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 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