GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Burkholderia phytofirmans PsJN

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate BPHYT_RS19375 BPHYT_RS19375 AMP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>FitnessBrowser__BFirm:BPHYT_RS19375
          Length = 576

 Score =  717 bits (1850), Expect = 0.0
 Identities = 353/565 (62%), Positives = 430/565 (76%), Gaps = 9/565 (1%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75
           S+ RG+TD+PL E T+G F  D  A  P+R A+V   Q  R+T+ +   E   LA+ LL 
Sbjct: 19  SYVRGSTDIPLSEATVGRFLRDTAASFPDRPAVVFREQLIRWTWKEFAEEVDILAAGLLT 78

Query: 76  MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135
           +G+  GDRVGIWS N  EW+L Q ATA++G VLVNINPAYR AE+EYALNKVGCK +++ 
Sbjct: 79  LGIAKGDRVGIWSPNRVEWLLTQFATARIGAVLVNINPAYRLAELEYALNKVGCKAIIAA 138

Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195
            RFKTS YL ML+ LAPE   Q PG L AA+LP+L+ V+ + D      + PG+L F+++
Sbjct: 139 ERFKTSMYLEMLQALAPELATQAPGELHAARLPELRYVIRMCD-----TETPGMLTFSDV 193

Query: 196 IARGNAA--DPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMK 253
           I RG       +L  + A L   +PINIQFTSGTTG PKGATLTH N++NN  +I   M+
Sbjct: 194 IERGRVCLDVAKLDAIGATLSCHEPINIQFTSGTTGNPKGATLTHSNVVNNARYIAMAMR 253

Query: 254 LTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGV 313
           L+  D LCIPVPLYHCFGMVL  LAC + GA +V+P +GFDP   L  V +E+CT LHGV
Sbjct: 254 LSEQDGLCIPVPLYHCFGMVLAVLACVSVGAKMVFPGEGFDPAATLAAVAEEQCTALHGV 313

Query: 314 PTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPV 373
           PTMFIAELDHP FA ++ S LRTGIMAGSPCP E MK+VV +M+L EITIAYGMTETSPV
Sbjct: 314 PTMFIAELDHPNFATYDFSRLRTGIMAGSPCPIETMKKVVSRMHLSEITIAYGMTETSPV 373

Query: 374 SCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDE 433
           S QSST  PL KR +TVG++QPHLEVKIVDP  GA+VP+G+ GE CT+GYSVM GYWGDE
Sbjct: 374 SFQSSTTDPLDKRTTTVGRIQPHLEVKIVDP-LGAIVPVGETGELCTRGYSVMQGYWGDE 432

Query: 434 AKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQ 493
           AKTRE+I + GWMHTGDLAT+DAEGY NIVGR+KDM+IRGGENIYPREIEEFL+RHP++Q
Sbjct: 433 AKTRESIVD-GWMHTGDLATLDAEGYCNIVGRLKDMLIRGGENIYPREIEEFLFRHPKIQ 491

Query: 494 DVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTV 553
            VQV GVPD KYGEE+CAW++ + G Q T ++I+ FC GQIAHYKVP+YIRFV   PMTV
Sbjct: 492 SVQVFGVPDTKYGEEVCAWVVLRSGEQVTAEEIQQFCHGQIAHYKVPKYIRFVDELPMTV 551

Query: 554 TGKIQKFKIRDEMKDQLGLEEQKTA 578
           TGK+QKF +R++M  +L L E KTA
Sbjct: 552 TGKVQKFIMREQMISELKLREDKTA 576


Lambda     K      H
   0.320    0.136    0.412 

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: 914
Number of extensions: 34
Number of successful extensions: 6
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: 578
Length of database: 576
Length adjustment: 36
Effective length of query: 542
Effective length of database: 540
Effective search space:   292680
Effective search space used:   292680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 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