GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Azospirillum brasilense Sp245

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate AZOBR_RS09405 AZOBR_RS09405 acyl-CoA synthetase

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



>lcl|FitnessBrowser__azobra:AZOBR_RS09405 AZOBR_RS09405 acyl-CoA
           synthetase
          Length = 544

 Score =  221 bits (562), Expect = 8e-62
 Identities = 177/575 (30%), Positives = 260/575 (45%), Gaps = 53/575 (9%)

Query: 10  SAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRL 69
           + P  +   R A  VPL   T   F        P++ A+V  +   R ++ +++  A  L
Sbjct: 4   TTPSAELSRRTANHVPL---TPLDFLRRSAMVYPDKTAVV--YGPLRRSWLEVEHRARAL 58

Query: 70  ASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGC 129
           ASA+   G+ PG+ V + + N    +         G VL  IN       V + L     
Sbjct: 59  ASAVSRAGVRPGEVVSVLAFNTPAMLEAHFGVPGAGAVLNAINTRLDPPAVAFILEHAES 118

Query: 130 KLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGL 189
           +L +            + R  AP                    VVWIDD A Q AD  G 
Sbjct: 119 RLFLVDRGLSAVARAALERMTAPP------------------RVVWIDDPAAQDADPVGD 160

Query: 190 LRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHR----NILNNG 245
           L + + +  G+   P            + I + +TSGTTG PKG    HR    N L N 
Sbjct: 161 LEYEDFLKTGDPEAPWRRPE----DEWESIALNYTSGTTGNPKGVLYHHRGAHLNALGNV 216

Query: 246 FFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDE 305
              G    L P       +P++HC G      A    GAT V      DP  + + + +E
Sbjct: 217 ITFG----LRPDSVYLWTLPMFHCNGWTYP-WAVTAVGATHVCLR-AVDPAAIFRLIAEE 270

Query: 306 RCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAY 365
           + T L G P +    +  P   +         +  G   P   +   +E+M  R +T  Y
Sbjct: 271 KVTHLCGAPVVLTMLIHAPDAVKRAFDHGPVQVATGGAAPPSAVIAGMERMGFR-LTHLY 329

Query: 366 GMTETSPVSC-----QSSTDTPLSKR-VSTVGQVQPHL---EVKIVDPDTGAVVPIGQR- 415
           GMTE    S      ++  + PL +R V    Q  P++   E  ++DPDTG  VP     
Sbjct: 330 GMTECYGPSTGCAWQEAWAELPLEERAVKMARQGVPNVTMSEQTVLDPDTGREVPADGET 389

Query: 416 -GEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGG 474
            GE   +G +VM GY  + A T EA+ +G W+HTGDLA +  + YV I  R KD++I GG
Sbjct: 390 LGELALRGNTVMKGYLKNPAATDEALRDG-WLHTGDLAVLHPDRYVEIKDRAKDIIISGG 448

Query: 475 ENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQ--PTEDDIRAFCKG 532
           ENI   E+EE LY+HP V +  VV  PD K+GE  CA++  KPG++   +E ++  +C+ 
Sbjct: 449 ENIASLEVEEVLYKHPHVMEAAVVARPDAKWGETPCAFVTLKPGSEGRVSEAEVIGWCRD 508

Query: 533 QIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMK 567
            +AH+K PR + F  + P T TGKIQKF +R++ +
Sbjct: 509 HLAHFKTPRTVVF-GALPKTSTGKIQKFVLREQAR 542


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: 716
Number of extensions: 41
Number of successful extensions: 9
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: 544
Length adjustment: 36
Effective length of query: 542
Effective length of database: 508
Effective search space:   275336
Effective search space used:   275336
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 paper from 2022 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