GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas fluorescens GW456-L13

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate PfGW456L13_1910 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1910
          Length = 562

 Score =  247 bits (631), Expect = 8e-70
 Identities = 172/536 (32%), Positives = 263/536 (49%), Gaps = 43/536 (8%)

Query: 52  HQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110
           + G   TYA+L+ ++   A  L     L  GDR+ +   N   + +      + GL++VN
Sbjct: 45  NMGVTLTYAELERQSAAFAGYLQAHTDLVAGDRIAVQMPNVLHYPIAVFGALRAGLIVVN 104

Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQ-----QPGHLQ-A 164
            NP Y   E+ +     G + LV +  F        ++E+ P+   Q     + G L  A
Sbjct: 105 TNPLYTAREMRHQFKDSGARALVYLNMFGQK-----VQEVLPDTDIQYLIEAKMGDLMPA 159

Query: 165 AKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFT 224
           AK   + TVV    +       P  + F   +  G     +  +V  GL   D   +Q+T
Sbjct: 160 AKGWLVNTVVSKVKKMVPDYSLPQAVSFKSALRMGRGLGIKPLKV--GLD--DIAVLQYT 215

Query: 225 SGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHCFGMVL 274
            GTTG  KGA LTH N++ N      C+    +D           +  P+PLYH +    
Sbjct: 216 GGTTGLAKGAMLTHGNLVANMQQARACLGQFGSDGQPLLREGQEVMIAPLPLYHIYAFT- 274

Query: 275 GNLACF----THGATIVYPND--GFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAE 328
            N  C      H   I  P D  GF     ++ +++ R + L G+ T+F+A +DHP F  
Sbjct: 275 ANCMCMMVTGNHNVLITNPRDIAGF-----IKELKNWRFSALLGLNTLFVALMDHPDFKT 329

Query: 329 FNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVS 388
            + S+L+     G+       +R  EQ+    IT  YG+TETSPV+C +        R+ 
Sbjct: 330 LDFSSLKLTNSGGTALVKATAERW-EQLTGCRITEGYGLTETSPVACTNPYGD--QSRIG 386

Query: 389 TVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHT 448
           TVG   P   +K+++ D G   P+G+RGE C KG  +M GYW     T E +D  GW  +
Sbjct: 387 TVGLPVPGTTLKVINDD-GVEQPLGERGELCIKGPQIMKGYWQKPDATAEVLDAEGWFKS 445

Query: 449 GDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEE 508
           GD+A +D +G+V IV R KDM+I  G N+YP EIE+ +  HP V +  V+GVPD++ GE 
Sbjct: 446 GDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPNVANCAVIGVPDERSGEA 505

Query: 509 LCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
           +  +++A+      E +++A+CK     YKVP++I    S PMT  GKI + ++RD
Sbjct: 506 VKLFVVAREAGVSLE-ELKAYCKENFTAYKVPKHIVLRESLPMTPVGKILRRELRD 560


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: 778
Number of extensions: 44
Number of successful extensions: 6
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: 562
Length adjustment: 36
Effective length of query: 542
Effective length of database: 526
Effective search space:   285092
Effective search space used:   285092
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