GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Acidovorax sp. GW101-3H11

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate Ac3H11_4115 Aromatic-amino-acid aminotransferase (EC 2.6.1.57)

Query= CharProtDB::CH_004054
         (397 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4115
          Length = 398

 Score =  397 bits (1021), Expect = e-115
 Identities = 205/397 (51%), Positives = 263/397 (66%), Gaps = 1/397 (0%)

Query: 1   MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60
           +F  V+    DPIL L E+F  D   +KVNL +G+Y++++G +P LQ V  AE  + + P
Sbjct: 3   LFTAVEMAPRDPILGLNEQFNADTNPNKVNLGVGVYFDDNGKLPLLQCVQAAEKTMMSTP 62

Query: 61  HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120
                YLP++G+  Y +A+  L+FGAD   +   RVAT+Q +GG+G LK+GADFLK+  P
Sbjct: 63  TARG-YLPIDGIVAYDNAVKSLVFGADSEPVTSGRVATVQAIGGTGGLKIGADFLKKVSP 121

Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180
            + V +SDP+WENH A+F  AGFEV TY +YD    GV F   LA+L      +IV+LH 
Sbjct: 122 SAKVLISDPSWENHRALFTNAGFEVDTYAYYDAEKRGVNFEGFLASLNAAAPGTIVVLHA 181

Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240
           CCHNPTG D+T  QWD VI  +KA+ L PFLD+AYQGFG G+ ED   I    +AGL   
Sbjct: 182 CCHNPTGYDITAAQWDQVIAAVKAKGLTPFLDMAYQGFGHGIAEDGAVIGKFVAAGLNFF 241

Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300
           VS SFSK FSLYGERVGGLSV+C D E A RVL QLK  +R NYS+PP  G  VVAAVLN
Sbjct: 242 VSTSFSKSFSLYGERVGGLSVLCADKEEASRVLSQLKIVIRTNYSNPPIHGGAVVAAVLN 301

Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360
           +  L+A W  E+ EMR RI AMRQ+LV  L     +++  ++  Q GMFSY+GLS  Q+ 
Sbjct: 302 NPELRAMWEQELAEMRVRIKAMRQKLVDGLKAAGVKQDMSFITTQIGMFSYSGLSKDQMV 361

Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397
           RLR EFGVY   +GRMCVA LN+ N+  V +A A V+
Sbjct: 362 RLRNEFGVYGTDTGRMCVAALNSKNIDYVCQAIAKVV 398


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: 434
Number of extensions: 22
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 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