Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate GFF3827 PS417_19595 3-methylcrotonyl-CoA carboxylase
Query= reanno::PS:Dsui_0516 (663 letters) >FitnessBrowser__WCS417:GFF3827 Length = 627 Score = 493 bits (1270), Expect = e-144 Identities = 287/660 (43%), Positives = 397/660 (60%), Gaps = 38/660 (5%) Query: 2 FKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61 F KILIANRGEIACR+ +TA+ +G +TVAVYS+AD AL V+MADEAV IGPA ++SYL Sbjct: 4 FSKILIANRGEIACRIQRTAQALGYRTVAVYSDADAQALHVQMADEAVHIGPAPVQQSYL 63 Query: 62 VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121 D I+ A + T A+A+ PGYGFLSEN +F+R ++ G+ FIGP +I MG K SK Sbjct: 64 NIDAILNAARVTSADAIPPGYGFLSENPDFARACQQAGLTFIGPSPEAIELMGSKRLSKL 123 Query: 122 LAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGF 181 ++A V I GY + A IGYP+MIKASAGGGG+G+R+ + E + Sbjct: 124 AMLDAGVPCIAGYQGSAQDDSTLQREADAIGYPLMIKASAGGGGRGMRLVQHPEELLDNL 183 Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241 + +EA+N+FG + +E+ +++PRH+EIQ+ GDSHG+ +YL ERDCSIQRRHQK+IEE Sbjct: 184 HTARSEAKNAFGSGELILEQALIDPRHVEIQLFGDSHGHLIYLGERDCSIQRRHQKIIEE 243 Query: 242 APSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVT 301 AP P + PE+R+AMGE A+ RAVNY AGTVEF++ FYFLEMNTRLQVEHPVT Sbjct: 244 APCPVMTPELRQAMGEAALNAGRAVNYVGAGTVEFLLD-RNGRFYFLEMNTRLQVEHPVT 302 Query: 302 ELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQP 361 ELITGLDLV+ +++A G+ LPLTQ DV +NG AME R+ AEDP +GFLP TG ++++ P Sbjct: 303 ELITGLDLVDWQLQIAAGQPLPLTQPDVSLNGHAMEVRLYAEDPAQGFLPQTGEVLRWDP 362 Query: 362 PAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSN 421 A VR+D GV +G IS +YD M+ K+I +GA+RE+A ++ A+ V+ G+++N Sbjct: 363 AA----GVRIDHGVTEGQRISPFYDPMLGKIIAYGATREEARRKLLRAVEDTVLLGVTTN 418 Query: 422 IPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRAA 481 P L++H F G F TGFIA+ + + + P A + +AA + Y A Sbjct: 419 QPLLVDLLKHPDFVGGDFSTGFIAEHF-----SEIRPLTPSAEHLALAAALF--YQHSAN 471 Query: 482 QVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLSDWRQGQSLFN 541 Q L G W RN P + G T N L +D R +FN Sbjct: 472 QHPQGLAG--------W---RNNTSAPCTYRLEVNGDTHTVNAAPLPLTTDGRHANHVFN 520 Query: 542 GTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSKFLLSPM 601 G R R Y L + ++ R ++ + + A S + +PM Sbjct: 521 GI-----------RRRTAYHLVGNQLWLPGLTVTDRTQQVAS----RQANVSSGTVKAPM 565 Query: 602 PGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSVDEIIIE 661 G + +V V+ G V G+ L V+EAMKME+ L A D +K + V AG + ++++E Sbjct: 566 DGAIVDVRVSAGDSVTKGQLLLVLEAMKMEHPLTAGIDGVIKGVQVIAGDQVRNRQVLLE 625 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: 995 Number of extensions: 44 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: 627 Length adjustment: 38 Effective length of query: 625 Effective length of database: 589 Effective search space: 368125 Effective search space used: 368125 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