GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Klebsiella michiganensis M5al

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate BWI76_RS00585 BWI76_RS00585 dihydrodipicolinate synthase family protein

Query= BRENDA::A9CL94
         (309 letters)



>FitnessBrowser__Koxy:BWI76_RS00585
          Length = 307

 Score =  370 bits (950), Expect = e-107
 Identities = 182/305 (59%), Positives = 232/305 (76%), Gaps = 1/305 (0%)

Query: 3   KRIEGIIPVMITPFR-DGKIDFEGVANLVEWYIANGSDALFAVCQSSEMMFLTLEERVEL 61
           K I GI+PVM+TPF  D +ID+  +A L++WY+  G DALFAVCQSSEM FL+LEERVEL
Sbjct: 2   KTINGIVPVMLTPFAADERIDYPALAKLIDWYLEKGVDALFAVCQSSEMQFLSLEERVEL 61

Query: 62  AAFVKRAAAGRIPVIASGHISEALEDQQKELNAIARTGVDGIVLVTNRMDARQEGGSKFL 121
           A FV +   GRIPVIASGHIS+ +E Q+ EL A+A+TG+D +VLVTN +D R EG   F 
Sbjct: 62  ARFVVQRVNGRIPVIASGHISDDIEAQKAELLAMAQTGIDALVLVTNHLDPRNEGSDVFY 121

Query: 122 DDLGWLLDRLPPNLPLGLYECPAPYRRLMTDAEISFCANSGRFVILKDVSCDLETVKRRV 181
             L  LL+ LP +LPLGLYECPAPYRRL+TD E ++CANSGRFV+LKDVSCDL TV+RRV
Sbjct: 122 AVLNTLLETLPASLPLGLYECPAPYRRLLTDDEFTWCANSGRFVVLKDVSCDLPTVERRV 181

Query: 182 ALTANTPLAIVNANAAIAFDAMKAGSRGFTGVFTNFHPDLYKWLLTEAGRKPELADELSV 241
            L   TPL ++NANAAIA+ A+ AGS+GF+GVFTNFHP+LY WL  E   +  LADEL++
Sbjct: 182 RLAQGTPLNVINANAAIAWPAILAGSQGFSGVFTNFHPELYSWLWREGKNQRALADELAI 241

Query: 242 YLALAAMAEPMGYPKLAKLYHQRLGTINDIESRAVTFDIQERFWAIEPLLDKIIQGTTDF 301
           +L+L A++E +GYPK AK+YHQRLGT + I  R    D+  ++W +  +LD+I  GT  +
Sbjct: 242 FLSLGAVSETLGYPKNAKIYHQRLGTFDSITCRVNKDDVLNKYWGLTVILDQIRAGTEQW 301

Query: 302 RQRIM 306
           RQRI+
Sbjct: 302 RQRIV 306


Lambda     K      H
   0.323    0.138    0.406 

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: 304
Number of extensions: 12
Number of successful extensions: 2
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: 309
Length of database: 307
Length adjustment: 27
Effective length of query: 282
Effective length of database: 280
Effective search space:    78960
Effective search space used:    78960
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 (21.9 bits)
S2: 48 (23.1 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