GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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