GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Acidithiobacillus ferrooxidans ATCC 23270

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_012536942.1 AFE_RS09520 O-succinylhomoserine sulfhydrylase

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



>NCBI__GCF_000021485.1:WP_012536942.1
          Length = 404

 Score =  365 bits (938), Expect = e-105
 Identities = 190/387 (49%), Positives = 257/387 (66%), Gaps = 2/387 (0%)

Query: 16  KPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEM 75
           +P T AIR G  R++  E SEA+F TS + +D A +AA RF+G   G  Y+R  NPTV  
Sbjct: 15  RPETIAIRAGIHRTQEQEHSEAIFPTSSFVFDSAEEAADRFAGRVPGNIYARFTNPTVRT 74

Query: 76  LEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFG 135
            E+R+A LEGAEAC ATASGMAA   A +  L AGDH++  R+ FG+   L    L +FG
Sbjct: 75  FEERLAALEGAEACVATASGMAACLTAFMGILKAGDHVVASRSIFGTTVQLLGNILSRFG 134

Query: 136 IETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAF 195
           +ET+ V   D   +  A+RPNT++ F ETP+NP  ++ D++A+  +A       VVDN F
Sbjct: 135 VETSFVPLADVPAWRAALRPNTRMLFLETPSNPLTEIGDMQALADLAHVHDAWLVVDNCF 194

Query: 196 ATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPF 255
            TPALQ+P+ FGAD+V +SATK +DGQGR L GAVCG+ E +N+    F R  GP+LSPF
Sbjct: 195 CTPALQQPLKFGADLVIHSATKYLDGQGRTLGGAVCGSTELLNSGPRNFVRTAGPSLSPF 254

Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAA 313
           NAWV LKGLETL LR++R   NA K+A +LE R  V RV +PGL SHPQ  LA  Q    
Sbjct: 255 NAWVQLKGLETLGLRMERHCANAQKIAEWLEARPEVARVYYPGLDSHPQQALAARQQRLP 314

Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373
           G I S +L GG+  A   +DAL L+ ++ N+GD+++ +THPASTTHS V+ + R   GVG
Sbjct: 315 GAILSFDLHGGQKAAWAFVDALRLLSLTANLGDAKTTITHPASTTHSRVSPEARAAAGVG 374

Query: 374 EGMLRLNVGLEDPEDLIADLDQALGSV 400
           +G+LR++VGLE  +DL  D+++   ++
Sbjct: 375 DGLLRISVGLEHADDLREDMERGFAAL 401


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: 441
Number of extensions: 14
Number of successful extensions: 2
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: 404
Length adjustment: 31
Effective length of query: 371
Effective length of database: 373
Effective search space:   138383
Effective search space used:   138383
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 Apr 10 2024. The underlying query database was built on Apr 09 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