Alignments for a candidate for acs in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Dyella japonica UNC79MFTsu3.2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate N515DRAFT_0016 N515DRAFT_0016 propionyl-CoA synthetase

Query= curated2:O93730
         (670 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0016
          Length = 630

 Score =  497 bits (1279), Expect = e-145
 Identities = 275/635 (43%), Positives = 397/635 (62%), Gaps = 19/635 (2%)

Query: 33  YFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRHV 92
           Y  F+R ++E  E+FW   A+ ++W  P  +VLD S PPF +WFVGG  NL Y A+DRH+
Sbjct: 3   YETFYRHSIEAPEAFWAEQAQLIDWQTPPRQVLDYSRPPFRRWFVGGTTNLCYNAIDRHL 62

Query: 93  KTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLY 152
           +  R ++LA+        E G     R+L+Y  L+REVN  A +L     V++GD++ +Y
Sbjct: 63  EA-RGDQLALVAIST---ETGLT---RELSYRQLHREVNVFAAVLAA-LDVQRGDRVVIY 114

Query: 153 LPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVRL 212
           LP + E    MLA  R+GAI SVVF GF+A  LA RI+D+Q +++I AD   R G+V+  
Sbjct: 115 LPNIAEAVFAMLACARLGAIHSVVFGGFAAHNLALRIDDAQPKLLIAADAGMRGGKVIPY 174

Query: 213 KEVVDAALEKATGVESVIVLPRLGLKDVPMTE--GRDYWWNKLMQGIPPNAYIEPEPVES 270
           K +VDAALE++      +++   GL D  MT   GRD  + +L +     A +    +ES
Sbjct: 175 KPLVDAALEQSAAPPPHVLIVDRGL-DPQMTRVAGRDLDYAQLRKA-HEQAEVPVAWLES 232

Query: 271 EHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSY 330
             PS++LYTSGTTGKPKGI  D GG+AV +  +++++FDI    + + T+D+GW  GHSY
Sbjct: 233 NEPSYLLYTSGTTGKPKGIQRDVGGYAVAMAMSVRYIFDIAPGQVMFSTSDVGWAVGHSY 292

Query: 331 VVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKH 390
            V GPL+ GAT ++YEG P  P P  WW + ERY V   ++SPT IR+  +    W RK+
Sbjct: 293 NVYGPLIAGATSLLYEGLPTRPDPGIWWYLCERYSVRTMFSSPTGIRVLKKQDPAWLRKY 352

Query: 391 DLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMK 450
           DLS+L+ +   GEP++     W    LG   V     +W TETG   I+  PGL L  +K
Sbjct: 353 DLSSLQWLFLAGEPLDEPTAHWITDGLG---VPVIDNYWQTETGWPAITLMPGLELKRVK 409

Query: 451 PGTNGPPLPGFEVDVVDE-NGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSR 508
            G+ G P PG+ + V+DE  G  A PG KG LV + P  PG L  +WGD ERY+ +Y+  
Sbjct: 410 FGSPGLPAPGYRMKVIDEATGEEAAPGHKGVLVFEPPLPPGCLSTVWGDDERYLSSYFGH 469

Query: 509 FPGMFYAG-DYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGV 567
           F  + Y+  D+AI+D+ GY  +LGR D+VI VAGHRLGT E+E ++ +HPAVAE+AV+GV
Sbjct: 470 FKELLYSSLDWAIRDEHGYTTILGRTDDVINVAGHRLGTREIEESVATHPAVAEAAVIGV 529

Query: 568 PDAIKGEVPIAFVVLKQGV-APSDELRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGK 626
            D +KG+VP+ F  LKQ     + ++ + +++ V   +G IA P++++ V  LPKTRSGK
Sbjct: 530 RDELKGQVPVVFATLKQDAGTQAGQVAQAMQQRVVDQLGGIARPSRVYVVNALPKTRSGK 589

Query: 627 IMRRLLKAVATGAPLGDVTTLEDETSVEEAKRAYE 661
           ++RR L+A+A     GD++TL+D  ++EE +RA E
Sbjct: 590 LLRRSLQALAEQRDPGDLSTLDDPGALEEIRRALE 624


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: 1307
Number of extensions: 86
Number of successful extensions: 9
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: 630
Length adjustment: 38
Effective length of query: 632
Effective length of database: 592
Effective search space:   374144
Effective search space used:   374144
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources