Align Uncharacterized protein (characterized, see rationale)
to candidate 207248 DVU1783 cysteine-rich domain protein
Query= uniprot:E4PLR5 (279 letters) >MicrobesOnline__882:207248 Length = 250 Score = 273 bits (699), Expect = 2e-78 Identities = 133/248 (53%), Positives = 169/248 (68%), Gaps = 1/248 (0%) Query: 25 YPEKPEAVTLFGTCVVDLFFPEAGLDTIRLLEREGVRVHFPQEQSCCGQPAWTSGYRDEA 84 YPE + V FGTC+VD+ FP+AG+ IRLL+R GV V FP QSCCGQPA+ SG+ DEA Sbjct: 4 YPEDIKTVYFFGTCLVDMSFPDAGMAGIRLLQRAGVEVVFPAAQSCCGQPAYNSGFFDEA 63 Query: 85 KAVARAQLDILDRSGLPVVVPSGSCAGMFRHHYPALFADEPDTLKRVEALAERTFELTEF 144 + VA Q++ P+VVPSGSCAGM R HYP LFA+ PD + V +ER FEL +F Sbjct: 64 RTVALRQVEAFSAHDWPIVVPSGSCAGMMRFHYPELFAEAPDYFE-VRRFSERVFELGDF 122 Query: 145 LLKVCRVQLADRGAPSKIALHTSCSARREMNTHLHARELLQQLEGVERIDHDHESECCGF 204 L D+GAP K+ H+SC A REM A+ L+ QL VE +D +E ECCGF Sbjct: 123 LCNALHQTYEDKGAPIKVTWHSSCHAMREMGAVAAAKTLIGQLANVELVDLPYEYECCGF 182 Query: 205 GGTFSVRMPEVSGAMVKDKTRSLIDSGAVEMVTADGGCLMNINGSLEKQKESFRGRHLAS 264 GGTFS++ PE+SGAMV DK ++ +GA +++ D GCLMNING++EKQ +G+HLAS Sbjct: 183 GGTFSIKQPELSGAMVSDKVANIRSTGAARVLSGDCGCLMNINGAMEKQSVPVQGQHLAS 242 Query: 265 FLWERTNG 272 FLWER NG Sbjct: 243 FLWERING 250 Lambda K H 0.320 0.134 0.406 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: 267 Number of extensions: 12 Number of successful extensions: 2 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: 279 Length of database: 250 Length adjustment: 25 Effective length of query: 254 Effective length of database: 225 Effective search space: 57150 Effective search space used: 57150 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 (21.8 bits) S2: 47 (22.7 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