GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Marinobacter adhaerens HP15

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF4204 HP15_4144 short chain acyl-CoA synthetase

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



>lcl|FitnessBrowser__Marino:GFF4204 HP15_4144 short chain acyl-CoA
           synthetase
          Length = 578

 Score =  231 bits (589), Expect = 6e-65
 Identities = 172/557 (30%), Positives = 273/557 (49%), Gaps = 50/557 (8%)

Query: 28  EQTIGAFFADMVARQPEREALVSVH----QGRRYTYAQLQTEAHRLASALLGMGLTPGDR 83
           ++ I  +F   VA  P+REA+V            TY +L  +  R+A+ L  MG+  G+ 
Sbjct: 47  DKIITDYFDQAVASTPDREAIVGYQVTSDTRNALTYRELNDKVTRMAAGLAAMGIGKGEV 106

Query: 84  VGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDY 143
           V     N  +   + LA  ++G +L  + P +R  E+ + L     KLLV    F+  DY
Sbjct: 107 VACQLPNWWQTTALHLACMRIGAILNPLMPIFRERELRFMLKHGEAKLLVIPKVFRDFDY 166

Query: 144 LGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLR--------FTEL 195
             M+  +  E             LP L+T++ I  E G+ + E  L+          T L
Sbjct: 167 EAMVDGIRGE-------------LPALETLLVIGGE-GERSFEQRLMETPWEKQQDITSL 212

Query: 196 IARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLT 255
            A               L A D I I +TSGTTG PKG   T   + +N     + + LT
Sbjct: 213 FAERQ------------LTADDAIQILYTSGTTGEPKGVMHTSNTLFSNVRPYADRLHLT 260

Query: 256 PADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPT 315
             D++ +  PL H  G + G +     G T +   D +D   V + +  E+        T
Sbjct: 261 SDDKVLMASPLAHQTGFMYGIMMPVYLGTTAIL-QDIWDADYVCKVIGAEK-PAFTMAAT 318

Query: 316 MFIAEL--DHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPV 373
            F+A+L    P+  E  L +LR  + AG+P P+ V+++  + +  + I  A+GMTE   V
Sbjct: 319 PFLADLVKTAPKH-EGELDSLRIFVSAGAPIPSAVVEQAGKVLKAK-IVSAWGMTENGAV 376

Query: 374 SCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDE 433
           +     D P  +   + G+  P +EVK+ D   G  +P G+ G    +G S+  GY   +
Sbjct: 377 TMTCPED-PAERASQSDGKAMPFMEVKVTDFQ-GNELPAGEEGSLLVRGSSLFVGYL--K 432

Query: 434 AKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQ 493
                 +DE GW +TGDLA MD + Y+ I GR KD+VIRGGENI   E+E  LY+ P + 
Sbjct: 433 RPELYGVDESGWFNTGDLARMDQDAYIRITGRTKDVVIRGGENIPVVEVENLLYKFPGIV 492

Query: 494 DVQVVGVPDQKYGEELCAWI-IAKPGTQPTEDDIRAF-CKGQIAHYKVPRYIRFVTSFPM 551
           DV +VG PD++ GE LCA++ + +  T  T + ++ +  + Q++   +P Y+  + + P 
Sbjct: 493 DVALVGCPDERLGERLCAYVTLDENATDLTLEQVKTYLTEQQLSKNYLPEYLEVIEAMPR 552

Query: 552 TVTGKIQKFKIRDEMKD 568
           T +GKIQKFK+R++ ++
Sbjct: 553 TASGKIQKFKLREQARN 569


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: 682
Number of extensions: 33
Number of successful extensions: 7
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: 578
Length adjustment: 36
Effective length of query: 542
Effective length of database: 542
Effective search space:   293764
Effective search space used:   293764
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 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