Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BPHYT_RS28825 BPHYT_RS28825 methylmalonate-semialdehyde dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__BFirm:BPHYT_RS28825 Length = 507 Score = 756 bits (1953), Expect = 0.0 Identities = 366/494 (74%), Positives = 419/494 (84%), Gaps = 1/494 (0%) Query: 7 VGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSL 66 +GHYI G A + R +VFNPATG V VALA VDAAV +A AAFPAWSE + L Sbjct: 15 LGHYIGGAPAAPTSGRFKDVFNPATGKVTGSVALASVEEVDAAVQAARAAFPAWSETAPL 74 Query: 67 RRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDF 126 +R+R++F+FKELL++HHDELA +I+REHGKV +DA GEV RGIE+VE+ACG PNLLKTDF Sbjct: 75 KRARILFRFKELLNQHHDELAMLITREHGKVFTDAQGEVVRGIEVVEFACGIPNLLKTDF 134 Query: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186 +D IGGGIDNWNLRQ LGV AG+TPFNFPVMVP+WM P+AL GN F+LKPSERDPSASL Sbjct: 135 TDQIGGGIDNWNLRQALGVVAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSASL 194 Query: 187 LMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKR 246 +A LL EAGLPDGVFNVV GDKVAVDAL+ HPD+ A+SFVGSTPIAEYIH + + +GKR Sbjct: 195 RLAELLKEAGLPDGVFNVVNGDKVAVDALIDHPDVAALSFVGSTPIAEYIHTEASKRGKR 254 Query: 247 VQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLP 306 VQALGGAKNH++VMPDADLDQA DALIGAAYGSAGERCMAIS+AVAVG+V D+LI KL+P Sbjct: 255 VQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGNVADKLIEKLVP 314 Query: 307 RIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFF 366 R+ L I NG+ +MGPLVTAEHKAKV G+I +G AEGA+LIVDGR V E+GFF Sbjct: 315 RVKSLVIKNGEHLDAEMGPLVTAEHKAKVTGYIASGEAEGAKLIVDGRAHPVTN-EEGFF 373 Query: 367 VGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIAR 426 VG TLFD V EM IY++EIFGPVL +VRVPDFA+AV LINAHEFGNGVS FT DGG+AR Sbjct: 374 VGGTLFDHVGTEMKIYKEEIFGPVLAVVRVPDFASAVDLINAHEFGNGVSLFTSDGGVAR 433 Query: 427 AFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPD 486 AF R I+VGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEG+RFY+RYKS+MQRWPD Sbjct: 434 AFGRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGVRFYTRYKSIMQRWPD 493 Query: 487 SIAKGPEFSMPTAQ 500 SIAKG EF+MP A+ Sbjct: 494 SIAKGAEFTMPVAK 507 Lambda K H 0.320 0.137 0.412 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: 816 Number of extensions: 27 Number of successful extensions: 2 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: 500 Length of database: 507 Length adjustment: 34 Effective length of query: 466 Effective length of database: 473 Effective search space: 220418 Effective search space used: 220418 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 (21.8 bits) S2: 52 (24.6 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