GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Dinoroseobacter shibae DFL-12

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate 3606714 Dshi_0145 Aspartate transaminase (RefSeq)

Query= CharProtDB::CH_004054
         (397 letters)



>FitnessBrowser__Dino:3606714
          Length = 392

 Score =  226 bits (577), Expect = 7e-64
 Identities = 146/398 (36%), Positives = 204/398 (51%), Gaps = 9/398 (2%)

Query: 1   MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60
           MF  +   A DPIL LM  F+ DPR  KV+L IG++ + +G  P   AV  AE RL  + 
Sbjct: 1   MFAHLRPQADDPILVLMRAFQADPRPGKVDLGIGVWRDAEGRTPVFGAVKTAEERL-WRT 59

Query: 61  HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120
                Y+   G   +  A+  LL G+    + + R  T  T GG+ A++      +   P
Sbjct: 60  QDTKSYVSFAGDPAFHAAVGDLLLGS----VTRPRAVTATT-GGTSAVQTLLALSQVARP 114

Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180
            + VW+   TW NH  +    G     + +      G+    LL  L    A  +V+LH 
Sbjct: 115 AAQVWIPAETWPNHRVLAEHLGLATRAFTYLAPEGTGIDREVLLRDLAQAQAGDVVILHA 174

Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLP-A 239
           CCHNPTG D   +    +++ L     +P +D AY GFGA  E DA  +R +AS  LP A
Sbjct: 175 CCHNPTGIDPDPELQAEIVDSLARTGAVPLVDCAYLGFGAVPEADAAFLRRLAS--LPEA 232

Query: 240 LVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVL 299
           +++ S SK F LY ERVG   V+ E       V  QL    R NYS PP+ GA+VV  +L
Sbjct: 233 MLAFSGSKSFGLYRERVGLALVLLEQPGVVEAVQSQLTRLNRVNYSFPPDHGARVVTEIL 292

Query: 300 NDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQV 359
            D AL+ +W AE+  +RT + A RQ L K L   +    FD L  Q GMF+   L   +V
Sbjct: 293 ADPALRTAWEAELAAIRTALSANRQALAKALRARLQSDRFDGLAAQSGMFAMLPLGKERV 352

Query: 360 DRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397
            R+RE+F VY + +GR+ +AG+      RVA+A AAV+
Sbjct: 353 MRMREDFAVYAVGTGRVNLAGVTPRTTDRVAEAIAAVL 390


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: 387
Number of extensions: 23
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: 392
Length adjustment: 31
Effective length of query: 366
Effective length of database: 361
Effective search space:   132126
Effective search space used:   132126
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 Sep 17 2021. The underlying query database was built on Sep 17 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