Align D-specific alpha-keto acid dehydrogenase; Vancomycin resistance protein VanH; EC 1.1.1.- (characterized)
to candidate WP_019867135.1 METMI_RS0115120 formate dehydrogenase
Query= SwissProt::Q05709 (322 letters) >NCBI__GCF_000384075.1:WP_019867135.1 Length = 400 Score = 104 bits (259), Expect = 4e-27 Identities = 80/236 (33%), Positives = 116/236 (49%), Gaps = 24/236 (10%) Query: 68 KRAGVKYISTRSIGCNHIDTTAAKRMGITVDNVAY-SPDSVADYTMMLILMAVRNVKSIV 126 K +K I T IG +H D AA GITV V Y + +SVA++ +M+ L VRN Sbjct: 111 KAKNLKMIVTAGIGSDHTDLQAAMERGITVAEVTYCNSNSVAEHVVMMTLALVRNYLPSY 170 Query: 127 RSVEKHDFRLDS--DRGKVLSDMTVGVVGTGQIGKAVIERLRGFGCKVLAYSRSRSIEV- 183 V K + + R L M VG V G+IG V+ L+ F K+ R R E Sbjct: 171 HWVIKGGWNIADCVARSYDLEAMHVGTVAAGRIGLRVLRLLKPFDVKLHYLDRHRLPEAV 230 Query: 184 -------NYVPFDELLQNSDIVTLHVPLNTDTHYIISHEQIQRMKQGAFLINTGRGPLVD 236 + + L + D+VTL+ PL+ +T ++I+ ++ K+GA+LINT RG L D Sbjct: 231 EQELNLTYHSSLESLTKVCDVVTLNCPLHPETEHMINEASLKNFKRGAYLINTARGKLCD 290 Query: 237 TYELVKALENGKLGGAALDVLEGEEEFFYSDCTQKPIDNQFLLKLQRMPNVIITPH 292 +V ALE+G+L G A DV + P D+ + + MPN +TPH Sbjct: 291 RDAIVNALESGQLAGYAGDVWFPQ---------PAPNDHPW----RTMPNHGMTPH 333 Lambda K H 0.319 0.135 0.383 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: 239 Number of extensions: 12 Number of successful extensions: 3 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: 322 Length of database: 400 Length adjustment: 29 Effective length of query: 293 Effective length of database: 371 Effective search space: 108703 Effective search space used: 108703 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: 49 (23.5 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