GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS11330
          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:

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