GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_0492
          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 (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