Alignments for a candidate for acs in Rubrivirga marina SAORIC-28

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Rubrivirga marina SAORIC-28

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_095511499.1 BSZ37_RS15895 AMP-binding protein

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_002283365.1:WP_095511499.1
          Length = 658

 Score =  459 bits (1181), Expect = e-133
 Identities = 262/638 (41%), Positives = 372/638 (58%), Gaps = 22/638 (3%)

Query: 30  IDAYFKFHRQTVENLESFWESVAKEL--EWFKPWDKVLDASNP-PFYKWFVGGRLNLSYL 86
           +D Y    R  ++++  FW+ V ++L  E+ +P+ + LDAS      +W VGGR+N+ + 
Sbjct: 34  LDGYAALERWALDDIGRFWDLVMEDLGIEFSQPYTRALDASGGIERPRWCVGGRMNVVHN 93

Query: 87  AVDRHVKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKG 146
            +DR   T    + AI +E E           R LTY +L+ EV   A  L+ + G+  G
Sbjct: 94  CLDRWAGTEAWERDAIRYESEE-------GTTRSLTYLELHAEVEACAAGLRAH-GLGAG 145

Query: 147 DKITLYLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRR 206
           D + LYLPM PE+ +  LA  RIG I   +FSG+ A+A+A R+ D  ++ ++ ADG  RR
Sbjct: 146 DAVGLYLPMTPEIVVAFLAVARIGGIILPLFSGYGAEAVATRLADGNAKALVVADGAPRR 205

Query: 207 GRVVRLKEVVDAALEKATGVESVIVLPRLG--LKDVPMTEGRDYWWNKLMQGIPPNAYIE 264
           GR V +K + D AL +A  V  V V+ R+G  L   P T GRD  W++L++    +    
Sbjct: 206 GRAVPMKAIADEALAEAPSVRHVFVVDRMGDELIGTPRTGGRDIPWSRLLEIGRQSTATG 265

Query: 265 PEPVESEHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGW 324
                +E P  ++YTSGTTG PKG VH   G+ +     M+   D+R  D+ W  +D+GW
Sbjct: 266 CADTAAEDPVLLIYTSGTTGTPKGAVHTHCGFPIKAAQDMRHPMDVRAGDVVWWMSDMGW 325

Query: 325 VTGHSYVVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGE 384
           + G  ++V G LL GAT V+++GAPD+P+ DR W+I ER+GVT+   SPT IR  M +G 
Sbjct: 326 MMG-PWLVFGALLNGATMVLFDGAPDFPEADRTWAICERHGVTLLGLSPTLIRALMPHGA 384

Query: 385 EWPRKHDLSTLRIIHSVGEPINPEAWRWAYR-VLGNEKVAFGSTWWMTETGGIVISHAPG 443
              + HDLS LR + S G P +PE+WRW +  VL + +     +     +GGIV     G
Sbjct: 385 GPVQAHDLSALRAVGSTGSPWDPESWRWLFSTVLDSNRPILNYSGGTEISGGIVC----G 440

Query: 444 LYLVPMKPGTNGPPLPGFEVDVVDENGNPAPPGVKGYLVIKKPWPGMLHGIWGDPE--RY 501
            ++  +KP     P+ G + DVVDE+G P   G  G L I++PW GM  G WGD +  RY
Sbjct: 441 NHVQSLKPTGFSGPVLGMDADVVDESGEPVR-GAVGELAIRQPWIGMTRGFWGDEDNARY 499

Query: 502 IKTYWSRFPGMFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAE 561
             TYW+R PG++  GD+A  D DG  ++LGR+D+ IKVAG RLG  E+ESAL + P V E
Sbjct: 500 HATYWARTPGLWVHGDFAAVDADGQWFLLGRSDDTIKVAGKRLGPAEVESALNAAPEVLE 559

Query: 562 SAVVGVPDAIKGEVPIAFVVLKQGVAPSDELRKELREHVRRTIGPIAEPAQIFFVTKLPK 621
           SA VGVPD +KG+  +AF VL  G   SD LR+ L   V   +G    P  + FV  LPK
Sbjct: 560 SAAVGVPDDVKGQAVVAFAVLAAGATESDALREALIGRVTDALGKALRPKAVLFVDALPK 619

Query: 622 TRSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRA 659
           TR+ K+MRR+++A      LG+VT LEDE +VE  +RA
Sbjct: 620 TRNAKVMRRVIRAAHLDGDLGNVTALEDEDAVEAIRRA 657


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: 1341
Number of extensions: 81
Number of successful extensions: 10
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: 658
Length adjustment: 38
Effective length of query: 632
Effective length of database: 620
Effective search space:   391840
Effective search space used:   391840
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 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