Alignments for a candidate for gatA in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Marinobacter adhaerens HP15

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF2395 HP15_2343 amidase signature enzyme

Query= curated2:Q7UT33
         (499 letters)



>FitnessBrowser__Marino:GFF2395
          Length = 495

 Score =  196 bits (497), Expect = 2e-54
 Identities = 160/499 (32%), Positives = 235/499 (47%), Gaps = 57/499 (11%)

Query: 4   SASEILKQLDSGEVTAVEVIAQSLAAIRASQPTINAFTHVAEETAMQAAEAVDADRKAGK 63
           SA ++LKQL++G +T+  +    L  IR   PTINA   + E+ A+  A   D +R AG 
Sbjct: 12  SAHDLLKQLEAGTLTSEALTTALLERIREHNPTINAVVTLDEQKALTNARRADEERAAGS 71

Query: 64  TLGPLAGLPVAIKDVLCTSDMPTTCSSKMLEGFVPPYDATVVARLKSAGAIVVGKTNMDE 123
             GPL GLP+ +KD    + M  T  +  L    P   A VV RL+ AGAI++GKTN+  
Sbjct: 72  ARGPLHGLPLTLKDTWEVAGMTCTAGAPALRDHKPNRHADVVQRLEDAGAIILGKTNVPI 131

Query: 124 FAMGASTETSAMGVTGNPWDTTKTPGGSSGGAAAAVAAGAVPLSLGTDTGGSIRQPAAFC 183
           +A    +     GVT NP +   TPGGSSGGAAAA+AAG  PL +G+D  GSIR PA FC
Sbjct: 132 YATDLQSYNKLFGVTNNPHNLAHTPGGSSGGAAAALAAGMTPLEVGSDLAGSIRTPAHFC 191

Query: 184 GITGLKPTYGRVSRYGLV------AFASSLDQAGPMGWSVDDVAIGLQAMAGYDPRDSTS 237
           G+ G KPT   VS  G +           L + GPM  S  D+ + +  +AG  P     
Sbjct: 192 GVFGHKPTRSLVSFRGHIPGPPGTQSRPDLVEGGPMARSAGDLELLMSVIAGPRP----- 246

Query: 238 VNAEVPDFTPAMAAEDVRGM---RIGVLREG----LDQDGISPAVRDALATAESVFREQG 290
             AE   ++ AMA  ++  +   R+G+  E     +DQ+     + +      +   E+G
Sbjct: 247 --AEERSWSLAMAPSELNSLDQARVGLWLEDPLCPIDQE-----LTEGYQNLGNALSERG 299

Query: 291 AEIVEVELP--HSKYWVPTYYVIAPCEASSNLSRFDGAHYGYRVADAEIAAADSGPLEAM 348
           A + E   P    ++ +P Y+ +     S++L         + +A  E      GP+   
Sbjct: 300 ALVTEARHPLLSLEHILPAYFNLLGALLSTSLKPAQRRQMKW-IARLEPWLKFLGPMTPF 358

Query: 349 YSLSRAGGFGSEVKRRIMVGTYALSEGYYDAYYNQALKVRRLIRNDYDAAFQQVDLMLGP 408
                 G +G  V + +     A SE            +R  +R + ++ FQ+VD++L P
Sbjct: 359 -----IGEYGRGVNQPV-YQWMAWSE------------MREKMRAEIESLFQEVDVLLTP 400

Query: 409 VTPSPAFALNEK----------TDDPIAMYLCDLFTVGANLAGVPAISLPGGFDAVGLPV 458
           VTP+ A   +               P A      +   A L G+PA S+P G    GLP 
Sbjct: 401 VTPTTAIRHDHSHPVFKRRITVAGQPRAYMDQFCWIAFATLLGLPATSVPIGRTKEGLPF 460

Query: 459 GVQ-LQAPVMEETRLLRAG 476
            VQ + AP M+ T +  AG
Sbjct: 461 NVQVIGAPGMDLTTIGFAG 479


Lambda     K      H
   0.316    0.132    0.381 

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: 584
Number of extensions: 30
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 499
Length of database: 495
Length adjustment: 34
Effective length of query: 465
Effective length of database: 461
Effective search space:   214365
Effective search space used:   214365
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: 52 (24.6 bits)

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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