GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:15923 b1805 acyl-CoA synthase (NCBI)
          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 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