GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Pedobacter sp. GW460-11-11-14-LB5

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate CA265_RS14465 CA265_RS14465 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__Pedo557:CA265_RS14465
          Length = 453

 Score =  376 bits (966), Expect = e-109
 Identities = 191/389 (49%), Positives = 258/389 (66%), Gaps = 2/389 (0%)

Query: 42  PPCTSDYYHFND-LLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGV 100
           PP   D+YH  D  L  E++ ++ KVR  +EKEV PI+  YW KAEFPF I PKL  + +
Sbjct: 64  PPIEGDFYHLGDEALKDEDRELQLKVRAFLEKEVKPIVNHYWNKAEFPFEIIPKLAELNI 123

Query: 101 AGGSIKGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYL 160
            G + KGYGCPG S     I   E+AR+D S STF  V S L M +I LCGSE QK+++L
Sbjct: 124 CGLTYKGYGCPGKSNLMEGILAMEMARIDTSISTFFGVQSGLAMGSIYLCGSEEQKQQWL 183

Query: 161 PSLAQLNTVACWALTEPDNGSDASG-LGTTATKVEGGWKINGQKRWIGNSTFADLLIIFA 219
           P + Q   +  + LTEP+ GS A+G L TT  KV+G W +NGQK+WIGN+TFAD+LII+A
Sbjct: 184 PLMQQFKIIGAFGLTEPEVGSAAAGGLTTTCKKVDGKWVLNGQKKWIGNATFADILIIWA 243

Query: 220 RNTTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQD 279
           R+  + ++ GFIVKKD PG    K+ +K+ LR+VQNG I L N  V + DRL   NSF+D
Sbjct: 244 RDEESGEVKGFIVKKDNPGFAVEKMQDKMALRIVQNGIITLTNCEVEEADRLQNANSFKD 303

Query: 280 TSKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQA 339
           T+KVL ++R  VAWQ +G + G Y+    Y + RKQFG P+A+FQL Q  LV+ML N+ A
Sbjct: 304 TAKVLQMTRAGVAWQAVGCARGAYENALDYTRTRKQFGKPIASFQLIQNHLVEMLSNLTA 363

Query: 340 MFLMGWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFC 399
           M  + +RL +L + G +    ASL K + S + R+  S  RE++GGNGIL ++ VA+   
Sbjct: 364 MQTLCFRLSQLQDQGLLKDEHASLAKVFCSLRTRDVVSRAREVMGGNGILLEYNVARFVA 423

Query: 400 DLEPIYTYEGTYDINTLVTGREVTGIASF 428
           D E IY+YEGT +INTL+ GR +TG ++F
Sbjct: 424 DAEAIYSYEGTKEINTLIVGRAITGFSAF 452


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: 449
Number of extensions: 18
Number of successful extensions: 3
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: 453
Length adjustment: 32
Effective length of query: 404
Effective length of database: 421
Effective search space:   170084
Effective search space used:   170084
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 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