GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Pseudomonas fluorescens FW300-N1B4

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Pf1N1B4_3385 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3385
          Length = 526

 Score =  819 bits (2116), Expect = 0.0
 Identities = 409/526 (77%), Positives = 451/526 (85%)

Query: 1   MNQILGHNYIGGARSAAGQTRLQSVDASTGEALPHDFIQATAEEVDAAAKAAAAAYPAYR 60
           M  +LGHNYIGG RSA G  +LQS+DASTG+ALP  F QAT  EVDAAAKAAAAAYP YR
Sbjct: 1   MTTLLGHNYIGGGRSANGTLQLQSLDASTGDALPGTFFQATEAEVDAAAKAAAAAYPVYR 60

Query: 61  SLSAVRRAEFLEAIADELDALGDEFVAVVCRETALPAARIQGERGRTSGQMRLFAKVLRR 120
           +LSA +RA FL+AIADE+DALG++F+A VCRETALPA RIQGER RTSGQMRLFAKVLRR
Sbjct: 61  NLSAEKRARFLDAIADEIDALGEDFIATVCRETALPAGRIQGERARTSGQMRLFAKVLRR 120

Query: 121 GDFYGARIDRALPERTPLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGC 180
           GDFYGARIDRALP+R PLPRPDLRQYRI LGPVAVFGASNFPLAFSTAGGDTASALAAGC
Sbjct: 121 GDFYGARIDRALPDRQPLPRPDLRQYRIALGPVAVFGASNFPLAFSTAGGDTASALAAGC 180

Query: 181 PVVFKAHSGHMATAEHVADAIIRAAEKTLMPAGVFNMIYGGGVGEWLVKHPAIQAVGFTG 240
           PVVFKAHSGHMATAE VADAIIRAAEKT MPAGV+NMIYGGGVGEWLVKHPAIQAVGFTG
Sbjct: 181 PVVFKAHSGHMATAEWVADAIIRAAEKTEMPAGVYNMIYGGGVGEWLVKHPAIQAVGFTG 240

Query: 241 SLKGGRALCDMAAARPQPIPVFAEMSSINPVIVLPQALETRAESVARDLTASVVQGCGQF 300
           SLKGG AL  MAA RPQPIPVFAEMSSINPV +LP+AL  R E +   L  SV  GCGQF
Sbjct: 241 SLKGGNALSHMAATRPQPIPVFAEMSSINPVFLLPEALAVRCEQIGAQLAGSVTLGCGQF 300

Query: 301 CTNPGLVIGIRSPQFTAFTQQVAALIGDQAPQTMLNAGTLQSYGKGLQKLLAHPGIEHLA 360
           CTNPGLVIG+RSPQF+ F +   A +  Q PQTMLNAG L SY KGL +L  HPG+ HLA
Sbjct: 301 CTNPGLVIGLRSPQFSTFLEMFCASMNQQPPQTMLNAGALASYSKGLVELHEHPGLTHLA 360

Query: 361 GRQQQGNQAQPQLFKADASLLINGDEALQEEVFGPTTVFVEVADQAQLTAALNGLHGQLT 420
           G+ QQGNQAQPQ+F+AD SLL+ GDE LQEEVFGPTT+ +EV D+AQLTAAL+GL GQLT
Sbjct: 361 GKPQQGNQAQPQVFQADVSLLLKGDELLQEEVFGPTTIVIEVEDRAQLTAALHGLRGQLT 420

Query: 421 ATMIGEPADFERFSELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSVG 480
           AT+IGE  +   +  L  LL++KVGRILLNGYPTGVEVC++MVHGGPYPATSD+RGTSVG
Sbjct: 421 ATLIGEADELLEYRWLAELLQEKVGRILLNGYPTGVEVCEAMVHGGPYPATSDSRGTSVG 480

Query: 481 TLAIDRFLRPVCFQNYPDSLLPEPLKNANPLGILRLVDGVPGREAL 526
           TLAIDRFLRPVCFQNYPD+LLP+ L+NANPLGI RLVDG   + AL
Sbjct: 481 TLAIDRFLRPVCFQNYPDALLPQALQNANPLGIRRLVDGEVSQLAL 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: 947
Number of extensions: 30
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