Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate CA265_RS12250 CA265_RS12250 enolase
Query= BRENDA::D4GP40 (412 letters) >FitnessBrowser__Pedo557:CA265_RS12250 Length = 388 Score = 155 bits (393), Expect = 1e-42 Identities = 110/370 (29%), Positives = 176/370 (47%), Gaps = 36/370 (9%) Query: 49 NYPWILVRVYTDAGVVGTGEAYWGGGDTAII--------ERMKPFLVGENPLDIDRLYEH 100 ++ LV + TD+G+ G GEA G I +KP L+G++ +I RL+E Sbjct: 30 SFDMTLVVITTDSGLQGFGEAKAAVGSCGICASIVNCIENELKPMLLGKSVKNITRLWEE 89 Query: 101 LVQKMSGEGSVS-----------GKVISAISGIEIALHDVAGKLLDVPAYQLVGGKYRDE 149 + ++S G ISA+SGI+ AL D+ GK+L+VP L+GG R + Sbjct: 90 MYNGTRDHYALSRGRKFPILGRRGLTISAMSGIDTALWDLKGKMLNVPVADLLGGACRTK 149 Query: 150 VRVYCDLHTEDEANPQACAEEGVRVVEELGYDAIKFDLDVPSGHEKDRANRHLRNPEIDH 209 + Y DE N E+ + V + G+ +K + V + NR Sbjct: 150 MPAYASGGWADEQN---IGEQLMGYVNK-GFKGVKMRVGVMDDTVQKSINR--------- 196 Query: 210 KVEIVEAVTEAVGDRADVAFDCHWSFTGGSAKRLASELEDYDVWWLEDPVPPENHDVQKL 269 V+A A+G + D H +F+ AK+ +ED +V+W E+P+ P+N Sbjct: 197 ----VKAARAALGPDIKLMVDAHGTFSVPEAKQFCRGVEDCNVYWFEEPISPDNRKGTAE 252 Query: 270 VTQSTTTPIAVGENVYRKFGQRTLLEPQAVDIIAPDLPRVGGMRETRKIADLADMYYIPV 329 V +T PIA GE+ + F LL+ +A+D++ PD +GG+ E +++ LA ++ + + Sbjct: 253 VRAATDIPIAAGESEFTSFDIHDLLQIRAIDVVQPDAAIIGGISEAMRVSHLASVHQVEL 312 Query: 330 AMHNVSSPIGTMASAQVAAAIPNSLALEYHSYQLGWWEDLVEEDDLIQNGHMEIPEKPGL 389 A H S MA VA A ++ +E+ DLV E + NG + P PGL Sbjct: 313 APHCWGSAFSFMAGLTVAFASASATIIEFSLGGNPMMYDLVNEQIAVVNGEISAPTAPGL 372 Query: 390 GLTLDLDAVE 399 GLT + D V+ Sbjct: 373 GLTPNWDFVK 382 Lambda K H 0.315 0.135 0.401 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: 368 Number of extensions: 21 Number of successful extensions: 5 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: 412 Length of database: 388 Length adjustment: 31 Effective length of query: 381 Effective length of database: 357 Effective search space: 136017 Effective search space used: 136017 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: 42 (22.0 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