Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate GFF3328 PS417_17030 3-methylcrotonyl-CoA carboxylase
Query= reanno::Dino:3607308 (681 letters) >FitnessBrowser__WCS417:GFF3328 Length = 641 Score = 462 bits (1188), Expect = e-134 Identities = 276/656 (42%), Positives = 371/656 (56%), Gaps = 40/656 (6%) Query: 5 ILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYIVID 64 +L+ANRGEIACRV++TA+ MG+ TVA++S DR+A H R AD V +G S A SY+ ID Sbjct: 7 LLVANRGEIACRVMRTAKAMGLTTVAVHSAIDRDARHSREADIRVDLGGSKATDSYLQID 66 Query: 65 KVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKKIAQ 124 K++ A + +GA+A+HPGYGFLSEN FA A+E G+ F+GPPA+AI+AMG K +K + + Sbjct: 67 KLIAAAQASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALME 126 Query: 125 EANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREGFQSS 184 A V VPGY G D + IGYPV++KA+AGGGGKGM++ + ++ E S+ Sbjct: 127 TAGVPLVPGYHGEAQDLETFRAACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 186 Query: 185 KNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVEEAPS 244 + EA +SFG+ ++ +EK++ +PRH+EIQV AD HG+C+YL ER+CSIQRR+QKVVEEAP+ Sbjct: 187 QREALSSFGNGQMLVEKYLLKPRHVEIQVFADQHGHCLYLNERDCSIQRRHQKVVEEAPA 246 Query: 245 PFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVTELIT 304 P L RKAMGE + AQA+GY AGTVEF++D F+F+EMNTRLQVEHPVTE IT Sbjct: 247 PGLSGEQRKAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 306 Query: 305 GVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRPPVEV 364 G+DLV IRVA GE LP+TQ+ V LTG AIE RLYAEDP +FLP+ GRL YR E Sbjct: 307 GLDLVAWQIRVAQGEALPITQEQVPLTGHAIEVRLYAEDPTNDFLPATGRLALYR---ES 363 Query: 365 AAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAIEAMR 424 A GP R D+GV +G +S +YDPM+ KL WG DR A + Sbjct: 364 APGP----------------GRRVDSGVEQGDSVSPFYDPMLGKLIAWGEDREQAQLRLL 407 Query: 425 NALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLTRLAA 484 LD F + G+ NL F+ ++ HP F E+ T FI P E + DL+ Sbjct: 408 AMLDEFAIGGLKTNLGFLRRIIGHPAFAAAELDTGFI----PRYQEELLPAPGDLSDEFW 463 Query: 485 AAAAMFRVAEIR------------RTRISGTLDNHERMVGTDWVVT-AQDA---RFDVTI 528 AA + + R + + H G D +VT A DA R + + Sbjct: 464 QAAGSAFIQSLPPEDGPWGDKRGFRAGLPAEVSLHLSCTGQDRLVTLAADAPPLRGEQLL 523 Query: 529 DADPGGSTVRFADGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVK 588 G A + V RW G+ D V G G+ V+ Sbjct: 524 IERQGVRRSHLAVRSEGSVFLRW-DGEMHGVTLFDPIAAVEANQSHQGGLTAPMNGSIVR 582 Query: 589 VHVRTPRQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVE 644 V V + + + + P G+V + + G+ V EG AL +E Sbjct: 583 VLVEVGQHVDAGTQLVVLEAMKMEHSIRAPQAGVVKALFCQEGEMVAEGCALVELE 638 Score = 47.4 bits (111), Expect = 2e-09 Identities = 25/67 (37%), Positives = 37/67 (55%) Query: 615 LLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRAEKTATVTKINAGAGDSLAVD 674 L PM G +V++ VEVG V G L +EAMKME+ +RA + V + G+ +A Sbjct: 572 LTAPMNGSIVRVLVEVGQHVDAGTQLVVLEAMKMEHSIRAPQAGVVKALFCQEGEMVAEG 631 Query: 675 DVIMEFE 681 ++E E Sbjct: 632 CALVELE 638 Lambda K H 0.318 0.134 0.392 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: 1111 Number of extensions: 53 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 681 Length of database: 641 Length adjustment: 38 Effective length of query: 643 Effective length of database: 603 Effective search space: 387729 Effective search space used: 387729 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.
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