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

GapMind for catabolism of small carbon sources

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

Align 2-ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate AO353_14870 AO353_14870 ketoglutarate semialdehyde dehydrogenase

Query= metacyc::MONOMER-18709
         (527 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_14870
          Length = 529

 Score =  788 bits (2036), Expect = 0.0
 Identities = 401/523 (76%), Positives = 450/523 (86%)

Query: 1   MTAILGHNFIGGARSAAGTLFLQSLDAASGEALPYRFVQATPEEVDAAAEAAASAYPHYR 60
           M+AI+GHNFIG  RSAAG   L S+DA SGE LPY F QA+ EE+D AA  AA+AYP YR
Sbjct: 1   MSAIIGHNFIGFGRSAAGDHVLHSVDAHSGEPLPYDFSQASAEEIDNAAHFAATAYPIYR 60

Query: 61  QLPASRRAEFLDTIAAELDALDDDFVAIVCRETALPATRIQGERSRTSGQLRLFAEVLRR 120
            LPA+ RA FL+TIA E+DAL DDF+AIVCRETALPA RIQGER+RTSGQLRLFA VLR+
Sbjct: 61  NLPATVRAGFLETIAEEIDALGDDFIAIVCRETALPAARIQGERARTSGQLRLFARVLRQ 120

Query: 121 GDFHGARIDRARPERKPLPRVDLRQCRIGLGPVAVFGASNFPLAFSTAGGDTAAALAAGC 180
           GDF GARIDRA PER+P PR D+RQ RIGLGPVAVFGASNFPLAFSTAGGDTAAALAAGC
Sbjct: 121 GDFLGARIDRALPERQPFPRPDVRQWRIGLGPVAVFGASNFPLAFSTAGGDTAAALAAGC 180

Query: 181 PVVFKAHSGHMATAERVAAAILRAAERTGMPAGVFNMIYGGGVGERLVRHPAIQAVGFTG 240
           PVVFKAHSGHMATAE VAAAI+RAA+R+GMP GVFNMIYG GVGE LV+HPAIQAVGFTG
Sbjct: 181 PVVFKAHSGHMATAELVAAAIIRAAQRSGMPEGVFNMIYGAGVGEALVKHPAIQAVGFTG 240

Query: 241 SLKGGRALCDMAAARAQPIPVFAEMSSINPVVLLPAALKKRGEAVADELSASVVLGCGQF 300
           SLKGGRALCDMAAAR QPIPVFAEMSSINPV+LLPAAL  R  ++A ELSAS+VLG GQF
Sbjct: 241 SLKGGRALCDMAAARPQPIPVFAEMSSINPVLLLPAALAARSASIASELSASIVLGGGQF 300

Query: 301 CTNPGLVIGIRSAQFSAFLERFAARMDDQPAQTMLNTGTLASYEKGLAALHAHPRVRHLA 360
           CTNPGL+IG+RSA FSAF+E+  A+++++P QT+LN+GT  SYE G+  L  HPRV  L+
Sbjct: 301 CTNPGLIIGLRSAAFSAFIEQLTAQINEKPPQTLLNSGTRRSYESGVQRLLEHPRVTRLS 360

Query: 361 GQPQEGRQARPQLFQADVSLLLEGDELLQEEVFGPASVVVEVADHAELKRALHGLHGQLT 420
           G    G Q +PQLF+ADVSLLLEGDE+LQEEVFGPAS+V+EVAD  EL+ AL  LHGQLT
Sbjct: 361 GNLVPGNQVQPQLFKADVSLLLEGDEVLQEEVFGPASIVLEVADERELRLALCALHGQLT 420

Query: 421 ATLIAEAEDLASFADLVPLLEQKAGRLLLNGYPTGVEVCDAMVHGGPYPATSDARGTSVG 480
           ATLIAE +DL   A L+P+LEQKAGRLLLNGYPTGVEVCDAMVHGGPYPATSDARGTSVG
Sbjct: 421 ATLIAEPQDLVLCAQLIPILEQKAGRLLLNGYPTGVEVCDAMVHGGPYPATSDARGTSVG 480

Query: 481 TLAIDRFLRPVCYQNYPDAWLPEALKDGNPLGIARLVDGIVTR 523
           +LAI+RFLRPVCYQN PD  LP+ALK+ NPLGI RLVDG+ TR
Sbjct: 481 SLAIERFLRPVCYQNCPDRLLPDALKNANPLGILRLVDGVNTR 523


Lambda     K      H
   0.321    0.136    0.397 

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: 864
Number of extensions: 25
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: 527
Length of database: 529
Length adjustment: 35
Effective length of query: 492
Effective length of database: 494
Effective search space:   243048
Effective search space used:   243048
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 (21.9 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)
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

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