Alignments for a candidate for leuC in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Pseudomonas fluorescens FW300-N2E3

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate AO353_21605 AO353_21605 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= curated2:B2V844
         (431 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21605
          Length = 866

 Score =  107 bits (266), Expect = 2e-27
 Identities = 127/473 (26%), Positives = 196/473 (41%), Gaps = 63/473 (13%)

Query: 2   GMTITEKIIAAHAGRDYVEPGELVTVKVDLAIANDITAPLAIKQLEKYGIDKVHDPNKIA 61
           G T+ +K++    G   V PG     K+    + D T P+   +L+    D         
Sbjct: 381 GFTLAQKMVGKACGVAGVRPGTYCEPKMTTVGSQDTTGPMTRDELK----DLACLGFSTD 436

Query: 62  LVMDHF-----FP-PKDIMSAQQIKISRDFAKKMGIKNYFEGQDSGVMHTLLPEKGFVVP 115
           LVM  F     +P P D+ +   +    DF    G  +   G   G++H+ L     ++P
Sbjct: 437 LVMQSFCHTAAYPKPIDVTTHHTLP---DFIMTRGGVSLRPGD--GIIHSWLNR--MLLP 489

Query: 116 GDLVIGADSHTCTYGGIGAFSTGVGSTDIAYIWATGETWLRVPESMKFVFYNKPQKWVGG 175
             +  G DSHT    GI   S   GS  +A+  ATG   L +PES+   F  K Q  V  
Sbjct: 490 DTVGTGGDSHTRFPMGI---SFPAGSGLVAFAAATGVMPLDMPESILVRFKGKMQPGVTL 546

Query: 176 KDFV-----------LTVIGKIGVDGALY-KAMEYQGEAIRALDIDNRLTIANMAIEAGG 223
           +D V           L  + K G   A   + +E +G    +++    L+ A+    A G
Sbjct: 547 RDLVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEGLDNLSIEQAFELSDASAERSAAG 606

Query: 224 ------KSGIIEPDEKTVDWVRKRTNREF--------------------KLYKSDPDAKY 257
                 K  I E     +  +R      +                    +L  +D DA+Y
Sbjct: 607 CTIKLSKESITEYLSSNITLLRWMIGEGYGDARTLERRAQAMEAWIANPELMVADADAEY 666

Query: 258 CCEYEFDASKI-EPVVACPSLPSNVKPVSEVAGTHIDQVFIGSCTNGRLSDLRIAAAILK 316
               E D + I EPV+  P+ P + + +S VAG  ID+VFIGSC    +   R A  +L 
Sbjct: 667 AEIIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMT-NIGHFRAAGKLLD 725

Query: 317 SKKVHPEVRCIVIPASDQIYKQALHEGIIEILADAGCLISTSTCGPCLGGHMGILAEGEV 376
             K     R  + P +     Q   EG   I   AG  +    C  C+G    +     V
Sbjct: 726 QVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVEPNSTV 785

Query: 377 CLSTSNRNFVGRMGHPKSQVYLSSPAVAAASAVLGRIAHPDEVAKY-EEVETL 428
            +STS RNF  R+G   + VYL+S  +A+ +++LGR+   +E   Y +E++T+
Sbjct: 786 -VSTSTRNFPNRLG-DGANVYLASAELASVASILGRLPTVEEYMAYAKEIDTM 836


Lambda     K      H
   0.319    0.137    0.407 

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: 843
Number of extensions: 43
Number of successful extensions: 7
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: 431
Length of database: 866
Length adjustment: 37
Effective length of query: 394
Effective length of database: 829
Effective search space:   326626
Effective search space used:   326626
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis