GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:14473
          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 (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