GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Klebsiella michiganensis M5al

Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate BWI76_RS01925 BWI76_RS01925 aromatic amino acid aminotransferase

Query= BRENDA::P04693
         (397 letters)



>FitnessBrowser__Koxy:BWI76_RS01925
          Length = 397

 Score =  679 bits (1752), Expect = 0.0
 Identities = 339/397 (85%), Positives = 360/397 (90%)

Query: 1   MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60
           MFQKVDAYAGDPIL+LMERFK+DPRSDKVNLSIGLYYNEDGIIPQLQ+VA AEARLNAQP
Sbjct: 1   MFQKVDAYAGDPILSLMERFKDDPRSDKVNLSIGLYYNEDGIIPQLQSVAAAEARLNAQP 60

Query: 61  HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120
           HGAS+YLPMEGLN YRHAIAPLLFGADH VL Q RVA+IQTLGGSGALKVGADFLKRYFP
Sbjct: 61  HGASVYLPMEGLNTYRHAIAPLLFGADHQVLAQNRVASIQTLGGSGALKVGADFLKRYFP 120

Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180
            S VWVSDPTWENH+AIF GAGFEVSTYPW+DE TNGVRF   L  L +L  R IVLLHP
Sbjct: 121 GSRVWVSDPTWENHIAIFEGAGFEVSTYPWFDEKTNGVRFAAFLEKLNSLAERDIVLLHP 180

Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240
           CCHNPTGADL+N QWD V+E+LKAR LIPFLDIAYQGFGAGMEEDAYAIRAIA+AG+P L
Sbjct: 181 CCHNPTGADLSNAQWDQVVEVLKARNLIPFLDIAYQGFGAGMEEDAYAIRAIANAGMPML 240

Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300
           VSNSFSKIFSLYGERVGGLS++CEDAE A RVLGQLKATVRRNYSSPPNFGAQVVAAVL+
Sbjct: 241 VSNSFSKIFSLYGERVGGLSIVCEDAETAIRVLGQLKATVRRNYSSPPNFGAQVVAAVLS 300

Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360
           D  LKASWLAEVE MRTRILAMRQELV VL   +P  NFDYLL QRGMFSYTG S AQVD
Sbjct: 301 DSELKASWLAEVEGMRTRILAMRQELVNVLKETVPGGNFDYLLKQRGMFSYTGFSLAQVD 360

Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397
           RLR+EFGVYLIASGRMCVAGLN+ NVQRVA+AFAAV+
Sbjct: 361 RLRDEFGVYLIASGRMCVAGLNSRNVQRVAQAFAAVI 397


Lambda     K      H
   0.320    0.135    0.401 

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: 585
Number of extensions: 5
Number of successful extensions: 1
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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