Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate WP_083492001.1 ABB28_RS10755 glycosyl hydrolase
Query= SwissProt::E7CY69 (757 letters) >NCBI__GCF_001431535.1:WP_083492001.1 Length = 928 Score = 263 bits (672), Expect = 3e-74 Identities = 205/690 (29%), Positives = 321/690 (46%), Gaps = 76/690 (11%) Query: 24 GDAWHLQGVESKGIPSYMITDGPHGLRKSLASSAGETDLDDSVPATCFPPAAGLSSSWNP 83 G A + GV GIP+ D G+ G+ AT P +SSWNP Sbjct: 268 GSAGFVPGVARLGIPAQQSADAGVGVTNPGGIRKGDF-------ATAMPSGPSTASSWNP 320 Query: 84 ELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSEDPYLAGHEAIGIVEGV 143 + + G M E Q++ ++LG VN++R+P GR FEY EDP L G + G+ Sbjct: 321 LIAYVGGATMGREAWQQRFNILLGGSVNLQRDPRNGRNFEYAGEDPLLGGVIVGESIRGI 380 Query: 144 QSKGVGTSLKHFAANNQETDRLRVDARISPRALREIYFPAFEHIVKKAQPWTIMCSYNRI 203 QS+ V +++KH+A N+ ET R +I +A+ E AFE ++ +P + MCSYN+I Sbjct: 381 QSQHVISTMKHYALNDMETRRNFHSVQIGDQAMHESDLLAFEIAIELGKPGSAMCSYNKI 440 Query: 204 NGVHSAQNHWLLTDVLRDEWGFDGIVMSDWGADHDRGASLNAGLNLEM------PPSYTD 257 NG++ ++ +L+ VL+ EW F G VMSDWG H + AGL+ + ++ D Sbjct: 441 NGIYGCEHPYLMNQVLKQEWKFPGFVMSDWGGVHSGSKAALAGLDQQSAGEVFDATTFFD 500 Query: 258 DQIVYAVRDGLITPAQLDRMAQGMIDLVNKTRAAM----SIDN----YRFDVDAHDEVAH 309 + AV G + A+LD D+V++ M + DN DV+A A Sbjct: 501 QPLRLAVAGGTVPQARLD-------DMVSRILRTMFLHGNFDNPPQHQPIDVEAGYAAAQ 553 Query: 310 QAAIESIVMLKNDDAILPLNAGPVANPSATPQKIAVIGEFARTPRYQGGGSSHITPTKMT 369 + E V+L+N+ +LPL + + ++I +IG A GGGSS + T Sbjct: 554 RTVEEGSVLLRNEGNLLPL--------ADSVKRIVIIGGHADKGVIGGGGSSMVGVTAK- 604 Query: 370 SFLDTLAERGIKADFAPGFTLDLEPADP--ALESE----------------AVETAKNAD 411 T A G+ PG + P+ P AL +E A A AD Sbjct: 605 ---GTNAVPGVMPTTWPGPVI-FHPSSPLEALRAERPDAQITYVDGRNPAAAARAAAQAD 660 Query: 412 VVLMFLGLPEAVESEGFDRDTLDMPAKQIALLEQVAAANQNVVVVL-SNGSVITVAPWAK 470 V L+F +E D + +P +Q AL+ VA AN VVVL +NG V T PW Sbjct: 661 VALVF---ATQWSAESVDLPDMQLPDQQDALISAVAKANPKTVVVLETNGPVRT--PWLA 715 Query: 471 NAKGILESWLLGQSGGPALADVIFGQVSPSGKLAQSIPLDINDDPSM----LNWPGEEGH 526 +L++W G GG +A ++ G+V+PSG+L + +D + P L + ++ Sbjct: 716 QVPALLQAWYPGIRGGEGIAALLTGKVNPSGRLPVTWVVDESQLPRPHVPGLGFNPKQPA 775 Query: 527 VDYG----EGVFAGYRYYDTYGKAVDYPFGYGLSYATFEITGVAVAKTGANTATVTATVT 582 VD EG GY++ G + FG+GLSY++F + V+ G + V Sbjct: 776 VDIFDFDIEGANVGYKWAAAKGLVPTFAFGHGLSYSSFAYENLQVSVEG-QRVVASVDVR 834 Query: 583 NTSDVDAAETVQVYVVPGKADVARPKHELKGFTKAFLKAGESKTVAIDLDERAFAYWSEK 642 NT A+ Q+Y+ + + L GF K L+ GE + + I+ + + A + Sbjct: 835 NTGARAGADVAQLYLKLPQGHTTPIR--LVGFDKVNLQPGEQRRIRIEAEPKTLADFDPT 892 Query: 643 YNDWHVEAGEYAIEVGVSSRDIADTVAVAL 672 +W + AG Y +++G ++ + V V L Sbjct: 893 AREWKIAAGTYQLQLGRNAAEPLQVVDVQL 922 Lambda K H 0.315 0.132 0.393 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: 1714 Number of extensions: 90 Number of successful extensions: 6 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: 757 Length of database: 928 Length adjustment: 42 Effective length of query: 715 Effective length of database: 886 Effective search space: 633490 Effective search space used: 633490 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: 56 (26.2 bits)
This GapMind analysis is from Sep 24 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