GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Salinicoccus carnicancri Crm

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_017548203.1 C792_RS0104225 aconitate hydratase

Query= curated2:O28084
         (416 letters)



>NCBI__GCF_000330705.1:WP_017548203.1
          Length = 644

 Score =  260 bits (664), Expect = 1e-73
 Identities = 144/415 (34%), Positives = 231/415 (55%), Gaps = 2/415 (0%)

Query: 1   MGKTIAEKILSEKSKS-DAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTH 59
           M   +A+K++ E   S +   G+ +  +IDQ   QD T  + + +L  +  +    + + 
Sbjct: 1   MQLNVAQKLIKEHLLSGEMTPGEEIGLKIDQTLTQDATGTMVMLELEAMDLDRVKTEVSA 60

Query: 60  FFVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADS 119
            +VDH          +D  F+   A+K G  ++ PG G+ H + ++    PG   +G+DS
Sbjct: 61  QYVDHNLIQDDYRNPDDHIFLRSAARKFGVHYSRPGNGVSHPVHMQELAIPGKTLLGSDS 120

Query: 120 HTCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIG 179
           HTC  G +G  + G G  DVA+A+A       +P    V+L G LP+ V AKDVIL+++ 
Sbjct: 121 HTCANGCMGMLAMGAGGIDVAMAMAGEAYHVEMPRVMGVKLTGELPEWVSAKDVILEMLR 180

Query: 180 DLGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGRE 239
              V G   + +E++G   +N++  +R  IANM  E GA A +F SD+  ++F+A+ GR 
Sbjct: 181 RHSVKGGVGRIIEYYGPGLDNLSAMDRHVIANMGAELGATATVFPSDDEVKRFMAQEGRG 240

Query: 240 GDFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNG 299
            ++ E+KADE AEY+    +++S LVP+++KP + DNV  ++E+EG  + Q YIG+  N 
Sbjct: 241 DEWVELKADEGAEYDDHDEINLSELVPLIAKPTSPDNVVPVTEIEGEPIYQSYIGSSANP 300

Query: 300 RLSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPC 359
              D  +A+ I++GR +  G+   + P SR++  Q ++ G I   + AGG +   GC  C
Sbjct: 301 GYRDFAIASLIVQGRYIANGISFDINPTSRQLLQQLVENGHIANLLGAGGRMHQAGCNGC 360

Query: 360 VGIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPRE 414
           +G+ Q   A G+  + T  RNF GR G     +FL SP  AAASA+ G I DPR+
Sbjct: 361 IGMGQA-PATGQNSLRTTPRNFPGRSGTKEDSVFLCSPEIAAASALYGVITDPRK 414


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: 637
Number of extensions: 34
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: 644
Length adjustment: 35
Effective length of query: 381
Effective length of database: 609
Effective search space:   232029
Effective search space used:   232029
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.

Links

Downloads

Related tools

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