GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Thermoactinomyces daqus H-18

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_033100144.1 JG50_RS0105805 AMP-binding protein

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_000763315.1:WP_033100144.1
          Length = 646

 Score =  470 bits (1209), Expect = e-136
 Identities = 255/631 (40%), Positives = 382/631 (60%), Gaps = 23/631 (3%)

Query: 33  YFKFHRQTVENLESFWESVAKEL--EWFKPWDKVLDASNP-PFYKWFVGGRLNLSYLAVD 89
           Y +F+ Q+++N+  FW+ V  +L   W  P+ +VLD S+   + +WFV G++N+S   +D
Sbjct: 30  YDRFYEQSIKNIAWFWDEVVNDLGLRWMMPYRQVLDMSDGIAWTRWFVDGKINISDNCLD 89

Query: 90  RHVKT-WRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDK 148
           R V+    +++LA+ WEG+           +K TY DL+ EVNR+A  LK+  GV  GD 
Sbjct: 90  RFVEEPAARHRLALIWEGDD-------GTTKKYTYRDLWLEVNRLACGLKK-LGVAAGDC 141

Query: 149 ITLYLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGR 208
           + +Y+PM+ E  I MLA  RIGAI +  FSG+ A+A+A RI   Q++ +ITADG+ RRG+
Sbjct: 142 VAIYMPMIAENVIAMLAVARIGAIFTPCFSGYGAEAVATRIQGCQAKWLITADGYLRRGK 201

Query: 209 VVRLKEVVDAALEKATGVESVIVLPRLGLKDVPMTEGRDYWWNKLMQGIPPNAYIEPEPV 268
           VV +KE  D A + +  VE V+V+ RLG +D P    RD  W++L   +     + P   
Sbjct: 202 VVAMKEEADRAADLSPSVEKVVVVSRLG-RDCPWNPDRDVKWDQLTAEMKT---LSPAVT 257

Query: 269 ESEHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGH 328
           ++  P  I+YTSGTTGKPKG VH   G+ +       + FD+   DI +   D+GW+ G 
Sbjct: 258 DANDPFMIIYTSGTTGKPKGTVHVHSGFPLKAAFDAGYAFDVGPGDILFWVTDMGWMMG- 316

Query: 329 SYVVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPR 388
            ++V G LL+G+T +++EG PDYP P R W + E++GVT    SPT IR  M++G  W  
Sbjct: 317 PWMVFGTLLLGSTMLVFEGTPDYPIPGRLWELTEKHGVTHLGISPTLIRALMKHGTSWFS 376

Query: 389 KHDLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTE-TGGIVISHAPGLYLV 447
           + DLS+LR+  S GEP NPE W W +  +G ++V   +    TE +GGI+ +H    +  
Sbjct: 377 QRDLSSLRVFGSTGEPWNPEPWHWLFEQVGGKRVPIFNYSGGTEISGGILGNH----FFK 432

Query: 448 PMKPGTNGPPLPGFEVDVVDENGNPAPPGVKGYLVIKKPWPGMLHGIWGDPERYIKTYWS 507
           P+ P     PLPG + +V D+ G     G  G LV+++PW GM  G W D  RY  TYWS
Sbjct: 433 PIVPCGFAGPLPGMDAEVFDDQGKTVR-GEVGELVLRQPWVGMTSGFWQDARRYEDTYWS 491

Query: 508 RFPGMFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGV 567
           R+P  +  GD+ I D+ G  ++ GR+D+ +K+AG RLG  E+ES L+ HP+V E+A +GV
Sbjct: 492 RWPKTWLHGDWVIVDEGGQWFITGRSDDTLKIAGKRLGPAEMESVLVDHPSVIEAATIGV 551

Query: 568 PDAIKGEVPIAFVVLKQGVAPSDELRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGKI 627
           PDA KGE  + FVV++        L +EL   V   +G   +P ++  V +LPKTR+GKI
Sbjct: 552 PDADKGESAVCFVVVRGDGEEVQSLTEELVRFVGERMGKALKPKRVHIVDELPKTRNGKI 611

Query: 628 MRRLLKAVATGAPLGDVTTLEDETSVEEAKR 658
           +RR+++A   G   GD+++LE+  +VE+ +R
Sbjct: 612 LRRVIRAAYLGENAGDLSSLENAHAVEKIRR 642


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: 1391
Number of extensions: 93
Number of successful extensions: 6
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: 646
Length adjustment: 38
Effective length of query: 632
Effective length of database: 608
Effective search space:   384256
Effective search space used:   384256
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