Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Echvi_1268 Echvi_1268 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Cola:Echvi_1268 Length = 632 Score = 712 bits (1839), Expect = 0.0 Identities = 344/618 (55%), Positives = 439/618 (71%), Gaps = 6/618 (0%) Query: 28 YQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCLDRHLQ 87 YQ+S+ P+ FW W K + KV F +V KW+ +G +N+ N L+RHL Sbjct: 15 YQKSVTEPEQFWARIADSFHWKKRWDKVLEWDFEGPDV--KWFVNGKVNITENILERHLF 72 Query: 88 ENGDRTAIIWEGDDASQS-KHISYKELHRDVCRFANTLLELGIKKGDVVAIYMPMVPEAA 146 GDR AIIWE +D ++ + ++Y++L+ +VC+F+N L GI KGD V IYMPMVPEAA Sbjct: 73 IMGDRPAIIWEPNDPNEEGRTLTYRQLYHEVCKFSNALKAKGIGKGDKVIIYMPMVPEAA 132 Query: 147 VAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKKNVDDAL 206 +AMLACARIGAVHSV+F GFS A+A RI D ++ V+TSD R + I +K VD+AL Sbjct: 133 IAMLACARIGAVHSVVFAGFSSSALADRINDCEAKAVLTSDGNFRGTKKIAVKDLVDEAL 192 Query: 207 KNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDPLFILYTSG 266 + ++E V+V +RT ++ EGRD+WWHD ++ D ++AE M++ED LFILYTSG Sbjct: 193 EKTK--TIETVIVYQRTKQEVKMVEGRDIWWHDAIDGQPDTNEAEVMDSEDMLFILYTSG 250 Query: 267 STGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPLACGAT 326 STGKPKGV+HTTGGY+VY+ TF+ VF Y PGD+YWCTAD+GW+TGHSY++YGPL GAT Sbjct: 251 STGKPKGVVHTTGGYMVYSKYTFENVFQYSPGDVYWCTADIGWITGHSYIVYGPLLAGAT 310 Query: 327 TLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLRILGSV 386 ++MFEGVP +P R +VDK+QVN YTAPTAIRAL A G K IE SL++LGSV Sbjct: 311 SIMFEGVPTYPDAGRFWAIVDKYQVNQFYTAPTAIRALEAHGTKPIEPYKLDSLKVLGSV 370 Query: 387 GEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRPFFGVQP 446 GEPIN EAW WY +G +CP+VDTWWQTETGG M++P+ G T K AT P GVQ Sbjct: 371 GEPINEEAWHWYHTHVGKNRCPIVDTWWQTETGGIMVSPIAGITPNKPAYATMPLPGVQL 430 Query: 447 ALVDNEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDGARRD 505 A+VD EG L+G A EG+L I WPG RT +GDH+R +QTYFS + MYF+GDG +RD Sbjct: 431 AIVDPEGKELKGKAVEGNLCIKFPWPGMLRTTYGDHDRCKQTYFSAYPGMYFTGDGVKRD 490 Query: 506 EDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIYAYVTL 565 DGYY I GRVDDV+NVSGHR+GTAEIE+A+ HPK+ E+AVVG PH +KGQ IYAYV Sbjct: 491 HDGYYRILGRVDDVINVSGHRMGTAEIENAINEHPKVIESAVVGYPHEVKGQGIYAYVIC 550 Query: 566 NHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDTSN 625 + L E+++ + K IGP+A PD + LPKTRSGKIMRRILRK+A G N Sbjct: 551 DLKNRTEENLIGEIKDTITKSIGPIAKPDKIQIVPGLPKTRSGKIMRRILRKVAEGSFDN 610 Query: 626 LGDTSTLADPGVVEKLLE 643 +GDTSTL DP VVE+++E Sbjct: 611 MGDTSTLLDPAVVEEIIE 628 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: 1299 Number of extensions: 72 Number of successful extensions: 5 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: 632 Length adjustment: 38 Effective length of query: 614 Effective length of database: 594 Effective search space: 364716 Effective search space used: 364716 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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