GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Burkholderia phytofirmans PsJN

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 BPHYT_RS02230 BPHYT_RS02230 acetyl-CoA acetyltransferase

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



>FitnessBrowser__BFirm:BPHYT_RS02230
          Length = 397

 Score =  516 bits (1328), Expect = e-151
 Identities = 259/389 (66%), Positives = 311/389 (79%)

Query: 6   DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65
           DPIVIV   RTPM  FQG+  +L+APQLG+ AI AAV+RAG+  + V+EV+ GCVL AGL
Sbjct: 7   DPIVIVGVARTPMAAFQGDFAALTAPQLGSVAIEAAVKRAGLKPEQVDEVVMGCVLPAGL 66

Query: 66  GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125
           GQAPARQAALGAGL  +T  TT+NKMCGSGM AA+ AHDML AGS DV+VAGGMESM+NA
Sbjct: 67  GQAPARQAALGAGLPLATGSTTVNKMCGSGMRAAMFAHDMLAAGSVDVIVAGGMESMTNA 126

Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185
           PYLL +AR+G RMGHG+V+DHMF DGLEDAY+KGRLMGTFAE+CA +  FTREAQD FA+
Sbjct: 127 PYLLPKARNGMRMGHGQVIDHMFYDGLEDAYEKGRLMGTFAEECAASFDFTREAQDAFAV 186

Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245
            S  RA++A +DGSF  EI P++V   K    I  DEQP KA  +KI +LKPAF   GTV
Sbjct: 187 ESLNRAKRANEDGSFGWEIAPVKVESRKGDVTIDRDEQPFKANPEKIPTLKPAFSKTGTV 246

Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305
           TAANSSSISDGAAAL++MR S A + G++P+A + GH+ FA  P  F  APVGAI+KL +
Sbjct: 247 TAANSSSISDGAAALVMMRESTARRLGVEPIARVVGHSTFAQEPAKFTTAPVGAIRKLFE 306

Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365
           K GW  DEV+L+EVNEAFAVV++  M +  +PH KVNV+GGACALGHPIGASGARILVTL
Sbjct: 307 KNGWRADEVDLYEVNEAFAVVTMAAMKEHHLPHEKVNVNGGACALGHPIGASGARILVTL 366

Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVE 394
           + AL+++GLKRGVA +CIGGGEATAM +E
Sbjct: 367 IGALKKRGLKRGVATLCIGGGEATAMGIE 395


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: 513
Number of extensions: 12
Number of successful extensions: 1
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: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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