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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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