GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas simiae WCS417

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF4309 PS417_22070 long-chain fatty acid--CoA ligase

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



>FitnessBrowser__WCS417:GFF4309
          Length = 562

 Score =  249 bits (635), Expect = 3e-70
 Identities = 173/540 (32%), Positives = 261/540 (48%), Gaps = 51/540 (9%)

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

Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTS----------DYLGMLRELAPEWQGQQPG 160
            NP Y   E+ +     G + LV +  F +           DYL  +     ++     G
Sbjct: 105 TNPLYTPREMRHQFKDAGVRALVYLNLFGSRVQEVCSDTEIDYL--IEARMGDFMPTAKG 162

Query: 161 HLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPIN 220
            L    + ++K +V            P  + F   +  G      L      +   D   
Sbjct: 163 WLVNTLVDKVKKMV-------PAYSLPRAVAFKRALHMGAG----LGVTRHPVTLDDIAV 211

Query: 221 IQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHCF 270
           +Q+T GTTG  KGA LTH N++ N   +  CM  T  D           +  P+PLYH +
Sbjct: 212 LQYTGGTTGLAKGAMLTHGNLVANMQQVRACMSQTGDDGHPLIKEGQEVMIAPLPLYHIY 271

Query: 271 GMVLGNLACF----THGATIVYPND--GFDPLTVLQTVQDERCTGLHGVPTMFIAELDHP 324
                N  C      H   I  P D  GF     ++ ++  R TGL G+ T+F+A +DHP
Sbjct: 272 AFT-ANCMCMMVSGNHNVLITNPRDIGGF-----IKELKKWRFTGLLGLNTLFVALMDHP 325

Query: 325 RFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLS 384
            F   + S L+     G+       +R  +Q+    I   YG+TETSPV+  S+      
Sbjct: 326 DFKSLDFSHLKLTNSGGTALIKATAERW-QQITGCAIGEGYGLTETSPVA--STNPYGNK 382

Query: 385 KRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGG 444
            R+ TVG   P   +K++D D G  +P+G+RGE C KG  VM GYW     T EA+D  G
Sbjct: 383 SRLGTVGIPVPATAMKVID-DHGVELPLGERGELCIKGPQVMKGYWQQPEATAEALDAEG 441

Query: 445 WMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQK 504
           W+ TGD+A +D EG+V+IV R KD++I  G N+YP EIE+ +  HP V +  V+GVPD++
Sbjct: 442 WLKTGDIAVIDEEGFVSIVDRKKDLIIVSGFNVYPNEIEDVVMAHPAVANCAVIGVPDER 501

Query: 505 YGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
            GE +  +++A+      E +++A+CK     YKVP++I    S PMT  GKI + ++RD
Sbjct: 502 TGEAVKLFVVARAEGVSLE-ELKAYCKTNFTGYKVPKHIVLRDSLPMTPVGKILRRELRD 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: 797
Number of extensions: 36
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
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