GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Shewanella amazonensis SB2B

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 6937938 Sama_2079 acetyl-CoA synthetase (RefSeq)

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__SB2B:6937938
          Length = 650

 Score =  964 bits (2493), Expect = 0.0
 Identities = 444/645 (68%), Positives = 535/645 (82%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
           MS    +++PA+IA   L+N +QY+ MYQ+S+  P+ FWGE  K +DWIKP+ +VK+TS+
Sbjct: 1   MSTQSLYSVPADIAANALVNNEQYQKMYQESVANPEGFWGEHAKRIDWIKPFTQVKDTSY 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
              N+ IKW+ DGTLN +ANCLDRHL   GD  AIIWEGDDAS+ + ++Y+ELH +VC+F
Sbjct: 61  DDQNLYIKWFHDGTLNASANCLDRHLASKGDDVAIIWEGDDASEQRKVTYRELHAEVCQF 120

Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
           AN L   G+K+GDVV IYMPMV EA VAMLACARIGAVHSV+FGGFSP+++A R+ID  S
Sbjct: 121 ANALKAEGVKRGDVVTIYMPMVVEATVAMLACARIGAVHSVVFGGFSPDSIASRVIDGKS 180

Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240
           +L+IT+DEGVR GR IPLK N+D+AL  P+VT+VE V+VLKRTGG ++W EGRD WWH +
Sbjct: 181 KLLITADEGVRGGRKIPLKGNIDEALNRPDVTTVETVIVLKRTGGAVNWVEGRDKWWHQV 240

Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300
            + A+ +   EEM AEDPLF+LYTSGSTG PKGVLHTTGGYLVYA++T +YVFDY PG++
Sbjct: 241 TDGAATECAVEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKPGEV 300

Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360
           YWCTADVGW+TGHSY++YGPLA GAT L+ EG+PN+P+PAR+ ++VD+HQVNILYTAPT 
Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATILIHEGIPNFPSPARLGEIVDRHQVNILYTAPTL 360

Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420
           IRALMAEG +  +  D  SLRI+GSVGEPINPEAW WY + IG+E CP+VDTWWQTETGG
Sbjct: 361 IRALMAEGKQHFDNFDGKSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIVDTWWQTETGG 420

Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480
            +ITPLPGAT+ K GSATRPFFGVQPALVDNEGN LEGATEG+LV+ DSWPGQ RT++GD
Sbjct: 421 ILITPLPGATDTKPGSATRPFFGVQPALVDNEGNILEGATEGNLVLLDSWPGQMRTVYGD 480

Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540
           HERF  TYF TF+ MYF+GDGARRDEDGYYWITGRVDDV+NVSGHRLGTAE+ESALVAH 
Sbjct: 481 HERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHD 540

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

Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
            LPKTRSGKIMRR LRKIAA + +NLGD STLADP V++ L+E +
Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEITNLGDASTLADPSVIDTLIESR 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: 1459
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 Aug 03 2021. The underlying query database was built on Aug 03 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