GapMind for catabolism of small carbon sources

 

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

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Pf1N1B4_1109 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1109
         (481 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1109 2-ketoglutaric
           semialdehyde dehydrogenase (EC 1.2.1.26)
          Length = 481

 Score =  949 bits (2454), Expect = 0.0
 Identities = 481/481 (100%), Positives = 481/481 (100%)

Query: 1   VADAKRYDNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWS 60
           VADAKRYDNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWS
Sbjct: 1   VADAKRYDNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWS 60

Query: 61  TSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR 120
           TSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR
Sbjct: 61  TSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR 120

Query: 121 LSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLV 180
           LSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLV
Sbjct: 121 LSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLV 180

Query: 181 PGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSC 240
           PGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSC
Sbjct: 181 PGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSC 240

Query: 241 VSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKF 300
           VSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKF
Sbjct: 241 VSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKF 300

Query: 301 VEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDT 360
           VEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDT
Sbjct: 301 VEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDT 360

Query: 361 EGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSL 420
           EGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSL
Sbjct: 361 EGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSL 420

Query: 421 KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG 480
           KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG
Sbjct: 421 KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG 480

Query: 481 S 481
           S
Sbjct: 481 S 481


Lambda     K      H
   0.318    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: 888
Number of extensions: 13
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: 481
Length of database: 481
Length adjustment: 34
Effective length of query: 447
Effective length of database: 447
Effective search space:   199809
Effective search space used:   199809
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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