GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E2

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf6N2E2_1879 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1879
          Length = 511

 Score =  244 bits (623), Expect = 6e-69
 Identities = 171/545 (31%), Positives = 266/545 (48%), Gaps = 35/545 (6%)

Query: 27  IEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGI 86
           +E +IG +     AR   + A++   +G+ +++  +  ++ RLA++L  MG+   D V I
Sbjct: 1   MEHSIGNWVGRSAARFGNKPAII--FEGKYWSFLDIDVQSSRLAASLESMGVKREDVVSI 58

Query: 87  WSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGM 146
           +S N+ EW++   A  ++G ++  +N      E  +A+   G     ++A F TSD L  
Sbjct: 59  YSPNSPEWIITYYAILKIGAIVNPLNTMLTAREAAFAIKNCG-----AVAVFSTSDKLLA 113

Query: 147 LRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRL 206
           L+E           H+   ++  L +          G    G+  F  L+    A     
Sbjct: 114 LQE-----------HIGPTEVISLISF--------DGITVAGMRHFNLLVDANVAVRE-- 152

Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPL 266
                G+Q  D   I +TSGTTG PKGA L+HR IL N          T +D     +PL
Sbjct: 153 -YPVTGIQKDDISTIGYTSGTTGQPKGAVLSHRCILTNVSMTATMHLRTASDIAVSALPL 211

Query: 267 YHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRF 326
            H +G V+ N A   +G T+V  +  FD   +L ++Q    T L GVPTM+I  L+ P  
Sbjct: 212 SHVYGNVVMNSA-IAYGMTLVL-HKTFDAEAILSSIQIYGATLLEGVPTMYIYLLNCPNL 269

Query: 327 AEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKR 386
             +++S+L    + G   P   M+ V   +  R + + +GMTE   +    S      +R
Sbjct: 270 GAYDVSSLTRCTVGGQMMPYTAMENVERALGCRLLEL-WGMTELGGLGTTHSLYG--ERR 326

Query: 387 VSTVGQVQPHLEVKIVDPDT-GAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGW 445
           + ++G   PHLE +I   +  G  +P+G+ GE   +G  VM  Y G    T E   + GW
Sbjct: 327 LGSIGVALPHLEARIAQLELDGDALPLGEIGELQIRGPVVMKHYLGRPDATAETKTDEGW 386

Query: 446 MHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKY 505
           + TGDLA MD+EG++ IV R+KDM I  G NIYP E+E  +  HP V  V V  V D+  
Sbjct: 387 LRTGDLARMDSEGFIYIVDRLKDMFITAGFNIYPAELERVIAEHPSVAMVAVGSVLDEIK 446

Query: 506 GEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDE 565
           GE   A+I+ K G +     I   C+ ++A YKVPR  + V   P T +GK+ +  +R  
Sbjct: 447 GELAKAYIVPKTGYEIDIQQIERHCRDRLAAYKVPRLFQIVEDLPKTSSGKVMRRMLRQI 506

Query: 566 MKDQL 570
            + +L
Sbjct: 507 FESKL 511


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: 581
Number of extensions: 26
Number of successful extensions: 4
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: 511
Length adjustment: 35
Effective length of query: 543
Effective length of database: 476
Effective search space:   258468
Effective search space used:   258468
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: 52 (24.6 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