GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Halomonas desiderata SP1

Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_086508794.1 BZY95_RS04550 amino acid aminotransferase

Query= BRENDA::P04693
         (397 letters)



>NCBI__GCF_002151265.1:WP_086508794.1
          Length = 395

 Score =  333 bits (855), Expect = 4e-96
 Identities = 167/396 (42%), Positives = 243/396 (61%), Gaps = 2/396 (0%)

Query: 1   MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60
           MF+ ++   GD IL L+E FK+D    KV+L +G+Y +  G  P ++AV EAEA L  + 
Sbjct: 1   MFEHIERVPGDAILGLIEAFKKDTNPQKVDLGVGVYKDAQGNTPVMRAVKEAEALL-LKN 59

Query: 61  HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120
                Y+   G   Y   + P++ G D PVL  +R +  Q+ GG+GAL++ ADF+    P
Sbjct: 60  ETTKTYIGSHGAPQYGEVVLPMVLGQDSPVLAAKRASATQSPGGTGALRLAADFISTQLP 119

Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180
              +WVSDPTW NH  IF  AG E+  YP+ D A N + F  +LA +K +PA  +++LH 
Sbjct: 120 GKSIWVSDPTWPNHHGIFKAAGIELHKYPYVD-AENRLDFAGMLAAVKQIPAGDVIVLHA 178

Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240
           CCHNPTG DL   QW  ++E+++ R L+P +D AYQGFG G++EDAY +R +A      +
Sbjct: 179 CCHNPTGFDLDRGQWQQILEVVRERNLLPLIDFAYQGFGEGLDEDAYGVRLMAENLDEVI 238

Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300
           +++S SK F +Y ER G L ++ +++E    V  Q+    R NYS+PP  G  +V+ +L+
Sbjct: 239 ITSSCSKNFGIYCERTGCLIMVAKNSEQMENVRSQVAIVARENYSNPPAHGGAIVSEILH 298

Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360
              L A W  E+ EMR RI  +R++ V+ L     ++ +  +  QRGMFSYTGL   QVD
Sbjct: 299 SAELAALWREELTEMRDRINTLRRDFVESLKPYGLDQKYACVAEQRGMFSYTGLKPEQVD 358

Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396
           RLR+EFG+Y++ SGR  VAG +  N+  +AKA AAV
Sbjct: 359 RLRDEFGIYMVRSGRANVAGFSHENLPYLAKAIAAV 394


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: 390
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: 397
Length of database: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
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