GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pseudomonas simiae WCS417

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF4259 PS417_21815 amidase

Query= curated2:A1K1T5
         (487 letters)



>FitnessBrowser__WCS417:GFF4259
          Length = 500

 Score =  184 bits (467), Expect = 6e-51
 Identities = 160/472 (33%), Positives = 217/472 (45%), Gaps = 42/472 (8%)

Query: 18  VSSVELATLFLDRIAERNPALNAFITIDREGALAAARAADARIAAGTA-GPLTGIPLAHK 76
           ++S +L T    RI   +P L+A I ++ + AL  AR  D   A G   GPL G+P+  K
Sbjct: 53  LTSADLVTHLQARIRRLDPQLSAIIELNPK-ALETARELDRERARGNVRGPLHGMPILLK 111

Query: 77  DLFCTEGVLTTCGSKMLADFVSPYDAHVVSRLKDAGAVSLGKTNMDE---FAMGSSNESS 133
           D   TEG+ T+ G+  L    +  +A +V  L   GAV LGKTNM E   F  G    SS
Sbjct: 112 DTIETEGMQTSAGAFGLVGASASKNAPLVDHLIQQGAVILGKTNMTEMAGFRGGPDGWSS 171

Query: 134 HYGAVRNPWDTTRIPGGSSGGSAAAVAARLVPLATGSDTGGSVRQPASHTGVTGIKPTYG 193
             G  RNP       GGSS GSAAAVAA L P+A G++T GS+  PA+  G+ G+KPT G
Sbjct: 172 RGGQTRNPHQRDADVGGSSSGSAAAVAAGLAPMAVGAETNGSIIVPAARNGIVGLKPTVG 231

Query: 194 VVSRYGMIAYASSLDQGGAFGASAEDCALLLTAMAGFDPRDSTCLDRP-AEDYAAALAPT 252
           ++ R G+I  +   D  G    S  D AL+L AM+G DP D   +  P   DY   L P 
Sbjct: 232 LLDRNGIIPASQYQDTPGPMTRSVFDAALMLNAMSGSDPADPASVGAPQGIDYTQLLVPG 291

Query: 253 AGGKPLAGLRIGLPREFFAEGMADDVR--AAVDAALDQYRALGAVTVEVSLPNAKLAVPA 310
           A    L G RIG P  F  EG    V      +  L+  R  GAV V V+L  A  +   
Sbjct: 292 A----LKGKRIGYPATFSKEGETLPVENSTTFNRTLEVLREQGAVLVPVNLRLADAS--R 345

Query: 311 YYVIAPAEASSNLSRFDGVRYGHRAAEYGDL---NDMYCKSRAEGFGAEVKRRILVGTYV 367
           Y  +  ++   +L+ + G R G       +L   ND   +  +E     V R I   T  
Sbjct: 346 YDELLLSDVKDSLNTYLGKRSGLPVKSLTELIRFNDE--RDGSETDHQPVLREISASTLT 403

Query: 368 LSHGYYDAYYLQAQKLRRLIAQDFQAAFAQCDVIAGPTSPTTAWAIGEKADDPVQMYLSD 427
            +           + L   + QDF+++            P  A    E  D  V  + ++
Sbjct: 404 PA---------ARKPLWEALIQDFRSSI---------DDPIKA----ENLDAMVSDFDTN 441

Query: 428 IYTIAVNLAGLPGLSHPCGFGAGRLPVGLQLIGNYFGESRLLATAHQYQQAS 479
            Y   V  AG PG++ P G     LP      G  + E  LLA AH Y+QA+
Sbjct: 442 SY-FGVAAAGYPGIAVPSGVDEDGLPTSAYFFGTQWAEPTLLAVAHGYEQAA 492


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: 527
Number of extensions: 22
Number of successful extensions: 3
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: 487
Length of database: 500
Length adjustment: 34
Effective length of query: 453
Effective length of database: 466
Effective search space:   211098
Effective search space used:   211098
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: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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