GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Shewanella oneidensis MR-1

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 201132 SO1971 AMP-binding family protein (NCBI ptt file)

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



>lcl|FitnessBrowser__MR1:201132 SO1971 AMP-binding family protein
           (NCBI ptt file)
          Length = 578

 Score =  620 bits (1600), Expect = 0.0
 Identities = 311/571 (54%), Positives = 391/571 (68%), Gaps = 7/571 (1%)

Query: 1   VTSSAAATNSAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYA 60
           VT+ A     +PL  S  RG     L+E+TIG +  D+    PE+ A+V  HQ  R+ Y 
Sbjct: 8   VTNQATNQTISPLKYSEFRGPNAPELVEKTIGQYLDDIANTYPEQLAVVVNHQDIRWNYR 67

Query: 61  QLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEV 120
           Q       LA+ LL +G+ PGDR+GIWS NN EW L Q ATA++G ++V INPAYR  E+
Sbjct: 68  QYLARIDALAAGLLKLGIGPGDRIGIWSPNNIEWCLTQFATAKIGAIMVCINPAYRPEEL 127

Query: 121 EYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEA 180
           +YAL  VGC+ ++   +FK+S+YL ML  LAPE +    G LQA  LP+L+ V+ +  E 
Sbjct: 128 QYALTNVGCRAVICADKFKSSNYLQMLYTLAPELKECAAGQLQAKALPELQFVIRMGAEK 187

Query: 181 GQGADEPGLLRFTELIARGNAADPR-LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHR 239
                 PG+L F +L+   +A D   L ++A GL   D INIQFTSGTTG PKGATL+H 
Sbjct: 188 S-----PGMLNFDDLLVEVSADDKAMLERIANGLSPYDAINIQFTSGTTGSPKGATLSHH 242

Query: 240 NILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVL 299
           NILNNG+ + E MK T  D+LCIPVPLYHCFGMVLGNL C   GA  V+P D FDPLT L
Sbjct: 243 NILNNGYLVAEAMKFTCDDKLCIPVPLYHCFGMVLGNLVCLAKGAAAVFPGDSFDPLTTL 302

Query: 300 QTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLR 359
           + V+ ERCT LHGVPTMFIAEL+HP F  F+LS+LRTG+MAG+ CP EVM+RV + M ++
Sbjct: 303 EVVERERCTALHGVPTMFIAELEHPEFTRFDLSSLRTGVMAGATCPEEVMRRVQQLMYMQ 362

Query: 360 EITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFC 419
           E+ I YG TE SP++  +  D+P+ KRV TVG+  PH EVKIVD + G V+PI Q GE C
Sbjct: 363 EVLIGYGQTECSPLNHITEIDSPVEKRVLTVGRALPHTEVKIVD-EFGEVLPINQPGEVC 421

Query: 420 TKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYP 479
           ++GY +M  YW D  KT   ID  GW+H+GD+  MD +GYV IVGRIKDM+IRGGENIYP
Sbjct: 422 SRGYCIMQCYWNDPEKTAATIDREGWLHSGDIGQMDEQGYVQIVGRIKDMIIRGGENIYP 481

Query: 480 REIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKV 539
           REIEE LY H  VQD  V GV   KYGEE+CAWI  + G    E+DIR F   + A++KV
Sbjct: 482 REIEEKLYTHKDVQDAAVFGVHSDKYGEEVCAWIKVRSGATIKEEDIRHFLTEKFAYFKV 541

Query: 540 PRYIRFVTSFPMTVTGKIQKFKIRDEMKDQL 570
           PRYI+FV  +PMTVTGKIQKFK+R+ M  +L
Sbjct: 542 PRYIKFVDQYPMTVTGKIQKFKMRELMYQEL 572


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: 857
Number of extensions: 32
Number of successful extensions: 3
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: 578
Length adjustment: 36
Effective length of query: 542
Effective length of database: 542
Effective search space:   293764
Effective search space used:   293764
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 paper from 2022 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