GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Escherichia coli BW25113

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate 14473 b0335 predicted propionyl-CoA synthetase with ATPase domain (NCBI)

Query= curated2:O93730
         (670 letters)



>lcl|FitnessBrowser__Keio:14473 b0335 predicted propionyl-CoA
           synthetase with ATPase domain (NCBI)
          Length = 628

 Score =  477 bits (1227), Expect = e-139
 Identities = 260/642 (40%), Positives = 394/642 (61%), Gaps = 26/642 (4%)

Query: 32  AYFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRH 91
           ++ +F+++++   E FW   A+ ++W  P+ + LD SNPPF +WF  GR NL + A+DR 
Sbjct: 2   SFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDRW 61

Query: 92  VKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITL 151
           ++   +    I    E  +E       R  T+  L+ EVN VA ML+ + GV++GD++ +
Sbjct: 62  LEKQPEALALIAVSSETEEE-------RTFTFRQLHDEVNAVASMLR-SLGVQRGDRVLV 113

Query: 152 YLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVR 211
           Y+PM+ E  IT+LA  RIGAI SVVF GF++ ++A RI+D++  ++++AD   R G+++ 
Sbjct: 114 YMPMIAEAHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIP 173

Query: 212 LKEVVDAALEKATGVESVIVLPRLGLKDVPMTEGRDYWWNKLM-QGIPPNAYIEPEPVES 270
            K+++D A+ +A      ++L   GL  +    GRD  +  L  Q I   A +    +ES
Sbjct: 174 YKKLLDDAISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHI--GARVPVAWLES 231

Query: 271 EHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSY 330
              S ILYTSGTTGKPKG+  D GG+AV +  +M  +F  +   +F+C +DIGWV GHSY
Sbjct: 232 NETSCILYTSGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSY 291

Query: 331 VVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKH 390
           +V  PLL G   ++YEG P +P    WW+I+E+Y V+  +++PTAIR+  ++     RKH
Sbjct: 292 IVYAPLLAGMATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKH 351

Query: 391 DLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMK 450
           DLS+L +++  GEP++     W    L    V     +W TE+G  +++ A GL   P +
Sbjct: 352 DLSSLEVLYLAGEPLDEPTASWVSNTL---DVPVIDNYWQTESGWPIMAIARGLDDRPTR 408

Query: 451 PGTNGPPLPGFEVDVVDE-NGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSR 508
            G+ G P+ G+ V +++E  G P     KG LV++ P  PG +  IWGD  R++KTYWS 
Sbjct: 409 LGSPGVPMYGYNVQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSL 468

Query: 509 FPGMFYAG-DYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGV 567
           F    YA  D+ I+D DGY ++LGR D+VI VAGHRLGT E+E ++ SHP VAE AVVGV
Sbjct: 469 FSRPVYATFDWGIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGV 528

Query: 568 PDAIKGEVPIAFVVLKQG-------VAPSDELRKELREHVRRTIGPIAEPAQIFFVTKLP 620
            DA+KG+V +AFV+ K+        VA S E  K +   V   IG    PA ++FV++LP
Sbjct: 529 KDALKGQVAVAFVIPKESDSLEDRDVAHSQE--KAIMALVDSQIGNFGRPAHVWFVSQLP 586

Query: 621 KTRSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRAYEE 662
           KTRSGK++RR ++A+  G   GD+TT++D  S+++ ++A EE
Sbjct: 587 KTRSGKMLRRTIQAICEGRDPGDLTTIDDPASLDQIRQAMEE 628


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: 1158
Number of extensions: 70
Number of successful extensions: 8
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: 628
Length adjustment: 38
Effective length of query: 632
Effective length of database: 590
Effective search space:   372880
Effective search space used:   372880
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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