Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_035704411.1 BA79_RS18200 AMP-binding protein
Query= BRENDA::Q2XNL6 (634 letters) >NCBI__GCF_000691145.1:WP_035704411.1 Length = 644 Score = 385 bits (988), Expect = e-111 Identities = 220/595 (36%), Positives = 338/595 (56%), Gaps = 18/595 (3%) Query: 43 YW--AEKAERLEWFRKWDRVLDESNRPFYRWFVNGKINMTYNAVDRWLDTDK-RNQVAIL 99 +W AEKA ++W + ++ L + + +W+ G +N+T AVD+W + ++ ++Q AI+ Sbjct: 46 FWREAEKAVGIQWKKPYEAALGHHSLMWPKWYQGGTLNITETAVDKWAEKEETKHQPAII 105 Query: 100 YVNERGDERKLTYYELYREVSRTANALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGA 159 + NE G+E+K ++ EL +VSR A G++KGD +Y+PM PE V MLA KIG Sbjct: 106 WSNEAGEEKKWSFLELQEKVSRLAAGFLKEGLQKGDVAIIYMPMLPETVAVMLAFTKIGV 165 Query: 160 VHSVIYSGLSVGALVERLNDARAKIIITADGTYRRGGVIKLKPIVDEAILQCPTIETTVV 219 + S ++SG L R+ + A I++TA+ RRG I ++ V +AI + T++ +V Sbjct: 166 IFSPVFSGYGSEPLAVRIRASGASIVVTANEMMRRGKTINMRECVADAINKTATVQKVIV 225 Query: 220 VKHTDIDIEMSDISGREMLFDKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHT 279 + + D+ ++L ++ I G A + EDPL ILYTSG+TG PKG +HT Sbjct: 226 HTSSHTGYQ-GDVLLNDLLQEQPITG------ATYVTNEDPLMILYTSGTTGTPKGAVHT 278 Query: 280 TGGYMVGVASTLEMTFDIHNGD-LWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDY 338 G+ + A + D+ GD L+W T D+GW+ G ++V+G L+ G +LY+GAPDY Sbjct: 279 HAGFPIKAAFDAGLCMDVAKGDRLFWLT-DMGWMMG-PFLVFGGLINGAAIVLYDGAPDY 336 Query: 339 PDPGVWWSIVEKYGVTKFYTAPTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWM 398 PD WS + + VT F +PT +R M+ + L +K + + GEP N W Sbjct: 337 PDEQQLWSFIHQKKVTHFGLSPTFVRSAMQ---QTIDGVELSHVKAIISTGEPWNEAPWQ 393 Query: 399 WYYRNIGREKCPIIDTWWQTETGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVP 458 W + IG++ PI++ TE ++ + P+KP + G+ ADV +E G V Sbjct: 394 WLFHTIGQKNIPILNYSGGTEVSGGIVGSTLLRPIKPILFNAAILGMAADVYNEAGQSV- 452 Query: 459 LGKGGFLVIRKPWPAMFRTLFNDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRS 518 + + G LV++KPW M +N+ +RY D Y+K+ G V+T GD + EDG F I GRS Sbjct: 453 MNEVGELVVKKPWVGMTCGFWNEPERYEDTYFKRFDG-VWTHGDWVMQTEDGEFHITGRS 511 Query: 519 DDVLNIAGHRIGTAEVESVFVAHPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALI 578 DDV+N AG RIG AE+ES+ HPAV EAAVIG D +KGE + F++ A LI Sbjct: 512 DDVINTAGKRIGPAEIESILTWHPAVHEAAVIGVKDEVKGEALVCFIVTSPHAFEEATLI 571 Query: 579 EELKRHLRHELGPVAVVGEMVQVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLE 633 +EL H+ G E+ + +LPKTR+GKI+RR+L+ E + D S+L+ Sbjct: 572 QELSAHVGSHAGKALTPKEVHLISALPKTRNGKIVRRLLKGAYEEKPSPDLSSLD 626 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: 1119 Number of extensions: 65 Number of successful extensions: 7 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: 644 Length adjustment: 38 Effective length of query: 596 Effective length of database: 606 Effective search space: 361176 Effective search space used: 361176 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