Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate GFF2122 PGA1_c21540 propionyl-CoA carboxylase alpha chain
Query= SwissProt::Q5LUF3 (681 letters) >FitnessBrowser__Phaeo:GFF2122 Length = 681 Score = 1201 bits (3106), Expect = 0.0 Identities = 601/681 (88%), Positives = 635/681 (93%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MF KILIANRGEIACRVIKTARKMGI TVAIYSDADKQ+LHV+MADEAVHIGPPPANQSY Sbjct: 1 MFEKILIANRGEIACRVIKTARKMGIKTVAIYSDADKQSLHVKMADEAVHIGPPPANQSY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 IVIDKVM AIRATGAQAVHPGYGFLSEN+KFAEAL AEGV FVGPP GAIE+MGDKITSK Sbjct: 61 IVIDKVMEAIRATGAQAVHPGYGFLSENAKFAEALAAEGVAFVGPPVGAIESMGDKITSK 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 KIAQEA VSTVPGYMGLI DADEAVKISN+IGYPVMIKASAGGGGKGMRIAW+D EAREG Sbjct: 121 KIAQEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSDAEAREG 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCD+HGNGIYLGERECSIQRRNQKVVE Sbjct: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDAHGNGIYLGERECSIQRRNQKVVE 240 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAPSPFLDE TRRAMGEQAVALAKAVGYASAGTVEFIVDG KNFYFLEMNTRLQVEHPVT Sbjct: 241 EAPSPFLDEDTRRAMGEQAVALAKAVGYASAGTVEFIVDGDKNFYFLEMNTRLQVEHPVT 300 Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360 ELITGVDLVEQMIR+A GEPLSITQ DVKL GWAIENRLYAEDPYRGFLPSIGRLTRYRP Sbjct: 301 ELITGVDLVEQMIRIAGGEPLSITQNDVKLNGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360 Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420 PAE AAGPL +GKWQGDAP+GE AVRNDTGV+EGGEISMYYDPMIAKLCTW PTR AAI Sbjct: 361 PAEVAAGPLHDSGKWQGDAPAGELAVRNDTGVFEGGEISMYYDPMIAKLCTWGPTRDAAI 420 Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480 AMR ALD FEVEGIGHNLPFLSAVMDHP FI+G MTTAFI E+YPEGF GV LPE DLR Sbjct: 421 AAMRDALDGFEVEGIGHNLPFLSAVMDHPIFIAGTMTTAFIEEQYPEGFNGVELPEQDLR 480 Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAADHDGSTVSFD 540 ++AAA+AAMHRVAEIRRTRVSGRMDNHER+VG++WVVTLQ F VT+ AD DGSTV FD Sbjct: 481 KIAAASAAMHRVAEIRRTRVSGRMDNHERKVGSDWVVTLQDVSFNVTVDADRDGSTVRFD 540 Query: 541 DGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVRTPRQAELA 600 DGS++RV SDWTPGDQLA L V LV+KVGKISGGFRIR+RGADLKVHVRTPRQAELA Sbjct: 541 DGSALRVASDWTPGDQLARLTVGDDSLVVKVGKISGGFRIRSRGADLKVHVRTPRQAELA 600 Query: 601 RLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKKGVV 660 +LMPEK+ PDTSK+LLCPMPGL+VK++VEVG EVQEGQALCTIEAMKMENILRAEKKGVV Sbjct: 601 KLMPEKIAPDTSKLLLCPMPGLVVKLEVEVGDEVQEGQALCTIEAMKMENILRAEKKGVV 660 Query: 661 AKINASAGNSLAVDDVIMEFE 681 + INA+AG+SLAVD+VIMEFE Sbjct: 661 SAINAAAGDSLAVDEVIMEFE 681 Lambda K H 0.317 0.134 0.387 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: 1455 Number of extensions: 43 Number of successful extensions: 1 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: 681 Length of database: 681 Length adjustment: 39 Effective length of query: 642 Effective length of database: 642 Effective search space: 412164 Effective search space used: 412164 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 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