GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Desulfatiglans anilini DSM 4660

Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.103; EC 1.2.1.106 (uncharacterized)
to candidate WP_035254042.1 H567_RS0110135 N-acetyl-gamma-glutamyl-phosphate reductase

Query= curated2:A0RWW0
         (348 letters)



>NCBI__GCF_000422285.1:WP_035254042.1
          Length = 353

 Score =  242 bits (618), Expect = 9e-69
 Identities = 142/355 (40%), Positives = 198/355 (55%), Gaps = 13/355 (3%)

Query: 1   MKVGVVGASGYVGGETLRLLVNHPDVEIAAVTSRQHVGEYLHRVQPSLRGFTDLTFSELD 60
           +KVG++GA GY G   + LL  HP+ EIAA+  +Q +G+ +  + P L GF DL      
Sbjct: 4   IKVGIIGAGGYGGCGAVELLNRHPEAEIAALIDQQDIGKAISDLYPHLTGFCDLPLRSPQ 63

Query: 61  YDRLSDSCDLVFTAVPHGTATDIVRALYDRDIKVIDLSADYRLHDP---ADYTKWYGWEH 117
              L ++ D+VF A P G           +  KV+D S D+R +DP   A Y    G   
Sbjct: 64  DPELPENFDVVFFATPDGVGQKEGPKWLRKGTKVVDYSGDFRFNDPDTYAGYAARIGRTE 123

Query: 118 PH--PDYLSKSVFGIPELHREEIRSAKLVSCPGCMAVTSILALAPPVREGLVDTEHIVVD 175
           PH  PD L +SV+G+ ELHRE I  + LV  PGC AV+ IL LAP V+EGL+D E I+ D
Sbjct: 124 PHASPDMLPRSVYGLAELHREGISRSDLVGNPGCFAVSCILGLAPAVKEGLIDLEGIICD 183

Query: 176 SKIGSSGAGAGAGTA--HAMRAGVIRPYKPAKHRHTGEIEQELSGIAGKKIRVSMSPHAV 233
           +K G SGAG        +  R   +  Y+ + H+H  EIE+EL  +AG  + ++ +PH V
Sbjct: 184 AKTGVSGAGKKPSPTFHYPARYEAMNAYRISGHQHVYEIERELGLLAGSAVTLTFTPHVV 243

Query: 234 DVVRGILCTNHVFLTREASEKDLWKMYRQAYGEERFVRLIRDKKGLYKFPDPKFLV-GSN 292
            + RGIL T +  L        +   YR  YG++ FVR+    K     P     V GSN
Sbjct: 244 PLCRGILSTIYGSLKPGKGLPQVLDAYRSFYGKDVFVRVFGPDK-----PQSSINVRGSN 298

Query: 293 FCDIGFDLDEDNNRLVAISASDNLMKGAAGSAIQNMNIMAGLDEMSGLRYTPLTP 347
           FC++  ++D+   +L+ +S  DNL+KG AGSA+QNMNIM GLDE +GL    + P
Sbjct: 299 FCNLSLNIDDRTGKLIVVSHIDNLVKGQAGSAVQNMNIMFGLDETAGLMNPGIFP 353


Lambda     K      H
   0.320    0.137    0.412 

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: 334
Number of extensions: 17
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: 348
Length of database: 353
Length adjustment: 29
Effective length of query: 319
Effective length of database: 324
Effective search space:   103356
Effective search space used:   103356
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: 49 (23.5 bits)

This GapMind analysis is from Jul 25 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