GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Pseudomonas fluorescens GW456-L13

Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate PfGW456L13_3585 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)

Query= metacyc::G1G01-1343-MONOMER
         (525 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3585
          Length = 525

 Score =  865 bits (2235), Expect = 0.0
 Identities = 432/524 (82%), Positives = 471/524 (89%)

Query: 1   MPLTGNLLIGQRPVTGSRDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRE 60
           M LTGN+LIGQ+ + G+R+AIR IDP T   LEPAY GG+GEHV QACALAW+A D+YR 
Sbjct: 1   MTLTGNMLIGQQAIAGNREAIRGIDPATDLPLEPAYHGGSGEHVEQACALAWSALDSYRA 60

Query: 61  TSLEQRAEFLEAIATQIEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAG 120
           TSLE RAEFLE IA++IEALGD LIDRAV ETGLP+ RIQGERGRTC QLRTFA TVRAG
Sbjct: 61  TSLEARAEFLETIASEIEALGDELIDRAVAETGLPRPRIQGERGRTCQQLRTFALTVRAG 120

Query: 121 EWLDVRIDSALPERQPLPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180
           EWLDVR+DSALPERQPLPR DLRQRQV LGPVAVFGASNFPLAFSVAGGDTASALAAGCP
Sbjct: 121 EWLDVRVDSALPERQPLPRPDLRQRQVPLGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180

Query: 181 VVVKAHSAHPGTSELVGQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFT 240
           V+VKAH AHPGTSELVG+A+A+AVK CGL EGVFSLL+GSGREVGIALV+DPRIKAVGFT
Sbjct: 181 VIVKAHGAHPGTSELVGRALARAVKLCGLHEGVFSLLFGSGREVGIALVTDPRIKAVGFT 240

Query: 241 GSRSGGMALCQAAQARPEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQ 300
           GSRSGG+ALC AAQARPEPIPVYAEMSSINPV LF AALQ+RAEALAQGFVASLTQGAGQ
Sbjct: 241 GSRSGGIALCNAAQARPEPIPVYAEMSSINPVLLFPAALQSRAEALAQGFVASLTQGAGQ 300

Query: 301 FCTNPGLVIARQGPALQRFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAI 360
           FCTNPGLVIARQGP L+RFI +AA  +Q+  AQTMLTPGIF AY+AG+ ALA++ HA+ +
Sbjct: 301 FCTNPGLVIARQGPDLERFIQSAAQLLQRSPAQTMLTPGIFKAYEAGVGALAEHAHAETV 360

Query: 361 TSGQAGQGPNQCQAQLFVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQ 420
             G  G+ PNQCQA LFVTQA  FLADPALQAE+FGAASL+V C  DEQ+RQV EHLEGQ
Sbjct: 361 AVGLKGETPNQCQAHLFVTQASEFLADPALQAEMFGAASLIVQCASDEQIRQVIEHLEGQ 420

Query: 421 LTATLQLDEADIDSARALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTS 480
           LTATL LD+AD++SARALLP LERKAGR+LVNGWPTGVEVCDAMVHGGPFPATSDARTTS
Sbjct: 421 LTATLHLDDADVESARALLPILERKAGRLLVNGWPTGVEVCDAMVHGGPFPATSDARTTS 480

Query: 481 VGTAAILRFLRPVCYQDVPDALLPQALKHGNPLQLRRLLDGKRE 524
           VGTAAILRFLRPVCYQD PDALLP ALKHGNPLQLRRLLDG+RE
Sbjct: 481 VGTAAILRFLRPVCYQDFPDALLPAALKHGNPLQLRRLLDGQRE 524


Lambda     K      H
   0.319    0.134    0.391 

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: 982
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: 525
Length of database: 525
Length adjustment: 35
Effective length of query: 490
Effective length of database: 490
Effective search space:   240100
Effective search space used:   240100
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