GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Marinobacter adhaerens HP15

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF1060 HP15_1039 acyl-CoA synthetase

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



>FitnessBrowser__Marino:GFF1060
          Length = 542

 Score =  213 bits (542), Expect = 2e-59
 Identities = 176/568 (30%), Positives = 265/568 (46%), Gaps = 52/568 (9%)

Query: 14  VDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASAL 73
           VD++    + V  IE+T   +        PE  A++  H   RY +AQ      RLASAL
Sbjct: 12  VDANYAVQSPVDFIERTATVY--------PEYPAVI--HGAIRYNWAQTYERCRRLASAL 61

Query: 74  LGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLV 133
            G G+  GD V +   N    V        +G VL  +N       + + L+    K+++
Sbjct: 62  KGRGIGRGDTVAVMLPNIPAMVEAHFGVPMIGAVLNTLNVRLDAEAIAFMLDHGEAKVVI 121

Query: 134 SMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDD-EAGQGADEPGLLRF 192
           +   F       ++R+               ++L     V+ +DD E G+G     L  +
Sbjct: 122 ADREFGE-----VIRDAV-------------SRLDTKPLVIDVDDPEYGEGVQVSDL-DY 162

Query: 193 TELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECM 252
              +  G   DP   Q +      D I++ +TSGTTG PKG    HR    N        
Sbjct: 163 EAFLQEG---DPTF-QWSFPENEWDAISLNYTSGTTGNPKGVVYHHRGAYINAIGNQTVW 218

Query: 253 KLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHG 312
            +         +P++HC G           G  +       DP  +LQ ++D + T + G
Sbjct: 219 SMDMHPVYLWTLPMFHCNGWCFPWTITAMAGTHVCLRR--VDPEKILQLIRDHQVTHMCG 276

Query: 313 VPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTET-S 371
            P +  A L+ P  A+  +      + AG+  P +V+   +E+M + ++T  YG+TE   
Sbjct: 277 APIVLNALLNVPESAKAGIDHDVKSMTAGAAPPAQVIG-AIEEMGI-QVTHVYGLTEVYG 334

Query: 372 PVSC---QSSTDT-PLSKRVSTVGQ--VQPHL--EVKIVDPDTGAVVPIGQR--GEFCTK 421
           PV+    +S  D  PL  R     +  V+ H      + DP+T   VP   +  GE   +
Sbjct: 335 PVTVCAWKSEWDALPLHDRARKKARQGVRYHTLAGTMVGDPNTMEPVPKDGKTIGEIFLR 394

Query: 422 GYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPRE 481
           G +VM GY  +   T EA   GGW HTGDLA    +GY+ I  R+KD++I GGENI   E
Sbjct: 395 GNTVMKGYLKNPKATEEAF-RGGWFHTGDLAVWHEDGYMEIKDRLKDIIISGGENISTIE 453

Query: 482 IEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP-GTQPTEDDIRAFCKGQIAHYKVP 540
           +E+ LYRHP V +  VV  PD+K+GE  CA++  KP     +E+DI  FC+  +A +KVP
Sbjct: 454 VEDTLYRHPAVLEAAVVARPDEKWGETPCAFVTLKPEAGDVSEEDIINFCREHLARFKVP 513

Query: 541 RYIRFVTSFPMTVTGKIQKFKIRDEMKD 568
           + I F +  P T TGKIQKF +RD+ K+
Sbjct: 514 KTIVF-SELPKTSTGKIQKFVLRDQAKE 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: 703
Number of extensions: 46
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 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