GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Dyella japonica UNC79MFTsu3.2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate N515DRAFT_3075 N515DRAFT_3075 acetyl-coenzyme A synthetase (EC 6.2.1.1)

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3075
          Length = 646

 Score =  883 bits (2281), Expect = 0.0
 Identities = 411/639 (64%), Positives = 508/639 (79%)

Query: 7   HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66
           + +    A +  I+ + YE +Y++S+  P+ FWG  G+ L+W +   K+KN S+ P N+ 
Sbjct: 5   YPVKPEFAAKARISKEDYERLYEESVRDPEGFWGRIGERLEWHRKPSKIKNVSYDPKNLH 64

Query: 67  IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126
           I+WYEDG LN++ANCLDRHL   GD+TAII+EGDD ++S+H++Y+ELH +VC+FANTL  
Sbjct: 65  IRWYEDGELNVSANCLDRHLASRGDKTAIIFEGDDPNESRHLTYRELHAEVCKFANTLKN 124

Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186
           LG+ KGD VAIYMPM+PEAAVAMLACARIGAVHSV+FGGFSP+++AGRI DS +++V+T+
Sbjct: 125 LGVAKGDRVAIYMPMIPEAAVAMLACARIGAVHSVVFGGFSPDSLAGRIADSTAKVVVTA 184

Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASD 246
           DEGVR G+ IPLK NVD AL+ P   SVE V+V++RTG  +  Q  RD ++H L+E  S 
Sbjct: 185 DEGVRGGKKIPLKANVDAALERPGTNSVETVIVVRRTGSAVPMQSPRDRYYHVLMEGQSA 244

Query: 247 QHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTAD 306
                 + AE PLFILYTSGSTGKPKGVLHT+GGYLV+A  T + VFD    D+YWCTAD
Sbjct: 245 DCPPTPVEAEHPLFILYTSGSTGKPKGVLHTSGGYLVFAGFTHEMVFDLREDDVYWCTAD 304

Query: 307 VGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMA 366
           VGWVTGHSY++YGPLA GATT+MF+GVPN+P  +R   VVDKH+V + YTAPTAIRALM 
Sbjct: 305 VGWVTGHSYVVYGPLANGATTVMFDGVPNYPDTSRFWNVVDKHKVTLFYTAPTAIRALMR 364

Query: 367 EGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPL 426
           EG+  ++   R+SLR+LGSVGEPINPEAWEWY++ +G+E+CP+VDTWWQTETGG MITPL
Sbjct: 365 EGEAPVKKASRASLRLLGSVGEPINPEAWEWYYRVVGDERCPIVDTWWQTETGGIMITPL 424

Query: 427 PGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQ 486
            GA + K GSAT+PFFG++PA+VD  G  LEGATEG+LVI DSWPGQ RT++GDH+RF +
Sbjct: 425 AGAIDAKPGSATKPFFGIRPAVVDAGGAVLEGATEGNLVIADSWPGQMRTVYGDHQRFVE 484

Query: 487 TYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAA 546
           TYF+ +   YF+GDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESALV+HPK+AEAA
Sbjct: 485 TYFTAYPGNYFTGDGVRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPKVAEAA 544

Query: 547 VVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTR 606
           VVG PH IKGQ IYAYVTL  GE+ S EL  E+  WVRKEIGP+ATPD L W   LPKTR
Sbjct: 545 VVGCPHEIKGQGIYAYVTLIAGEQGSDELRKELVAWVRKEIGPIATPDYLQWAPGLPKTR 604

Query: 607 SGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           SGKIMRRILRKI       LGD STLADP VV+ L+EE+
Sbjct: 605 SGKIMRRILRKIGENQPDQLGDISTLADPSVVKNLVEER 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: 1438
Number of extensions: 60
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: 646
Length adjustment: 38
Effective length of query: 614
Effective length of database: 608
Effective search space:   373312
Effective search space used:   373312
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:

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