GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Klebsiella michiganensis M5al

Align fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate BWI76_RS00790 BWI76_RS00790 bifunctional aspartokinase II/homoserine dehydrogenase II

Query= ecocyc::ASPKINIIHOMOSERDEHYDROGII-MONOMER
         (810 letters)



>FitnessBrowser__Koxy:BWI76_RS00790
          Length = 810

 Score = 1482 bits (3836), Expect = 0.0
 Identities = 741/810 (91%), Positives = 778/810 (96%)

Query: 1   MSVIAQAGAKGRQLHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINW 60
           MSVIAQAGAKGRQLHKFGGSSLAD KCYLRVAGIM EYSQ  DMMVVSAAGSTTNQLI+W
Sbjct: 1   MSVIAQAGAKGRQLHKFGGSSLADAKCYLRVAGIMTEYSQAGDMMVVSAAGSTTNQLISW 60

Query: 61  LKLSQTDRLSAHQVQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLDSGINDA 120
           LKLSQTDRLSAHQVQQ+LRRYQ DLISGLL  + AD+LI+ F+ DLERLA LLD G+ DA
Sbjct: 61  LKLSQTDRLSAHQVQQSLRRYQMDLISGLLSPDAADTLIATFIQDLERLAGLLDGGVTDA 120

Query: 121 VYAEVVGHGEVWSARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLL 180
           VYAEVVGHGEVWSARLM+AVLN  G+ AAWLDAR FLRAER+ QPQVDEGLSYPLLQQL+
Sbjct: 121 VYAEVVGHGEVWSARLMAAVLNHLGVEAAWLDARSFLRAERSPQPQVDEGLSYPLLQQLM 180

Query: 181 VQHPGKRLVVTGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADP 240
            QHP KRLVVTGFISRNNAGETVLLGRNGSDYSATQIGALAG SRVTIWSDVAGVYSADP
Sbjct: 181 AQHPNKRLVVTGFISRNNAGETVLLGRNGSDYSATQIGALAGASRVTIWSDVAGVYSADP 240

Query: 241 RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIER 300
           RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSGS+IDLQLRCSYTPDQGSTRIER
Sbjct: 241 RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSDIDLQLRCSYTPDQGSTRIER 300

Query: 301 VLASGTGARIVTSHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLL 360
           VLASGTGARIVTSHDDVCLIEFQVP  QDFKLAHKE+D ILKRAQ+RPLAVGVH DR+LL
Sbjct: 301 VLASGTGARIVTSHDDVCLIEFQVPGGQDFKLAHKELDAILKRAQLRPLAVGVHADRKLL 360

Query: 361 QFCYTSEVADSALKILDEAGLPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPV 420
           QFCYTSEVADSALK+LDEAGLPGELRLRQ LALVAMVGAGVTRNPLHCHRFWQQLKGQPV
Sbjct: 361 QFCYTSEVADSALKLLDEAGLPGELRLRQKLALVAMVGAGVTRNPLHCHRFWQQLKGQPV 420

Query: 421 EFTWQSDDGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFARE 480
           EFTWQS++GISLVAVLR GPTESLIQGLHQS+FRAEKRIGLVLFGKGNIGSRWLELFARE
Sbjct: 421 EFTWQSEEGISLVAVLRAGPTESLIQGLHQSLFRAEKRIGLVLFGKGNIGSRWLELFARE 480

Query: 481 QSTLSARTGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPY 540
           Q+TLSARTGFEF+LAGVVDSRRSLL+Y+GLDASRALAFFNDEA+EQDEESLFLWMRAHPY
Sbjct: 481 QTTLSARTGFEFILAGVVDSRRSLLNYEGLDASRALAFFNDEAIEQDEESLFLWMRAHPY 540

Query: 541 DDLVVLDVTASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYN 600
           DDLVVLDVTAS QLADQYLDFASHGFHVISANKLAGAS S+KYRQIHDAFEKTGRHWLYN
Sbjct: 541 DDLVVLDVTASAQLADQYLDFASHGFHVISANKLAGASSSSKYRQIHDAFEKTGRHWLYN 600

Query: 601 ATVGAGLPINHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLT 660
           ATVGAGLP+NHTVRDLIDSGDTIL++SGIFSGTLSWLFLQFDG+VPFT+LVDQAWQQGLT
Sbjct: 601 ATVGAGLPVNHTVRDLIDSGDTILALSGIFSGTLSWLFLQFDGTVPFTDLVDQAWQQGLT 660

Query: 661 EPDPRDDLSGKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNE 720
           EPDPR DLSGKDVMRKLVILAREAGY+IEPDQVRVESLVPAHCE GS+DHFFENG+ LN+
Sbjct: 661 EPDPRVDLSGKDVMRKLVILAREAGYDIEPDQVRVESLVPAHCEEGSVDHFFENGEALND 720

Query: 721 QMVQRLEAAREMGLVLRYVARFDANGKARVGVEAVREDHPLASLLPCDNVFAIESRWYRD 780
           QM+QRLEAAREMGLVLRYVARFDANGKARVGVEAVRE+HPLA+LLPCDNVFAIESRWYRD
Sbjct: 721 QMLQRLEAAREMGLVLRYVARFDANGKARVGVEAVREEHPLAALLPCDNVFAIESRWYRD 780

Query: 781 NPLVIRGPGAGRDVTAGAIQSDINRLAQLL 810
           NPLVIRGPGAGRDVTAGAIQSDINRLAQLL
Sbjct: 781 NPLVIRGPGAGRDVTAGAIQSDINRLAQLL 810


Lambda     K      H
   0.320    0.135    0.397 

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: 2072
Number of extensions: 50
Number of successful extensions: 1
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: 810
Length of database: 810
Length adjustment: 41
Effective length of query: 769
Effective length of database: 769
Effective search space:   591361
Effective search space used:   591361
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: 56 (26.2 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