Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate 3607832 Dshi_1240 SMP-30/Gluconolaconase/LRE domain protein (RefSeq)
Query= uniprot:B2UIY8 (300 letters) >FitnessBrowser__Dino:3607832 Length = 286 Score = 120 bits (302), Expect = 3e-32 Identities = 97/289 (33%), Positives = 127/289 (43%), Gaps = 26/289 (8%) Query: 17 CGVGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTN-NWPLPEMAGCIAMAPNGWAM-A 74 C +GE P+WH Q L+W DI G+ + + G T W EM + + A Sbjct: 11 CALGEGPLWHPERQQLFWFDITGQRMLSRD---GDTPLEWQFDEMVSAAGWVDHDTLLIA 67 Query: 75 METGIFLAPPPSPGIELGPLQRLATVAHARPDMRFNDGRCDRQGRFWAGTMVLDTSLGLP 134 ET + + G + +A + RP+ R NDGR D G FW GTM G Sbjct: 68 SETALVTFD-----LAEGESRFVAPLEADRPETRSNDGRADPWGGFWIGTMGKSAEPGA- 121 Query: 135 LGKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDSHASRQTVWAFDYDIDT 194 G +YRL G + V+ D+ + N L F Y +D+ +RQ V D D Sbjct: 122 -GAIYRLF-----DGTLRRVVRDVTISNALCFDAAQSCAYYADT-PTRQ-VMRLPLDGDG 173 Query: 195 GTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDAGFVHRFTPDGRLDRSIAIPTSKP 254 V +D+ A PDGA DA G WI AG V PDG R++A Sbjct: 174 WPSGPATVAVDLRAEGLNPDGAVTDAAGNLWIAQWGAGRVACHAPDGTFLRALACGGRHS 233 Query: 255 AMCAFGGPGLDTLFVTSIRIG---DD----PLSGATFAVRPGVTGLPEP 296 + AFGGP LD LF+T+ R G DD P +G FA GLPEP Sbjct: 234 SCPAFGGPDLDQLFITTAREGLSADDIAAAPENGCVFAAEGVARGLPEP 282 Lambda K H 0.322 0.140 0.466 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: 317 Number of extensions: 23 Number of successful extensions: 3 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: 300 Length of database: 286 Length adjustment: 26 Effective length of query: 274 Effective length of database: 260 Effective search space: 71240 Effective search space used: 71240 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 (21.9 bits) S2: 48 (23.1 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