GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Burkholderia phytofirmans PsJN

Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate BPHYT_RS02230 BPHYT_RS02230 acetyl-CoA acetyltransferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982
         (397 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS02230 BPHYT_RS02230 acetyl-CoA
           acetyltransferase
          Length = 397

 Score =  523 bits (1346), Expect = e-153
 Identities = 264/389 (67%), Positives = 314/389 (80%)

Query: 6   DPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVLPAGL 65
           DPIVIV   RTPM  FQG+  +LTAPQLG+ AI+AAV+RAG+  + VDEV+ GCVLPAGL
Sbjct: 7   DPIVIVGVARTPMAAFQGDFAALTAPQLGSVAIEAAVKRAGLKPEQVDEVVMGCVLPAGL 66

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

Query: 126 PYLLDRARAGYRMGHGRVQDSMFLDGLEDAYDKGRLMGTFAEDCAETNGFSREAQDAFAI 185
           PYLL +AR G RMGHG+V D MF DGLEDAY+KGRLMGTFAE+CA +  F+REAQDAFA+
Sbjct: 127 PYLLPKARNGMRMGHGQVIDHMFYDGLEDAYEKGRLMGTFAEECAASFDFTREAQDAFAV 186

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

Query: 246 TAANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIKKLMK 305
           TAANSSSISDGAAALV+MR+S A++ G++P+A + GH+ FA  P  F  AP+GAI+KL +
Sbjct: 247 TAANSSSISDGAAALVMMRESTARRLGVEPIARVVGHSTFAQEPAKFTTAPVGAIRKLFE 306

Query: 306 KTGWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARILVTL 365
           K GW  ++VDL EVNEAFAVV MAAM    +PHEK+NV+GGACALGHPIGASGARILVTL
Sbjct: 307 KNGWRADEVDLYEVNEAFAVVTMAAMKEHHLPHEKVNVNGGACALGHPIGASGARILVTL 366

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


Lambda     K      H
   0.318    0.132    0.376 

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: 550
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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