Alignments for a candidate for aacS in Klebsiella michiganensis M5al

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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources