GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Pseudomonas stutzeri RCH2

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate GFF765 Psest_0779 Aspartate/tyrosine/aromatic aminotransferase

Query= CharProtDB::CH_004054
         (397 letters)



>FitnessBrowser__psRCH2:GFF765
          Length = 398

 Score =  307 bits (787), Expect = 3e-88
 Identities = 171/396 (43%), Positives = 230/396 (58%), Gaps = 2/396 (0%)

Query: 2   FQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQPH 61
           F ++    GDPIL LM+ ++ DP   K++L +G+Y +  G+ P  +AV  AE RL     
Sbjct: 3   FGQIPRVPGDPILGLMDLYRADPNPAKLDLGVGVYKDAQGLTPIPRAVKLAEQRLVDGEQ 62

Query: 62  GASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFPE 121
             S Y+   G   +   +     G+    L +QR    Q  GG+GAL++  +F+ +  P 
Sbjct: 63  SKS-YIGGHGDAQFGALLLRQALGSRAIALGEQRAGCTQAPGGTGALRLAGEFIAKCLPG 121

Query: 122 SGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHPC 181
             +W+SDPTW  H  +FA AG  V  YP Y  A N +    +LA L+ +P   +VLLH C
Sbjct: 122 RSIWLSDPTWPIHETLFAAAGLRVQHYP-YVGADNRLDVEGMLAALQQVPPGDVVLLHAC 180

Query: 182 CHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPALV 241
           CHNPTG DL +D W  V+E+++AREL+P  D AYQGFG G+EEDA+A+R  A      L+
Sbjct: 181 CHNPTGFDLNHDDWLRVLEVVRARELLPLFDFAYQGFGDGLEEDAWAVRLFAETLPEMLI 240

Query: 242 SNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLND 301
           + S SK F LY ER G L  +  DAE    V  QL +  R  +S+PP  GA VVA +L D
Sbjct: 241 TTSCSKNFGLYRERTGALIAVTSDAERLLDVRSQLASLARNLWSTPPAHGAAVVATILAD 300

Query: 302 EALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVDR 361
           E L+  W  EVE MR RI ++RQ LV+ L        F ++  QRGMFSYTGL+A QV R
Sbjct: 301 EPLRQIWQGEVERMRRRIASLRQGLVEALMPYGLAERFAHIAQQRGMFSYTGLTAEQVRR 360

Query: 362 LREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397
           LR E  VYL+ SGR  VAGL+   +  +AKA A V+
Sbjct: 361 LRAEDSVYLVESGRANVAGLDAERLDALAKAIARVV 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: 411
Number of extensions: 16
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: 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