Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein
Query= reanno::psRCH2:GFF2388 (503 letters) >NCBI__GCF_000504245.1:WP_034273599.1 Length = 496 Score = 254 bits (649), Expect = 5e-72 Identities = 162/487 (33%), Positives = 255/487 (52%), Gaps = 11/487 (2%) Query: 11 KLLIDGEFIEST-TQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAF--KTWRKTP 67 +L IDG ++++T T R V+NPA LA V A +++D AVA+ ++AF WR T Sbjct: 3 ELFIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATT 62 Query: 68 IGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIGNLQLG 127 R + + +L++ + + LA + + GKT+A+ DV V + A + + + G Sbjct: 63 ARERGELLREIARLLQRDKEHLARTESLDTGKTMAEGRVDVDDVTSVFRYYANLADNEAG 122 Query: 128 ELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 187 + + A V + + +P+GVC+ I P+N+P + W A+A GNT V+KPSE P+ Sbjct: 123 RVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTPLT 182 Query: 188 TMRLCELALEAGVPPGVLNVVHGGPDVVNA-ICDHPDIKAVSFVGSTKVGTHVYNRASQA 246 T+ L L EAGVP GV+N+V GG V A + HPD+ VSF G + G + A++ Sbjct: 183 TIELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMAMAAEG 242 Query: 247 GKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEA-QAWIPD 305 KRV +G KN +V DA + ++ AAF +GQ C A S +++ + ++ + Sbjct: 243 VKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEFVAE 302 Query: 306 LVAKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGYEN 365 L +A +++ G++ T+ GPL S D+V IE EGA+L + G P+ + Sbjct: 303 LARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPELAD 362 Query: 366 GNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTRSGA 425 G F+ PT+F+ REM + Q+E+FGPV+ V T DEAI L N G A++T + Sbjct: 363 GYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTSDAS 422 Query: 426 AARHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLG-DLGPYG----KQVVQFYTQTK 480 A+ + G V IN P +P + G S +G +LGP G ++ Y + Sbjct: 423 RAQRVAGALRHGTVWINDFHPY-LPQAEWGGFGKSGIGRELGPSGLEEYRETKHIYQNIR 481 Query: 481 TITERWF 487 RWF Sbjct: 482 PAPMRWF 488 Lambda K H 0.318 0.134 0.394 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: 585 Number of extensions: 26 Number of successful extensions: 4 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: 503 Length of database: 496 Length adjustment: 34 Effective length of query: 469 Effective length of database: 462 Effective search space: 216678 Effective search space used: 216678 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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