GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Klebsiella michiganensis M5al

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate BWI76_RS10680 BWI76_RS10680 tartrate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>FitnessBrowser__Koxy:BWI76_RS10680
          Length = 372

 Score =  211 bits (536), Expect = 3e-59
 Identities = 137/356 (38%), Positives = 203/356 (57%), Gaps = 30/356 (8%)

Query: 4   RICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAE-AGWETFERRGTSVPEETVEK 58
           RI  I GDGIG EV+P   RVL+A     GL L F   E A  + + + G  +P++   +
Sbjct: 6   RIAAIPGDGIGKEVLPEGVRVLQAAAERWGLALSFEHFEWASCDYYAQHGAMMPDDWRAQ 65

Query: 59  ILSCHATLFGAATSPTRKVP---GFFGAIRYLRRRLDLYANVRPAK-----SRPVPGSRP 110
           + +  A  FGA   P   VP     +G++   RR  D Y N+RP +       P+ G +P
Sbjct: 66  LQTFDAIYFGAVGWPDI-VPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQP 124

Query: 111 G-VDLVIVRENTEGLY------VEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPR 163
           G +D  +VRENTEG Y      V     + +V I ++V +++  +RI R A  +A+ RPR
Sbjct: 125 GDIDFYVVRENTEGEYSALGGHVNPGTEH-EVVIQESVFTRRGVDRILRYAFELAQSRPR 183

Query: 164 KTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTT 223
           +TL  A K+N L ++   +   V+ +A+++P V      +D    + V++PERFDV+V +
Sbjct: 184 RTLTSATKSNGLAISMPFWDQRVEAMAQEYPEVKWDKQHIDILCARFVLQPERFDVVVGS 243

Query: 224 NLLGDILSDLAAGLVGGLGLAPSGNIG-DTT--AVFEPVHGSAPDIAGKGIANPTAAILS 280
           NL GDILSDL     G +G+APS N+  D T  ++FE VHGSAPDI GK IANP A I +
Sbjct: 244 NLFGDILSDLGPACTGTIGIAPSANLNPDRTFPSLFEAVHGSAPDIYGKNIANPIATIWA 303

Query: 281 AAMMLDYLGEKEAAKR-----VEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331
            AMMLD+LG  +A  +     +  A++  +  GP+TPD+ G A+T+   EA+ +A+
Sbjct: 304 GAMMLDFLGNGDARYQAAHDGILAAIEQTIASGPKTPDMQGTASTQQVGEAICQAI 359


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: 322
Number of extensions: 18
Number of successful extensions: 6
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: 372
Length adjustment: 29
Effective length of query: 305
Effective length of database: 343
Effective search space:   104615
Effective search space used:   104615
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