GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Phyllobacterium endophyticum PEPV15

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_106719629.1 CU100_RS26290 amidase

Query= curated2:A7NKM0
         (490 letters)



>NCBI__GCF_003010935.1:WP_106719629.1
          Length = 492

 Score =  213 bits (541), Expect = 2e-59
 Identities = 163/483 (33%), Positives = 237/483 (49%), Gaps = 39/483 (8%)

Query: 15  MLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARRAAGDASPLLG- 73
           M A G+ISS E+T A L+RIA  + K+ A++ V    AR  A + D          L G 
Sbjct: 1   MRAAGQISSAEITHAYLSRIAKFDGKLNAYVEVYEQEARFAATSLDTGSNGRIEGGLAGG 60

Query: 74  IPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLNCDEFAMGSST 133
           IP+ +KD++   G  TT  S           A+   RL A+G++ILGK    E A     
Sbjct: 61  IPIALKDLLEVDGKITTAGSAHFRGRRSRVTASLATRLIASGSIILGKTQTVELAYSGWG 120

Query: 134 ENSAFQQTRNPWN--LERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPAALCGITGL 191
            N       NPW+  ++R PGGSS GSA AV+AG AP A+GTDTGGS+R PAA CGITGL
Sbjct: 121 INPQMGTPWNPWDEDIQRDPGGSSSGSAVAVSAGLAPWAVGTDTGGSVRLPAAFCGITGL 180

Query: 192 KPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTDYPAPDYEAA 251
           K T G+++  G++  + + D  GP+ R+V D AI+  ++ G+    A  +         A
Sbjct: 181 KTTAGQIATDGIIPLSKTFDTPGPITRSVLDAAILYNLMLGSKSQFAFGSG-TVSGISRA 239

Query: 252 LTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHTPYALPVYYL 311
           L G ++GL++G   +    G++PDV  A   ++E L   GA++ EI+LP        + L
Sbjct: 240 LEGGVQGLKLGSLPKAEREGVEPDVLGAYDRSLETLSNLGADIVEINLP--------FRL 291

Query: 312 IAPAEASANLARFDGVRYGLRV--PGESYFDELERTRGAGFGPEVRRRIMLGTYALSAGY 369
                A + +   +   Y   V   G S  DE  R+ G   G     R +   ++L A  
Sbjct: 292 NDCRTAHSTIINSEAYSYFYDVIEDGSSLIDESTRS-GISTG-----RTISPQHSLDA-- 343

Query: 370 YDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGA--HTDDPLAMYLEDVCT 427
               +K+  ++++ I      A   VD +  PTT +VA  +     T  P         T
Sbjct: 344 ----FKQIWRLKSQI----SGALLNVDALLTPTTESVAIPVEGLDRTKSPARF------T 389

Query: 428 LPLNLAGLPGLVVPCG-FAEGLPIGLQLIGRAFDEESLLRVGDAYQRVTDWHTRMPEVRE 486
             +N  G+ GL +P G  AE LP  LQ++ R   E   LR+G A+Q  TDWH   P +  
Sbjct: 390 RFVNALGMCGLAIPNGKSAEALPTSLQIVCRQHQERLALRIGLAFQNATDWHLGYPPMCR 449

Query: 487 DGS 489
           D +
Sbjct: 450 DAA 452


Lambda     K      H
   0.320    0.136    0.398 

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: 499
Number of extensions: 21
Number of successful extensions: 5
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: 490
Length of database: 492
Length adjustment: 34
Effective length of query: 456
Effective length of database: 458
Effective search space:   208848
Effective search space used:   208848
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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. 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:

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:

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