GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Streptacidiphilus oryzae TH49

Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate WP_037570303.1 BS73_RS06160 aconitate hydratase

Query= curated2:Q9WYC7
         (418 letters)



>NCBI__GCF_000744815.1:WP_037570303.1
          Length = 661

 Score =  253 bits (646), Expect = 1e-71
 Identities = 151/416 (36%), Positives = 220/416 (52%), Gaps = 6/416 (1%)

Query: 4   TLAEKIFSEHV--GRDVKAGEIVLARVDIAMAQDGTGPLMINEFRELGFKEVKVPKAFLF 61
           +LA ++ ++H+  GR + AGE +  RVD  + QD TG L++ E   LG    +   +  +
Sbjct: 14  SLAYRLIADHLVEGR-MTAGEEIALRVDQTLTQDATGTLVMQELEALGLDRAQTEVSVQY 72

Query: 62  IDHASPSPRKELSNSQKMMREFGKEMGVKVFDAGDGISHQILAEKYVKPGDLVAGADSHT 121
           +DH      +  +     +R      G+     G+G+SH +  +++  PG  +AG+DSHT
Sbjct: 73  VDHNLLQADERNAEDHAFLRSAAHRYGLWYSKPGNGVSHPVHMQRFGVPGRSLAGSDSHT 132

Query: 122 CTAGGLGAFGTGMGSTDVAIIFGLGQNWFKVPETIKVVVNGKLQDGVYAKDIILEIARIL 181
           C AG LG    G+G  +VA+          +P    + + G+L   V AKD+ILE+ R  
Sbjct: 133 CAAGALGMLAVGVGGLEVALAIAGQPLHLVMPRIRGIRLTGQLPPWVSAKDVILELLRRH 192

Query: 182 GSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFLKKMGREED 241
           G  G     LE+HG  +++++  DR  I+NM  E+GA A + PSD  TR+FL+  GR ED
Sbjct: 193 GVKGGVGWILEYHGPGLDHLSAMDRHVIANMGAELGATASVFPSDRVTRDFLRAQGRGED 252

Query: 242 FRELKADPDAVYETEIEIDATTLEPLVSLPHYVDNVRKVSEVEKEKIKIDQVFIGTCTNG 301
           F  L A PDA Y+   EID +TLEPL++ P    +V  V EVE E+I   Q  IG+  N 
Sbjct: 253 FAMLTAGPDARYDETEEIDLSTLEPLIARPSSPGDVVPVGEVEGEEIA--QSVIGSSANP 310

Query: 302 RLQDLEIALKILEKHGKHPDVRLIVGPASRKVYMDALEKGIIKKFVELGAAVIPPGCGPC 361
            L+D  +A  I+      P V L V P SR++  D    G +   +  GA +   GC  C
Sbjct: 311 GLRDFAVAAGIVAGRQTAPGVSLDVNPTSRELLQDLARSGAVLDLIAAGARLHQAGCLGC 370

Query: 362 VGIHMGVLGDGERVLSTQNRNFKGRMGNPNAEIYLASPATAAATAVTGYITDPRRF 417
           +G+       G   L T  RNF GR G     ++L SP TAA +A+TG ITDPRR+
Sbjct: 371 IGMGQAPAA-GRNSLRTFPRNFPGRSGTEEDAVWLCSPETAAVSALTGRITDPRRW 425


Lambda     K      H
   0.318    0.137    0.395 

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: 610
Number of extensions: 23
Number of successful extensions: 3
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: 418
Length of database: 661
Length adjustment: 35
Effective length of query: 383
Effective length of database: 626
Effective search space:   239758
Effective search space used:   239758
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