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) >FitnessBrowser__psRCH2:GFF1047 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:
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