Aligments for a candidate for aacS in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for aacS in Shewanella oneidensis MR-1

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 201721 SO2581 long-chain-fatty-acid--CoA ligase (NCBI ptt file)

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



>lcl|FitnessBrowser__MR1:201721 SO2581 long-chain-fatty-acid--CoA
           ligase (NCBI ptt file)
          Length = 557

 Score =  214 bits (544), Expect = 1e-59
 Identities = 159/545 (29%), Positives = 259/545 (47%), Gaps = 30/545 (5%)

Query: 35  FADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAE 93
           F   VA+  ++ A +++  G   TY +L+  +   A+ L   + L  GDRV +   N  +
Sbjct: 29  FETAVAKYADQPAFINM--GATLTYRKLEERSRAFAAYLQNELKLQKGDRVALMMPNLLQ 86

Query: 94  WVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPE 153
           + +      + G+V+VN+NP Y   E+++ L   G K +V ++ F  +     L E+  +
Sbjct: 87  YPIALFGILRAGMVVVNVNPLYTPRELKHQLIDSGAKAIVVVSNFART-----LEEVVDQ 141

Query: 154 WQGQQP------GHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLA 207
              +          L A K   +  VV    +     D P  L   E ++RG     R+ 
Sbjct: 142 TPVKSVIITGLGDLLSAPKRTLVNFVVKYIKKLVPKYDLPHALSMRETLSRGR----RMQ 197

Query: 208 QVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR-----LCI 262
            V   +   D   +Q+T GTTG  KGA LTH N++ N          +PA R     +  
Sbjct: 198 YVKPVITGDDLAFLQYTGGTTGVSKGAMLTHSNVVANVLQANGAY--SPALRDGSEFVVT 255

Query: 263 PVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELD 322
            +PLYH F + +  L     G+  +   +  D    +  ++    T L GV T+F A ++
Sbjct: 256 ALPLYHIFALTVNCLLFLHKGSQNLLITNPRDIPGFVAELKKYPFTALTGVNTLFNALVN 315

Query: 323 HPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382
              F+E + S L+  I  G      V  +  + +    +   YG+TE SP+   +     
Sbjct: 316 SSDFSELDFSRLKLSIGGGMAVQKAVADKW-QNITKTRLLEGYGLTEASPLL--TCCPYN 372

Query: 383 LSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDE 442
           L     ++G   P   +++ D D G V+P G+ GE   KG  +M GYW    +T + ID 
Sbjct: 373 LDGYNGSIGFPAPSTLIQVRD-DAGNVLPQGETGELFGKGPQIMKGYWQRPEETAKVIDN 431

Query: 443 GGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPD 502
            GW+ TGD+  MD +G+  IV R KDM++  G N++P E+EE +  HP+V +V  VGVP+
Sbjct: 432 DGWLATGDIGYMDEQGFFYIVDRKKDMILVSGFNVFPNEVEEVVALHPKVIEVAAVGVPN 491

Query: 503 QKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKI 562
              GE +  +++ K  +   ED I+  C+  +  YKVP+ + F    P T  GKI + ++
Sbjct: 492 DASGELVKVFVVKKDKSLTAEDIIK-HCRVHLTGYKVPKLVEFRDELPKTNVGKILRREL 550

Query: 563 RDEMK 567
           RDE+K
Sbjct: 551 RDEVK 555


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: 717
Number of extensions: 41
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: 557
Length adjustment: 36
Effective length of query: 542
Effective length of database: 521
Effective search space:   282382
Effective search space used:   282382
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 preprint 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