Align maltose phosphorylase (MapA) (EC 2.4.1.8) (characterized)
to candidate N515DRAFT_1906 N515DRAFT_1906 alpha,alpha-trehalose phosphorylase
Query= CAZy::BAD97810.1 (768 letters) >FitnessBrowser__Dyella79:N515DRAFT_1906 Length = 1036 Score = 355 bits (911), Expect = e-102 Identities = 239/760 (31%), Positives = 383/760 (50%), Gaps = 65/760 (8%) Query: 8 DEWSIIEEGFDPHTHEISESVFSIGNGFMGQRANFEEAYSGSSLQGSYMAGVYYPDKTRV 67 D W++I G DP ES+F++ NG +G R EE S S Q S+++ + ++T + Sbjct: 27 DPWTLIRRGTDPAGFAQDESLFALANGALGVRGGLEEGDSPS--QASFLSAAW--ERTPI 82 Query: 68 GWWKN--GYPEYFAKVLNSTNWIGIDIQIDGTPLDLAKCTVKDFVRELNMKEGFLSRRFT 125 + + G+ + + + I +++ P+ LA+ DF R L+++EG R Sbjct: 83 EYHERFPGFAAHTDTRIPVADATRIQLRLGDVPVRLAEGEWLDFERRLDLREGCYRRFLR 142 Query: 126 AVTEDGKELKVEAIRFVSIVRHEIGAIRYAVTPLNFKGELT------------------- 166 + G+ L++EA R VS+ + A+RY V +++ G +T Sbjct: 143 WRSPAGETLEIEAERIVSLDEPGLLALRYRVRSVDYTGPVTLESAISTARDAAEQGDDPR 202 Query: 167 ITPYLDGDVKNKDSNYDEKF-WLEVFKEATQG------SAAVTVKTKKLDFHVTSVMSYT 219 I LDG + D+ + F W+ ++ T + A + LD H ++ + Sbjct: 203 IGTRLDGGLHTVDAAAEPDFAWVR--QQTTHSGIRLACAQAHRAQDGGLDCHFANLAQHG 260 Query: 220 ILKNGEKLELQAELVEKEKYAGNRVSMPVSEGETVTVYKYVANVTSRNHGFGE---LVEA 276 ++ + Y G ++ G+ VT+ KYVA + HG L+ Sbjct: 261 VVHS---------------YTGM-----LTPGQAVTLEKYVAYAWTEPHGDDADDALLAR 300 Query: 277 ARAVLEPAVETGFEQLLKEQADAWGDKWKESDIVIEGDVAAQQAIRFNIFQLNQTYSGED 336 R +LE A + LL+ Q A W +D+ I+GD A +QA+RFN+F L Q+ S D Sbjct: 301 TRGILEAAAHLRYAGLLERQRQALAPLWDGADLAIDGDAATEQALRFNLFHLFQS-SCRD 359 Query: 337 DRLNIGPKGFTGEKYGGSTYWDTEAYCLPFYLSTADASISRNLLIYRYKHLEKAKENAKK 396 + + KG TGE Y G +WD EA+ LP L+T ++R +L+YR++ L++++ +A++ Sbjct: 360 GQGSAAAKGLTGEGYEGHYFWDAEAFILPV-LATVAPELARGMLLYRHRILDRSRRHARE 418 Query: 397 LGFTKGALYPMVTMNGEECHNEWEITFEEIHRNGAIAYAIYNYVNYTGDFSYLGQYGLEV 456 L +GALY T++G+EC + + H N AIA+AI YV+ +GD +L +G E+ Sbjct: 419 LNHPRGALYAWRTISGDECSAYYPGGSAQYHINAAIAWAISLYVDASGDTDFLRDHGAEI 478 Query: 457 LVEISRFWEERVNYVAAK-DQYMMLGVTGPNEYENNVNNNWYTNRIASWTMEYTLDVLEY 515 L E +R W + ++ A + D + + VTGP+EY V+NN YTNR+A + + Sbjct: 479 LFETARVWLDIGHFNARRGDAFCIHEVTGPDEYSALVDNNHYTNRMAQRHLRDAAATALW 538 Query: 516 LKENENARYDELTAKLALQEAETTKWQDIIQKMYYPVDEELGVFLQQDGFLDKELVP--- 572 + Y L A++ L E E +W+ + MY P D LGVF Q DGFLD+ +P Sbjct: 539 MAGAAPVEYGALCARIGLGEDEVAQWRRAAEAMYLPEDPRLGVFPQDDGFLDRPRLPDHL 598 Query: 573 -VKELDPVHLPLNQNWSWDRILRSVYIKQADVLQGLFFLGDRYDLATKKRNFDFYEPFTV 631 K D H PL I R KQAD L L GD + A K+RNFD+YE TV Sbjct: 599 AAKPGDGKH-PLLLRLHPLTIYRHQVCKQADTLLALMLAGDGVERAAKRRNFDYYESVTV 657 Query: 632 HESSLSPCVHSILACELGYQEKAYEMYLRTARLDLDNYNNDTEDGCHTTSMAGTWMSVVH 691 H+S+LS ++A E+G KA+ + + R+DLD+ + + G H +MAG+W+ +V Sbjct: 658 HDSTLSASTFGVIAAEVGLAAKAWRYFQDSLRVDLDDSHGNAAHGVHMAAMAGSWLGLVW 717 Query: 692 GFGGLRVKDGVLHLNPFIPGHWSSFSFKVMFRGSRLKVSV 731 GFGG R DG L P +P W + F + + ++L+V V Sbjct: 718 GFGGFRTIDGQPALAPRLPAAWHGYRFGLRWGRAQLRVEV 757 Lambda K H 0.317 0.135 0.404 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: 1702 Number of extensions: 93 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 768 Length of database: 1036 Length adjustment: 43 Effective length of query: 725 Effective length of database: 993 Effective search space: 719925 Effective search space used: 719925 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 (21.6 bits) S2: 56 (26.2 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