GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Stenotrophomonas chelatiphaga DSM 21508

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_057507944.1 ABB28_RS06925 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_001431535.1:WP_057507944.1
          Length = 382

 Score =  167 bits (422), Expect = 7e-46
 Identities = 114/376 (30%), Positives = 180/376 (47%), Gaps = 6/376 (1%)

Query: 56  TPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKG-YGCPGLS 114
           T E+  ++   R   ++++AP    +    EFP      LG  G+ G  +   YG  G+ 
Sbjct: 6   TEEQLMLQDVARRIAQEKIAPSAEHHDRTGEFPLANIQLLGENGLMGIEVPAEYGGAGMD 65

Query: 115 ITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWAL 174
             A  +A  E+A  DA+ ST + V++SL    I   G+EAQK+KY+ ++A+   +  +AL
Sbjct: 66  PIAYVLAMVEVAAGDAAHSTIMSVNNSLFCNGILTHGNEAQKQKYVRAIAEGTAIGAFAL 125

Query: 175 TEPDNGSDASGLGTTATK-VEGGWKINGQKRWIGNSTFADLLIIFARNTT---TNQINGF 230
           TEP +GSDA+ +   A K  +G + ING+K WI +   A  +++FA          I+ F
Sbjct: 126 TEPQSGSDATAMRCRAVKQADGSYVINGKKSWITSGPVAKYIVLFAMTDADKGARGISAF 185

Query: 231 IVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNS-FQDTSKVLAVSRV 289
           ++  D  G    K   K+G+R     +I   +     ED L      F+    VL   R+
Sbjct: 186 LIDTDNAGFGRGKTEPKLGIRASATCEIEFNDYVAQAEDLLGQEGEGFKIAMGVLDAGRI 245

Query: 290 MVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCK 349
            +A Q IGI+   Y+    Y+KERK FGA +  FQ+ Q K+  M   + A  L+  R   
Sbjct: 246 GIASQAIGIARAAYEATLEYVKERKAFGAAIGTFQMTQAKIADMKCKLDAALLLTLRAAW 305

Query: 350 LYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEG 409
           +   G+    +A++ K   S  A        ++ GG G   +  + + F D +    YEG
Sbjct: 306 VKGEGKRFSNEAAIAKLTASEAAMWITHQAVQIHGGMGYSKEMPLERYFRDAKITEIYEG 365

Query: 410 TYDINTLVTGREVTGI 425
           T +I  LV  R  TG+
Sbjct: 366 TSEIQRLVIARNETGL 381


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: 352
Number of extensions: 17
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: 382
Length adjustment: 31
Effective length of query: 405
Effective length of database: 351
Effective search space:   142155
Effective search space used:   142155
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 24 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