GapMind for Amino acid biosynthesis

 

Aligments for a candidate for serB in Pedobacter sp. GW460-11-11-14-LB5

Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 3.1.3.3 (characterized, see rationale)
to candidate CA265_RS22635 CA265_RS22635 phosphoserine phosphatase

Query= uniprot:A0A1X9ZBA8_9SPHI
         (433 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS22635 CA265_RS22635
           phosphoserine phosphatase
          Length = 433

 Score =  861 bits (2225), Expect = 0.0
 Identities = 433/433 (100%), Positives = 433/433 (100%)

Query: 1   MPKQKAYYIIDFDSTFTQVEALDELARISLKNHPDKEAIFQKIEDYTNFAMEGKLSFSES 60
           MPKQKAYYIIDFDSTFTQVEALDELARISLKNHPDKEAIFQKIEDYTNFAMEGKLSFSES
Sbjct: 1   MPKQKAYYIIDFDSTFTQVEALDELARISLKNHPDKEAIFQKIEDYTNFAMEGKLSFSES 60

Query: 61  LAQRVKLLEANEDHLKQLIKHLKKKVSTSFSRNAEFFKKHADEVLIVSGGFKEFITPVVS 120
           LAQRVKLLEANEDHLKQLIKHLKKKVSTSFSRNAEFFKKHADEVLIVSGGFKEFITPVVS
Sbjct: 61  LAQRVKLLEANEDHLKQLIKHLKKKVSTSFSRNAEFFKKHADEVLIVSGGFKEFITPVVS 120

Query: 121 QYHIKKENIYANTFVTTGDGKIIDYDHANPLSEEGGKVKLLQHLKLEGELFGIGDGYSDF 180
           QYHIKKENIYANTFVTTGDGKIIDYDHANPLSEEGGKVKLLQHLKLEGELFGIGDGYSDF
Sbjct: 121 QYHIKKENIYANTFVTTGDGKIIDYDHANPLSEEGGKVKLLQHLKLEGELFGIGDGYSDF 180

Query: 181 QLRESGIINKFFAFTENIARESIVSKADHVTPSFDEFLYVNDLPRAISYPKNRILCLVIG 240
           QLRESGIINKFFAFTENIARESIVSKADHVTPSFDEFLYVNDLPRAISYPKNRILCLVIG
Sbjct: 181 QLRESGIINKFFAFTENIARESIVSKADHVTPSFDEFLYVNDLPRAISYPKNRILCLVIG 240

Query: 241 DVDPLTIAILKNDGLSIRHKTSFEDKYVKDVGIILLADGEKINKEQLKNAAKLKTIGYLG 300
           DVDPLTIAILKNDGLSIRHKTSFEDKYVKDVGIILLADGEKINKEQLKNAAKLKTIGYLG
Sbjct: 241 DVDPLTIAILKNDGLSIRHKTSFEDKYVKDVGIILLADGEKINKEQLKNAAKLKTIGYLG 300

Query: 301 NAKNKIDLDLCTKQGIVVFDDPKNNPRNIDFIPKRVADFMNTGATYLSSNFPNLQLPKIE 360
           NAKNKIDLDLCTKQGIVVFDDPKNNPRNIDFIPKRVADFMNTGATYLSSNFPNLQLPKIE
Sbjct: 301 NAKNKIDLDLCTKQGIVVFDDPKNNPRNIDFIPKRVADFMNTGATYLSSNFPNLQLPKIE 360

Query: 361 KSHRLIHIHKNVPGIMAKINTVFAKHDINIVSQFLMTNPEIGYAITDINAEYDKQLFKSL 420
           KSHRLIHIHKNVPGIMAKINTVFAKHDINIVSQFLMTNPEIGYAITDINAEYDKQLFKSL
Sbjct: 361 KSHRLIHIHKNVPGIMAKINTVFAKHDINIVSQFLMTNPEIGYAITDINAEYDKQLFKSL 420

Query: 421 KKIEHTIKFRVLY 433
           KKIEHTIKFRVLY
Sbjct: 421 KKIEHTIKFRVLY 433


Lambda     K      H
   0.319    0.138    0.389 

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: 882
Number of extensions: 18
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: 433
Length of database: 433
Length adjustment: 32
Effective length of query: 401
Effective length of database: 401
Effective search space:   160801
Effective search space used:   160801
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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