GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Dechlorosoma suillum PS

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate Dsui_1904 Dsui_1904 aspartate/tyrosine/aromatic aminotransferase

Query= CharProtDB::CH_004054
         (397 letters)



>FitnessBrowser__PS:Dsui_1904
          Length = 398

 Score =  525 bits (1353), Expect = e-154
 Identities = 268/397 (67%), Positives = 307/397 (77%), Gaps = 1/397 (0%)

Query: 1   MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60
           MF+ VDAYAGDPILTL+E F +D R+ KVNL IGLYY+E G IP L +V +AEA + A P
Sbjct: 1   MFEHVDAYAGDPILTLVETFHKDSRTTKVNLGIGLYYDEQGRIPLLGSVRQAEAAIAAAP 60

Query: 61  HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120
              S YLPMEG   YR  +  LLFGAD   LK  R+ATIQTLGGSGALKVGAD LKRYFP
Sbjct: 61  APRS-YLPMEGAADYRAVVQKLLFGADSAALKAGRIATIQTLGGSGALKVGADLLKRYFP 119

Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180
           +S  WVS+PTW+NH +IF GAG  V  YP+YD  T GV F  ++A LK LP +SIVLLHP
Sbjct: 120 KSEAWVSNPTWDNHRSIFEGAGIAVHDYPYYDANTGGVDFTGMVACLKGLPEQSIVLLHP 179

Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240
           CCHNPTG DL+ +QW  VI I+  R+LIPFLDIAYQGFG G++EDAYAIRA+A +GLP L
Sbjct: 180 CCHNPTGVDLSREQWQQVIAIVAERKLIPFLDIAYQGFGDGLDEDAYAIRALADSGLPFL 239

Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300
           VSNSFSK  S YGERVGGLSV+C+DAE AGRVLGQLK TVRRNYSSPP  G  V   V+N
Sbjct: 240 VSNSFSKNLSFYGERVGGLSVVCKDAEEAGRVLGQLKFTVRRNYSSPPIHGELVTTIVMN 299

Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360
           D AL A W+ EV EMRTRI AMRQ+L +VL+  +P ++F Y   QRGMFSYTGLS AQVD
Sbjct: 300 DAALHAEWVKEVTEMRTRIQAMRQKLYEVLTARVPGKDFSYFTKQRGMFSYTGLSPAQVD 359

Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397
           RLREEFGVYL+ SGRMCVAGLNT NV  VA+A AAV+
Sbjct: 360 RLREEFGVYLVRSGRMCVAGLNTGNVAYVAEAMAAVL 396


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: 489
Number of extensions: 11
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: 397
Length of database: 398
Length adjustment: 31
Effective length of query: 366
Effective length of database: 367
Effective search space:   134322
Effective search space used:   134322
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 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