GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Paraburkholderia bryophila 376MFSha3.1

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate H281DRAFT_06132 H281DRAFT_06132 acetyl-CoA C-acetyltransferase

Query= reanno::pseudo3_N2E3:AO353_25685
         (397 letters)



>FitnessBrowser__Burk376:H281DRAFT_06132
          Length = 395

 Score =  528 bits (1361), Expect = e-155
 Identities = 268/393 (68%), Positives = 322/393 (81%), Gaps = 1/393 (0%)

Query: 3   MSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLS 62
           M++DPIVIVSA RTPMGGFQGEL  L+AP LGA AI+AA+ERAGV+   V+E+  GCVLS
Sbjct: 1   MNNDPIVIVSAARTPMGGFQGELNLLTAPALGAVAIKAALERAGVSGSQVDELTLGCVLS 60

Query: 63  AGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESM 122
           AGLGQAPARQAA+ AGL  S  C+T++K+CGSGM+A ++AHD L AGSA V+VAGGMESM
Sbjct: 61  AGLGQAPARQAAIAAGLPLSVHCSTVSKVCGSGMKAVMVAHDALAAGSASVIVAGGMESM 120

Query: 123 SNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAY-DKGRLMGTFAEDCAEANGFTREAQD 181
           SNAPYLL +AR+G RMGH   LDHMF DGLEDAY D+GRLMGTFAEDCAE   FTR  QD
Sbjct: 121 SNAPYLLPKARAGLRMGHAAALDHMFFDGLEDAYFDRGRLMGTFAEDCAERFCFTRGDQD 180

Query: 182 EFAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRD 241
            +AIAST +AQQAI+ G+F+ EI P+ V     +K +  DEQPPKA+LDKI SLK AF+ 
Sbjct: 181 SYAIASTVKAQQAIESGAFDWEIAPVTVTSKVGEKTVDTDEQPPKARLDKIQSLKAAFKK 240

Query: 242 GGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIK 301
            GTVTAANSSSISDGAAAL+LMR S AE++GL+PLAV+ GH+ +AD P LF  AP+GAI+
Sbjct: 241 DGTVTAANSSSISDGAAALVLMRLSTAERQGLQPLAVVVGHSTYADEPRLFTTAPIGAIR 300

Query: 302 KLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARI 361
           KLL +T WS+ +V+L+E+NEAFAVVS+    +L I   +VN+HGGACALGHPIGASGARI
Sbjct: 301 KLLDRTEWSIGDVDLWEINEAFAVVSMACTKELGIAPERVNIHGGACALGHPIGASGARI 360

Query: 362 LVTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394
           LVTLL ALRQ G KRG+A++CIGGGEATA+A+E
Sbjct: 361 LVTLLGALRQTGGKRGIASLCIGGGEATAVAIE 393


Lambda     K      H
   0.318    0.133    0.378 

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: 492
Number of extensions: 10
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: 397
Length of database: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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