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 WP_025199990.1 BIBO1_RS06830 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= SwissProt::P0DTA4 (730 letters) >NCBI__GCF_000182725.1:WP_025199990.1 Length = 673 Score = 487 bits (1253), Expect = e-142 Identities = 301/674 (44%), Positives = 402/674 (59%), Gaps = 30/674 (4%) Query: 63 FDKILIANRGEIACRVIKTCKKMGIKTVAVHSDVDASSVHVTMADEAVCVGPAPTSKSYL 122 F KILIANRGEIACRVI+T +K+G+ TVA++SD DA ++HV MADEAV VGPA +++SYL Sbjct: 20 FQKILIANRGEIACRVIRTARKLGVVTVAIYSDADARALHVEMADEAVRVGPAASAQSYL 79 Query: 123 NMDAIMEAVRTTRAQAVHPGYGFLSENKEFAKCLAAEGVIFIGPDTHAIQAMGDKIESKL 182 N+DAI++A T AQA+HPGYGFLSEN F + G+IFIGP AI+AMG K +K Sbjct: 80 NVDAIIKAALETGAQAIHPGYGFLSENPAFVDAVEEAGLIFIGPSAKAIRAMGLKDAAKA 139 Query: 183 LAKKAKVNTIPGFDGVVKDADEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGF 242 L +KA V +PG+ G +D A I YPV+IKA AGGGGKGMR + Sbjct: 140 LMEKAGVPVVPGYHGDNQDGAFLKSEADRITYPVLIKARAGGGGKGMRRVDSAADFAAAL 199 Query: 243 RFSSQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVVEE 302 + +EA +SFGD +L+EK++ PRHIE+QV GD HGNA+ L ER+CS+QRR+QKV+EE Sbjct: 200 ESARREAEASFGDGAVLVEKYMAKPRHIEVQVFGDNHGNAVHLFERDCSLQRRHQKVIEE 259 Query: 303 APSIFLDSETRRAMGEQAVALAKAVNYSSAGTVEFLVDSKK-----NFYFLEMNTRLQVE 357 AP+ + E R AMGE AV A A+ YS AGTVEF+ D + F+F+EMNTRLQVE Sbjct: 260 APAPGMTEEMRAAMGEAAVKAALAIGYSGAGTVEFIADVSEGLRPDRFFFMEMNTRLQVE 319 Query: 358 HPVTECITGLDLVQEMIRVAKGYPLRHRQADIPINGWAVECRVYAEDPYKSFGLPSIGRL 417 HPVTE ITGLDLV+ +RVA G L RQ ++ INGWA E R+YAEDP + F LP+ G+L Sbjct: 320 HPVTEAITGLDLVEWQLRVASGEALPKRQDELSINGWAFEARLYAEDPARDF-LPATGKL 378 Query: 418 SQYQEPIHLPGVRVDSGIQPGSDISIYYDPMISKLITYGSNRMEALKRMENALDNYVIRG 477 + + P RVDSG++ G I+ +YDPMI+K+IT+G+ R EAL R++ AL+ I G Sbjct: 379 ALFVPP---ENARVDSGVRTGDTITPFYDPMIAKIITHGAMRDEALNRLDAALNKTRIAG 435 Query: 478 VTHNIALLREVIINSRFVEGDINTKFLSDVYPDGFKGHKLTEDERNQLLAIA-SSLFVAS 536 + N L + F GD++T + G + L D + +A A ++L Sbjct: 436 LVTNRQFLSALCNLEAFRTGDVDTGLI------GRETAALFTDAQPSDIAFALAALGALD 489 Query: 537 QLRAQRFQEPENSRVPIIKPQVANWELSIRLHDEVHTVTASNSGPTFSVEVDGSKLNVTS 596 L A +P + A+ + I H + TV+ + G G Sbjct: 490 LLDAPEKSDPWSGLRGFRLWGEASRSVLIEHHGKRRTVSFTARGDRHF----GFAFGTMD 545 Query: 597 TWNLASPLLSVSIDGTQRTIQCLSRDAGGNMSIQFLGTVYKVHILTKLAAELNKFMLEKA 656 + L+ +IDG R + G ++++Q G H + A E+ Sbjct: 546 IRKHKNGLVRFAIDG--RVSEASVLRIGHDVTVQIEGHDAIFHHVQATGA-------EED 596 Query: 657 AEDTSSILHSPMPGVVVAVSVKPGDLVAEGQEICVIEAMKMQNSMTAGKTGKVKSVHCKA 716 A S IL SPMPG+V + V G VA+G + +EAMKM+ S+TA + GKV SV A Sbjct: 597 ASSESRIL-SPMPGLVRLICVVEGASVAKGDPLVTMEAMKMELSLTAPRDGKVASVTVAA 655 Query: 717 GDTVGEGDLLVELE 730 GD V EG LLVELE Sbjct: 656 GDQVNEGALLVELE 669 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: 1079 Number of extensions: 46 Number of successful extensions: 4 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: 730 Length of database: 673 Length adjustment: 39 Effective length of query: 691 Effective length of database: 634 Effective search space: 438094 Effective search space used: 438094 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 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