Align D-glucosaminate dehydratase (EC 4.3.1.9) (characterized)
to candidate HSERO_RS08720 HSERO_RS08720 amino acid deaminase
Query= reanno::pseudo5_N2C3_1:AO356_00450 (405 letters) >FitnessBrowser__HerbieS:HSERO_RS08720 Length = 430 Score = 377 bits (967), Expect = e-109 Identities = 204/406 (50%), Positives = 266/406 (65%), Gaps = 5/406 (1%) Query: 5 IPNAGVEKGAATVGAHLL-KDVSLPALVLHRAALEHNIRWMQAFVTDSGAELAPHGKTSM 63 +P A A TV +LL +D+SLPA VL+ + HN++WMQ FV +LAPHGKT+M Sbjct: 25 LPQALPPGQAGTVRWNLLNEDISLPAAVLYEEKIAHNLKWMQEFVGQYQLKLAPHGKTTM 84 Query: 64 TPALFRRQLDAGAWGLTLATAVQTRAAYAHGVRRVLMANQLVGTPNMALIADLLADPAFE 123 P LF RQLD GAWG+TLATA QT A Y HGVRRV+MANQLVG NMA+I++LLADP+FE Sbjct: 85 APKLFARQLDTGAWGITLATAHQTLAGYHHGVRRVIMANQLVGKRNMAIISELLADPSFE 144 Query: 124 FHCMVDHPDNVADLGAFFASRGMKLNVMIEYGVVGGRCGCRTEAEVLALAEAIRSQPALA 183 F C+VD V LG FFA R LNV++E G GGR G R EA+ A+ EAI ++A Sbjct: 145 FFCLVDSAALVDQLGRFFAERKQTLNVLLELGPTGGRTGVRDEAQQQAVLEAISRWDSIA 204 Query: 184 LTGIEGYEGVIHGDHAISG-IRAFAASLVRLAVQLQDDDAFAIDKPIITASGSAWYDLIA 242 L G+E YEGV+ + I ++ A L LA Q Q A ++T +GSAWYD++A Sbjct: 205 LAGVEVYEGVLKEEVDIRRFLQRAVACLQDLAAQGQLARRLARGPAVLTGAGSAWYDVVA 264 Query: 243 ESFEAQNAHGRFLSVLRPGSYVAHDHGIYKEAQCCVLERRSDLH---EGLRPALEVWAHV 299 E F + VLRPG Y+ HD GIY+ AQ + R H L+PAL++WA+V Sbjct: 265 EEFGQADIGAALDVVLRPGCYLTHDVGIYRAAQAQIQVRNPVAHSMRSQLQPALQLWAYV 324 Query: 300 QSLPEPGFAVIALGKRDVAYDAGLPVPLKRYTPGSDSVPGDDVSGCKVTAVMDQHAFMSV 359 QS+PE A+IALGKRD A+DAGLP+P+ R+ PG D+ P + +VT +MDQHA++ + Sbjct: 325 QSIPESDKAIIALGKRDAAFDAGLPMPVSRFRPGRDTGPQATPAHWEVTGMMDQHAYLKI 384 Query: 360 AAGVELRVGDIIAFGTSHPCLTFDKWRVGCLVDEQLRVVESMETCF 405 AAG ++ VGD+IAF SHPCLTFDKWR +VD + V + ++T F Sbjct: 385 AAGDDIEVGDMIAFDISHPCLTFDKWRHLVVVDGRFDVTDIVQTFF 430 Lambda K H 0.322 0.136 0.414 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: 509 Number of extensions: 16 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: 405 Length of database: 430 Length adjustment: 32 Effective length of query: 373 Effective length of database: 398 Effective search space: 148454 Effective search space used: 148454 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 (21.9 bits) S2: 50 (23.9 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