GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Marinobacter adhaerens HP15

Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.- (uncharacterized)
to candidate GFF354 HP15_352 N-acetyl-gamma-glutamyl-phosphate reductase

Query= curated2:A8AAF8
         (356 letters)



>FitnessBrowser__Marino:GFF354
          Length = 388

 Score =  263 bits (671), Expect = 7e-75
 Identities = 151/353 (42%), Positives = 214/353 (60%), Gaps = 17/353 (4%)

Query: 1   MTYEVAIVGASGYTGGELLRVLAVHPDVNVKVVTSREYANKPVYYAHPHLRGIYPASLKF 60
           M  +V IVG +GYTG ELLR+LAVHP+V+V  +TSR  A  PV   +P+LRG Y  +   
Sbjct: 43  MVIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFS- 101

Query: 61  KRLDDPDQLSDVVGDVDLVFLALPHKVSLHYVPKALEVGYKVVDLSADYRLKRVEDYKTW 120
               +PD   +V+G  DLVF A PH V++  VP+ +  G +VVDLSAD+RLK ++ +  W
Sbjct: 102 ----EPDV--NVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANW 155

Query: 121 YGYEHPYPDLLEKAVYGLPELYGDKIRGAQLVANPGCNATSSILAVLPPAAERIIDLDRI 180
           YG  H  P+  EKAVYGLPE+  D+IR AQLVANPGC  T+  L  LP   + ++D  R+
Sbjct: 156 YGMAHESPEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRL 215

Query: 181 VVDVKVGSSEAGAKPYRGGHHPEREGTARPYDAEGHRHVAELEQVIRDYTGRDVKVGFTP 240
           + D K G+S AG +   G  H E   + + Y A GHRH+ E+ Q +    G DV V F P
Sbjct: 216 IADAKSGASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVP 275

Query: 241 HAVSMIRGSLASAYSWLTKDLAPLD-VQRIYAKYYAGKKFVKIVRGAPMPY---PDVKNV 296
           H + MIRG  A+ Y+ L K+ A  D +Q ++ + +  + FV +     MP+   P+ ++V
Sbjct: 276 HLIPMIRGIEATLYAEL-KNPADFDRLQALFEQRFDDEPFVDV-----MPFGSHPETRSV 329

Query: 297 YGSNYAEVGFALDKRVGRLAMFAAIDNLMKGAAGTAVQNMNLMLGMDEDEGLK 349
            G+N   +     ++   + + + IDNL+KGAAG AVQNMN+M G+ E  GL+
Sbjct: 330 RGANQCRMALHRQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLE 382


Lambda     K      H
   0.319    0.138    0.410 

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: 452
Number of extensions: 23
Number of successful extensions: 3
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: 356
Length of database: 388
Length adjustment: 30
Effective length of query: 326
Effective length of database: 358
Effective search space:   116708
Effective search space used:   116708
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 (21.7 bits)
S2: 49 (23.5 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