GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Caulobacter crescentus NA1000

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate CCNA_03696 CCNA_03696 acetyl-coenzyme A synthetase

Query= SwissProt::P27550
         (652 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03696 CCNA_03696 acetyl-coenzyme A
           synthetase
          Length = 647

 Score =  826 bits (2134), Expect = 0.0
 Identities = 397/637 (62%), Positives = 488/637 (76%), Gaps = 2/637 (0%)

Query: 9   IPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIK 68
           +PA++A    I+   Y+A   +    P+ +W +    LDWI P  K+K+ S+A  +  I+
Sbjct: 10  VPADLARDAHIDAAAYDAALARVEADPEGYWRDIAARLDWITPPTKIKDVSYAKEDFRIR 69

Query: 69  WYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELG 128
           WYEDG LN++ANC+DRHL    D  A+++EGD+   S  ++Y +LH +VCR AN L   G
Sbjct: 70  WYEDGVLNVSANCIDRHLPAKKDDVALVFEGDEPGTSSTLTYGQLHEEVCRMANVLKAQG 129

Query: 129 IKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDE 188
           +KKGD V IY+PMVP AAVAMLACARIGAVHSV+FGGFSP+++AGRI D  S  VIT+DE
Sbjct: 130 VKKGDRVTIYLPMVPLAAVAMLACARIGAVHSVVFGGFSPDSIAGRIQDCASHFVITADE 189

Query: 189 GVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQH 248
           G R GR +PLK N+D+ALK+     V  V++++ TG  +  + GRD+ W D+ +  S   
Sbjct: 190 GRRGGRRVPLKANIDEALKH--CPWVGKVLMIRWTGADVPLKAGRDIVWQDVRDTVSADC 247

Query: 249 QAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVG 308
             E MNAEDPLFILYTSGSTGKPKGVLHTTGGYL +A+ TF  VFDY PG+++WCTADVG
Sbjct: 248 PPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLAWASWTFWAVFDYKPGEVFWCTADVG 307

Query: 309 WVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEG 368
           WVTGHSY++YGPLA G T+L+FEGVPN+PTP+R  +V+DKHQV+I YTAPTA+RALM EG
Sbjct: 308 WVTGHSYVVYGPLANGGTSLIFEGVPNYPTPSRFWEVIDKHQVSIFYTAPTALRALMREG 367

Query: 369 DKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPG 428
           D  +   D SSLR+LGSVGEPINPEAW WY + +G EK P+VDTWWQTETGG +ITPLPG
Sbjct: 368 DAHVTKNDLSSLRLLGSVGEPINPEAWLWYHRVVGKEKLPIVDTWWQTETGGMLITPLPG 427

Query: 429 ATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTY 488
           AT LK GSA++P  GV+P LVD EG  L+GATEG+LVITDSWPGQ RT++GDH+RF +TY
Sbjct: 428 ATALKPGSASKPLPGVKPQLVDAEGKFLDGATEGNLVITDSWPGQMRTVYGDHQRFFETY 487

Query: 489 FSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVV 548
           FST+   YF+GDG RRD DGYYWITGRVDDV+NVSGHRLGTAEIESALVAH  +AEAAVV
Sbjct: 488 FSTYPGKYFTGDGCRRDADGYYWITGRVDDVINVSGHRLGTAEIESALVAHETVAEAAVV 547

Query: 549 GIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSG 608
           G PH+IKGQ +YAYVTL  G E +  L  ++  WVR EIGP A PDV+ W   LPKTRSG
Sbjct: 548 GYPHDIKGQGVYAYVTLKAGIEATDALRKDLVLWVRHEIGPFAAPDVIQWAPGLPKTRSG 607

Query: 609 KIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           KIMRRILRKIA  +  +LGDTSTLADP VV+ L++ +
Sbjct: 608 KIMRRILRKIAENELGSLGDTSTLADPSVVDDLVKNR 644


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: 1510
Number of extensions: 56
Number of successful extensions: 2
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: 647
Length adjustment: 38
Effective length of query: 614
Effective length of database: 609
Effective search space:   373926
Effective search space used:   373926
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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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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