GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Acidovorax sp. GW101-3H11

Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate Ac3H11_1140 Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)

Query= curated2:Q9WYC7
         (418 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1140
          Length = 980

 Score = 89.4 bits (220), Expect = 5e-22
 Identities = 65/202 (32%), Positives = 94/202 (46%), Gaps = 26/202 (12%)

Query: 60  LFIDHASPSPRKELSNSQKMMR-----EFGKEMGVKVFDA------GDGISHQILAEKYV 108
           + IDH       +L+   +  R     EF K  G++ FD       G GI HQ+  E Y+
Sbjct: 142 IMIDHYGKKNSLDLNMKLEFQRNRERYEFMK-WGMQAFDTFGVVPPGFGIVHQVNLE-YL 199

Query: 109 KPG-----------DLVAGADSHTCTAGGLGAFGTGMGSTDVAIIFGLGQN-WFKVPETI 156
             G           D + G DSHT    G+G  G G+G  +      LGQ  +F  P+ +
Sbjct: 200 ARGVHKRKDGVFYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAAM-LGQPVYFLTPDVV 258

Query: 157 KVVVNGKLQDGVYAKDIILEIARILGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEV 216
              + G+L++GV A D++L +  +L       K +EF G     + + DR TI NMA E 
Sbjct: 259 GFEMTGRLREGVTATDLVLTVTELLRKHKVVGKFVEFFGEGTRTLALPDRATIGNMAPEY 318

Query: 217 GAKAGLMPSDEKTREFLKKMGR 238
           GA  G  P DEKT ++ +  GR
Sbjct: 319 GATMGFFPVDEKTIDYFQGTGR 340



 Score = 40.8 bits (94), Expect = 2e-07
 Identities = 38/135 (28%), Positives = 59/135 (43%), Gaps = 20/135 (14%)

Query: 295 IGTCTNGRLQDLEIALKILEKHGKH------PDVRLIVGPASRKVYMDALEKGIIKKFVE 348
           I +CTN     + +A  +L K          P ++  + P SR V     E G++    +
Sbjct: 494 ITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTEYLSETGLLPYLEK 553

Query: 349 LGAAVIPPGCGPCVGIHMGVLGDGERVLSTQ-----------NRNFKGRMGNPNAEI-YL 396
           LG ++   GC  C+G + G L        TQ           NRNF+ R+ +PN +  +L
Sbjct: 554 LGFSIAGYGCTTCIG-NAGDLTPELNEAITQNDLVCAAVLSGNRNFEARI-HPNLKANFL 611

Query: 397 ASPATAAATAVTGYI 411
           ASP    A A+ G +
Sbjct: 612 ASPPLVVAYAIAGTV 626


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: 845
Number of extensions: 36
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 418
Length of database: 980
Length adjustment: 38
Effective length of query: 380
Effective length of database: 942
Effective search space:   357960
Effective search space used:   357960
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: 54 (25.4 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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