Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_091300298.1 BLV57_RS42120 acetoacetate--CoA ligase
Query= BRENDA::Q2XNL6 (634 letters) >NCBI__GCF_900107045.1:WP_091300298.1 Length = 658 Score = 247 bits (631), Expect = 1e-69 Identities = 177/590 (30%), Positives = 297/590 (50%), Gaps = 23/590 (3%) Query: 30 WEAELEKGKDHENYWAEKAERL--EWFRKWDRVLDESNRPFYRWFVNGKINMTYNAVDRW 87 WE +++ + +WA AE L W ++ VL + P +WF G +N +A+ Sbjct: 45 WEFSVQRVPE---FWAAVAEFLGMRWHQQPGEVLSGA-MPQAKWFDGGTLNYAEHALTPG 100 Query: 88 LDTDKR--NQVAILYVNERGDERKLTYYELYREVSRTANALKSLGIKKGDAVALYLPMCP 145 + + +++A+++ E G R+LTY +L +V+ AL S G+ KGD V P CP Sbjct: 101 VAGASKADDELAVIFHREDGLTRQLTYGKLRAQVAAFRAALVSSGVGKGDRVVALAPNCP 160 Query: 146 ELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKIIITADGTYRRGGVIKLKPIVD 205 + +V+ LA A +GAV S V A+ +R K+++ +G G + + Sbjct: 161 QTLVAFLATASLGAVWSSCSPDFGVRAISDRFTQIEPKVLVAVNGYVYNGRSFDTRSTIS 220 Query: 206 EAILQCPTIETTVVVKHTDIDIEMSDISGREMLFDKLIEGEGDRCDAEEMDAEDPLFILY 265 + Q P++E TV++ + + + G D L +G E +D PL++LY Sbjct: 221 QLREQIPSLEATVLIDY----VGGGSLDGTLDFDDLLAAHDGAELAFEPVDFAHPLWVLY 276 Query: 266 TSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDLWWCTADIGWITGHSYVVYGPLLL 325 +SG+TG PKG++H GG + + L + D+ GD ++ GW+ ++++ G LL+ Sbjct: 277 SSGTTGLPKGIVHGHGGITIELLKALALQSDLGPGDRFFWFTTTGWMM-WNFLISG-LLV 334 Query: 326 GTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTAIRHLMRFGDKHPKRYNLESLKIL 385 GTT +L++G+P +PD V W + E++ VT F T+ I+ ++ G K +Y+L +L+ + Sbjct: 335 GTTIVLFDGSPGHPDLNVLWHLAEQHRVTFFGTSAPFIQSCLKEGIKPSSKYDLTALRAI 394 Query: 386 GTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGMHLIAPLPVTPLKPGSVTKPLPGI 445 G+ G P++ E + W G+ I T+ +A P P+ G ++ G Sbjct: 395 GSTGSPLSVEGFRWLVNEFGK-SVQICSVSGGTDLCAAFVAASPDLPVWLGELSCRALGA 453 Query: 446 EADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDE--QRYIDVYWKQIPGGVYTAGDM 503 + DE G+ V + + G LV+ +P P+M +ND R + Y++ P G++ GD Sbjct: 454 AVESFDEAGNSV-IEEVGELVVTQPMPSMPVYFWNDPDGSRLREAYFEMYP-GIWRHGDW 511 Query: 504 ARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHPAVAEAAVI--GKADPIKGEVI 561 R + G I GRSD LN G R+GTAE V +VA++ VI A G+++ Sbjct: 512 IRITKRGSAVIYGRSDSTLNRGGVRMGTAEFYRVVEGFASVADSLVIDTSAAGNEDGQLL 571 Query: 562 KAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVDSLPKTRSGK 611 FL+LK G L A + L++ LR L P V V V +P+T +GK Sbjct: 572 -CFLVLKSGASL-ADVEPSLRKELRGALSPRHVPDRFVVVTEIPRTLNGK 619 Lambda K H 0.319 0.138 0.428 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: 1082 Number of extensions: 58 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: 634 Length of database: 658 Length adjustment: 38 Effective length of query: 596 Effective length of database: 620 Effective search space: 369520 Effective search space used: 369520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 24 2021. The underlying query database was built on Sep 17 2021.
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