GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Dinoroseobacter shibae DFL-12

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 3610022 Dshi_3403 AMP-dependent synthetase and ligase (RefSeq)

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



>FitnessBrowser__Dino:3610022
          Length = 579

 Score =  666 bits (1718), Expect = 0.0
 Identities = 324/564 (57%), Positives = 404/564 (71%), Gaps = 7/564 (1%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75
           SH  GA + PL+E TI        AR P   A +   QG R+TY  L  E   LA  LL 
Sbjct: 22  SHVLGAQEPPLLELTIPELLVQTAARFPNHVAAIFEAQGIRWTYRDLIREVDALAGGLLQ 81

Query: 76  MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135
           +GL PGDRVG+W+ N AEW+L Q ATA++G++LVN+NPAYR  E+ YAL K GC  L+  
Sbjct: 82  LGLKPGDRVGVWAPNCAEWLLAQFATARLGIILVNVNPAYRPFELSYALKKTGCTALILA 141

Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195
           A+FK SDY+ ML E+ PE     PG L AA+LP L+ V+  + EA  G     ++ F +L
Sbjct: 142 AQFKNSDYVAMLSEVVPEIAASDPGALHAAELPDLRAVIVTEAEAPDG-----MIAFPDL 196

Query: 196 IARGNAADPR-LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254
           IA+G A   + L  +   L   DPINIQFTSGTTG PKGATLTHRNI+NN   +   +KL
Sbjct: 197 IAKGRAVVAKDLDAITRKLDCHDPINIQFTSGTTGLPKGATLTHRNIVNNAASVTSAIKL 256

Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314
              D LCIPVP YHCFGMV+G L C T GA IV P  GFDP+T L TV   RCT L+GVP
Sbjct: 257 IEQDMLCIPVPFYHCFGMVMGTLGCVTKGAAIVVPGPGFDPITTLDTVSKHRCTALYGVP 316

Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374
           TMF+  L+HPRFAE++LS+LRTGIMAG+PCP E+M++V  +M++ E+TIAYGMTETSPVS
Sbjct: 317 TMFVGMLEHPRFAEYDLSSLRTGIMAGAPCPIEIMRQVQSRMHMSEVTIAYGMTETSPVS 376

Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434
            QS+TD P+ KRVS+VG++QPH+EVKIVD D+  VVP+G +GE  T+GYSVM GYW +  
Sbjct: 377 FQSATDDPVQKRVSSVGRIQPHVEVKIVDEDS-VVVPVGAQGELLTRGYSVMQGYWDEPD 435

Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494
           KT EAID  GWMHTGDLAT+D +G+  I GR+KDM++RGGEN+YPREIEEFLY HP +  
Sbjct: 436 KTAEAIDADGWMHTGDLATLDVDGFCKITGRVKDMIVRGGENVYPREIEEFLYTHPAISQ 495

Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVT 554
           VQV G+PDQK+GE + AW++AKPG  PTE +I  FC+  IAH+KVP  +RF  S PMTVT
Sbjct: 496 VQVFGIPDQKFGEIVVAWLVAKPGADPTEAEILDFCRDSIAHFKVPAMVRFKNSLPMTVT 555

Query: 555 GKIQKFKIRDEMKDQLGLEEQKTA 578
           GK QKF +R +M ++LGLEE +TA
Sbjct: 556 GKPQKFIMRAQMVEELGLEEIETA 579


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: 897
Number of extensions: 27
Number of successful extensions: 3
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: 579
Length adjustment: 36
Effective length of query: 542
Effective length of database: 543
Effective search space:   294306
Effective search space used:   294306
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