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_2521 Long-chain fatty-acid-CoA ligase (EC 6.2.1.3), Mycobacterial subgroup FadD3

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2521
          Length = 526

 Score =  283 bits (725), Expect = 9e-81
 Identities = 181/539 (33%), Positives = 277/539 (51%), Gaps = 32/539 (5%)

Query: 30  TIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSH 89
           TI   FA+      +R A+         +Y QL     + A ALL + +  GDRV IW+ 
Sbjct: 9   TIAQLFANAAQAYGDRPAIEDADH--TISYRQLDQLRRQAARALLALDVQVGDRVAIWAP 66

Query: 90  NNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRE 149
           N  EW++   A   VG  LV +N   + +E  Y L + G  +L ++  F  +DY GML  
Sbjct: 67  NVWEWIVAAGALQSVGAALVPLNTRMKGSEAGYILRESGTCVLFAIGEFLGADYPGML-- 124

Query: 150 LAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLL--RFTELIARGNAADPRLA 207
             PE             LP L+ +V +     +GA+   L   RF +L A       R  
Sbjct: 125 -TPE------------DLPALRHIVSV-----RGANSGTLAWERFMDLAADVPQLALRTR 166

Query: 208 QVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLY 267
           + + G QA    ++ FTSGTTG PKG   +H   L       + + L   DR  I  P +
Sbjct: 167 EQSVGPQALS--DVLFTSGTTGKPKGVMTSHGQNLRIVRDWSDIVGLREGDRYLIVNPFF 224

Query: 268 HCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFA 327
           H FG   G LA    G T++ P   FD   VL+ VQ ER T L G PT++ + L HP+ +
Sbjct: 225 HSFGYKAGWLAALMRGCTLL-PQQVFDVQAVLECVQRERITVLPGPPTLYQSLLAHPQRS 283

Query: 328 EFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS--CQSSTDTPLSK 385
           EF+LS+LR  +   +  P E++ R+ +++    I  AYG+TE    +  C+S     L  
Sbjct: 284 EFDLSSLRVAVTGAAAIPVEMIHRMRDELGFATIVTAYGLTEVCGFATICRSGDSAELV- 342

Query: 386 RVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGW 445
             +T G+  P ++V+ V  ++G   P    GE   +GY++M GY  +   ++E +D  GW
Sbjct: 343 -ANTSGRAMPGVQVRCVG-NSGRSQPANIPGEVQIRGYNLMQGYLNNPEASQEILDADGW 400

Query: 446 MHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKY 505
           +HTGD+  +D +GY+ I  R+KDM I GG N+YP EIE+ L  +P V    V+G+PD++ 
Sbjct: 401 LHTGDIGMLDEQGYLRITDRLKDMFITGGFNVYPAEIEQCLLTYPGVAQAAVIGIPDERL 460

Query: 506 GEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
           GE   A+++  PG +  +    A+C+ Q+A+YKVPR ++ +   P+   GK+ K  +R+
Sbjct: 461 GEVAMAFLLPAPGMEIEQTRFLAWCREQMANYKVPRRVQVLQKMPINAAGKVTKNVLRE 519


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: 688
Number of extensions: 35
Number of successful extensions: 5
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: 526
Length adjustment: 36
Effective length of query: 542
Effective length of database: 490
Effective search space:   265580
Effective search space used:   265580
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