GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__MR1:201132
          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:

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