Aligments for a candidate for gatA in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Aligments for a candidate for gatA in Pseudomonas fluorescens FW300-N2E2

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate Pf6N2E2_3403 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)

Query= curated2:A1K1T5
         (487 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3403
          Length = 475

 Score =  253 bits (645), Expect = 1e-71
 Identities = 185/488 (37%), Positives = 245/488 (50%), Gaps = 40/488 (8%)

Query: 5   SVSELRRALDTRQVSSVELATLFLDRIAERNPALNAFITIDREGALAAARAADARIAAGT 64
           S+ +LR+AL++  ++S  L    L+RI   N  LNA++    + AL AA AAD + AAG 
Sbjct: 11  SIGQLRQALESGTLTSESLVGAQLERIERFNGQLNAYVEAYPQRALGAAIAADRQRAAGV 70

Query: 65  -AGPLTGIPLAHKDLFCTEGVLTTCGSKMLADFVSPYDAHVVSRLKDAGAVSLGKTNMDE 123
             GPL GIP+A KDLF  +G   T GS      +S   A  V RL+ AGA+ +GKT+  E
Sbjct: 71  HLGPLHGIPIAIKDLFEIDGKAITGGSLAQTPRISRLTATAVQRLERAGAIIMGKTHTVE 130

Query: 124 FAMGSSNESSHYGAVRNPWD--TTRIPGGSSGGSAAAVAARLVPLATGSDTGGSVRQPAS 181
           FA G    ++  G   NPWD    R PGGSS GSA AVA  L   A G+DTGGSVR PA 
Sbjct: 131 FAFGGWGTNAVMGTPWNPWDHEVHRAPGGSSSGSAVAVAGGLASAALGTDTGGSVRIPAG 190

Query: 182 HTGVTGIKPTYGVVSRYGMIAYASSLDQGGAFGASAEDCALLLTAMAGFDPRDSTCLDRP 241
             G+ G+K T G+VSR+G+I    SLD  G    + ED A +L A+ G DP D      P
Sbjct: 191 MCGLVGLKTTRGLVSRHGLIELCPSLDSVGPITHTVEDAAWMLDALLGPDPLDPVSAKSP 250

Query: 242 AEDYAAALAPTAGGKPLAGLRIGLPREFFAEGMADDVRAAVDAALDQYRALGAVTVEVSL 301
               AA L       P+AGLRI +  +   E +A  V AA D  L+Q  ALG   VE  L
Sbjct: 251 VFSAAAGL-----NLPVAGLRIWVLPQTEREHIAPGVLAAYDQGLEQLAALGMHLVEQPL 305

Query: 302 PNAKLAVPAYYVIAPAEASSNLSRFDGVRYGHRAAE-YGDLNDMYCKSRAEGFGAEVKRR 360
           P                  ++L +   V  G  +AE Y  L  ++ +     F   V+RR
Sbjct: 306 P------------------TSLEQCMRVAGGLMSAEGYASLGSLFERDDLR-FDPHVQRR 346

Query: 361 ILVGTYVLSHGYYDAYYLQAQKLRRLIAQDFQAAFAQCDVIAGPTSPTTAWAIGEKADDP 420
           +L G  + +     A Y+     RR   Q    A +Q D  A PT+     AIG      
Sbjct: 347 VLSGRAIDA-----AAYIHLHNQRRAARQAMDEAMSQVDACAFPTN-----AIGSVPLSQ 396

Query: 421 VQMYLSDIYTIA--VNLAGLPGLSHPCGFGAGRLPVGLQLIGNYFGESRLLATAHQYQQA 478
           V  Y + +  +    NL  L  ++ P GF   R+PV +Q++G  F E  +L  AH YQQ 
Sbjct: 397 VDEYGTPLALLGRFANLLNLCSVALPVGFDEQRMPVSMQIVGRAFAEPLVLRIAHAYQQV 456

Query: 479 SDWHLQRP 486
           SDWH +RP
Sbjct: 457 SDWHQRRP 464


Lambda     K      H
   0.318    0.133    0.392 

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: 533
Number of extensions: 25
Number of successful extensions: 6
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: 487
Length of database: 475
Length adjustment: 34
Effective length of query: 453
Effective length of database: 441
Effective search space:   199773
Effective search space used:   199773
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, 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

GapMind for Amino acid biosynthesis