  VPNNPIIPFIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEVYTGEKSTQVYGQDV 82

Query: 56  -LTDSDLAALAQHDAILLGAVGGDPRDARLAGGIIERGLLLKLRFAFDHYINLRPTALLP 114
            L    L  + ++   + G     P    + GGI  R L + LR   D Y+ LRP     
Sbjct: 83  WLPAETLDLIREYRVAIKG-----PLTTPVGGGI--RSLNVALRQELDLYVCLRPVRYYQ 135

Query: 115 GVASPLAAPGQVDFVVVREGTEGPYAG-------------------NGGVLRRGTEHEIA 155
           G  SP+  P   D V+ RE +E  YAG                     GV +        
Sbjct: 136 GTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSAEADKVIKFLRDEMGVKKIRFPEHCG 195

Query: 156 TEVSVNTAHGVERTVRFAFELAEKRDRKRVTLVHKTNVLTFAGSLWQRTVDRVAAEH--- 212
             +   +  G +R VR A E A   DR  +TLVHK N++ F    ++    ++A E    
Sbjct: 196 IGIKPCSEEGTKRLVRAAIEYAITNDRDSLTLVHKGNIMKFTEGAFKDWGYQLAREEFGG 255

Query: 213 -----------------PDVTVDYLHVDATMIFLVTDPSRFDVIVSDNLFGDIITDLAAA 255
                             ++ V  +  DA +  ++  P+ +DVI   NL GD I+D  AA
Sbjct: 256 ELIDGGPWLKIKNPNTGKEIVVKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAA 315

Query: 256 ISGGIGLAASGNVNPTGAFPSMFEPVHGSAPDIAGQQKADPTAAILSVALLLDHLGLSEA 315
             GGIG+A   N+    A   +FE  HG+AP  AGQ K +P + ILS  ++L H+   EA
Sbjct: 316 QVGGIGIAPGANIGDECA---LFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMQWFEA 372

Query: 316 AARVSAAVSDDLAA--------RATGDAAPRSTAEVGDAIL 348
           A  +       +AA        R    A     +E GDAI+
Sbjct: 373 ADLIVKGTEGAIAAKTVTYDFERLMEGAKLLKCSEFGDAII 413


Lambda     K      H
   0.319    0.136    0.389 

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: 292
Number of extensions: 20
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: 355
Length of database: 416
Length adjustment: 30
Effective length of query: 325
Effective length of database: 386
Effective search space:   125450
Effective search space used:   125450
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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