GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Marinobacter algicola DG893

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_007151877.1 MDG893_RS01200 acyl-CoA synthetase

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



>NCBI__GCF_000170835.1:WP_007151877.1
          Length = 542

 Score =  211 bits (536), Expect = 8e-59
 Identities = 165/531 (31%), Positives = 244/531 (45%), Gaps = 42/531 (7%)

Query: 51  VHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110
           +H   RYT+ Q      RLASAL   G+  GD V     N    V        +G VL  
Sbjct: 39  IHGAIRYTWGQTYERCRRLASALSSRGIGRGDTVAAMLPNIPAMVECHFGVPMIGAVLNT 98

Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQL 170
           +N       + + L     K++V+   F      G++R+               ++L   
Sbjct: 99  LNVRLDAEAIAFMLEHAEAKVVVADREFG-----GVVRDAV-------------SRLDSK 140

Query: 171 KTVVWIDD-EAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTG 229
             V+ +DD E G+G     L  +   +  G   DP   Q        D I++ +TSGTTG
Sbjct: 141 PLVIDVDDPEYGEGIQMSDL-DYEAFLQEG---DPEF-QWNLPENEWDAISLNYTSGTTG 195

Query: 230 FPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYP 289
            PKG    HR    N         +         +P++HC G           G  +   
Sbjct: 196 NPKGVVYHHRGAYLNSLGNQAVWSMGQHPVYLWTLPMFHCNGWCFPWTVTAMAGTHVCLR 255

Query: 290 NDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVM 349
               DP  +LQ ++D + T + G P +  A L+ P  A+  +      + AG+  P +V+
Sbjct: 256 R--VDPEKILQLIRDHQVTHMCGAPIVLNALLNVPESAKAGIDHEVKAMTAGAAPPAQVI 313

Query: 350 KRVVEQMNLREITIAYGMTET-SPVSCQSSTDTPLSKRVSTVGQVQPHLEVK-------- 400
              +E+M +  IT  YG+TE   PV+  +       K +     ++    V+        
Sbjct: 314 G-AIEEMGIA-ITHVYGLTEVYGPVTVCAWKAEWDEKTLDERATIKARQGVRYHTLAGTM 371

Query: 401 IVDPDTGAVVPIGQR--GEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEG 458
           + DP T   VP   +  GE   +G +VM GY  +   T EA   GGW HTGDLA    +G
Sbjct: 372 VGDPSTMEPVPNDGKTIGEIFLRGNTVMKGYLKNPKATEEAF-RGGWFHTGDLAVWHEDG 430

Query: 459 YVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP- 517
           Y+ I  R+KD++I GGENI   E+E+ LYRHP V +  VV  PD K+GE  CA+I  KP 
Sbjct: 431 YMEIKDRLKDIIISGGENISTIEVEDTLYRHPAVLEAAVVARPDAKWGETPCAFITLKPE 490

Query: 518 GTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKD 568
            ++ +E+D+  FC+ ++A +KVP+ I F T  P T TGKIQKF +RD+ K+
Sbjct: 491 ASEVSEEDLIDFCRERLARFKVPKTIVF-TDLPKTSTGKIQKFVLRDQAKE 540


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: 706
Number of extensions: 45
Number of successful extensions: 7
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: 542
Length adjustment: 36
Effective length of query: 542
Effective length of database: 506
Effective search space:   274252
Effective search space used:   274252
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 24 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