Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate HSERO_RS05225 HSERO_RS05225 gluconolaconase
Query= uniprot:B2UIY8 (300 letters) >FitnessBrowser__HerbieS:HSERO_RS05225 Length = 292 Score = 166 bits (421), Expect = 5e-46 Identities = 107/292 (36%), Positives = 148/292 (50%), Gaps = 32/292 (10%) Query: 19 VGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPLPEMAGCIAMA--PNGWAMAME 76 +GE +W Q+++WTDI LW + +G T +W +PE C A P + +E Sbjct: 13 LGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAFTADPQQLLIGLE 72 Query: 77 TGIFLAPPPSPGIELGPLQRLATVAHARPDMRFNDGRCDRQGRFWAGTMVLDTSLGLPLG 136 + + + G + + + P R NDGRCDRQGRF GT+ D P+ Sbjct: 73 SRLAFF-----NLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDAGRA-PIA 126 Query: 137 KLYRLDAAAARTGRVDAVIDDLIVP-----NGLAFSPEGKTMYLSDSHASRQTVWAFDYD 191 YRL+ D ++ L +P N + FS +GK MY DS A + + DYD Sbjct: 127 SFYRLNT--------DLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGK--IMVCDYD 176 Query: 192 IDTGTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDAGFVHRFTPDGRLDRSIAIPT 251 +G +RVF D+ A PG PDG+ +DA+G W V R+ PDGR+DR +AIPT Sbjct: 177 TASGAVGGQRVFADV-AQPGGPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPT 235 Query: 252 SKPAMCAFGGPGLDTLFVTSIRIG-------DDPLSGATFAVR-PGVTGLPE 295 S+P+ AFGG DTL+VT+ G DP +GA FAV V GLPE Sbjct: 236 SQPSCVAFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPE 287 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: 303 Number of extensions: 22 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: 300 Length of database: 292 Length adjustment: 26 Effective length of query: 274 Effective length of database: 266 Effective search space: 72884 Effective search space used: 72884 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