Alignments for a candidate for aceA in Beijerinckia indica subsp. indica ATCC 9039

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Beijerinckia indica subsp. indica ATCC 9039

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_012383064.1 BIND_RS00235 isocitrate lyase

Query= BRENDA::Q9I0K4
         (531 letters)



>NCBI__GCF_000019845.1:WP_012383064.1
          Length = 530

 Score =  835 bits (2157), Expect = 0.0
 Identities = 412/528 (78%), Positives = 453/528 (85%)

Query: 3   AYQNEIKAVAALKEKNGSSWSAINPEYAARMRIQNRFKTGLDIAKYTAAIMRKDMAEYDA 62
           +YQ++I  V+ L +    +W  IN E   RMR+QNRFKTGLDIAKYTAAIMR+DMA YDA
Sbjct: 2   SYQDQITEVSQLIKSKNGTWDGINAEAVVRMRLQNRFKTGLDIAKYTAAIMRRDMAAYDA 61

Query: 63  DSSVYTQSLGCWHGFIGQQKLISIKKHLKTTNKRYLYLSGWMVAALRSDFGPLPDQSMHE 122
           D++ YTQSLGCWHGFIGQQK+ISIKKH  TT +RYLYLSGWMVAALRS+FGPLPDQSMHE
Sbjct: 62  DTTKYTQSLGCWHGFIGQQKVISIKKHFGTTERRYLYLSGWMVAALRSEFGPLPDQSMHE 121

Query: 123 KTAVSGLIEELYTFLRQADARELDLLFTGLDAARAAGDKAKEAELLAQIDNFETHVVPII 182
           KT+V  LIEELYTFLRQADAREL+ +F  +DAAR AGD AK  ELL Q +N +THV+PII
Sbjct: 122 KTSVPALIEELYTFLRQADARELNDIFRAIDAARKAGDSAKAKELLTQAENHQTHVIPII 181

Query: 183 ADIDAGFGNAEATYLLAKKMIEAGACCIQIENQVSDEKQCGHQDGKVTVPHIDFLAKINA 242
           ADIDAGFGNAEATYLLAKKMIEAGA  +QIENQVSDEKQCGHQDGKVTVPH DFLAK+ A
Sbjct: 182 ADIDAGFGNAEATYLLAKKMIEAGAGALQIENQVSDEKQCGHQDGKVTVPHEDFLAKVRA 241

Query: 243 VRYAFLELGVDDGVIVARTDSLGAGLTKQIAVTNEPGDLGDLYNSFLDCEEISESELGNG 302
            RYAFLELGVDDG++V RTDSLGAGLTKQIAV+++PGDLGD YNSFLD EE+      NG
Sbjct: 242 CRYAFLELGVDDGIVVTRTDSLGAGLTKQIAVSHKPGDLGDQYNSFLDVEEVPAGGGANG 301

Query: 303 DVVIKREGKLLRPKRLASNLFQFRKGTGEDRCVLDCITSLQNGADLLWIETEKPHVGQIK 362
           DV+I R+GKL RPKRL SNLFQFRKGTGEDRCVLD ITSLQNGADLLWIETEKPHV QI 
Sbjct: 302 DVIINRDGKLFRPKRLPSNLFQFRKGTGEDRCVLDSITSLQNGADLLWIETEKPHVEQIA 361

Query: 363 AMVDRIREVIPNAKLVYNNSPSFNWTLNFRQQVFDAFVAEGKDVSAYDRNKLMSVEYDDT 422
            M+DRIR VIPNAKLVYNNSPSFNWT+NFRQQV+DA+   GKDVSAYDR  LM V+YD +
Sbjct: 362 GMMDRIRAVIPNAKLVYNNSPSFNWTINFRQQVYDAWKEAGKDVSAYDRAGLMDVKYDGS 421

Query: 423 ELAKVADEKIRTFQRDGSAHAGIFHHLITLPTYHTAALSTDNLAKGYFADEGMLAYVKGV 482
           +LA  ADEKIRTFQ D S  AGIFHHLITLPTYHTAALSTDNLAK YF ++GML YV  V
Sbjct: 422 DLAAEADEKIRTFQADASKRAGIFHHLITLPTYHTAALSTDNLAKEYFGEQGMLGYVLNV 481

Query: 483 QRQELRQGIACVKHQNMAGSDIGDNHKEYFAGEAALKASGKDNTMNQF 530
           QRQE+RQ IAC KHQNMAGSDIGD+HKEYFAGEAALKA G DNTMNQF
Sbjct: 482 QRQEIRQKIACAKHQNMAGSDIGDDHKEYFAGEAALKAGGADNTMNQF 529


Lambda     K      H
   0.318    0.134    0.388 

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: 888
Number of extensions: 21
Number of successful extensions: 1
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: 531
Length of database: 530
Length adjustment: 35
Effective length of query: 496
Effective length of database: 495
Effective search space:   245520
Effective search space used:   245520
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 25 2024. The underlying query database was built on Jul 25 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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