Alignments for a candidate for glnA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Synechococcus elongatus PCC 7942

Align glutamine synthetase type III subunit (EC 6.3.1.2) (characterized)
to candidate Synpcc7942_0169 Synpcc7942_0169 glutamate-ammonia ligase, glutamine synthetase type III

Query= metacyc::SYNPCC7942_0169-MONOMER
         (723 letters)



>FitnessBrowser__SynE:Synpcc7942_0169
          Length = 723

 Score = 1433 bits (3709), Expect = 0.0
 Identities = 723/723 (100%), Positives = 723/723 (100%)

Query: 1   MSGNAARVNAVHQITNREPLPSKPPMSLEAIWAENVFDLSKMQARLPKAVFKSIKNTIVT 60
           MSGNAARVNAVHQITNREPLPSKPPMSLEAIWAENVFDLSKMQARLPKAVFKSIKNTIVT
Sbjct: 1   MSGNAARVNAVHQITNREPLPSKPPMSLEAIWAENVFDLSKMQARLPKAVFKSIKNTIVT 60

Query: 61  GQKLDPSVADAVATAMKDWAMSKGALYYAHVFYPMTNVTAEKHDGFISVQGDGKVISEFS 120
           GQKLDPSVADAVATAMKDWAMSKGALYYAHVFYPMTNVTAEKHDGFISVQGDGKVISEFS
Sbjct: 61  GQKLDPSVADAVATAMKDWAMSKGALYYAHVFYPMTNVTAEKHDGFISVQGDGKVISEFS 120

Query: 121 GKVLVQGEPDGSSFPNGGIRDTFEARGYTGWDVTSPAYIMETDNGSTLCIPTVFVSWTGE 180
           GKVLVQGEPDGSSFPNGGIRDTFEARGYTGWDVTSPAYIMETDNGSTLCIPTVFVSWTGE
Sbjct: 121 GKVLVQGEPDGSSFPNGGIRDTFEARGYTGWDVTSPAYIMETDNGSTLCIPTVFVSWTGE 180

Query: 181 ALDKKVPLLRSIAAMDKAARKVLTLLGNTEVSQVNSSCGAEQEYFLVDANFAAQRPDLLL 240
           ALDKKVPLLRSIAAMDKAARKVLTLLGNTEVSQVNSSCGAEQEYFLVDANFAAQRPDLLL
Sbjct: 181 ALDKKVPLLRSIAAMDKAARKVLTLLGNTEVSQVNSSCGAEQEYFLVDANFAAQRPDLLL 240

Query: 241 AGRTLFGRPSAKGQEFDDHYFGAIPERVQVFMQDVEETLYKLGIPAKTRHNEVAPGQFEI 300
           AGRTLFGRPSAKGQEFDDHYFGAIPERVQVFMQDVEETLYKLGIPAKTRHNEVAPGQFEI
Sbjct: 241 AGRTLFGRPSAKGQEFDDHYFGAIPERVQVFMQDVEETLYKLGIPAKTRHNEVAPGQFEI 300

Query: 301 APFFEAANVASDHQQLIMTVLKQTAKKHGFMCLLHEKPFAGINGSGKHVNWSVGNATQGN 360
           APFFEAANVASDHQQLIMTVLKQTAKKHGFMCLLHEKPFAGINGSGKHVNWSVGNATQGN
Sbjct: 301 APFFEAANVASDHQQLIMTVLKQTAKKHGFMCLLHEKPFAGINGSGKHVNWSVGNATQGN 360

Query: 361 LLDPGDSPHDNAQFLVFCGAVIRGVHKYGPLMRAAIATASNDHRLGANEAPPAIMSVYLG 420
           LLDPGDSPHDNAQFLVFCGAVIRGVHKYGPLMRAAIATASNDHRLGANEAPPAIMSVYLG
Sbjct: 361 LLDPGDSPHDNAQFLVFCGAVIRGVHKYGPLMRAAIATASNDHRLGANEAPPAIMSVYLG 420

Query: 421 TQLEEVFEQIKTGTVTESKQKGIMDLGVDVLPYLTKDAGDRNRTSPFAFTGNRFEFRAVG 480
           TQLEEVFEQIKTGTVTESKQKGIMDLGVDVLPYLTKDAGDRNRTSPFAFTGNRFEFRAVG
Sbjct: 421 TQLEEVFEQIKTGTVTESKQKGIMDLGVDVLPYLTKDAGDRNRTSPFAFTGNRFEFRAVG 480

Query: 481 ASQSVSGPLIVLNTILADSLDWIGNRLESELAKGLDLNTAILTVLKEVMEEHGNVIFGGN 540
           ASQSVSGPLIVLNTILADSLDWIGNRLESELAKGLDLNTAILTVLKEVMEEHGNVIFGGN
Sbjct: 481 ASQSVSGPLIVLNTILADSLDWIGNRLESELAKGLDLNTAILTVLKEVMEEHGNVIFGGN 540

Query: 541 GYSEEWHREAVEKRGLANLPTTADALPVLKEEYIEDLFKKTGVLTPVELESRFEVYAEQY 600
           GYSEEWHREAVEKRGLANLPTTADALPVLKEEYIEDLFKKTGVLTPVELESRFEVYAEQY
Sbjct: 541 GYSEEWHREAVEKRGLANLPTTADALPVLKEEYIEDLFKKTGVLTPVELESRFEVYAEQY 600

Query: 601 ILSIEVEAKLAVSIAKTIIYPAAVEYLAKLSGTIASLSGLGIDFEKESARKIAELTSSLV 660
           ILSIEVEAKLAVSIAKTIIYPAAVEYLAKLSGTIASLSGLGIDFEKESARKIAELTSSLV
Sbjct: 601 ILSIEVEAKLAVSIAKTIIYPAAVEYLAKLSGTIASLSGLGIDFEKESARKIAELTSSLV 660

Query: 661 GAATQLSEALEHESSDTVEHLQYCAKTLRPLMDNVRTYADALEAEVADSFWPLPTYQEML 720
           GAATQLSEALEHESSDTVEHLQYCAKTLRPLMDNVRTYADALEAEVADSFWPLPTYQEML
Sbjct: 661 GAATQLSEALEHESSDTVEHLQYCAKTLRPLMDNVRTYADALEAEVADSFWPLPTYQEML 720

Query: 721 FIK 723
           FIK
Sbjct: 721 FIK 723


Lambda     K      H
   0.316    0.133    0.383 

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: 1645
Number of extensions: 33
Number of successful extensions: 3
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: 723
Length of database: 723
Length adjustment: 40
Effective length of query: 683
Effective length of database: 683
Effective search space:   466489
Effective search space used:   466489
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 (21.6 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis