Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_109940824.1 DLD82_RS09165 AMP-binding protein
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_003173335.1:WP_109940824.1 Length = 616 Score = 431 bits (1108), Expect = e-125 Identities = 236/538 (43%), Positives = 335/538 (62%), Gaps = 23/538 (4%) Query: 38 FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97 FN+ DV + K+R +K A++W + GEE ++ ++S SN +++ + K+ + KGD Sbjct: 79 FNFGFDVVDAWAKKDR-NKIAMVWTN-QKGEEKFFTFRDISRRSNEIVNMMIKYKIGKGD 136 Query: 98 VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157 V +M P W + +A+IK G + +P+ T LT ++ YR + + +I+D A + Sbjct: 137 RVLIMLHRVPEWWFMTVALIKIGAIYIPAPTMLTPKDIAYRVNTAEAKMVITDMENAHKV 196 Query: 158 EEALGSLK--VEKFLIDGKRETWNSLEDESSNAEP-----------EDTRGEDVIINYFT 204 +E +G V K ++DG+ + W S E P T+ + ++ +F+ Sbjct: 197 DEIVGDCPTLVTKMVVDGECDGWLSYTRELMYPAPVSSRIINLKGMRKTKSSEPMVIFFS 256 Query: 205 SGTTGMPKRVIHTAVSYPVGSITTASIV-GVRESDLHLNLSATGWAKFAWSSFFSPLLVG 263 SGTTG PK V H+ SYP+G I TA VR +DLH +S TGWAK AW F + G Sbjct: 257 SGTTGEPKMVQHSH-SYPLGHIVTARFWHDVRNNDLHFTVSDTGWAKSAWGKLFGQWIEG 315 Query: 264 ATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGE 323 A + +Y + + L +E G+T+FCAPPT +R I DL ++ F LR VSAGE Sbjct: 316 AAIFVYDYRSRFNATELLPLIEKYGITTFCAPPTIYRMLIMADLRKWDFSELRHCVSAGE 375 Query: 324 PLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEG 383 +NPEVIK WKD L I + YGQTET VG FP ++ K GSMGKP P ++I L D++G Sbjct: 376 LINPEVIKAWKDATGLEIYEGYGQTETVLCVGTFPCMEPKYGSMGKPSPGWEIELHDEDG 435 Query: 384 KEITKPYEVGHITVKLNPRPIGLFLGY-SDEKKNMESFREGYYYTGDKAYFDEEGYFYFV 442 ++ KP E G I +K PRP+G F+ Y +E+ N SF+ GYYYTGD+A D +GYF+FV Sbjct: 436 NQV-KPGEEGSIAIKTEPRPVGFFMEYWGNEEANANSFKGGYYYTGDRAMKDNDGYFWFV 494 Query: 443 GRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSK 502 GR DDVIK S YR+GPFEVESA++EHPAV EAAVVG PD +R +VKA++VLK G+ PS+ Sbjct: 495 GRDDDVIKASGYRIGPFEVESAIIEHPAVQEAAVVGSPDIIRGFIVKAFVVLKAGFEPSE 554 Query: 503 ELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELR----KREEEKRKKGE 556 +++ +I+E +K +PYK PR IEF+ ELPKTISGKI+R +LR KR E ++K G+ Sbjct: 555 KISRDIQEYVKNSTAPYKYPRKIEFIKELPKTISGKIKRKDLRELEMKRFEVEQKNGD 612 Lambda K H 0.318 0.137 0.402 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: 852 Number of extensions: 40 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: 564 Length of database: 616 Length adjustment: 37 Effective length of query: 527 Effective length of database: 579 Effective search space: 305133 Effective search space used: 305133 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: 53 (25.0 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