GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pco in Dyella japonica UNC79MFTsu3.2

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate N515DRAFT_0492 N515DRAFT_0492 hypothetical protein

Query= BRENDA::Q96329
         (436 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0492 N515DRAFT_0492
           hypothetical protein
          Length = 386

 Score =  179 bits (453), Expect = 2e-49
 Identities = 119/380 (31%), Positives = 189/380 (49%), Gaps = 10/380 (2%)

Query: 56  TPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKG-YGCPGLS 114
           T ++ +I+   R+  +K + P+  E   K EFP     ++G +G+ G  +   YG  G+ 
Sbjct: 6   TEDQLSIQSIARDFAQKRIVPVAAELDAKGEFPLENIREMGQLGLMGIEVPHEYGGAGMD 65

Query: 115 ITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWAL 174
             A  +A  EIA  DA+ ST + V++SL    I   G+E QK+KY+ ++AQ   +  +AL
Sbjct: 66  PIAYVLAMIEIAAADAATSTVMSVNNSLFCNGILKHGNEEQKQKYVRAIAQGEAIGAYAL 125

Query: 175 TEPDNGSDASGLGTTATK-VEGGWKINGQKRWIGNSTFADLLIIFARNTT---TNQINGF 230
           TEP +GSDAS + T ATK  +G W ING+K WI +   A  +++FA +T       ++ F
Sbjct: 126 TEPQSGSDASAMHTRATKNADGDWVINGKKSWITSGPVARYIVLFAISTPGIGARGVSAF 185

Query: 231 IVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL-PGVNSFQDTSKVLAVSRV 289
           I+    PG  A K   K+G+R     +I   +   P E+ L      F     VL   R+
Sbjct: 186 IIDTQLPGFAAGKTEPKLGIRASATCEIEFSDYVCPKENLLGEEGKGFSIAMGVLDAGRI 245

Query: 290 MVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLM----GW 345
            +A Q +GI+   Y+   ++ ++RK FG  + +FQ+ Q K+  M   + A  L+     W
Sbjct: 246 GIASQSVGIARAAYEATLQWSRDRKAFGQAIGSFQMTQAKIADMKCKLDAATLLTLRAAW 305

Query: 346 RLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIY 405
              +  + G     +AS+ K   S  A   A    ++ GG G   +  + + F D +   
Sbjct: 306 TKGQAEKNGGRFGTEASVAKLVASEAAMWIAHQAVQIHGGMGYSKEMPLERYFRDAKITE 365

Query: 406 TYEGTYDINTLVTGREVTGI 425
            YEGT +I  LV  R  TG+
Sbjct: 366 IYEGTSEIQRLVIARAETGL 385


Lambda     K      H
   0.319    0.133    0.399 

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: 377
Number of extensions: 20
Number of successful extensions: 5
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: 436
Length of database: 386
Length adjustment: 31
Effective length of query: 405
Effective length of database: 355
Effective search space:   143775
Effective search space used:   143775
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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