Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate RR42_RS29420 RR42_RS29420 3-methylcrotonyl-CoA carboxylase
Query= reanno::PS:Dsui_0516 (663 letters) >FitnessBrowser__Cup4G11:RR42_RS29420 Length = 666 Score = 444 bits (1141), Expect = e-129 Identities = 284/676 (42%), Positives = 380/676 (56%), Gaps = 43/676 (6%) Query: 2 FKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61 F+KILIANRGEIA RV+++A +G +TVAVYS AD A VE A +AV IG A +SYL Sbjct: 7 FQKILIANRGEIALRVMRSATALGYRTVAVYSSADAGARHVEEAGQAVYIGQAQPAQSYL 66 Query: 62 VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121 D II A +++GA+AVHPGYGFL+ENA F+R E G+ FIGP SI MG+K +K+ Sbjct: 67 RIDAIIEAARRSGADAVHPGYGFLAENAAFARACREAGLVFIGPSAESIVAMGNKAGAKR 126 Query: 122 LAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGF 181 L + A V IPGY A++IG+PVMIKA+AGGGG+G+R+ + E Sbjct: 127 LMMAADVPCIPGYQGEDQDEARLCAEAERIGFPVMIKATAGGGGRGMRLVPHARAFPELL 186 Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241 S +EA+ +FGD V +E+ V+EPRHIEIQ+L D +GN ++L ERDCS+QRRHQK+IEE Sbjct: 187 RSARSEAQGAFGDPEVILERAVVEPRHIEIQILADRYGNAIHLGERDCSVQRRHQKLIEE 246 Query: 242 APSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVT 301 APSP V E+R MG AVA +A+ YE AGT+EF++ +YF+EMNTRLQVEHPVT Sbjct: 247 APSPAVSAELRARMGATAVAAVKAIGYEGAGTLEFLLD-RDGNYYFMEMNTRLQVEHPVT 305 Query: 302 ELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ- 360 E ITGLDLV +R+A GE LPL Q DV+ +G A+E R+ AED +GF+P +G + +Q Sbjct: 306 EAITGLDLVALQLRIAAGEPLPLRQEDVRFSGHAIEVRLCAEDADQGFMPQSGEIALWQA 365 Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420 PPA +RV+ + G I YYDSMIAKLI +G +R++A ++ L V G+++ Sbjct: 366 PPA-----LRVEHALGSGAAIPPYYDSMIAKLISYGGTRDEARRKLSQGLEDLVALGVTT 420 Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFV-------- 472 N F + H F +G T FI + DA + P D AL AA Sbjct: 421 NQVFLGRCLAHPAFAAGEATTAFIGQHQ----DALLQP--DAALRQRAAALAALLLYETS 474 Query: 473 -HRRYIDRAAQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLS 531 R+ AA ++ LP +G + V NG H G GE Sbjct: 475 PERQPGAPAASLAPTLP-----IGLRYRV--NGAEHQASLAYGAGNRFAVAMGESRFAFE 527 Query: 532 DWRQGQSLFNGTCNGEEFTLQVERHRMTYQLFHWGT----RADMMVMSARAAELLALMPE 587 G +C+G + R T L + GT +ARA E Sbjct: 528 TIALGAHSVRFSCDGLVESATFHRDASTLLLHYQGTPLRIEDHTRAAAARAGE------- 580 Query: 588 KAAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISV 647 AA D L + M G + V VA G +V+AG+ + +EAMKME+I A +V + V Sbjct: 581 -AAGDGK--LRASMNGRVVNVMVAAGDQVEAGQPMVTLEAMKMEHIHVAPAAGRVGAVHV 637 Query: 648 TAGSSLSVDEIIIEFE 663 G + +I E E Sbjct: 638 QVGDQAAAMRVIAEIE 653 Lambda K H 0.319 0.135 0.391 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: 1044 Number of extensions: 54 Number of successful extensions: 5 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: 663 Length of database: 666 Length adjustment: 38 Effective length of query: 625 Effective length of database: 628 Effective search space: 392500 Effective search space used: 392500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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