GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF4204
          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:

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