Align Phosphopentomutase; EC 5.4.2.7; Phosphodeoxyribomutase (uncharacterized)
to candidate 17443 b3380 predicted mutase (NCBI)
Query= curated2:Q67ND8 (393 letters) >FitnessBrowser__Keio:17443 Length = 408 Score = 134 bits (338), Expect = 4e-36 Identities = 122/423 (28%), Positives = 189/423 (44%), Gaps = 59/423 (13%) Query: 6 RVVLIVIDSVGIGAMPDAA--DWGDAGANTLGNMARQRGGLPLPNLGRLGLGNLCAIEGT 63 R V++VIDS G+GAM D DAGANT G++ Q L LP L LGL N Sbjct: 3 RFVVLVIDSFGVGAMKDVTLVRPQDAGANTCGHILSQLPHLQLPTLETLGLINALGYAPG 62 Query: 64 PPVDAPAGAYGRMAIFSHGKDTMTGHWEMVGIRP----EAPFRTYPDGFPEDLIA---EF 116 + + +G + G DT GH E++G RP PFR D + L++ + Sbjct: 63 DMQPSDSATWGVAELQHEGGDTFMGHQEILGTRPLPPLRMPFRDVIDRVEQALVSAGWQV 122 Query: 117 CRRAG-LEGVLGNK-VASGTEIIKELGEEHLRTGWPIVYTSADSVFQVAAHEERFGLERL 174 RR L+ + N+ VA G + +LG+ V+ + A+ + Sbjct: 123 ERRGDDLQFLWVNQAVAIGDNLEADLGQ----------------VYNITANLSVISFDDA 166 Query: 175 YEVCRIARDLLRPPHRVGRVIARPFVGTDRTNFTRTANRHD------------------- 215 ++ RI R+ ++ VGRVI + TD A + Sbjct: 167 IKIGRIVREQVQ----VGRVITFGGLLTDSQRILDAAESKEGRFIGINAPRSGAYDNGFQ 222 Query: 216 -----YALEPPRMLLDEVKDAGLSVLAVGKISDIFSG-HGITYSVHTKSNADGIEKIHEC 269 Y ++ + ++ +AG+ + VGK++DI + +G+++ S ++E Sbjct: 223 VVHMGYGVDEKVQVPQKLYEAGVPTVLVGKVADIVNNPYGVSWQNLVDSQRIMDITLNE- 281 Query: 270 LDRQEPGLIFANLVDFDMLYGHRRDVEGYARAMLEFDAALPAIMAKLGPEDVLVVTADHG 329 + I N+ + D L GH DV YA + D L ++ + P+D LVV ADHG Sbjct: 282 FNTHPTAFICTNIQETD-LAGHAEDVARYAERLQVVDRNLARLVEAMQPDDCLVVMADHG 340 Query: 330 NDPTYIGTDHTREYVPVLLYGEPIKPGVDVGTRASLADLGATVADLLGVPQTGFGESFAD 389 NDPT + HTRE VPVL+Y + + +G R +L+D+GATV + P G SF Sbjct: 341 NDPTIGHSHHTREVVPVLVYQQGM-IATQLGVRTTLSDVGATVCEFFRAPPPQNGRSFLS 399 Query: 390 QIR 392 +R Sbjct: 400 SLR 402 Lambda K H 0.321 0.141 0.426 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: 409 Number of extensions: 25 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: 393 Length of database: 408 Length adjustment: 31 Effective length of query: 362 Effective length of database: 377 Effective search space: 136474 Effective search space used: 136474 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: 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