Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate WP_017549877.1 C792_RS0112915 galactonate dehydratase
Query= reanno::BFirm:BPHYT_RS16405 (382 letters) >NCBI__GCF_000330705.1:WP_017549877.1 Length = 382 Score = 545 bits (1404), Expect = e-160 Identities = 252/382 (65%), Positives = 304/382 (79%) Query: 1 MKITKLETFIVPPRWCFLKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYLIGKDPLLI 60 MKI E F VPPRW FLK+ETD G+VGWGEPV+EG+A TV AAV E+ + LIG+DPL I Sbjct: 1 MKIKSYELFTVPPRWLFLKVETDAGLVGWGEPVIEGKAATVKAAVIEMMETLIGRDPLEI 60 Query: 61 EDHWQVMYRSGFYRGGPITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYSWI 120 E W +YRSGFYRGGPI MSAI+G+DQALWDIKGK++G P+H LLGG+ RD IKVYSW+ Sbjct: 61 EGIWNELYRSGFYRGGPILMSAISGIDQALWDIKGKYYGAPVHELLGGRARDSIKVYSWV 120 Query: 121 GGDRPSDVANNARAVVERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREAVGPNIGI 180 GGDRP+DV + + +G AVKMN +EELQ ID++ KV V+ V ++R + G + GI Sbjct: 121 GGDRPADVGEASLELKNQGITAVKMNATEELQYIDSYSKVDMVLERVDSIRRSCGTDFGI 180 Query: 181 GVDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSR 240 G+DFHGRVHKPMAKVLA+EL+ ++ +FIEEP L EN E LRDI T PIA GER++S+ Sbjct: 181 GIDFHGRVHKPMAKVLARELEQFRPMFIEEPALPENNENLRDIAMHTAIPIATGERMFSK 240 Query: 241 WDFKHILSGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPLGPIALATCLQID 300 W FK +L GY DIIQPD SHAGGITEC+KI SMAEA+DVA A HCPLGPIALA+CLQ+D Sbjct: 241 WQFKTLLQDGYADIIQPDLSHAGGITECKKIMSMAEAFDVAAAPHCPLGPIALASCLQVD 300 Query: 301 AVSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYEDGFVSIPQGPGLGIEVNEEKVREM 360 A +NA IQEQSLGIHYN+GND+LDYIK+ VF+Y DG V IP GPGLGIE+NE+ VRE Sbjct: 301 ATCHNAIIQEQSLGIHYNKGNDILDYIKDASVFEYTDGHVKIPDGPGLGIEINEDYVRER 360 Query: 361 AKVGHRWRNPVWRHEDGSVAEW 382 + +GH W+NPVWRH DGS+AEW Sbjct: 361 SHIGHNWKNPVWRHADGSIAEW 382 Lambda K H 0.319 0.139 0.428 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: 529 Number of extensions: 7 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: 382 Length of database: 382 Length adjustment: 30 Effective length of query: 352 Effective length of database: 352 Effective search space: 123904 Effective search space used: 123904 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: 50 (23.9 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