Alignments for a candidate for prpE in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Sphingomonas koreensis DSMZ 15582

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Ga0059261_1313 Ga0059261_1313 acetyl-coenzyme A synthetase (EC 6.2.1.1)

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Korea:Ga0059261_1313
          Length = 645

 Score =  844 bits (2181), Expect = 0.0
 Identities = 401/640 (62%), Positives = 491/640 (76%), Gaps = 3/640 (0%)

Query: 7   HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66
           H +PA  A     +   YE +Y +SI  P +FW +Q K LDW+K  +   + SF   +  
Sbjct: 6   HPVPAEWAREARYDAAGYEQLYGRSIADPGSFWLDQAKRLDWVKRPELAGDWSFDESDFR 65

Query: 67  IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDD-ASQSKHISYKELHRDVCRFANTLL 125
           I+W+ DG LN+AANC+DRHL   GD  AIIWE DD A  S+  +Y+ELH +VCRFAN L 
Sbjct: 66  IEWFADGKLNVAANCIDRHLASRGDEVAIIWEPDDPAEASRQFTYRELHEEVCRFANVLK 125

Query: 126 ELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVIT 185
             G+KKGD V IYMPM+PEAA A+LACAR+GA+HSV+FGGFSPEA+AGRI D +S +VIT
Sbjct: 126 GQGVKKGDRVTIYMPMIPEAAFAILACARLGAIHSVVFGGFSPEALAGRITDCDSSVVIT 185

Query: 186 SDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQAS 245
           +DEG R G+ I LK NVD A +     ++E V+V+K TGG +    GRD+W+H+      
Sbjct: 186 ADEGRRGGKRIALKANVDAAAER--APALEKVIVVKATGGHVTMTPGRDVWYHEAAAGVG 243

Query: 246 DQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTA 305
               AE MNAEDPLFILYTSGSTGKPKGVLHT+ GYL++A+LT +  FDY PG+++WC A
Sbjct: 244 TDCPAETMNAEDPLFILYTSGSTGKPKGVLHTSAGYLLWASLTHELAFDYRPGNVWWCAA 303

Query: 306 DVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALM 365
           D+GWVTGHSY+LYGPLA GATTLM+EG+PNWP  +R+ QVVD+H V+ ++TAPTA+RALM
Sbjct: 304 DIGWVTGHSYILYGPLANGATTLMYEGLPNWPDASRIWQVVDRHNVHTIFTAPTALRALM 363

Query: 366 AEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITP 425
            +GD  +  T R+SLR+LG+VGEPINPEAW WY + +G  +CP++DTWWQTETGG MI P
Sbjct: 364 KDGDDFVTKTSRTSLRLLGTVGEPINPEAWRWYHEVVGESRCPIIDTWWQTETGGAMIAP 423

Query: 426 LPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFE 485
           +PGAT+LK GSATRP  GV P LVD+EG  L GATEG+LVI  SWPGQ RT++GDHERF 
Sbjct: 424 MPGATDLKPGSATRPLPGVDPQLVDSEGAVLHGATEGNLVIARSWPGQMRTVWGDHERFF 483

Query: 486 QTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEA 545
           QTYF+T+   YF+GDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESALV HPK+AEA
Sbjct: 484 QTYFTTYPGKYFTGDGCRRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVLHPKVAEA 543

Query: 546 AVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKT 605
           AVVG+PH++KGQ IYAYVTLN G      L AE+  WVR EIGP+ATPD L +   LPKT
Sbjct: 544 AVVGMPHDVKGQGIYAYVTLNAGCAADDALRAELVKWVRTEIGPIATPDALQFAPGLPKT 603

Query: 606 RSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           RSGKIMRRILRKIA GD S+LGDTSTLADP VV+ L+  +
Sbjct: 604 RSGKIMRRILRKIAEGDVSSLGDTSTLADPSVVDDLVANR 643


Lambda     K      H
   0.317    0.135    0.421 

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: 1497
Number of extensions: 71
Number of successful extensions: 3
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: 652
Length of database: 645
Length adjustment: 38
Effective length of query: 614
Effective length of database: 607
Effective search space:   372698
Effective search space used:   372698
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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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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