GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Shewanella amazonensis SB2B

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate 6938304 Sama_2423 isocitrate dehydrogenase (RefSeq)

Query= curated2:O27441
         (329 letters)



>FitnessBrowser__SB2B:6938304
          Length = 336

 Score =  280 bits (717), Expect = 3e-80
 Identities = 152/335 (45%), Positives = 209/335 (62%), Gaps = 8/335 (2%)

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

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

Query: 117 TEDLYVG-DEEYTPEGAVAKR--IITRTASRRISQFAFQYAQKEGMQKVTAVHKANVLKK 173
           TE +Y G  ++ + +G+ A+   IITR  + +I+ FA++ A+KEG +KVT VHKAN++K 
Sbjct: 121 TEGMYSGYGQKVSDDGSTAEATSIITRQGAEQITTFAYELARKEGRKKVTIVHKANIMKS 180

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

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

Query: 294 EKALQKTLAEG-LVTPDLGGKLGTMEMAAEIARHL 327
             A+   + EG   T DLGG  GT +    +   L
Sbjct: 301 RNAVAAVIEEGDRTTRDLGGTHGTTDFTQAVLDRL 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: 267
Number of extensions: 8
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.

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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