GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Amycolatopsis xylanica CPCC 202699

Align Acyl-CoA synthetase short-chain family member 3, mitochondrial; Acetate--CoA ligase 3; Acyl-CoA synthetase short-chain family member 3; Propionate--CoA ligase; EC 6.2.1.1; EC 6.2.1.17 (characterized)
to candidate WP_091290483.1 BLV57_RS18395 propionyl-CoA synthetase

Query= SwissProt::Q9H6R3
         (686 letters)



>NCBI__GCF_900107045.1:WP_091290483.1
          Length = 625

 Score =  675 bits (1742), Expect = 0.0
 Identities = 330/624 (52%), Positives = 439/624 (70%), Gaps = 3/624 (0%)

Query: 61  EYKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRH 120
           +Y      S+ DPE FW +AAE I W +  T+ L++  +P  RWF +G LN   NA+DRH
Sbjct: 3   DYAEAHRRSLEDPEGFWLEAAEAIDWSRKPTRALDDSGAPLYRWFPDGELNTSVNALDRH 62

Query: 121 IENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQ 180
           ++ G+G++ A+I+DSPVT     FTY E+L +V++ AG L    + KG+ V+IYMPM+P+
Sbjct: 63  VQAGRGERTALIWDSPVTGQTRRFTYAELLYEVTRFAGALASLHVDKGERVIIYMPMVPE 122

Query: 181 AMYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEE 240
           A+  MLACAR+GA+HS++FGGFA KEL++R+D  KP+V+V AS GIEP R VEY P+++E
Sbjct: 123 AVIAMLACARLGAVHSVVFGGFAPKELAARVDDAKPRVIVAASCGIEPTRTVEYKPIIDE 182

Query: 241 ALKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTS 300
           AL +  H+PD+++I  R   +A      RD+DW+E +  A     VPV +  PLYILYTS
Sbjct: 183 ALAMSAHQPDRVVILQRDRHKAE--LGERDVDWNELIEHAPPAQAVPVAATDPLYILYTS 240

Query: 301 GTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGN 360
           GTTG PKGV+R TGG+AV L WSMS+IY +QPG+VWW ASD+GWVVGHSYI Y PLL G 
Sbjct: 241 GTTGKPKGVVRDTGGHAVALAWSMSAIYDIQPGDVWWTASDVGWVVGHSYIVYAPLLVGA 300

Query: 361 TTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKT 420
           T+VLYEGKPVGTPDAGA++RV+AEHGV ALFTAPTA+RAI++ DP A    +Y L+RF+T
Sbjct: 301 TSVLYEGKPVGTPDAGAFWRVIAEHGVKALFTAPTALRAIKKVDPEAKELAKYDLSRFQT 360

Query: 421 LFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAGKSVP 480
           LF+AGER D ET  W+      PV+DHWWQTETG PI A+  GL       PG A K VP
Sbjct: 361 LFMAGERLDPETYHWASEHLGTPVIDHWWQTETGWPIAANPRGL-EPMPVKPGSATKPVP 419

Query: 481 GYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDA 540
           G++V ILD   + + A   G I +KLPLPPG+   LW + E +K  Y  ++ GYY T D+
Sbjct: 420 GWDVRILDQAGESVPAGREGAIAIKLPLPPGSLPTLWGDDERYKETYLSRYDGYYLTGDS 479

Query: 541 GYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVPLA 600
           GY+DE+GYL+VM R DDVINVAGHR+S G++E  + SH  VA+CAV+G +D LKG +P  
Sbjct: 480 GYLDEDGYLFVMGRTDDVINVAGHRLSTGSMEAVLASHPAVAECAVIGVKDQLKGQLPRG 539

Query: 601 LCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAIVN 660
           L VL+  +  TE  +  E+V  VR++IGPVAAF++   V+ LPKTRSGKI R  +  I +
Sbjct: 540 LVVLKAGVEVTEADLKAELVALVRRDIGPVAAFKDVSIVEALPKTRSGKILRKTMRGIAD 599

Query: 661 GKPYKITSTIEDPSIFGHVEEMLK 684
           G+   + STIED S+   ++ +L+
Sbjct: 600 GRDEAVPSTIEDASVLEALKVVLR 623


Lambda     K      H
   0.318    0.136    0.422 

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: 1219
Number of extensions: 57
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: 686
Length of database: 625
Length adjustment: 38
Effective length of query: 648
Effective length of database: 587
Effective search space:   380376
Effective search space used:   380376
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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