GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Methylocella silvestris BL2

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_012592297.1 MSIL_RS16900 PLP-dependent transferase

Query= reanno::Korea:Ga0059261_3194
         (402 letters)



>NCBI__GCF_000021745.1:WP_012592297.1
          Length = 392

 Score =  197 bits (502), Expect = 3e-55
 Identities = 129/384 (33%), Positives = 202/384 (52%), Gaps = 10/384 (2%)

Query: 16  KPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEM 75
           +PAT +  G T        S  +F TS + +D   D A  ++G  + + YSR  NPTV  
Sbjct: 12  EPATGSA-GRTRAYALDAASPPIFQTSSFFFDNFDDMADVYAGRSRRLIYSRGDNPTVME 70

Query: 76  LEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFG 135
            E+ +A L+GAEA RA +SGM A+ A ++  +SAGD ++  R  +     L +  L KFG
Sbjct: 71  FERVMAELDGAEAARAFSSGMGAIAATIIAFVSAGDRIVTVRNVYSDAYRLFELVLAKFG 130

Query: 136 IETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAF 195
           +    +D  D      A+ P  K+ + ETP + T ++ D+  + A+AR +G+V+V+DN++
Sbjct: 131 VTVDYLDGADAGAIAAAL-PGAKLLYLETPTSLTFELQDIATLAALARAQGVVSVIDNSW 189

Query: 196 ATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPF 255
           ATP  Q+P+  G D+V ++A+K + G    +AG V G+ E +       +   G  LSPF
Sbjct: 190 ATPQFQKPIAHGVDLVIHAASKYLGGHSDTVAGVVSGSAEHVARINAGAYAYLGAKLSPF 249

Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQMAAA 313
            AW++L+GL TL+LR+ R  ++ L +A  L+    V  V  P    HP      + ++  
Sbjct: 250 EAWLLLRGLATLELRLPRHMQSGLLIAGRLKAHPNVSLVRHPAYSDHP----GKATLSGF 305

Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373
             +FSIE+ G         +AL L  +  + G   SL+  PA         +     GV 
Sbjct: 306 SGLFSIEV-GENIDVRTFANALKLFRLGVSWGGPESLVV-PALAPLQLRTANCFARFGVS 363

Query: 374 EGMLRLNVGLEDPEDLIADLDQAL 397
             ++RL+VGLED E L  DL++AL
Sbjct: 364 PRLIRLHVGLEDAEALWDDLERAL 387


Lambda     K      H
   0.319    0.134    0.396 

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: 361
Number of extensions: 20
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: 402
Length of database: 392
Length adjustment: 31
Effective length of query: 371
Effective length of database: 361
Effective search space:   133931
Effective search space used:   133931
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: 50 (23.9 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