Align UPF0280 protein MA_1715 (characterized, see rationale)
to candidate WP_011308597.1 MBAR_RS19645 UPF0280 family protein
Query= uniprot:Y1715_METAC (253 letters) >NCBI__GCF_000195895.1:WP_011308597.1 Length = 253 Score = 427 bits (1098), Expect = e-124 Identities = 215/253 (84%), Positives = 232/253 (91%) Query: 1 MPEPTQKPAKEPVRAPIKEHFQLRETIVTIAADDPAHIEAAKEAIRVHRATLETYILADP 60 M +P + A EP PIKEHFQL+ETIVTIAAD+ AHIEAAKEAIR+HRA LETYI +DP Sbjct: 1 MSDPINEHANEPASFPIKEHFQLKETIVTIAADNLAHIEAAKEAIRIHRAALETYIFSDP 60 Query: 61 YFQFTLEPYECPENAPEVVRRMVKAGNTMGIGPMSAVAGTISALAVEAMVKAGAKYAIVD 120 YFQ TLEPYECPENAPEVVRRMVKAGNTMGIGPMSAVAGTISALAVE+MVKAGAKYAIVD Sbjct: 61 YFQLTLEPYECPENAPEVVRRMVKAGNTMGIGPMSAVAGTISALAVESMVKAGAKYAIVD 120 Query: 121 NGGDIALINDRSVVVGIYAGQSPIKNLGLIFEPRDSITGVCTSAGTVGPSISFGMADAAA 180 NGGDIALINDR VVVGIYAGQS IKNLGL+FEPR SITGVCTSAGTVGPSISFGMADAAA Sbjct: 121 NGGDIALINDRPVVVGIYAGQSTIKNLGLVFEPRGSITGVCTSAGTVGPSISFGMADAAA 180 Query: 181 IFSDDVSLADAAATALGNEVGIGKEAVEVAFKVVKTVQGIKGALVIQGEYIGMWGKVPKI 240 +FSDDVSLADAAATALGNEV IGKE+VE +FK VK + IKGALVIQGEYIGMWG+VP++ Sbjct: 181 VFSDDVSLADAAATALGNEVNIGKESVEASFKAVKGIPEIKGALVIQGEYIGMWGQVPRV 240 Query: 241 TRAEVRHEYITKA 253 TRA+VR+EYITKA Sbjct: 241 TRADVRYEYITKA 253 Lambda K H 0.317 0.133 0.379 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: 314 Number of extensions: 10 Number of successful extensions: 1 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: 253 Length of database: 253 Length adjustment: 24 Effective length of query: 229 Effective length of database: 229 Effective search space: 52441 Effective search space used: 52441 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: 46 (22.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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