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_007153301.1 MDG893_RS08275 acyl-CoA synthetase

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



>NCBI__GCF_000170835.1:WP_007153301.1
          Length = 542

 Score =  201 bits (511), Expect = 6e-56
 Identities = 175/570 (30%), Positives = 258/570 (45%), Gaps = 53/570 (9%)

Query: 13  LVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASA 72
           L  + A  AT  PL       F A   +  PE  A++  H   R  + Q      RLASA
Sbjct: 9   LEPTDANNATLTPL------DFLARTASVYPEYPAVI--HGATRRNWQQTYERCRRLASA 60

Query: 73  LLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLL 132
           L   G+  GD V     N    +        +G VL  +N       + + L     K+L
Sbjct: 61  LADRGVGKGDTVAAMLPNIPPMLECHFGIPMLGAVLNALNTRLDAKAIAFMLEHGEAKVL 120

Query: 133 VSMARFKT--SDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGAD-EPGL 189
           ++   F    ++ +GML           P        PQ   V+ ++D    GA  +   
Sbjct: 121 IADREFGDVINEAVGML---------DNP--------PQ---VIDVNDPEFSGAGTQVSD 160

Query: 190 LRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIG 249
           L +   +A G+ A     Q+ A     D I++ +TSGTTG PKG    HR    N     
Sbjct: 161 LDYDAFVASGDPAFDW--QMPA--DEWDAISLCYTSGTTGNPKGVVYHHRGAYENAMGNQ 216

Query: 250 ECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTG 309
               +         +P++HC G           G  +       +P  +LQ + + + + 
Sbjct: 217 AVWSMGMHPVYLWTLPMFHCNGWCFPWTITAFAGTHVCLRK--VEPEKILQLISEHKVSH 274

Query: 310 LHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTE 369
           + G P +    L     A+ + S     + AG+  P +V++  +E M  R +T  YG+TE
Sbjct: 275 MCGAPIVLNTLLGASEAAKSSFSHTVQAMTAGAAPPAKVIE-AIENMGFR-VTHVYGLTE 332

Query: 370 T-SPVSC----QSSTDTPLSKRVSTVGQ--VQPHL--EVKIVDPDTGAVVPIGQR--GEF 418
              PV+         D P+  R     +  V+ H    + + DP+T   VP      GE 
Sbjct: 333 VYGPVTVCAWKSEWDDLPVEDRARIKARQGVRYHTLAGMMVGDPETMEAVPKDGNTIGEI 392

Query: 419 CTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIY 478
             +G +VM GY  +   T EA   GGW HTGDLA   A+GY  I  R+KD++I GGENI 
Sbjct: 393 FLRGNTVMKGYLKNPKATEEAF-RGGWFHTGDLAVWHADGYAEIKDRLKDIIISGGENIS 451

Query: 479 PREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP-GTQPTEDDIRAFCKGQIAHY 537
             E+E+ LYRHP + +  VV  PD+K+GE  CA++  KP   + +EDDI AFC+ ++A +
Sbjct: 452 TIEVEDVLYRHPDILEAAVVARPDEKWGETPCAFVTLKPEAGEVSEDDIIAFCRERMAKF 511

Query: 538 KVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567
           KVP+ I F +  P T TGKIQKF +RD+ K
Sbjct: 512 KVPKTIVF-SELPKTSTGKIQKFVLRDDAK 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: 728
Number of extensions: 45
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
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