Align Methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Ac3H11_2278 Methylmalonyl-CoA mutase (EC 5.4.99.2)
Query= reanno::PS:Dsui_0519 (721 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2278 Length = 722 Score = 1182 bits (3057), Expect = 0.0 Identities = 579/705 (82%), Positives = 645/705 (91%) Query: 15 NLDAWAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPYADTLPGFAPYLRGPQ 74 +L+AWAKAAAKSAPGGDV+ALNW+TP+G+TVKPLYT +D LPYA+TLPGF PYLRGPQ Sbjct: 16 SLEAWAKAAAKSAPGGDVSALNWVTPDGITVKPLYTAEDTASLPYANTLPGFEPYLRGPQ 75 Query: 75 ATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSDNPRVLGD 134 ATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSD+PRV GD Sbjct: 76 ATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSDHPRVTGD 135 Query: 135 VGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVAAEEQGVSQEQLSGT 194 VGKAGVAIDSVEDMKILFD IPLDK+SVSMTMNGAVLP+LAGY+VAAEEQGVSQ++LSGT Sbjct: 136 VGKAGVAIDSVEDMKILFDQIPLDKVSVSMTMNGAVLPVLAGYVVAAEEQGVSQDKLSGT 195 Query: 195 IQNDILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISISGYHIQEAGANQAIE 254 IQNDILKEFMVRNTYIYPPKPSM+II DI GYTA++MPKFNSISISGYH+QEAGANQA+E Sbjct: 196 IQNDILKEFMVRNTYIYPPKPSMRIIGDIIGYTAKNMPKFNSISISGYHMQEAGANQALE 255 Query: 255 LAFTLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKMRAGRMLWHRIMSQF 314 LAFTLADG EYV+T +ASGLDVD FAGRLSFFWA+GMNFYLE+AKMRA R+LW RIM + Sbjct: 256 LAFTLADGKEYVKTAMASGLDVDEFAGRLSFFWAIGMNFYLEVAKMRAARLLWCRIMKET 315 Query: 315 NPKSAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAIALP 374 K+ KSLMLRTH QTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAIALP Sbjct: 316 GAKNPKSLMLRTHCQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAIALP 375 Query: 375 TEFSARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAWSIIQEIEAMGGMTK 434 TEFSARIARNTQLIIQEETHI NV+DPWAGSYMMEKLTQDM D AW II+E+EAMGGMT+ Sbjct: 376 TEFSARIARNTQLIIQEETHITNVIDPWAGSYMMEKLTQDMMDAAWKIIEEVEAMGGMTQ 435 Query: 435 AVESGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDILDIDNHAVREAQIAR 494 AV+SGWAK+++E AA+KQARIDSGKDVIVGVNKYKLAKED +DIL IDN VR+ QIAR Sbjct: 436 AVDSGWAKLKIEAAAAEKQARIDSGKDVIVGVNKYKLAKEDPVDILQIDNMKVRDGQIAR 495 Query: 495 LKKIRASRDSAAVQAALDALTQCAESGEGNLLDLSVKAIRLRATVGEVSDALEKVFGRFR 554 L+KIRA+RD+A VQAALDALT AESGEGNLL+LS+ A+RLRATVGEVSDALEKVFGR R Sbjct: 496 LEKIRATRDAAKVQAALDALTAAAESGEGNLLELSINAVRLRATVGEVSDALEKVFGRHR 555 Query: 555 ANNQTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMIAKLGQDGHDRGAKVVATA 614 A+ Q ++GVY + E W+ +K +I FAEE+GRRPR+MIAKLGQDGHDRGAKVVATA Sbjct: 556 ADTQKVTGVYAAAYDSAEGWDKLKTEINAFAEEQGRRPRVMIAKLGQDGHDRGAKVVATA 615 Query: 615 FADLGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHKTLLPALVNSLKEQGADDI 674 FADLGFD+DMGPLFQTPEE ARQA+ENDVHA+GVS+LAAGHKTL+PA++ SL++QGADDI Sbjct: 616 FADLGFDVDMGPLFQTPEECARQAIENDVHAVGVSTLAAGHKTLVPAIIQSLRDQGADDI 675 Query: 675 IVFAGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEIRKS 719 IVF GGVIPAQDYD LY +G K ++GPGT I SAK VLE+IRK+ Sbjct: 676 IVFVGGVIPAQDYDFLYESGVKGVYGPGTPIPASAKDVLEQIRKA 720 Lambda K H 0.317 0.132 0.380 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: 1568 Number of extensions: 50 Number of successful extensions: 1 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: 721 Length of database: 722 Length adjustment: 40 Effective length of query: 681 Effective length of database: 682 Effective search space: 464442 Effective search space used: 464442 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 (21.6 bits) S2: 55 (25.8 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