Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate BWI76_RS13985 BWI76_RS13985 urea carboxylase
Query= metacyc::MONOMER-13589 (666 letters) >FitnessBrowser__Koxy:BWI76_RS13985 Length = 1201 Score = 382 bits (980), Expect = e-110 Identities = 233/579 (40%), Positives = 330/579 (56%), Gaps = 40/579 (6%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 MF +LIANRG IACR+++T R M ++ VAVYS+AD ++LH+ ADEA+ +G PA Q+Y Sbjct: 1 MFDTLLIANRGAIACRILRTLRAMQVKGVAVYSEADLSSLHIRDADEALSLGDGPAAQTY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + +KI+ A + SGA A+HPGYGFLSE FA A EAAG+ F+GP + G K T++ Sbjct: 61 LATEKIIAAAQQSGARAIHPGYGFLSENAAFAEACEAAGLAFVGPTPRQLRVFGLKHTAR 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 LAK GV + G L+AD+DEA + + +GYPVM+K++AGGGG GMR+ E+ E Sbjct: 121 ALAKAEGVPLLEG-SELLADSDEACRAAEAVGYPVMLKSTAGGGGIGMRVCRDARELTEA 179 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 F + + N+F D +F+EK++ + RH+E+Q+ D G+ + L R+CS+QRRNQKVIE Sbjct: 180 FATVQRLGQNNFSDAGVFLEKYIERARHLEVQIFGDGRGDVIALGVRDCSVQRRNQKVIE 239 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDG-QKNFYFLEMNTRLQVEHPV 299 E P+P L E T +A+ A AL KAV Y SAGTVEF+ D + FYFLE+NTRLQVEH V Sbjct: 240 ETPAPNLPEGTAQALCAAAIALGKAVSYRSAGTVEFVYDSTARQFYFLEVNTRLQVEHGV 299 Query: 300 TELITGIDLVEQMIRVAAGEKLPFQ--QSDLKINGWAMESRLYAEDPYRNFLPSIGRLTR 357 TE + G+DLV MI +AAG+ P + L+ G A+++RLYAEDP R F PS G LT Sbjct: 300 TEQVWGVDLVRWMIELAAGDLPPLDVLAAGLRPQGHAIQARLYAEDPGRQFQPSPGLLTE 359 Query: 358 -YRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFE 416 PP + + +R D V G E+ ++DPM+AK W P+R+ AI + AL Sbjct: 360 AIFPPADG----AALRIDRWVEAGCEVPPFFDPMLAKTIAWRPSRDEAIAGLAQALAETR 415 Query: 417 VEGIGHNLPFVGAVMDHPRFVKGDITT---------AFIAEEYPDGFQGAVLDEPTLRRV 467 + G+ N ++ ++ F +G+ T A E G Q +V D P Sbjct: 416 LYGVETNRLYLLQILGFAPFTEGEPWTRCLEQLRYRAATVEVLSAGTQTSVQDYPGRLGY 475 Query: 468 AAAAAAMNRVAEIRRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSD- 526 A SG M++ +G + +GE+ ++ G T+ F+ Sbjct: 476 WAVGVPP-----------SGPMDDRALRLGNRLLGNAEGEA---ALEITLNGPTLKFNTD 521 Query: 527 ------GSSLRVTSDWTPGQPLASLMVDGRPLVMKVGKI 559 G+ L VT D QPL + +K+G I Sbjct: 522 VQAVVCGAPLAVTLDGV-DQPLDRVFTIPAGATLKLGAI 559 Score = 38.5 bits (88), Expect = 2e-06 Identities = 18/55 (32%), Positives = 32/55 (58%) Query: 603 PMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGASLR 657 P+ G + ++ A G V+ G L +E+MKME L A G ++++ PG+++R Sbjct: 1134 PISGNLWQVQTAAGSRVRAGDVLVVLESMKMEIPLLAPCDGVIQQVHVQPGSAVR 1188 Lambda K H 0.318 0.134 0.386 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: 1775 Number of extensions: 85 Number of successful extensions: 7 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: 666 Length of database: 1201 Length adjustment: 43 Effective length of query: 623 Effective length of database: 1158 Effective search space: 721434 Effective search space used: 721434 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: 56 (26.2 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