GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pseudomonas putida KT2440

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate PP_0613 PP_0613 Amidase family protein

Query= curated2:Q1DCA3
         (486 letters)



>FitnessBrowser__Putida:PP_0613
          Length = 469

 Score =  240 bits (613), Expect = 7e-68
 Identities = 171/488 (35%), Positives = 236/488 (48%), Gaps = 35/488 (7%)

Query: 5   DLTMLELAAKLAAGEASSEEATRASLARIQQVDPKVRAFLRVDEAGALAAARASDARRKS 64
           +LT +EL       + S  E     LARI   +P V AF  VD  GA AAARAS+ R + 
Sbjct: 9   ELTAVELLELYHRRQLSPVEVVDDVLARIDLHNPAVNAFCHVDGEGARAAARASEQRWQR 68

Query: 65  GSPASALDGVPLGLKDIFLTEGVETTAGSRILEGFVP-PYDATVVRLLKEAGLPLVGKLN 123
           G P   LDGVP  +KD+ LT G+ T  GSR   G  P   DA     ++EAG  LVGK  
Sbjct: 69  GQPCGRLDGVPASIKDLTLTRGMPTRKGSRTTSGAGPWEIDAPFSAFMREAGAVLVGKTT 128

Query: 124 MDEFAMGSSNESSAFFPSHNPWDVSRTPGGSSGGSAAAVAAREVFGALGTDTGGSIRQPA 183
             EF      ++  +  + NPWD   T GGSSGG+AAA A        G+D GGSIR P 
Sbjct: 129 TPEFGWKGVTDNPLYGITRNPWDTRLTAGGSSGGAAAAAALNLGVLHQGSDAGGSIRIPC 188

Query: 184 ALTNTVGLKPTYGRVSRFGVIAFASSLDQPGPMTRTVADAAALLQVIARPDAQDATSADA 243
           A T T G+KPT+G V ++   A  + L   GPMTRTV D+  +L  +ARPDA+D   A A
Sbjct: 189 AFTGTFGIKPTFGYVPQWPASAM-TVLSHLGPMTRTVDDSVLMLDCVARPDARDGL-AGA 246

Query: 244 PVPDYSADLEAGVRGLKLGVPREYFTEGMDPEVEAAVREALREYERLGATLVDVSLPHTK 303
           P        +  + GL++     +    +DP+++A V +A++   RLGA + +V      
Sbjct: 247 PRQAPWLSQQQDLSGLRIAYSANFGYVQVDPQIQALVAQAVQRLARLGAQVEEVD----- 301

Query: 304 YALATYYLIAPAEASSNLARYDGVRFGLRAKDARSLRDVYALTREQGFG--AEVKRRIML 361
                         S  L  ++ + F   A+ A +L D      + G    AE   +I L
Sbjct: 302 -----------PGFSDPLETFNTLWFAGAARLASALSDEQKALLDPGLRWIAEQGAQISL 350

Query: 362 GTFALSSGYYDAHYLRAQKVRTLIREDFTRAFQQVDALLSPTSPVPAFKLGEKVEDPLSM 421
           G            Y +A + R  +        Q+ D L+SP  P+ AF+ G  V     M
Sbjct: 351 G-----------EYTQALEARAELIAKMNAFHQRYDVLVSPMLPLVAFEAGHNVPPGSGM 399

Query: 422 YLMDIYT---LPCNLAGLPGLSVPCGFTKAGLPVGLQILGRPFDEAGLLRIARAYEREHD 478
                +T    P NL   P  SVPCGFT+ GLPVGLQ++   F +  +LR+ + YE+ + 
Sbjct: 400 AQWMEWTPLSYPFNLTQQPAASVPCGFTREGLPVGLQVVAGRFADEQVLRVCKVYEQHYP 459

Query: 479 FFRRSAPL 486
                AP+
Sbjct: 460 SRHLQAPI 467


Lambda     K      H
   0.318    0.134    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: 553
Number of extensions: 37
Number of successful extensions: 7
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: 486
Length of database: 469
Length adjustment: 34
Effective length of query: 452
Effective length of database: 435
Effective search space:   196620
Effective search space used:   196620
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.

Links

Downloads

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:

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