GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Lentibacillus jeotgali Grbi

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_010529220.1 ON01_RS01390 aconitate hydratase

Query= curated2:O28084
         (416 letters)



>NCBI__GCF_000224785.1:WP_010529220.1
          Length = 651

 Score =  248 bits (634), Expect = 3e-70
 Identities = 141/414 (34%), Positives = 222/414 (53%), Gaps = 2/414 (0%)

Query: 1   MGKTIAEKILSEKSKS-DAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTH 59
           M   I +K++ +   + +  +G+ +  +IDQ   QD T  L + +L  +  +    + + 
Sbjct: 1   MPLNITQKLIKDHLVTGEMTSGEEIGLKIDQTLTQDATGTLVMLELEAMELDQAKTEVSA 60

Query: 60  FFVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADS 119
            +VDH       +  +D  F+    ++ G  F+ PG G+ H + ++R  KPG   +G+DS
Sbjct: 61  QYVDHNLIQEDSKNPDDHLFLQSATERFGLYFSRPGNGVSHPVHMQRLAKPGKTLLGSDS 120

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

Query: 180 DLGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGRE 239
              V G     +E+ G   EN++  +R  IANM  E GA   +F SD+  ++FL    RE
Sbjct: 181 RHDVKGGVGSVIEYFGPGVENLSAMDRHVIANMGAELGATGTVFPSDKEVKRFLKAQDRE 240

Query: 240 GDFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNG 299
            D+ E+ AD+ A Y+    +D+S L P+++KP +  NV  + E+ GT + Q Y+G+  N 
Sbjct: 241 DDWIELTADKGAAYDILEEVDLSELEPLIAKPSSPGNVVAVRELAGTPIYQSYVGSSANP 300

Query: 300 RLSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPC 359
              D  +AA I+ G  + +GV   + P SR++    + +  I   ++AG  +   GC  C
Sbjct: 301 GYRDFAIAAEIVNGMNIADGVSFDINPTSRQMLTDLVQESHIASLLQAGARMHQAGCNGC 360

Query: 360 VGIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPR 413
           +G+ Q   A G   + T  RNF GR G     +FL SP TAAASA+ G I DPR
Sbjct: 361 IGMGQA-PATGRNSLRTTPRNFPGRSGTREDSVFLCSPETAAASALTGQITDPR 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: 611
Number of extensions: 33
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: 651
Length adjustment: 35
Effective length of query: 381
Effective length of database: 616
Effective search space:   234696
Effective search space used:   234696
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