Aligments for a candidate for dopDH in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for dopDH in Pseudomonas putida KT2440

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate PP_2585 PP_2585 Alpha-ketoglutaric semialdehyde dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_612
         (526 letters)



>FitnessBrowser__Putida:PP_2585
          Length = 526

 Score =  779 bits (2011), Expect = 0.0
 Identities = 394/519 (75%), Positives = 434/519 (83%)

Query: 8   NYIGGARSAAGQTRLQSVDASTGEALPHDFIQATAEEVDAAAKAAAAAYPAYRSLSAVRR 67
           N+I G  S  G   L S+DA TGE LP+ F QAT +EV+AAA+AA  AYP+YRS    +R
Sbjct: 8   NHIAGQLSGHGDVLLHSLDAHTGETLPYAFHQATGDEVEAAAQAAEVAYPSYRSTRPDQR 67

Query: 68  AEFLEAIADELDALGDEFVAVVCRETALPAARIQGERGRTSGQMRLFAKVLRRGDFYGAR 127
           A FL+AIA ELDALGD+F+  V RETALP ARI+GER RTS Q+RLFA+V+RRGDFY AR
Sbjct: 68  AAFLDAIASELDALGDDFIQDVMRETALPEARIRGERSRTSNQLRLFAEVVRRGDFYAAR 127

Query: 128 IDRALPERTPLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGCPVVFKAH 187
           IDRALP+RTPLPRPDLRQYRIG+GPVAVFGASNFPLAFSTAGGDTASALAAGCPVVFKAH
Sbjct: 128 IDRALPQRTPLPRPDLRQYRIGVGPVAVFGASNFPLAFSTAGGDTASALAAGCPVVFKAH 187

Query: 188 SGHMATAEHVADAIIRAAEKTLMPAGVFNMIYGGGVGEWLVKHPAIQAVGFTGSLKGGRA 247
           SGHM TA HVA AI RA   + MPAGVFNMIYG GVGE LVKHPAIQAVGFTGSL+GGRA
Sbjct: 188 SGHMLTAAHVAAAIDRAVTGSGMPAGVFNMIYGAGVGEALVKHPAIQAVGFTGSLRGGRA 247

Query: 248 LCDMAAARPQPIPVFAEMSSINPVIVLPQALETRAESVARDLTASVVQGCGQFCTNPGLV 307
           LCDMAAARPQPIPVFAEMSSINPV+VLPQAL+ R E VA +L ASVV GCGQFCTNPGLV
Sbjct: 248 LCDMAAARPQPIPVFAEMSSINPVVVLPQALQARGEQVATELAASVVLGCGQFCTNPGLV 307

Query: 308 IGIRSPQFTAFTQQVAALIGDQAPQTMLNAGTLQSYGKGLQKLLAHPGIEHLAGRQQQGN 367
           +GIRSP F  F Q + A + DQ PQTMLNAGTL+SY   +Q LLAHPGI+HLAG+ Q GN
Sbjct: 308 VGIRSPHFEHFLQTLVARMADQGPQTMLNAGTLRSYQNAVQHLLAHPGIQHLAGQPQTGN 367

Query: 368 QAQPQLFKADASLLINGDEALQEEVFGPTTVFVEVADQAQLTAALNGLHGQLTATMIGEP 427
           QAQPQLFKAD SLL+NGD  LQEEVFGP TV VEVAD  QL  AL  L GQLTAT+I EP
Sbjct: 368 QAQPQLFKADVSLLLNGDPLLQEEVFGPCTVVVEVADAQQLAEALRHLQGQLTATLIAEP 427

Query: 428 ADFERFSELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVGTLAIDRF 487
            D   F+ L PLLE+K GR+LLNGYPTGVEV D+MVHGGPYPATSDARGTSVGTLAIDRF
Sbjct: 428 DDLRTFASLVPLLERKAGRLLLNGYPTGVEVSDAMVHGGPYPATSDARGTSVGTLAIDRF 487

Query: 488 LRPVCFQNYPDSLLPEPLKNANPLGILRLVDGVPGREAL 526
           LRPVCFQNYPD+LLP+ LKNANPLGI RL++GV  REA+
Sbjct: 488 LRPVCFQNYPDALLPDALKNANPLGIARLLEGVSSREAV 526


Lambda     K      H
   0.319    0.135    0.395 

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: 980
Number of extensions: 33
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: 526
Length of database: 526
Length adjustment: 35
Effective length of query: 491
Effective length of database: 491
Effective search space:   241081
Effective search space used:   241081
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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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