GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Allochromatium vinosum DSM 180

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_012969354.1 ALVIN_RS00525 N-acetyl-gamma-glutamyl-phosphate reductase

Query= curated2:A8AAF8
         (356 letters)



>NCBI__GCF_000025485.1:WP_012969354.1
          Length = 340

 Score =  243 bits (621), Expect = 4e-69
 Identities = 152/353 (43%), Positives = 202/353 (57%), Gaps = 26/353 (7%)

Query: 5   VAIVGASGYTGGELLRVLAVHPDVNVKVVTSREYANKPVYYAHPHLRGIYPASLKFKRLD 64
           V IVG +GYTG ELLR+LA HP     V+TSR  +  PV    PHLRG         RLD
Sbjct: 4   VGIVGGTGYTGAELLRLLARHPQAAPAVITSRSESGLPVAEMFPHLRG---------RLD 54

Query: 65  ----DPDQLSDVVGDVDLVFLALPHKVSLHYVPKALEVGYKVVDLSADYRLKRVEDYKTW 120
               +PD  +  + + DLVF A P+  ++  VP+ LE G +V+DL+AD+RLK    ++ W
Sbjct: 55  LCFSEPD--TGALAECDLVFFATPNGTAMQSVPELLERGTRVIDLAADFRLKDPALWERW 112

Query: 121 YGYEHPYPDLLEKAVYGLPELYGDKIRGAQLVANPGCNATSSILAVLPPAAERIIDLDRI 180
           YG  H  PDLL + VYGLPE+  D IR A+L+ANPGC  T+  L  LP    R +D   +
Sbjct: 113 YGMPHQCPDLLAETVYGLPEVNRDAIRRARLIANPGCYPTAVTLGFLPLLERRAVDPSWL 172

Query: 181 VVDVKVGSSEAGAKPYRGGHHPEREGTARPYDAEGHRHVAELEQVIRDYTGRDVKVGFTP 240
           + D K G S AG K        E   + + Y   GHRH+ E+ Q ++ + G +V + F P
Sbjct: 173 IADAKSGVSGAGRKAETSLLMAEVGESFKAYSVSGHRHLPEITQNLQTFAGIEVGLTFVP 232

Query: 241 HAVSMIRGSLASAYSWLTKDLAPLDVQRIYAKYYAGKKFVK-IVRGAPMPYPDVKNVYGS 299
           H V MIRG  A+ Y+ LT D   LD+  +Y   YA + FV  +V G+    PD ++V GS
Sbjct: 233 HLVPMIRGIEATLYARLTDD--GLDLAALYQSRYADEPFVDFMVSGS----PDTRSVRGS 286

Query: 300 NYAEVGFALDKRVGRLAMF-AAIDNLMKGAAGTAVQNMNLMLGMDEDEGLKNL 351
           N   +  A   R G + +  + IDNL+KGAAG AVQNMNLM G DE  GL+ L
Sbjct: 287 NDCRIAVA---RQGDIVIVQSVIDNLVKGAAGQAVQNMNLMFGFDETLGLEAL 336


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: 383
Number of extensions: 21
Number of successful extensions: 4
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: 340
Length adjustment: 29
Effective length of query: 327
Effective length of database: 311
Effective search space:   101697
Effective search space used:   101697
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 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