Aligments for a candidate for iolA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for iolA in Burkholderia phytofirmans PsJN

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BPHYT_RS28150 BPHYT_RS28150 methylmalonate-semialdehyde dehydrogenase

Query= reanno::pseudo5_N2C3_1:AO356_23175
         (500 letters)



>FitnessBrowser__BFirm:BPHYT_RS28150
          Length = 505

 Score =  717 bits (1850), Expect = 0.0
 Identities = 341/493 (69%), Positives = 405/493 (82%)

Query: 7   VGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSL 66
           + H+IDGR  A  + R  +VF+PA G V ARV +A  + VDAAVA+A AAFPAWSE + L
Sbjct: 12  LSHFIDGRRAAGASGRFGDVFDPAQGRVAARVPVANATEVDAAVAAAKAAFPAWSETAPL 71

Query: 67  RRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDF 126
           +R+R+MF+FKELL+ H DELA++I+R+HGK+LSDA GEV RGIEIVE+ACG PNLLKTDF
Sbjct: 72  KRARLMFRFKELLEAHSDELAELITRDHGKLLSDAKGEVVRGIEIVEFACGIPNLLKTDF 131

Query: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186
           +D I GGIDNWNLRQPLGV AGVTPFNFP++VP WM  +A   GN F+LKPSER PSAS+
Sbjct: 132 TDQISGGIDNWNLRQPLGVAAGVTPFNFPMVVPCWMFVMAAACGNTFVLKPSERTPSASI 191

Query: 187 LMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKR 246
            +A L  EAG P GVFNVV G K  VDAL++HPD+ AIS VGSTP+AEYI+ +   +GKR
Sbjct: 192 RLAELFIEAGFPKGVFNVVHGGKAVVDALIEHPDVAAISVVGSTPVAEYIYSESAKRGKR 251

Query: 247 VQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLP 306
           VQALG AKNH++VMPDADLDQA DALI ++YGSAGERCMA S+AVAVG +GDELI +L P
Sbjct: 252 VQALGSAKNHLVVMPDADLDQAVDALIASSYGSAGERCMATSVAVAVGRIGDELIERLAP 311

Query: 307 RIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFF 366
           R+  L+IG G +P  DMGPL++A H+AKV G+IDAGVA GARL+VDGRG  VPG E GFF
Sbjct: 312 RVRSLRIGGGMEPDLDMGPLISAAHRAKVLGYIDAGVAAGARLVVDGRGHSVPGHEAGFF 371

Query: 367 VGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIAR 426
           +G +LFD V  +MSIY++EIFGPVL +VRVPD A+A+AL+NAHE GN VS FT DGG AR
Sbjct: 372 LGGSLFDDVKPDMSIYREEIFGPVLSVVRVPDLASAIALVNAHELGNCVSLFTSDGGAAR 431

Query: 427 AFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPD 486
           AF+R I++GMVGINVP PVP AWHSFGGWKRSLFGDHHAYGEE +RFY+ YKSVMQRWPD
Sbjct: 432 AFSRQIQIGMVGINVPSPVPPAWHSFGGWKRSLFGDHHAYGEEAVRFYTHYKSVMQRWPD 491

Query: 487 SIAKGPEFSMPTA 499
           SIAKG EF+MP A
Sbjct: 492 SIAKGAEFAMPVA 504


Lambda     K      H
   0.320    0.137    0.412 

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: 782
Number of extensions: 23
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: 505
Length adjustment: 34
Effective length of query: 466
Effective length of database: 471
Effective search space:   219486
Effective search space used:   219486
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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Candidates (tab-delimited)
Steps (tab-delimited)
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, or view the source code.

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