GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2521 Long-chain
           fatty-acid-CoA ligase (EC 6.2.1.3), Mycobacterial
           subgroup FadD3
          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 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