GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Chryseobacterium arthrosphaerae CC-VM-7

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_065400887.1 BBI00_RS21510 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_001684965.1:WP_065400887.1
          Length = 452

 Score =  359 bits (921), Expect = e-103
 Identities = 182/429 (42%), Positives = 267/429 (62%), Gaps = 4/429 (0%)

Query: 4   LSSADRASNEKKVKSSYFDLPPMEMSVAFPQATPAST---FPPCTSDYYHFNDLLTPEEQ 60
           LSS     +  K+  ++  L   ++S       P       PP   D+Y     L+PE++
Sbjct: 23  LSSISEKVDLPKLMQNFSKLDDKQLSGLMKMLDPEKKKKELPPIDGDFYDIYHTLSPEQR 82

Query: 61  AIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKGYGCPGLSITANAI 120
            I+ KVR+ MEKEV P++  YW + EFPF + PK   + + G + +GYGCPG+      +
Sbjct: 83  EIQLKVRDFMEKEVKPLVNHYWLRDEFPFELIPKFQKLNICGVTYEGYGCPGMPFLMEGV 142

Query: 121 ATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNG 180
              E+AR+DAS +TF  V S L M +I +CGSE QK+K+LP + +   +  + LTEP+ G
Sbjct: 143 IAMEMARIDASIATFFGVQSGLAMGSIYICGSEEQKQKWLPQMQKFEKIGAFGLTEPEVG 202

Query: 181 SDASG-LGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQINGFIVKKDAPGL 239
           S A+G L  T  K   GW +NGQK+WIGN+TFADL+II+AR+  + ++ GFIV+KD PG 
Sbjct: 203 SGAAGGLTVTCKKTPEGWILNGQKKWIGNATFADLVIIWARDLDSGEVKGFIVEKDNPGY 262

Query: 240 KATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAWQPIGIS 299
              KI  K+ LR+VQNG I L++  V +E+RL   NSF+DT KVL ++R  VAW   G +
Sbjct: 263 SVEKIKGKMALRIVQNGLITLKDCLVTEENRLQNANSFKDTGKVLRMTRAGVAWMATGCA 322

Query: 300 MGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQMTPG 359
            G Y+    Y ++R+QFG P+A+FQ+ Q  LV+ML N+ AM  M +RL ++ + G +   
Sbjct: 323 RGAYESALDYTRKREQFGRPIASFQMIQGHLVEMLSNLTAMQTMVFRLSEMQDEGILKDE 382

Query: 360 QASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDINTLVTG 419
            ASL K + + + R+  S  RE++GGNGIL ++ VA+   D E IY+YEGT +IN+L+ G
Sbjct: 383 HASLAKVFCTLRTRDIVSRAREVMGGNGILLEYDVARFVADAEAIYSYEGTKEINSLIVG 442

Query: 420 REVTGIASF 428
           R +TG ++F
Sbjct: 443 RSITGFSAF 451


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: 483
Number of extensions: 18
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: 436
Length of database: 452
Length adjustment: 32
Effective length of query: 404
Effective length of database: 420
Effective search space:   169680
Effective search space used:   169680
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: 51 (24.3 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