GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS19375 BPHYT_RS19375 AMP-binding
           protein
          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 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