GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Klebsiella michiganensis M5al

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate BWI76_RS17800 BWI76_RS17800 long-chain-fatty-acid--CoA ligase

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



>FitnessBrowser__Koxy:BWI76_RS17800
          Length = 572

 Score =  234 bits (598), Expect = 5e-66
 Identities = 164/544 (30%), Positives = 266/544 (48%), Gaps = 17/544 (3%)

Query: 29  QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALL-GMGLTPGDRVGIW 87
           Q++   F   V R  ++ A +++  G   TY +L+  +   A+ L  G+GL  GDRV + 
Sbjct: 34  QSLVELFEHAVRRYADQPAFINM--GEVMTYRKLEERSRAFAAYLQEGLGLQKGDRVALM 91

Query: 88  SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFK-TSDYLGM 146
             N  ++ +      + G+++VN+NP Y   E+E+ LN  G   +V ++ F  T + +  
Sbjct: 92  MPNLLQYPVALFGILRAGMIVVNVNPLYTPRELEHQLNDSGAAAIVIVSNFAHTLEKVVD 151

Query: 147 LRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRL 206
             ++      +    L  AK   +  VV            P  + F   +  G     R+
Sbjct: 152 KTQVKHVILTRMGDQLSPAKGTVVNFVVKYIKRLVPKYHLPDAISFRSALQHGY----RM 207

Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGEC---MKLTPADRLCIP 263
             +   +   D   +Q+T GTTG  KGA LTHRN+L N   +      +     + +   
Sbjct: 208 QYIKPEIVPQDLAFLQYTGGTTGVAKGAMLTHRNMLANLEQVNGTYGPLLHRGKELVVTA 267

Query: 264 VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDH 323
           +PLYH F + +  L     G   +   +  D   +++ +     T + GV T+F A L++
Sbjct: 268 LPLYHIFALTMNCLLFIELGGQNLLITNPRDIPGLVKELAKYPFTAMTGVNTLFNALLNN 327

Query: 324 PRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPL 383
             F + + S+L      G P    V +R V+ +  + +   YG+TE +P+   +  D  +
Sbjct: 328 KEFQQLDFSSLHLSAGGGMPVQQVVAERWVK-LTGQYLLEGYGLTECAPLVSVNPHD--I 384

Query: 384 SKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEG 443
                ++G   P  E K+VD D   V P G+ GE C KG  VM GYW     T E I +G
Sbjct: 385 DYHSGSIGLPVPSTEAKLVDDDDNEVPP-GEPGELCVKGPQVMLGYWQRPDATAEIIKDG 443

Query: 444 GWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQ 503
            W+HTGD+A MD EG++ IV R KDM++  G N+YP EIE+ + +H  VQ+V  VGVP  
Sbjct: 444 -WLHTGDIAVMDEEGFLRIVDRKKDMILVSGFNVYPNEIEDVVMQHAGVQEVAAVGVPSG 502

Query: 504 KYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563
             GE +  +++ K  T  TE+ +  FC+ Q+  YKVP+++ F    P +  GKI + ++R
Sbjct: 503 SSGEAVKIFVVKKDPTL-TEEMLITFCRRQLTGYKVPKHVEFRDELPKSNVGKILRRELR 561

Query: 564 DEMK 567
           DE +
Sbjct: 562 DEAR 565


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: 772
Number of extensions: 38
Number of successful extensions: 8
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: 572
Length adjustment: 36
Effective length of query: 542
Effective length of database: 536
Effective search space:   290512
Effective search space used:   290512
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