GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS09405
          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:

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