Alignments for a candidate for aacS in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Cupriavidus basilensis 4G11

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate RR42_RS26915 RR42_RS26915 AMP-binding protein

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



>FitnessBrowser__Cup4G11:RR42_RS26915
          Length = 573

 Score =  718 bits (1854), Expect = 0.0
 Identities = 352/563 (62%), Positives = 431/563 (76%), Gaps = 8/563 (1%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75
           SH RG+TD+PL E T+ A  A+ VAR P+REA+V   QG R+++ +       +A  L  
Sbjct: 18  SHVRGSTDIPLSELTVPALLAETVARFPDREAVVFREQGIRWSWREFAQVVDAMAGGLRL 77

Query: 76  MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135
           +GL  GDR+GIWS N  EW++ Q ATA++GLVLVNINPAYR AE+EYALNKVGCK +V+ 
Sbjct: 78  LGLERGDRIGIWSPNRVEWLVTQFATARLGLVLVNINPAYRLAELEYALNKVGCKAIVAA 137

Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195
             FKTS YL ML+ LAPE +  +PG LQAA+LP L+ V+ +  E       PG+L +  L
Sbjct: 138 ESFKTSRYLEMLQTLAPELKSCEPGTLQAARLPALRWVIRMGAER-----TPGMLNYDAL 192

Query: 196 IARG-NAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254
           +A G +A    L  + A L   DPINIQFTSGTTG PKGATLTHRNI+NN  FI   M+ 
Sbjct: 193 LAHGTHALTSELDALTAQLDRYDPINIQFTSGTTGAPKGATLTHRNIVNNARFIAMAMRF 252

Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314
           +  D+LCIPVP YHCFGMVL  LAC + GA +V+P + F+P   +  V +ERCT LHGVP
Sbjct: 253 SEQDKLCIPVPFYHCFGMVLAVLACVSTGACMVFPGEAFEPAATMAAVSEERCTALHGVP 312

Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374
           TMFIA+LDHP FA+++ STLRTGIMAGSPCP E MKRV+ QM++ ++TIAYGMTETSPVS
Sbjct: 313 TMFIAQLDHPDFAKYDFSTLRTGIMAGSPCPIETMKRVISQMHMAQVTIAYGMTETSPVS 372

Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434
            QSST  PL KRV+TVGQ+QPHLEVK+VD  TG +VP+G++GE CT+GYSVM GYW DE 
Sbjct: 373 FQSSTTDPLDKRVTTVGQIQPHLEVKLVD-GTGEIVPVGEKGELCTRGYSVMQGYWDDEP 431

Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494
           +TREAI + GWMHTGDLAT+DAEGY NIVGR+KDM+IRGGEN+YPREIEEFL+RHP+VQ 
Sbjct: 432 RTREAIRD-GWMHTGDLATIDAEGYCNIVGRVKDMLIRGGENVYPREIEEFLFRHPKVQA 490

Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVT 554
           VQV GVPD KYGEE+CAWI+ KPG   TEDDIRAFC+ QIAHYK+PRYIRFV   PMT+T
Sbjct: 491 VQVFGVPDPKYGEEVCAWIVLKPGDTATEDDIRAFCRDQIAHYKIPRYIRFVDEMPMTIT 550

Query: 555 GKIQKFKIRDEMKDQLGLEEQKT 577
           GK+QKF +R+ M  +LGL ++ T
Sbjct: 551 GKVQKFVMRERMTLELGLGDKTT 573


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: 915
Number of extensions: 34
Number of successful extensions: 4
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: 573
Length adjustment: 36
Effective length of query: 542
Effective length of database: 537
Effective search space:   291054
Effective search space used:   291054
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources