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_RS23695 BWI76_RS23695 putative acyl-CoA synthase

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



>FitnessBrowser__Koxy:BWI76_RS23695
          Length = 518

 Score =  171 bits (434), Expect = 5e-47
 Identities = 149/543 (27%), Positives = 231/543 (42%), Gaps = 65/543 (11%)

Query: 40  ARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGM-GLTPGDRVGIWSHNNAEWVLMQ 98
           AR P+  AL    + RRY Y        R  + L  +  L  GDR+ +   N+  +  + 
Sbjct: 20  ARSPD--ALALAFEDRRYLYRDFHLRVQRAMAQLDRIWSLRKGDRILLAWGNHPAFCEVL 77

Query: 99  LATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQ 158
            A   +G+ +V  +   + AE E  +  +  + ++  A  +             +W  Q 
Sbjct: 78  FAALGLGIEVVPFSTKLKQAESEELVGHIAPRAVLFDATVQ-------------DWLKQT 124

Query: 159 PGHL-------QAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAA 211
           P  L       QA  LP                                  DP L ++  
Sbjct: 125 PDALCVSLSEWQALSLP----------------------------------DP-LTRLPT 149

Query: 212 GLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFG 271
            +   D   + FTSGTTG PKGA +TH N+L       + + LT AD   + VP+YH  G
Sbjct: 150 PVNRDDTAVMMFTSGTTGEPKGAIITHHNLLCAIDAYAQKLNLTAADSTILAVPIYHITG 209

Query: 272 MVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFI----AELDHPRFA 327
           +    LA F      ++    F+   V+ T++++  T LHG PT+FI    A  +     
Sbjct: 210 LS-ALLALFISLGASLWLQHRFNAPQVINTLREQNITFLHGSPTIFILLCQAAREQSASH 268

Query: 328 EFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRV 387
             +   LRT           ++  +        I   YG+TET+  +     D   S + 
Sbjct: 269 PGDFPALRTIACGAGHLSDGLIAELKTLFPHTAIQPIYGLTETTSPATIFPGDVWGSDKC 328

Query: 388 STVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMH 447
            + GQ  P L + I + D    +P GQ G    KG  V+  YW   ++ R + D  GW  
Sbjct: 329 GSSGQAIPGLAIAIRN-DRQQPLPAGQIGHIWLKGDVVIREYW-QHSERRPSCDAQGWFC 386

Query: 448 TGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGE 507
           TGDL  +D EG++ I  R KDM+ RGGE IY  E+E  L  +  V++V V+  P   YGE
Sbjct: 387 TGDLGYLDDEGWLYIKDRSKDMINRGGEKIYSLELENILSTYRGVREVAVIPTPSPVYGE 446

Query: 508 ELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567
           E  A+I+       T ++I  + K +IA +K+P  I F    P T  GK+ K +++  + 
Sbjct: 447 EPVAFIVPDGQHHLTSEEILGWLKVKIARFKLPARIIFTRVLPRTHNGKVSKQQLKARLA 506

Query: 568 DQL 570
           + +
Sbjct: 507 ESI 509


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: 650
Number of extensions: 38
Number of successful extensions: 6
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: 518
Length adjustment: 36
Effective length of query: 542
Effective length of database: 482
Effective search space:   261244
Effective search space used:   261244
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