GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMa1450 SMa1450 thiolase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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