Align Propionyl-CoA carboxylase alpha chain, mitochondrial; PCCase subunit alpha; Propanoyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.3 (characterized)
to candidate GFF1047 Psest_1080 Acetyl/propionyl-CoA carboxylase, alpha subunit
Query= SwissProt::P0DTA4 (730 letters) >lcl|FitnessBrowser__psRCH2:GFF1047 Psest_1080 Acetyl/propionyl-CoA carboxylase, alpha subunit Length = 633 Score = 493 bits (1269), Expect = e-143 Identities = 286/669 (42%), Positives = 403/669 (60%), Gaps = 46/669 (6%) Query: 66 ILIANRGEIACRVIKTCKKMGIKTVAVHSDVDASSVHVTMADEAVCVGPAPTSKSYLNMD 125 +L+ANRGEIACRV++T K MG+ TVAVHS +DA++ H AD + +G A + SYL +D Sbjct: 5 LLVANRGEIACRVMRTAKAMGLTTVAVHSAIDATARHAREADIRIDLGGAKPADSYLRID 64 Query: 126 AIMEAVRTTRAQAVHPGYGFLSENKEFAKCLAAEGVIFIGPDTHAIQAMGDKIESKLLAK 185 +++A + + AQA+HPGYGFLSEN EFA+ + G+IF+GP AI AMG K +K L + Sbjct: 65 KLIDAAKASGAQAIHPGYGFLSENAEFARAIEQAGLIFLGPPASAIDAMGSKSAAKALME 124 Query: 186 KAKVNTIPGFDGVVKDADEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGFRFS 245 +A V +PG+ G +D + A +IGYPV++KA+AGGGGKGM++ + + + + Sbjct: 125 EAGVPLVPGYHGEAQDVETFRAAAEKIGYPVLLKATAGGGGKGMKVVEREADLAEALASA 184 Query: 246 SQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVVEEAPS 305 +EA SSFGD R+L+EK++ PRH+EIQV D+HGN L+LNER+CSIQRR+QKVVEEAP+ Sbjct: 185 QREAQSSFGDWRMLVEKYVLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 244 Query: 306 IFLDSETRRAMGEQAVALAKAVNYSSAGTVEFLVDSKKNFYFLEMNTRLQVEHPVTECIT 365 L E RRAMGE AV A+A+ Y AGTVEFL+D++ F+F+EMNTRLQVEHPVTE IT Sbjct: 245 PGLTPELRRAMGEAAVKAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 304 Query: 366 GLDLVQEMIRVAKGYPLRHRQADIPINGWAVECRVYAEDPYKSFGLPSIGRLSQYQEPIH 425 GLDLV IRVA+G PL Q +P+ G A+E R+YAEDP F LP+ G L Y+E Sbjct: 305 GLDLVAWQIRVARGEPLPISQEQVPLIGHAIEVRLYAEDPDNDF-LPATGTLDLYREAAE 363 Query: 426 LPGVRVDSGIQPGSDISIYYDPMISKLITYGSNRMEALKRMENALDNYVIRGVTHNIALL 485 PG RVDSG+ G +S +YDPM+ KLI +G NR EA R+ LD + GV N+A L Sbjct: 364 GPGRRVDSGVAEGDTVSPFYDPMLGKLIAWGENREEARLRLLAMLDETAVGGVRTNLAFL 423 Query: 486 REVIINSRFVEGDINTKFLSDVYPDGFKGHKLTEDERNQLLAIASSLFVAS-QLRAQRFQ 544 R V+ + F E +++T F+ ++LL A L A Q A+ F Sbjct: 424 RRVVGHRAFAEAELDTAFI--------------PRHESELLRPAGELSDAFWQQAAECFV 469 Query: 545 EPENSRVPIIKPQVANWELSIRLHDEVHTVTASNSGPTFSVEVDGSKLNVTSTWNLASPL 604 + E ++V D+ H+ + SG F + +++++ N S Sbjct: 470 QTEPTKV---------------RGDDAHSPWSKRSGLRFGMP---AQISLHLQCNGESRR 511 Query: 605 LSVSIDGTQ---RTIQCLSRDAGGNMSIQFLGTVYKVHILTKLAAELNKFMLEKAAEDTS 661 L V Q RT + + + G + +Q+ G V +A +A+ Sbjct: 512 LKVDPAAPQPNVRTPKAIRQ--GDALYLQWNGEWLAVRAFDPIAE-------AEASHQHH 562 Query: 662 SILHSPMPGVVVAVSVKPGDLVAEGQEICVIEAMKMQNSMTAGKTGKVKSVHCKAGDTVG 721 L +PM G +V V V+ G V G + V+EAMKM++S+ + + G VKS+ C G+ V Sbjct: 563 GGLTAPMNGSIVRVLVEAGQHVEAGTALIVLEAMKMEHSIRSAQAGVVKSLFCSEGEMVS 622 Query: 722 EGDLLVELE 730 EG +L+E+E Sbjct: 623 EGAVLLEME 631 Lambda K H 0.318 0.134 0.385 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: 1036 Number of extensions: 41 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 730 Length of database: 633 Length adjustment: 39 Effective length of query: 691 Effective length of database: 594 Effective search space: 410454 Effective search space used: 410454 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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