GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Shewanella sp. ANA-3

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 7025363 Shewana3_2523 acetyl-CoA synthetase (RefSeq)

Query= SwissProt::P27550
         (652 letters)



>lcl|FitnessBrowser__ANA3:7025363 Shewana3_2523 acetyl-CoA
           synthetase (RefSeq)
          Length = 650

 Score =  979 bits (2531), Expect = 0.0
 Identities = 453/645 (70%), Positives = 539/645 (83%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
           MS    + +  NIA   L+N  QY+ MYQ+SI  P+ FW E GK +DWIKPY K+K T+F
Sbjct: 1   MSSQSLYKVSGNIAANALVNNDQYKKMYQESIVNPEGFWREHGKRIDWIKPYTKIKKTTF 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
              N+SI W+ DGTLN +ANCLDRHL E+ DR AIIWEGD+AS+ + I+Y ELH  VC+F
Sbjct: 61  DDHNLSINWFYDGTLNASANCLDRHLAEHSDRVAIIWEGDNASEQRQITYGELHTQVCKF 120

Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
           AN L   G+++GD+V IYMPMVPEAAVAMLACARIGAVHSV+FGGFSP+++A R+ID  S
Sbjct: 121 ANALRSQGVRRGDIVTIYMPMVPEAAVAMLACARIGAVHSVVFGGFSPDSIASRVIDGKS 180

Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240
           ++VIT+DEG+R GR+IPLK+N+DDALK+P+VTSVE V+VLKRTGGK+DW EGRD+WWH L
Sbjct: 181 KVVITADEGMRGGRAIPLKRNIDDALKHPDVTSVEKVIVLKRTGGKVDWVEGRDVWWHSL 240

Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300
           VE AS+    EEM AEDPLF+LYTSGSTG PKGVLHTTGGY+VYA++T +YVFDY PG+I
Sbjct: 241 VETASEHCAIEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYASMTHEYVFDYKPGEI 300

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360
           YWCTADVGW+TGHSY++YGPLA GAT L+ EG+PN+P+PAR+ +++D+H+VNILYTAPT 
Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATVLIHEGIPNYPSPARLGEMIDRHKVNILYTAPTL 360

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420
           IRALMAEG +  +  D SSLRI+GSVGEPINPEAW WY + IG+E CP+VDTWWQTETGG
Sbjct: 361 IRALMAEGKQHFDKYDGSSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIVDTWWQTETGG 420

Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480
            +ITPLPGAT+ K GSATRPFFGVQPALVDN GN LEGATEG+LV+ DSWPGQ RT++GD
Sbjct: 421 ILITPLPGATDTKPGSATRPFFGVQPALVDNMGNILEGATEGNLVLLDSWPGQMRTVYGD 480

Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540
           HERF  TYF TF+ MYF+GDGARRDEDGYYWITGRVDDV+NVSGHRLGTAE+ESALV+H 
Sbjct: 481 HERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVSHE 540

Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600
            +AEAAVVG PH+IKGQ IYAYVTL  G E S EL  E+R WVRKEIG LATPD++ W  
Sbjct: 541 LVAEAAVVGYPHDIKGQGIYAYVTLTRGTEESEELRQELRQWVRKEIGALATPDLIQWAT 600

Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
            LPKTRSGKIMRR LRKIAA + +NLGD STLADP V+E L+E +
Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVTNLGDASTLADPAVIETLIETR 645


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: 1447
Number of extensions: 55
Number of successful extensions: 1
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: 650
Length adjustment: 38
Effective length of query: 614
Effective length of database: 612
Effective search space:   375768
Effective search space used:   375768
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