GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Bacteroides thetaiotaomicron VPI-5482

Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate 351451 BT1923 O-acetylhomoserine (thiol)-lyase (NCBI ptt file)

Query= BRENDA::L7N4M1
         (449 letters)



>FitnessBrowser__Btheta:351451
          Length = 426

 Score =  394 bits (1011), Expect = e-114
 Identities = 204/415 (49%), Positives = 271/415 (65%), Gaps = 4/415 (0%)

Query: 19  ETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTRIGNPTTDVV 78
           ET  + AG  P      R LPIY +T++ +D +   A LF LE  G  YTR+ NPT D V
Sbjct: 8   ETLCVQAGWTPKKG-EPRVLPIYQSTTFKYDTSEQMARLFDLEDSGYFYTRLQNPTNDAV 66

Query: 79  EQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAKLGI 138
             +IAALEGGVAA+  SSGQAA  +AI N+  AGDH V S  +YGGT+NLF  ++ KLGI
Sbjct: 67  AAKIAALEGGVAAMLTSSGQAANFYAIFNICQAGDHFVCSSAIYGGTFNLFGVTMKKLGI 126

Query: 139 EVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVDNTI 198
           +V+FV+     +   AA +PNTKA F ETISNP +++LD    + +AH +GVPLIVDNT 
Sbjct: 127 DVTFVNPDASEEEISAAFQPNTKALFGETISNPSLEVLDIEKFARIAHSHGVPLIVDNTF 186

Query: 199 ATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDWT--QGRFPGFTTPDPSY 256
            TP   +P   GADI+VHS TKY+ GH  ++ G IVD GNFDW     +FPG  TPD SY
Sbjct: 187 PTPINCRPFEWGADIIVHSTTKYMDGHATSVGGCIVDSGNFDWDAHADKFPGLCTPDESY 246

Query: 257 HGVVFAE-LGPPAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQRVA 315
           HG+ + +  G  A+  KA  QL+RD GS  SP N+FL+  GLETL LR+ +H  NAQ+VA
Sbjct: 247 HGLTYTKAFGKGAYITKATAQLMRDLGSIQSPQNSFLLNLGLETLHLRMPQHCRNAQKVA 306

Query: 316 EFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAFVNALKLHS 375
           E+L+  + V  VNY GLP + ++  A++  P G+  V+SF L GG +    F+++L+  +
Sbjct: 307 EYLSKNEKVAWVNYCGLPDNKYYALAQKYMPNGSCGVISFGLKGGRDVSIKFMDSLEFIA 366

Query: 376 HVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLE 430
            V ++ D RS V+HPAS TH QLS  + +  GV P L+RL+VGIE  DDI+AD+E
Sbjct: 367 IVTHVADARSCVLHPASHTHRQLSDEQLMEAGVRPDLIRLSVGIENADDIIADIE 421


Lambda     K      H
   0.318    0.134    0.394 

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: 503
Number of extensions: 13
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: 449
Length of database: 426
Length adjustment: 32
Effective length of query: 417
Effective length of database: 394
Effective search space:   164298
Effective search space used:   164298
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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