Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate Pf1N1B4_225 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= reanno::PS:Dsui_0516 (663 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_225 Length = 653 Score = 502 bits (1293), Expect = e-146 Identities = 299/674 (44%), Positives = 406/674 (60%), Gaps = 36/674 (5%) Query: 2 FKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61 F KILIANRGEIACR+ +TA+ +G +TVAV+S+AD DAL V+MADEAV IGPA ++SYL Sbjct: 4 FSKILIANRGEIACRIQRTAQALGYRTVAVFSDADADALHVQMADEAVNIGPAPVQQSYL 63 Query: 62 VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121 II A ++TGA+A+HPGYGFLSENAEF+R ++ GI FIGP +I MG K SK Sbjct: 64 NIQAIIDAARRTGADAIHPGYGFLSENAEFARACQQAGIIFIGPSPEAIELMGSKRLSKL 123 Query: 122 LAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGF 181 I+A V I GY + A++IGYP+MIKASAGGGG+G+R+ ++ E E Sbjct: 124 AMIKAGVPCIKGYQGSEQDDATLSREAERIGYPLMIKASAGGGGRGMRLVHSAGELLEQL 183 Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241 + +EA++ FG D + +E+ +++PRH+E+QV GD HGN +YL ERDCSIQRRHQK+IEE Sbjct: 184 RTARSEAQHGFGSDELILEQALIDPRHVEVQVFGDQHGNLIYLGERDCSIQRRHQKIIEE 243 Query: 242 APSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVT 301 AP P + ++R+AMGE A+ RAVNY AGTVEF++ A +FYFLEMNTRLQVEHPVT Sbjct: 244 APCPVMTADLRQAMGEAALKAGRAVNYVGAGTVEFLLD-ARGQFYFLEMNTRLQVEHPVT 302 Query: 302 ELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQP 361 ELITGLDLV VA G LPL Q VQ+NG AME R+ AEDP +GFLP TGR+ ++P Sbjct: 303 ELITGLDLVAWQFHVAEGLPLPLQQEQVQLNGHAMEVRLYAEDPAQGFLPQTGRIAAWEP 362 Query: 362 PAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSN 421 + G VR+D G+ +G +S +YD M+ KLI HGA+RE+A ++ A+ V+ G+ SN Sbjct: 363 --ALPGGVRIDHGLIEGQSVSPFYDPMLGKLIAHGATREEARRKLLRAVQDSVLLGVQSN 420 Query: 422 IPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRAA 481 A L++H +F SG F TGFI + + PH A + +AA + + +A Sbjct: 421 QRLLACLLEHPQFISGKFSTGFIPTHFAD--HPCLHPHVPSAEELAIAAALFYQASAQAH 478 Query: 482 QV-------SGQLPGHERKVG---DEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLS 531 + + +P H R +G +W V N E KP Y EL Sbjct: 479 RTPLAGWRNNASVPLHYR-IGLEDQDWPVELNAE----PGKP----YRAQIGARTLELKV 529 Query: 532 DWRQGQSLFNGTCNGEEFTLQVE--RHRMTYQLFHWGTRADMMVMSARAAELLALMPEKA 589 C+G TL+++ R R Y+L S R + + Sbjct: 530 I----------QCDGRWATLEIDGIRQRHAYRLKAGQLWLFTRPGSLRLVDRTQALVSGQ 579 Query: 590 APDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTA 649 A S L +PM G + +V V+ G V G+ L V+EAMKME+ LK+ D +K++ V Sbjct: 580 ASVSSGTLKAPMDGAIVDVLVSEGSPVSKGQLLVVLEAMKMEHPLKSGIDGVLKRLQVRV 639 Query: 650 GSSLSVDEIIIEFE 663 G + +I++E E Sbjct: 640 GDQVKNRQILLEVE 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: 1067 Number of extensions: 51 Number of successful extensions: 5 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: 663 Length of database: 653 Length adjustment: 38 Effective length of query: 625 Effective length of database: 615 Effective search space: 384375 Effective search space used: 384375 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