GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuB in Shewanella sp. ANA-3

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate 7025740 Shewana3_2890 isocitrate dehydrogenase (RefSeq)

Query= curated2:O27441
         (329 letters)



>lcl|FitnessBrowser__ANA3:7025740 Shewana3_2890 isocitrate
           dehydrogenase (RefSeq)
          Length = 336

 Score =  281 bits (719), Expect = 2e-80
 Identities = 153/335 (45%), Positives = 206/335 (61%), Gaps = 8/335 (2%)

Query: 1   MKSMKIAVIPGDGIGVEVMEAALHILNTLDLDLEFIHADAGDACLKRTGTALPEETLEAV 60
           M    I VIPGDGIG  ++++AL IL+    D E+  ADAG   L++ G  LP+ TLE +
Sbjct: 1   MSKRTITVIPGDGIGPSIIDSALKILDKAGCDFEYEFADAGLTALEKQGELLPQRTLELI 60

Query: 61  GEARATLFGA----AGESAADVIVRLRREFDLFANLRPVKSLPGVPCLYPDLDFVIVREN 116
            + R TL G      GE    + V LR++F L+AN+RPV S  G    Y ++D + VREN
Sbjct: 61  EKNRITLKGPLTTPVGEGFTSINVTLRKKFGLYANVRPVLSFKGTQARYENIDIITVREN 120

Query: 117 TEDLYVGDEEYTPEG---AVAKRIITRTASRRISQFAFQYAQKEGMQKVTAVHKANVLKK 173
           TE +Y G  +   E    A A  I+TR  + +I+ FA++ A+KE  +KVT VHKAN++K 
Sbjct: 121 TEGMYSGHGQKVSEDGTTAEATSIVTRQGAEQIATFAYELARKENRKKVTIVHKANIMKS 180

Query: 174 TDGIFRDEFYKVASEYPQMEATDYYVDATAMYLITQPQEFQTIVTTNLFGDILSDEAAGL 233
           T G+F     +V+  YP ++  +  VDAT M L+  P+ F  IVTTNLFGDILSD  AGL
Sbjct: 181 TSGLFLKVAREVSQRYPDIKTEEMIVDATCMKLVMNPENFDVIVTTNLFGDILSDLCAGL 240

Query: 234 IGGLGLAPSANIGEKNALFEPVHGSAPQIAGKNIANPTAMILTTTLMLKHLNKKQEAQKI 293
           +GGLG+AP ANIG   A+FE VHGSAP IAGKN+ANPT++IL +  ML++L    +A  I
Sbjct: 241 VGGLGMAPGANIGRDAAIFEAVHGSAPDIAGKNLANPTSVILASIQMLEYLGMADKADLI 300

Query: 294 EKALQKTLAEG-LVTPDLGGKLGTMEMAAEIARHL 327
            KA+   + EG   T DLGG  GT +    +   L
Sbjct: 301 RKAVSAVIEEGDRTTRDLGGTHGTTDFTQAVLDRL 335


Lambda     K      H
   0.317    0.134    0.374 

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: 262
Number of extensions: 10
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: 329
Length of database: 336
Length adjustment: 28
Effective length of query: 301
Effective length of database: 308
Effective search space:    92708
Effective search space used:    92708
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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