GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Marino:GFF1060 HP15_1039 acyl-CoA synthetase
          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 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