GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Caldicellulosiruptor kronotskyensis 2002

Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate WP_013431026.1 CALKRO_RS10670 aconitate hydratase

Query= curated2:O28084
         (416 letters)



>NCBI__GCF_000166775.1:WP_013431026.1
          Length = 643

 Score =  327 bits (837), Expect = 8e-94
 Identities = 175/414 (42%), Positives = 247/414 (59%), Gaps = 2/414 (0%)

Query: 1   MGKTIAEKILSEKS-KSDAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTH 59
           MG T+A+KI+ +   K +   G  +   IDQ   QD T  +A  Q   +G +     R+ 
Sbjct: 1   MGLTVAQKIIKQHLVKGEMIPGKEIAIRIDQTLTQDSTGTMAYLQFEAMGIDRVKTKRSV 60

Query: 60  FFVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADS 119
            ++DH       E ++D  +I   AKK G  F+ PG GI HQ+ +ER+  PG   +G+DS
Sbjct: 61  AYIDHNTLQTGPENADDHLYIQTVAKKYGIYFSKPGNGICHQVHLERFAVPGQTLLGSDS 120

Query: 120 HTCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIG 179
           HT T GGIG  + G G  DVAVA+  G+ +  +P+  +V L G L   V AKD+IL+L+ 
Sbjct: 121 HTPTAGGIGMLAIGAGGLDVAVAMGGGEYYLIMPKIVKVNLKGKLQPWVSAKDIILELLR 180

Query: 180 DLGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGRE 239
            L V G   K  E+ GE  + +++ ER TI NM  E GA   IF SDE T +FL   GRE
Sbjct: 181 RLTVKGGVGKIFEYTGEGVKALSIPERATITNMGAELGATTSIFPSDEVTYEFLKAQGRE 240

Query: 240 GDFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNG 299
            DF E+  D DA+Y++EI +D+SSLVP+ + PH+ DNV  +SE++G +V+QV IG+CTN 
Sbjct: 241 ADFVEILPDPDAQYDEEIEIDLSSLVPLAACPHSPDNVVPVSELKGIKVDQVAIGSCTNS 300

Query: 300 RLSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPC 359
              DL   A+IL+G+ + E V L++ P S++V       G +   V AG  +L   CGPC
Sbjct: 301 SYKDLMKVAKILEGKTIAEHVSLVISPGSKQVLNMLAQNGALASMVAAGARILECACGPC 360

Query: 360 VGIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPR 413
           +G+ Q     G + + T NRNF+GR G P+A+++L SP TAAASA+ GYI DPR
Sbjct: 361 IGMGQAPRTGG-ISLRTFNRNFEGRSGTPSAKVYLVSPETAAASAITGYITDPR 413


Lambda     K      H
   0.318    0.136    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: 653
Number of extensions: 30
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: 416
Length of database: 643
Length adjustment: 35
Effective length of query: 381
Effective length of database: 608
Effective search space:   231648
Effective search space used:   231648
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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