Alignments for a candidate for iolA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolA in Burkholderia phytofirmans PsJN

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BPHYT_RS19500 BPHYT_RS19500 methylmalonate-semialdehyde dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_515
         (500 letters)



>FitnessBrowser__BFirm:BPHYT_RS19500
          Length = 512

 Score =  758 bits (1958), Expect = 0.0
 Identities = 362/499 (72%), Positives = 424/499 (84%)

Query: 2   SDAPVVGHYLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWS 61
           + A  + H++NG   +  S RF +VFNPA G+V ARV LA    VDAAVA+A AAFPAWS
Sbjct: 14  TSARALTHFINGKTFEGTSGRFGDVFNPAQGSVSARVPLASVAEVDAAVAAAKAAFPAWS 73

Query: 62  EQSSLRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNL 121
           E + ++R+RV+FKFKELLDRHHDELA++I+REHGKV SDA GEV RGIEIVE+ACG PNL
Sbjct: 74  ETAPIKRARVLFKFKELLDRHHDELAELITREHGKVFSDAKGEVMRGIEIVEFACGIPNL 133

Query: 122 LKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERD 181
           LKTDF+D IGGGIDNWNLRQPLGV AG+TPFNFP+MVP WM P+A+  GN F+LKPSERD
Sbjct: 134 LKTDFTDQIGGGIDNWNLRQPLGVVAGITPFNFPMMVPCWMFPVAIACGNTFVLKPSERD 193

Query: 182 PSASLLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGT 241
           PS S  +A LL EAGLPDGVFNVV GDKVAVDALL HP++ A+SFVGSTPIAEYI+ +GT
Sbjct: 194 PSCSNRLAELLKEAGLPDGVFNVVHGDKVAVDALLVHPEVSALSFVGSTPIAEYIYTEGT 253

Query: 242 AHGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELI 301
            HGKRVQALGGAKNH++VMPDADLDQA DALIGAAYGSAGERCMAIS+AVAVG + DELI
Sbjct: 254 KHGKRVQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGHIADELI 313

Query: 302 AKLLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGA 361
            +L PR+  LKI NG +   +MGPLVTA H+ KV G+ID+GV  GA+L+VDGR  +V G 
Sbjct: 314 ERLTPRVKSLKILNGMESDAEMGPLVTAVHREKVVGYIDSGVEAGAKLVVDGRGHQVSGH 373

Query: 362 EQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRD 421
           E+GFF+G TLFD V+ +M IY++EIFGPVL +VRVPDFA+AV LINA+EF NGVS FT D
Sbjct: 374 EKGFFLGGTLFDNVSTDMKIYREEIFGPVLCVVRVPDFASAVELINANEFANGVSLFTSD 433

Query: 422 GGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVM 481
           GG+ARAF+R I++GMVGINVPIPVPMAWHSFGGWK+SLFGDHHAYGEEG+RFY+RYKS+M
Sbjct: 434 GGVARAFSRQIQIGMVGINVPIPVPMAWHSFGGWKKSLFGDHHAYGEEGVRFYTRYKSIM 493

Query: 482 QRWPDSIAKGPEFSMPTAQ 500
           QRWPDSIAKG EF+MP A+
Sbjct: 494 QRWPDSIAKGAEFTMPVAK 512


Lambda     K      H
   0.321    0.137    0.415 

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: 821
Number of extensions: 27
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: 500
Length of database: 512
Length adjustment: 34
Effective length of query: 466
Effective length of database: 478
Effective search space:   222748
Effective search space used:   222748
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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

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 catabolism of small carbon sources