Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate Echvi_2982 Echvi_2982 Phosphomannomutase
Query= SwissProt::O74478 (587 letters) >FitnessBrowser__Cola:Echvi_2982 Length = 575 Score = 283 bits (724), Expect = 1e-80 Identities = 181/558 (32%), Positives = 290/558 (51%), Gaps = 23/558 (4%) Query: 12 WFKLDQDETTRNEVSQLIKAEDYATLKQIMHPRIGFGTSGLRAEIGAGFARMNCLTVIQA 71 W + D+ ++ ++ QL+ A D + L + + FGT GLR +G G RMN TV A Sbjct: 13 WLNSNIDQESKTKIQQLLDASDSSELVDAFYKDLEFGTGGLRGVMGIGSNRMNVYTVGMA 72 Query: 72 SQGFAEYLLQTVPSAAKLGVVIGHDHRHKSNTFARLTAAVFLQKGFKTYFFDHLVHTPLV 131 +QG A YLL P + V I HD R + FA TA V G K +F+ + TP++ Sbjct: 73 TQGLANYLLACFPGE-DIKVAITHDSRINNTLFAETTANVLTANGIKVKYFEEMRPTPML 131 Query: 132 PFAVKTLGTAAGVMITASHNPAAYNGYKVYWGNGCAIIPPHDKGIAACIE--KNLTPITW 189 +A++ G +GVMITASHNP YNGYK YW +G I+ PHDK I ++ K++ + W Sbjct: 132 SYAIRHYGCKSGVMITASHNPKEYNGYKAYWEDGGQIVAPHDKNIIMEVQKIKSIDDVKW 191 Query: 190 DKN--LVENHKLADRDFAVGLLKNYWSQLHEFHSENNFSLEMKSLKFVYTPIHGVGLPFV 247 DKN L+E + A+ D Y + + +F L + + V++PIHG V Sbjct: 192 DKNDALIE-YIGAEMDL------TYLNDIKKFSLSPKAILNQRDMCIVFSPIHGASGKMV 244 Query: 248 TSALHLFGEQGDMISVPLQDSPNPDFPTVKFPNPEEEGALDLAYEQADANGISYVLATDP 307 +AL FG + + V Q++P+ FPTV +PNPEE AL L+ + A VLA DP Sbjct: 245 PAALKTFGFENIHV-VKEQEAPDGTFPTVVYPNPEEAEALSLSLKLAKEVNAELVLACDP 303 Query: 308 DADRFAFA-EKINGAWRRFTGDEVGCILAYFIFQEYKNVGKPIDDFYVLSTTVSSAMVKS 366 D DR+A A G + G++ G IL Y++ +++ G D ++++T V++ +++ Sbjct: 304 DGDRYAAAIPNEKGEYELLNGNQTGSILTYYLLNQWREHGLFTGDQFMVNTIVTTELIEE 363 Query: 367 MAKVEGFHHVETLTGFKWLGNKALELEKQGKFIGLAYEEALGYMVGSIVRDKDGVNALIT 426 + LTGFK + ELE + +F+G EE+ G++VG VRDKDGV+A Sbjct: 364 ICHGFNIPCYRVLTGFKNIAAIIRELEGKKQFVG-GGEESYGFLVGDAVRDKDGVSACAM 422 Query: 427 FLHLLKRLQLQNLSITEVFEQMSKKYGYYTTQNSYFLSRDTPKLRALVDALRHYDTKSGY 486 ++ + + +++ +V ++ + YG+Y ++ +++ + L H ++ Sbjct: 423 LAEVVAYYKEKGMTLFDVLAEIYQSYGFY-KESLISVTKKGKDGAEQIQQLMH-GFRTNR 480 Query: 487 PATLGSKKITNVRDLTTGYDSSSTDGKATLPVSKSSDNVTFELENGEVIMTIRTSGTEPK 546 P + K+ V D+ + DG S+ + F LE+G I + R SGTEPK Sbjct: 481 PEAINGTKVVKVVDVKESKVYNIADGTEEDLDLDKSNVIQFYLEDGSKI-SARPSGTEPK 539 Query: 547 LKFYICARGHSLEDSIKN 564 +K+YI S+ +S+ N Sbjct: 540 IKYYI-----SVNESLPN 552 Lambda K H 0.318 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: 830 Number of extensions: 42 Number of successful extensions: 7 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: 587 Length of database: 575 Length adjustment: 36 Effective length of query: 551 Effective length of database: 539 Effective search space: 296989 Effective search space used: 296989 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: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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