GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Epibacterium ulvae U95

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_090218894.1 CV091_RS11625 methionine gamma-lyase

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



>NCBI__GCF_002796795.1:WP_090218894.1
          Length = 401

 Score =  293 bits (749), Expect = 8e-84
 Identities = 162/384 (42%), Positives = 237/384 (61%), Gaps = 4/384 (1%)

Query: 18  ATQAIRGG-TARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEML 76
           +T+AI  G  A    G  +  ++LTS + ++ A    A F+G+QQG  YSR+ NPT++ L
Sbjct: 9   STRAIHHGYDAGQHQGSLNPPVYLTSTFTFETAEAGGAMFAGEQQGHFYSRISNPTLDQL 68

Query: 77  EQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGI 136
           E+RIA LEGAEA  ATASGM A+T+     + AGD +I  +  +G         L KF +
Sbjct: 69  EERIANLEGAEAGLATASGMGAITSVFWTLVKAGDEVIIDKTLYGCTFAFLSHGLTKFDV 128

Query: 137 ETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFA 196
           + T VD  DP+   DAI   T+V +FETPANP   +VD+ A+  IA  +G   VVDN +A
Sbjct: 129 KVTPVDLTDPENLTDAITDRTRVVYFETPANPNNRLVDIAAISRIAHAKGAKVVVDNTYA 188

Query: 197 TPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGT-EEFINNTLLPFHRNTGPTLSPF 255
           TP L RP++ GAD+V +SATK + G G ++AG + G+ E+     L+     TG  +SPF
Sbjct: 189 TPVLTRPLEHGADIVLHSATKYLGGHGDLVAGLIAGSAEDMTQVRLVGLKDMTGSVMSPF 248

Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAA 313
            A ++L+GL+TL+LR++R   +A+++A+ LE    V  V++PGL S PQ +LA  QM+  
Sbjct: 249 TAMLLLRGLKTLELRVERHCRSAMQIAQMLEDHPSVASVHYPGLDSFPQADLARRQMSDF 308

Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373
           G +   E+ GG+     +++ L LI  + ++GD+ SL+ HPAS THS     +R   G+ 
Sbjct: 309 GGMIPFEVVGGKDGGIAMMNRLKLIQRAVSLGDAESLIQHPASMTHSTYTPQERAEHGIA 368

Query: 374 EGMLRLNVGLEDPEDLIADLDQAL 397
           EG++RL+VGLE  +DLI DL  AL
Sbjct: 369 EGLVRLSVGLETADDLIDDLMAAL 392


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: 399
Number of extensions: 13
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: 402
Length of database: 401
Length adjustment: 31
Effective length of query: 371
Effective length of database: 370
Effective search space:   137270
Effective search space used:   137270
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 26 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