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_010530341.1 ON01_RS07160 aconitate hydratase

Query= curated2:O28084
         (416 letters)



>NCBI__GCF_000224785.1:WP_010530341.1
          Length = 650

 Score =  249 bits (637), Expect = 1e-70
 Identities = 143/411 (34%), Positives = 220/411 (53%), Gaps = 5/411 (1%)

Query: 3   KTIAEKILSEKSKSDAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTHFFV 62
           K I + ++S + K  A  G     +IDQ   QD T  + + +L  +G +    + +  +V
Sbjct: 8   KLIKDHLVSGEMKPGAEIG----LQIDQTLTQDATGTMVMLELEAMGLDYAKTEASAQYV 63

Query: 63  DHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADSHTC 122
           DH       +  +D  F+   A++ G  F+ PG G+ H + ++R   PG   +G+DSHTC
Sbjct: 64  DHNLIQEDNKNPDDHLFLESAAQRFGLHFSRPGNGVSHPVHMQRLAIPGKTLLGSDSHTC 123

Query: 123 TYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIGDLG 182
             G +G  + G G  DVA+AI     + ++PE   V+L G LP  V AKDVIL+++    
Sbjct: 124 ANGCMGMLAMGAGGIDVAMAITGEPIYIKMPEVMGVKLTGKLPDWVSAKDVILEMLRRHD 183

Query: 183 VDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGREGDF 242
           V G   K +E++G   +++T  +R  IANM  E GA A +F SD   ++FL+   RE D+
Sbjct: 184 VKGGVGKIIEYYGPGLDDLTAMDRHVIANMGAELGATATVFPSDNEVKRFLSMQDRENDW 243

Query: 243 REVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNGRLS 302
            E+ AD +A Y+    +++S L P+V+KP +  NV    E+ GT + Q YIG+  N    
Sbjct: 244 VELTADNNAAYDIHEEINLSELEPLVAKPSSPGNVVPARELAGTPIYQSYIGSSANPGYR 303

Query: 303 DLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPCVGI 362
           D  +AA I+K R +  GV   + P SR++    + +  I   +++G  +   GC  C+G+
Sbjct: 304 DFAIAAEIVKDRNIATGVSFDINPTSRQMLTNLVKEMHIASLLQSGARLHQAGCNGCIGM 363

Query: 363 HQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPR 413
            Q   A G   + T  RNF GR G     +FL+SP TAA SA+ G I DPR
Sbjct: 364 GQA-PASGRNSLRTTPRNFPGRSGTKEDSVFLSSPETAAVSALTGEITDPR 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: 616
Number of extensions: 29
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: 650
Length adjustment: 35
Effective length of query: 381
Effective length of database: 615
Effective search space:   234315
Effective search space used:   234315
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