GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Sinorhizobium meliloti 1021

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 SMa1450 SMa1450 thiolase

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



>FitnessBrowser__Smeli:SMa1450
          Length = 396

 Score =  555 bits (1431), Expect = e-163
 Identities = 276/389 (70%), Positives = 327/389 (84%)

Query: 6   DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65
           DP+VIV   RTP+G FQGELK LSA  LGAAAI  A++RAG+A DAV+EV+FGCVL+AG 
Sbjct: 5   DPVVIVGQARTPLGSFQGELKDLSAADLGAAAIVDALKRAGLAPDAVDEVMFGCVLTAGQ 64

Query: 66  GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125
           GQAPARQAALGAGL      TT+NKMCGSGM+AA+LAHD++ A SA +VVAGGMESM+NA
Sbjct: 65  GQAPARQAALGAGLPPGVGATTVNKMCGSGMKAAMLAHDLIKAESASIVVAGGMESMTNA 124

Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185
           PYLLDRAR GYR+GH KVLDHMFLDGLEDAYDKGRLMG+FAEDCAEA  FTR AQDE+AI
Sbjct: 125 PYLLDRARQGYRIGHQKVLDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTRSAQDEYAI 184

Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245
           AS  +AQ+A  DGSF  EIVPL +  GK ++ +  DEQP KA+LDKI  LKPAFRDGGT+
Sbjct: 185 ASLEKAQKASADGSFAEEIVPLSIASGKGERTVNLDEQPQKARLDKIPLLKPAFRDGGTI 244

Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305
           TAAN+SSISDGAAAL+LMRRS A+K+G+ PLAVI GHA  AD P LFP AP+GAIK L +
Sbjct: 245 TAANASSISDGAAALVLMRRSAADKQGIGPLAVICGHATHADAPSLFPTAPIGAIKALCR 304

Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365
           + GW + EV+LFE+NEAFAVV +  M +L +   KVNVHGGACALGHPIGASGAR++VTL
Sbjct: 305 RIGWDIGEVDLFEINEAFAVVPMAAMRELGLDAEKVNVHGGACALGHPIGASGARVIVTL 364

Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVE 394
           ++ALR++GL+RG+A++CIGGGEATA+AVE
Sbjct: 365 VNALRRRGLRRGIASVCIGGGEATAVAVE 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: 546
Number of extensions: 17
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: 396
Length adjustment: 31
Effective length of query: 366
Effective length of database: 365
Effective search space:   133590
Effective search space used:   133590
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