GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hcs in Burkholderia phytofirmans PsJN

Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate BPHYT_RS13280 BPHYT_RS13280 2-isopropylmalate synthase

Query= curated2:P05345
         (381 letters)



>FitnessBrowser__BFirm:BPHYT_RS13280
          Length = 572

 Score = 70.5 bits (171), Expect = 1e-16
 Identities = 102/388 (26%), Positives = 159/388 (40%), Gaps = 49/388 (12%)

Query: 9   TTLRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMG--DEEIARIQLVRRQLPD 66
           T LRDG QS         K+ + + L   G   +EV  P+    D    R  +    +PD
Sbjct: 36  TDLRDGNQSLFEPMDAQRKMRMFKTLVQIGFKEIEVAFPSASQTDFNFVRELIEGGHIPD 95

Query: 67  AT---LMTWCRMNALEIRQSADLGIDWVDISIPAS------------DKLRQYKLREPLA 111
                ++T  R + +E    +  G+    + +  +            +K    +L +  A
Sbjct: 96  DVTIEVLTQARDDLIERTFESLRGVPRAIVHLYNATAPEFRKIVFNLEKSGVKELAQNAA 155

Query: 112 VLLERLAMFI---HLAHTLGLKVCIGCEDASRASGQTLRAIAEVAQNAPA--ARLRYADT 166
             ++R+A  +           +V  G E     + +   A+ +V Q  P   A +    T
Sbjct: 156 RTMKRIAATMPETQFTFQYSPEVFSGTE--IEFAKEVCDAVFDVWQPTPEHKAIVNLPAT 213

Query: 167 VGLLDPFTTAAQIS------ALRDVWSGEIEMHAHNDLGMATANTLAAVSAGATSVNTTV 220
           V +  P   A QI       A RD  S  I +H HND G A A    AV AGA  +   +
Sbjct: 214 VEMSTPNIYADQIEWMHRNLARRD--SLIISVHPHNDRGTAVAAAELAVMAGADRIEGCL 271

Query: 221 LGLGERAGNAAAWKPSALGLERCLGVETGVHFSALPALCQRVAEAAQRAIDPQQPLVGEL 280
            G GER GN       AL L    GV+ G+ FS +  + +   E  Q  I P+ P VG+L
Sbjct: 272 FGNGERTGNVDL-VTLALNLYT-QGVDPGLDFSNINEVARTAEECTQLPIHPRHPYVGDL 329

Query: 281 VFTHESGVHVAALLRD----------SESYQSIAPSLMGRSYRLVL--GKHSGRQAVNGV 328
           VFT  SG H  A+ +              Y  I P+ +GR+Y  V+     SG+  +  +
Sbjct: 330 VFTAFSGSHQDAIKKGFAVQKPDAVWEVPYMPIDPADLGRTYDSVIRVNSQSGKGGIAYL 389

Query: 329 FDQMGYHLNAAQINQL--LPAIRRFAEN 354
            +Q GY +   +  Q+    A++RF ++
Sbjct: 390 LEQ-GYGVVLPRRLQVDFSSAVQRFTDD 416


Lambda     K      H
   0.319    0.132    0.384 

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: 370
Number of extensions: 17
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 381
Length of database: 572
Length adjustment: 33
Effective length of query: 348
Effective length of database: 539
Effective search space:   187572
Effective search space used:   187572
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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