GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Duganella sacchari Sac-22

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_072790532.1 BUA36_RS28615 propionate--CoA ligase

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_900143065.1:WP_072790532.1
          Length = 622

 Score =  484 bits (1246), Expect = e-141
 Identities = 254/631 (40%), Positives = 394/631 (62%), Gaps = 18/631 (2%)

Query: 33  YFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRHV 92
           Y +F+++++   E FW+  A  ++W  P+ +VLD + PPF +WFVGG  NL + AVDR  
Sbjct: 3   YAEFYQRSIVTPEQFWQDEAALIDWNTPFTQVLDYAKPPFARWFVGGHTNLCHNAVDRWC 62

Query: 93  KTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLY 152
            T       I    E   E  Y       ++ +L  EV R A M+ Q+ GV+KGD++ +Y
Sbjct: 63  ATQGDQPALIAISTETNTERCY-------SFNELRAEVERWAAMM-QSLGVRKGDRVLIY 114

Query: 153 LPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVRL 212
           +PM+ E    MLA  RIGA+ SVVF GF+A++LA RI+D++  ++++AD   R G+ +  
Sbjct: 115 MPMIAEAAFAMLACARIGAVHSVVFGGFAANSLASRIDDAKPVLIVSADAGSRNGKAIPY 174

Query: 213 KEVVDAALEKATGVESVIVLPRLGLKDVPMTEGRDYWWNKLMQGIPPNAYIEPEPVESEH 272
           K ++D A+  ++   S ++L   GL  + M EGRD  +  L +     A++    +ES  
Sbjct: 175 KPLLDEAIALSSAKPSRVLLVDRGLAPMAMVEGRDVDYAAL-RAAHLAAHVPVTWLESNE 233

Query: 273 PSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSYVV 332
           PS+ILYTSGTTGKPKG+  D GG+AV + A+MK+ F  +  + F+ T+DIGWV GHSY+V
Sbjct: 234 PSYILYTSGTTGKPKGVQRDVGGYAVALAASMKYNFCGKAGETFFATSDIGWVVGHSYIV 293

Query: 333 LGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHDL 392
            GPL+ G   ++YEG P  P P  WWSI+E+Y VT  +++PTAIR+  +   E+ RK+D 
Sbjct: 294 YGPLIAGMATIMYEGLPICPDPGIWWSIVEKYKVTRMFSAPTAIRVLRKQAPEFMRKYDK 353

Query: 393 STLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMKPG 452
           S+L+ ++  GEP++     W   +     V     +W TETG  ++S A G+   P + G
Sbjct: 354 SSLKALYLAGEPLDETTSSW---IADELNVPIIDNYWQTETGWPILSIAKGIEDTPTRLG 410

Query: 453 TNGPPLPGFEVDVVDE-NGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSRFP 510
           + G  + G++V +++E NG       KG ++++ P  PG +  ++GD +R++ TYWS   
Sbjct: 411 SPGLAMYGYKVRLINEINGQECGANEKGVVMVEGPLPPGCMQTVYGDDQRFVDTYWSEHD 470

Query: 511 G--MFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGVP 568
           G  ++   D+ ++D DGY ++LGR D+VI VAGHRLGT E+E ++ SHP V+E AVVGV 
Sbjct: 471 GKMVYSTFDWGLRDADGYYFILGRTDDVINVAGHRLGTREIEESITSHPNVSEVAVVGVE 530

Query: 569 DAIKGEVPIAFVVLKQGVAPSDELRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGKIM 628
           D +KG+V +AF +LK   A + E  +++   V R +G +A PA+++FVT+LPKTRSGK++
Sbjct: 531 DKLKGQVAVAFAILKDANAATSE--QDVMSVVDRQLGAVARPARVYFVTQLPKTRSGKLL 588

Query: 629 RRLLKAVATGAPLGDVTTLEDETSVEEAKRA 659
           RR ++A+  G   GD+T +ED  S+++ +RA
Sbjct: 589 RRSIQAICEGRNPGDLTAIEDPASLQQIQRA 619


Lambda     K      H
   0.319    0.138    0.440 

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: 1226
Number of extensions: 65
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: 670
Length of database: 622
Length adjustment: 38
Effective length of query: 632
Effective length of database: 584
Effective search space:   369088
Effective search space used:   369088
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 (21.7 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