GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Shewanella sp. ANA-3

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 7025225 Shewana3_2386 long-chain-fatty-acid--CoA ligase (RefSeq)

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



>FitnessBrowser__ANA3:7025225
          Length = 557

 Score =  221 bits (562), Expect = 8e-62
 Identities = 162/545 (29%), Positives = 262/545 (48%), 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  YPIALFGILRAGMVVVNVNPLYTPRELKHQLVDSGAKAIVVVSNFART-----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 YVKPVITGDDLAFLQYTGGTTGVSKGAMLTHKNVVANVLQANGAY--SPALRDGNEFVVT 255

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

Query: 323 HPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382
              FAE + S L+  I  G      V  +  + +    +   YG+TE SP+   +     
Sbjct: 316 SSDFAELDFSRLKLSIGGGMAVQKAVADKW-QSITKTRLLEGYGLTEASPLL--TCCPYN 372

Query: 383 LSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDE 442
           L     ++G   P   +++ D D G V+P G+ GE   KG  +M GYW    +T + ID+
Sbjct: 373 LDGYNGSIGFPAPSTLIQVRD-DAGNVLPQGETGELFGKGPQIMKGYWQRPEETAKVIDK 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 +  +++AK  +  T DDI   C+  +  YKVP+ + F    P T  GKI + ++
Sbjct: 492 DASGELVKVFVVAKDKSL-TADDIIKHCRAHLTGYKVPKLVEFRDELPKTNVGKILRREL 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: 722
Number of extensions: 42
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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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