GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Escherichia coli BW25113

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 15923 b1805 acyl-CoA synthase (NCBI)

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



>FitnessBrowser__Keio:15923
          Length = 561

 Score =  244 bits (622), Expect = 9e-69
 Identities = 173/551 (31%), Positives = 269/551 (48%), Gaps = 25/551 (4%)

Query: 29  QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALL-GMGLTPGDRVGIW 87
           Q++   F   VAR  ++ A V++  G   T+ +L+  +   A+ L  G+GL  GDRV + 
Sbjct: 23  QSLVDMFEQSVARYADQPAFVNM--GEVMTFRKLEERSRAFAAYLQQGLGLKKGDRVALM 80

Query: 88  SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARF-----KTSD 142
             N  ++ +      + G+++VN+NP Y   E+E+ LN  G   +V ++ F     K  D
Sbjct: 81  MPNLLQYPVALFGILRAGMIVVNVNPLYTPRELEHQLNDSGASAIVIVSNFAHTLEKVVD 140

Query: 143 YLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAA 202
              +   +      Q    L  AK   +  VV            P  + F   +  G   
Sbjct: 141 KTAVQHVILTRMGDQ----LSTAKGTVVNFVVKYIKRLVPKYHLPDAISFRSALHNGY-- 194

Query: 203 DPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMK--LTPADRL 260
             R+  V   L   D   +Q+T GTTG  KGA LTHRN+L N   +       L P   L
Sbjct: 195 --RMQYVKPELVPEDLAFLQYTGGTTGVAKGAMLTHRNMLANLEQVNATYGPLLHPGKEL 252

Query: 261 CIP-VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIA 319
            +  +PLYH F + +  L     G   +   +  D   +++ +     T + GV T+F A
Sbjct: 253 VVTALPLYHIFALTINCLLFIELGGQNLLITNPRDIPGLVKELAKYPFTAITGVNTLFNA 312

Query: 320 ELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSST 379
            L++  F + + S+L      G P    V +R V+ +  + +   YG+TE +P+   +  
Sbjct: 313 LLNNKEFQQLDFSSLHLSAGGGMPVQQVVAERWVK-LTGQYLLEGYGLTECAPLVSVNPY 371

Query: 380 DTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREA 439
           D  +     ++G   P  E K+VD D   V P GQ GE C KG  VM GYW     T E 
Sbjct: 372 D--IDYHSGSIGLPVPSTEAKLVDDDDNEVPP-GQPGELCVKGPQVMLGYWQRPDATDEI 428

Query: 440 IDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVG 499
           I + GW+HTGD+A MD EG++ IV R KDM++  G N+YP EIE+ + +HP VQ+V  VG
Sbjct: 429 I-KNGWLHTGDIAVMDEEGFLRIVDRKKDMILVSGFNVYPNEIEDVVMQHPGVQEVAAVG 487

Query: 500 VPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQK 559
           VP    GE +  +++ K  +  TE+ +  FC+ Q+  YKVP+ + F    P +  GKI +
Sbjct: 488 VPSGSSGEAVKIFVVKKDPSL-TEESLVTFCRRQLTGYKVPKLVEFRDELPKSNVGKILR 546

Query: 560 FKIRDEMKDQL 570
            ++RDE + ++
Sbjct: 547 RELRDEARGKV 557


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: 765
Number of extensions: 36
Number of successful extensions: 8
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: 561
Length adjustment: 36
Effective length of query: 542
Effective length of database: 525
Effective search space:   284550
Effective search space used:   284550
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